A science teacher questions
the party line…
Please feel free to reproduce this work in its entirety and distribute it freely,
as I am giving it away at no charge to you. I believe it contains some important truths
that should be shared (and I don’t have the means to make unlimited copies!),
but selling the truth is a big no no, so please don’t sell it or alter it in any way!
I will trust your integrity and good will on this. Thank you, and enjoy! 
©2014
Preface…………………………………………………………………………………………………………………………………………….............1
An introduction of sorts… …………………………………………………………………………………………………………………………..2
Honor where honor is due……………………………………………………………………………………………………………...2
It doesn’t always work properly……………………………………………………………………………………………………..3
The limitations of science………………………………………………………………………………………………………………..4
Truth is like an asymptote……………………………………………………………………………………………………………….5
Surely this isn’t still happening, is it?..................................................................................................8
Whether it’s good, bad or ugly is up to us…………………………………………………………………………………….…9
What this writing is not for……………………………………………………………………………………………………………...9
No arm twisting possible………………………………………………………………………………………………………………...10
Part 1: The prevailing theories don’t really cut it…………………………………………………………………………………….….11
Life, where it all begins….…………………………………………………………………………………………..…………………...11
Popcorn strings, trains and balsa wood planes….…………………………………………………………………...........11
On Persian rugs and Archimedes………….............................................................................................14
Rolling rocks uphill………………………………………………………………………………..………………………………………...15
The ultimate enigma………………………………………………………………………………..………………………………….….17
Part 2: Just a few examples of evidence to the contrary………………………………………..……………………….……….…18
Zippers and self-aware chemicals?!...................................................................................................18
Label makers………………………………………………………………………………………………..…………………….…………..19
Transcription and crocheting…………………………………………………………………………..…………………............20
Paint shakers and Lego sets without instructions?............................................................................21
Backup files……………………………………………………………………………………………………………………..….………….21
Fort Knox, NORAD and sunscreen……………………………………………………………………….…..….….……………..22
Redundant systems and maintenance robots to the rescue!............................................................23
Stovepipes and Japanese cartoon cat robots………………………………………………………..…….…….…………..25
Control, control, you must learn (?)control!......................................................................................26
Coin operated…………………………………………………………………………………………………………..….………………..28
Hydro-electric dams and lasagna noodles…………………………………………………………………..………………….28
Metabolic poisons and mothballs…………………………………………………………………………..……..……………….32
Solar arrays, reactor cores and Thin Mint™ Girl Scout cookies…………………………..………….…...…………32
The cellular pony express and old fashioned switchboards.............................................................. 35
Automated assembly lines... is everyone on coffee break?.............................................................. 36
Getting the biggest bang for the buck, and sometimes junk... isn’t junk!......................................... 40
Reduce, re-use and recycle!...............................................................................................................42
Unbalanced washing machines, Archimedes’ screws and electric football....................................... 45
Bull whips and their little brothers, sky scrapers and their footings................................................. 47
Warehouse roofs, monorails, movable scaffolding and sacrificial security guards........................... 49
Swimming in peanut butter, 3-point turns and hypodermic needles............................................... 51
Donation funnels............................................................................................................................... 54
Row upon row of rowers................................................................................................................... 54
Warehousing and value added distribution centers.......................................................................... 56
Mouse traps, the wave and pigs in a blanket.................................................................................... 57
Golf balls, doughnut holes and the larger world............................................................................... 62
Wrong place, wrong time, wrong language....................................................................................... 63
Cops on the beat and military police................................................................................................. 64
Retirement planning, the self-destruct sequence, and burning the embassy files........................... 65
Contingency against cellular psychopaths: conscience and counseling............................................ 66
A seared conscience and taking candy from a baby.......................................................................... 67
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The wrong kind of immortality and six steps to social destruction................................................... 68
Weld plates, zigzag stitches, and the ECM........................................................................................ 69
Storm sewers, homeland security, and a peak at the arsenal........................................................... 70
Listen to what hearing is saying and what vision is revealing…………………………………………………….....72
So why do your fingers get wrinkled in the bathtub?........................................................................ 77
Life is more remarkable than going to the moon.............................................................................. 77
Blood pressure cuffs, hydraulic dampeners and waste water treatment plants.............................. 78
Speaking of engineering.................................................................................................................... 80
Duck feathers, cat hair and those weird pictures.............................................................................. 82
The miracle of flight........................................................................................................................... 83
The unimind and Bose Einstein condensates.................................................................................... 85
The social intelligence of ants, bees, termites, birds, whales and people......................................... 86
Atomic level assembly and some 3-D designing................................................................................ 87
We’ve only just begun... ................................................................................................................... 88
Part 3: Some important considerations in view of the evidence................................................................. 88
What do similarities mean? Your presuppositions matter!.............................................................. 88
What if we weren’t considered alive, only our machines were?...................................................... 89
Skepticism, bait-and-switch, smoke and mirrors and sleight-of-hand.............................................. 95
My (?)conclusion?.......................................................................................................................................... 98
Which came first, really?................................................................................................................... 98
What’s it all for?................................................................................................................................ 101
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Willing to look behind the curtain?
A science teacher questions the party line…
Preface
A couple of things should be said before I dive in to what I want to talk about. First of all, this is not
meant to be a scholarly work, but a discourse, and as such you’ll see that I don’t quote any studies. I’m
paraphrasing what I have learned over many years, and it may very well be that my understanding is lacking or
not totally up to date, though I am doing some “fact checking” as I write (like “am I remembering this
correctly?”). I think the content is pretty accurate, but I would be happy to stand corrected on specific details
that I somehow misunderstood or misconstrued. It’s certainly not my desire to misrepresent anything, and I
will try to be as accurate as I can without pouring over a ton of primary sources to confirm what I remember.
Now, the conclusions I draw are a different matter entirely. Those I make without qualification, even if you
disagree. 
Secondly, I have inserted many graphics into the text as an aid to visualize the complicated structures I
am trying to describe. When it comes to the proteins and their intricate folding, it really is true that a picture is
worth a thousand words! Seeing them really drives home what I want to convey. Having said that, please be
aware that I have done my best to take these from the public domain, and as far as I know they are not
copyrighted. If I am mistaken about any of these and you are aware of it please let me know and I will delete
any copyrighted images ASAP. It’s not my intention to infringe or use material without the owner’s permission.
Thirdly, though I want to make the thoughts herein as readable and accessible to those without a
formal science education as possible, it’s going to be necessary to use some technical terms that are required
to appreciate the points being made, and I just want you to know it’s not my intention to speak over anyone’s
head or be showy with science lingo. It’s science teachers/professors and students I hope will be reading this,
but the majority of ordinary folks who have had some science in school (assuming you paid attention in class!)
should also be able to “get it” as well. Some of the terms we use in science aren’t exactly common speech, and
I apologize in advance if some of this becomes bewildering or too technical. Also, those of you who are already
well-versed in science may be dissatisfied with the level of detail (hey, you forgot this or that!). For you, please
understand that I’m trying to strike a balance for a wide audience, so don’t be insulted by my analogies or lack
of fine-grained detail as I’m trying to summarize and make the concepts more accessible. Remember, I am a
teacher by trade after all.  Since I really enjoy science myself, I encourage you to bone up on it if something I
discuss is still confusing. Try not to zone out if I lose you. In fact, please research this stuff yourself rather than
just taking my word for anything. Clear thinking is so important, and the arena of scientific investigation can
“sharpen your pencil” mentally just keeping up with the latest advances and discoveries. If you learn a few
things in this reading that’s great, but what I really intend to do is re-examine with you so many things we take
for granted. I invite you to explore some well-known and not-so-well known discoveries from a different
perspective and cultivate wonder and awe at the Mind which conceived them in the first place.
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An Introduction of Sorts…
Science has been a wonderful tool for figuring out how things work, and though there is more left
unanswered than what has been discovered so far, still we have come to understand some astounding things.
As the years of studying and teaching have passed, I have become more and more amazed--even
dumbfounded at the engineering and architecture that exists in nature, especially at the cellular level. I could
easily use the word design, but I’ll avoid that for now because it instantly brings to mind the public debate
surrounding “intelligent design” being taught in classrooms. I’m not advocating teaching religion in public
schools, which is a serious mistake and wrong on a number of levels, but I do want to offer you my thoughts
about what I believe the universe, and life in particular is virtually shouting to us. Before I attempt to do so,
you may be wondering how I figure into the scientific community. Where am I coming from?
Honor where honor is due
Let me begin by saying that I genuinely appreciate the efforts of myriads of others who have done the
heavy lifting in science, whether they are my contemporaries or those who pre-date me by decades or
centuries. Honestly, we science teachers/adjunct professors pass on what others have worked hard to learn,
and even though we are often the most public face of science, we aren’t usually the ones who contribute to
scientific knowledge. I have the luxury of being able to learn all about the things that have been discovered
and then teach this knowledge to my students without really getting my hands dirty. The closest I get to actual
research are the times I have to write a research paper for a graduate class! When I wanted to investigate the
link between biodiversity and the prevalence of diseases in an ecosystem, it was wonderful to find that a
multitude of studies dealing with the question from a variety of angles were already published. For one thing,
it was a relief that there were plenty of primary sources for my research paper, but it was also kind of exciting
that so many other people had already asked the same question and done so much in the field. They beat me
to the question and had been really productive! The answer to the question still has far reaching
consequences for our generation, and there are people “on it” already. That’s kind of reassuring to know.
A glimpse at my classroom would reveal the fact that I also respect and honor past generations of
scientists who have given us so much. I have a podium at the front of the room stenciled colorfully with some
of the names of great physicists and chemists (Schrödinger, Boyle, Rutherford etc.) on whose shoulders I
stand. In the corner of my room I have a coat rack with an Einstein doll sitting at the top, and each week I
switch out the quote he is saying for the students’ consideration. By the way, he and his contemporary
Schrödinger had some insightful, and at times unpopular, things to say that were valuable even beyond the
realm of science. It seems that the keenest minds are often the most productive in many “fields” of inquiry,
because they have the courage to ask hard questions and follow reason where it leads them.
We often think of reason when we think of science, but without courage and one other crucial
ingredient, faith, modern science would never have taken off as it did. Courage might come to mind in relation
to science, but faith is certainly not something we typically associate with it. However, it really was vital in the
early days of modern science and has continued to fuel the efforts of many (though certainly not all) other
scientists up to the present. In post-renaissance Europe there was a fundamental belief that the universe was
created by a God who was orderly. This was instilled in men like Davinci, Galileo, and Copernicus who had
confidence that their efforts would be fruitful because an orderly God had created an orderly, and therefore
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understandable, universe. They believed that learning the way nature worked enabled them to glimpse the
mind of God, so they were highly motivated in their investigations. But their curiosity also required courage,
because the religious powers of the day frowned violently upon dissent, as Copernicus and Galileo soon found
out.
Thankfully, those who encountered religious opposition during the fledgling stage of science were not
deterred in their desire to understand reality better, in spite of intimidation from those who misrepresented
God. They knew their belief in God was legitimate, even if the religious “authorities” opposed them. Pursuing
scientific inquiry did not disqualify them from having genuine faith. It’s ironic that the religious majority
opinion and “authority” in the early days of science was difficult to overcome, as the tables have now turned.
Scientists who profess faith in God today find it difficult to survive amidst the “authority” of atheistic
humanism in the scientific community. Still, having faith in God does not disqualify a person from being a
legitimate scientist any more than being a scientist in the renaissance disqualified one from having faith in
God. The two are NOT incompatible, in spite of the apparent contradictions at times. I believe that these
conflicts are man-made, due to a faulty understanding of who God really is, or a deficiency or
misinterpretation of scientific knowledge (or both). Working through these conflicts requires courage, because
anyone who finds himself opposing the majority view invariably draws criticism or even hostility. Our
forerunners had the courage of their convictions, both scientific and religious, and it served them well. In fact,
it’s amazing how much they were able to accomplish in the face of strong opposition with so little to work
with. Often times they had only relatively crude instruments, pencil and paper, keen powers of observation,
sound reasoning and an insatiable curiosity. In spite of many challenges, they made great strides and set the
stage for the rest of us.
Because of the ground work that was laid by those science pioneers, subsequent generations were
able to add their contributions to a growing foundation of knowledge. If it weren’t for the diligent efforts and
breakthroughs of past scientists, our understanding of the universe would be shallow, our standard of living
would be greatly diminished, and our capability to do useful things would be far less than it is. Thanks to the
scientific progress our generation has inherited, we are able to keep the momentum going and work on real
issues confronting us. The welfare of millions of people will be affected by the work on crop yields, the spread
of old and new diseases, and toxins in our environment, just to name a few. Moreover, the everyday
technologies we take for granted in our lives (cell phones, modern medical care, commercial flight, etc.) would
not be possible if it weren’t for scientific inquiry. As the majority of what you are about to read deals with
some of what we have learned about cellular physiology, I wouldn’t even be able to write it without the
intense labors of many superb biochemists over the last 50 years. But for all its merit, Science has its
limitations and flaws.
It doesn’t always work properly
Science has one great weakness. It’s performed by people. Being a scientist does not automatically
make one virtuous. An arrogant person will be an arrogant scientist. A greedy person will be a greedy scientist.
An immoral person will be an immoral scientist. A dishonest person will be a dishonest scientist, though a
dishonest scientist is usually discovered fairly quickly and shunned. Science is supposed to be empirical and
objective, but it doesn’t always work out that way because of human foibles. Two of my past colleagues, one
at the high school level and one at the college level, expressed frustration about their experiences with
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cutting-edge research they had been involved in. They both said there was no clear evidence to support either
conclusion they could have reached. The high school teacher complained that her PhD supervisor told her that
“we already know what conclusion we want to make, so pick the data that looks like it”. She confided to me
that there was a lot of pressure on the research team to get the intended results because more grant money
was riding on it. The college professor said in an e-mail to many of us that it was exasperating to find
seemingly valid data that supported exactly opposite conclusions, and it made her want to quit, but that she
stuck with her research because “in the end it comes down to what you believe”. Wow. This doesn’t exactly
sound like pure objectivity is always the guiding principle.
How the process actually works is unlike the posters which we science teachers put on our walls,
showing a rigid step-by-step “scientific method” with its systematic progression in a perfectly orderly way
without any of these “hiccups.” Most progress comes via other avenues than the way we portray it. Scientists
tend to find things because they are looking or thinking, and then at some stage they usually transition over to
forming a hypothesis that can be tested. Sometimes there is a fuzzy line between what qualifies as a theory
rather than a hypothesis, and some “theories” are only tested mentally or are never really tested at all. There
is sloppiness and questionable motives at times, but we count on the larger community to weed out the “bad
eggs.” Unfortunately, it works the other way around sometimes, and you are pressured to overlook things
because of conclusions that have already been drawn. Oops, that’s supposed to be the last step on the poster
(the conclusion), not the first! Even so, we have managed to make steady progress in a lot of areas of science,
and for the most part it is a self-correcting enterprise. Plain and simple, science is hard work, and even if there
were no graft, egos, hidden agendas or other obstacles, it is still a tough endeavor to do well. And it is worth
doing well. Those who have done it with integrity, objectivity and perseverance deserve our respect and
appreciation. When it works well it works pretty good, but even at its best it can only tell us so much. Why is
that?
The limitations of science
As science seeks to know the truth about the how the material world works, it cannot prove or
disprove anything immaterial. By definition, teleological (ultimate “why?”) questions, or things of a
supernatural, or transcendent nature cannot be investigated with empirical methods. Anyone who says
otherwise should be considered a pseudoscientist at best. They are probably more likely a charlatan. Good
scientists are innately skeptical, and you should be especially skeptical if a person were to say, for instance,
that they had a scientific instrument capable of detecting ghosts. Nah, don’t believe them, and hold on to your
wallet!
However, we all know there are things that are very real which cannot be accounted for with material
considerations only. Intense hatred, sacrificial love, appreciation of beauty, the joy found in good music, good
food and good company, or even our personalities all fall into this territory. You could say these are issues of
the “soul.” Spiritual issues, such as the existence/activity of good and evil, God, Satan, angels, demons etc. are
also beyond the purview of science. Issues of soul or spirit must be apprehended, searched out and
experienced with something other than a microscope or Bunsen burner, but they are no less real than the
elements on the periodic table. Not only is this so, but I believe the MOST important issues in life are things
science, by its very nature, is actually incapable of addressing. Whether or not I love people is of far more
4
value than how well I can teach them to balance chemical equations. What science textbook or study
published in a research journal can teach me how to love?
There is some overlap to be sure. We can talk about the amygdala being the part of the brain where
emotions are “centered,” but few people would accept the notion that their thoughts and feelings are nothing
more than a complicated series of chemical reactions, or that who they are can be reduced to a couple of bags
of charcoal briquettes (carbon), a few dozen boxes of matches (phosphorus), six cases of bottled water, a
couple of bags of fertilizer (nitrogen) and a smattering of other elements. Most would insist there is more to
our existence than just the sum of our physical parts. I certainly agree.
Even staunch atheists are hard-pressed to explain why they feel it would be wrong to murder their
family members. After all, the perpetrator is just a bag of chemicals who is the product of past chemical
reactions, leading up to the current situation which they cannot be held morally responsible for, right? I mean,
if there is nothing but matter then there is no objective basis for right and wrong, no free will, in fact no
unique or “sentient” mind of your own, only electrical impulses, hormones, electrolyte levels and so forth.
Running you over with my car has no more significance than smelling a flower or eating lunch in a purely
materialistic world view, because it’s all just chance encounters of complex aggregates of matter interacting
with other matter or energy. Though the newest insanity defense based on this dribble, dubbed “my brain
made me do it”, is gaining some momentum in our courts, nobody really believes that when push comes to
shove. Not when it’s their loved ones. Don’t tell me it’s merely a learned response to physical stimuli that
makes you feel the need to defend your family, or that because our “genome is selfish”, that’s what accounts
for the fierce protectiveness that instantly rises up in your heart and mind as they are threatened. The notion
that it’s just a complicated demonstration of your DNA preserving itself through natural selection is hogwash.
There is more going on here. Though science might be able to tell us something about a chemical imbalance in
the criminal’s brain, it cannot address those more profound issues of what makes something right or wrong.
Hitler and Stalin CHOSE to mercilessly murder millions of their own people, and you cannot convince me that
they were not truly evil men.
So, we live in a reality where material considerations are important, but not ALL- important.
Consequently, science is useful as a way of seeking truth, but it’s not the exclusive way, because it can only
investigate material phenomenon. However, material things are not the only things that are important, and
definitely not the only things that are REAL. Two-time Nobel laureate Linus Pauling said science should be the
pursuit of truth. Is there a difference between truth and reality?
Truth is like an asymptote
Interestingly, the ancient Greeks used the same word for truth and reality, “alethia”, and there’s a lot
to be said for that. It’s a bit like that set of lines you draw on a graph of a hyperbola, called asymptotes. They
form an x, and the curves approach them, getting closer and closer but never touching it. Science is a logical,
methodical attempt to get to that line in the natural world. There have been long periods of time in our
history where we really didn’t know our place on the curve, and we had no way to get any traction to make
progress. Then suddenly, someone would have an insight that they believed to be true, and perhaps they or
someone soon thereafter would develop the tools to test their idea.
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A great example of this was our lack of understanding about the way matter is constructed. Some
Greek philosophers thought it could be subdivided infinitely, while others said there was a lower limit
(“atomos”, meaning indivisible). All they could do was argue philosophically. No one could prove anything.
Then Aristotle threw his ignorance onto the pile (four elements), and since he was so well respected about so
many things, nobody dared question his views. He actually set us back badly for a long time, but thousands of
years later, after alchemists had groped around in the virtual dark, there seemed to be a breakthrough in
scientific progress.
A rich Irish aristocrat Robert Boyle, with his insatiable curiosity, careful observations and use of
instruments that he could afford, proved, among many other things, that cold was not a substance. A German,
Proust, who like Boyle with his painstaking experiments, was able to formulate the law of definite proportions,
meaning that there are exact ratios that matter combines in. Then a relatively poor English teacher, John
Dalton, who relied mainly on deductive reasoning, was able to make some even greater strides, and the
atomic theory was developed. But where on the hyperbola of seeking reality did we stand at that point? How
close to the “truth” were we?
Well, you know that there was still a lot to learn. Flash forward to J.J. Thompson and Earnest
Rutherford and you find that atoms were in fact not like tiny indestructible billiard balls, and atoms of the
same element are not all identical. From a distance, it looked like the atomic theory got us pretty close to that
asymptote, but when we “zoomed in” we realized that we were still far away from reaching it. That’s ok, it
was a step. Meanwhile, others had joined the fray, like Sir Humphrey Davies using a voltaic pile to separate
compounds into elements. His greatest discovery though was his understudy Michael Faraday, who did more
amazing things to advance scientific knowledge than I can possibly tally. By the way, Faraday was also a
devout Christian, demonstrating that the two (being an excellent scientist and possessing faith in God) were
not in the least incompatible. Though his former boss seemed more interested in getting inebriated with
laughing gas, Michael was forever trying to find out what God was up to, how He had fashioned the universe,
working feverishly to discover the principles at work behind phenomenon that others just shrugged their
shoulders at. I find it intriguing that his faith actually made him a more productive scientist, not less.
Meanwhile, Lavoisier got science off the ground in France, also working tirelessly with his wife doing
carefully planned experiments. He ingeniously proved the conservation of matter by rusting a gun barrel
within a closed system. He also proved that the Englishman Joseph Priestly was mistaken about the theory of
phlogiston, but Lavoisier was himself mistaken about the caloric theory. He was such a great scientist in other
respects that it was very difficult to question his conclusion about what makes matter change into its various
states. Even though he lost his head in the French revolution and could no longer be an active voice in the
scientific community, it was still extremely difficult to disprove his theory. It seemed to work so well and
account for so many things. You could even say that he was respected too much, because even after Count
Rumford plainly demonstrated with cannon boring that you could generate indefinite amounts of heat with
motion, the caloric theory still stood. It wasn’t until an English brewer, James Joule, demonstrated again that
mechanical motion really is interchangeable with heat energy that Lavoisier’s theory finally died, and we could
move forward. Afterwards, through the efforts of Carnout and Lord Kelvin, the ultra-important first and
second laws of thermodynamics could be formulated, but not until the caloric theory had been debunked.
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This process has repeated itself over and over again through the centuries. We think we have things
more or less figured out, only to find that new data shifts our paradigm dramatically. Sometimes it’s
particularly difficult to make these shifts though, especially when the established/accepted theories seem to
explain things so well, or are the work of someone prestigious such as Lavoisier or Newton. It wasn’t until
Einstein came along that we would have even thought to question Newton, and in fact Einstein’s theories
were so radical that the Nobel Prize committee was afraid to mention his general and special theories of
relativity. They opted to award him the prize for his work on Brownian motion instead. This was no small
thing, as he proved once and for all the existence of atoms, but it had nowhere near the revolutionary impact
of relativity.
Later he had to come up with a “fudge factor” for his equations called the cosmological constant. He
knew his theories were based in reality, and yet this adjustment was necessary to make the numbers work
out. Toward the end of his life he thought that he had made a huge blunder in doing so, when in fact he had
not. We know now that this constant is crucial for the structure of the universe! Einstein wasn’t satisfied with
“good enough” or agreeing to disagree. He went to his grave trying to find a unifying principle that could
harmonize the world of the very large, where relativity made sense, and the realm of the very small, Quantum
Mechanics. Big things seemed to operate smoothly and predictably, but the quantum world was chaotic. He
was convinced that “God doesn’t play dice,” and because the world of the very large consisted of the very
small, he refused to believe that there was no explanation for the seeming incongruity between these two
worlds. Like Michael Faraday before him, Albert was driven by the desire to “know God’s thoughts” and would
not believe that the creator of the universe would leave us unable to comprehend the problem. By the way,
we still don’t know the answer to this riddle. 
Other examples of surprises and unsolved phenomenon abound. Because of the work of Einstein, we
thought nothing in the universe could travel faster than light, but then we found really big structures near the
edge of the visible universe that forced us to reconsider. Now cosmologists believe that during the first
fraction of a second of the big bang things must have expanded faster than the speed of light to account for
this. Oops. I don’t think it would really bother Einstein that his theory has been contradicted, as he had done it
to Newton too. It was also assumed that the expansion of the universe after the big bang would be slowing
down due to the mutual attraction of gravity, only to discover by studying type “A” supernovas that the rate of
expansion is actually speeding up. Uh…how do we account for this? Well, cosmologists and astronomers now
believe there is such a thing as dark matter and its counterpart, dark energy, behind this radical shift in our
previous understanding, but we can’t really study these directly because they are “dark.” Hmm, you mean
there are things which can and must be at work in order for the universe to exist as it is, but we don’t
understand them, can’t observe them or really even prove their existence? Is it possible for something to be
reasonable without being verifiable through empirical methods? Believing in something we cannot see…Well,
how about that!
That pretty much sums up the march of progress in science. Just when we think we’ve done all but
work out a few minor details, along comes a major kink in the works that causes us to frantically scramble to
figure out what’s actually going on. It’s like someone keeps moving the goal posts while we’re playing the
game! We are not daunted though, and we spare no expense of time or effort or money to get to the bottom
of things the way they really are. The large Hadron collider is proof of this! Perhaps it will unravel the mystery
7
of gravity for us, because even though we can quantify it, we still don’t have a clue what causes it! Perhaps
they’ll find gravitons, perhaps not.
Despite setbacks and delays, what we hope is going on as we search for greater understanding of the
universe is that we are creeping closer and closer to that line of material “truth” or reality. Sometimes we
come to find that we were not nearly as close as we thought, and we have to go back to the drawing board.
That’s ok, because if we remain curious and humble then we won’t be an obstacle for progress, and even if we
can’t quite figure something out it’s likely that someone else will and we all benefit. That’s how science is
supposed to work ideally. However, strong personalities and reputation sometimes get in the way. Sometimes
the blockage goes on for tens, hundreds, or even thousands of years. The most difficult theories to challenge
are those which have gained almost universal acceptance.
Surely this isn’t still happening, is it?
There is one theory which will probably never be successfully challenged. These days, few people
question Darwinian evolution. The difficulty is that his theory has gained so much momentum because it
seems to be supported by a large body of evidence and appears to explain so many things. It is far more
difficult to challenge than Aristotle’s physics, or Lavoisier’s caloric theory, or Newtonian physics ever were. It is
heralded as an established and incontrovertible fact. Consequently, most scientists either don’t want to
question Darwin because they agree with him, or they’re afraid to because it will make them look like some
backwoods hick and destroy their credibility within the scientific community. It’s a classic example of the “tall
poppy syndrome”. As they say in Japan, “the tall nail gets hammered down.” Nevertheless, I question Darwin,
and it doesn’t make me less of a scientist. I’m vastly outnumbered, but that’s ok. What matters is that I have
good reason to. My reasons for rejecting Darwinian evolution are rational. I don’t reject his theory because my
gran-pappy did, or because some religious group that I align myself with is against it. His theory is deeply
entrenched and widely accepted without second thought, but I don’t buy it. I have peeked behind the curtain
of the great and powerful Oz, and I see enormous problems.
Most don’t realize that Darwin knew absolutely nothing about cells, and I believe his theory would
have been a tough sell if others in his day had known what we do now about biochemical complexities, but
maybe not. Perhaps it would have gained just as much support because of what it seems to offer, namely,
autonomy from God. Therein lies its real appeal. Carl Marx absolutely loved the theory, because it justified his
own social theory of an evolving society, with the proletariat rising up to overthrow the rich, and communism
replacing capitalism. It is the darling theory of humanists today, because it makes them feel secure in their
faith in humanity. I haven’t quite figured that one out in view of our supposed “progress.” Just one viewing of
the evening news puts a severe dent in that sentiment. To be fair, Darwin did have one great insight that I can
see; that of natural selection. It’s just that it doesn’t do what he thought it did. While natural selection
explains quite well how species adapt to pressures they encounter by shifting allele frequencies within their
populations, it does not explain how each species would have gotten their genome in the first place. As a
satisfactory explanation for how life as it is could have come to exist, it falls way short. Nevertheless, it’s held
together by the bubble gum and bailing wire of needing it to be correct. Because of humanity’s unwillingness
to give up this hard-fought independence from any accountability to God, his theory is almost impossible to
dislodge now.
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Whether it’s good, bad or ugly is up to us
Having said all this, I find that science is a bit like fire in the sense that you can either cook your food,
warm yourself, make steam and harness it to do useful work, or you can burn your house down around your
own ears! We have gained the capability to destroy the world many times over, and many ethical questions
surround some of the other technologies that we have developed. As I like to tell my students, science is
neither moral nor immoral but amoral. The “good” of science depends on what you do with it! Many great
minds have grappled with complex riddles in nature and made great strides, but I do not deify science as if it
were the ultimate source of all truth. In spite of the overly optimistic and self-reliant spirit that science tends
to encourage, there are many important things that science will never be able to answer. Not only is it
incapable of leading us into all truth, its purpose has also shifted gradually. Other agendas have entered into
the picture. You may think of the “military industrial complex” or other commercial and political interests
hijacking science, and I suppose this does happen sometimes. But there is another agenda that has become
more and more dominant.
The most destructive development I have observed as an upshot of scientific progress is that it has
emboldened vast numbers of people to feel arrogantly defiant towards God (“who needs God, we have
science!”) and to pressure others to join with them. There has been a groundswell of antagonism against faith
in God, and the form it takes is by insinuating that anyone who believes in Him is by very nature superstitious,
unreliable, unstable, and sub-par intellectually. There is a not-so-subtle attack on the scientific credentials of
anyone professing faith in God, as if it’s not possible to believe in Him and be a genuine scientist. This is
shameful, and though I doubt it will lessen, it at least needs to be seen clearly for what it is: using science to
proselytize for the alternate religion of atheism. I am not alone in this conviction in the scientific community.
As I have already mentioned, some of history’s greatest scientific minds have acknowledged God as the
creator of the universe, and some great minds still do. I have seen a document signed by over 600 PhD science
professors/researchers from reputable universities who question Darwin, and it’s reassuring to know that I’m
not crazy.  But here’s the sad part; their views are brushed aside, marginalized or even viciously attacked
these days because they are an inconvenience or embarrassment. The fact that great scientific minds of the
past such as Kepler, Boyle, Galileo, Copernicus, Davinci, Newton, Faraday, Einstein and Schrödinger among
many others, professed belief in God is also not a foil against the aggressive agenda of so many scientists
today. You don’t have to look far and wide to find a prominent scientist using their “pulpit” to denounce or at
the very least belittle faith in God. It’s a good thing truth does not require consensus.
What this writing is not for
In any case, I want you to know that even though there have been innumerable scientific discoveries
over the years which have confirmed my faith in God, I wouldn’t and don’t need to know all the cool science
stuff as a pre-requisite for believing in Him. I don’t lean on science as some kind of crutch to reassure myself.
Unfortunately, I have gotten that feeling when reading other writings that you could call “Christian
apologetics,” and it feels like some authors really are apologetic, grasping somehow to use science as a way to
lend credibility to their faith.  Some even go so far as to try to use scientific explanations for miracles so that
they will be more palatable, which is absurd. Believing that God can perform miracles just means that you
acknowledge that He has the right and the ability to do as He wishes with His creation. You don’t suddenly
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lose your scientific credentials for believing that God can do as He wills. Besides, there are more profound
reasons that I have come to have confidence in God’s existence and character than the wonders of His
creation or other miracles, as much as I appreciate both. Simply put, I have experienced His love and mercy.
I’m not writing this book to reassure myself that He is real and the legitimate creator of the universe. Besides,
God Most High is not up for a vote anyway, and nothing I could say would improve on the reality of His eternal
self. He doesn’t need my “defense” of Him! I just want to declare what I have been graciously allowed to see
because I can’t help it! 
No arm twisting possible
Funny thing is, the universe seems to be set up in such a way that there is no irresistible proof of God’s
existence, and perhaps that’s just how He wants it. There are some very loud and influential voices in the
scientific community who feel justified in their denial of Him by claiming that if He did exist, it’s unfair that He
does not somehow overpower them with irrefutable or undeniable evidence (and implying therefore that He
in fact is not real). As it is, nobody who refuses to believe in Him can be convinced regardless of persuasive
evidence, because in the end we all believe what we want to for various reasons. Conversely, nobody who is
convinced that “He is, and that He is a rewarder of those who diligently seek Him” can be dissuaded either.
Ironically, there are scientific studies that demonstrate this well-documented human phenomenon. We
actually become even more deeply entrenched in our views BECAUSE of the efforts of others to “prove” we
are mistaken. Our views get reinforced over time regardless of evidence to the contrary unless something
radical changes on the inside.
In light of all that, I know I can’t prove anything to you, and you may conclude that I am the one who is
way off! I realize that many who encounter this writing will just blow it off without even reading it, while
others will perhaps read it skeptically, ready to pounce. Maybe you’re already so mad that I would dare to
question Darwin that you want to tear me to pieces, I don’t know. Perhaps you will reconsider after you’ve
finished reading. Maybe, but I’m not counting on it. So much has already been said, minds made up, and
hostility fanned on both sides of an ongoing debate. Even so, I invite you to consider some things with me,
especially if you are a science teacher, professor or student. Try to give it a fair hearing, and I think you’ll find
sound reasoning which is difficult to ignore with honesty or integrity.
However, I really don’t want to argue with anyone, only tell you what I see. Judge for yourself, but I
believe that the bulk of the scientific community has gone out of its way to overlook some profound things,
and I will try to elucidate them to you. It is my hope and prayer that I can offer what follows in humility, and
that in reading and digesting this with an open mind and soft heart you can benefit in some way by seeing the
magnificence of the God who “with wisdom, created the heavens and earth” and of His Son who “apart from
Him nothing was made which has been made. Remember that Greek word “alethia”? It’s the same word Jesus
used when he said of Himself “I am the way, the truth and the life. No one comes to the Father but by Me”
and “you shall know the truth, and the truth shall set you free”. My hope is that you will acknowledge Him for
who He is and submit to His rightful rule of your life.
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Part 1: The Prevailing Theories Don’t Really Cut It
Life, where it all begins…
I’m going to start and end this discourse talking about the origin of life. Without a doubt, one of the
greatest difficulties scientists have had is finding a natural explanation for where life came from. How could it
have gotten off the ground in the first place? We are familiar with the theories of forces such as radiation and
electricity acting on simple molecules to build more complex ones like amino acids (Stanley Millers’ famous
experiment) which could presumably be used to assemble even more complex proteins. The theories go on to
offer explanations for how lipid microspheres could have self-assembled to form rudimentary cell membranes,
and how nucleic acids could have formed with clay acting as a catalyst. The most modern theories place the
origin of life in the deep oceans, where chemical energy from thermal vents could drive the formation of the
first cells.
Problem is, there are several very fundamental and unavoidable glitches in these theories which make
them untenable explanations. Before going into it, first let me reiterate that I’m not here to argue. I’ll just spell
out the impasse as I see it, and then move ahead to the stuff I really want to talk about! Essentially, there
are two root issues that the theories fail to address, and without grappling with these core questions, no
theory can explain the origin of life by mechanistic means. However, if one acknowledges that the universe
was fashioned by God and that “all things are from Him, through Him and to Him”, the perspective changes
dramatically. Like I said before, nothing I can say will convince you of this, but since I already believe in His
loving greatness, everything I encounter by way of learning new things about the universe (especially the
intricacies of life) inspires admiration and appreciation for His vast genius and creativity. A large number of
scientists express wonder and awe at how all this complexity could have arisen by chance while scoffing at
what they see as backwards and superstitious worship of a God as the creator of everything (and with this, the
implication that anyone who does so is, by definition, unscientific). So be it. You can pick your world view, but I
believe it is far more reasonable to credit His boundless imagination than to try and “work around Him” and
write Him out of the script. I opt to worship as I learn, and I hope to infect you with the same sense of
staggering bewilderment.  So first, the two reasons why I don’t buy the party line, and then on to the good
stuff!
Popcorn strings, trains and balsa wood planes
The first core problem is one of information. I spent many years in a different career as a structural
inspector, working closely with engineers, architects and builders to ensure that structures were being built
according to the plans. My role was to ensure that the contractors were actually executing what was in the
blue prints, down to minute details. If corners were cut, materials incorrect or craftsmanship sub-par there
could be disastrous consequences for the future occupants because it would not be built as it was intended to
be. You can probably make the connection with life, with DNA (or its transcript RNA) serving as the blue prints,
ribosomes and transfer RNA being like the contractors, amino acids as the building materials and so forth. All
that is well and good, and cells do what they are supposed to when the plans are executed properly. If not,
you have disease, deformation or death. But who wrote the plans?!
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Darwinian evolution cannot possibly explain the final outcome that we call life. Though natural
selection is a really important mechanism that keeps life going strong, it could not have generated all the code
that exists. It does a wonderful job of ensuring that life can respond to pressures, changing the allele
frequencies within a population so that it can adapt and continue on. However, the Darwinian theory relies
solely on one thing for the creation of new code for natural selection to act on, namely, mutation.
Unfortunately, mutations make a mess of the code and are not credible as a source of creative power,
regardless of what the textbooks say. In short, they (mutations) almost always make you either less fit or dead
outright! The rare instances that they are “neutral,” or even more rarely “helpful” cannot account for the vast
addition of well-oiled and fine-tuned instructions that it takes to make a mammal as compared to a bacteria.
In fact, even bacteria are too intricate and sophisticated for me to stomach the notion that they could be
happenstance. More importantly, mutations are random accidents that occur to an already existing set of
instructions, and the question of where the blueprints for even the simplest life forms came from is not
answered by believing that it could be amended successfully in a gigantic way.
Maybe it would be good to spend a moment examining how the code works in order to gain an
appreciation for the insurmountable task at hand which mutation would have to account for. You are
probably aware that nucleic acids are code for protein synthesis, but accidental assemblies of these large and
complex molecules cannot explain the reverse engineering that would be necessary in order to accomplish the
creation of even the simplest functional cell. The most basic bacteria are incredibly complicated when you
consider their structure and function. It’s a really large “pill to swallow” that the working proteins which cells
are built out of could randomly occur and accomplish anything meaningful. Allow me to explain what I mean.
Let’s grant the existence of ribosomes and the other machinery such as transcription factors, spliceosomes
and tRNA which are necessary to translate nucleic acids into proteins (how they could arise spontaneously is
another story). If all this is in place in a functional cell, the main issue at stake in the genetic code is the
sequence of the instructions.
Each nucleotide subunit of the DNA (or RNA if you believe it came first) specifies which amino acid
comes next in the strand of protein which is being built. Three letters of the code specifies one amino acid for
protein synthesis. These three letter units are called a codon. In some ways it’s a bit like the sequence of box
cars on a train, where some are red, some yellow, some blue, some carry coal or autos and so forth, and yet
it’s not like that, because the locomotive will pull the train to its destination regardless of the sequence of the
cars. But what if the locomotive couldn’t move unless the order was right? That would be weird, but in
proteins the sequence of the amino acids, and hence the three letter codons in the DNA, really does matter
intensely.
In order to make a functional protein there has to be an ultimate shape that it ends up forming. This
shape determines what the protein is able to do, and in fact, what it is intended to do within the cell, or
outside the cell sometimes in the case of multicellular organisms. But what does this final shape have to do
with the sequence of the amino acids? Well, as it turns out, the protein won’t hold its shape after being
folded, twisted and bunched up unless the right amino acids end up being across from each other and can
make a bridge-like bond which keeps it from unfolding and unraveling. Some amino acids have a sulfur atom in
a region of the molecule called the “R group” which is the part that distinguishes between them. There are 20
different amino acid building blocks, and most lack the sulfur atom. Only when these amino acids are placed in
the long chain of amino acids in the right position do you maintain the final shape. The problem is, these
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particular amino acids have to be sometimes hundreds of units away from each other
in the single file line that the ribosomes chug out as they read and translate the code.
If they are in the wrong position in the sequence (called the primary structure), then
the twisting and folding (such as alpha helixes and beta pleats called secondary
structures) won’t be able to give rise to three-dimensional shapes (tertiary structures)
which will “stay” when they themselves fold up. It would be a bit like the rubber band
engine on a balsa wood airplane (you know, the kind with a plastic propeller). When
you turn the prop it twists the rubber band into thicker and thicker wads that take on
a three- dimensional lumpy shape, but there is nothing keeping it in that shape when
you let go, so it just unwinds again.
Another analogy may help make this clear. Imagine a child threading popcorn on a needle and string. If
some of the pieces were Velcro and the child randomly sequenced them hundreds of pieces long, what would
the odds be that a specific shape required for final structure and function would be achieved if it could be
maintained only when certain positions had a Velcro piece? In fact, this would have to be true many times
down the length of the string, where if a Velcro piece was missing from any of the right spots, the ultimate
shape could not be preserved once it was attained. Not only that, the child would have to make thousands if
not tens or even hundreds of thousands of other strings with just the right sequence in order to make a
working cell. Remember, the ones that can make a sulfur bridge (disulfide bond) have to end up opposite each
other once all the folding and twisting is done or the protein will not work properly. So, you have to know
what the final three-dimensional shape has to be in order to program the code to achieve it. Moreover, you
have to know how many proteins are needed and what their jobs will be in order to pull it all off! So the
question is not just one of whether or not the complex molecules of RNA and DNA could arise by random
chance, but more fundamentally, it is a question of information, foreknowledge, planning and intent.
To grasp the magnitude of this accomplishment, let’s consider the size/length of the code for a
generic, rod-shaped bacterium like E. coli. If you were to type the nitrogenous base sequence in 12 point font,
it would fill the entire collection of one of those old-fashioned sets of encyclopedias! If just one of the letters
in the code was goofed up it might seriously harm the bacteria. Take a guess how long the code is in OUR
genome? Would you believe we have 3 billion base pairs?! When you realize that there are debilitating
diseases such as Tay-Sachs that result from a single point mutation (just one letter of the code being wrong) it
staggers the mind! Granted, some mutations are more “survivable” than others (like a letter being switched
out for a different letter) because of the redundancy that’s built into the code to ward off these outcomes, but
others are horribly destructive. Omissions (deletions) or additions wreak havoc, because they shift all the
instructions “downstream” one spot. As an illustration, try reading this sentence if you take out a letter e in
the first word the, and shift everything back a spot (remember, codons are read in groups of three): the dog
ate her bags. It would read “thd oga teh erb ags”. Gibberish. When this happens to the DNA, the sequence of
amino acids will probably be wrong, a deformed protein is likely and its function is subsequently lost. And
there is another kind of mutation called a translocation that is especially devastating. This is when portions of
the code get misplaced to some other location in the DNA and the coordination/control that previously
existed is shattered.
Organisms fight these alterations tenaciously with attempts at repair, and the maintenance systems
which perform this invaluable service are absolutely mind bending. The genetic code is jealously guarded for a
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reason. Suffice it to say for now that DNA isn’t called “the miracle of life” (mind you, by professed atheists) for
no reason. To me, it seems more reasonable right at the outset to conclude that the genetic code, just as with
all codes containing information, has a writer. I see enormous evidence that an author has “written” it for a
specific purpose, and reject the proposition that it arose randomly, with accidental serendipity creating
delicate and incredibly precise structures, complete with a host of specific functions which must work in a
coordinated fashion in order to create even the simplest living cell. You are free to conclude that is the case if
you want, and I’m not trying to insult you if you do, honestly. I’m just calling it like I see it, that’s all! There are
actually more serious and convincing reasons to reject the materialistic world view, but let’s save that till the
end of the discussion. For now, trying to explain how this level of complexity, harmony and order could arise
from chaos is only one of the huge holes in the theories for the origin of life from non-life.
On Persian rugs and Archimedes
Before moving on to the second great fallacy of Atheistic materialism, I want to drive home the point
that the information required to achieve the sophistication in life is in fact deliberately programmed, not
accidental. Around 1800, there was a French inventor named Jacquard who came up with a revolutionary way
to manufacture Persian rugs. He devised a loom that was controlled by punch card instructions which greatly
increased the speed of manufacturing the highly intricate patterns that had once been so painstaking. His
ingenious mechanism was one of the earliest computers, because it utilized input (the cards) to create output
(the finished rug). Though he could not have been aware that it was the harbinger of things to come in the
information age, it was certainly an industrial breakthrough at the time. Prior to his invention, a team of two
highly skilled weavers could only produce an inch or two of rug in an entire day! However, whether it was the
original artisans who were painfully slow or his analog computer (that’s what the loom was after all) which
could mass produce the rugs, someone had to conceive of the intended outcome. The design which was
created had to be envisioned first and then executed. In the case of Jacquard’s loom, there is a striking parallel
between the punch cards and DNA. It is simply inconceivable that the final outcome of a gorgeous rug or a far
more intricate living thing could be produced randomly. The loom could not even construct itself, let alone
write a program that would control its operation. A mind HAD to be involved, from the artistic vision of the
intended rug design to the creation of a machine that could execute pre-programmed commands that would
produce this design automatically. Life required a far more ingenious designer, because it is not just a static
two-dimensional pattern for which code had to be written. DNA contains all the instructions for constructing,
regulating, repairing, and coordinating a whole host of interrelated structures and functions within a
continuously changing organism. Why would we come to any other conclusion but that life was indeed
designed by a programmer who wrote OUR code? If a mind is required to make a Persian rug (whether by
hand or by automation), why not life? We see Jacquard’s loom in action and know without a doubt that he
painstakingly designed it, marveling at his genius. The evidence is unmistakable.
Along these lines, there was no question as to who the mind was behind a vast number of
mathematical insights and ingenious mechanical devices in ancient Greece. Archimedes was renowned for not
only his calculations of such things as the distance to the moon and the volumes of shapes like the cylinder
and sphere, but also the design and construction of practical devices. He conceived of a way to lift water from
rivers which utilized an auger inside a cylinder, and designed huge war machines to defend Syracuse from the
Romans. He was so successful, with such devastating machines as a giant claw that could reach out from the
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city walls and lift ships by the prow and then drop them, that the generals became terrified of his intellect and
capabilities. But the most amazing machine which has been attributed to Archimedes is the Antikythra
mechanism. Whether he was responsible for this invention or not; the ancient device, which was capable of
being programmed to predict solar and lunar eclipses, the phases of the moon and the motions of the planets,
was astounding in its complexity. I highly encourage you to investigate this device, because it is a great
example of unmistakable design by someone truly brilliant. The intricacy of the brass gears, with their
diameter, number of teeth, complex interconnections, and the sheer number of how many were packed into
such a tiny compartment is astounding. The desired outcome had to be known in advance in order for the
machine to be designed in such a way to account for such challenges as the eccentricity of the moon’s orbit,
the discrepancies between the lunar and solar calendars, etc. An ancient wooden box full of tiny gears, labeled
with program inputs, complete with output dials, capable of phenomenally complicated celestial
computations was obviously a great achievement; the work of a great mind and skilled craftsman. Why would
we come to any other conclusion about the sophistication observed in life?
Darwin scoffed at it having been planned in advance and proposed his theory in an attempt to explain
how it could have arisen by an undirected process. But then lo and behold we discovered that it is the product
of a code, which makes life look an awful lot like a directed process with an architect! So why do so many still
stubbornly refuse to acknowledge that something far more complex than Jacquard’s loom or Archimedes’
machines had a designer? It’s logical to see a mind behind the programming found in such analog computers,
which, though impressive, don’t even hold a candle to life. Why the obdurate and illogical switch in reasoning
when it comes to DNA and its output? Hmm…
Rolling rocks uphill
The second gigantic problem with the scientific theories attempting to explain life arising from non-life
is one of thermodynamics. It has been said that nothing more than gravity is needed to account for the origin
of life, because the collection of raw materials into a localized area is all that is required to provide the
opportunity for life to arise spontaneously. Others have cited the second law of thermodynamics, the fact that
heat moves from areas of high concentration to low and that randomness in the universe is always increasing,
as reason enough to reject accidental creation of life, since it implies that left to their own, the raw materials
would tend toward disorder and decay. This “arrow of time” we observe in the universe seems to be a
powerful argument against life arising spontaneously, but it doesn’t quite refute the prevailing scientific
theories. Even though the odds of a system becoming more organized randomly are astronomically low
according to the law of entropy, proponents of life arising accidentally still rest their case on the miniscule
chance, relying on large amounts of time utilizing random events to even the odds. Before delving into more
detail about thermodynamics and why it really is impossible that life occurred randomly, perhaps it would be
helpful to consider the basics of the law of entropy.
When the universe began, it was as organized as it will ever be, and has been becoming more
disordered ever since. The highly ordered “initial conditions” of this event are what dictate the one way
passage of time, from past to present and the ever increasing chaos in matter and energy. The way the
universe has been developing ever since its inception can be described by a famous equation developed by
Boltzmann, S=k log w. S stands for entropy (randomness), k is “Boltzmann’s constant”, log is the natural
logarithm, and w stands for the number of “microstates” possible in a system. For example, if you were to
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yank the cover off one of Shakespeare’s works and throw the pages up in the air, there would be an
unimaginable number of possible outcomes for the way the pages landed (probably more ways than there are
atoms in the universe), because of the number of degrees of freedom inherent in the system. Only one of the
possibilities is that the pages would spontaneously come back together inside the cover and land in the exact
order, right side up, turned with the page numbers at the bottom corners, etc. We are understandably
dubious about the chances of this occurring, because we don’t observe non-living matter behaving this way,
yet this is exactly the proposition that has to be accepted in order for the spontaneous generation of life to
occur. Actually, it doesn’t even come close to describing the “long odds,” because the number of possible
microstates in the matter required to build a cell is far beyond this illustration with the book tossing. But,
however unlikely, atheists have no alternative but to believe it must have actually happened. Even so, the
reason that life could not simply arise spontaneously is a bit more complex than that. You have to dig a little
deeper into thermodynamics, beyond just enthalpy changes (movement of heat) and changes in entropy
(randomness) according to the second law, and consider something called Gibbs free energy.
The interactions between various forms of matter, such as chemical reactions, happen the way they do
because there is a continual effort on the part of the universe to achieve lower states of free energy. That’s
the energy that’s available to do stuff. Without getting too complex, the question of whether or not a process
will be spontaneous (happen on its own without outside intervention or expenditure of energy to force it to) is
a combination of considering enthalpy/temperature, entropy and free energy changes in a system. For
example, nails will rust when exposed to oxygen and water because the products have less free energy and
more randomness (entropy). Most exothermic processes (those that have negative enthalpy changes/ which
give off heat) are spontaneous and most endothermic processes are not. Most processes that result in an
increase in disorder are spontaneous too. Even so, it is possible for an endothermic process or one that
reduces entropy to be spontaneous, so long as there is an overall reduction in free energy. Also, in all of these
scenarios there can never be reduction of the overall entropy of the universe, even if a system became more
organized. There has to be some increase in entropy that is equal to or greater than this localized reduction in
order to offset it. Anyway, what’s all this got to do with the origin of life?!
Well, to answer that question we have to consider what life does thermodynamically. Life organizes
itself. It goes to great lengths to reduce its own entropy, technically speaking. This is obvious to all of us,
whether it is plant, animal or bacterial life. But how do we accomplish this self-organization? As mentioned,
this continual maintenance of our cells, cellular work and so forth requires an energy input from outside,
because the reduction of entropy would not occur spontaneously otherwise. So far so good, but where does
the energy come from? Well, we know that autotrophs (plants) get the energy needed to build their own food
from the sun, and we heterotrophs (animals) get it from eating autotrophs. Here’s the amazing thing though.
All living things recruit free energy from their environment so they can order themselves and get stuff done,
but the process of recruiting the outside energy IS SPONTANEOUS! Whoa, did you catch the significance of
that? Nothing else in the universe performs this feat! What’s more, this recruitment of outside energy goes on
continuously. Without this non-stop grabbing of external energy to fight the second law, life quickly dies. This
process is so commonplace to us that we take it for granted, but the conundrum has not been lost on scientific
minds. We know it’s strange, which is why scientists are in a headlong pursuit to confirm if it could have arisen
spontaneously elsewhere. If you conclude that life would inevitably arise of its own accord given sufficient
time and the right conditions, then it should be no big deal, but it is a big deal! In fact, finding life elsewhere
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would not remove the basic problems of thermodynamics and the origin of information. It’s just as unlikely to
have arisen randomly anywhere. Not here, not elsewhere. Not an accident.
The ultimate enigma
The existence of life is tantamount to a rock rolling itself uphill spontaneously. We know that doesn’t
happen, so how could the rock pull it off? This occurs on a daily basis no less, because the rock keeps rolling
back down every day! Well, it could recruit the local wind to push it uphill of course! Before you scoff at that
notion, this is exactly what life does all the time. Since it already exists, we just accept that it does this amazing
feat, but the problem lies in how the rock could have ever developed this capability in the beginning. It’s
extraordinary. Nothing else in the known universe does this, and life makes it look easy! Life is a serious
anomaly, owning the ability to decrease its own entropy but operating within the second law of
thermodynamics. It’s not breaking any laws, just taking advantage of a loophole! It decreases its own entropy
by increasing the overall disorder of the universe at the expense of its environment (think waste products and
landfills). It’s like an island of order surrounded by an increasingly tumultuous ocean, and it helps to make the
ocean more a jumbled mess by the process of harvesting energy and subsequent activities to maintain itself.
An even more stupefying fact is that life goes on even though no individual organism can stave off the second
law indefinitely. We all eventually succumb to decay and death, our final equilibrium state in the universe. But
life has an ace up its sleeve! Seemingly aware of the inexorable march of the universe toward chaos, it has a
way of prolonging its existence by passing on the method for self-organizing to another generation through
reproduction. Huh? That’s an enigma and a half! So anyone who blithely states their mechanistic explanations
of how life could have arisen randomly must pass the harder test of explaining how an unintelligent
hodgepodge of chemicals could have known this would be a necessity, and developed a contingency plan for
its own propagation as well. Wow, now THAT is a real horse pill to swallow! Again, it’s much more reasonable
to conclude that life was, in fact, NOT a random occurrence.
Even some scientists who are atheists have acquiesced on this point, and they are prepared to
consider that it was perhaps “seeded” from elsewhere, like bacteria falling to the planet on an asteroid from
somewhere that life already existed. This doesn’t really answer the question though, just postpones it briefly.
Life only comes from life, and in order to be alive you have to consist of at least one functional cell. Just like
we learned in high school biology, the cell theory is the bedrock of our understanding of all of life. Living cells
only come from other living cells, plain and simple. We debunked abiogenesis long ago (remember Pasteur
and the meat with maggots?). Even if it were possible for bacteria to develop into all the living things we
know, which as I said is a stretch that I am convinced goes way beyond credibility, you would still have no way
of making the first cell just because you have all its essential ingredients. How can I be so sure? Well, after
Humpty Dumpty falls off the wall, is there really any way to put him back together again from his parts, even
when they are all present and accounted for? No. If you lyse a cell (break it open and let the insides gush out)
there is no way to restore life back to it just a moment later. Even though all the perfectly formed structures
necessary for life are still there (never mind how they were created in the first place), you can’t quickly stuff all
the guts back in and call it good! We’ve all seen things die, but what’s the difference chemically and
structurally between a live person and a corpse the moment after death? Nothing has changed physically
when you get right down to it.
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But wait a minute. We hear stories of people falling into freezing cold water whose core temperature
drops to 70 degrees, dying clinically, but then being “brought back to life”, right? Have we really considered
the root cause of the difference? I recently read an amazing, but not surprising, article in a popular magazine (I
think it was Newsweek) that was written by a neurosurgeon. He gave an account of how he had been clinically
dead for seven days due to a severe infection in his brain stem, but he was resuscitated and claimed he had
been aware of everything that went on during his clinical death. Prior to his experience he was of the school of
thought that our minds are just the sum of the electrical impulses going on in our brains, but there was
documented proof that these had all ceased during this time. Needless to say, he has changed his “mind!”  I
realize that his and other “back from the dead” stories are anecdotal, but there really does seem to be some
special, even bizarre phenomenon going on with living things. Consequently, some are even willing to
attribute the origin of life to the intervention of an “alien” intelligence. Still, this only pushes back the question
a notch. Why would we “go there” with aliens but not God? Hmm, now THAT’S a good question to ask! Let’s
revisit it later, but now, on to the good stuff.
Part 2: Just a Few Examples of Evidence to the Contrary
Zippers and self-aware chemicals?!
Ok, I want to try and explain why even atheists call DNA a
miracle. Though it is a fairly complicated and really long molecule,
nobody in their right mind would attribute intelligence to it, let alone
a consciousness of its own shape. We can’t see the backs of our own
heads without two mirrors, but this stuff seems to know exactly how
it’s shaped. You know how you learned in high school biology that
DNA replicates during the S phase of the cell cycle? Well…how does
that happen exactly? You may have covered that part of the
curriculum in great detail and learned that there is an enzyme called
helicase that mounts the DNA and starts to unzip it. In conjunction
with helicase, another enzyme called DNA polymerase mounts the
DNA Polymerase in action
unzipped DNA to begin replicating the separate sides. More
accurately, two of these usually work together, one on each
side of the DNA, and to speed things up several pairs of these mount it at some distance apart and work
toward each other in a coordinated fashion. Together with another enzyme called ligase, which connects the
new sections together, the work of making duplicate strands that are exact replicas begins. The building blocks
are called nucleotides. These consist of one of the nitrogenous base “letters” in the code bonded to a sugar
called deoxyribose and a phosphate group. The sugar and phosphate make up one unit of the backbone which
is created when the nucleotides bond covalently with each other, while the base that’s connected to the sugar
points inward. A series of three of these constitutes a “codon”, which codes for an amino acid. The two
original sides of the double helix serve as templates for new base pairing to occur. You remember A with T and
C with G, right? Since the originals are just duplicates of each other running upside down, the two new double
helixes that are created are exact copies of the original. That’s why DNA is said to be “semi-conservative”,
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because each new molecule has one of the old strands plus a new one. The new strands are then wound back
up for protection.
Anyway, in order for this whole process to work, the enzymes (helicase, DNA polymerase and ligase)
have to be form-fitted to do their jobs. Remember, enzymes are proteins, and their shape determines their
ultimate function. Fine, they’re shaped right to accomplish this particular purpose in keeping with that
mysterious ability that life possesses called reproduction, whether at the cellular level to repair damage to the
organism, to grow, to reproduce altogether in the case of unicellular organisms, or to make reproductive cells
in the case of multicellular organisms. You have to double your DNA before you can do any of that, because
the new cells have to have a copy of the plans too.
So far it all sounds familiar and nothing has blown your mind, though it should if you see where I’m
going. How does DNA know its own shape such that it can code for the very proteins that work on it?!?
Remember, we’re talking about a double helix here, not an easy shape to configure a protein to conform to.
Helicase has to have the ability to break the hydrogen bonds that hold the two sides together, advancing in a
corkscrew fashion, while DNA polymerase advances forward, holding all the new components together. The
best analogy I can think of is one of those zipper puller thingies that form fit to the two sides and hold the
teeth while spreading the oncoming teeth apart. It’s not a perfect picture, because it’s not twisting as it goes,
and it doesn’t account for the new assemblage going on at the back side from the new raw material cruising in
place against the existing half(s). But the fact that there is really no other good use for that gizmo other than
unzipping and zipping, and the fact that it couldn’t do its job without the right shape captures it pretty well.
Add to that the fact that the zipper itself would have to contain the code for the creation of the zipper puller
thingy and you start to feel a little dizzy. Now, to make things more wonderful, add another layer of realizing
that the whole purpose of this exercise ultimately is to go on valiantly fighting entropy by reproduction! Can
we really attribute that kind of foreknowledge, planning and self-awareness to a mere chemical? I don’t know
about you, but I certainly won’t.
Label makers
There is another enzyme that works somewhat like DNA
polymerase but it has a different job. This enzyme is RNA polymerase
and it also has help performing its function. This time we’re making RNA
which has a unique structure, and the purpose for its special shape is
entirely different. Now it’s the expression of the code, not just its
replication we’re talking about, and this requires different means. RNA is
called that because the sugar in the backbone is altered (ribose instead
of deoxyribose). It also has some other structural modifications. Most
notably, it’s only single-sided/stranded. That’s important. Also, one of
the nucleotide building blocks has been substituted out for a different
one. Instead of Adenine, Thymine, Cytosine, and Guanine, RNA has
RNA Polymerase in action
Uracil in the place of Thymine. To be honest with you, I don’t know
what the significance of this alteration is in RNA. But I do know this;
the RNA is the go-between for expressing the code, the manufacturing of proteins. To be specific, it’s mRNA
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that gets transcribed from the DNA. There are other types or roles that RNA plays. What tRNA, rRNA and RNAi
do will be fun to talk about down the road, but let’s focus on mRNA and the RNA polymerase that makes it.
Do you remember those old-fashioned label makers that look like guns, where the blank label feeds
through one space at a time? You select the letter, squeeze the trigger and it makes an impression which
matches what you chose. Then it advances the ribbon forward and you do the next letter you want to imprint
over and over, and in the end you cut the label off and the finished message is done. Once again, it’s not a
perfect analogy, but it does an ok job at capturing the purpose of the enzyme. You are acting like the DNA
code when you select the letters on the dial and the growing ribbon is like the mRNA. RNA polymerase still has
to unzip the DNA as it progresses, just like DNA polymerase, but this time it’s kind of holding/feeding the
growing chain of mRNA at the back end, and when it gets to the “stop codon” (the place in the code that
triggers RNA polymerase to dismount) the process is finished. A really cool thing about the enzyme is that it
also re-zips the DNA back together as it passes through! Remember, all these critical functions are shapedependent, and again, the DNA seems to know all of these other tasks that have to be going on
simultaneously. Its code is written for the construction of the enzyme accordingly to get it all done. When a
gene (a portion of the DNA that codes for a specific protein) needs to be expressed, the code has to send a
message to be converted into a protein that will do a specific job somewhere. This is necessary because the
DNA remains housed safely and permanently in the nucleus (until cell division anyways), but the actual
translation of the protein occurs outside the nucleus in the cytoplasm.
Transcription and crocheting
Before we move on to that, we should stop and take a closer look at the transcription process. As I
mentioned, RNA polymerase has help in doing its job. It would not be possible except for the aid of a
collection of protein subunits called transcription factors. They hang around in the nucleus, typically waiting
for a command which enters the nucleus from the outside to initiate their assembly. This is actually a
safeguard that genes will not be expressed willy-nilly without prompting. Once assembled into a larger
structure, they form something like a “jig”
that holds the DNA and helps feed it
through the RNA polymerase. It reminds
me of the way my wife crochets yarn to
make a blanket or something. She has to
use two hands to accomplish the task,
because one hand holds the upcoming yarn
while the other one holds and works the
crochet hook. The hook would be like the
enzyme, and the other hand would be the
helping jig created out of the transcription
factors. These factors are proteins coded for by the DNA, but the extra craziness comes with the fact that they
exist as separate subunits that won’t work until they get their cue, in order to insure that no untimely
transcription of the code is going on uninitiated. They get “phosphorylated” to get the process started, which
requires the attachment of a phosphate group from ATP (adenosine triphosphate). That’s the little nucleic acid
that’s only one nucleotide long, but has the sugar adenosine and three phosphate groups instead of just one.
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There are tons of these little guys in a cell who act like tiny batteries and are continuously being discharged
and recharged as work is done. But, getting back to the topic at hand: could the DNA possibly know that
chaotic transcription and translation of itself must be prevented in order to avoid the waste of limited
resources or even worse yet, diseases? No way. This clearly implies some really amazing engineering is going
on here!
Paint shakers and Lego sets without instructions?
As I was describing all of this to my children, one of them came up with an analogy of their own, and I
want to share it with you. He and his brother have a bunch of Lego sets they have enjoyed playing with over
the years. Sometimes they like to use the instructions and assemble what the people at Lego headquarters
dreamt up, sometimes they like to make their own creations from scratch. Either way, there is a mind at work
who devises the final outcome, which is fashioned out of some basic building blocks (bricks) put together in a
sequence to make an ultimate three-dimensional structure, like a ship or an airplane. He asked me, “How
would the pieces know what they’re supposed to end up building if they didn’t have the instructions to read?”
It was absurd to him that unintelligent pieces of plastic could ever make something meaningful, let alone a
specific outcome, even if you granted that they could self-assemble, because they wouldn’t even know that
they were supposed to perform such a feat. They would have no awareness of what they are, or that they
could stack tighter to make something bigger. They could certainly never say to themselves, “I know, let’s
come together and make a Millennium Falcon!” They would have to be aware of the intended design, then
execute it without the benefit of directions. Yeah…right… A similar question was then asked; “What do you
think the likelihood is that the pieces could fall into the right configuration if you put them into a mechanical
paint shaker (you know, those ones in the paint department store)?” If we assume that any parts that came
together would not get destroyed by continuous shaking, how long would it take for even a simple model to
be completed correctly? What if we had duplicate sets of bricks in a trillion different shakers and gave the
process a trillion years, would it ever be accomplished? Good questions.
Backup files
In view of these insightful questions, let’s dwell for a moment on the extreme importance of our DNA.
Whether we realize it or not, we are its caretakers, but if we had to actively perform all the protection and
maintenance of it we’d be sunk. Do you have extra car keys? Where did you put those come to think of it?
How about your wallet or purse? Uh…Good for us there are built in features for preserving our DNA. It’s
wonderful that its care is mostly on “auto pilot”, though if we do stupid stuff like volunteer to shovel up
nuclear waste then we only have ourselves to blame! In a similar fashion, we certainly value data, whether we
think much about it or not, and live in a society that is heavily information dependent. Millions of jobs are
either directly or indirectly related to the “tech sector”, and we rely on our gadgets to get by in life. From the
laptop I’m typing on, to the electronic banking and cell phones we use every day, data is super important.
That’s why everyone is so up in arms about that 17-year-old whiz kid hacker in Russia that just stole
everyone’s credit card numbers! I don’t type for long without pressing “control s” for fear that my progress
will be lost, and I’m planning on getting this on an external flash drive ASAP in case my hard drive crashes! So,
how are the “data files”/encoded information in DNA backed up?
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Remember the fact that it’s a double helix for protection sake? Well, it’s also constructed that way as
a method to back up the files! DNA is essentially a mirror image molecule, with the two sides of the ladder
being identical but upside down relative to each other. The technical term for this phenomenon is that the 3’
(three prime) and 5’ (five prime) ends face opposite directions. So, when the cell needs to retrieve a “file” but
it happens to be corrupt (I’m using computer lingo now, but you get the point), the information can be
recovered by looking up or down stream and comparing the damaged section to the intact one. The double
helix design physically protects the code, facilitates the elegant transcription/translation of itself, while
providing for built in file backup AND recovery of damaged files! Whoa, that’s four birds with one stone. God is
truly the original and master architect.
Fort Knox, NORAD and sunscreen
Before we move on to the next step in the process of expressing genes, let’s pause and talk more
about this architecture of DNA. The most valuable part of the molecule is the nitrogenous bases. They are the
code for protein synthesis and must be protected at all costs. That’s why DNA is a double helix. The sugar
phosphate backbone is pretty tough, with covalent bonds holding it together, and once the molecule is
twisted, the code tucks neatly inside a fortress. This is really important, because the hydrogen bonds that hold
the “rungs” of this corkscrew ladder molecule are relatively weak and easily shattered. Cool thing is, the
molecule can be untwisted and those weak bonds can be broken momentarily (and gently) when it needs to
be read or copied, but then it’s immediately twisted back up for good measure. Another plus to this
configuration is that it enables the molecule to be coiled up on itself without being damaged, which saves
space and keeps it packed away in a tidy fashion. Imagine how tangled it would get if it weren’t stored in an
organized manner. It would become like that wad of hopelessly tangled fishing line at the bottom of your
tackle box! Not only this, but it also provides a method for regulating gene expression. One superstructure
serves two purposes at the same time, a theme I have seen over and over again in nature. Good engineers and
architects do that every chance they get.
You know how they have all our gold reserves underground in a well-guarded place we call Fort Knox?
We can’t just leave our most valuable asset sitting out in the open, now can we? In a similar way, the cell
possesses nothing more valuable than its code, and it is positioned as far out of harm’s way as possible; at the
physical core, well protected from the outside world. Granted, plant cells have their nucleus shoved to one
side because of that enormous central vacuole they need for storing water, but they also have something akin
to armor plating around the cell in the form of a cell wall. In animal cells, the central location of the nucleus
places it ideally to control all of the functions of the cell. It is surrounded by the highway of manufacturing
tunnels, the endoplasmic reticulum, which connect to the openings on the surface of the nucleus (the nuclear
pores),with plenty of space left between there and the cell membrane (the outer boundary of the cell) for
other structures.
It reminds me of that bunker they have in the basement of the White House or better yet, that
sprawling underground complex somewhere in the middle of the country deep underground called NORAD
where vital persons can go in times of unimaginable war so they can continue functioning. The truth is, our
cells are perpetually under attack from a range of outside threats like bacteria, viruses, or radiation which
threatens to turn them into the traitorous cancer cells that come to behave as if “it’s all about them.” The
more dangerous threats are the shots to the heart; like nasty chemicals we absorb, breathe or ingest such as
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pesticides, or invisible but highly-penetrating ionizing radiation. What makes carcinogenic chemicals, ionizing
radiation and other wrecking balls like neutron radiation so devastating an enemy is that it alters the code,
which by the way is what gives rise to the cancer in the first place! When we smoke, eat food with chemical
residues, work or play around carcinogens, we run the risk of harming our code. While we sleep or take a
flight, especially those that go close to the poles, radiation from space bombards us mercilessly. We always
knew that wearing sun screen was a good idea when we go outside to prevent painful sunburns, but the real
problem is not the burn to our skin. Rather, it’s the damage that the UV rays do to our DNA that we should be
concerned about.
Having foreseen this, we have been equipped with built-in sun screen as a species, and natural
selection sorts out just how much we need in each region of the planet. Hence, populations near the equator
(think Nigeria) have a lot, since those who didn’t have dark skin died of melanoma long ago and failed to pass
on their genes, and those near the poles are pasty white (think Finland and Norway) because they need to
synthesize all the vitamin D they can with what little skin is exposed to the sun while outside wearing warm
clothing. Rickets (a painful and debilitating disease caused by vitamin D deficiency) is what got the darker folks
up there! The people who live in the middle latitudes have tan skin because the intensity of the sun is average.
Funny how the flexibility and capacity in our gene pool provides for this range of variation, eh? God knew in
advance that we would spread out over the face of the earth and need to be able to adapt. This wide range of
possible skin colors and a myriad of other traits which can adjust to suit the need is made possible because our
code was written with all sorts of contingency plans in mind by our creator. All of this operates like clockwork
without us even realizing it, and our most precious commodity is being safe guarded all the time with yet
another layer of redundancy and active maintenance. That’s where we’re going next.
Redundant systems and maintenance Robots to the rescue!
So, how do we keep up with repairing all the damage incurred to our code? Well, we don’t actually
have to repair all of it because of some built-in redundancy in the system. Most amino acids are specified by
multiple codons (sets of three of the letter codes), where the second and third letter end up being the most
critical ones. If the first one is messed up it can be ok in many cases. It’s a bit like the way there are many ways
to pronounce certain words and others will still understand what you mean. If you go to the deep south, that
stuff you put in your car to lubricate the engine is pronounced “ole”, but we still understand them. 
However, there are many instances that the damage MUST be repaired or there will be horrible
consequences. Before I discuss the repair process though, let me go into a more complex level of redundancy
that’s built into the system.
Have you ever noticed that almost all cancers develop late in life? It’s not a coincidence. By the time
we are old, we have started to lose the fight against the law of entropy, and our efforts to repair our DNA
can’t keep up with the rate at which it’s being damaged. Though the campaign is a valiant one we still lose,
and the damage ends up accumulating until finally some of our cells careen out of control and become selfserving, malevolent, and even psychopathic. So sad. Hence, the need is urgent to reproduce while we’re
young, before the irreparable damage has occurred, and that is in fact how it works. We are designed to pass
our genes on to the next generation relatively early in life before our code gets too damaged (during the time
that the maintenance robots can keep up with the rate of harm pretty well). As we know, those who
postpone reproduction until later in life run a greater risk of passing on genetic damage to their children. But
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what causes the cancers that occur earlier in life? They are most often due, tragically, to some genetic damage
being passed on to us through our parents’ reproductive cells, or gametes, not by accumulated damage
incurred during our own lifetime. For example, the BRCA1 and BRCA2 genes that predispose women to
certain cancers are inherited and “pre-damaged”. It’s like that gene is already half way wrecked. They (the
women) can be ok if they have only one defective gene, but the odds of developing the cancer are greater
because they’ve already lost half the war. The mutation occurred sometime in the past and did not get
repaired, so now it is an ongoing problem as it gets passed on, but the fact that people still have a chance at
being disease-free points to this deeper level of redundancy we possess. It has to do with our chromosomes,
the superstructures of twisted and greatly coiled up DNA that are formed when cells are about to divide, the
vehicles by which the code is inherited.
We have almost all our genes in sets of two, each one on a chromosome that came from one parent.
The 46 chromosomes we have in our genetic make-up are actually 2 sets of 23. For example, you have a giant
chromosome we call number one, and you get one of those from mom and one from dad. They look alike and
have instructions for the same trait stored on them at the same geographic location (called a locus) along their
length, and so we call them homologous chromosomes. The “versions” of the genes can be different on
homologous chromosomes, but what trait they code for is the same. This system of getting multiple copies of
a gene for the same trait from separate parents is the main way that populations stay healthy genetically. For
some traits it doesn’t seem to matter what you get or what is ultimately expressed, as with eye color or
attached/detached earlobes. But the presence or absence of other traits can be very critical in obvious ways,
such as with Hemophilia or sickle cell anemia. By the way, all these life-threatening diseases are the result of
mutations, and illustrative of the point that mutations are destructive in nature, not constructive, because
they mess with the instructions that already exist for some specific purpose. In the case of genetic predisposition to a disease such as some form of cancer, one of the homologous chromosomes has a damaged
gene and the other one is still normal, but with only one good copy there is a greater likelihood of both ending
up damaged sooner in life. This is called the “two hit” hypothesis, where if the gene you inherited from one
parent is damaged you will probably be fine until the second copy on the other chromosome gets damaged,
and then you’re in trouble.
I don’t know if you can see where I’m going with all of this, but the fact that most traits depend on the
information located on both of the homologous chromosomes, and that just one healthy copy can “save” you,
points to a built-in redundancy that is extremely farsighted. This provides not only for protection against
diseases being automatic when just some of your DNA is damaged, but also for the variation that natural
selection can work on in order to respond to the circumstances that living things encounter. That’s why family
members resemble each other but are not identical. The genetic deck has been shuffled, and that’s a good
thing. We have a set of instructions that is pretty resilient by virtue of the way it’s set up physically. In keeping
with that theme of efficiency (accomplishing multiple tasks with one feature), this same system of redundancy
also makes reproduction a randomization of traits, so that populations can adjust to the rigors of life. Truly
good stuff.
So, about those “maintenance robots”- what are they and how do they work to protect you? They have
been given the name of “tumor suppressor proteins”, because they work to prevent the formation of
cancerous tumors. Since fixing the damage before it can do any harm is urgent, and the damage is occurring all
the time from a host of sources, you could well say that “a tumor suppressor proteins’ work is never done.”
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This is especially true since there is another source of corruption to the code that I failed to mention earlier.
During the replication of DNA, copying errors sometimes occur. As with all machines, the micro machine DNA
polymerase sometimes malfunctions for some reason, and a letter in the code ends up altered from the
original. This contingency, as well as the damage caused by external threats was foreseen and a system was
programmed into the code to resist this degradation. Genes called tumor suppressor genes code for the
production of proteins that mount the DNA and check for damage, repairing any if they find it.
They are able to do this because of the redundancy present in the
double helix mirror image design. They can compare one side to the other
and detect the alterations, fixing them according to the healthy portion of
the code that remains. I’m not sure of the exact method for this, but it has
something to do with the fact that some series of base pairs mean nothing,
and they detect it as nonsense, so they have a good idea of which side is
the intact/original one and which one has been altered. I do know that not
all tumor suppressor proteins are the same, but perhaps the most famous
one is the p53 tumor suppressor protein. It has been called “the caretaker
of our genome” by cancer researchers. This large protein has multiple
“domains” that do different tasks, and it is long enough to check the DNA
down or upstream for comparison and repair purposes. Without these
P53 tumor suppressor protein in action
work horses we have a greatly increased risk of developing cancer. In
fact, we’re really in trouble when the genes that code for these
caretakers get mutated, because then they end up misshapen, and consequently can’t do their duty. As you
recall, a protein’s function is all about its shape, and without these little robots being precisely shaped in an
intricate three-dimensional configuration, we become helpless in fighting mutations. 
The very presence of the instructions for these marvelous repair robots being written into the larger
code that they serve to protect is a powerful testimony to extraordinary planning. The genius that went into
fashioning organisms that could take a pummeling and still go on with a high level of resilience is beyond
reckoning. Timex watches could “take a lickin’ and keep on tickin’,” but they aren’t even in the same ball park
as life! The designs such as watches, computer chips and rudimentary nano-machines of ours are a nice
attempt at making smaller and smaller functional creations (like a little boy imitating his daddy’s work), but
the biological ones that God conceived and built are far superior not only in construction but also in
capabilities. We have found that as we have gotten down to the molecular level we can no longer design and
build machines with moving parts. We have had to settle for utilizing the properties of the materials
themselves to do anything useful at the ultra-tiny level. Not so with the fascinating cellular world. There’s a
whole plethora of genuine robots working away all the time without us even being aware of what they’re up
to. Let’s dig into the next series of them, shall we? 
Stovepipes and Japanese cartoon cat robots
Let’s go back to that strand of mRNA that just got transcribed from the DNA. You might be aware of
the fact that at this stage of the game it’s not quite ready to go out of the nucleus and get translated into a
protein. First, it has to be trimmed and given a protective cap and tail. Sections of the transcript we call introns
have to be removed while the exons get to stay (I know, the names are backwards, go figure!). The final result
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is a strand of mRNA that will code for the manufacture of a protein, while the parts that got removed are
dismantled into nucleotides, ready to be used again. So, how is this snipping and addition of a cap and tail
accomplished? As you might guess, there are multiple protein subunits waiting to get the command through
phosphorylation to assemble into a much larger machine that will mount the immature mRNA and get the job
done. This final assembly is called the “spliceosome” because it removes the introns and splices the exons
together, but as with the transcription factors it doesn’t assemble until ordered to.
It reminds me of a Japanese cartoon that used to be on when I was a child where these cool robots
that looked like big cats (lions I think) could come together to form a giant and ultra-cool robot. One cat made
up the left leg, one the right, one each for the arms, and one for the torso and final head (sorry, childhood
flash back…you get the point). This big robot could do amazing things which the smaller ones couldn’t do
alone, once it was all assembled and ready to go. It’s the same with
the spliceosome, and once all of its various subunits come together
and assemble on the immature mRNA strand, one final
phosphorylation gets it started. It holds on to the beginning of the
mRNA and then feeds the rest through, in effect moving down the
line, cutting out the unwanted sections and splicing them back
together.
This is amazing enough, but then it does something else
almost unimaginable when it’s time to put on the cap and tail. The
subunits undergo what’s called a conformational change, or in other
words, they twist on the joints between themselves and reconfigure
into a totally new shape. When this occurs, the far end of the RNA
The assembled spliceosome
ends up right next to the start in kind of a u shape. If you’ve ever
fooled around with stove pipe, you know how it’s possible to twist it at the joints and get this new horse shoe
configuration from the initially straight shape. Since the spliceosome is still attached to the start of the RNA,
what this accomplishes is that the 5’ and 3’ ends are brought into close proximity. In one final operation, the
spliceosome finishes the job by adding the cap and tail simultaneously, then it dismounts the mature RNA and
disassembles into the separate parts, waiting for the next command to do it all over again with a different
immature strand. We wouldn’t want the giant Japanese cat robot going around chopping things up arbitrarily
now would we? 
Now, lest the significance of that whole thing be lost on us, let’s consider what it would take to achieve
it. The code for the subunits would have to be written in such a way as to foresee the need to not only do the
cutting and splicing operations, but also to have the capability to twist on its joints. This is another one of
those efficiency-in-design examples to be sure, as being constructed from separate pieces gives it both the
ability to do the conformational change, and for the overall process to be initiated and terminated by
assembly and disassembly of the parts. All of this has to be programmed into the code. Miraculous? You
betcha.
Control, control, you must learn (?) control!
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Cells have very elaborate control systems incorporated into every aspect of what they do, and they are
very purposeful. Chaos is death for cells, and they are not random or disorganized in the slightest. There’s a
poster I want to get for my classroom wall that shows all the common biochemical pathways that occur within
a cell, and the sheer number of complex reactions is astonishing. There are seemingly innumerable numbers
of interrelated pathways, with products of multiple processes becoming raw materials in another process.
Chemical intermediates go through an elaborate waltz of temporarily being modified for a certain purpose
before they revert back to the original compound and start their part of a crucial chain of events all over again.
Our high school biology teachers tried to explain some of the prominent examples to us, like the steps of the
Citric acid/Krebs cycle, portions of the light and dark reactions within plant cells, or the steps in glycolysis and
fermentation, but the obscure names of compounds in these processes and the sheer number of steps to
memorize was pretty daunting or maddening, and most of us probably “checked out” at that point. 
Even if we went to the great pains of committing all of that stuff to memory, let alone really
understand it within the bigger picture of what was going on, we probably didn’t realize that all of it would be
impossible without extreme measures of both control and speed. In the macroscopic world of the chemistry
lab, we tinker with reactions that are relatively uncontrolled and go slowly enough to visualize, but not so at
the cellular level. The rate of biochemical reactions is actually so fast that we have a difficult time explaining
how it could possibly work at all, let alone harmoniously. For example, we have an enzyme called “carbonic
anhydrase” which can catalyze the production of 600,000 hydrogen carbonate ions per enzyme per second.
And this is by no means the only enzyme working at blistering speeds. So how do cells make the things they
need, like ATP for cellular work, proteins, complex carbohydrates and so forth with such speed and precision?
Virtually all cellular processes are regulated, facilitated, enabled, sped up, or prevented by biological
catalysts. We have already encountered some of these, and they tend to bear names with the “-ase” ending
(DNA polymerase for example). Enzymes are the molecules that make life both possible and manageable.
Molecules that would not have an easy time finding each other or being joined together in the desired way at
any useful rate can suddenly form crucial products in a very short period of time, as opposed to a glacial rate
or not at all. They do this by having something called an active site that has a specific shape which
accommodates the perfect fitting together of two reactants. In this way, the “energy barrier” that must be
overcome in order to get something accomplished is greatly lowered. In technical terms this is called lowering
the activation energy for a reaction, and enzymes do a superb job at this due to their highly specific active site.
An enzyme that will catalyze one reaction will be useless for other processes, and this turns out to be one of
the key features of a cell’s control system. When you realize that a different enzyme is usually required for
each step in a chain of complex biochemical processes, it begins to dawn on you just how stupefying that
poster I mentioned really is.
Not only are there so many overlapping chemical subsystems in a cell as to be completely disorienting
when you try to take it all in, but the level of planning that had to go into the code in order to orchestrate it all
makes me just shake my head in wonder. Remember, all the enzymes that control this stuff had to be
designed in advance so that their shapes would get each particular job done and no other. Miss a step in any
of the processes that depend on each other and everything comes to a screeching halt, and that’s exactly what
would happen if we didn’t have all the right machinery in place, doing what it does constantly. Death, or at the
very least, disease ensues otherwise.
27
But there’s another level of control that goes beyond this, and I’ve mentioned it a few times already.
Many cellular processes will not operate unless a protein is activated, and this requires a process called
phosphorylation. All sorts of cool structures and functions become well-regulated and productive due to this
method of operating our machinery, and that’s the next topic I want to delve into. But first, let me say that it’s
impossible for the profound depth of control, and coordination we see in cells to have been developed or
“learned” through chance development in a step-wise fashion via natural selection acting on mutations. Not
trying to argue, just calling it like I see it. What I DO see is God’s handiwork.
Coin-operated
We were taught that ATP is the energy currency for cells, and that’s why it has to be produced in
copious amounts for life to function. Just about all cellular processes require activation by phosphorylation
reactions, and there are many profound reasons for this. First, as we have been examining, the need to
regulate and control the timing and sequence of actions is paramount. Phosphorylation satisfies this need
nicely, because no action which requires it will occur randomly, ensuring there will be no chaos with these
subsystems. Secondly, a fascinating thing occurs when most proteins are phosphorylated, and that is that their
shape changes temporarily. The shape reverts back so that the action can be repeated as many times as
necessary, and work can continue on when triggered.
Perhaps the most profound thing that phosphorylation accomplishes is the coupling of spontaneous
processes with ones that are not spontaneous. At the beginning of the book we took a quick look at the issues
of enthalpy, entropy, free energy and spontaneity. Most of the processes that need to occur within a living
thing will not happen without being forced to, from a thermodynamics’ point of view, and this creates an
exquisite opportunity for regulation and control. The whole reason we need ATP is that the reaction of
detaching a phosphate group is exothermic and spontaneous, so it can drive other processes that are not.
When a biochemical process needs to stay in a “holding pattern,” the cell just leaves it alone, then activates it
through phosphorylation when it’s needed. It’s like one of those coin-operated car washes or tire pumps that
sit there until someone puts the money in, and THEN it will work. Of course, the frequent expenditure of ATP
leaves a lot of ADP needing to be “recharged”, and that’s where we’re going next.
Hydro- electric dams and lasagna noodles
Cells consume/recycle phenomenal quantities of ATP. We need it to contract muscles, to generate
nervous impulses, make cilia wave in our trachea, transport cellular cargo, send messages within cells, build
proteins, etc. Did I tell you we use a lot of this stuff? We’re talking an average of 1x1020 per cell per second, or
to put it in other terms, your body weight in ATP per day. Uh… how is this superhuman feat possible? Well, we
essentially convert the energy that’s contained in our food by “burning” it with oxygen, and utilizing the
release of energy to reattach a phosphate group to ADP. What an understatement. If you write the ultimate
balanced equation, without any of the fine-grained detail of the little steps that occur, it looks like an ordinary
combustion reaction. You may recognize it:
𝐶6 𝐻12 𝑂6 + 6𝑂2 → 6𝐶𝑂2 + 6𝐻2 𝑂 + 36𝐴𝑇𝑃
I’ll try not to bore you with too much detail, but the process is broken down into three phases which
accomplish different things, and each occurs in different locations of the cell. The work horse of the whole
thing is a kidney bean-looking structure in our cells called mitochondria. Among other assigned tasks (see
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“military police” and “contingency against cellular psychopaths”), they are prodigious makers of ATP. If it were
not for these organelles, and chloroplasts in plant cells, eukaryotic cells (as opposed to bacteria only) would be
impossible.
So, the initial step in respiration is called glycolysis. It does not harvest all the energy possible from
glucose, but it doesn’t have to as it is a preliminary process. The cell invests 2 ATPs to get the process started,
but gets 4 back in return. Bacteria can manage to get by with just this relatively simple process (actually, it’s
not simple at all, but compared to the second and third stage it is), and although only a net gain of 2 ATPs can
be generated with this biochemical pathway, it’s ok because they don’t need much compared to our cells.
Plus, the hardware required to extract the lion’s share of energy out of glucose takes up as much space as the
whole bacteria itself, so it would be impractical anyway. There’s one more thing that is accomplished during
glycolysis in the final stage that becomes relevant later on. When glucose is broken in half, two molecules
called pyruvate are created, and two molecules called NAD+ “accept” two electrons each (becoming NADH2).
In chemical terms they are “reduced” temporarily.
In the case of bacteria, this is the end of the road , and the electron acceptors must be stripped of
these electron passengers so that they can be converted back into NAD+ and utilized again for another round
of glycolysis. Sometimes this is achieved by using oxygen (an “aerobic” process), but bacteria (and yeast) can
also switch to a process called fermentation, where the electron carriers are reset without oxygen. The result
of this is the production of alcohol, and that’s what brewers want going on. When you have to settle for doing
only glycolysis because your cells aren’t getting enough oxygen to continue on with the other two stages of
cellular respiration, you make a different by-product. Rather than making alcohol, you make lactic acid when
there’s insufficient oxygen. This is why your muscles get so sore the day after you exerted yourself a lot and
you couldn’t get oxygen to your muscles fast enough. The acid actually damages your muscles where the
anaerobic respiration had to occur (think sprinting and heavy weight-lifting).
For those of you who know the whole story, you recognize that I’m making a huge simplification here,
and the actual process of glycolysis is much more complicated. It involves 10 separate steps which each
require their own unique enzyme to enable it to happen. Going back to the previous discussion about control,
that’s pretty impressive, but it pales in comparison to the second and third stages which occur in the
mitochondria.
So, let’s dig into the mitochondria, shall we? It’s one of
my all–time favorites. This highly specialized organelle
essentially picks up where glycolysis leaves off. As previously
noted, the glucose, a six-carbon molecule, has already been split
into two three-carbon molecules called pyruvate. Since glycolysis
occurs in the cytoplasm, they have to move into the
mitochondria, to the fluid-filled central area called the matrix.
That’s where the next series of biochemical steps occur. Now,
the biochemical pathway of glycolysis is pretty involved, but it’s
nowhere near as complex as the citric acid (or Krebs) cycle that
makes up the second stage of cellular respiration. I’m not even
going to try and explain the biochemical pathway of the citric acid cycle here. It’s WAY too complicated, so I’ll
29
just summarize it. In a very complex revolving door of chemical steps, two more ATPs are generated as well as
6 molecules of waste carbon dioxide (which have to be disposed of). The most valuable products during this
stage of the game are not the paltry 2ATPs but a whole bunch of hydrogen ions (protons), and many more of
those electron-carrying molecules of both the NADH2 variety previously mentioned, and another called FADH2
full of electrons. These, along with those made during glycolysis are going to power something phenomenal
which we call the electron transport system.
The ETC is a marvel of biological engineering. It is the
third and final stage of respiration, where we get 32 out of the
36 ATP molecules from our initial glucose molecule. It takes place
in the inner mitochondrial membrane. Like all membranebound organelles, the mitochondria have two layers of
phospholipids facing each other to create an outside boundary
facing the cytoplasm, but mitochondria also have a second
double-layered membrane deeper inside. In the very center is
the fluid-filled matrix I mentioned, where the citric acid cycle
takes place. Unlike the outermost membrane, this inner
membrane is highly convoluted, like a partition made of lasagna
noodles. The folded structures that the inner membrane form
are called “cristae.” The folding of the cristae greatly increase
A simplified diagram of the inner and outer membranes
the amount of surface area inside the mitochondria, and this
provides sufficient space for a tremendous number of the functional assemblies that I’m about to describe.
Embedded in the inner membrane are a series of proteins called cytochromes that act as proton
(hydrogen ion) pumps. At the end of this series of cytochrome pumps there is an enzyme called ATP synthase.
Allow me to explain how it all
works together. You remember
during the previous steps of
respiration, there were a lot of
protons generated as a byproduct,
and they become highly
concentrated in the mitochondrial
matrix. Here’s where the electron
carrying molecules of NADH2 and
FADH2 come into play. They
essentially dump their cargo of
electrons into the first protein in
A close up view of the ETC
the series of pumps, and then the
electrons cascade from one protein
to the next like a domino effect, or
like falling down a series of stairs. Some have used the analogy of a slinky falling down steps, or like water
down a wheel, but however you visualize it, the critical thing is that the energy of the “falling” electrons
powers the pumps. As the electrons pass down the series of pumps, protons are pumped through them in a
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one-way direction (from the matrix side to the space between the two membranes). What this accomplishes is
an altering of the proton concentration on either side of the inner membrane. It used to be that there were
more protons on the matrix side, but now, the concentration of protons in the space between the inner and
outer membranes is greater than it is in the matrix. This generates something called “chemiosmotic pressure”,
because the protons want to get back across to equalize the concentration, but they can’t right away.
Ok, so why? Here’s the amazing purpose…so that copious
amounts of ATP can be made automatically. How so? As you
might have guessed by now, it involves that enzyme ATP
synthase. As with other complex enzymes we’ve examined, ATP
synthase is constructed of many protein subunits, and it extends
through the inner membrane. Its top opening is toward the space
between the membranes, and the bottom opening is towards the
matrix. It provides the only pathway for the protons who, due to
the law of diffusion, will take advantage of any opportunity to get
back across the inner membrane to an equilibrium state of equal
concentrations. ATP synthase functions somewhat like a vending
machine. Three protons are inserted into the top part of the
assembly, and then the lower shaft spins and allows them to
move the rest of the way through. For every three protons that
come through it, the enzyme uses the energy of their passage to
An even closer look at ATP Synthase
reconnect one phosphate group to an ADP, regenerating an ATP
(notice all the tertiary and quaternary structure and
molecule. Then, as the protons move the rest of the way through,
imagine the programming that had to go into making
they rejoin with the electrons that have finished falling down the
this nano-machine!)
cytochrome cascade, and together they bond to oxygen. Each one of
these functional units (the protein pumps and the ATP synthase) can generate 1,000 ATP molecules per
second, and you have a whole lot of them embedded in that convoluted inner membrane. Each cell usually
has many mitochondria, and we have trillions of cells. Now we can start to grasp how that huge figure for the
number of ATP you make each day is possible.
As you recall, this whole process of aerobic respiration is not possible without oxygen. Here’s why. The
oxygen bonds with the hydrogen atoms to form water, and this keeps the system from building up too many
protons in the matrix, resulting in insufficient chemiosmotic pressure at the top side of the membrane. If you
look back at the balanced chemical equation, you see that six water molecules are produced for every glucose
molecule, and without the formation of this “metabolic water” we could not keep up with our demands for
ATP consumption.
But let’s take a step back and consider this whole set up. To me it looks an awful lot like one thing…a
hydroelectric dam (the “pumped storage” type to be exact). Only we are making ATP instead of electricity.
Pressure is built up behind the dam for the intended purpose of giving it only one way to get through, namely,
the penstock. That’s the tunnel that dams have which permit water to pass from the high side to the low, and
as it does, the energy of the water is transformed into mechanical energy (turning the turbine which turns the
generator). It took a long time for people to figure out how to construct hydroelectric dams, and nobody
would look at the Itaipu, the Grand Coulee, the Aswan or Hoover and attribute their existence to anything
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other than the fact that someone very ingenious was behind it. So why would we look at this wonder of
planning and execution called cellular respiration and conclude anything else?
Metabolic poisons and mothballs
Before we look at what metabolic poisons are, I want to point out that a single point mutation in ATP
synthase can have devastating consequences. Since their operation is a mechanical one, they don’t work right
unless the parts move properly. And as we covered at the start, a mutation to the code can change the final
shape of the protein and its ultimate function. Even minor alterations in the code for ATP synthase have been
documented to cause such things as epilepsy. That’s the level of fine-tuned detail we’re dealing with here.
But what if everything is perfectly formed according to the original plans and something comes along
and sabotages the process? That’s what the infamous poisons do to us. Some poisons latch on chemically to
the cytochrome pumps and stop them from building up the chemo-osmotic pressure. No difference in proton
concentration, no impetus to get back across the membrane, no ATP synthase activity. No ATP synthesized
and we are rather quickly dead. Poisons like Rotenone, carbon monoxide and hydrogen cyanide all fall into
this category. Then there’s the poison oligomyacin which bonds to the ATP synthase and prevents it from
operating. Even though all the other machinery is working right, without ATP synthase it’s all pointless! An
altogether different poisonous effect happens when DNP soaks into the inner mitochondrial membrane and
makes it porous to protons. The cytochrome pumps keep working away, but the wall is leaky. Without the
ability to maintain the difference in concentration from one side of the membrane to the other, everything
falls apart. Having all the enzymes functioning properly accomplishes nothing. Death ensues.
Obviously, life is quite fragile in some ways, even though it seems resilient in other respects. It doesn’t
take much to damage to the cellular systems that we depend on. They are exquisitely designed and must be
working per the specifications of the code or disease and death result. Ever heard of the mean trick of putting
mothballs in someone’s gas tank? The normal combustion of fuel and air can’t take place because the ensuing
goo clogs everything up. It’s the same idea as metabolic poison. Pulling off just one vacuum hose from a part
of your engine will keep it from running too, although it’s
less cruel because it doesn’t destroy your engine. Point
being, a car was designed for a useful purpose and can’t
do what it was designed to if you mess with it, even in
small ways. A crack in a dam can also be a serious
problem, especially for communities downstream! But a
log in the penstock can be detrimental too. No turning of
the turbine, no electricity. I think you see my point. Cars
and hydroelectric dams are really cool inventions,
designed by some smart people to serve us, but these
creations and their makers aren’t even in the same league
as the maker of the designers and His inventions!
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Solar Arrays, reactor cores and Thin Mint Girl Scout cookies™
The other organelle that eukaryotic organisms couldn’t live without is the chloroplast. Obviously plants
need them to convert the simple molecules of carbon dioxide and water into high energy sugars, but we
heterotrophs would be dead without them too. Not only would there be no food (plants), but there would
also be no oxygen to burn it with if it weren’t for photosynthesis. In fact, the overall chemical equation for
photosynthesis is exactly the same as respiration except backwards. We give the plants what they need, and
they give us what we need. That’s cool. That’s not a coincidence. So how do they get the job done?
Well, in a similar fashion to mitochondria, chloroplasts have an external membrane and internal
structures which greatly increase their available surface area. They have stacks of membrane-bound structures
called grana (the stacks of grana are called thylakoids). To me they look like a sleeve of Thin Mint Girl Scout
cookies. Chloroplasts have a lot of these stacks, and the amount of surface area they provide dwarfs that of
the mitochondria. That’s because the machinery required to accomplish photosynthesis takes up more space.
The grana are interconnected so that the substances in their inner fluid called lumen can move about. The
fluid outside the grana is called the stroma. Embedded in the grana membrane is a system of extraordinary
protein sub-systems which each execute a different portion of the overall process of manufacturing ATP.
Wait. I thought that’s what the
mitochondria did? Well, as it turns out,
chloroplasts make ATP too, but they make it
from the energy they harness from sunlight, not
from breaking the bonds in sugar. In fact, they
will use the ATP made during these “lightdependent” reactions in order to make sugars in
the “dark” reactions, which do not require light.
In some ways the manufacture of ATP is similar
to what takes place in mitochondria. Both use
the enzyme ATP synthase, powered by
chemiosmotic pressure, and both use cytochrome protein pumps to build up concentrations of protons. Both
use falling electrons to power the pumps. But that’s where the similarity ends, and things become even more
wonderful.
First of all, the payoff at the end is upside
down. ATP synthase is oriented with the spinning
shaft facing the outside (the stroma) rather than
the inside (the lumen). That’s because ATP is
needed on the stroma side of the thylakoid
membrane to power the dark reactions that make
sugars. Another big difference is that at the
beginning of each functional unit is a solar farm.
There is a solar array of light-harvesting protein
complexes which are embedded in the thylakoid
membrane. These surround a reactor core, which
Photosystem II
33
contains chlorophyll. As light strikes the protein harvesting complexes, they pass the light’s energy on to the
reactor core. If you’ve ever seen one of those solar power plants where the mirrors bounce the sunlight to a
tower in the middle, which in turn generates electricity, it’s a
pretty good analogy for the “photosystem” that plants use.
The chlorophyll uses the energy of the photons in the red
range of the visible spectrum (680nm) to split water that is on
the lumen side, producing oxygen, protons and electrons. The
protons formed in this step provide for some of the
chemiosmotic pressure on the lumen side, but more are
needed. The electrons that are produced have 2 tasks to
accomplish, and they do it in stages. First, the electrons are
“boosted” to the top of a series of cytochrome proteins
(these have some unusual names like plastoquinone), and as they cascade down, more protons are pumped
from the stroma side to the lumen side of the thylakoid membrane. This first stage of the process is called
“photosystem 2”. By the end of photosystem two, the electron needs its energy boosted again, in order to
power the next stage of the process.
That’s where the second photosystem comes in, called “photosystem 1”. I know, they are backwards in
numerical order. I think it’s because photosystem one was discovered first, even though it’s second in the
action. Anyway, this second photosystem is powered by light of a
Reactor core in Photosystem II
higher wavelength (around 700nm, or “far red”). By utilizing
(Again, think of the programming required to make
photons that were not used by photosystem 2, it is able to give
this and the entire photosystem it is a sub-system of!)
the electron another kick. The newly energized electron now has
the energy to power a second and shorter cytochrome chain which accomplishes something different. This
time the energy is used to produce the molecule NADPH, from NADP+ and a proton. This molecule carries
electrons to be used in the dark reactions, and uses up some of the protons that pass into the stroma side of
the membrane through ATP synthase, so that the concentration of protons can be kept low on the stroma
side. Together with the ATP that is produced on the stroma side via the ATP synthase, production of NADPH
completes the light reactions. They have accomplished what they need to.
During the dark reactions, a very complex
series of biochemical steps called the Calvin cycle
takes place in the stroma. This is powered by the
ATP and NADPH created during the light
reactions, and it essentially uses carbon dioxide
as a building block to manufacture sugar. It’s
crazy complicated, and I won’t go into all the
details. The crucial thing is that the waste product
of respiration is being used to rebuild the fuel
that life needs to keep on going. Also, the need
for a source of protons and electrons during the
Photosystem I
light reactions necessitates the usage of water,
which produces oxygen as waste. This is disposed of by the plant and used by us to “burn” the food we get
34
from them. Though plants need to keep some oxygen too to do their own respiration in their mitochondria,
where they burn some of the sugar they produce, they make a surplus of oxygen. Without the splitting of
water during the light reactions, we heterotrophs would be unable to perform cellular respiration.
I have heard biologists comment on how it’s “interesting” that these cycles of photosynthesis and
respiration provide exactly what the other one needs. Hmmm. When you consider that each part of the
photosynthetic and respiration processes, all the cytochromes, the ATP synthase, the enzymes for the dark
reactions, citric acid cycle, glycolysis etc., has to be coded for by DNA, that it all has to be coordinated in a
biochemical dance of gigantic proportions, and that the code has no way to devise master plans for cycling
energy through an ecosystem, it becomes clear that it’s waaaay more than interesting, it’s miraculous.
Without plants there would be no fuel OR chemically active oxygen to bond with the hydrogen that’s formed
in the ETC and respiration would be impossible. Take a wild guess which kind of living thing is listed as having
been created first in the Genesis account. Yep, plants. But plants need water and carbon dioxide to do this,
and sure enough, water and sky were made just before they were. I don’t believe that Moses (who is credited
as having written Genesis) had a clue about all of this, but God certainly did. 
The cellular pony express and old fashioned switchboards
Let’s go back to the coordination and control of executing the code for a moment. Since the DNA is not
arbitrarily transcribed and translated into proteins, what triggers the process for gene expression? We looked
at the fact that the transcription factors have to be phosphorylated in order to be sent into action, but why
does this happen? In order to execute gene expression, a messenger molecule has to enter the nucleus from
the cytoplasm and initiate the transcription of a specific gene. But what prompted the sending of the
messenger molecule in the first place?
As it turns out, there is a system of relay proteins or other messenger molecules such as AMP
(adenosine mono phosphate) which trigger one another to be phosphorylated and energized to move to their
appointed destination in the chain. It’s a bit like the mail carrying system we relied on early in U.S. history
during westward expansion called the “pony express”. Each messenger waited with a fresh horse to make
their leg of the journey, and carried the messages they received on a pre-determined route to the next
messenger and so forth, until the message arrived at its ultimate destination.
The message can originate within the cell, or it can come from outside the cell. For example, if a
cellular structure has gotten worn out (that ever-present second law of thermodynamics at work!) and needs
to be dismantled, a new assembly will need to be constructed to replace it. At that point, a message is sent to
the nucleus to initiate the production of the proteins to build the replacement. This is really important,
because the cell does not have unlimited resources, nor does it have any spare room for unnecessary
structures just sitting around or getting in the way of other vital processes even if it had an unlimited supply of
amino acids at its disposal (which it doesn’t).
Messages can also come from outside the cell. Let’s say that you have suffered an injury. Your skin has
been lacerated, and the epithelial cells are no longer in contact with each other due to an enormous canyon
that’s been created between them. This lack of contact initiates the sending of a message through the cell
membrane, down into the cytoplasm and finally into the nucleus, saying “hey, it’s time for cell division!” The
genes that are required to move the cell out of its normal state of affairs into the mode of replicating itself are
35
activated, and the cell divides. This process will continue until the cells are touching each other and then the
message to divide stops being sent.
The process of delivering a message from outside the cell is called signal transduction, and it’s a highly
sophisticated process. The kind of message that gets sent is dependent on the shape of the messenger
molecule that lands on receptor proteins which are embedded in the cell membrane. The protein has an active
site with a particular shaped indentation which protrudes from the cell surface, facing outward. If the shape of
the messenger molecule doesn’t match the active site of the receptor, then it doesn’t trigger that particular
transduction pathway. A different pathway might be triggered by that messenger molecule, which has a cell
surface receptor of a matching shape, but not one that doesn’t match. In this way, no arbitrary messages are
sent into the cell. When the right receptor protein is activated, it in turn triggers the activation of another
protein adjacent to it which is also embedded in the cell membrane, but it protrudes into the cytoplasm
instead of toward the exterior of the cell. This protein activates another messenger molecule, and the tag
team sequence continues on, deeper into the cell until a final messenger enters the nucleus, prompting the
intended action.
This is extraordinary, because it means that the cell is set up to receive a variety of specific messages
in anticipation that they will be sent for specific purposes. All the intermediary messenger molecules have to
be coded for by the DNA, as well as all the cell surface receptors with their specially shaped active sites which
correspond to the shape of external messenger molecules. All of this had to be planned for in advance, or
none of it would work properly.
It reminds me of those old-fashioned switch boards you see from the early days of telephone service.
The ladies would listen with their headphones and switch wires from one hole to another in order to make the
connection and enable the conversation to occur. It’s not a perfect analogy, but a pretty decent one, because
the ends of the plugs had to match the shape of the receptacles, and there was selectivity in the process. Not
just any old way of routing the wires would do. Without a way to control the flow of information, everything
would be chaos. More importantly, someone had to devise the whole system in the first place, foreseeing the
need to put people in contact with each other and route the messages appropriately. Otherwise the baker
would be getting fire alarm calls, and the police would be getting orders for bagels. Telephone poles had to be
installed, fiber optic cables laid, cell phone towers constructed, and the phones themselves had to be
designed. All the infrastructure that enables cells to communicate is amazing enough, but envisioning the
need for them to have this capacity, and planning appropriately so that it can be executed is what makes me
stand amazed. Before there were phone companies there was God.
Automated assembly lines… is everyone on a coffee break?
Though I’ve mentioned the process of translation, where the mature mRNA is read and its instructions
are executed to make the specified protein, I haven’t gone into the details of how this is accomplished. It’s
quite magnificent.
First, the mature mRNA strand passes out of the nucleus through an opening called a nuclear pore.
Surrounding the nucleus is a network of membrane-bound tunnels called the endoplasmic reticulum.
Embedded in this convoluted maze of flattened, interconnected passageways are many little machines called
ribosomes. These nano-wonders of the cell are made primarily of protein, but they also have some RNA in
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their make-up that we call rRNA. The responsibility of these little machines is to hold the mRNA while and feed
it though itself while it is interpreted one codon at a time. So the mRNA inserts into one of the ribosomes and
the process of translation begins. Here’s how the ribosome, and its partner machines, tRNA, get the job done.
The ribosome’s construction enables it to securely hold the mRNA strand because it’s composed of two
subunits. The smaller subunit hugs the bottom of the strand, while the much larger one towers above it,
forming a groove that the mRNA nestles into. The reason the top subunit has to be much larger is that it has
two alcoves oriented side by side to accommodate incoming tRNA molecules. These transfer RNA (that’s what
the “t” stands for) are like tiny vehicles which carry a specific amino acid piggy back. Which amino acid they
carry depends entirely on the “anti-codon” at the bottom of the molecule. So what’s an anti-codon? Well, like
the three nitrogenous base codons, the anti-codon is also comprised of three bases in a row, but they are
called “anti” because they have the opposite letters. Remember, A pairs with U, and C with G in RNA. So, if the
first codon on the mRNA happened to be AUG (actually, that’s always the first codon ), then the
corresponding tRNA anti-codon would be UAC, and the amino acid which it carries on its back would be
Methionine. This tRNA carrying Methionine is called the initiator tRNA, and when it pairs up with the start
codon, only the bottom subunit of the ribosome is attached to the mRNA. Then the top and larger subunit
mounts the bottom one and the initiator tRNA fits into the left hand alcove. The next tRNA with the correct
anti-codon to match the second codon will then automatically cruise into position in the second or right hand
alcove. It’s at this point that a chain of amino acids begins to be formed.
The bond between amino acids, called a peptide bond, will not normally form on its own. They typically
do not result when amino acids simply bump into each other. The two have to be held together in close
proximity because the orientation of both molecules has to be just right, and this is a difficult proposition. For
those of you who are curious, it’s the carboxylic acid on one molecule and the amino group of another that
have to be adjacent and they both have to be rotated just right so that a “dehydration synthesis” can occur.
It’s the close proximity and correct orientation between amino acids that’s achieved by the nestling side by
side of the tRNA molecules into these alcoves above the mRNA that makes it possible. Because the amino
acids on their “backs” (the top of the tRNA) are sitting right next to each other in just the right orientation, a
peptide bond forms and you now have a two-unit “poly peptide” started, which can keep growing longer and
longer. The fledgling polypeptide is now being held by the second tRNA molecule that came into that right
hand alcove, and the initiator tRNA is ready to leave and go find another Methionine to carry.
What happens next is that the ribosome feeds the mRNA through to the next codon, and as it does so,
the initiator tRNA dislodges, the second tRNA slides over into the left hand alcove, leaving the right hand
alcove empty and ready for another tRNA molecule to
cruise in, and by the base pairing rules for the correct
anti-codon, bring the next amino acid in on its back to
be bonded to the first two. The mRNA is fed forward
once again, with the left hand alcove being vacated, the
right hand tRNA shifting over to the left, a new tRNA
replacing it by matching the newly encountered codon
and so forth. This team of machines keeps doing their
work until the ribosome reaches what is called a “stop”
codon (there are three possible ones), at which point it
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disassembles, and the mRNA comes away, either to be broken down and recycled into nucleotides, or to go
repeat the process with another ribosome. Meanwhile, the amino acid chain has been getting longer one unit
at a time on the top side, forming new peptide bonds to make a longer and longer polypeptide. Technically
speaking we don’t call this long string of amino acids a protein at this stage because it hasn’t folded up into its
secondary and tertiary shapes, but it is certainly ready to because the sequence is right, based on the codons
that were fed through and interpreted by the team of ribosome and tRNA molecules.
To envision this whole process you have to see clearly in four dimensions. You could even argue that five or six
dimensions of planning are required. Not only does one have to design the ribosome subunits by coding for
their ultimate shape, complete with the groove for the mRNA to slide in, and the alcoves especially shaped to
form fit the tRNA molecules, but also the places where rRNA can nestle into the overall structure to make the
ribosome structure complete. Not only do the three-dimensional shapes of the two subunits need to be
correct, but the matching shape of tRNA must be accounted for. It also achieves its final shape by folding and
twisting, but this time it’s the nucleotide sequence within the molecule itself that determines the final
outcome, as the tRNA isn’t translated into anything. It’s the RNA that it’s made out of that creates the
necessary configuration, by base pairing with itself! Because the molecule is single-stranded, it can fold up and
twist, aligning some of its bases opposite and facing each other. The ensuing hydrogen bonds that form are
strong enough to maintain the three-dimensional shape that gets created.
To make things more complicated, there are two “active” locations on the molecule where a threeletter sequence of nucleotides must be exposed, rather than being hydrogen bonded to other bases in the
strand. What’s more, they have to be twisted to face outward, in the case of the anti-codon, or extend beyond
the end of the rest of the molecule, as in the case of the amino acid attachment site. As if that weren’t
enough, they have to be the right three letters in order to create both an anti-codon (at the bottom of the
molecule) and the amino acid attachment site (at the top of the molecule) that match. Here’s another doozie
to chew on. Even though there are only 20 amino acids to build from, due to the built-in redundancy of the
code intended to protect against the effects of mutations, there are actually 61 codons that code for these 20
amino acids. What that means is, no less than 61 DNA sequences must be planned such that when they are
transcribed to create the adequate number of tRNA molecules to work together with the ribosomes for
achieving translation to protein, they will end up forming to all these required specifications! The forethought
required to conceive of such a system, with the code specifying not only the machines which can replicate and
transcribe it, but also the machines which can translate the transcript into protein in an automatic, assembly
line fashion is astounding.
Allow me to describe another automated assembly line that completely blew me away the first time I
learned of it. This time it exists not in a big eukaryotic cell, but in an itsy bitsy bacteria. Even though they are
tiny by comparison, they still have elaborate control mechanisms to regulate their cellular activities. In fact,
since they only consist of one cell, it is imperative that these mechanisms work properly or the bacteria will
quickly run out of resources. The need to husband their limited supply of amino acids for constructing proteins
is acute, and the system they use to accomplish this is called an operon.
Operons are actually a fairly long series of genes (for a prokaryote anyway) that are regulated more or
less as a group. Often these operons exist as part of a plasmid, or circular piece of DNA. I want to tell you
about a particular one, called the lac Operon. The term operon comes from a region of the DNA that forms
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what is called an operator. Ok, so what does it do? Well, it doesn’t do anything actively really, but it serves as
an attachment point for a protein called a regulatory protein. This protein is coded for by a gene called the
regulatory gene which is “upstream” from the operator region (it comes before it). The regulatory protein that
is translated from it has a very important job to do. It must mount the operator stubbornly and not come off
unless triggered to. With the regulatory protein in place, it isn’t possible for the downstream genes to be
read/transcribed, because the RNA polymerase cannot mount the DNA. The reason for this is that the site for
this to occur, the promoter region, is just behind the operator, and the regulatory protein is gumming up the
works! So what good is this thing anyway? Great question, and the answer is astounding.
The downstream genes code for the production of digestive enzymes for the sugar lactose. Even
though the bacteria needs the ability to digest lactose as a food source for energy to maintain itself, it can’t
afford the cost of making the enzymes to digest it unless there is some around to digest. Making proteins costs
the bacteria ATP to phosphorylate machines like RNA polymerase, and it has a limited supply of amino acids to
build stuff out of. If a protein isn’t being used for a current purpose, it tends to get recycled so the amino acids
it’s made of can be utilized for other things. Ok, so the regulatory protein prevents the wasteful manufacture
of digestive enzymes. But what if the bacteria comes across a bunch of lactose and suddenly needs to digest it,
what then? Here’s the beautiful part.
When lactose is present, it binds to the regulator protein in a place form-fitted to receive it (a lactoseshaped depression). When a lactose molecule docks into this depression that matches its shape, the shape of
the protein is altered (kind of like a push button being activated), and the new shape will no longer stay bound
to the operator. The regulator protein falls off the operator, clearing the way for the promoter region to be
used. Now the RNA polymerase can mount the DNA at the promoter site and begin transcribing the
downstream genes. As a result, the enzymes which are able to digest the lactose can be manufactured
(bacteria have ribosomes too), and the bacteria can gobble up the sugar and reap the energy rewards. As soon
as the lactose is all gone, the regulatory protein remounts the DNA at the operator, effectively shutting off the
digestive enzyme genes again. The bacteria can then dismantle the digestive enzymes whose services are no
longer required, and the amino acids they were made of can be put to good use elsewhere! The design of the
lac operon demonstrates God’s provision for these tiny guys to be able to conserve their diminutive resources
with an elegant and ingenious feedback mechanism.
Now I don’t know about you, but if I were to walk into a factory and see an assembly line going
gangbusters, with robots doing their appointed tasks, until no more raw material was coming down the line
and then it stopped abruptly, only to start back up when more started to flow in again, I would be impressed.
Wow, all this elaborate planning, just to save electricity and wear and tear on the machines! If there was
nobody around manning the whole thing it would make me wonder if everyone was on a coffee break at the
same time! Surely somebody has to be monitoring this whole complex process, right? If there was in fact
nobody around, not in the break room or restrooms, I would be astonished at the achievement and want to
meet the industrial engineer who invented the thing.
The truth is, He actually is monitoring these automatic assembly lines all the time, both those which
manufacture proteins in us and the ones that bacteria possess. He is also monitoring every other aspect of the
creation which He thoroughly enjoyed making, and I’d like to go on sharing more of the remarkable highlights
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that have gotten my attention after we plumb the depths of this issue of coordination and control just a bit
more.
Getting the biggest bang for the buck, and sometimes junk…isn’t junk!
These impressive examples of automation are enough to make a worshipper of me, but I want to go
deeper down the rabbit hole with you. Did you know that you have about 24,000 genes that code for protein
synthesis? It sounds like a lot until you realize that a mouse or a goldfish have about the same number, and
rice plants have around 60,000. What’s going on here? Aren’t we far more complex than a goldfish or at the
very least a rice plant? Yes, most definitely. So how can our code achieve so much with relatively so little to
work with? Everything we’ve examined so far is
undoubtedly awe-inspiring, but that question
takes us to a depth of complexity that staggers
the mind. The answer comes in several layers,
and to be honest with you scientists don’t have it
all figured out yet. We have a pretty good idea
for part of the explanation, so I’ll start there.
First, the complex and organized
packaging of our DNA provides multiple
opportunities to amplify what can be
accomplished by the code. Many traits depend
Coiling of DNA around histones and epigenetic control mechanisms
on whether the code can even be accessed in the
first place. The DNA is housed in a tightly coiled superstructure which either permits or denies access to
certain regions of the code for particular reasons. For example, all the genes that code for the kinds of cellular
machinery which are peculiar to being a pancreas cell are permanently inaccessible to muscle cells, and vice
versa. Both cells possess the same code, owing to the fact that they all came from the same original zygote.
But at some point in the development of the organism, the genes for being one kind of cell as opposed to
another were permanently shut off and cannot be accessed. If this were not the case, all our cells would be
identical and we would just be a generic ball of goo (and a small one at that). This permanent shut down of
genes is fascinating, and has to do with a phenomenon called “switches”, which once flipped are highly
resistant to change. A chemical straight jacket has been placed on the portions of the code which prevents its
access, and once installed it’s virtually impossible to alter. Nerve cells cannot morph into liver cells at some
point in their existence, and it’s a good thing. Though at first glance it may seem like permanently deactivating
some of our code would give rise to less complexity as an organism, it actually enables more. Without this
selective and permanent switching off of certain genes in certain groups of cells during our embryonic
development, there would be no tissues, organs, or systems possible.
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Another opportunity to regulate gene expression is provided for by the way DNA is coiled up. It is
wrapped around spherical proteins called “histones”, and when examined under an electron microscope this
arrangement has the appearance of a string of pearls. Being wound around histones creates a structure which
facilitates not only the organized packing/compression and physical storage of the code (the string of pearls
can itself be wound up into supercoils), but also a chance to further regulate gene expression. If the DNA is
wound tightly around the histones then it remains inaccessible for the process of transcription because there
isn’t enough room for the transcription factors and RNA polymerase to mount and read it. Here’s the really
special part.
Just how tightly the DNA is wound around the histones is a reversible process. When the DNA is
“methylated” with chemical tags, it is winds more tightly around the histone proteins in the region where the
methyl markers are added. These markers can be removed however, permitting access to the code in the
previously inaccessible portion. Methylation or the removal of methyl markers can be triggered by
environmental exposure to various substances, and genes are turned on or off accordingly. This mechanism
demonstrates the efficiency principle which is so common in life. The coding for histone proteins enables our
large quantity of DNA to be stored in an organized fashion while also creating a way for cells to activate or
deactivate certain genes in response to what they are encountering. As if this were not marvelous enough, a
whole host of additional methods for regulating gene expression are built into the system, enabling the cell to
maximize how much complexity it can squeeze out of a limited set of instructions.
One opportunity to make the most of the code exists in the fact that more than one strand of mature
mRNA can be made from a single gene. Rather than making one long finished strand, the spliceosome can
make multiple shorter pieces of mRNA, depending on where the caps and tails are added. This would result in
smaller proteins that have completely different shapes and functions.
Then, the cell can regulate the quantity of protein which is manufactured by a given strand of mRNA by
allowing it to continue to be translated, or by dismantling it back into nucleotides sooner rather than later.
Just how much protein is manufactured from a particular gene can have profound effects on how a trait is
expressed.
Still another way genes are regulated is in the “finishing” of proteins after they have been translated
from the mRNA. Often times, proteins remain inactive until some tailoring is done to their structure. Without
a snip here or there which is performed in a structure called the “Golgi apparatus”, a protein may remain
inactive because its ultimate shape has not been achieved. A good example of this is the protein known as
insulin. The translation process does not result in the active form of this crucial substance (it’s what enables
cells to take sugar in for food). The pancreas cells which manufacture it must first modify it into the active
form before it is ready to be shipped out, and this does not have to be performed immediately. This enables
pancreas cells to meter out the rate at which they produce insulin very precisely.
Even after the active form of a protein is created, how long it remains active can be regulated by the
cell. If the protein is disassembled fairly quickly back into its constituent amino acids, then the trait does not
end up being expressed for very long. By permitting the protein to function for longer periods of time, the
same gene has a different effect. Truly, this all gets a bit dizzying, but the next mechanism is where we see the
greatest feat of controlling gene expression.
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This one relates to the fact that not all of our DNA actually codes for protein synthesis. Huh? I thought
that’s what it was for! Yes and no. If you recall, we have around 3 billion base pairs in our code, and the vast
majority of this information is actually not for specifying amino acid sequences. Well, what’s it for then? We
used to think that it was just “junk,” like remnants of mess ups from previous copying errors, or viral DNA that
has found its way into our code (we really do have some of that). What we have come to realize after the
human genome project was completed is that identifying the code for protein synthesis is child’s play
compared to figuring out how the rest of the genome operates. We’re not sure, but this may be what
accounts for the control of all of the control mechanisms I just described (I wondered if you were wondering
how it knew when to do all that stuff).It’s actually software that runs the software! What was once assumed
to be extraneous genetic material figures to be the most vital part of our DNA, because it actually controls the
part of the code that codes for proteins. By determining when, why and how long our genes are in operation,
we can use many of the same genes which make a goldfish or a mouse, or even some that make a rice plant
for that matter, and accomplish something vastly different as an organism. It is this software that runs the
code which makes the difference between most living things, not just the differences in the various codes for
protein synthesis (although there are usually enormous differences here too). Scientists have called this the
epigenome. The prefix “epi” means surpasses or above, and deciphering our epigenome will keep us occupied
for quite a while.
What this epigenome points to is perhaps the most profound issue we’ve contemplated. If knowing
what the code must be in order to construct the countless numbers of proteins that it takes to make a
functional organism, then programming the software to run the code is an unimaginably difficult task.
Foreseeing how long a gene must be expressed in order to achieve a desired effect, while considering the
effects of tens of thousands of others simultaneously being expressed in trillions of cells such that the desired
organism can work properly in all respects requires an intellect that goes beyond anything we can conceive of.
All the other words I’ve used in celebration of God’s character aren’t quite enough at this point. Glorious, holy,
omniscient, and almighty are more appropriate.
Reduce, re-use and recycle!
Long before there were any of those blue garbage cans with the triangular arrow picture, cells were
keen on all this. Their recycling program makes our most efficient and well- planned recycling program look
like child’s play. We have difficulty getting “buy in” by all the members of the community to participate,
despite all our education efforts, but cells “get it.” The effects of the second law of thermodynamics were
foreseen, and the equipment required to dismantle worn out parts and re-use the building blocks was
programmed into the code in anticipation of this vital need. Digestive enzymes are produced by our cells not
only to break down food, but also to recycle raw material. But you can’t exactly have this stuff cruising around
the cytoplasm breaking all your good stuff down indiscriminately, so a method for doing this in a controlled
fashion had to be devised.
Enter the lysosome. It gets its name from the word “lyse”, to break open, and it is a membrane-bound
vesicle full of digestive enzymes. The membrane keeps the dangerous digestive enzymes safely housed, and
when something needs to be broken down it moves toward it and engulfs the item. That way, the digestion
takes place on the inside, where no harm will come to outside structures unintentionally. It is created by the
production of digestive enzymes in the endoplasmic reticulum via the ribosomes and tRNA which are then
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sent in a vesicle to another structure called the Golgi apparatus. The enzyme is modified into its final form and
then shipped out inside a new vesicle, and this enzyme/vesicle combo is the lysosome. The lysosome is
capable of taking on very large digestive jobs, even the break-down of such things as an entire mitochondria. I
have even seen electron microscope images of one working on a mitochondria and another organelle called a
peroxisome simultaneously! All the raw material that these digested organelles were constructed out of can
then be utilized to make new structures to replace the old ones or to make whatever else the cell may
urgently need. By way of efficiency, the lysosomes are also capable of digesting food that is brought into the
cell, so there is no need to create a second kind of digestive organelle to do this job. The food vacuole and
lysosome merge together, and the digestive enzymes go to work. You could call this ability to perform multiple
jobs the “reduce” part of the program, and the raw materials which are again available would be the “recycle”
part. 
So how about the “re-use” part of the program? A great example of this is the way cells use
membranes over and over again for all sorts of jobs. It all starts with the endoplasmic reticulum. The way the
endoplasmic reticulum ships newly-made cargo is to move the product to the end of one of its membranous
tunnels and then “pinch” the end of the tunnel off with the product inside, forming a vesicle. In this way, what
has been manufactured will not get lost by diffusion into the cytoplasm and it can be sent to its destination
with an added bonus. Rather than being like the plastic bag we buy bread in which is discarded to go into
some land fill, the membrane packaging that a product is shipped in will merge with the Golgi apparatus, also
a membrane-bound organelle, and replenish its membranes. This is crucial, because without a new shipment
of membrane that comes along with the product, the Golgi apparatus would not be able to keep sending
finished products out from itself in vesicles, as it would rapidly run out of membrane material. As it is, the
membranes end up being used and re-used many times and in many locations, including the exterior cell
membrane, because products which exit the cell do so by shipment within a vesicle which merges together
with the cell membrane, thereby dumping its cargo to the exterior of the cell.
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Biologists call this scheme of interconnected/interrelated membrane-bound organelles the
“endomembrane system”. The ubiquitous use of cellular membranes is made possible by the endoplasmic
reticulum, and the cool thing is that the packaging for a product ends up becoming packaging for something
else later on, or the boundary for an organelle, or an addition to the cell membrane itself which keeps the cell
separate from its environment. Wow. We try to do this kind of thing with our recycling efforts. I’m wearing a
pair of shoes made from 70% plastic soda bottle material and they’re actually comfortable.  We do pretty
well with paper and glass, and ok with plastics and metals, but none of our
efforts rival what the cell does so ingeniously with membranes, amino acids and
nucleotides.
Before we leave our discussion of the cellular recycling program, I want
to tell you about one other component in the cell’s architecture that actually
resembles one of those blue garbage cans. It’s called the “proteasome”. This
one made me laugh and shake my head all at the same time when I learned
about it. The need to recycle proteins is so regular that the lysosomes could not
possibly keep up with the demand for their services. They tend to do the big
jobs, and the countless little jobs go to this machine which is designed solely to
shred proteins, one at a time.
There are three reasons this capability is so crucial to the cell. First, the
second law of thermodynamics takes its toll on everything over time, and
proteins tend to wear out. For example, if cells experience heat stress, there’s a
good chance that some of their proteins have “denatured”, or partly unraveled.
These have to be disposed of and replaced. Secondly, when a cell has made a lot
of a certain protein for a particular reason but no longer needs so many of them,
Proteasome side view
the proteasome reduces their concentration in the cell to required levels to
regulate the activity level of that protein. Thirdly, as we have examined many times, proteins are complex
three-dimensional structures whose function depends on their ultimate shape, but sometimes the twisting
and folding goes awry, and the misshapen protein is then either useless or even harmful and must be disposed
of by recycling its raw materials.
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The Protease is a rather large structure made of many protein subunits
that are basically rings stacked on top of each other. It resembles the blue
recycling can in that it has a top part like a lid, a center hollow portion, and a
bottom. One important difference is that the sides have openings though
which the shredded protein fragments can pass out of, back into the
cytoplasm so that they can be re-used for other purposes. The hollow center
acts kind of like the garbage disposal you have in your sink because it won’t
chew up proteins unless it’s activated. The way that the “switch” to initiate the
recycling is flipped is fascinating, because it provides for both on/off control of
the device and the selection of which protein is going to be shredded.
Proteasome cross section
Since you wouldn’t want this giant machine shredding just any protein
it encounters, there needs to be a way to regulate its operation. First, the
protease won’t operate unless a complex of regulatory particles is affixed to
the top and bottom. This is just like other systems we’ve looked at that
require the assembly of subunits to permit a larger function. But even after
the regulatory particles have been attached, it will not open its lid and begin
functioning arbitrarily. Having the lid closed is the principle way the “on/ off”
is controlled, but interestingly, even if a protein enters the “mouth” of the
shredder nothing usually happens (there are a few exceptions) unless it has
been attached to a small protein called “ubiquitin”. Ubiquitin was given that
name because it’s a really tough protein, and since it is durable you seem to
find it all over the place in living things (it’s ubiquitous).
The ubiquitin attaches to both the lid and the protein that has been
designated for recycling. As you might expect, a protein that has been
A protease in action with lid open,
showing attached regulatory particles
selected for recycling will have this hardy ubiquitin attached to it by
and ubiquitin chains
phosphorylation. Remember, non-spontaneous cellular actions require
phosphorylation to get them going so that they can be controlled. Ok, so once the ubiquitin is bound to the
protein, this triggers the addition of many other ubiquitin molecules to be added, forming a chain of them.
The resulting assembly of the ubiquitin chain attached to the protein that has
been tagged for digestion will then be transported to the mouth of the
proteasome and the ubiquitin will dock onto the proteasome’s lid in a special
location that form fits the shape of the ubiquitin. This prompts the lid to
open and the chain to then feed the tagged protein down the hatch into the
grinder. With the lid activated, the middle part goes into action and shreds
Ubiquitin
the protein into short pieces. The pieces then exit outward from the center
and can be used elsewhere. Once the digestion is complete, the ubiquitin dismounts the lid, it closes, and the
monstrous protein superstructure goes dormant again.
The first reason I chuckled when encountering a detailed account of this creation was that the images
it evoked were humorous. I mean, a giant trash can looking thing with a shredder in its belly lying dormant
until the proper “secret knock” was given at the lid, at which time it awoke, opened up its pac man mouth and
then gobbled up the offering, spitting the debris out its sides! The second reason I laughed was that there is
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no conceivable way that this monster could be accidental. In fact, it’s very existence speaks of the awareness
that parts are going to wear out and require replacement, that there will be some misshapen proteins, due to
improper folding, that are useless or dangerous. The amino acids they are made of need to be used elsewhere.
Then there’s one final amusing consideration for anyone who thinks this thing arose spontaneously.
The proteasome is so complicated that its own assembly requires the aid of other little machines that
have been called “chaperones”, which ensure the proper folding of the secondary and tertiary structures so
that the final quaternary structure (the finished functional assembly of all the subunits) will be achieved. So…
you have to serendipitously code through billions of years of random mutation for the machines which can
guide the construction of the larger machine that you are writing code for, so that you can ensure that it can
avoid the fate of the proteins it is being built to recycle (being misshapen), as well as provide for the
maintenance of the cell through recycling raw materials AND regulating protein concentrations within the
cell…Right! No, it was planned in advance, and honestly, this flabbergasts me. The mind that conceived of such
an “over-the-top” thing and the means by which to accomplish it is beyond my reckoning.
Unbalanced washing machines, Archimedes’ screws and electric football
I want to go back to the mechanism whereby life passes on its code to the next generation. Not only is
the forethought which went into the need for cells to reproduce in the first place impressive, but so is the
machinery that enables it to happen. Let’s go back down memory lane to high school biology class during the
unit on cellular reproduction. Remember all those stages of mitosis and meiosis you had to memorize in the
right order? You many have forgotten them after the test, but interphase, prophase, metaphase, anaphase,
teleophase and cytokinesis (and in the case of meiosis you had to use either a Roman numeral I or II) are all
really important. I’m not going to bore you with a review of all that occurs during the overall process, but I do
want to highlight a couple of structures and their functions that are super cool.
Recall a diagram of a eukaryotic cell. There are these two inconspicuous bundles off to one side of the
nucleus that seem to do nothing, that is, until it’s time for cell division. The centrioles, which are packed full of
microtubules, play an important role in the process of those stages we had to memorize. As the nuclear
membrane is dissolving and the chromosomes are forming during prophase, the centrioles are already
migrating toward opposite poles of the cell and extending these thin but strong structural fibers. They sort of
telescope them out toward the center, or equator, of the cell until the fibers meet and complete a structure
we call the “spindle”, which to me looks like a hollow football, or a blimp with no skin. Meanwhile the
centrioles have anchored themselves at the poles by radiating out shorter sections of the microtubule fibers
immediately around them.
During this time, the chromosomes have migrated to the equator and anchored themselves at the
waist to the spindle fibers by a structure called a centromere. The centromere temporarily holds the sister
chromatids together. These are the two identical copies of the chromosome which together form the classic X
appearance. In the case of mitosis, which is used for growth and repair, these chromatids are about to be
yanked apart (after an enzyme splits the centromere) and moved to opposite ends of the cell. This is also true
during the second cell division of meiosis, but in the first stage of meiosis they stay together, because it’s the
homologous chromosomes that are being separated. In any case, I want to examine what happens during the
stage we call anaphase, where the chromosomes quickly travel to the poles in opposite directions.
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If your teacher showed you actual footage of anaphase, you may have noticed a couple of things. One,
the chromosomes move to the poles so fast that they bend in the middle, with the ends trailing behind. Two,
they jiggle as they are moving. We now know what causes the vibrating motion you observed. Here’s where
reality is once again stranger than fiction…
Those centrioles which are parked at the poles of the cell brought something extraordinary with them.
There is a simple machine (actually it’s a compound machine but who cares at this point) called an
“Archimedes’ screw” which was used in ancient times to draw water from rivers, and is still used in many
applications today. Essentially, it’s a cylinder with an auger inside which can rotate freely but comes close to
contacting the sides. When the auger spins, anything it is in contact with at one end will be drawn down the
shaft, cradled in the threads of the screw and prevented from falling out sideways by the cylinder. In this way,
you can convey liquids or loose crumbly solids up or down the screw length, depending on which way you turn
the shaft. We see these used to draw coal uphill into train cars, to convey gravel uphill onto piles, or even to
transport liquids uphill, though the seal between the auger and the cylinder has to be pretty tight for this
application. We never expected to see a molecular-sized one in a functional cell. But its presence isn’t the
most unexpected and wonderful thing, rather, how it works to get those chromosomes moving.
If you attach the cylinder to a fixed point at one end and then turn the auger inside, what happens is
that the whole Archimedes’ screw assembly will rotate on its eccentric axis. But because the rotation is not
about the center of its mass, it causes forceful vibrations. This is akin to what happens when all the towels or
blue jeans are stuck on one side of your washing machine when it goes into the “spin cycle”. If this occurs, the
machine vibrates violently and will walk itself away from the wall and out into the hallway if you let it! And
that’s EXACTLY the intended outcome with this little machine, because it is attached to that network of fibers
which create the spindle. When the screw is activated through phosphorylation, it begins to make the spindle
rattle and shake, and if it weren’t for those radiating fibers around the centrioles anchoring it to the rest of the
cytoskeleton it would probably self-destruct.
As it is, the shaking is able to go on because of the reinforcement. The machine continues to spin in
this wobbly fashion due to its eccentric (off-centered) loading, and that’s why the chromosomes move toward
the poles. If you recall, they were all aligned in single file along the equator, which is the part of the spindle
where its circumference is largest. The chromosomes are attached to the spindle fibers, so they aren’t going to
go flying off randomly, but since the whole structure is shaking, and it’s “downhill” to move toward either pole
from the equator, that’s the direction they migrate.
This reminds me of a really old game we used to play when I was a boy called electric football. There
were little plastic players on a rectangular base that you would set up on the line of scrimmage. The
quarterback had this little felt football which you could use to make a pass or hand off to a running back, but
the “play” began by turning on the switch. An electric motor buzzed loudly and vibrated the table, and the
players would jiggle around chaotically while you endured the noise. If a defender touched the little guy with
the ball the play was dead, or if the offensive player wanted to he could temporarily turn off the switch to
make a hand off or pass. It was maddening, because you couldn’t control what the players did, but also funny
because they did weird and unpredictable things.  It cracked me up to see a line of players who had “run”
out of bounds, just banging up against the edge of the field.
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Now imagine setting this kind of thing up to deliberately get half the playing pieces at one end zone
and the other half at the opposite one EVERY PLAY. How would you do it? You’d bow the playing surface
severely and make the 50 yard line the high point, lining up one team on their half of the field and the other
on their half. Then, just to make sure, you would run a bunch of lines perpendicular to the equator that the
players would attach to but be able to slide on. This is what God did, but He wasn’t playing football!
It’s interesting to note that the PhD who discovered this mechanism credits the design to God, and the
Neo-Darwinian community has shown little interest in it. They have studied the way the spindle forms, with
“kinetochores” connecting opposite sides of the growing spindle once they contact each other, but this thing
with the rotating Archimedes’ screw smacks just a little too much of engineering, so for the time being the
response has been to “hear no evil, see no evil, speak no evil.” Curious.
Bull whips and their little brothers, sky scrapers and their footings
Ok, you’re still in high school biology class with me, and we’re taking turns looking at one-celled
organisms swimming in pond water. Some of them are gliding around smoothly, while others are jerking
rather violently. Some aren’t actually swimming but are anchored by a type of stalk to nearby debris. You
zoom in with your highest objective and notice that these guys have little hairs waving around the rim of their
“head”, and this is creating a little circular current in the water above them. Closer inspection of another
critter reveals that it possesses one giant bull whip-like tail that wiggles back and forth the same way a fish
undulates its body. We find yet another one shaped like a cigar, and zoom in on it to find the same kind of
little hairs that the stationary protist had, and they’re waving all around it. These hairs look like little brothers
of the bull whip structure you just looked closely at, and the creature with
these undulating hairs reminds you of one of those old galley ships with
oars sticking out of the sides.
All these protists have something in common with each other, and
for that matter with the cells lining your own upper respiratory tract. They
all have external structures composed of bundles of microtubules in a 9+2
arrangement, sheathed in an extension of the cell membrane. In other
words, they all have either cilia or flagella. These superstructures are
designed to convert chemical energy into mechanical and kinetic energy,
and the way they do it is really neat.
Cross section of Cilia and Flagella
As with so many other cellular structures, it’s a combination of specifically-shaped proteins arranged
and interacting in a particular way that enables the desired outcome. The structure is essentially the same for
both cilia and flagella, only the flagella are much longer. They both have the 9+2 arrangement of microtubules,
a structural protein that gets its strength and rigidity from the fact that it is a tightly-coiled chain of amino
acids that form a tube. Tubes are the most efficient structural member, considering strength-to-mass ratio and
the fact that they are equally resistant to bending stress in all directions (it has no “weak axis”). But if tubes
resist bending, then how can such wiggly structures be constructed out of them?
It all has to do with their configuration, and the additional components which work in tandem with it.
There are 9 bundles of two that are arranged in a ring around the perimeter of the shaft. The bundles do not
contact each other, but have gaps between them, and there is an even larger gap between the outside ring of
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bundles and the one bundle of two microtubules in the center. This open configuration permits the flow of
ATP molecules and other material up and down the shaft. Spanning between the two microtubules in the
central axis and the bundles of two that are stationed around the perimeter are spokes of flexible proteins.
This maintains the spacing between them while also providing for internal traction (anti-slippage). Vertical
rows of two motor proteins called “dynein arms” are installed between each of the 9 bundles of microtubules
at the perimeter, down the entire length of the shaft. These are attached on one end to a microtubule at the
perimeter of the shaft, and oriented horizontally so they can reach up or down to grab the microtubule across
from it.
This results in a pulling action similar to when an oar is placed in the water and the shaft is pulled. The
boat moves through the water because the ratcheting oar pushes/pulls on the “stationary” water and the oar
ratchets its way on by. This ratcheting or rowing action occurs when the dynein arm is phosphorylated as you
might have guessed. When combined with the contractions of neighboring dynein arms, one bundle of two
microtubules “walks” up or down relative to its neighboring bundle, and this teamwork is capable of flexing
the shaft in any direction perpendicular to its length. The central spokes support this action by bracing against
the central bundle of microtubules and preventing slippage. If the microtubules weren’t fairly rigid, then there
would be nothing useful to exert forces on because there would be nothing solid to give a reaction force, or
“push back” (remember Newton’s third law!)
This is a little difficult to visualize, but the truly amazing part is that there must be a coordinated effort
on the part of the dynein arm contractions or there will be no useful motion. Alternating sides of the shaft
have to be either relaxing or contracting at different locations along the length of the shaft in order to
generate the wiggling effect which in turn pulls the overall structure
through the water. The motion really looks like a fish swimming, only
that one end of the structure is stationary. The tension that all this
wiggling/waving creates is considerable, especially at the base of the
flagella or cilia. Without some kind of beefed up attachment into the
cell, the cilia, but especially the flagella would literally rip itself out at
the base. This called for an additional support structure at the junction
of the cell and the flagella/cilia.
You could think of this reinforcing structure as something like
the foundation of a skyscraper, bracing it into the surrounding earth.
The base of the flagella/cilia couples with this foundation structure
1 and 5 are the bundles of microtubules in
called a basal body, by protruding into it. This is possible due to the
the flagella shaft (5 also shows dynein
arms), 2 is the extended cell membrane, 3
slightly different arrangement of microtubules in the basal body. 9
shows the transport of ATP and ADP, and 4
bundles of three microtubules are arranged in a ring of overlapping
and 6 are the basal body
bundles, creating a very strong structure. In the case of the basal body,
there is no need for the central bundle of two. From a structural engineering perspective, having mass in the
middle of a member which is resisting bending stress doesn’t help the strength due to the fact that the center
of rotation does not deflect. It’s more beneficial to have greater mass further away from your center of
rotation so as to create a greater moment of inertia. In other words, a thick walled pipe (which is essentially
what a basal body is) with a larger diameter is stronger than a pipe with a smaller diameter, thinner walls and
a useless piece in the middle. But wait, I thought the bundle of two microtubules in the flagella and cilia was a
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crucial part of the structure? It is, for the flagella or cilia which have to have a mechanism for flexing back and
forth, but not for the basal body which responsible for anchoring it back into the cell and has to fight bending.
I find it fascinating that some of the exact same building members can be arranged differently to
achieve a totally different purpose. In the case of the cilia and flagella, bundles of microtubules are
interspersed with motor proteins in an arrangement that provides rigidity along the length while allowing
flexibility horizontally so that undulating motion can be produced. But in the case of the basal body, larger
bundles without gaps between them are arranged in an overlapping ring to achieve the maximum resistance
to bending stress!
True masters of engineering and architecture are the ones that find ways to use the same raw
materials in different applications, maximizing their structural capabilities and seeing the opportunities for
possible uses in combination with other materials to accomplish unforeseen things. This is very challenging for
us, yet the good ones can pull it off now and then. I don’t know who came up with the notion of reinforced
concrete for instance, but it’s brilliant. Concrete is a relatively cheap material that is happy in compression but
pretty awful in tension, whereas steel is great in tension but tends to get expensive when made into large
enough members to hold anywhere near the vertical load that concrete can. Their epiphany was to embed
cheap grade steel with deformations (ridges) into the concrete when it was wet and place it in the locations
where its high resistance to tension could compensate for the concrete’s weakness. By placing the steel at the
places where the bending stresses were the greatest, like the bottom of a beam or the outside of a column or
caisson footing, the presence of the concrete around the deformations in the concrete would ensure that the
steel would not be simply bent over (steel doesn’t deal with that well either), but rather have to be stretched
before the concrete could crack and crumble. Meanwhile, the tops of beams and centers of columns that
experience compression forces are just fine without the more expensive steel. The same holds true for
“spread footings” which act like giant snow shoes for a building and counterweights to hold it down. It’s these
kind of creative applications of some simple materials which make our sky scrapers possible. We’re catching
on, but God has been doing this routinely for a long time. And we’ve only just begun to explore the uses for
structural proteins that He has devised. 
Warehouse roofs, monorails, movable scaffolding and sacrificial security guards
We can’t quite leave our discussion of the basal body, because alone it would not be enough of an
anchor to hold the flagella or cilia securely in place. It has to be braced even further back into the network of
scaffolding that exists in the cytoplasm, and that’s where we’re going next.
Have you ever taken a look at the internal roof structure in one of those “big box” warehouse stores?
What you will see is some really big structural members called girders that span long distances (from column
to column), supporting some medium-sized members called joists that span from girder to girder. Then,
spanning in between the joists there are the smallest members called purlins. The purlins carry the smallest
amount of load, but there are an awful lot of them. There are quite a few joists, and these are capable of
carrying greater loads, namely all the purlins plus the weight of local air conditioning units, and very few
girders, but they ultimately hold up everything. This organized structure may have struck you before,
especially if you find geeky science stuff more interesting than shopping, but what you might not know is that
it is the roof structure of such a large building that holds up the walls. Huh? I thought the roof rested on the
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walls at the perimeter of the building!? Yes, but without the roof making what is structurally dubbed a
“diaphragm” between all the walls, they would have no way to stay upright when the wind blows against
them. The rigid skeleton that the roof provides, working together with the walls that they tie into creates a
very strong, versatile and durable structure.
Cells have a similar kind of construction plan except that it’s
not just a two-dimensional diaphragm that lends stiffness to the
structure but a three-dimensional network of structural members
running though the cytoplasm. The largest and least numerous
members are made of the same microtubules that create flagella
and basal bodies. Spanning between them are proteins called
intermediate filaments, and crisscrossing all over the place between
them are the smallest but most numerous members called
microfilaments. These structural members anchor to proteins that
are embedded in the cell membrane, they anchor organelles into
their positions within the cell and provide overall shape and
stability to the cell. Going back to the basal body, they anchor it into
this network, and with the combination of its rigidity and the bracing into the whole network of structural
proteins, it’s not going anywhere, and neither are the cilia or flagella that are connected to it!
Collectively, this varied network of structural proteins is called the “cytoskeleton” for obvious reasons.
That’s quite a different conception of the cell than we had 80 years ago. We knew about some of the
organelles and their basic functions, but had no idea that they were tied into a cytoskeleton. The original
notion of cellular architecture that some students create as a model of the cell when they make a Jell-o mold
with fruit and gummie bears suspended in the goo. Back then nobody had seen these proteins because they
are so thin and special staining techniques had to be developed in order to identify and visualize them. When
we did, we found that in reality the cell is much more like a city with a complex structural infrastructure which
provides for support and much more.
When I was a boy we went to Disneyworld, and I got to see a real “monorail”. Having a train wrap
around a central guide ridge obviously made an impression on me, but it comes to mind for good reason at
this moment. Those structural proteins, particularly the thinner ones, also serve as a transportation system of
monorail lines for cellular transport. When we speak of an item being transported from one place to another
in the cell, it’s actually these intermediate filaments that serve as the monorails. The trains are especially
designed transport proteins, and the “fare” to ride is the phosphorylation of these little machines. That’s why
exocytosis, the process of moving a vesicle full of some cellular product to the cell membrane and dumping it
outside, falls into the category of “active transport.” It costs the cell ATP to move freight from point A to point
B within the cell, because the vesicle isn’t aimlessly wandering about but being actively pulled to a destination.
This is one way to utilize the cytoskeleton to provide for movement; keep the frame still and ride along it to
get where you want to go within the network. But there is another fascinating way to utilize the cytoskeleton
to create locomotion.
Do you remember watching amoebas oozing around under the microscope? They actually use their
cytoskeleton to do this! By extending their structural proteins to one side, their external shape changes. A
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“pseudopod” is formed, and then the rest of the cell is moved when the rest of the cytoskeleton is pulled
along to catch up. Imagine a large set of construction scaffolding covered with giant tarps (that would be the
cell membrane). Normally scaffolding has to be taken down piece by piece and rebuilt to move it, but wouldn’t
it be amazing if it could ratchet sideways, one section at a time and then pull the rest with it? I guarantee that
construction workers would love it! This movable scaffolding does not generate a particularly fast way to get
around, but the amoeba doesn’t need speed. It needs extreme flexibility and a way to combine movement
with eating (here’s that wonderful efficiency principle again). To eat, it extends multiple portions of the
cytoskeleton around the object to be ingested until it has the thing surrounded. Then the cell membrane
closes/merges with the food on the inside of the amoeba, creating a food vacuole. The contents of the vacuole
are then digested by a lysosome. Of course it costs the amoeba a lot of ATP to move all this structure around,
but it’s well worth it because there is a meal waiting at the end and a net gain of energy.
The process of engulfing an object in this manner is called phagocytosis, and it’s not just single-celled
organisms that utilize it. We have immune cells called phagocytes that also utilize their cytoskeleton for
locomotion and phagocytosis, but they engulf things for a completely different purpose. Phagocytes are quite
literally search and destroy eating machines who engulf enemies and digest them with powerful lysosomes to
valiantly protect the greater good of the organism. They follow chemical trails directing them to invaders,
engulf and digest them, and repeat the process over and over until they have eaten themselves “to death.”
Whereas amoebas are making a living by using their cytoskeletons to move and eat, phagocytes are
functioning as self-sacrificial security guards. Certainly they have no conscious altruistic motives, but their
designer does.
Swimming in peanut butter, 3-point turns and hypodermic needles
At the opposite end of the size continuum from amoebas in the world of one-celled organisms are the
bacteria. These prokaryotic organisms (having no membrane-bound organelles) are teensy weensy compared
to eukaryotic cells. They are about the size of a mitochondria or chloroplast yet have to fend for themselves.
One of the challenges they face in life is just getting around. They certainly can’t use amoeboid motion for a
number of reasons, the most obvious one being that their cell wall makes them rigid! How about the cilia or
flagella that protists use? This is close to the answer, because they do in fact utilize flagella, but theirs has to
be different in both structure and function.
The whip or wiggle motion that an ordinary flagella produces is inadequate to propel a bacteria
because at their small scale, something odd occurs with the dynamic of the fluid they have to move through.
The same pond water that a paramecium and its cilia swim through rather nicely is far more viscous to
something as small as a bacteria. They have to do something akin to swimming though peanut butter! So how
would one do such a thing? The answer is to auger their way through their surroundings like a drill. The
bacterial flagella achieve this drilling motion in an amazing way.
Unlike the eukaryotic flagella, the bacterial flagella do not have motor proteins in the shaft itself to flex
it like a swimming fish. Rather, the motor proteins that create the spinning motion are located under the
surface of the bacteria. The shaft passes through a protein ring embedded in the outer membrane (bacteria
have a membrane just outside and just inside their cell wall), then through a second ring embedded in the cell
wall and finally through a third ring embedded in the inner membrane. These rings keep the shaft
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perpendicular to the surface of the bacteria and reinforce the area while providing a “race” that the shaft can
spin smoothly inside of, but they do not generate the rotational motion.
This is accomplished by a complex set of proteins that are arranged in a way that looks an awful lot like
the alternator under my car hood. The shaft of the flagella terminates just under the inner membrane and has
a thick cylindrical protein connected to its base. This protein sits within another protein which is larger and
forms a ring around it (they don’t touch). Another set of smaller proteins are embedded within the cell wall in
a circle around the protein that formed one of the “races”. These proteins extend down to terminate in the
inner membrane, but they also protrude into the cytoplasm and make contact with the large protein ring that
surrounds the protein on the flagella shaft base. This circle of smaller proteins serves to both anchor the outer
ring and keep it isolated from the shaft base protein. For those familiar with motor terminology, the outer
assembly that is formed would be the stator (it’s the stationary part), and the inner protein attached to the
shaft is the rotor (the part that spins within the stator).
In the case of my car’s alternator, the rotor turns
because of electromagnetic attraction and repulsion
between the magnetic fields that are being generated.
In the case of the bacterial flagella, the rotational force
is provided by the flow of ions moving past the rotor due
to a proton ion gradient that is established in the inner
membrane by the bacteria’s metabolism. Hmm…that
sounds familiar!  This deliberate creation of
chemiosmotic pressure so that chemical energy can be
converted to rotational motion is ingenious and
reminiscent of ATP synthase with its rotating shaft
powered by a concentration gradient. This time, the
ultimate purpose was not to turn one kind of chemical
energy into another (the bonds in glucose into the more
readily usable bonds in ATP) but to give the bacteria the ability to move within its viscous environment. Not
only this, but it does so with great efficiency because there is no middle step of synthesizing ATP which in turn
power motor proteins. The chemiosmotic pressure directly runs the motor proteins in the case of the bacterial
flagella. That’s some awesome engineering.
There’s another incredible component in this system. You may have picked up on the fact that just
spinning a shaft will not create the desired corkscrew action so that the bacteria can auger its way around.
This was foreseen. Without one more crucial component the system would accomplish nothing. As the shaft of
the flagella exits the cell it couples to a bent “hook” piece, which in turn transitions to the long filament we
recognize as the flagella. The hook causes the filament to take an outward swing, momentarily perpendicular
to the surface of the cell before straightening out. This achieves the corkscrew action that the bacteria needs
in order to move forward. But what about when the bacteria has to go somewhere other than directly
forward, what then?
When my children heard about this, they instinctively asked if the direction of the spin made any
difference. As it turns out, it does matter a great deal. The clockwise direction produces the outcome I’ve just
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described, but the counter-clockwise direction, which is instantly achieved by a slight modification (rapid and
temporary) of the motor protein, does not produce the same corkscrew action. This is due to the fact that the
filament is composed of long protein strands (protofilaments) that corkscrew around a central connection in a
helix arrangement. The direction of the winding is clockwise, so when the filament is being turned clockwise
the protofilaments lay down smoothly and the overall corkscrew motion is achieved. However, when the
filament is turned counter-clockwise, the protofilaments fling outward from the center and causes the
corkscrew to be shorter in length (more bunched up) due to increased friction between the surrounding fluid
and the filament. What results is a more random motion, but the bacteria uses this option to its advantage,
much in the way we do three-point turns.
By alternating smooth forward corkscrew motions via turning the flagella clockwise, with more random
motion when the flagella is turned counter-clockwise, the bacteria can selectively drift in the direction they
need to go. If the general direction they need to move is forward, then they will spin their flagella clockwise
most of the time, but if they need to change course then they will reverse the direction of the spin more often
to gradually shift their course. Some people use a 5-point turn to change direction because they aren’t
comfortable with only 3, and it may take a bacteria far more of these adjustments but at least it’s better than
always going the same direction! The efficiency of design is what astounds me here, because with a little
tweak of the exact same equipment a different outcome can be achieved! Again, we see some splendid
engineering.
The bacterial flagella have been a favorite of many who want to cite complexity in nature as evidence
of God’s involvement. It’s a good example, but certainly not the most complex one (some of the others I have
mentioned are my favorites, like the proteasome or spliceosome). Even so, because it played a prominent role
in debate over “intelligent design” being taught in schools, there are many who protest the use of the
bacterial flagella in this manner. They claim that it is not at all difficult to propose a step wise evolution of this
system from another bacterial system, because the two systems share a strong similarity in their protein
subunits.
The system is called a type III secretory system, and what it amounts to is a weapon that bacteria
possess which resembles a hypodermic syringe. The base of the system has ring proteins that are very similar
to those in the flagella base, and there is also a shaft which passes through them to the outside of the cell,
only this time it is short, rigid and deliberately hollow for the purpose of delivering toxins. It’s the means by
which many harmful bacteria protect themselves and it is very important, though unpleasant for us! So, why
the argument surrounding the two systems?
Well, the idea was that the flagella wouldn’t work without all its parts, and that there would be no
selective advantage to developing only part of a system, so a bacteria that wasted its resources on making
something which didn’t help it would die off. Those wanting to refute this idea point to the type III secretory
system to demonstrate that bacteria could make other useful things with only some of the parts, and the
flagella could have developed later on. Honestly, I think it’s moot, because neither one could arise by a series
of chance mutations, and if you believe that God designed them both, then you can see His wisdom in utilizing
some of the same features for some of the same reasons.
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Let me put it to you this way. If you were the one designing various bacteria components and needed
to come up with a way to anchor a shaft that passes through the cell wall and membranes, would YOU devise
a completely novel way to do it each time? Nah, good engineers don’t reinvent the wheel every time they
create something, but they do make variations on ideas to accomplish different things. Case in point! 
Donation funnels
Most of us have heard of cystic fibrosis but few
know what causes it. Some people are aware of the
debilitating effects of the disease, that mucosal
membranes of those suffering with the condition become
thick and sticky. The epithelial linings of the lungs and
digestive system don’t work right, and the tragic thing is
that it often comes down to just a single point mutation
in a very complex protein called an ion channel.
When I first saw a depiction of this ion channel it
staggered me, because of the three-dimensional thinking
that had to go into the creation such an enormous
protein. It’s not just that it’s big. There are a lot of really
big proteins, but this one has a lot going on. There is a
stationary part and two separate moving parts that all
articulate together. Just trying to imagine the code to
accomplish this is inconceivable to me. Here’s what you
would have to know in advance that you have to code for
in the primary structure in order to pull it off.
The secondary coiling of the protein begins on one side of the system (under the cell membrane) then
takes a bend up into and through the membrane, then makes a u turn and then comes back down, then up,
then down etc. This continues until it the first half of the funnel is formed, then it exits the cell membrane on
the opposite side it started from to form a hinge and arm with the ball plug wad, then goes back to the elbow
and turns back up into the cell membrane to continue its back and forth u turning pattern to complete the
funnel, before finally exiting the cell membrane on the same side it started, to form the latch and its
elbow/arm on the underside of the cell membrane before terminating. Whew!
It reminds me of those donation funnels you sometimes see at the local shopping mall. You know, the
kind designed to roll coins down. I don’t know if the chlorine ions come through the channel at greater speeds
due to the funnel shape or if the funnel shape just provides a good seal for the spherical plug. I wonder if it’s
funnel-shaped in order to produce something called the “Venturi effect”, where fluids moving though the
funnel shape swirl and accelerate, creating an associated drop in fluid pressure which in effect makes even
more fluid move through due to the difference in pressure outside versus inside the cone. This makes the
passage of the fluid very efficient and keeps the hole from getting clogged. You can roll innumerable coins
down those donation funnels and they all go through without getting in each other’s way, but if you dump the
same number of coins into the mouth simultaneously they will jam up at the opening. A good contrast would
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be the way an old-fashioned carburetor worked in a car to quickly and efficiently swirl the fuel/air mixture into
the intake manifold, as opposed to your kitchen funnel that clogs when you try to pour sugar straight through
it. It’s an interesting question, and I’d love to ask someone who studies this channel protein if they have
noticed the Venturi effect. It wouldn’t surprise me if they had, but for now, it’s just a guess. 
Either way, there are several mutations which can cause the disease, but all of them alter the code for
some part or “domain” of this elaborate funnel and plug. The mutations typically occur on one of the arms
that bend/flex to open and shut the plug mechanism or the latch that keeps it secure. If the flow of chlorine
ions cannot be controlled through the channel then the proper concentration outside the cell relative to inside
cannot be maintained, and the consistency of the mucosal lining becomes too thick and sticky. Somehow, the
moisture content of the mucous is altered, and the digestion of food and breathing becomes difficult.
As I mentioned previously, the action that a protein is intended to perform will not occur until it is
phosphorylated because the phosphorylation alters its shape. In the case of the arms that control the plug and
latch for the plug, a point mutation that omitted an amino acid in the region of the coiled up elbow interferes
with the flexing (coiling and uncoiling), and the channel either remains open or closed but cannot be
controlled as intended. That’s profound. The deletion of just one amino acid (phenylalanine) is enough to
disfigure and disable the “elbow” on the arm. When the system works properly we take it for granted, but a
single point mutation can cause a horrible disease state, and this scenario replays itself over and over again
with diseases. A tiny alteration to the code and you are either chronically sick with some debilitating disease
or worse, dead. It kind of takes you back to the absolute necessity to protect the code as it was written, let
alone God’s unimaginable intellect in being able to design all this stuff. As king David said long ago, “we are
fearfully and wonderfully made”.
Row upon row of rowers
I first learned of the details of muscle contraction
when I was an undergrad student getting my B.S. in Biology.
It blew me away. Z lines, actin, myosin, sarcomeres,
sarcoplasmic reticulum, action potentials,
phosphorylation…all of it set up so that I could flex my
muscles with varying degrees of force, from gently holding a
rose petal to gripping hard enough to support my own
weight! I was amazed at the organization of the protein
subunits into banks of ratcheting fibers possessing little
motor proteins on the myosin fibrils, that would attach the
adjacent walls of actin filaments and flex when
One sarcomere from Z line to Z line
phosphorylated (just like those little dynein arms) so that
the length of the unit they are in would shorten. Because the myosin is pulling actin fibers toward each other
from opposite ends, the gap between the actin ends is reduced. Rows of these subunits were combined, and
back-to-back groups of the units which shared a common “z line” wall at each end were added together to
create more force and smooth, linear contraction of a substantial length on the macro scale.
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It made me think of those rowing teams you see competing at the Olympics, but this time half the
rowers would be facing one end of the boat and half would be facing the other end. And the boat is not really
moving, but rather it is pulling the walls of the housing it’s installed into past itself. To the left and right are
another boat with rowers, and in the next room behind and in front, more banks of rowing teams are all doing
the same thing!
My immediate reaction to this whole set up was that it was a masterful design. The awe only
intensified when I learned more of the details. An action potential is established through sodium ion
concentration levels (created by the action of ion pumps), and when a nerve impulse is sent it triggers the
phosphorylation of the myosin, and release of calcium ions from the sarcoplasmic reticulum (a specialized
version of endoplasmic reticulum which surrounds the sarcomeres) that initiates contraction. When the signal
is terminated, calcium ions are pumped back into the sarcoplasmic reticulum, allowing relaxing/resetting of
the fibers. It’s actually a lot more complicated than this, with acetylcholine being involved with the release of
the action potential, and a series of intermediate steps with the phosphorylation of myosin which involves
calcium ions interacting with actin, producing a “state of rigor” between the myosin and actin, and a whole lot
more. But the essential point was not lost on me the first time I saw it, and I still get the overall picture (I hope
you do too!) 
These cells and their sarcomere units exist for one purpose, to provide pulling force and work in
conjunction with an elaborate system of levers and pulleys (the skeletal system) to propel the larger organism
that they are a part of around and accomplish useful work. The engineering and creativity required to
accomplish this is marvelous. At the cellular level, we have row upon row of rowers. At the macro scale, we
walk. Stupendous.
Warehousing and value-added distribution centers
Something I want to focus on for just a moment is the way cells control the flow of proteins that are
manufactured. Just how do the products know where to go and what to do? What larger process or structure
are they supposed to be a part of? Surely it’s not random and chaotic, right?
The organelle that is responsible for modifying proteins is also where they are “tagged” for shipment to
their final destination and use. As I previously mentioned, The
Golgi apparatus receives vesicles full of recently manufactured
products from the endoplasmic reticulum, specifically the
“rough” ER (endoplasmic reticulum studded with ribosomes).
These vesicles merge with the “back” side of the Golgi
apparatus that faces the ER and then the process of
modification begins. The Golgi is a stack of interconnected
membrane structures that look sort of like pancakes, and as the
proteins pass through the layers, chemical modifications are
performed. This may entail snipping of the inactive form in
order to create the active form of a protein. It may also be the
addition of a group of sugars to create a “glycoprotein”. This is
often the chemical “tag” that identifies the final destination for the glycoprotein macromolecule. When the
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finished product is ready it may be packaged in a vesicle that exits the side or the “front” of the Golgi, where it
will be transported along the cytoskeleton by motor proteins. We aren’t exactly sure of how this all works, but
it appears that this key stage of entering and exiting the Golgi is what modifies, sorts and ships products for
their final destination. However it all works, the Golgi definitely has a ton of “value-added” features. The
ability to receive, modify, process, tag for shipment, package and ship products all in one location is very
efficient. Engineers are always looking for ways to make a process do more with less, whether it is time, space,
or material that is conserved, and the Golgi is a model of these kinds of efficiencies rolled up into one
structure.
The Golgi apparatus is also a really good example of how we try to get closer to that “asymptote” of
reality, only to realize that there is still so much we don’t understand. It’s not just the process of chemical
tagging for shipment we haven’t fully figured out. There is another funny phenomenon which has stumped us.
During mitosis the Golgi apparatus disappears, only to reappear later once cell division is finished. As far as I
know, nobody has figured out what happens to it or how it is re-established, but it’s a good thing it does or
cellular chaos would ensue! I know somebody must be working on the intricacies and mysteries of this weird
looking organelle, and I will be excited to hear what they find out when they learn more. Whatever the finegrained detail is, it was well thought out as a part of a larger scheme to provide for the orchestration of the
cells’ needs. That realization keeps me humble, though I would certainly love to know more. 
The Golgi apparatus, like muscle cells, plays a crucial role in many macroscopic structures and
functions. For example, our pancreas cells manufacture insulin, but it is the Golgi apparatus that turns the
inactive form into the active form. Also, the formation of vesicles full of insulin also provides for a method of
delivering large doses of insulin into the blood stream when needed. This is accomplished by gathering the
insulin-laden vesicles into a staging area between the Golgi apparatus and the cell membrane. There they
await the reception of a chemical message from outside the cell that more insulin is needed in the body, at
which time the vesicles are transported by the motor proteins on the cytoskeleton to merge with the cell
membrane and dump their cargo outside the cell (exocytosis). Without this dose of insulin our cells cannot
take in glucose, and without the capability to provide a large enough quantity in spurts which correspond to a
sudden influx of sugar from a newly-digested meal, the system would all break down and the organism would
soon die. The dedication of certain cells within a larger organism for the purpose of performing a task that is
vital to the survival of all the other cells in that organism, and designing the equipment on the cellular level to
make it possible demonstrates a level of planning and execution that inspires me to worship our Maker.
Mouse traps, the wave, and pigs in a blanket
Nerve cells, oh boy. I’m about to go into deep waters here, where the details are bewildering, but the
magnificence is worth a look, so I’ll try to summarize the best I can. What we’re going to see is that control on
a larger scale requires extreme measures. When it comes to creating just about every kind of multicellular
organism, you have to have nerve cells (only sponges don’t have them), or life isn’t manageable.
A nerve cell has one job in the overall scheme of an organism, that of control and coordination. It
sends and receives messages so that feedback can exist between the organism’s brain (however simple) and
the rest of its body. As with a muscle cell, there simply is no way to understand the nerve cell’s existence and
purpose outside of the context of serving a greater whole. Since the control of macroscopic functions usually
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has to be focused in one location, the nerve cells are required to have a structure that is capable of spanning
physical distance. You can’t monitor and coordinate what you aren’t in contact with, so the nerve cells must
have substantial length, but if the length is considerable then the signal they carry weakens. Maintaining signal
strength becomes a challenge, and this becomes more acute with larger and larger organisms. The size of
most organisms necessitates the linking together of multiple nerve cells end to end, and this creates
challenges for propagating signals from one nerve cell to the next. There must also be specialized nerve cells
on the sensory end of the system to differentiate between various kinds of stimuli, and a plan for branching
into the various parts of the body to ensure that no part is out of contact.
These considerations are quite similar to those facing city planners when working with power
companies, or data transmission lines. Interestingly, the engineering that went into the construction of the
first trans-Atlantic cable is used by biologists to understand the physics behind nerve conduction (relating
cable diameter to resistance etc.). Lord Kelvin’s work on “cable theory” is still useful today in studying axon
length vs. diameter! Anyway, the point is that forethought is absolutely essential to make this all work
properly. Another thing that is unavoidable is the use of copious amounts of energy. No less than 20% of our
energy resources are consumed by nerve transmission, but it’s “money well spent.” So how does it all work?
At the most basic level, no electrical impulse will move without something called voltage, or electric
potential. This is the “push” that makes electricity flow, and it’s created
by a difference in charge from one side of a system to another. This can
be accomplished by having a surplus of electrons on one side of a system
(as in your car battery), or a difference in concentration of ions from one
side of a membrane to another. This is how your nerve cells create
voltage. As you may recall from biology class, your nerve cells have many
active transport pumps that ferry sodium and potassium ions across the
cell membrane. Like other protein pumps, they operate when
phosphorylated, and the shape of the protein changes. The expenditure
of energy through phosphorylation and subsequent alteration of the
pump’s shape enable it to force 3 sodium ions out and then allow 2
potassium ions in, kind of like a squeeze bulb expelling a liquid first, then
filling with air. The internal shape of the pump is selective to sodium ions
on the cytoplasm side, and after the conformational (shape) change it
The sodium potassium pump (the cell
becomes selective to potassium ions outside the cell. These active
membrane is between the red and blue lines)
transport pumps operate ceaselessly to create the difference in sodium
and potassium ion concentrations across the nerve cell membrane, and this difference in concentration is
maintained by the “selective permeability” of the membrane. Sodium ions cannot come in without passing
through special voltage-regulated protein “gates” and the potassium ions cannot exit the cell without passing
through gates especially shaped for them. The cooperation of all these specialized proteins creates what is
known as a “resting potential”. The cell is ready to send a signal because the ions want to establish equilibrium
in their concentrations again but aren’t being allowed to.
Ok, here’s where it starts to get complicated.  One end of the cell is set up to receive messages. The
surface area of the end of the cell is increased with a “dendritic” or branching cell membrane shape.
Embedded in the cell membrane are specialized receptor proteins which are activated in some specific way by
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the message source. The origin of the message could be your skin, where “hot” or “pain” messages are being
sensed, or your brain, where directions are being sent out to the body. The “trigger” could be physical
pressure on your fingertip or the detection of heat moving in our out of the vicinity. I don’t know exactly how
the pressure/pain and hot/cold nerve endings work but it relates to their structures: a coiled loop, a flailed out
end or some other configuration. Most nerve cells are triggered by receiving a chemical messenger molecule
such as acetylcholine on specialized receptors. The cell is triggered to allow ions to pass through specialized
gates in the membrane down the length of the cell, and this wave of migrating ions is the signal that is sent
down the long body, or axon, of the cell. At the opposite end of the neuron the set-up is reversed so that the
message can be relayed to the next neuron or the final destination. Chemical messenger molecules await the
arrival of a wave of ions, at which time they are sent out of the end of the nerve cell to transmit the message.
The target of the message could be somewhere in the body, like a muscle cell needing to contract, or the brain
receiving a pain message.
In any case, the messages won’t be sent unless a certain “threshold voltage” is reached on the
receiving end of the neuron. A signal strength under a certain voltage will not be sufficient to open the gates
that regulate the permeability of the membrane to either sodium or potassium ions. If the gates remain closed
then no signal is sent. However, if the threshold voltage is achieved then the gates do open in a cascade, first
the sodium gates, followed by the potassium gates. The signal propagates down the length of the axon
because the ion channels are triggered to open in sequence down the line. The ensuing wave of ion migration
across the membrane is similar to the “wave” that you see sometimes at a football stadium when the crowd is
in a silly mood. As each portion of people in the stands jumps up and flings their arms in the air, the next
section senses it’s their turn and they do the same, with an obvious pulse traveling around the stadium. Then
they sit back down and are ready to do it again (if they are feeling especially silly). But there has to be an
initiation to the event, such as a persuasive or charismatic individual talking his neighbors into going along
with him. If insufficient numbers of people start the wave, it quickly dies out and goes nowhere.
This phenomenon in nerve cells has been called the “all or nothing” response for nerve impulses. Even
though a resting potential exists, an “action potential” cannot be established unless enough voltage has been
applied to the ion gates/channels (specifically the sodium channels). Once the gates open though, they ALL
open due to a chain reaction of sorts. The sodium gates open first, which triggers the potassium gates to open,
and the intensifying signal activates the next series down the line. Otherwise, no signal at all is sent. Like a
mouse trap that has been set, a tiny nudge won’t set it off. But give it a strong enough bump and WHAM, it
goes off completely! No half measures with mousetraps or nerve cells, and it’s a good thing. You wouldn’t
want a cockroach to set off the trap, and you don’t want your pain receptors all screaming “ouch” just
because a feather touches you.
In addition to the all or nothing response nerve cells have built in to their architecture to prevent
unwarranted signals, we have another layer of sensitivity that enables us to function. We need the ability to
not only distinguish between a variety of types of stimuli but also their intensity. This is accomplished by
placing a higher density of receptors in locations that need to give feedback between the brain and the
environment, such as fingers and lips, but not as many in other areas which need a higher tolerance to pain,
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such as elbows. Imagine the nightmare of your elbows having the same sensitivity as the bottoms of your feet
and vice versa!
A few more details bear mentioning. When axons are long they tend to experience a voltage drop and
require insulation. However, the insulation cannot be
continuous or there would be no way for ions to migrate
through the opened voltage-regulated channels and the
signal would die. The solution for both the insulation
and propagation problems was to wrap the axons
intermittently with fatty cells called Schwann cells. The
A peripheral neuron in purple, with Schwann
cells surrounding the axon in yellow
outcome resembles the food we call “pigs in a blanket”,
where in cross section the hotdog would be the axon
and the dough wrapped around it would be like the
Schwann cell. This process of wrapping nerve cells with insulating Schwann cells is called “myelination” and it’s
vital for nerve function. In the gaps between the Schwann cells called “nodes of Ranvier”, enough ion channels
can be opened to keep the impulse propagating. In fact, the mode of propagation (called salutatory
conduction) that this creates, where the impulse jumps from node to node is actually FASTER (up to 10x) than
in unmyelinated nerve cells. The “myelin sheath” made of
Schwann cells also helps nerve cells to regenerate and to
produce an extracellular matrix for tissue formation. In the
brain this becomes even more important because of the
proximity of each cell to its neighbor. In the brain, additional
cells called satellite cells encase the main body of the neurons
(leaving gaps between them) and perform a similar function to
the Schwann cells. So much electrical activity occurs in such a
densely packed area that without myelination the signals
would short circuit. This is in fact what occurs in diseases
A highly insulated neuron from the brain
where the myelin sheath degenerates, such as ALD and
muscular dystrophy.
Another crucial detail in the design of nerve cells is the function of the
synapses between nerve cells. In some cells where the impulse needs to
travel as fast as possible (as in some areas of the brain), there actually is
no synapse but rather a direct connection with special gates called a gap
junction to permit the propagation to continue unimpeded. In most
cases though, the signal is propagated from cell to cell by the
secretion of a neurotransmitter molecule like acetylcholine. Vesicles
with the neurotransmitter wait on the inside of the terminal end of
the neuron, ready to merge with the cell membrane by exocytosis.
The molecule quickly diffuses across the gap and lands on receptor
proteins that match its shape, triggering the action potential of
Diagram of a synapse showing the cycling of acetylcholine
the next cell.
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However, the gates of the triggered cell then need to be closed, which necessitates the breakdown of
the messenger molecule. The neurotransmitter molecule is cleaved by an enzyme that is present in the
synapse (actually embedded in the same membrane as the receptor proteins) to deactivate it. The hydrolyzed
(broken-down) molecule can then be pumped back into the neuron that sent the signal and reassembled back
into fresh neurotransmitter molecules by a different enzyme. With the synapse cleared of neurotransmitter
molecules, and restored neurotransmitter molecules ready to go, a new
impulse can be sent. This process has to be able to repeat rapidly to keep up
with the demand to propagate new impulses, and to allow for the cessation of
the previous impulse and/or its effects. For example, in muscle cells the
sodium gate needs to be closed and calcium needs to be pumped back into
the sarcoplasmic reticulum, so that the muscle fibers can relax. Without
elimination of the signal, the calcium ions stay bound to the actin fibers and
no new contraction can occur. Thanks to the action of acetylcholinesterase,
neurotransmissions to our muscles can be quickly halted and reset. One
Acetylcholinesterase
enzyme hydrolyzes about 25,000 molecules of acetylcholine per second.
That’s a quick turnover rate considering the complexity of the molecule it’s working on! Going back to our
examination of poisons, this is another one of the ways that they can harm us. Poisons like sarin gas or some
pesticides bind to acetylcholinesterase, interfering with its activity. Without the cessation of the impulse to
contract, our muscles will remain in a state of rigor mortis. That’s bad news. No relaxation of muscle
contractions means no diaphragm and intercostal muscle contractions and no breathing. 
It’s easy to learn the details of such a system and lose track of the wonder of it all. Without sodium
potassium pumps and a selectively permeable membrane, no voltage would exist. Without the design of
protein channels that only open with sufficient voltage (more specifically, whose conformations change with
voltage), nerve cells would be firing prematurely all the time.
Without the architecture of elongated axons and dendritic ends
with receptor proteins and neurotransmitters, the signal wouldn’t
be able to propagate. Without super-fast enzymes to break down
neurotransmitters, protein pumps to recover the pieces, and more
enzymes to reassemble them we would not be able to repeat the
process over and over again. Without myelination the impulses
would short circuit, wouldn’t go far enough or fast enough, and
nerve tissue couldn’t form or repair itself. Without a variety of
Diagram of a gap junction between adjacent cells
nerve endings we wouldn’t be able to distinguish between heat
and pressure. Without varying the density of these nerve cells in
specific locations in the body, the information they send wouldn’t be useful. All of this planning and provision
was performed so that our minds could control our bodies. All of this had to be written into the code. All of
this is a miracle of vast proportions.
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Golf balls, doughnut holes, and the larger world
Let’s take a look at what we have learned about red blood cells and
hemoglobin and then explore the mechanism that was designed to make
sure that oxygen gets precisely where it’s needed most. We learned that red
blood cells are full of a protein called hemoglobin, and that it was given that
name because of the “heme” groups within the larger “globular” mass of
proteins. We also learned that in the center of these heme groups is an iron
atom, and that this iron is what temporarily bonded to oxygen and carried it
along. This is what gives oxygenated blood the red color it has, just like rust.
What we probably didn’t learn (we didn’t know about this when I was in
biology class) is the reason why the oxygen stays on the hemoglobin until it’s
time to get off. I’m excited to tell you, because this is absolutely amazing.
3D structure of deoxygenated
hemoglobin, with heme units
shown in green (iron atoms
omitted for clarity)
The iron atom is initially too large in diameter to fit into the middle of the
heme group, so it rests on top, like a golf ball sitting over the hole in a doughnut. However, when the iron
atom bonds to oxygen it loses valence electrons (those are its outermost ones) and it shrinks in diameter.
Once it shrinks, it is small enough to fit into the hole and it settles into it. But as it does, the heme group
distorts from this movement of the iron, and the flexing pulls on the larger protein superstructure that it is
connected to. This in turn makes the protein undergo a conformational change, and that’s where the
selectivity comes in.
The altered shape of the protein hugs against the heme units and makes it difficult for the oxygen to
leave the hemoglobin, so it stays attached to the iron atoms until the original shape of the overall
superstructure is restored. You can probably guess when this occurs and
you’re right. When the blood encounters areas of high carbon dioxide
concentration, the pH of the environment causes the protein
superstructure to revert back to the original shape. It’s not immediately
obvious why high carbon dioxide levels affect the acidity of the extra
cellular fluid, but carbon dioxide is highly soluble in water, and when it
dissolves it immediately reacts to form carbonic acid. The carbonic acid
dissociates into a proton and a hydrogen carbonate ion, and it is the
high level of protons that cause the protein to denature (unwind) slightly. Oxygenated hemoglobin (note the iron
atoms sunken into the hemes and the
This allows the oxygen atoms to dismount and the carbon dioxide
flexed shape of the globular protein)
molecules to bind to a different site on the hemoglobin for the return
journey back to the lungs.
However, the carbon dioxide carrying capacity of the hemoglobin is not sufficient to rid the body of
this waste, even when combined with the volume of carbon dioxide that can dissolve into the blood. Another
method had to be devised to increase the ability of the blood to carry carbon dioxide away from the cells
producing it. The answer was in an enzyme called carbonic anhydrase. This converts carbon dioxide to
carbonic acid, which in turn dissociates on its own into the hydrogen carbonate ion and a proton. Afterwards,
the automatic action of shifting the chemical equilibrium takes care of the rest. When we exhale carbon
dioxide, some of the hydrogen carbonate ions spontaneously recombine with a proton to become carbonic
63
acid again, which then immediately decomposes into carbon dioxide and water to compensate for the loss.
Here’s a look at the equilibrium:
𝐶𝑂2+𝐻2 O↔ 𝐻2 𝐶𝑂3 ↔ 𝐻𝐶𝑂3− +𝐻 +
When the equilibrium is stressed by adding or removing a reactant or product, it will respond by using
what is present to replace what was removed, or remove what was added by generating more of the product
that can be made from what was added. This built-in response to stresses in chemical equilibria is called Le
Chatelier’s principle, and along with the work of carbonic anhydrase and breathing it keeps the levels of
carbon dioxide in the body under control.
The creation of hydrogen carbonate ions also serves another crucial role in the larger organism. The
blood needs to be chemically buffered to protect it from extremes in pH. Enzymes will denature (come
unwound) and lose their ability to function if the pH in our body is too high or too low. The hydrogen
carbonate has the ability to either neutralize acids by absorbing excess protons and becoming the relatively
harmless molecule carbonic acid, or neutralize bases by releasing a proton and becoming the carbonate ion.
Consider with me the meaning of all this. There is really no way to view all these features except as
part of a larger plan to acquire oxygen at a location which is distant to the final location where it is needed,
and dispose of waste carbon dioxide. This was essential so that large multicellular organisms could meet their
demand for oxygen through the use of specialized and highly efficient tissues and organs (lungs and heart)
that could obtain it and transport it. Given this need, there had to be a mechanism whereby oxygen would
automatically mount and dismount from the vehicle that carried it. The placement of the iron and heme units
within the larger protein was the solution for ensuring that oxygen would be delivered where it is needed
most, to the cells that have been performing cellular respiration and are running low. The design of the
hemoglobin also provided the ability to also transport some of the waste of cellular respiration back to the
lungs for disposal. The strategy which was devised to increase the uptake of carbon dioxide into the blood to
dispose of the rest, while also creating a blood buffer is so impressive because it provides for several needs
with the same solution. This highly efficient and automated system is yet another one of those creations that
pays tribute to God’s ingenuity.
Wrong place, wrong time, wrong language
I want to go back and take another look at the way in which the code for all the complexity we’ve been
examining is coordinated and controlled. Actually, it’s the malfunctioning of these control systems I want to
take a closer look at. As we saw, even simple organisms have genes that control other genes. Prokaryotic cells
tend to control several genes with one regulatory gene in a system called an operon, but unlike Prokaryotes,
each gene in a Eukaryotic multicellular organism tends to have its own regulatory gene. If you recall, the
regulatory genes code for the production of regulatory proteins which in turn control the operation of the
downstream genes. In most instances, the default condition of a gene is “off” due to the action of these
regulatory genes and the proteins they create. This ensures that genes are only expressed when they need to
be, via some kind of feedback mechanism, as we saw with the bacterial lac operon, or by the reception of a
chemical messenger. The messenger triggers the deactivation of the regulatory protein and subsequent
transcription and translation of the gene.
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There are some genes that are always “on” deliberately, such as those that are responsible for the
operation of glycolysis, because cells always need the process running. This can be accomplished by the
presence of a “weak promoter” region on the DNA that does not interfere with transcription of the
downstream genes. But what would happen when a gene is supposed to be in the default condition of “off”,
but the regulatory gene which normally controls it is mutated or even missing/misplaced due to translocation?
If the regulatory gene is mutated, then the regulatory protein it codes for will be deformed and not
work properly. Uncontrolled gene expression is the result. If the regulatory gene is translocated (misplaced
somewhere else in the genome), then it won’t be controlling the downstream genes that it was intended to,
and expression of those genes will not be regulated. Even though the regulatory gene isn’t mutated, being
placed next to genes it was not intended to control makes it useless, or interferes with their operation. Couple
with this the fact that most of or our genes are actually expressed in concert with other groups of genes and
this poses a real problem. Polygenic expression of traits is pretty common in multicellular organisms, with
genes being activated simultaneously to express a trait. If the regulatory genes are not working in a
coordinated fashion, traits are not expressed properly and chronic diseases or cancer ensues. This is especially
true if the regulatory genes for those that control the cell cycle (mitosis) are not operating properly, or if the
genes that code for tumor suppressor proteins are mutated. If the regulatory genes for the genes that code
for growth factors which stimulate cells to reproduce (oncogenes) are mutated or translocated the cell has a
greater chance of becoming cancerous. The regulation of the cell cycle could also be disturbed if the
oncogenes are mutated because a misshapen growth factor can be “hyperactive”. A real nightmare scenario
would be the misfortune of having translocated or mutated regulatory genes for oncogenes AND tumor
suppressor genes. In that case there is a high probability that cancer will develop.
To get a picture of the ensuing chaos, imagine being a police officer who is teleported to a foreign
country. The way that country operates is different and he doesn’t know the laws. Being in the wrong place at
the wrong time, speaking the wrong language would result in a lot of criminal activity going unchecked! That’s
what it would be like at the cellular level, with potentially terrible consequences for the larger organism. While
we’re thinking about police officers, let’s move on to talk about the systems that have been put in place to
monitor the cell for suspicious activity.
Cops on the beat and military police
Police officers have a territory called a “beat” that they are responsible to patrol. In some places they
walk their beat and have intimate contact with the people they serve, enabling them to instantly recognize
when something is wrong. Our cells have similar servants which are designed to protect against unusual
activity.
There is a version of RNA that we have not examined yet, RNAi. This particular form of RNA has a
unique responsibility, and that’s where it gets its name. It interferes with the activity of viral DNA by patrolling
the cytoplasm, looking for unusual segments of other RNA. The RNAi has the ability to recognize foreign
instructions, and when it sees that something is amiss it destroys the foreign RNA. This helps to ward off the
invasion by viruses, and without it we would be much sicker, much more often. Obviously, the need to protect
us from invaders was foreseen and a line of defense was created to counter their presence.
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There is another, perhaps more sober kind of police officer in our cells. Mitochondria have their own
DNA for many reasons, one of which is to play the role of independent monitoring of the activity in the cell’s
nucleus. The mitochondria are able to detect when there are serious problems with the regular DNA in our
cells. Like military police on a high security base, who have the job of arresting our own officers when they are
acting in contradiction with their orders, the mitochondria will issue the order for the cell to self-destruct
when things aren’t right in order to protect us from cancer. As grim as it sounds, the likelihood of irreparable
damage accumulating in our DNA was foreseen and planned for. No cell is allowed to live on and jeopardize
the whole organism when it is heading towards becoming cancerous.
Retirement planning, the self-destruct sequence, and burning the embassy files
There are genes in both our mitochondria and our nucleus that exist for one purpose, that of organized
cell death, or apoptosis. This is different than unexpected cell death, or necrosis, that might occur to cells that
are poisoned or starved for oxygen or some other cause. Programmed cell death is planned for by the code.
Before we get into the details of how this works, we need to take a step back and look at the larger view of
things.
To understand apoptosis, we first need to revisit the fact that the second law of thermodynamics will
always “win” in the end, with an accumulation of damage to the code necessitating it’s destruction so that life
in its healthy state can be perpetuated. One of the ways that this was planned for was a limit on the number
of times that a cell is allowed to divide. When the cell has reached its predetermined limit on number of
divisions, a series of events triggers the onset of apoptosis. Simply put, immortality for our cells was ruled out
from the beginning.
But what establishes the limit on the number of times a cell is permitted to undergo mitosis? The
mechanism for determining this is the existence of protective caps on the ends of our chromosomes called
telomeres. Each time a cell divides, the length of these protective caps is degraded a little, and when no
telomeres are left the cell goes into a “crisis.” Crazy things begin to happen in the nucleus, like chromosomes
fusing together end to end, and erratic execution of instructions that results in the production of deformed
proteins. The mitochondria recognize by the products resulting from the
dysfunctional nucleus that all is not well, and they secrete a protein
called apoptosis inducing factor (AIF). Ironically, the gene for this protein
is actually located on the X chromosome in the nucleus. After the
mitochondria secrete the AIF it makes its way to the nucleus, and its
arrival triggers the condensation and fragmentation of the DNA. Like an
embassy that is about to be overrun, the files must be destroyed. The
DNA is programmed to prevent its own use in the event that the cell
attempts to become cancerous. Now that is a powerful testament to
deliberate design!
There is another sequence in the self-destruct mechanism initiated by the release of AIF. It’s not
enough that the out-of-control DNA is being destroyed, the cell must also dispose of the myriads of proteins it
possesses, and this duty is performed by a special family of proteases called
Apoptosis inducing factor
caspases. Caspases are made in preparation for the day that they will be
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called upon to participate in apoptosis. When that time comes, they spring into action and start destroying
proteins in a similar fashion to the way regular proteases do in their maintenance of the healthy cell, only this
time the destruction is final. Imagine that. A cellular doomsday machine created for the day it is summoned.
Wow.
The cell possesses yet another mechanism to initiate apoptosis. There are lipids embedded in the cell
membrane called ceramides that have the ability to sense severe stress in the form of high doses of radiation
entering the cell. They can trigger the onset of apoptosis before the nucleus even has a chance to become
cancerous. The levels of radiation that cause the ceramides to initiate apoptosis correlate to severe damage
that would kill the cell or damage it to the point of becoming cancerous, and since the cell membrane is the
first place in the cell that the radiation would encounter, it makes perfect sense that it would be given the
equipment to send this alarm message if necessary.
It was once thought that when a cell needed to self-destruct it would simply release the digestive
enzymes in its lysosomes. We know now there is much more to it than that, but it is believed that there are
special vacuoles that are similar to lysosomes which do play a role in the orderly dismantling of the cell. This
would be akin to the existence of the caspases in addition to normal proteases. As various enzymes work, the
cell begins to break down its organelles and digest its proteins, and it starts to shrivel and pinch off into small
chunks. Chemical messages of the cell’s death are sent out, and at this point, phagocytes arrive to engulf and
digest the bits and pieces of the dismantled cell.
With all this specialized equipment ready to shut down operations in the cell it becomes apparent just
how important this capability must be. Cancer is a truly hideous enemy, and its prevention is paramount. I had
a graduate professor once say that the mutations in cancer were an excellent example of evolution in action
for anyone who doubts the theory. As it turns out, it’s actually one of the strongest arguments against it.
Contingency against cellular psychopaths: conscience and counseling
All the pre-arranged measures the cell possesses to ward off cancer could be considered something
akin to a cellular “conscience”. The cell knows when it is too old and damaged to go on and it “gets its affairs
in order”. But there is another layer of defense our cells possess against becoming cancerous, and that is the
fact that they are not alone.
In a multicellular organism, cells are a part of a larger whole, and their existence only makes sense
within this larger context. No cell exists solely to serve itself, and the community that they are a part of
actually helps them not only to survive, but also to know when it’s time to die. Because cells are
interconnected via their extracellular matrix and chemically through messenger molecules, they monitor each
other’s well-being. When a cell is starting to become cancerous, its cell surface proteins begin to be disfigured,
and neighboring cells recognize this. If the cell has not already initiated apoptosis on its own, other cells will
send chemical messages to the cell in an attempt to initiate the process. While this seems morbid for us to
council anyone to commit suicide, cells do it in order to protect the good of the community. Cellular
psychopaths are the worst kind, because the enemy is “us”.
Ironically, some of our most promising therapies take advantage of the fact that cancer cells still have a
“conscience” by trying to awaken it so to speak. The problem is that they are ignoring the programming to die,
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so we have to try to reactivate the mechanisms for self-destruction through diplomacy. It’s sort of like trying
to talk a maniac out of his heinous plans by reminding him of the fact that he was once a peaceful member of
a beautiful society, and that community is what he was meant to serve, not dominate. His useful lifespan is
done, and now it’s time to die or he will inevitably destroy the society and himself with it. I don’t mean to
make light of cancer whatsoever. It really is hideous, and we have probably all been affected by the loss of
someone we love to cancer. To give us an appreciation of the lengths God went to in order to protect us from
it we need to examine how it develops.
A seared conscience and taking candy from a baby
When a cell has too much genetic damage, one of two possible outcomes will occur. Either all the
systems that are in place to ward off cancer through apoptosis will work properly to avert disaster, or the cell
will begin to find ways to circumvent programmed cell death.
Normally, when apoptosis is initiated, the molecules that prevent programmed cell death are disabled.
For example, enzymes that inhibit AIF are deactivated, as are those that protect the cell from digestive
enzymes in the event of a leaky lysosome. Cells that become cancerous find a way to keep these enzymes
active. They also find a way to keep on dividing without going through the crisis that ensues when their
telomeres are degraded.
You may have objected earlier when I said that no cell can divide indefinitely (kudos if you caught it!).
Actually, there ARE healthy cells that have no “retirement plan”, and can go on dividing without their
telomeres degrading. We have special cells called “stem cells” which are responsible for regenerating tissues
by replacing worn out cells through their own division, and they can keep on dividing as long as you live. An
example of this would be the adult stem cells you have in the marrow of your “long” bones, like the femur.
These cells have not differentiated into specific blood cell types yet, and when they divide they can produce
red blood cells, platelets or a host of white blood cells. But how is this possible?
Stem cells utilize an enzyme called telomerase which maintains the length of the telomeres on their
chromosomes. When we are first developing as an embryo, this enzyme is active in all cells to enable the
many cell divisions required for rapid growth. However, at a certain stage of development, after the cells have
already differentiated into what they will be in the larger scheme of things, this enzyme is turned off.
Permanently. The only cells who retain the use of telomerase are the stem cells, because again, control in an
organism is paramount.
We simply can’t allow every cell the ability to go on dividing forever. It’s too risky. It’s even too risky to
have cells around that have no level of differentiation at all. Embryonic stem cells can become anything
because there are no genes permanently shut off which would prevent them from producing whatever they
need to make. They also have active telomerase and this, together with their lack of differentiation, makes
them very appealing to researchers seeking therapies for degenerative diseases. What a cancer cell does in its
quest for immortality is to somehow reactivate the genes for the production of telomerase that used to be
needed during embryonic development. This “evolution” of the cancer cell is a very bad idea, and re-opening
forbidden capabilities has disastrous consequences for both itself and the larger organism it was originally
meant to serve.
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The wrong kind of immortality and six steps to societal destruction
I want us to delve a little more into the nightmare we call cancer, just to draw attention to the fact that
it highlights the destructiveness of mutations. The life of a cell in a multicellular organism only makes sense in
terms of its programmed role within a larger “society” of cells. As in a human population, cells have narrow
duties and responsibilities that they must fulfil if the organism is to thrive. Some cells are devoted to being a
part of the squamous epithelial layer lining the lungs, working in close cooperation with the cells who
constitute the capillary beds adjacent to them, so that gases can be exchanged. Linked with our previous
examination of hemoglobin and blood buffering, as well as the dimpled shape of red blood cells to maximize
surface area, the picture starts to emerge that there is a grand orchestration which makes life on this scale
possible. Multiply this macrocosm over and over with all the interconnected and interdependent systems,
along with the necessary microcosm of what has to be occurring at the cellular level in order for it all to
happen in a controlled fashion, and the complexity becomes truly staggering. But this wonder we call life all
comes crashing down when cells forgets why they exist.
Rogue cells cast off the constraints that were set in place to protect against chaos. It is the code that is
meant to go on and on through generations of cells, organisms, and populations, not the individual cells which
carry and execute it. Cancer cells seek the wrong kind of immortality. They cease serving in their appointed
role, as a skin cell, lung cell, liver cell etc. and begin functioning as if their existence is all about their own
propagation. The first and second steps toward destroying the community they once served is completed
when they find a way to ignore signals to voluntarily die, and then find a way to preserve their chromosome
integrity and avoid crisis. They are now ready to find a way to “self-initiate” their own division and start
dividing out of control to form a tumor. Step 3 accomplished. They could continue on to the fifth and sixth
steps to complete their domination, except for one problem.
Large groups of cells cannot survive without the services of other cells. A fourth step is necessary. They
must find a way to deceive the healthy cells who still do the useful work of building blood vessels to do their
bidding. Without vascularization, a tumor is very limited in its size because the cells on the interior will begin
to starve. Once the recruitment of endothelial cells is accomplished, angiogenesis can begin and the tumor can
grow dramatically.
Step five is to break through the boundaries which normally exist between tissues. For example, a
polyp in the large intestine is not really life-threatening unless it has started to invade through the basement
membrane. In order to do this, the cancer cells have to recruit a type of healthy cell that is quite shocking.
There are certain types of immune cells who are experts at worming their way through layers of tissues, and
the cancer cells find a way to hoodwink them into leading the way into areas adjacent to the growing tumor.
Destruction of the organism is imminent. Only one final step in their “evolution” remains.
The cancer cells must find a way to colonize entirely new areas in their quest to serve themselves and
be all important. As they migrate into nearby tissues and take over they may be fortunate enough to find a
large blood vessel. If they can find a way to live apart from the tumor they have been confined to and enter
the vessel, then step six will be initiated. Metastasis. This is the term oncologists use for the stage of cancer
where cells from the tumor have managed to get into the blood stream and migrate to entirely new areas. The
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end of the organism is near, because once the cancer cells lodge somewhere else they will grow new tumors
and repeat the process exponentially. Once self-serving tumors dominate the landscape, the systems that
were designed to serve each other start to break down, and death for all cells, including the cellular free
loader megalomaniac cancer cells comes swiftly.
I asked my graduate classmates and professor how this exemplified Darwinian evolution. Since the
“evolution” of the cancer cell spelled doom for itself, this gave it no selective advantage--even though it was
able to live a little longer than it would have otherwise. The weird response I received was that there are lines
of cancer cells that have achieved immortality outside the body by invading tissue cultures in labs or by being
deliberately sustained by technicians who grow them in petri dishes. Hmm…do we really want to consider this
an improvement?!? No, cancer is rather a perfect example of how mutations are a very bad thing for an
organism. Cancer is not an example of an organism mutating the code to create completely new genes and
improve itself, but rather a commandeering of existing code to use in a way that was never intended.
Unauthorized use of the existing code for a purpose beyond what it was designed for is NOT a good thing for
the organism. Life was programmed to know this. It fights mutations vigilantly, and for good reason.
Functioning within the confines that were originally set is what a cell exists for. In a multicellular organism,
unity is what matters, not independence.
Weld plates, zigzag stitches, and the ECM
I want to take a closer look at how some of this unity is achieved between cells. What enables them to
work together to form tissues anyway? I’ve already made mention of one key component in cellular structure
that makes cooperation between cells possible. The jungle of proteins, glycoproteins and carbohydrates that
extend from the surface of the cell, called the extracellular matrix, serves a tremendous variety of functions. In
addition to the cell surface receptors already discussed, there is a forest of sugar molecules which extend
outward from the surface of the cell called the “glycocalyx”. Cells recognize each other via this complex web of
macromolecules, and it plays an important role in healing and regeneration. When cells are too far apart to
make contact with each other after an injury, the body resorts to filling in the gap with that multipurpose
patch of collagen fibers we call scar tissue. This explains why it’s important to stich wounds tightly together to
minimize scaring, and why you get a big “caterpillar” scar when you don’t (when cells don’t know who belongs
where, they just use generic collagen fibers to fill in the gaps).
There are other structures that play a very important role in connecting cells together to form tissues,
and these are called “structural proteins.” Cells that need strong connections in order to form resilient tissues
have complex proteins embedded in their cell membranes that face each other. These proteins have a large
surface area to make contact with and connect to a plate like itself in the adjacent cell. The plates are
anchored back into the cytoskeleton with reinforcing fibers, creating a very strong connection between the
cells. When many cells are anchored to each other with this type of connection, a very tough tissue results.
These structural proteins remind me of a kind of connection that engineers design for places in
buildings that have to join dissimilar materials and withstand tremendous stresses. They were commonly
known as “weld plates”, “embed plates”, or “drag struts,” and what they consisted of was a thick steel plate
with rebar welded to the back which would be deeply embedded into fresh concrete. The plates could be
welded to each other where a connection between two concrete members had to be joined together, or they
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could be used as a point of attachment for a steel beam via welding and bolting. Engineers had to consider the
pulling forces that would be acting on the desired connection and make the design sturdy enough to
withstand what it might encounter (like long and thick enough rebar extending off the back). God also
designed these structural proteins to enable cells to hold together and endure stress in order to maintain
tissue integrity.
Another kind of connection between cells is not as strong in tension, but better in “shear” (side to side
sliding force). They are called “tight junctions” and to me they resemble the zig zag stitching that someone
using a sewing machine can use to make a sturdy hem in fabric. The protein “stitching” between cells resists
slippage sideways. It also reminds me of the “puddle welding” and “button punching” that connected
individual sheets of metal roof decking down to their supporting joists and horizontally to each other. These
connections aren’t all that strong individually, but there are a lot of them, and in total they can withstand
tremendous shear stress. The tight junctions between the cells also achieve this, but with the added benefit of
creating water tight connections for tissues that need to be impervious to liquid infiltration.
Yet another kind of connection was designed for connecting cells in order to form specialized tissues.
Sometimes cells need a very fast way to share information, and rather than going through the slower process
of being transported by diffusion across the cell membrane, a permanent tunnel is installed between them
that has a rapid opening/closing mechanism reminiscent of the shutter on an old camera. These are called
“gap junctions”, and I alluded to these in the discussion of nerve cells (nerve tissue in the brain often utilizes
these connections).
What stands out to me with all of this variety of cellular connection and communication is that there
was deliberate intent to create a hierarchy of organization that begins at the cellular level but extends upward
in greater and greater levels of complexity until the whole functional organism is created. This required
contemplation of the final outcome and what it would take to accomplish it. Architects and structural
engineers do this when they are attempting to create complex structures, with consideration of the grades of
steel, the size and number of bolts in a connection, the amount of welding needed, the depth of a beam
needed to span a given distance, the diameter and embedment length of rebar into concrete, the compressive
strength of concrete and the mixture of sand, cement and aggregate (gravel) required to achieve it, etc. But all
this pales in comparison to the attention to detail that God exhibited when He created living things. Though
we have focused primarily on cellular structures so far, I’d like to take a moment to look at a few organs and
systems that amaze me.
Storm sewers, homeland security, and a peek at the arsenal
We aren’t aware of all the terrorist plots that never happened because they were thwarted by the FBI,
CIA, NSA and Homeland Security agencies. Sadly, only the ones they didn’t prevent are the ones we
remember. We don’t know all the inner workings of what the agents do to protect us, they just do their job in
the background, utilizing the infrastructure they possess (spy satellites, intelligence agents, internet
monitoring, phone tapping capabilities, etc.). Our immune system operates in much the same way, with a
wide array of infrastructure and weapons at its disposal, and it prevents most illnesses before they even gain a
foothold.
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One feature of the immune system that many are not aware of is a system of drainage tunnels called
lymph vessels that run parallel to our veins. They serve to drain bodily fluids back into the blood stream, acting
a bit like storm sewers. But they also provide a means for our immune cells to take short cuts between various
points in our bodies to quickly deal with threats. Because our blood vessels run in a giant circuit from the heart
to the lungs, back to the heart, out to the arteries, branching into capillaries, back out to veins, and back to the
heart, every square inch of our body is reached by them. But without a way to hop on and off the highway of
blood vessels, immune cells would have to take a very long journey to get where they need to go. Instead,
they take advantage of the one-way drainage valves, and enter the veins at the ideal location to save time.
Another feature of the lymph vessels which plays an important role in the immune system is that they
have “nodes” at the intersections of the vessels. These widened intersections are strategically placed at the
places where our extremities attach to our trunk. They provide an ideal location for the stationing of the
immune cells which are responsible for the production of antibodies to identify intruders (B cells). The cells
who initially identify invaders (T cells) can quickly take the specifications for the antigens (surface features on
the enemies) to the cells who will use the information to create the matching tags. The antibodies are then
mass produced and sent into the bloodstream so that the invader can be identified by other lymphocytes and
destroyed. The antibodies immediately latch onto the intruder’s surface features (antigens) and flag them with
the clear message “destroy me” to the other immune cells.
It’s worth taking a peek at some of the weapons in the arsenal of our immune system, because it’s
some really cool stuff that God invented. We already know about phagocytes who move about and engulf
intruders by phagocytosis, but they are actually of two types, monocytes and neutrophils. The monocytes are
far more numerous and widespread in the body but not as “heavy duty.” They can “eat” about 4 intruders
before dying and becoming a part of the pus we see at the site of an infection. The neutrophils are larger and
have the ability to regenerate their lysosomes. They are active for longer periods and can destroy a greater
range of invaders. Yet another type of cell called a natural killer makes ingenious use of its Golgi apparatus to
destroy intruders. When the killer cell identifies a foreigner, it comes up next to it and turns its Golgi
apparatus to face the doomed cell, then literally shoots vacuoles of digestive enzymes out by exocytosis to
obliterate it! Together, the phagocytes and these killer cells form a first line of defense, and buy time for the
production of antibodies so that mass destruction of the invaders can take place.
Meanwhile, the production of antibodies has begun, and when they arrive and latch on to the antigens
of the invader, something amazing happens. Yet another kind of immune cell (a different type of T cell) senses
the antibody flags on the invaders and produces another protein factor that combines with the antibodies to
form a kind of shoe horn drill rig which wedges the cell wall of the bacteria open. Since this is occurring all
over the cell’s surface, it causes all the cytoplasm to leak out though the numerous perforations that have
been created. Because healthy cells do not have the same cell surface proteins as foreign cells, the antibodies
will not attach to them and there is no risk that the drill rig assemblies will form on them. Once the invasion is
quelled, the level of antibodies drops because the B cells go back into waiting mode, but provision has been
made in case that same invader ever rears its head again. Special “memory” cells are programmed to retain
the information about the invader’s antigens, and they do not require as much time to recognize the threat.
They immediately trigger the B and T cells to go into action. The response is swift and automatic destruction
next time. We call this memory acquired immunity.
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The complexity of the immune system is actually far greater than this brief summary, and I encourage
you to dig in to the finer details yourself. The huge number of specialized cells with their complimentary
functions working in concert with the lymphatic system is superb. I stand in awe of the mind that provided so
well for our protection.
Listen to what hearing is saying, and look at what vision is revealing…
Newton once said of life in his famous work Principia, “Blind metaphysical necessity, which is certainly the
same always and everywhere, could produce no variety of things. All that diversity of natural things which we find suited
to different times and places could arise from nothing but the ideas and will of a Being, necessarily existing.” When he
studied the systems of living things more closely he came to this conclusion: “How came the bodies of animals to be
contrived with so much art, and for what ends were their several parts? Was the eye contrived without skill in Opticks,
and the ear without knowledge of sounds?...and these things being rightly dispatch’d, does it not appear from
phænomena that there is a Being incorporeal, living, intelligent...?” His ultimate conclusion about all this was that “He
who thinks half-heartedly will not believe in God; but he who really thinks has to believe in God.” Whoa, and to think
that Atheists have placed his image on a propaganda poster as an example of someone in their camp!? He examined the
way the eye and ear worked and came to this logical conclusion, and I can’t help but think that if he had known all that
we do today about their structure and function that he would have proclaimed God’s genius even more forcefully. Here
are some of the more fine-grained details he would have certainly attributed to their architect…
The retina of the eye contains highly specialized cells that are capable of translating light into nervous impulses.
We have known about rods and cones for a long time, and some of the earliest compound light microscope sketches
display their external complexity. What’s more amazing is that these cells are a part of a much larger scheme that takes
advantage of not only macroscopic strategies but also the very nature of matter at the most fundamental level. Without
utilizing almost unimaginable biochemical complexities combined with large scale architecture we would not be able to
see with the exquisite capabilities we enjoy, if at all.
First, the rod cells, which are extremely sensitive (some have
proposed that they are triggered by the presence of just a single
photon) but do not convey colors, make up the vast majority of the
sensory cells on our retina. They are present everywhere except on
the fovea, the place where light is optimally focused. The cone cells,
which work best in more intense lighting, are scattered in small
numbers on the retina except on the fovea where they are the only
sensory cells present. They require six photons to stimulate, but
have higher resolution (produce a sharper image) and convey color
to our brains. They possess three different pigments which have
peak sensitivities to blue, green or red light. Their range of responses to
different wavelengths extends beyond their optimal abilities, so that the
orange, yellow, indigo and violet light can be detected, and these ranges of
sensitivities overlap. The amazing thing is that the three different pigments
can actually be triggered by any color, but the intensity of the light has to
be greater if it is outside the peak range. Because of this, each cone doesn’t
exactly send a signal that says “red” or “blue”, but rather groups of them
send signals, and the brain has to perform an algorithm which interprets
the signals and translate the messages into the colors we sense based on
the relative signal strength from different cones! What is even more
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dumbfounding though is the series of biochemical changes that occur
when light strikes the retina, which ultimately rely on the quantum
properties of just two atoms and the bond between them.
The structure that actually changes in response to being struck by
a photon is called Rhodopsin. It is made up of a protein unit called opsin,
and a light sensitive molecule called retinal. The retinal has a “double
bond” in the center, which gives rigidity to the large molecule. The retinal
is unable to “twist” because there are four electrons being shared
between two atoms, and it is difficult to rotate due to a quantum effect
called “pi” bonding. The first pair of electrons shared creates a “sigma”
bond that is a direct overlap of orbitals (hybridized s𝑝2 orbitals), and if
alone, the sigma bond would permit twisting around a central axis
between two carbon atoms. But the second pair that is shared creates an
overlapping of orbitals (unhybridized p orbitals) in a side-to-side fashion
both above and below the axis of rotation, lending stiffness to the bond.
When sufficient energy from protons is gained by retinal, the pi bond is
broken and the molecule rotates, undergoing a change in shape (a
conformational change) from essentially straight to bent. This bent form is
chemically active, and the retinal then triggers a cascade of events that is
quite remarkable and complicated. In fact, for those who are acquainted
with the process, you already know I’ve left out a lot of detail!  The opsin
which retinal is embedded in responds to the change and in turn
triggers a change in a large protein structure below the membrane
called transducin. A series of chemical messengers are then
activated, amplification of the response occurs, and an impulse is
generated in an inverse fashion to the way our normal nerve cells
operate. It’s a long story, but the ion potential is basically upside
down, with sodium pumps working to build up a membrane
potential, but with a modified system that uses calcium ions and a
reduced response to stimuli rather than in increased one.
Essentially, this provides for a “noiseless” system that can be
extremely sensitive. Unlike a TV set that shows “snow” when not
tuned into a channel because of the microwave background
radiation in the universe, our eyes see nothing when there is no
light. To accomplish this, the setup necessitates a tremendous
number of these Rhodopsin units, because it takes 45 seconds
for the double bond to be restored by an enzyme-mediated
reaction, and we would quickly become blinded if there weren’t
enough of these available to sustain the capability. To provide for
this need, rods and cones have stacks of membrane structures
similar to those in chloroplasts (recall thylakoids) with a
tremendous number of rhodopsin/transducin subsystems,
enabling continuous vision. Of course, the system can be
overwhelmed in the presence of a very bright light, but
eventually vision returns as the retinal is reset.
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Rhodopsin is the combination of opsin, the protein
coils oriented vertically through the cell membrane,
and retinal, the little black image between the
second and third vertical coils of the opsin
superstructure. The conformational change triggers
alterations in the associated proteins shown below
the membrane known as transducin (where the
next step of signal transduction occurs)
The point is easy to lose in the midst of all this phenomenal complexity. We have been equipped with the
structures which enable us to see high resolution color images in the daytime when the light is more intense, and highly
sensitive night vision for when there is little light and colors aren’t as important. The sensitivity and lack of noise in the
system is due to special modifications to the way the channel proteins and sodium pumps operate (as opposed to
normal nerve cells), which all had to be programmed into the DNA. The code required for all this (and I haven’t even
scratched the surface of just how complicated it all is) is stupefying. Moreover, all this complexity would be for nothing if
it weren’t for the way it takes advantage of quantum mechanics. The system is predicated on the ability of photons to
break a double bond in retinal and clearly implies foreknowledge of the fundamental nature of chemical bonds.
Recently, another even more bizarre quantum effect has been observed in the vision of some migrating birds.
They appear to be able to literally “see” magnetic fields due to a strange phenomenon called quantum entanglement.
These birds have a light sensitive pigment called cryptochrome which, when struck by light, causes the formation of two
“radicals” (chemically active molecules), each possessing one of two electrons that had been “paired” together in the
cryptochrome molecule before being stripped from it. These electrons, though now a part of two separate molecules,
are inextricably linked to each other. If one is spinning “down”, the other is automatically spinning “up”, and the
differences in the spin directions makes one radical chemically active for a slightly longer time than the other. Somehow,
the biochemical and structural architecture of the bird’s eyes is set up to take advantage of this effect in order to
visualize magnetic fields. Specifically, they can see the angle of the field lines relative to the surface of the earth. Field
lines closer to the poles are oriented more vertically, whereas those closer to the equator are more parallel to the
surface. The birds utilize this to determine where they are with respect to their journey! Again, programming code in
order to take advantage of this quantum phenomenon is an extraordinary testament to God’s genius as a designer.
There is no way that a system which depends on “spooky action at a distance” (Einstein’s nickname for quantum
entanglement) for its very ability to function could have accidentally developed by random mutation. It simply had to be
deliberate planning.
Let’s go back to our human sense of vision and look at another system that works together with it in a crucial
way. It might not be immediately obvious, but the design and function of our inner ear is vital to our sense of vision. We
need to keep our head steady so that we can maintain the stable focus on an image, allowing for the kind of
concentration we are capable of and accustomed to. Without some amazing structures called semi-circular canals, we
would be unable to keep our balance and become so disoriented that seeing would become a chaotic mess, akin to
when you’re watching video footage where the camera is constantly moving. The layout of the skull provides for the
placement of three tiny membranous fluid filled loops in the x, y, and z planes of three-dimensional space. The
configuration is so complex that they have been called “labyrinths” (both osseous and membranous). The loops function
as little accelerometers, detecting changes in motion in all three planes of three-dimensional space. When we spin our
head, the inertia of the fluid inside keeps it stationary initially, but since the canal has moved, along with the sensory
hairs attached inside of it, the hairs are forced to lay down for a moment. The nerve endings at their base transmit a
signal to the brain that an acceleration has occurred one way or the other in that particular plane of motion. Though it’s
possible to trick the system by maintaining a constant spinning motion, it works remarkably well, considering that the
brain is able to keep track of “which end is up” when we tilt our heads or do complex gymnastics. But this is only reliable
when combined with sight. Without visual verification we can become disoriented, because eventually the speed of the
fluid will catch up if the motion continues, at which point the hairs stand erect giving the false indication that the motion
has stopped. But we DO have visual verification, and that’s the point of the coordination of the systems, to be a sort of
check and “balance” against the other. We rely on both systems working in concert. When the vestibular system (that’s
what this system of semi-circular canals is called) isn’t working properly we can become violently ill and desperately
disoriented.
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A student of mine described an episode that his sister had when her sensory hairs were stuck in the down
position (vomiting, the inability to walk, etc.), and the treatment it took to remedy. She had to lie on her back with her
head hanging over the edge of the bed while shaking it
a certain way for four hours in order to get them to
reset to the upright position. Then, everything was
back to normal. It’s a great example of how
sophisticated our bodies are, and how EVERYTHING
has to work right in order for us to function properly.
Just one glitch and we become incapacitated. The
chance of such a high performance biological system
called a human being to be anything other than
designed is zero. ALL the structures have to be just
right, with phenomenal levels of fine tuning, able to
work together smoothly to create the intended
outcome (a clear image and sense of balance).
As in a car, unplug just one sparkplug wire and
the car won’t work right because all the systems
depend on each other. The engineers planned for the
interconnectedness of the systems in an automobile to
produce the final outcome. It’s no accident that the
chemical reaction of combustion is harnessed mechanically, and some of this mechanical energy is converted back into
electrical energy which in turn serves to ignite more chemical reactions. It’s deliberate. They understood combustion,
how to utilize mechanical advantage within compound machines, how to generate electrical current by rotating a
permanent magnet through a coil of wire, how to step up the voltage by using a primary and secondary coil, the proper
stoichiometric ratios of fuel and air, and when to make the spark within the cycles of intake and exhaust strokes. This
foreknowledge of chemistry and physics enabled them to successfully design a functional car, and the fact that it all
works harmoniously is evidence of the engineers’ involvement! If this level of interconnected complexity is proof of an
engineers’ handiwork for a car, how much more for life? God obviously understood the principles of inertia,
acceleration, chemical architecture and bonding, optics (we haven’t even talked about the refractive index, focal length
and requisite placement of the cornea and lens!), electrical conductivity, the electromagnetic spectrum (different light
frequencies/wavelengths) and the amazing mathematical algorithms required to interpret all the data. The only way our
vision and inner ear, or the subsystems in a car can work together to produce a successful outcome is because of the
prior knowledge, planning, and implementation of all these principles by an engineer! This was Newton’s point. So,
point well made. Let’s go back to the inner ear for a second helping and dessert, because there’s even more complexity
and ingenuity to be seen there!
The other fluid-filled structure located adjacent to the vestibular system is called the cochlea. It is responsible
for hearing rather than balance, and is no less remarkable than the semi-circular canals--perhaps even more so. This is
especially true when the design and functions of the outer and middle ear are taken into consideration. The sound
waves that strike our eardrum must be converted into electrical impulses somehow, and the cochlea is where this final
translation takes place. Inside the spiraling fluid-filled structure is a partition of actually two fluid-filled chambers
separated by the basilar membrane. The membrane has a varying degree of tightness, starting with very tight at the
beginning and becoming less taut as it progresses toward the end. When the fluid is pushed by the bones of the middle
ear via the oval window of the cochlea, the fluid vibrates and the frequency of the vibrations sets up sympathetic
vibrations in the membrane at locations which correspond to the wavelengths (this includes all the overtones contained
within the vibrations). The force of the vibration is related to the amplitude (how loud) the sound is. On the opposite
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side of the membrane, these vibrations create pressure in the fluid there that is detected by sensory hairs which register
the force of the vibrations and the frequencies they correspond to. This is possible because of the fact that along the
length of the tube, other hairs which correlate to the overtones are also being stimulated, and the brain is able to
recognize the pattern. To make things more complicated, it’s not just one “note” that is setting up vibrations in the
cochlea, but a multitude. What’s more incredible is that the physics of wave dynamics known as constructive and
destructive interference are also at play, with either “dampening” or amplification of sound waves taking place.
Impulses from all these hairs is sent to our brain via the auditory nerve, and it somehow (through an incomprehensibly
complicated algorithm) is able to recognize all these factors and take them into account while processing the massive
amount of data. It does this in a way that particular groups of vibrations are identified as belonging together, being such
things as an engine running, a person singing, an electric guitar, a bird chirping etc. Not only can it decipher all the inputs
to recognize which ones go together to mean something, but it can process them all from the cacophony inside the
cochlea simultaneously. Our best computer algorithms can’t even come close to this ability. What’s more important is
that the foreknowledge of fluid dynamics and the physics of wave behavior were all programmed into the DNA in such a
way as to build structures that utilize these so that we could interface with sound and make sense of it. Without an
understanding of the physics of sound on the part of the designer, we would not be able to detect or interpret sound in
any meaningful way at all. But that’s not the end of the story.
Remember how I said that the outer and inner ear really make this system remarkable? It would be fair to say
that they shout out the evidence of the intellect of their designer. To begin, the force that air exerts on the ear drum is
not nearly strong enough to overcome the inertia of the fluid in the cochlea. It simply wouldn’t budge without a serious
force multiplier, and that’s where the middle ear comes into play.
It’s necessary to increase the pressure on the oval window to 20
times the pressure exerted on the ear drum, and the way that’s
accomplished is an engineering marvel. First, the series of three
bones that we learned about in biology class (the Malleus, Incus
and Stapes in that order) all work to provide not just a mechanical
connection from the eardrum to the oval window on the cochlea
but also leverage. Hinged together and supported/suspended in
the middle ear by ligaments, they transmit and multiply the force
of the air striking the eardrum. But this alone would not provide
enough of an improvement, so the surface area of the oval
window was made to be 1⁄16 the size of the eardrum. Since
pressure is equal to force divided by area, the greater force
distributed over a smaller area creates a much higher pressure on
the fluid in the cochlea. When you combine these engineering
solutions with the shape of the outer ear which funnels sound into
the ear canal, the whole system can be seen for the masterpiece that it is. Remember, the DNA had to be programmed
to create a space (rightly called the labyrinth) in the skull for all this equipment, code for the all the structures and
sensory cells, and give the brain extraordinary calculating abilities.
There is no way that an unintelligent and undirected process could take advantage of the fundamental physics
involved with forces, pressure, fluid mechanics, chemical bonding, quantum mechanics and so much more to create
these ingeniously collaborating auditory and visual systems. The architecture which grants us the ability to perform such
demanding tasks as driving, to appreciate the sights and sounds of a good movie, symphony or fireworks display, or
most importantly, to do something like recognize the distressed cry of a child and be able to run to their aid while
navigating through a crowd, is all a gift lavished on us by God. We tend to utilize all these and many other marvelous
abilities without giving a second thought to their wonder. Though we do not always appreciate or, sadly in the case of
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many, even believe in the existence of the Genius behind their origin, still He permits us to go on using these capabilities
in hopes that we will…
So why DO your fingers get wrinkled in the bathtub?
This might seem out of the blue, but I want to mention the phenomenon of how and why our fingers
get wrinkly when they are submerged for prolonged periods of time. It was widely believed for a long time
that this was simply a natural response to the “tonicity” of the environment relative to our cells. In other
words, if the concentration of solutes inside the skin cells was greater than outside, water would diffuse into
them and make them swell. While there is some truth to taking in extra water in a hypotonic environment
(ever notice how often you have to use the bathroom when swimming in your pool for a long time?), that’s
not the reason your fingertips get wrinkly. As it turns out, it’s actually a nervous response. I don’t know who
studied the effect with severed hands, but they found that the wrinkles didn’t happen unless there was a
connection to the brain! There is some kind of feedback loop that enables your brain to trigger the formation
of prune-like fingerprints in response to being continuously wet, but why is this mechanism in place to begin
with?
Here’s the other thing they found. The prune-like fingerprints enable you to grip objects better when
they are wet and slippery than the ordinary “dry” fingerprints. In other words, without the feedback
mechanism in place, we wouldn’t be able to continue grasping wet things if we were going to be in the water
for a long time. If you just get wet temporarily and then dry off, your brain is programmed not to respond with
this course of action. Only if you need to be able to keep functioning in a wet environment do the wrinkles
form. THAT is planning, and certainly worth an “honorable mention”! 
Life is more remarkable than going to the moon
When people wanted to go to the moon, the Saturn V rocket had to be designed. Without going into all
the details (I don’t know all of them anyway!), the aerospace engineers had to have a “big picture” in mind
that would guide their planning and execution, but they also had to give great attention to detail in all the
subsystems that went together to make the vehicle and mission successful. Everything had to work in concert
with all the other parts, fitting together and servicing the needs of each other. For example, the payload of
astronauts, command module and lunar lander had to be husbanded across the vast distance between here
and the moon by the service module. Inside the service module were fuel cells that would combine oxygen
and hydrogen to produce electricity and water for cooling and drinking. The cryogenic oxygen tanks had to be
designed with magnetic stirrers, and the wiring to control these stirrers remotely from the command module
had to be routed to an interface, and there had to be a switch and gauge in the capsule that the crew could
utilize. This is just one tiny subsystem among thousands that had to be integrated into the overall design in
order to get the men to the moon and back.
I bring up the oxygen tanks because they were what malfunctioned on the Apollo 13 mission with
almost fatal consequences. The fact that one tiny part did not operate properly causing the entire mission to
be “scrubbed” is similar to the way we develop a disease when some tiny part of one subsystem malfunctions.
But the more meaningful point in this example is not just what can go wrong when even a tiny part fails, it’s
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the monumental task of designing all the subsystems such that they can work successfully! A virtual army of
engineers had to work for years to develop everything from the massive engines and giant fuel tanks down to
the cabin lights that enabled the crew to see what they were doing. The real accomplishment with the Apollo
program was that they were able to design and integrate myriads of parts, all with their different functions,
into a successful vehicle that achieved the overall purpose. It was all designed with one ultimate purpose in
mind, and when it all worked, something previously thought impossible became history.
There are some striking similarities between such a complex system as the Saturn V rocket and our
bodies. Even though the act of “living” is a far greater achievement than going to the moon from an
engineering standpoint, a hierarchy of organization exists in both. It would not be possible for us to function
without the coordination and cooperation between some extremely complex systems. We’re all familiar with
the skeletal, muscular, cardiovascular, nervous, endocrine, excretory, integumentary and digestive systems,
but we might not appreciate the extreme levels of organization and all the minute details that make them
possible. The systems consist of organs with unique functions that are very specific to the larger role that they
are supposed to play within the system and organism as a whole. The organs consist of multiple types of
tissues working closely with each other, giving rise to the function of the organ. As we have already examined,
tissues are created by the close cooperation of specific types of cells connected together and working in
concert. To appreciate the magnitude of what this all means, it’s helpful to think backwards with the overall
“mission” in mind, just as the Apollo engineers had to.
To make a human, you have to design systems that can exchange gases, digest food and transport it,
oxygen and dissolved ions throughout the body, rid the body of wastes, sense and respond to external stimuli,
perform the homeostasis of osmotic regulation (water balance) while maintaining a narrow range of internal
temperature, that can move around to find food and escape danger, etc. Most importantly, you have to design
a system for central control of all these other systems, so that a person can THINK and MAKE DECISIONS. To
accomplish all of this, organs and the tissues and cell types that make them work have to be planned in
advance and designed accordingly. Moreover, the mechanism for growing all this architecture from a single
fertilized cell has to be devised. Genes have to be turned on and off so that stratified squamous, simple
cuboidal, ciliated columnar, and simple squamous epithelial tissues can be made for different uses, not to
mention dense and irregular connective tissue, smooth, skeletal and cardiac muscle tissue, osseous tissue,
areolar tissue, nervous tissue, etc. You have to know what you are trying to build so that every minute detail
can be attended to in order to get it done. Not only this, specialized applications of these tissues must be
contemplated in order to meet the needs of different species. It boggles the mind, especially when you get
into the really fine details. I highly encourage you to get a hold of an anatomy and physiology book and read
up on all the hierarchy in your body. It is astonishing and as far from accidental as one could imagine. The
scope of this writing does not permit me to delve into very many of the details, but I do want to mention a few
that pertain to one of our most incredible organs, the heart.
Blood pressure cuffs, hydraulic dampeners and waste water treatment plants
To get the blood circulating around the vast network of blood vessels in our body we need a powerful
heart. A lot of consideration went into the creation of such a powerful and durable pump. There had to be a
special kind of interwoven muscle designed exclusively for this organ, as well as one-way valves, complete
with chords that automatically open or close them as the various chambers contract and relax, and a complex
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network of blood vessels and “pace maker” nerve cells embedded in the exterior walls to feed the muscle and
trigger contractions. We could spend pages discussing the way that the heart collaborates with the lungs, the
architecture of the lungs and many other marvelous design features in the cardiovascular system, but I want
to take a look at just a few consequences that had to be taken into account when the heart was planned, and
one other system which was designed to take advantage of such a powerful pump.
The walls of our arteries have to be thick to resist the blood pressure that is generated from the
powerful contraction of the left ventricle, and the diameter of the aorta had to be large enough to permit a
sufficient volume of blood to move down our trunk. So far so good, but having our head so close to our heart
poses a problem. The blood vessels that feed into our head come right off the top of the aorta. The diameter
of the vessels branching off the carotid arteries has to reduce rather quickly as they begin branching out and
servicing the brain. The smaller diameter vessels would not be able to withstand the constant pounding
without bursting unless a solution was found. The answer was the installation of strategically placed coiled
blood vessels in our heads that act as hydraulic dampeners. When the heart pumps, they compress like shock
absorbers so that we will not be suffering aneurisms and death. That’s some wonderful engineering.
A giraffe’s anatomy creates a very different engineering challenge. Because its head is much further
from its heart, their heart has to be far more powerful than ours to provide adequate blood flow way up to
their brains. But when they want to take a drink, the level of their head drops below their heart, and this poses
a problem. The heart continues to pump just as forcefully as ever, but without gravity to fight, the giraffe
would suffer aneurisms and death. They need a way to reduce the flow of blood to their head when stooping
to drink, and the solution was the addition of tissue under the skin called sclera that acts like a blood pressure
cuff. They also have tight skin on their long legs to prevent blood from pooling below their trunk.
The other system that takes advantage of the heart’s power is the excretory system. The high blood
pressure in the descending aorta is utilized to enable the kidneys to filter blood. Kidney function is paramount,
and without continuous cleaning we are quickly overcome by accumulated toxins, much like a community that
has to recycle its own waste water without treatment plants. Stationing the kidneys on the descending aorta
provides for efficient filtering because high blood pressure forces liquid out of the blood stream in our
nephrons (in the Bowman’s capsules). However, there had to be a way to recover the water, sugar and
electrolytes that we need in the blood. I won’t go into all the details, but only summarize (here’s one you
should dig into on your own and not take my word for it!). The medulla of your kidneys is made salty by
selective permeability of different portions of your collecting tubules, so that the law of diffusion can be
utilized to cause water to come back into the blood stream through a portion of it called the “loop of Henle”.
In species where the maximum amount of water must be recovered, the loop of Henle is especially long, but
shorter in those who have ample water in their environment. Blood pressure forces the filtrate out of the
blood stream, and osmotic pressure recovers the portion we want to keep, thanks to a changing permeability
of the collecting tubules. Trust me, if you will research the structure and function of the nephrons in the
kidneys, it will astonish you.
As you look at the diagrams and learn about the shape of the Bowman’s capsule, routing of the distal
and proximal ends of the collecting tubule, the positioning of the capillaries and much more, ask yourself the
question: are all these structural features and their highly specific functions a result of natural selection acting
on successive mutations, or are they some ingenious feats of engineering? You decide.
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Speaking of engineering…
Some of our greatest accomplishments tend to be copies of the structures and systems found in living
things. This is taken for granted, but what does not occur to most people is that it takes an extreme effort by
our best engineers to accomplish results that are inferior by comparison. For instance, the robotic arms used
on assembly lines, which are based on our own limbs, required many generations of development by an army
of really intelligent designers to make anything useful. Mechanical engineers, computer programmers,
materials experts, etc. all had to put their creative energies together to make a functional robotic arm. Even
though they can articulate, weld, paint, etc.; they are typically very dangerous to be around because they
wield large forces and have a lot of mass. To make a robotic arm that is gentle in its motions and safe to be
around, engineers studied the musculature of an elephant’s trunk and imitated it with interconnected,
lightweight accordion tubes of compressed air. By making a triangular configuration of three long tubes
connected around a central flexible spine, movement in any direction was made possible by differential
pressures in the tubes.
Outfitting the end of the tubes with a grasping “hand” which was gentle yet strong enough to pick up
fragile objects without dropping them required engineers to study the structure and function of a fish’s tail,
which actually moves toward a pressure which is applied to it. Using two articulating “fins” made of a soft but
firm plastic which could open or close toward each other on command, the hand would wrap around the
object and grasp it firmly without damaging it. This simulated the gentle dexterity of the tip of an elephant’s
trunk without risk to people working nearby.
But is this robotic trunk is an improvement over the dangerous robotic arms that work on an
automobile assembly line? No, it’s just different, because it can’t do any heavy lifting or other tasks that
require rapid movements and endure “heavy duty” applications. Still, both borrow from the architecture of
living things, and yet the living things are far superior. An elephant’s trunk can take on either kind of work,
whether it be lifting a 400 pound log and tossing it aside, or picking up individual peanuts and gently lifting
them into their mouth and then caressing their baby afterwards.
The engineering of the imitations seems impressive, but their complexity is rather dull by comparison.
An elephant’s trunk has both longitudinal and transverse muscles which encircle the lengthwise muscles, and
it is all surrounded by a tough but flexible sclera and hide which make it extremely durable. Not only can they
switch back and forth between extremes in force and dexterity on command from the central nervous system,
but the appendage can also heal damage to itself. As a bonus, the trunk also has air lines running through its
length to provide for breathing and drinking, making the efficiency of the structure even greater! We venture
to borrow from just some of these structures with specific tasks in mind and can’t even come close to their
elegant efficiency. Ironically, most who observe the intelligent efforts of teams of top engineers to copy the
originals would be amazed at their accomplishments without recognizing that the far superior living models
were intentionally designed as well. If our attempts to imitate them still fall short of the capabilities and
exquisite features of the originals, why would we conclude that the real ones came about accidentally?
Wouldn’t it be more reasonable to just admit that we are inferior designers, even though we try real hard? 
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While mechanical engineers have worked diligently to design copies of macroscopic structures in
nature, biochemical engineers have been hard at work to do the same at the cellular level. However, the
systems are so complex that there is no way to reproduce them, and all we can do is modify them to our
advantage. We do this with bacterial transformation (splicing genes into them that are not original) to produce
vital substances like insulin to treat diabetes. Commercial products for recreation are also manufactured by
enslaving bacteria to do our dirty work, such as proteins that can be sprayed on snow to maintain ski slopes.
Even whimsical agendas have taken advantage of gene-splicing technology, such as creating fluorescent
aquarium fish by adding a glow-in-the-dark gene from jellyfish. Adding genes to crops that give them a
chemical defense against pests is a more practical application of DNA technology, but other genetically
modified organisms are also being utilized to manufacture such things as spider silk for bullet proof vests (this
is grown in the udders of genetically engineered goats of all things!).
There are even genetic engineers who are working on a way to use ordinary plants to detect bombs. By
splicing a gene into a bacteria that infects the plant, the gene ends up in the plant’s DNA, and it codes for a cell
surface receptor that is shaped like the explosive’s molecule. When a bomb is brought past the plant, the
shape-activated receptors then trigger a series of biochemical messengers to cause the plant to lose its
chlorophyll. It’s amazing that a terrorist could be caught as they walk by the flower beds in the airport
(everything turning white as they pass by would certainly make them stand out!), but what’s even more
amazing is that we have developed the technologies to take advantage of the cellular machinery without
acknowledging the fact that even relatively simple living things like bacteria possess structures and processes
that are far too complex for us to build from scratch. We can only “tweak” what is already established to
accomplish what we want, because the existing engineering is way beyond our capabilities. If our “best and
brightest” engineers can only hijack the pre-existing infrastructure of a cell, why would we attribute all of it to
anything other than exquisite engineering that we are pirating? The level of sophistication is just too much to
be accidental.
Yet another example of our best and brightest engineers borrowing from the design features in an
organism is that of hagfish slime. A hagfish has a defense mechanism to protect it from being eaten by sharks
which defies any notion of accidental serendipity. Most consider them direct descendants of the jawless fish
that would be predecessors of all other fish, amphibians, reptiles, birds and mammals on Darwin’s “tree of
life,” because they have an extremely simple body plan. Without jaws or eyes, they play the role of garbage
men on the sea floor, eating the remains of dead animals. They attach to the carcass and then tie themselves
in a knot that slides toward the mouth, which effectively tears off a piece to ingest. Without some special
provision for defending themselves, they would quickly be hunted to extinction because they are very
vulnerable while eating in this manner.
The answer was to equip their skin with a chemical counter attack which deters anything from biting
them lest they suffocate to death on a slime which engulfs the attacker’s mouth and gills. The equipment for
the slime defense mechanism comes in the form of thousands of packets of concentrated proteins which
create super hydrophilic mucous combined with a network of super tough filaments to keep it together. When
bitten, the packets eject their contents into the surrounding area (the attacker’s mouth) and just a tiny
amount of the powder combines with a large amount of readily available water to form the goo, with another
protein polymer forming an immediate network of ultra-tough stringy strands throughout the suffocating
mass. All sorts of practical applications await the replication of this wonder material on a large scale. Since the
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hagfish won’t reproduce in captivity, we have had to settle for imitating the proteins in this concoction, but
the fact that the hagfish have the system in place at all is what impresses me.
Since their vital role in the marine ecosystem needed to be preserved, the equipping of these simple
fish with an elaborate defense was crucial. The existence of the alternating subcutaneous packets of
complicated slime-forming powder with packets of filament constructing powder shouts out the message of
intentional planning, but we tend to be so preoccupied with trying to commercialize it that we don’t see the
significance. If the ratio of materials was not correct, the final outcome of tough slime would not be achieved.
Creating the network of fibers dispersed through a gelatinous mass required a knowledge of the desired
outcome in order to program the hagfish DNA to build both types of complicated molecules PLUS the delivery
system of exploding packets just under the skin.
There is simply no way that this could have evolved in a step wise fashion over millions of years. The
blind and preoccupied hagfish would have become extinct long ago without the finished and fully-functional
system installed right where it needed to be. ALL the components had to be planned in advance to protect
these creatures. We have not always known about these essential little guys who dwell in the dark ocean
depths, but the One who planned their ecosystem certainly did, and He didn’t miss a single detail required to
make it work well. Perhaps biochemical engineers can apply some of His “know how” to make life saving
bandages for burn victims or some other unforeseen application, but I doubt they will credit the ultimate
source of the technology.  I hope I’m wrong, because if there was ever a case of “intellectual property”, this
is it. Perhaps someone really will “pay royalties” without committing copyright infringement. 
Duck feathers, cat hair and those weird pictures
I was taking a walk with my wife and children in our neighborhood one day and noticed a duck feather
on the sidewalk. When I picked it up and looked more closely I saw that it was a short body feather that had
only the top half “zipped” up with the bottom half being like down (all fluffy). It was mostly white, but had
some horizontal brown stripes toward the end. In that instant, something struck me.
As I looked up at the female ducks in the water nearby and saw their camouflaged coloration, it
became clear that their overall appearance, which looked nothing like the feather I was holding, was
accomplished by the conglomeration of hundreds and hundreds of these individual feathers. The code for
coloring one feather had to work together with all the other feathers, each with their slight pattern variations
to achieve something far different and greater. You would have to know what the finished camouflage needs
to look like in order to program all the individual pieces such that it gives the final outcome. When I called my
family over to look at the feather and contemplate the whole amazing thing with me, one of my children
pointed out that our cat’s fur is the same way. Each individual hair has little stripes on it, but her fur coat has
definite patterns that are created by the combination of thousands of these little things. She wouldn’t be able
to hunt nearly as well without her camouflage, or keep warm without the same fur for that matter. As with
many anatomical features a living thing possesses, many things are accomplished with one structure.
Going back to the duck feather, an even greater number of capabilities are provided for by these
individual structures. The one I saw was a short “contour” feather, with the bottom half providing insulation
due to the fluffiness, and the upper half laying tightly against other feathers to create a smooth waterresistant contour. This is accomplished by the zipping together of the individual barbs by little “barbule” hooks
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which are installed on both sides of each barb to act like Velcro. When the duck spreads oil from its preening
gland over the surface of these zipped and overlapping feathers it creates the ability to shed water, which is
essential to its survival in an aquatic environment. Its flight feathers have a different purpose. They were given
a slightly curved strong central shaft that penetrates much further into the skin (no downy fluff needed so far
from the body), and zipped up barbs which are shorter on the “leading edge” side of the wing than on the
“trailing edge” to create an airfoil shape. They are placed in an overlapping arrangement beginning with the
part of the wing closest to the body, and when the all the feathers work together the duck can successfully
generate lift.
All of this and a million other design considerations had to be made beforehand in order to program
the DNA to produce the features which make a functional creature we call a duck. Not only this, the fact that
the feathers would take a beating and cease to perform properly was foreseen, so the DNA was programmed
to cause “molting” periodically to replace them! The point is, there is no way to create the entire organism
from tiny parts without envisioning the finished product. Only then can you know what each part must look
like, what structures and functions it must have in order to pull it all off. There’s just no way to make anything
meaningful or useful from a jumbled assemblage of parts that couldn’t possibly know what they are or what
they are doing together.
It’s like one of those crazy pictures you see where from a distance it makes a person’s face, but up
close it’s composed of a thousand little separate pictures which had the right colors and were positioned in
the right location within the grand scheme of the larger image that was being created. There have been artists
who can paint giant murals of some scene by just using polka dots of various colors. When you are up close
you only see tiny dots of color, but when you back up you see a pond with lily pads, a dragon fly, a frog, etc.
The artist had to know what he wanted all the dots to end up forming. God knew, whether it was a duck or my
cat or me, what He wanted all the little dots to create. 
The miracle of flight
Since the subject of ducks came up, I want to tell you about a book I read some years ago. It’s entitled
The Miracle of Flight, and I highly recommend it. I’m sure the author would like you to buy his book, so I hope
he doesn’t mind me encouraging you to get a copy. It’s written from a neo-Darwinian perspective but I don’t
mind because the wealth of information about bird and insect flight is truly amazing. I do find the title amusing
in light of the fact that miracles imply God’s involvement, but it’s not the first time I’ve heard that kind of
exclamation from a scientist when confronted with stupendous designs that seem so impossible to have
happened by undirected processes. In fact, if you listen closely to television programs about nature, you’ll
often hear the words miracle and design used. Of course, the speakers/authors mean that natural selection
was responsible for the miraculous designs, but I can’t help but note the “Freudian slip” that keeps occurring.

Anyway, I want to mention some of the stupefying things I remember from the book. The first was the
existence of a structure on the leading edge of the wings of some birds of prey. The ones who have a relatively
small wing surface area cannot maintain enough lift during the slow speeds just before landing. Without some
kind of extra feature to compensate, they wouldn’t be able to land without falling out of the sky. To avoid this
“stall”, they have the ability to open up a little channel for air at the top of their wings’ leading edges. As they
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slow down to land, this provides just enough extra lift to prevent the stall, then the opening closes back up. If
you have ever flown on a large jet and sat at the window next to the wing, you have seen structures like this in
operation, but the birds had it first. Both were ingenious aeronautical solutions.
Another engineering solution for birds was how to position all the flight muscles in a way that would
keep the weight of the skeleton to a minimum while still providing enough structural strength to resist the
forces the flight muscles generate. We all know that birds have special weight-saving features in their skeletal
systems to conserve weight, such as hollow bones and fused vertebrae. Cutting down on the number of joints
saves mass because the joints have to be thicker, but the addition of a large sternum called the “keel” adds
weight. The keel is as thin as possible by having an “I beam” cross section, but it’s still something that birds
need to make the best use of so as not to waste this weight expenditure. The flight muscles for both the
upstroke and down stroke are nestled into either side of the keel, but since muscles only pull, how could birds
accomplish the upstroke? The solution was to route tendons up through a gap in their shoulder blades, and
around the back to then attach to the top side of the wing. This creates a pulley arrangement where the
direction of the force is altered to up instead of down!
The other mind-boggling subject had to do with insect flight. The veins that feed the wing tissue act as
the structural members to provide rigidity, with a thin membrane stretched between. This is ingenious, but
they don’t have airfoil-shaped wings the way a bird does, and when you do the math, it appears that they
shouldn’t even be able to fly based on their relative body weight. Their wings don’t seem able to generate
enough lift until you consider an unlikely trick they have up their sleeve. Little hairs project from the wing
surface which disturb the “boundary layer” of the air flowing around the wing, and this generates the
additional lift they need to fly successfully. Aerospace engineers have experimented with this idea on fixed
wing aircraft by affixing little tabs here and there on the wing, but have not gotten the same “bump” that
insects seem to get from it.
I think it’s pretty cool that we have looked at the flight structures on birds and insects and tried to copy
them, even though the degrees of success have varied. But there is one structure that insects utilize which we
will probably never imitate successfully. The flight muscles of most insects are located inside their thorax but
do not connect to the wings directly. They are arranged in an amazing way to produce both speed and power.
Unlike a bird, insects have an exoskeleton, and its construction in the thorax
region is like a box with two hinges, one down each side. The thorax can be
flexed and it will automatically “click” back to the way that it was on its own
because of the tension stored in the thorax due to the flexing. The flight
muscles are arranged vertically and attach to the floor and ceiling of the thorax.
They pull the floor and ceiling toward each other, which flexes the “box” and
causes the wings, which are attached to the outside of the thorax just above
the hinges, to pivot up. When the muscles relax, the box clicks back to the
a=wings, b=hinges between thorax and
original shape on its own and the wings pivot back down for free. The cycle of wings, c and d=flight muscles (vertical and
longitudinal)
up and down is very rapid and requires only one contraction of the flight
muscles. The extremely high rpms that an insect can achieve with this
configuration enable it to quickly take off to avoid danger (that’s why house flies are so hard to swat!). Maybe
I’m wrong and someday an engineer will successfully replicate this design to make a little flying surveillance
robot. If they do, I hope they give credit to the original aerospace engineer who came up with it. 
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The unimind and Bose Einstein condensates
There is another book I highly recommend entitled What is Life? by Erwin Schrödinger. Be sure to get
the edition that has the companion book called Mind and Matter, because it’s only when you read both works
that you get the big picture of what he is trying to say.
You may recall that Schrödinger was the quantum physicist who came up with the psi equations which
described electron orbitals, the areas of probability for locating an electron around the nucleus. Without going
into detail, it’s fair to say he was a really smart guy. Though he was not a biologist by training, he ventured into
the question of what life really was from the standpoint of its building blocks, atoms and molecules and
quantum physics (his area of expertise).
He knew that life was enigmatic from the perspective of thermodynamics, because the amount of
molecular motion that exists at normal body temperatures is extremely chaotic. And yet, he knew that life
exhibited an orderliness that seemed to defy the randomness that should exist at these temperatures. DNA
had not been discovered yet, and though scientists suspected that there must be some molecular mechanism
for transmitting genetic information from one generation to the next, nobody knew what it was or how it
worked. One thing was certain to Schrödinger though: the molecule that carries hereditary information must
be extremely durable and thin, so as to avoid the effects of damaging radiation which continuously bombards
us (they knew about radiation after World War II!). He calculated the probability of collisions with radiation
with the incidence rate of inherited diseases and concluded that there must be very few actual collisions, and
that when they did occur there must be some explanation for the resilience of the molecular mechanism.
Nobody knew that DNA was in fact very thin and constructed in such a way as to make it difficult to damage.
They certainly had not suspected in their wildest dreams that it was designed with built-in redundancy and
contained the instructions for the assembly of nano machines that could use this redundancy to repair the
code!
What Schrödinger did know was that only one thing in the universe resembled the harmony exhibited
by all the parts in a living thing; a Bose Einstein condensate. At that point nobody had ever created one of
these states of matter that exist just above absolute zero, but theoretically they would behave just like the
cells in a living thing. They lose their individual identity and all cooperate to do the same thing! Close to
absolute zero atoms were predicted to behave strangely due to their lack of motion, and their quantum
properties would start to be more influential. We have now created Bose Einstein condensates and know that
the predictions are true; that the atoms in the condensate begin to exhibit wave properties and lose their
identity. Their wave functions begin to overlap and each atom begins to act as if it is everyone else until they
become just one big quantum system. It reminds me of the little green alien toys in a popular animated movie,
who operate like a “unimind,” even though there are many of them.
That is exactly how life behaves, and Schrödinger knew it. He just didn’t know how all the cells of the
body could be “of one mind,” obedient to a master plan that caused them to all cooperate at such high
temperatures. This led him to the next logical step in his considerations, and that was the fact that matter
does not normally do anything of the sort. Even though aggregates of matter will operate together chemically
in a reaction, there is no centralized control of what matter does all the time, except in a living thing. He knew
that our bodies obey the commands of our minds, and this led him to another logical conclusion. Our minds
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must be something greater than just the matter our bodies are made of, and by necessity must pre-date it.
Our minds must be immortal, and they must have been created by one ultimate mind, God. He was right.
The social intelligence of ants, bees, termites, birds, whales and people
The weird phenomenon of how our minds can command our bodies gets even stranger when you
examine populations of certain species. The farming that leaf cutter ants know how to do with their
underground fungus gardens, the way that army ants build bridges from their bodies to cross streams, and
many other ant behaviors seem to defy logic. No single ant knows the overarching purpose to their activities,
yet they execute their individual jobs to get it done.
The same can be said for the architecture of a honey bee hive, the dance they use to communicate
with each other, the roles of “wax maker” or “guard” or “air conditioner” for ordinary bees all seem so
mysterious. Who directed bees to hang in chains from the ceiling until wax was secreted from between the
segments of their abdomen while others come and grab it to fashion hexagonal shaped cubicles for storing
honey and growing grubs? Who told them that the hexagon was the most efficient structural shape to
approximate a cylinder without wasting valuable space? How does one worker know it’s supposed to station
itself at the entry and check the chemical identification of all who pass? Who tells some of the bees on a hot
day to gather water and deposit it within the hive while others station themselves at the entrance and exit
and hold on to the floor while they beat their wings furiously so as to create airflow through the hive to
provide evaporative cooling?
Who directs a million blind termites to move dirt a mouthful at a time to create a giant structure with
chimneys around the perimeter, a central shaft that runs down deep underground to an evaporative coil
which was strategically placed over a water source? No individual termite knows the plan, yet the resulting
convection currents keep the mound a constant temperature inside where the queen is busy laying eggs and
others are busy feeding her and tending the grubs. Instinct, some will say, but who programmed that instinct?
Who directs a flock of birds in a tight formation to move as one unit in avoiding predators without
hitting each other? Who told migrating birds that the v shape is the most efficient for reducing drag, but that
the lead bird takes the brunt of the work and needs to be “spelled” and go to the easiest place in the rear so
that the overall expenditure of energy ends up being less than if they flew as individuals?
Who taught a group of ducks sleeping on a log that the ones in the center are safe to sleep with both
eyes closed so long as the two on the ends sleep with one eye open (the eye facing the end they are on) to
keep watch for the rest? How do they know halfway through their nap that the other half of their brain needs
to sleep too, such that they get up, pivot 180 degrees, and then open the other eye and close the first?!
Why is it that no individual person trying to guess how many jelly beans are in a jar can get it right, but
the average guess of a group of guessers always gets extremely close to the correct answer? How is it that two
mobs of people crossing an intersection from opposite sides of the street always find the most efficient way to
pass by each other to get to the other side?
Who taught humpbacked whales to think three-dimensionally and strategically when they hunt
cooperatively? How did they learn to take turns corralling fish with “bubble nets” into a tighter and tighter
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circle until others suddenly rush up from below on signal with their enormous mouths open to scoop up the
fish? For that matter, who gave them that long pleated skin under their mouth so that it could expand in that
manner to enable this hunting method in the first place? These are so delightful to ponder, because they give
me a glimpse of the higher intelligence at work in the creation. Truly, God’s ways are beyond tracing out.
Atomic level assembly and some 3D designing
Have you ever wondered how it is that a spider can make silk that is far stronger than Kevlar out of
ordinary food under normal body temperatures, when Kevlar requires such extreme conditions to
manufacture? We use concentrated sulfuric acid, high temperatures and pressures, and complex starting
ingredients and end up with an inferior product. It’s because the spider is a living thing and can assemble
molecules an atom at a time with great precision. The methods for making Kevlar are very crude by
comparison.
Abalone make an extremely hard pearlescent lining for their shells with nothing but chalk and proteins.
Ok, proteins can be pretty complicated, but they aren’t hard. How does crumbly chalk help?! The key is that
they lay the material down in layers, one molecule at a time, and the composite result is astounding when you
consider the building material. As we’ve seen in so many examples, life is all about controlling processes, and
the results it achieves are pretty remarkable. But again, you have to know what you are trying to accomplish
before designing the processes that will get the job done.
Let’s look at two more examples of this profound engineering at the macroscopic level. I want to tell
you about a dolphin’s sonar capabilities. Their jaws are equipped with teeth that serve not only for eating fish,
but also as a sonar array. We are familiar with their adorable clicks, squeaks and chatter, but it blew me away
when I learned that they can tell where the objects are in three dimensions because of the architecture of the
jaws and teeth. The teeth are positioned within the jaws in such a way that they are offset by exactly half a
sound wavelength relative to the teeth on the other side of the jaw. Their brain takes the difference in the
timing for a sound wave to strike and vibrate one tooth as opposed to its neighbors and “triangulates” where
the echo came from!
In a similar fashion, owls depend on sound reception to locate prey. We typically think of those big
facial disks of feathers which catch sound like a funnel, but may not be aware of the fact that the ears that
those disks direct sound to are offset both vertically and horizontally relative to each other. What this enables
the owl to do is calculate precisely where a sound is coming from by the difference in the time that it took to
reach each ear. They turn their heads in the direction the sound is coming from, then “triangulate” the exact
location. Somehow their brain is able to store the location in memory so that they don’t lose track of it once
they take off and get closer!
Consider the conclusion that you would have to draw if you buy into the “tree of life” explanation for
the origin of the dolphin and owl. One organism is a bird and one is a mammal, each on completely different
branches of the tree. Both organisms would have had to evolve completely different structures in order to
adopt this identical strategy of auditory triangulation for locating prey. The speed of sound in water is faster
than air, and one set up uses a sonar array while the other uses funneling of sound with offset ear canals. Each
circumstance requires complex calculations that are different. Now add the auxiliary structures that must
coordinate with these “adaptations” in order for the organisms to survive. The ends of the primary feathers of
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an owl must be frizzy to make their flight silent to the unsuspecting prey, and the curved spear-like talons
must be able to spread out wide to capture and dispatch the prey. The dolphin must possess a hydrodynamic
shape, and powerful swimming muscles and fins, or the sonar array would all be for naught. I’m sorry, but the
likelihood of all these necessary components arising by natural selection acting on accidental mutations, and
ending up with the exact same strategy for catching prey TWICE on two unrelated “branches” is just not
credible. I choose rather to credit the unfathomable mind that designed them.
We’ve only just begun…
My feeble attempts to proclaim a few examples of God’s infinite wisdom displayed in His creation have
only scratched the surface. Thousands more pages could be filled with the marvels He envisioned and then
gave form to. As I said at the outset, nothing I could say can “prove” this point I’ve been trying to make, so
perhaps it’s time to move on to some other important considerations relative to all this. I will try to treat the
questions that many have asked with fairness, because they warrant reasonable answers.
Part 3: Some Important Considerations In View of the Evidence
What do similarities mean? Your presuppositions matter!
When we look at a dolphin’s tail and a fish’s tail, we aren’t surprised that they have these structures,
because they need them to survive in their environment. Neo-Darwinian theory calls these analogous
structures because they have a similar function but are not “derived” from the same physical structure. On the
other hand, a lizard’s front leg and your arm would be considered homologous structures because the arm is
believed to be the same structure, only modified by successive mutations acted upon by natural selection. The
first example of tails would be called “convergent evolution” because the structures ended up similar via
different pathways, but the second would be considered “divergent evolution” because the structures ended
up different but shared a common origin.
The presupposition of the theory of Neo-Darwinism is that the existence of all structures must be
explained by undirected processes (meaning that no outside intervention was involved), and that mutation
coupled with natural selection is the driver of all the variation we see in living things. With that as your starting
place the theory seems very reasonable and necessary, even if the “odds” seem astronomical. Before talking
about a very different starting place and profoundly different conclusion about it all, let’s look at more
similarities and the conclusions that Neo-Darwinians have drawn.
The most obvious similarity between all living things is that they all have DNA or RNA. Simpler
organisms have less DNA than more complex ones, so it seems reasonable that the simple ones were the
ancestors of the more complex ones. So how could the more complex cells and multicellular organisms have
arisen?
Let’s recall our examination of mitochondria and chloroplasts. I want to focus on a widely-accepted
theory about them called endosymbiosis. This theory postulates that mitochondria and chloroplasts were
once bacteria themselves that were engulfed by the very first eukaryotic cells, staying together thereafter due
to mutual advantage. On the surface this seems logical for a couple of reasons. The similar size is the most
obvious one. There’s also another similarity between these organelles and bacteria. They both have DNA in
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circular structures called plasmids. Because we have developed the technology which enables us to sequence
the genes of just about anything we want, we’ve found that the DNA of simple bacteria, chloroplasts and,
mitochondria is quite similar. This all seems like strong evidence from the perspective of materialism.
Many genes are shared in common between eukaryotic organisms. Much of what makes a mouse also
makes a human. Blocks of genes called “homeotic genes” or “homeoboxes” which build basic structures in a
developing organism, such as limb buds, are virtually identical. The more similar the organism the more genes
they share in common. For example, the human and chimp genomes are 76% the same (not 98% as previously
thought). We even have one less chromosome pair because two of their pairs appear to be fused together to
make a gigantic chromosome in our genome as compared with theirs. This seems like strong evidence to
indicate we are recently derived from a shared ancestor (this conclusion actually fails on close inspection).
Along these lines, a gene was discovered which pertains to the size of the jaw muscles, the ones
located on the top of their heads, in great apes. The gene we have for much smaller jaw muscles, the ones in
our “temples”, appears to be a mutated version of the same gene for the more massive muscles that great
apes possess on top of their heads. From a materialistic view, it seems logical to assume that after our
ancestor’s gene was mutated it allowed the evolution of a much bigger brain case, since the muscle space and
large bony ridge on top of the skull was no longer necessary to attach the muscles to. Presumably, this
increased brain space permitted the evolution of a brain that is large and complex enough to contemplate the
series of random events which enabled it to be aware of itself. This seems reasonable from a Neo-Darwinian
perspective.
The scales on a bird’s legs look an awful lot like reptilian scales, and the genes to produce both are
quite similar. Feathers really are modified scales, and birds have jerky motions just like a lizard. They have
many other anatomical similarities and they both lay eggs. Then there are those fossil remains of the
archaeopteryx. Never mind the dramatic differences in the skeletons or the warm-blooded metabolism. They
would have evolved by means of successive “successful” mutations and natural selection. It has to be so if
your beginning assumption is that all life originated from prokaryotic single-celled organisms in the deep
ocean. But what if your presupposition were drastically different? Would it be possible to come to a radically
different conclusion about it all? Yep.
What if we weren’t considered alive, only our machines were?
Imagine with me a race of intelligent machines that came to visit our planet searching for “life” as they
know it. As they looked around they would be see all sorts of machines, from ships and trains, to cars and
copying machines. They wouldn’t consider us or any other organic life to be truly alive, and would look at us
the way we do an interesting rock or crystal formation. As they surveyed all the machines on the planet they
would note that some are more similar to each other, and being intelligent they would want to make sense of
it all. They might ask, “How did all this life come to be?” They might conclude that because machines can only
be spawned by other machines that it might make sense to classify all the machines on the planet based on a
timeline of machine evolution. With their careful observation they notice that all machines are based in some
way on just a few simple machines such as the inclined plane and lever. All other machines seem to be
derivations of these or complex combinations of them. The machines that move about seem to utilize a
particular form of the lever in a circular configuration that we call the wheel, or wheel and axle. They decide to
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focus just on the moving machines for now, and on the basis of the wheel and axle they start their cladistics
scheme. It goes something like this:
The simplest form of moving life is the unicycle. This appears to be the oldest living mobile machine
and the ancestor of all other vehicles. It persists to the present, apparently unchanged, but must also have
given rise to two-wheeled vehicles. Its simplicity gives it the ability to turn on a dime, but in order to remain
upright it must be in almost continuous motion and it is not particularly stable.
Bicycles appear to have evolved from unicycles, and the selective advantage of a second wheel for
balance greatly enhanced the stability of this life form though it still had to be moving to remain upright.
These life forms are still very maneuverable, since they have retained the original unicycle in the front but the
bicycle has adapted to include levers at the top to aid turning. The frame and back wheel having been added
through mutation and favored by natural selection due to the advantages they provide over the unicycle.
Though the form with pedals continues to the present, other more advanced forms powered by internal
combustion engines evolved from them as well.
The bicycle also was the ancestor of tricycles of various kinds, but these all seem to be evolutionary
dead ends. Like the bicycle, the unicycle parts were retained in the front, and having two extra wheels in the
rear enabled it to stand upright without needing to be in motion. However, the tricycle has the tendency to tip
over when executing high speed turns, a definite disadvantage from an evolutionary perspective. Perhaps this
is why so few variants of this family have been discovered.
From the bicycle also came the four-wheeled cars and trucks. These organisms adapted to their
environment by developing a second pivoting wheel in the front of the vehicle which worked in tandem with
the first, as well as two extra wheels in the back. This resulted in a great deal of stability during maneuvering
as well as good stability while stationary. Because they were so successful from an evolutionary standpoint,
there are many successful variations of them that have filled every ecological niche. One example is a side
branch off the four-wheeled trucks with an extra set of wheels on the back axle and a diesel internal
combustion engine rather than gasoline. These must have evolved due to the selection pressure to carry
heavier loads. From these, an even more advanced life form evolved that have eighteen wheels and larger
diesel engine that is slow to accelerate but is tremendously powerful. These adaptations resulted from
selection pressures to carry even heavier loads over long distances.
A less common but even more advanced form of life was discovered that seems to be a derivation of
these large trucks. They have lost the ability to pivot their front wheels and have lost the rubber on the rims,
but they are far more massive and powerful. The hard wheels ride on a fixed track which is not attached to the
vehicle. The origin of the tracks is unknown, but this vehicle has evolved to take advantage of their prevalence.
The heavy loads are supported by transverse structures underneath, which spread out the weight and prevent
sinking into the ground. Utilizing these has both advantages and disadvantages. Extremely heavy loads can be
accommodated, but mobility is severely limited. The vehicle can only travel where the tracks exist. Exactly
what conditions gave rise to these unusual structures is still being studied, and how to classify this organism is
still open for debate. One puzzling phenomenon is the way it pulls other vehicles behind it that can detach
from it. Some propose that these are simply extensions of the same organism while others suggest that they
are symbiotic passengers, since the entire volume of the larger vehicle is dedicated to engine space while they
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have no engine of their own. This would create a competitive advantage for both. Most favor the first
hypothesis, since the unpowered segments have the same kind of wheels as the front part that is all engine.
Interestingly, the engine has somehow developed a secondary electric motor that works in combination with
the tremendously strong diesel engine. In spite of the unsolved mysteries of these adaptations, it has been
placed in the scheme above the large truck due to the retention of the diesel engine and apparent trend of
selection pressures which favored mutations enabling heavier and heavier loads.
Another life form they are having difficulty fitting into the classification scheme is an entire family of
flying vehicles. The earliest flying machines are now extinct, and the only fossil remains were found in a
museum, but strangely, they appear to have been without wheels, using a pair of skids on the bottom instead.
Perhaps this is why they went extinct. It appears that small single prop engine flying machines with two fixed
wheels in the front under the wing are the ancestors of surviving examples of these kinds of organisms. This
common ancestor gave rise to flying machines with multiple wings (these were evolutionary dead ends too),
multiple engines and jet engines. The jet engine was particularly successful in its environment and many
species of this family developed, including supersonic and massive cargo carrying variants. Though some of
these planes have the ability to lift their wheels up into their bodies after take-off, it is clear that they all
descended from the original wheeled vehicles.
One kind of life that has been quite challenging to place in the evolutionary scheme is a family of
aquatic machines. The have lost their original wheels altogether as a means to move about. It appears that the
original wheels have evolved into a form of wheel without a rim which is divided into four twisted segments.
This unusual wheel is positioned at the back of the craft and is attached to a shaft that turns it, which appears
to pull it through the water in some way. Obviously, the transition from land to water selected against having
the original wheel shape and favored a mutation that occurred which altered the orientation of the axle from
parallel (to the direction of motion) to perpendicular. In this way, the wheel would no longer be creating
friction by contacting the ground but by converting turning force into forward thrust, just like a twisted
inclined plane. Because the entire phylum of vehicles evolved from the wheel and axle not the inclined plane,
this must be an example of convergent evolution. The best guess so far for the origin of these aquatic vehicles
is that it shared a common ancestor with the giant diesel electric powered vehicles previously mentioned. If
you recall, these had lost their rubber wheel coverings and the ability to steer, and it seems that they were
already in the process of losing some of their land mobility. The most convincing piece of evidence for this
placement on the cladistics scheme is that the aquatic vehicles have retained the diesel electric power plant. It
is not known how the transition from land to water would have occurred, but more clues about this will no
doubt surface as the fossil record continues to be searched.
It is believed that a side branch of this aquatic form of life has been discovered that moves under the
water, but as this environment is difficult to explore, their precise ancestry is unclear. However, closer
inspection of the few specimens we do have has revealed that the diving of these underwater boats is
accomplished by an interior wheel that is more like the ancestral type. In the case of the surface boats, there
is also a wheel located in a centralized room of the machine which resembles the wheel found in cars and
trucks. All of these control wheels operate in a similar manner. How the organism could have evolved this
anatomy is still being studied, but it is obvious that there is a link with all of these wheels and the levers on a
bicycle. Even the flying vehicles retain this feature of a truncated wheel to control their motion, though in
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their case it makes flaps on their wings pivot. This curious range of uses for the original bicycle levers is a good
example of divergent evolution.
On a side note, the underwater vehicles appear to have flaps which move up and down like those of
the flying vehicles, which has only caused more consternation. The two competing theories accounting for this
are that the water flaps are due to convergent evolution, and that the flying machines actually evolved from
these underwater aquatic machines. Though this would necessitate another transition back to land and then
to the air, there is another piece of evidence in favor of this theory. The control wheel for diving and surfacing
has a structure and function almost identical to those found in the flying machines for controlling their wing
flaps. If this is true, the current scheme which shows the flying machines evolving from four-wheeled cars
would have to be radically altered. For now we are holding to the original theory due to the evidence of
gasoline-powered engines and rubber-rimmed wheels appearing in both the four-wheeled land vehicles and
flying vehicles.
Finally, the most advanced form of vehicle that was catalogued had no vestiges of wheels at all.
Curiously, there is a symbiotic relationship between this advanced flying machine and a giant vehicle that
transports it to its launch pad. This enormous machine still had many large wheels that were encompassed by
a wide track. This tracked configuration must have evolved in order to spread the enormous load over a
greater surface area so as not to sink into the ground under the tremendous pressure. Other vehicles that do
not appear to tow advanced flying machines have also been found with the track adaptation. Some of these
have articulating levers and scoops, others have a large blade on the front, while others have a dome on top
with a long thin cylinder protruding from the dome. It is unclear what the function of the cylinder is, but the
other adaptations appear to be for moving dirt. The evolution of this family of tracked vehicles is still being
studied, but they all seem to have the same basic adaptation for reducing ground pressure, and therefore
must share a common ancestor with the enormous one that hauls the advanced flying machine.
One theory is that they share a common ancestor with the previously mentioned diesel electric
powered vehicle which can haul tremendous loads. The evidence for this theory is that the wheels on the
tracked vehicles often lack the rubber on their rims, and almost all have a diesel power plant. Some even have
the same diesel electric combination, which supports the theory even further. However, the tracked vehicle
with the dome and protruding cylinder sometimes has a gasoline engine and rubber on the rims like the four
wheeled vehicles. However this anomaly evolved, it is certainly a side branch, since they do not move dirt and
have unusually thick bodies.
In any case, there is an intriguing hypothesis that the track is actually a derivation of a section of the
thin fixed track that the wheels of the heavy hauling vehicle traveled on. It is proposed that at some point the
vehicle lifted a loose section of the track as it traveled which subsequently bent around the perimeter of the
wheels. This would have enabled the vehicle to move into areas without the fixed tracks, providing a clear
competitive advantage. Over time, the selection pressures for greater mobility would have favored wider
modifications of the track, reduced vehicle sizes, as well as the capability to turn by developing separate
controls for the wheels on the left and right side of the vehicle. By making one side roll forward while the
opposite side rolls backwards these vehicles have evolved the ability to pivot or even turn slightly while in
forward or reverse motion by adjusting the speed of one side of wheels relative to the other. This is an
example of the remarkable structures that evolutionary processes can create. Some argue that the tracked
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vehicles must have evolved via some other pathway. They assert that it is implausible they evolved from the
massive diesel electric vehicles because the ground pressure of the initial combination of thin track and
extremely heavy vehicle would completely immobilize the vehicle, and it would not have survived long enough
for successive generations of mutations to occur. However, proponents of the theory point out the fact that
there are areas of the fixed tracks which occur on very hard ground, and that this may have been the site for
the initial generation. They could have remained in these areas until the adaptations were developed which
allowed successful forays into adjacent areas with softer ground. This is still being hotly debated. But back to
the advanced flying machine, the internal combustion engines have evolved into a surprising type of engine
that still burns fuel, but shoots flame out of the bottom to create a reaction force similar to that of the jet
engine, only this time no air is drawn into the front of the engine, and the circular blades inside the jet engines
which are derived from the wheel are missing altogether. It is believed that these vehicles which use a vertical
form of flight must have evolved from the jet family, but since they evolved for travel beyond the atmosphere,
there would be no air to pull against and the blades became vestigial and then disappeared over many
generations. Since the craft never makes contact with the ground it no longer had need for wheels and these
also became vestigial over time. The most surprising thing about these vehicles is that they obviously have
undergone adaptive radiation from the atmosphere into the habitat of space, but they have severely limited
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capabilities once they exit the atmosphere. Evidently, they have not yet evolved the capability to perform
interstellar travel. Perhaps in another 3 billion years they will have achieved this and come to visit us instead…
So, let’s
get the point. 
be sarcastic, but
illustrate that
great deal as we
in living things. It’s
ludicrous this
know full well that
designed the
exactly why each
it does. And yet,
this absurd
exactly the same
applied in forming
for life on earth.
get back to reality. You
My intention was not to
to use this allegory to
assumptions matter a
consider the similarities
easy to see how
analogy is because we
we are the ones who
vehicles. We know
one has the structures
the reasoning used in
fictional account is
reasoning that has been
a classification scheme
The reason it seemed
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ludicrous to organize the vehicle “life” in this manner was not the logic, but the omission of the designer in the
accounting. The logic was sound when you subtract us out of the equation. Darwinian evolution seems
reasonable when we subtract a designer out of our considerations, but a completely different and RATIONAL
conclusion can be drawn when a designer is credited for common features.
So then, why do all living things utilize nucleic acids (DNA and RNA) to encode for protein synthesis? Is
that proof that they all evolved from a common primitive single-celled organism, or is it proof that good
engineers do not “reinvent the wheel” when making a new design. No, they hit upon a good idea that works
and keep using variants of the same theme over and over again. Keep this in mind as you consider questions
like “why is the DNA of mitochondria and chloroplasts similar to some bacteria? Why do we share homeotic
genes with other vertebrates? Why do chickens look and act like big feathered lizards? Why are humans and
great apes so similar genetically?”
Could it be that we need similar physical features with only slight variations because we inhabit a
similar environment? Is the gene for our jaw muscle a mutation of one shared by a common ancestor with
great apes, or were we designed with a larger brain and less powerful jaws to begin with? Is our upright
posture intentional and original? Were our larger gluteus muscles, longer femurs and altered pelvis which
enable this all accidental mutations, or were these anatomical differences deliberate? Were we meant to sit
and contemplate, to walk and run on two feet, rather than swing through the trees and walk on our knuckles?
Were we meant to have the capacity to write symphonies and comprehend the mysteries of the universe?
Do all the similarities prove that everything evolved from a common ancestor, or do they mean that
what we have in common is the same creator who values efficiency and sees no need to use a completely
different design to accomplish similar outcomes? It all depends on your presuppositions. I think what you’ll
find when considering this question is that our convictions and passions are based on our world view, because
the same observations can be interpreted in VERY different ways, depending on our starting assumptions.
Let’s go back and re-examine the theory of endosymbiosis. Though the similarities between
chloroplasts, mitochondria and prokaryotes seem initially convincing, there are some serious problems with
stopping there and calling it a slam dunk of evidence. In fact, there is far more reason to reject this proposition
than to accept it. The most obvious one is that both are nothing like bacteria in structure or function. Their
architecture is blatantly designed for one purpose, even to the point of a caricature. They possess so much
specialized structure for maximizing surface area to facilitate the tremendous amount of exquisite machinery
to make enormous quantities of energy that they couldn’t possibly have been anything else “in a previous
life.” In fact, they make so much energy, as servants of the gigantic eukaryotic cells they are a part of, that the
very thought of the two ever being separate is impossible. Many would object by saying that the first
Eukaryotic cells were small by comparison and did not have the large energy requirements that the specialized
structures of chloroplasts and mitochondria provide for, and they would have “co-evolved” over time.
But this is preposterous, because there would be no selection pressure to favor such extreme
measures of energy production if it wasn’t needed. And if it wasn’t needed, then by what mechanism would
they be favored to develop them, if such a thing were even possible (they are far too deliberate in structure to
be anything but designed anyway). And I would argue that it is in fact NOT possible for an undirected process
to favor the creation of such elaborate equipment when it isn’t even needed in the first place! That’s like
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saying “since we know they had to arise by evolution, the structures must be adaptations.” I would ask then,
adaptations in response to what? This absurd circular reasoning was described to me by a fellow college
adjunct professor years ago when he exclaimed about photosynthetic bacteria: “now all they had to do was
figure out how to extract the other 34 ATP out of a molecule of glucose and a Eukaryotic cell would be
possible!” So… are we ready to attribute both problem-solving prowess and foresight to a prokaryote?! Even if
a bacteria could see the future and know that it would someday become a part of a behemoth of a cell that
would require it to morph into the equivalent of a muscle-bound cellular superhero, how could it possibly
design the optimal structure and function and write the code to get it all done? Just one look at the
photosystems, thylakoids, cytochromes, the Krebs cycle, ATP synthase, etc. and it just sounds like nonsense
honestly. These extreme complexities in both structure and biochemical pathways are so “over the top” that
believing they evolved gradually really is “blind faith.” I have to say it again, it’s FAR more reasonable to
believe that God was the architect of it all.
Many will object strongly by asserting that belief in a creator is unscientific, and that special creation is
not a materialistic mechanism. This assertion is absolutely true. I’m not using science to prove God’s existence
or to try and marry the two with a compromise like “theistic evolution.” I’m only drawing the conclusion that
all we have learned about the universe through our diligent searching cannot be attributed to materialism. I’m
crediting all the magnificence we have discovered to Him, rather than trying to find a way around Him. I simply
do not believe that either the universe or the immense complexity of life are their own causes. Remember,
just because something cannot be explained by science does not mean it is illogical, unreasonable, invalid or
untrue.
Some will still object by asserting that Darwinian evolution is strongly supported by evidence and that
there really aren’t multiple ways to view the data. The theory is virtually proven beyond a shadow of doubt,
right? Well, actually no. I doubt that many in the Neo-Darwinian camp would still be reading at this point, but,
I feel obligated to push back just a bit for the sake of those who don’t have “the other side of the story.” As
always in life, in order to make an informed decision, we need full information. It’s difficult to question the
“authority” of the majority, but courage and boldness are in order here.  So, if you’ll permit me, I’m going to
play the role of that little dog Toto and pull back the curtain...
Skepticism, bait-and-switch, smoke-and-mirrors and sleight-of-hand
One mark of a good scientist is a skeptical attitude. Being intimidated by the majority view has never
served scientists well, and doubts can be very fruitful when used in an honest search for the truth. It was my
high school biology teacher, Mr. Keller, who unwittingly helped me to be skeptical about Darwinian evolution.
I went to an ordinary public school, not a religiously-affiliated one, but Mr. Keller had an obvious distaste for
the theory. I don’t know if he was religious, because we didn’t know much about our teachers’ personal lives
in those days. It wasn’t so much what he said but what he didn’t say that caught my attention. He flew
through the chapter on evolution after saying he wasn’t going to spend much time on it. In those days,
evolution wasn’t taught as the “central unifying theme” in biology as it is now. He devoted so little time to the
theory that the only thing I remember him talking about was how foolish Lamarck’s initial theory was. He used
the example of a giraffe stretching its neck to reach food having no effect on its gametes.
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I got the distinct impression that he wanted to spend time on other more important things. I know, I
know, to the majority of biologists there is nothing more important than evolution. But Mr. Keller didn’t see it
that way. He focused his energies on other topics and activities, like di hybrid crosses, dissections, and
microscope drawings. He taught us how to handle our microscopes with care, because they were sensitive
instruments capable of making wonderful observations. And, boy, did he teach us to be careful in making
those observations! I will never forget how he would ask us if what we had just drawn was what we actually
had seen (no doing loop-dee-loops to fill space!), and encourage us to look again and draw things more
accurately!  We did a lot of cool stuff in his class, like examining blood flow through the capillaries in a
goldfish tail (a wet paper towel around its gills kept it alive), and independent research projects. I did my
project on Planarian regeneration, though I never could get one to grow two heads! This energetic and
enthusiastic teacher got me genuinely excited about science, and he subtly planted the seed that you didn’t
have to tow the party line in order to be a good scientist. I went on to get a B.S. in Biology with a minor in
Chemistry, largely due to the love this man had for what he did.
It wasn’t until college that I learned all the ins and outs of Neo-Darwinian theory (I was a Biology major
after all!). That was when I became a genuinely informed skeptic. I really did, and still do, understand the
theory. It’s just that I didn’t buy into it. Just so you know that my rejection of Darwinism isn’t personal, my
favorite college professor, Dr. Plummer, was an adherent to the theory. He was a great teacher, a very hardworking, intelligent and personable man. I just believe he was badly mistaken, even though he had a PhD and I
don’t.  You know, it would be easier to oppose the mainstream view if everyone I disagree with were nasty
individuals who were uneducated morons, but they aren’t.
This is why it’s so difficult for young minds to get any kind of footing when they have nagging feelings
of doubt about evolution. Their teachers are usually nice people who are definitely more educated and seem
to know so much. Who are students to question such authority, right? The not-so-subtle message that is
impressed upon young minds is that real scientists don’t believe in God now, because we have learned that He
is unnecessary. Only religious “Bible thumpers” who are ignorant about science stand on the side of
“superstition.” Besides, the textbooks, television and the internet agree, so they can’t be wrong. After all,
science deals with facts, not beliefs, right? Hmm…Let’s take a closer look…
Most high school and college biology texts use some classic examples of natural selection to explain
Darwinian evolution. Galapagos finches and peppered moths are typically used to demonstrate how allele
frequencies shift due to selection pressures. Ok, it’s well-documented that the white moths that used to
survive well prior to the industrial revolution became easy targets for predators, and that the dark ones that
were once rare were then favored due to the soot on the trees and they became the ones to pass on their
genes instead. Fine. If you show this on a graph, the previous bell curve distribution of traits in the population
has now been severely shifted to one side, and the traits that used to be “outliers” are now the most
commonly expressed trait. This example, or one with the finches’ beak types, is intended to give a satisfactory
explanation for how all species on earth would have evolved. We are supposed to nod our heads and move
on, but there is an enormous problem with these examples being used in this manner, and it borders on
dishonesty.
All they did was demonstrate that the range of possible traits which already existed within the original
gene pool was utilized by selection pressures to shift the frequency of the traits that are expressed. Perhaps
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some traits were not even expressed in the population initially, but their genetic potential existed in a latent
form in the population’s genome. A whole range of beak sizes was possible, but stabilizing selection had
originally narrowed the beak type down to one common shape in the original breeding pair that migrated to
the islands. Only when competition for different types of food drew out the variety of possible traits did the
array of beak shapes and sizes emerge. The potential had always been there in the original finches. But in the
end, no new species were created! The finches were still finches, not birds of prey. Dark peppered moths as
opposed to white peppered moths are still moths, not dragonflies. No new genetic material was added to
either population. Going back to the graphs, there was no new genetic material added which was outside the
original curve! We are meant to accept these examples of natural selection as proof that everything evolved
from single-celled organisms, but I have to call it what it is: classic “bait-and-switch” tactics. I have a hard time
believing that the authors and the larger community of adherents to Neo-Darwinian teaching are not aware of
how disingenuous this is.
Another example is often cited to demonstrate the evolution of a species that we can relate easily
with; dogs descending from wolves. The species Canus lupus “evolved” into Canus familiaris because of the
selection pressure of free food for those wolves with a smaller “flight distance” being favored over those who
feared humans. But the problem is the same as with the moths and finches. The wolves had all the range of
possibilities from Great Danes to Chihuahuas inherently built into their genome, and the combination of
natural selection (to make the first “proto dogs”) and selective breading in successive generations did the rest.
Plus, wolves and dogs can still interbreed to produce viable offspring anyway, so can they legitimately be
considered to have evolved? Even when you allow for the definition of a new species to be stretched to “a
new population that is reproductively isolated” (meaning that dogs and wolves don’t normally encounter each
other and interbreed), this example still fails dismally. Sorry, no new genetic material.
So, directional selection doesn’t sell me on the notion of Darwinian evolution. But wait, what about
“disruptive selection.” Nope, this only explains how an existing population can be separated into subgroups by
some barrier and become reproductively isolated from each other, with the two new populations ending up
with different allele frequencies. A classic example of this is the squirrels in the Grand Canyon area. One group
ends up with pointy ear tufts and a different coat color. They are all still squirrels afterwards. Still more smokeand-mirrors. 
What about genetic drift and gene flow? How about the Hardy Weinberg principle? What about the
overproduction of young? No, if you examine these closely you will see that they are all sleight-of-hand to try
and justify a theory that relies on one premise: the creative power of mutation. Without the generation of
brand new material for natural selection to act upon which increases fitness, the theory completely falls apart.
But isn’t evolution supported by the fossil record? Oops, it might surprise you that this is the worst
possible “proof” one could bring into the discussion. The fossil record completely destroys Darwin’s popular
“tree of life.” The record shows nothing but single-celled organisms initially with a sudden explosion of
different life forms appearing simultaneously in the Cambrian strata. All the major phyla show up all at once,
including animals with a spine, articulated bodies and limbs and compound eyes. There is no evidence of a
slow evolution from single-celled organisms to multicellular ones, let alone ones with complex structures. The
truth is that you have to bend the data severely to fit a preconceived notion of all life sharing a common
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ancestor, because the “tree of life” is not supported by the evidence. So why does this theory continue to
enjoy such widespread acceptance when it is contradicted by the data?
As I suggested at the beginning, it’s because the idea of all life evolving in a branching fashion of
gradual and successive steps from a one-celled organism NEEDS it to be true for so many. Let’s call a spade a
spade. The “Cambrian explosion” falsifies this hypothesis. Now if Darwin had speculated a “lawn of life” the
data would support him, but even that would not provide an appealing explanation for atheistic humanism to
publish. It would raise too many “unsavory” questions. There would be no crowing about belief in God being
unnecessary, unscientific and superstitious. I find it amazing that textbooks make mention of the Cambrian
explosion, but never inform the reader of its implications! However, even without this bone in the throat of
the theory created by the fossil record, there are the far larger problems with the theory that I discussed at
the outset (information and thermodynamics) and the obvious engineering and architecture that is blatantly
evident. I have discussed just a few examples among millions. So then, you may ask with a measure of
incredulity, where DID life come from then?!
My (?) Conclusion
Which came first, really?
I will give you what I believe to be the truth about that question shortly, but first allow me to frame the
question with a few more important considerations. To those loyal to Darwin and the false sense of security
he provides, everything I have said has been rubbish anyway, so I’m going to give you all the more reason to
write me off as a lunatic when I do answer the question. For the rest of you, a few more paragraphs won’t
hurt. 
It comes down to this. You can believe that the universe is eternal, with alternating oscillations of
expansion and contraction and the accompanying formation of matter from energy and space from the
nothingness of a singularity, and future annihilation of the universe back into a singularity (or “the big rip” due
to the expansion of dark energy, pick your poison). Or, you can believe that there is an omnipotent eternal
being who made it from Himself somehow on command. Adherents to both views can ask the other group
where the entity they believe is eternal came from, and both have to admit that it would be uncreated and
pre-existent. Both can tell themselves that because their opponents are unable to answer this ultimate
question, it proves that they are wrong. But let’s be reasonable. Both groups of believers must follow their
choice to its logical outcome and re-evaluate whether they can accept the necessary implications and
repercussions of where it all leads them.
Those who believe matter and energy are eternal find solace in believing that the properties of the
universe would spontaneously lead to the formation of life as we know it without having to “conjure up” what
to them seems like a cop out to explain its origin. They also find relief from the craziness of religion that swirls
around them, because it seems like once you accept the existence of anything supernatural, reason goes out
the window and everything deteriorates into a “free-for-all” of competing doctrines with a million
contradictory beliefs to choose from. They would rather not open Pandora’s Box. Instead, they mistakenly
equate atheism with empiricism, intellectual stability, rational thought and scientific progress. Atheism seems
much more manageable and trustworthy, but it is a false sense of security.
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When you adopt this view, there are other nagging questions that continue to crop up, other
“wrenches in the works” that keep coming to the fore. For instance, why is it that the universe is so distinctly
mathematical? Life itself uses profound mathematical patterns, such as fractals to create structures like the
branching patterns in the airways and alveoli of lungs, blood vessels, limbs on a tree, the distribution of trees
in a forest, veins in a leaf and so on. Why does the Fibonacci series keep coming up in the patterns of such
things as pinecones, leaf arrangements, pineapples, sunflower seeds etc.? Is it an accident that the
distribution of growth hormones at the apical meristem of a plant creates this mathematical pattern? Without
the pattern, the optimal spacing for gathering light or tightly packing seeds with maximum efficiency would
not occur. There certainly is a “smoking gun” here, as there is no possible way that a mindless plant could plan
for this (even with a mind it couldn’t program its own DNA!), and random mutation does not give rise to
consistent mathematical patterns. Why does the golden ratio keep showing up in the proportions of living
things? For that matter, why are even non-living features of the earth and greater universe exquisitely
mathematical in nature? Mountains and other topography is fractal, as is the turbulence behind a wing.
It’s ironic that even though math is the highly structured “language” of science, so few recognize the
obvious intelligence behind the mathematical structure. Working with the complex equations that describe
the universe requires intelligence, so isn’t it obvious that it took a far superior intellect to create it in the first
place?! Funny thing is, we haven’t even scratched the surface of the math that exists. The few examples of
“transcendent numbers” (wow, what an ironic term!) we have discovered such as pi, e, i, tau, and psi
represent just a taste of another kind of mathematics beyond algebra waiting to be discovered. Leibnitz and
Newton didn’t really invent calculus, they discovered it. It was already there waiting for them to figure it out.
Einstein discovered relativity. It was there all along. Schrödinger discovered the psi equations which describe
electron probability, but electrons had always obeyed these descriptions, and Newton discovered the way to
describe gravitational attraction, even though the inverse square law was always in effect for it and
electrostatic forces (Coulomb’s law). Why is all this intrinsic structure that we keep finding more and more
about woven into the universe such that it all works so elegantly? For that matter, why do the properties of
the universe support life? If one believes that these properties would automatically give rise to life, then what
are these properties? Let’s examine them…
As it turns out, the values for gravity, the mass of the fundamental particles in the universe (e.g.
electrons and quarks), the charge on electrons and protons and the cosmological constant (hypothesized to be
the rate of expansion of dark energy), just to name a few, have to be so finely tuned to permit the existence of
life that it seems unreasonable for it to be a coincidence. The cosmological constant, which deals with the rate
of expansion of the universe, is fine-tuned down to a level of precision that is almost incomprehensible, 1x
10120 !! When you add that requirement to the level of fine tuning for the strength of gravity, it becomes a
joke to conclude it was random chance. To give you an idea of how finely tuned gravity is, imagine a yard stick
that spans the entire length of the known universe. The precise value of gravity would be represented by a
segment only one inch long. If the value were any more or less than this exact spot, life as we know it could
not exist. Now throw the required values for all the other physical constants into the mix, and it becomes very
unsettling for atheistic cosmologists. How do they get around the degree of fine tuning exhibited in our
universe?
The most popular theory is that there are just as many parallel universes in existence as there are
possible combinations for all these variables (infinite), because this would breathe new life into the prospect
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that our universe is not special or fine-tuned at all, it only looks like it is. Probability gets another opportunity
to work its wonders in this scenario, but there is one serious problem with the multiverse theory. There is no
way to test it. There is no way to detect the existence of these supposed parallel universes empirically. So, are
we then talking about a scientific theory, or are we talking about religion and philosophy, or worse yet, science
fiction? Why would we call a conjecture that cannot be verified empirically a “scientific theory” and lend it
credibility by granting it this term, but disparage faith in God? Isn’t that talking out of both sides of our
mouth?! Those who propose these ideas cite “indirect evidence” by way of reason and what the math seems
to point to, but there is extremely compelling “indirect evidence” that God made all that we see, yet that
evidence is rejected out-of-hand because it is not empirical! Let’s at least be consistent, right?! Again, it is the
NEED for the “theory” to be true that gives it strength, because the alternative is so distasteful!
Another new theory that supposedly explains how the universe could exist apart from God’s
involvement is based on black hole theory. It is believed that digital (two-dimensional) information would be
stored on the surface of a black hole when an object is pulled in and annihilated, and that the object could be
“recreated” from the stored information as a three-dimensional image. Some cosmologists propose that the
entire three-dimensional universe is an illusion, projected from the edge of the universe which contains the
two-dimensional digital information for the three-dimensional “reality” we experience. The obvious problem
with this proposition, even if it could be demonstrated that our three-dimensional universe really could be a
hologram (that’s what our existence would be), is that it actually points to a creator who made the digital code
such that it could make the hologram in the first place! Even worse, you cannot have a hologram without an
original object to make it from, so what would the original universe have been, and why does our universe
keep changing if it’s an inward facing projection? If the digital information on the outside surface of the
universe is changing, rather than static, then who is changing it?! There would have to be some kind of
elaborate and active involvement by some enormously powerful and intelligent being who could orchestrate
such a thing. This leads us to the conclusion that these same cosmologists end up making. They asked the
same questions I just did, and they concluded that an alien race must be behind the trickery.
This ties into what I alluded to early on in the opening pages. Some cosmologists have considered the
possibility that aliens in fact were involved somehow in the origin of life, and a few have taken the proposition
a step further into the truly surreal. Some famous cosmologists have suggested that reality may not be what it
appears to be, and that the entire universe is not only a holographic projection, but that it is also generated
and controlled by an unimaginably intelligent and powerful alien race. They postulate that we may be
participants in a giant multiplayer simulation designed and manipulated by these beings. They aren’t joking.
These are people with PhDs coming up with this stuff! They realize, and are at least honest, that the structure
of the universe and especially the existence of life can’t possibly be an accident, but they have devised a
benign ultra-powerful intelligence to account for it. The notion that we would be somebody’s avatar, even
though we have no possible way to test this, is more palatable to some atheistic cosmologists than the
existence of God, because it avoids any accountability to obey Him.
This option seems strange and whimsical, but most importantly, non-threatening. Even if it does turn
us into a plaything for some alien behind a glorified joystick, it is preferable to be living an illusion than to be
answerable to our maker. We want to do whatever we please, even if it isn’t real. Besides, belief in an
omnipotent creator seems terrifying. Not only that, wasn’t this whole idea of God invented by those who want
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to manipulate the masses in order to extort money or gain power? The fact that history is full of religious
hypocrisy is used as proof that God is a human construct, but honestly, that seems mighty convenient.
On that note, there is an Irish physics professor I genuinely enjoy watching video clips of (he is really
enthusiastic and animated) who was “turned off” of any belief in God as a boy when he was told that
communion wafers had been transformed into the body of Jesus. He innocently and excitedly wanted to see
this under his brand new microscope, but was scolded for it, and that was the end of religion for him. I actually
think it was a GREAT idea! Why not let the boy look, right? Unfortunately, it never occurred to him as a boy or
adult that those teaching him were wrong! The truth has nothing to hide!! On one video clip when he was
speaking about Erwin Schrödinger and his prediction of a molecule that carried genetic instructions even
before DNA was discovered (I told you Schrödinger was a smart guy!), the Irish professor had the honesty to
admit that DNA “smacked of God”. I hope he reconsiders, because rather than hide behind the excuse of
abuse, it behooves us to find out who God really is. The terror is not misplaced for those who reject and hate
Him, but know this: He does not hate us in return. Quite the contrary.
It is God, the source of our dread when our conscience is not clean, the one whom we do not usually
respond properly to, who created life from non-life. He is the source of all life, because “in Him was life”
before the creation of the universe. He is the answer to the conundrum. Life came first, not matter. LIFE HAS
ALWAYS EXISTED. God is eternal, not the universe which he spoke into existence. THAT was the “big bang” by
the way! Biological life did not arise spontaneously from chemicals, it was deliberately formed. Our language
fails here, but you could say that He bestowed, or endowed or breathed life into the first living things, which
were created with the capability to reproduce. It was God who foresaw the need to grant this ability in order
to perpetuate life. He wanted it to survive from generation to generation, and it was He who designed all the
marvelous biological structures with their beautiful functions that we have been graciously permitted to
discover.
What’s it all for?
He wants us to take it all in with profound wonder, appreciating what He has done, and in doing so
turn to Him and acknowledge His creativity and genius. You know, if we were to seek recognition, honor, and
worship we would be megalomaniacs. Only God can legitimately seek worshippers without being guilty of
vanity. If you aren’t a worshipper already, I hope you will become one very soon. He was not content just to
fashion the universe with all its intricacies, wind it up like a clock and then remain aloof while it winds down.
What’s more, He must be actively involved. Without the continual exertion of His might, the universe would
cease to exist as we know it. Deism is not only inaccurate, it does God an injustice.
You may be aware that the most powerful force that we have identified in the universe, the strong
nuclear force, holds the nucleus of all atoms together. We have been able to quantify the magnitude of the
strong force and have found that it is almost unfathomable (releasing just a little of it is what we call a nuclear
blast). We know that without it the mutual repulsion of the protons would rip atoms apart, but scientists have
no idea what generates it in the first place. God is the source of this force that holds atoms together; “in Him
all things consist and are held together”. Can you imagine the amount of power it takes to maintain every
atom in the universe? Moreover, consider how much energy was required to create all the matter that is in
the known universe. Using Einstein’s famous equation, 𝐸 = 𝑚𝑐 2 , we can attempt to wrap our minds around
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this by converting the mass (which is really just highly condensed energy after all) backwards into energy by a
factor of the square of the speed of light (that’s a really big conversion factor!). Only a being who is limitless in
His power could form the trillions of galaxies, each with their billions of stars, and each of these with their
billions of tons of matter from His inexhaustible store! It’s bewildering, staggering, and frightful.
Here’s the most awesome thing. Though He is inconceivably powerful, He does not force us to obey
Him! If we possessed His power we would become tyrants. He, however, does not crush us with His might.
Rather, He wants us to know who He is and He reaches out tenderly to express Himself in a million ways. He
appeals to our sense of reason, and vies for our attention every day. Though it is fitting for Him to demand our
immediate obedience, He does not coerce us, because he has granted us the choice to believe what we want
to. We have enough evidence of His awesome power and genius, but He prefers to win us over with love and
kindness. The most intimate and amazingly gentle and humble way he has done this was by putting himself in
our shoes, by sending His own Son in the form of a man, experiencing our weakness, feeling our pain and
absorbing our rebellion so that we could return to Him in love and submission.
Though Jesus occasionally displayed his mastery over the forces and laws of nature, He did not
overpower anyone. He demonstrated mastery over the weather when He calmed storms on command. He
defied gravity when He walked on water. He exercised authority over disease, healing innumerable people
with every imaginable kind of sickness and disfigurement. He defied the second law of thermodynamics when
he raised a VERY dead Lazarus to life. He even manipulated matter at the most fundamental level of quantum
physics, vanishing after talking to friends on the road to Emmaus (after His resurrection) or walking through
locked doors to visit with them (by the way, he also had them touch the nail holes in his hands and ate fish
with them to prove that He was not a ghost). He also showed his control over relativity. A quick (and
conservative) calculation of the energy required to create just a pound of food for each of 5,000 men (not
including women and children), using the mass energy equivalence of 4𝑥1016 joules per pound reveals that He
expended the same amount of energy released in 3,000,000 atomic bombs (using 6.8𝑥1013 joules for the
Hiroshima bomb as a reference). When I first did the calculations I thought I had made a mistake, and
recalculated (actually making a math error the second time) and got an answer of 60. For some reason I
thought that was more reasonable (my draft version of the book has this wrong answer!) Obviously, my own
gut feeling about His power was wrong, and it shouldn’t have surprised me that the One who could create the
mass of the entire universe from His infinite store of energy (without being diminished) could easily create
enough food to feed a relatively small crowd of people, regardless of how big the number initially seemed.
Converting 20 million trillion joules into mass was not a problem!
Amazingly, He was able to not only do the reverse of 3,000,000 Hiroshima bombs discreetly (wielding
that much power right under everyone’s noses in complete safety!), but He also did it in a highly controlled
fashion, making bread and fish! Our best efforts to convert energy into matter with nuclear accelerators yields
only a few random particles. We have little control over what we’re doing. We can make an electron, a quark
or boson and the like here and there from energy, but certainly not an entire loaf of bread or a fully-formed
fish, let alone thousands of them, with no trace of radioactivity, carefully, inside a bunch of wicker baskets. No
giant 10 mile underground track of monstrous electromagnets required, just His surprisingly gentle hands.
Boy. When people DID catch a glimpse of just how much power and authority He possessed it made them wild
with excitement, and they wanted to make Him an earthly King so they could overthrow the Romans! He
wasn’t interested in any of that, but He does want our hearts, and He deserves our allegiance. We really are
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accountable to Him, and rightly so, but He wasn’t content to just judge us without providing a way back to
Him. He is the way back, and He is worth following. To hear the creator and sustainer of the universe invite us
by saying “come to Me all of you who are weary and I will give you rest…take on my yoke and learn of me, for I
am gentle and humble of heart” is an offer we can’t afford to refuse!
I can best end this effort to honor Him by quoting what one of Jesus’ first disciples said about all of
this…“The life became the light of men… and the light came and dwelt among us, but we did not recognize
Him…but to all who received Him, to those who believed on His name, He gave the power to become the
children of God.” That’s why we are here, so we would have the opportunity to believe what His friend John
said and make that choice. I choose to believe in Him and obey Him, and I hope you will too.
Sincerely,
Bill Faint
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