If Microbes begat Mind
© Zann Gill , 2008
PO Box 4001
Los Altos, CA 94024
Email: [email protected]
http://zanngill.com
http://desyn.com
CHAPTER NOTES —
TO BE REVISED W/ GALLEY PROOF
FOREWORD
1
p. 3. The term recognize is typically used to describe the conscious act of making implicit pattern
explicit. Although nonliving systems don’t “recognize” patterns in this conscious sense, implicit
pattern is made explicit in diverse nonliving systems, from crystals to tornadoes and tsunamis,
and sand on a vibrating plate.
INTRODUCTION : DESIGNING HYPOTHESES
3–7
p. 3. Quote:
Carl Sagan. 1987. “The Burden of Skepticism” first published in Skeptical Inquirer. 12. Fall.
Kenneth Snelson http://www.kennethsnelson.net/
Buckminster Fuller and E. J. Applewhite, 1975. Synergetics. New York: Macmillan.
The term creative is applied to a range of processes that produce innovative results, whether
driven by human consciousness or not. If we allow ourselves to see creativity as a dynamic
operating both in human consciousness and of non-human, non-living processes we discover
unpredicted connections.
p. 4. Darwinism is theory that species originate by descent, with variation from parent forms,
through the natural selection of individuals best adapted for successful reproduction. Darwin did
not claim to explain how parent forms originated.
I use the term “collaboration” to connote the mechanistic dynamic through which diverse
behaviors achieve an outcome that is greater than any individual behavior or than their sum.
Some scientists disagree, e.g. NASA Ames Chief Scientist for Human-Centered Computing,
William Clancey said: “You write that ‘arguments collaborate.’ In reality, only people
collaborate. Arguments are not agents at all. . . My specific work in the past few years has been to
elucidate why robots cannot collaborate with people either, until they have higher order
consciousness.” But to decide that “only agents collaborate” is an arbitrary designation of
language, leaving us without a term to characterize how diverse behaviors or elements with
implicit behaviors (e.g. arguments) mutually contribute to a shared, synergistic outcome. I use the
verb “collaborate” to show how this dynamic applies across domains. Although similarity of
concepts and entities can be wrongly implied by using the same name in multiple contexts, using
different terms spawns a proliferation of specific terms, which acts as a barrier to recognizing
similarities across disciplines. Numbering alternative usages adds complication, e.g., parts of an
organism collaborate (1) to make life alive, but arguments also collaborate (2) to construct a new
hypothesis with subscripts complicates. Private correspondence. November 2005.
p. 5. Herbert Spencer has been wrongly represented as someone who merely appropriated
Darwin’s theory. He had been working on his own theory before Darwin’s publication of Origin
of Species. Spencer extended Darwinist philosophy to develop a theoretical justification of
capitalism and coined the expression “survival of the fittest” in 1864 in his book Principles of
Biology, which drew parallels to free market economics, making “survival of the fittest”
philosophically appealing to those in power.
Richard Hofstadter in Social Darwinism in American Thought (1944) expounded on the capitalist
abuses of Social Darwinism. His argument has been attacked as an “appeal to consequences
184
fallacy.” Detractors argue that, although the concept of survival of the fittest might have be used
to justify Nazism or other violence, these negative consequences after-the-fact cannot be used to
disprove the theory of evolution by natural selection. But Social Darwinism is a modus operandi
for humans. So linking Social Darwinism to the Tragedy of the Commons is not an “appeal to
consequences fallacy” because Social Darwinism has been put forward as one explanation of
“how things work.” The Tragedy of the Commons is clear evidence that this modus operandi
leads to consequences that do not work. Whether Darwinism itself has limitations will be shown,
not by the Tragedy of the Commons, but by findings of biologists studying the mechanisms of
evolution itself.
Darwin and Alfred Russel Wallace both agreed that “survival of the fittest” overcame the
anthropomorphism of “selecting” though it “lost the analogy between nature's selection and the
fanciers'." Darwin employed the phrase “survival of the fittest” in the 5th edition of The Origin
published on 10 February 1869, in the subsection of Chapter 4 on natural selection. Several
decades later in The Man Versus the State Spencer expanded on the social implications: “Thus by
survival of the fittest, the militant type of society becomes characterized by profound confidence
in the governing power, joined with a loyalty causing submission to it in all matters whatever.”
Herbert Spencer. 1864. Principles of Biology. 2 vols. London: Williams and Norgate.
Herbert Spencer. 1884. The Man Versus The State, with Six Essays on Government. London:
Williams and Norgate.
Richard Hofstadter. 1944. Social Darwinism in American Thought. Philadelphia: University of
Pennsylvania Press.
On religious controversy:
Ashley Montagu. Ed.1984. Science and Creationism. Oxford University Press.
p. 6. Because If Microbes begat Mind documents its own origination experiment, obvious
organizational strategies for this book would have merely produced books about the origin of life:
• If I organized this book by chronology, a cut across what occurred in any particular year
would reveal intriguing juxtapositions. We might focus on how knowledge is built up over
time and its lineages.
• If I organized this book by disciplines, and how each brings its particular worldview, biases,
and tools to unravel the origin and synthesis of life, I might weave threads together across
disciplines.
• If I focused on leading thinkers, their methods, and how they relate or debate with others, I
might contrast “slash the Gordian knot” theorists with methodical “unravel the details”
experimenters. Focusing on personalities, and individual trajectories, I would then structure
this material in a very different way, producing a useful, but more conventional book.
• Or I might have focused on key hypotheses. Although If Microbes begat Mind is about
hypothesis generation, my aim was not to structure this book around the stories of how the
big hypotheses about the origin of life were developed, making a case for one over others,
arguing why evidence proves or disproves that hypothesis over its competitors.
To compile ideas of origin of life and artificial life thinkers to survey the field, I might have
adopted one of the organizational strategies listed above. Each of these books would be different
from the others. If Microbes begat Mind, though constrained by the linearity of text, exploits
linearity as a chance to convey the mystery of discovery where one cannot see what lies around
the next bend.
p. 7. J.D. Bernal. The Origin of Life. N.Y.: World Publishing Company. 1967.
P ART I.
THINKING ABOUT H OW W E THINK
8 – 11
p. 8. Quote: See discussion in
Karl Jaspers. Kant [from The Great Philosophers, Volume 1]. Ed. Hannah Arendt. Trans. Ralph
Manheim. N.Y.: Harcourt Brace. 1962. p. 91f. What I am working on in the Critique,” wrote
Kant on May 11, 1781, “is not metaphysics, but a totally new and hitherto unattempted science,
185
namely the critique of a reason that judges a priori.” No longer would concepts take their form
from objects; rather objects would take their form from concepts.
The metaphor of the Gordian knot refers to the city of Gordium, now called Gordion, which lies
about a hundred miles west of Ankara and was the capital of ancient Phrygia. A peasant named
Gordius became one of its rulers and gave his name to the city after fulfilling an oracle of Zeus.
After years of civil unrest and aimless wandering, the Phrygian Elders High Council met to
decide which warring clan would rule next. An ancient oracle foretold that a man with a wagon
would come and end the civil unrest. Midas wandered into town with his ox-cart while the High
Council met. So he was appointed king. To thank the gods for his rule, Midas erected a shrine,
dedicated his wagon to Zeus, and yoked it to a pole in the center of the acropolis with a large knot
made of an intricate complex of tightly interwoven thongs of bark. When the bark hardened, it
became very difficult to untie. The knot was moved to the temple of Zeus Basileus in an ancient
city called Gordium, ruled by Midas’ father Gordius. Untying the knot came to be seen as a
symbolic act. An oracle foretold that whoever could untie the Gordian Knot would rule Asia.
Alexander (the Lion of Macedon), a general who had never lost a battle, heard of the challenge to
untie the Gordian knot, came, and slashed the knot with his sword. Later he became Alexander
the Great, who ruled all of Asia.
Sir James George Frazer discusses the magic virtue ascribed to the Gordian knot as a talisman —
a symbol that the scepter of Asia would fall to whomever could untie this knot. 1959. The New
Golden Bough. NY: Criterion Books. 187.
On my use of the term “choice”: Resistance to generalizing terms, and tendency to specialize and
narrow their usage, is evident with the term “choice.” Organisms selecting mates exercise choice.
Choice may be deliberative (involving logical argument), or emotional, determined by non-verbal
reactions (e.g. he chose to spank the dog). I use “choice” broadly to describe electing one option
over other alternatives, regardless of whether that choice is preprogrammed or cognitive.
p. 9. C.P. Snow. 1993. [1959]. The Two Cultures. Cambridge University Press.
On how methods change in science:
Thomas S. Kuhn. 1970. The Structure of Scientific Revolutions. Second Enlarged Edition.
University of Chicago Press. I thank Thomas Kuhn for his critique of an early version of this
manuscript in the 1980s and for encouraging me to build on the work of Michael Polanyi.
p. 10. I use “concept” to connote a mental pattern applied to interpret, make decisions, and act. A
concept “ready to test” is a hypothesis.
Scientists debate first life’s constituents, principles, and behaviors. What were the ingredients of
first life? Whether clues to the origin of life lie in an inventory of the ingredients for life, or in a
context where life might have begun, theorists differ about which prerequisites they deem crucial
to make the leap from non-life to life.
p. 11. An early experimenter on the synthesis of life was Sidney W. Fox.
1991. Synthesis of Life in the Lab? Defining a Protoliving System. Quarterly Review of Biology.
Vol. 66. No. 2. June.
More recently, see J. Craig Venter Institute http://www.jcvi.org/ , Synthetic Genomics
http://www.syntheticgenomics.com/; Craig Venter’s TED Talk — “On the verge of creating
synthetic life.” February 2008 on “digitizing biology” and “designing life.”
Chapter 1. design as guided emergence
12 – 18
p. 12. Quote: Sherrington, Sir Charles. 1951 [1937-8]. Man on His Nature. Gifford Lectures.
Cambridge University Press.
p. 13. On nestedness: Russian matryoshka, nested wooden dolls are a metaphor for nested,
ordered hierarchies — solving a problem from inside out, or outside in. The innermost
matryoshka represents how origin of life theorists address this problem from particular
disciplines, using concepts and tools to come up with different hypotheses. On the next level,
general principles emerge that characterize how the human mind tackles complex problems that
186
are still a mystery to science. Amongst evolutionary theorists, these colorful dolls are reduced to
nested black boxes, where a “black box,” describes a device that does something but whose inner
workings are mysterious: the organism, its organs, their cells, their organelles, the molecules that
comprise them.
Kirschner, Marc W. and John C. Gerhart. 2005. The Plausibility of Life. New Haven: Yale
University Press. 122.
p. 14. In 1931 Lewis Mumford listed C.S. Peirce as a “forgotten American” whom he believed
played a key role in creating a revolution in thinking in the 1870s. In 1934, twenty years after
Peirce’s death, philosopher Paul Weiss described Peirce in the Dictionary of American Biography
as “the most original of American philosophers and America’s greatest logician.” In a 1959
Scientific American review Ernest Nagel referred to Peirce as a “little known American
philosopher,” ushering in a resurgence of interest in the man who actually invented both
semiotics and Pragmatism (and coined the term) but was little known in his lifetime. Peirce’s
close friend William James tried to secure him an appointment at Harvard, but President Eliot
would not hire him, despite the fact that his father, Benjamin Peirce, was also a distinguished
professor at Harvard. British logician William Kingdon Clifford viewed Peirce as a logician on a
par with Aristotle and George Boole. Logician B.E. Kent compared Albert Einstein and CS
Peirce in their visual and diagrammatic way of thinking, using both hemispheres equally to create
their thought experiments. Noam Chomsky considered Peirce to be the key inspiration for his
generative and transformational grammar. Ilya Prigogine credited Peirce with anticipating the
“new physics.” As early as 1866 Peirce originated the idea of abduction, which he first called
hypothesis, giving serious meaning to what we colloquially call lateral thinking. In 1885 Peirce
wrote to his friend William James, “I have something very vast now. I shall write it for Mind.
They will say it is too vast for them. It is. . . an attempt to explain the laws of nature, to show their
general characteristics. . . The new philosophers will say, ‘How crude!’” Peirce was convinced
that he had discovered a method of thinking with the power to transform philosophical inquiry.
Peirce’s biographer Brent describes Peirce as a polymath, at home in the physical sciences,
especially chemistry, geodesy, metrology, and astronomy, experimental psychology,
mathematical economics, logic and mathematics, inventor of the field of semiotics, dramatist and
actor. But Peirce died a poverty-stricken outcast. Brent sees Peirce as a heroic example of an
individual spurned in his own time and later rediscovered. See Joseph Brent. Charles Sanders
Peirce, A Life. Indiana University Press. 1993. (This book is based on Brent’s Ph.D. dissertation
of 1960, which he wanted to publish then. Harvard University, which owns the Peirce papers,
gave permission for publication only in 1991).
Charles Sanders Peirce. 1934. Collected Papers of Charles Sanders Peirce, vol. 5. Ed. Charles
Hartshorne and Paul Weiss. Harvard University Press.
_______. 1955. Philosophical Writings of Peirce. Ed. Justus Buchler. N.Y.: Dover.
p. 15. Jean Piaget raises the question of how the implicit becomes explicit in his introduction to
Howard E. Gruber. 1974. Darwin on Man: A Psychological Study of Scientific Creativity. N.Y.:
E.P. Dutton.
Charles Darwin. 1959 [1872]. Origin of Species. Sixth edition. Chapter XV. “Recapitulation and
conclusion.” For reference to changes in the various editions, see The Origin of Species: A
Variorum Text, edited by Morse Peckham. Philadelphia: University of Pennsylvania Press. 1959.
p. 16. Stuart Kauffman uses the buttons and thread metaphor for Random Boolean Networks:
Stuart Kauffman. 2000. Investigations. Oxford University Press. p. 35. This metaphor is based on
the theory of random graphs of mathematicians Erdös and Rényi in 1959 describing complex
networks.
Ricardo Solé, and Brian Goodwin. 2000. Signs of Life: How Complexity Pervades Biology. N.Y.:
Basic Books. p. 234.
Iris Fry. 1995. “Are the different hypotheses on the emergence of life as different as they seem?”
Biology and Philosophy. 10:389 – 417.
187
Harold J. Morowitz. 2002. The Emergence of Everything. Oxford University Press.
p. 17. Study of phase transitions in combinatorial problems from this work of Erdös and Rényi on
random graphs spurred growing interest in phase transitions, applied to algorithmic performance
on computationally hard problems, which shows how theoretical tools addressing critical
phenomena in the mathematical and physical sciences can contribute to understanding
computation and mind.
p. 18. Sherrington, Sir Charles. 1951 [1937-8]. Man on His Nature. Gifford Lectures. Cambridge
University Press.
Chapter 2. was there a leap to life?
19 – 24
p. 19. Quote:
Crick, Francis. 1994. The Astonishing Hypothesis: The Scientific Search for the Soul. New York:
Charles Scribner’s Sons.
I thank Cairns-Smith for reviewing an early draft for this book and arguing that defining life is a
bogus problem, which prompted me to explore why it’s a bogus problem.
On the Newton example and discussion of the difficulties of defining: Carol Cleland and
Christopher Chyba. 2002. “Defining Life.” ISSOL 2002.
Sherrington, Sir Charles. 1951 [1937-8]. Man on His Nature. Gifford Lectures. Cambridge
University Press.
p. 20. On the definition problem. Jack Szostak interview. May 12, 2006.
Quote translated: Nature makes no jumps, a dictum of Darwin, originally penned by Linnaeus in
his Philosophia Botanica (1751). Gottfried Leibniz (1646 - 1715) (New Essays, IV, 16) and
Isaac Newton (1642 – 1727), almost simultaneous inventors of infinitesimal calculus, were both
inspired the Law of Continuity. Leibniz believed that it was not possible to put organisms into
discrete categories.
C. D. Broad and C. Lewy. 1975. Leibniz: An Introduction. London: Cambridge University Press.
p. 21. On Wohler’s discovery:
P.J. Ramberg. 2000. The death of vitalism and the birth of organic chemistry: Wohler’s urea
synthesis and the disciplinary identity of organic chemistry. Ambix. Nov. 47(3):170-95.
Scientists debate about first life’s constituents, principles, and behaviors. Each argues his case
and “disproves” his colleagues. What were the ingredients of first life? Whether clues to the
origin of life lie in an inventory of the ingredients for life, or in a context where life might have
begun, theorists differ about which prerequisites they deem crucial to make the leap from non-life
to life.
Oparin and Haldane were not aware of each other’s work when they published their two
landmark papers expressing similar views. Oparin, A.I. The Chemical Origin of Life. Trans. Anne
Synge. Fort Lauderdale, FL: Thomas Books. 1964[1924] and J.B.S. Haldane. 1929. “The Origin
of Life.” first published in The Rationalist Annual, reprinted in 1986 On Being the Right Size and
other Essays. Oxford University Press. 101– 112 and excerpted in J.D. Bernal. 1967 [1929]. The
Origin of Life. London: Weidenfeld & Nicolson. 242 –249.
Gerald F. Joyce. 1992. Directed Molecular Evolution. in Scientific American, Vol. 267, No. 6,
December. 90-97.
Leslie Orgel. 1994. The Origin of Life on Earth. Scientific American. Volume 271, Number 4.
October. 53 – 61.
p. 22. Lovelock, J. 1979. Gaia: A New Look at Life on Earth. Oxford University Press.
Lovelock, J. and L. Margulis. 1974. Atmospheric homeostasis by and for the biosphere: the Gaia
hypothesis. Tellus. 26:2 – 10.
On extremophiles:
Christopher Wills and Jeffrey Bada. 2000. The Spark of Life: Darwin and the Primeval Soup.
Cambridge, MA: Perseus Books.
From a biochemical perspective:
188
Robert M. Hazen. 2005. gen•e•sis: The Scientific Quest for Life’s Origin. Washington, D.C.:
Joseph Henry Press.
From a philosophical perspective:
Iris Fry. 2000. The Emergence of Life on Earth. NJ: Rutgers University Press.
On using limits to define life, e.g. size, temperature, chemical bonds:
R.L. Folk.1997. “Nanobacteria: Size limits and evidence. Response.” Science 276:1777. Robert
Folk’s research on nanobacteria has entered them as candidates for possible precursors for life.
J.W. Szostak.1999. Constraints on the sizes of the earliest cells. In, “Size Limits of Very Small
R.L. Folk and F.L. Lynch. 1997. “Nanobacteria are alive on Earth as well as Mars.” Ed. R.B.
Hoover, Proceedings SPIE, San Diego. 3111:406 – 419.
Microorganisms,” Proceedings of a Workshop of the Space Studies Board, National Research
Council. National Academy Press.
Radu Popa. 2004. Between Necessity and Probability: Searching for the Definition and Origin of
Life. NY.: Springer.
Committee on the Limits of Organic Life in Planetary Systems, Committee on the Origins and
Evolution of Life, National Research Council. 2007. The Limits of Organic Life in Planetary
Systems. Washington, D. C. National Academies Press.
p. 23. On the definition of life:
Debates on the origin of life are a window on cross-disciplinary problem-solving. Theorists don’t
agree on which question takes priority are driven by questions about closed versus open systems,
chance versus necessity, spontaneous self-organization versus Intelligent Design. Where did life
begin? is not only about where life began but also about problem context, which uniquely
determines what buttons can be tied together and how a problem can be solved. If we ask, What
does life require? we might assume that the basic constituents were coincidentally assembled.
How did life begin? concerns method, asking how life’s basic constituents might be assembled in
the process of becoming alive. What method did pre-life use to gather what it needed to bring
itself to life? After the basic constituents were in place, in sufficient concentration, something had
to get the action going. What triggered the scenario that turned life on? If life was autonomous,
How did life begin? observes the dynamics of problem-solving: How does evolving life preserve
gains and avoid backsliding? What motivated self-assembly? Why did life naturally progress
toward increasing complexity?
p. 24. N. W. Pirie. 1937. “The meaninglessness of the terms life and living.” In J. Needham and
D. E. Green, Perspectives in Biochemistry. Cambridge University Press.Karl Jaspers. Kant [in
The Great Philosophers, Volume 1]. Ed. Hannah Arendt. Trans. Ralph Manheim. N.Y.: Harcourt
Brace. 1962.
Chapter 3. calling it life if it acts “alive”
25 – 34
p. 25. Quote:
Graham Cairns-Smith. 1996. Evolving the Mind: on the nature of matter and the origin of
consciousness. Cambridge University Press. 278.
Kirschner, Marc W. and John C. Gerhart. 2005. The Plausibility of Life. New Haven: Yale
University Press. 45, 69.
p. 26. On defining water:
Carol Cleland and Christopher Chyba. 2002. “Defining Life.” ISSOL 2002.
Carl Sagan. 1998. “Life.” The New Encyclopedia Britannica. vol 22. Macropaedia. 15th edition.
p. 27. Christian de Duve. 1995. Vital Dust: The Origin and Evolution of Life on Earth. N.Y.:
Basic Books.
J. Maynard Smith and Eors Szathmary. 2000. The Origins of Life: from the birth of life to the
origins of language. Oxford University Press.
Many scientists have been puzzled by the question of the origin of the genetic code:
Eigen, Manfred. 1992. Steps towards Life. N.Y.: Oxford University Press.
189
Francis. H. C. Crick. 1968. The Origin of the Genetic Code. Journal of Molecular Biology.
38:369 – 370. http://www.evolvingcode.net/uni_code.php3
Cairns-Smith, A.G. and G. L. Walker. 1974. “Primitive Metabolism.” Biosystems. 5. 173 – 186.
Cairns-Smith, A.G. 1975. A case for an alien ancestry, Proceedings of the Royal Society. B. 189.
249 – 74.
Eigen on the ur-gene:
Eigen M. 1971. Self-Organization of Matter and the Evolution of Biological Macromolecules.
Naturwiss. 58:465 – 523.
p. 28. JBS Haldane on fire:
1949 book. What is Life? New York: Boni and Gaer.; London: Alcuin Press. 58 – 62.
Chyba, Christopher F. and Kevin P. Hand. 2005. Astrobiology: The Study of the Living
Universe. Annual Review of Astronomy and Astrophysics. 43:31 – 74.
The Time Machine scenario captures the gist of why we have such difficulty defining life and
distinguishing it from non-life. Interview with Scott Sandford. April 9, 2004.
p. 29. On biological autonomy:
Francisco Varela. 1979. Principles of Biological Autonomy. N.Y.: McGraw Hill/ Appleton Lange.
On the biochemical definition of life as autonomous:
Pedro Ruiz-Mirazo, Juli G. Pereto, and Alvaro Moreno. 2002. Proposal for a Universal Definition
of Life. International Symposium of the Society for the Origin of Life (ISSOL) 2002.
On far from equilibrium thermodynamics:
J.S. Wicken. 1987. Evolution, Thermodynamics and Information. N.Y.: Oxford University Press.
Ilya Prigogine and I. Stengers. 1989. Order Out of Chaos: Man’s New Dialog with Nature. N.Y.:
Bantam Doubleday.
p. 30. On autonomous agents:
Patti Maes. Editor. 1991. Designing Autonomous Agents: Theory and Practice from Biology to
Engineering and Back. M.I.T. Press.
p. 31. On life as expressing information: Jack Szostak interview. May 12, 2006.
On life as defined by its capacity to die:
Christopher Wills and Jeffrey Bada. 2000. The Spark of Life: Darwin and the Primeval Soup.
Cambridge, MA: Perseus Books.
For an accessible discussion of Kant, see Karl Jaspers. Kant [from The Great Philosophers,
Volume 1]. Ed. Hannah Arendt. Trans. Ralph Manheim. N.Y.: Harcourt Brace. 1962. 58f.
p. 32. On life as expressed by its performance: Deconstructing Life: Interview with Dimitar
Sasselov. Astrobiology Magazine. March 13, 2006.
p. 33. Scott Turner. Private communication and his 2007 book, The Tinkerer’s Accomplice: How
Design Emerges from Life Itself. Harvard University Press.
p. 34. Stuart Kauffman. 2008. Beyond Reductionism: Reinventing the Sacred. NY: Basic Books.
Chapter 4. the miraculous “as”
35 – 46
p. 35. Quote:
Douglas Hofstadter. 1985. Metamagical Themas: Questing for the Essence of Mind and Pattern.
N.Y.: Bantam Books, p 254. Hofstadter’s extensive discussion on “Variations on a Theme” as the
crux of creativity. He concedes that genius may not lie initially in twiddling the knobs but in
spotting them (p. 251). Recognition again.
To say that abstract concepts precede and help to generate hypotheses requires defining the term
“concept.” Not easy. A six hundred-page tome on this subject shows how hard it is to pin down
this term. Whether a concept is a bundle of features, a theory, a mental representation, an abstract
entity, an object or a behavior makes considerable difference in deciding what conceptual
approach to take. For a thorough treatment of the term “concept” see
Eric Margolis and Stephen Laurence. 1999. Concepts: Core Readings. Cambridge, MA: MIT
Press.
190
Story about Stanislaw Ulam:
Heinz Pagels: 1988. The Dreams of Reason: The Computer and the Rise of the Sciences of
Complexity. N. Y. Simon and Schuster.
Nobel laureate Emil Fischer conceived the lock and key metaphor (1894).
This chapter focuses on the role of metaphor in the creative process. Several seminal thinkers
paved the way for appreciation of the role of metaphor in creative thinking such as
C.S. Peirce abduction triggered my study of metaphor and
Arthur Koestler. 1964. The Act of Creation. N.Y: Macmillan. This study, on which he labored for
several decades, saw the foundation for creativity in “bi-sociation,” his version of abduction or
metaphor-making.
Cognitive scientist George Lakoff made the study of metaphor the focus of his career.
George Lakoff and Mark Johnson. 1980. Metaphors We Live By. University of Chicago Press.
_______. 1999. Philosophy in the Flesh. N.Y.: Basic Books.
Lakoff and Rafael E. Nunez. 2000. Where Mathematics Comes From: How the Embodied Mind
Brings Mathematics into Being. N.Y.: Basic Books.
On the role of metaphor in inspiring scientific breakthroughs:
Gerald Holton. 1988. Thematic Origins of Scientific Thought. Cambridge, MA: Harvard
University Press, 2nd ed. and
_______. 1998. The Scientific Imagination. Cambridge, MA: Harvard University Press.
p. 36. Vannevar Bush. 1945. “As We May Think.” The Atlantic Monthly. July.
Douglas R. Hofstadter. 1979. Gødel, Escher, Bach: an Eternal Golden Braid. N.Y.: Basic Books.
See also his description of the 1995 work of his Fluid Analogies Research Group described in
Fluid Concepts and Creative Analogies: Computer Models of Fundamental Mechanisms of
Thought. N.Y.: Basic Books.
On analogy-making and attempts to simulate this process with computers:
Douglas R. Hofstadter and the Fluid Analogies Research Group. 1995. Fluid Concepts and
Creative Analogies: Computer Models of Fundamental Mechanisms of Thought. N.Y.: Basic
Books.
Hofstadter, D. R. and M. Mitchell. 1994. The Copycat project: A model of mental fluidity and
analogy-making. In K. Holyoak and J. Barnden Eds. Advances in Connectionist and Neural
Computation Theory. vol 2: Analogical Connections. Norwood, NJ: Ablex Publishing
Corporation.
Mitchell, M. 2005. Self-awareness and control in decentralized systems. In Working Papers of
the AAAI 2005 Spring Symposium on Metacognition in Computation. Menlo Park, CA: AAAI
Press.
Mitchell, M. 1993. Analogy-Making as Perception: A Computer Model. Cambridge, MA: MIT
Press.
Mitchell, M. 2001. Analogy-making as a complex adaptive system. In L. Segel and I. Cohen
(editors), Design Principles for the Immune System and Other Distributed Autonomous Systems.
New York: Oxford University Press.
p. 37. Anatol Rapoport. 1991. Ideological commitments in evolutionary theories. Journal of
Social Issues. Issues in Evolutionary Psychology. 47. 3: 83 – 100. Fall.
Lovejoy, Arthur O. The Great Chain of Being: A Study of the History of an Idea. Cambridge,
MA: Harvard University Press. 1936.
Darwin metaphors:
Great Tree: Origin of Species. Chapter IV. "Natural Selection; or The Survival of the Fittest";
p. 38. Tangled Bank: Origin of Species. Chapter XV. “Recapitulation and Conclusion”
For a comparison of Darwin, Marx, Frazier and Freud as literary writers see
S. E. Hyman. 1966.The Tangled Bank: Darwin, Marx, Frazer, and Freud. N.Y.: The Universal
Library, Grosset and Dunlap.
von Neumann’s machine-tape metaphor:
191
John von Neumann.1966. Theory of Self-Reproducing Automata. Urbana, Illinois: University of
Illinois Press.
p. 39. Graham Cairns-Smith. 1982. Genetic Takeover. Cambridge University Press.
Cairns-Smith built his hypothesis on a foundation of specific chemical experiments, e.g. A. G.
Cairns-Smith, P. Ingram and G.L. Walker. 1972. “Formose production by minerals, possible
relevance to the origin of life.” Journal of Theoretical Biology. 35. 601 – 4.
p. 40. Crick’s metaphor: 1981. Life Itself: Its Order and Nature. N.Y.: Simon and Schuster.
I’m indebted to Graham Cairns-Smith for suggesting that I explore how genetic memory might
relate to my argument. If “evolving a winning hand” requires genetic memory, then we have
already presupposed a mechanism for the origin of life that we associate with consciousness.
p. 41. The lock and key metaphor, now taken for granted, was conceived in 1894 by Nobel
laureate Emil Fischer.
p. 42. Hoyle golf metaphor:
Fred Hoyle Intelligent Universe. 1984. NY: Holt Rinehart, Winston.
Herbert Simon. Essay “The Architecture of Complexity.” Proceedings of the American
Philosophical Society. 106(6). 467 – 482.
Herbert A. Simon. The Sciences of the Artificial. Cambridge: M.I.T. Press. 1998. 47.
p. 43. Charle’s Lyell’s use of the Gordian knot;
Charles Lyell. [1830-33]1909 – 14. “II. Uniformity Of Change.” Scientific Papers. The Harvard
Classics.
Darwin’s use of the Gordian Knot as a metaphor for means of dispersal:
Chapter XII. Geographical Distribution: Means of Dispersal. Origin of Species. Harvard
Classics. 1909–14.
E.O. Wilson’s Gordian knot metaphor from his study of the complexity of the Attini:
E.O. Wilson. Attini: transition from hunter-gatherer to agriculture. Behavioral Ecology and
Sociology. 7:143-156. For the story of how E.O. Wilson was convinced to change his view by
reading W.D. Hamilton’s 1964 paper, see Wilson’s autobiography, Naturalist (p. 319-20). N.Y.:
Warner Books. 1995.
W.D. Hamilton. 1964. The genetical evolution of social behaviour I and II. Journal of Theoretical
Biology. 7: 1-16 and 17-52.
p. 44. Replicators and the target of selection:
E. Szathmary and L. Demeter. 1987. Group selection of early replicators and the origin of life. J.
Theor. Biol. 128:463 – 486.
On the target of selection debate:
Elliott Sober. 1983. “Holism, Individualism, and the Units of Selection,” Conceptual Issues in
Evolutionary Biology, Ed. Elliott Sober, M.I.T. Press.Cosmides, L. and J. Tooby. Cytoplasmic
inheritance and intragenomic conflict. Journal of Theoretical Biology. 89: 83 – 129.
Richard Dawkins. 1989. Dawkin’s new preface to this edition of The Selfish Gene contains his
Necker cube modification of his “selfish gene” metaphor, first published by Oxford University
Press in 1976. The Selfish Gene. Oxford University Press.
On the need for a revision of neo-Darwinism:
Peter A. Corning. 1996. The Co-Operative Gene: On The Role of Synergy in Evolution.
Evolutionary Theory. 11. 183-207.
and 2005. Holistic Darwinism: Synergy, Cybernetics, and the Bioeconomics of Evolution.
University of Chicago Press.
p. 45. Jeff Hawkins with Sandra Blakeslee On Intelligence: How a New Understanding of the
Brain will Lead to the Creation of Truly Intelligent Machines. NY: Henry Holt. 2004.
192
Per Bak’s sandpile model for self-organized criticality:
Per Bak.1996. How Nature Works. N.Y.: Springer-Verlag.
A popular rendition of self-organized criticality applied to social systems:
Malcolm Gladwell popularized Per Bak’s work in 2000. The Tipping Point. N. Y. Little Brown.
Chapter 5. chance versus necessity (or choice?)
47 – 57
p. 47. Quote:
Jacques Monod. 1971. Chance and Necessity. translated by A. Wainhouse. N.Y.: Knopf.
Scientists have introduced a range of metaphors to grapple with the concepts of chance, necessity,
and order in the origin of life.
Contradictory arguments drive the chance versus necessity debate. Lest we forget, Democritus
overruled that debate well before the rest of the debaters said a word when he asserted that
“everything existing in the Universe is the fruit of chance and necessity.” Democritus’ quote on
chance and necessity supported his atomic theory of matter. He maintained that nothing in the
universe exists except atoms and the empty space within which they move. All changes in the
world are the result of changes in the motion of atoms, in the way they are packed together and in
how, their random motion, they collide to form larger bodies. So necessity in the world derives
from the nature of the atoms themselves. Whatever comes about is due to the chance initial
arrangement of atoms, while their mechanical interactions follow laws (necessity).
Democritus fr. 164, Sextus Empiricus Against the Mathematicians VII 116-118. xxx
Some claim that minerals couldn’t carry enough information to be the first genetic material.
Cairns-Smith’s hypothesis of “genetic takeover” addressed this problem: while mica-type clay
could have been a precursor material, able to demonstrate evolutionary principles, it would later
have been replaced through “genetic takeover” by other materials able to carry more information.
Some question why if clays were once the basis of life, we don’t find traces of them inside us
today. Cairns-Smith addressed this question with his “genetic takeover” hypothesis: the precursor
clay would long since have been entirely replaced by other materials and mechanisms better able
to perform the required functions. See his 1982 book, Genetic Takeover.
Paul Davies’ dynamite, brick-building, and spilling beans metaphors to highlight why energy
alone, without pattern, is meaningless:
Paul Davies. 1999. The Fifth Miracle. N.Y.: Simon and Schuster. But would Crick have agreed?
p. 48. de Duve, like Davies, notes that, while random events must be meaningful, this complex
set of events need not occur at once (it’s not like tipping beans from a jar). He uses his Boeing
747 to draw the opposite conclusion: the assembly of a cell, like the assembly of a Boeing 747,
occurs piecemeal in a very large number of steps. The sequence of those steps is not rigid; so he
thinks it possible that evolution could have produced this complexity in the time allotted:
Christian de Duve. 1995. Vital Dust: The Origin and Evolution of Life on Earth. N.Y.: Basic
Books.
Fred Hoyle. Intelligent Universe. 1984. NY: Holt Rinehart, Winston.
Paul Coppock suggested that complex assembly can be accomplished simply. . .
p. 49. Robert Shapiro cites Haldane and develops the metaphor of Charlie the Chimp in his 1987
book Origins: A Skeptic’s Guide to the Creation of Life on Earth. N.Y.: Bantam Books. Books.
p. 50. Hoyle uses his typewriter with a dozen mistakes metaphor to explore the transcription error
problem. The “400 words” metaphor is Hoyle’s. The critique is mine. For his perspective on the
odds of miscopying DNA links:
Fred Hoyle. Intelligent Universe. 1984. NY: Holt Rinehart, Winston.
Fred Hoyle. 1997. Life on Mars? The Case for a Cosmic Heritage. Clinical Press Limited.
Redland Green Farm. Redland, Bristol, UK.
Leonard Troland. 1914. The chemical origin and regulation of life. Monist. 24: 92 –103.
193
p. 51. Christian de Duve questions whether there would be enough time for life to evolve on a
planet revolving around a Sun much bigger than our own and argues the case against panspermia
in
_______. 1995. Vital Dust: The Origin and Evolution of Life on Earth. N.Y.: Basic Books.
_______. 1995. “The Beginnings of Life on Earth.” The American Scientist. Sept. – Oct.
Francis Crick and Christian de Duve debate as to whether there was sufficient time to develop
advanced life on Earth. Crick takes up “shipping us all the right stuff”:
Francis H. C. Crick. 1981. Life Itself: Its Order and Nature. N.Y.: Simon and Schuster.
Hoyle was a not-enough-information debater in Intelligent Universe (1984).
A star more massive than the Sun will live a shorter lifetime on the main sequence. In rough
numbers the fuel supply goes as the Mass while the rate of burn goes as Mass to the power of 4 so
the lifetime goes as 1/M^3. So a star with M = 1.5xMsun will live 1/(1.5)^3 = 0.3 times the life of
the sun. The sun's Main Sequence lifetime is about 10 Gyr so a 1.5 M sun star would have a
lifetime of about 3 Gyr years. Could an oxygen rich atmosphere and complex life develop in that
shorter timeframe? This is a good question and if one looks only at the example of the Earth the
answer would be no. Oxygen was just beginning to rise on the Earth when the Sun was 3 Gyr old
and complex live was still a billion years in the future. But the time it takes to develop an oxygen
rich planet may be a function of the planet size. The Earth may not be optimal in this regard.
Chris McKay has argued that smaller planets could have oxygen rich atmospheres faster,
estimating that because Mars is so much smaller (1/10 the mass of the Earth), it could have
developed an oxygen rich atmosphere a thousand times faster than the Earth. Instead of 3 – 4 Gyr,
it might have only taken 3 – 4 Myr on Mars. But Mars is too small to have plate tectonics. McKay
maintains that the optimal size for a planet to develop life would be the smallest planet size that
can still sustain plate tectonics (possibly 1/2 the Mass of the Earth). A planet this size could have
an oxygen rich atmosphere, perhaps 100 times faster than the Earth, so maybe in a few hundred
million years. Time enough for a star as massive as 4 times the mass of the Sun.
C.P. McKay. Oxygen and the rapid evolution of life on Mars, In “Chemical Evolution: Physics of
the Origin and Evolution of Life", Edited by J. Chela-Flores and F. Raulin, Kluwer, 1996. pp 177
– 184.
p. 52. On life arising almost instantaneously when conditions were right:
Wanda L. Davis and Chris McKay. 1996. Origins of Life: A Comparison of Theories and
Application to Mars. Origins of Life and Evolution of the Biosphere. 26. 61 – 73.
V. R. Oberbeck and G. Fogelman. 1989. Origins Life Evol. Biosphere 19. 549.
_______. 1990. Origins Life Evol. Biosphere 20. 181.
Lou Allamandola. Interview. March 9, 2004.
Kirschner, Marc W. and John C. Gerhart. 2005. The Plausibility of Life. New Haven: Yale
University Press.
Aleksandr I. Oparin. 1964[1924]. The Chemical Origin of Life. Trans. Anne Synge. Fort
Lauderdale, FL: Thomas Books and published in English in 1967 by J.D. Bernal.
_______. [1936]1953.The Origin of Life. Translated and annotated by Sergius Morgulis. N,Y.:
Dover. Here Oparin describes how he changed his view.
_______. 1957 [1936]. The Origin of Life on the Earth. Oliver & Boyd, Edinburgh,
Jacques Monod, 1971. Chance and Necessity. translated by Austryn Wainhouse. N.Y.: Knopf.
de Duve’s counterargument is in Vital Dust. p. 8.
p. 53. Colin Pittendrigh coined the term teleonomy:
A. Roe and G.G. Simpson. Eds. 1958. Behavior and Evolution. New Haven: Yale University
Press. Pittendrigh wrote: “Today, the concept of adaptation is beginning to enjoy an improved
respectability for several reasons: it is seen as less than perfect; natural selection is better
understood; and the engineer-physicist in building end-seeking automata has sanctified the use of
teleological jargon. It seems unfortunate that the term ‘teleology’ should be resurrected and, as I
think, abused in this way. The biologists’ long-standing confusion would be more fully removed
194
if all end-directed systems were described by some other term, like ‘teleonomic,’ in order to
emphasize that the recognition and description of end-directedness does not carry a commitment
to Aristotelian teleology as an efficient causal principle” (384).
p. 54. Kirschner, Marc W. and John C. Gerhart. 2005. The Plausibility of Life: Resolving
Darwin’s Dilemma. New Haven: Yale University Press. 128.
Harold J. Morowitz. 2002. Beginnnings of Cellular Life: Metabolism Recapitulates Biogenesis.
Yale University Press. p. 1, 3.
Harold J. Morowitz. 1985. Mayonnaise and the Origins of Life: Thoughts of Minds and
Molecules. N.Y.: Charles Scribner’s Sons. p. 29 – 30
p. 55. Manfred Eigen and Ruthild Winkler. 1981. Laws of the Game: How the Principles of
Nature Govern Chance. N.Y.: Knopf. 18.
Henri Bergson (1859 – 1941), born the year Darwin published Origin of Species, is known for his
much-disputed ideas about élan vitale (life force), e.g. see his book Creative Evolution (1932).
Pierre Teilhard de Chardin, Jesuit, (1881 – 1955) developed Vladimir Vernadsky’s concept of the
noosphere and influenced the stance of the Church on evolution.
J.D. Bernal recounts his discussion with Einstein in his 1967 book, The Origin of Life. N.Y.:
World Publishing Company.
p. 56. Evolvability and fidelity of replication:
Mark Bedau and Norman Packard. 2003. “Evolution of Evolvability via adaptation of mutation
rates.” Biosystems. 69. 143-162.
ALife studies explore mutation versus fidelity of reproduction tradeoffs, e.g. see Mytilinaios,
Efstathios, Mark Desnoyer, David Marcus, and Hod Lipson. 2004. “Designed and Evolved
Blueprints for Physical Self-Replicating Machines.” Artificial Life IX.
For a discussion of why natural selection cannot preserve non-functional characters see
Horowitz, N.H. 1945. On the Evolution of Biochemical Syntheses. Proc. Nat’l Acad. Sci. U.S.A.
31.153 –7.
On “exploration vs. exploitation” and evolvability:
Marc Bedau. 1996. “The nature of life.” In M. Boden. Ed. The Philosophy of Artificial Life.
Oxford University Press. 332 – 357.
_______. 1997. “Weak Emergence.” Philosophical Perspectives. 11. 375 – 399.
_______. 1997. “Emergent Models of Supple Dynamics in Life and Mind.” Brain and Cognition.
11. 5 – 27.On modeling sustained evolution:
M.A. Bedau, J.S. McCaskill, N.H. Packard, S. Rasmussen, C. Adami, D.G. Green, T. Ikegami, K.
Kaneko, T. S. Ray. 2000. Open problems in artificial life. Artificial Life. 6(4):363 – 376. The
origin of life is highlighted as one of the open problems of ALife.
Gerald Joyce on how an RNA-based evolving system might bootstrap itself toward metabolic
complexity: 1991. “The Rise and Fall of the RNA World.” The New Biologist. 3. 399 – 407.
PART II.
CLUES TO OUR ORIGINS
58 – 59
p. 58. Quote:
Graham Cairns-Smith. 1985. Seven Clues to the Origin of Life. Cambridge University Press. p. x.
Thomas S. Kuhn, 1970. The Structure of Scientific Revolutions. Second Enlarged Edition.
University of Chicago Press. I am grateful to Thomas Kuhn for his comments on an early draft of
this manuscript (1986).
p. 59. Popper, Karl Raimond. [1935] 1959. The Logic of Scientific Discovery. London:
Hutchinson.
_______. 1963. Conjectures and Refutations. London: Routledge.
Wächterhäuser, Günther. The Uses of Karl Popper in Laura Dassow Walls. 1995. Seeing New
Worlds: Henry David Thoreau and Nineteenth-Century Natural Science. University of Wisconsin
Press. 177-189.
195
Iris Fry. 2000. The Emergence of Life on Earth. NJ: Rutgers University Press. Fry contrasts
hypotheses and gives an excellent historical account of Wächterhäuser’s role in the playoff of
ideas in this space.
Robert Hazen’s “Interlude — Where are the Women?” in his book gen•e•sis. Women are
permitted to carry out experiments; the barrier comes when they want to be accepted as original
thinkers — to put forward their own hypotheses.
Lucretius (Titus Lucretius Carus, c. 99 - c. 55 BCE). Roman poet and author of the philosophical
epic poem De Rerum Natura (On the Nature of the Universe) on the origins and atomic structure
of matter and anticipating biological mutation and survival of the fittest in the emergence and
evolution of life forms.
Chapter 6. hypothesis “worlds”
60 – 69
p. 60. Quote:
Niles Eldredge. 1995. Undreamt Philosophies. Foreword to Lynn Margulis and Dorion Sagan.
What is Life? N.Y.: Simon and Schuster.
For a good tour through these hypothesis worlds from an informational perspective:
John Maynard Smith and Eors Szathmary. The Origins of Life: from the birth of life to the origins
of language. Oxford University Press. 2000.
George Wald. 1954. The origin of life. Scientific American 191:46. This pivotal article introduced
the expression “RNA World.”
Woese is best known for his discovery of the third group of single-celled organisms, in addition
to the prokaryotes and eukaryotes, which were already known) — the archaea, a group that
contains both methanogens and numerous organisms that grow at extremely high temperatures (in
some cases above 100°C). As such, they provide potential insights into mechanisms of
thermophilia and methanogenesis.
Carl Woese. 1967. The Genetic Code – The Molecular Basis for Genetic Expression. N.Y.:
Harper and Row.
Woese, C.R., 1979. A proposal concerning the origin of life on the planet Earth: Journal of
Molecular Evolution. 13:95 – 101.
On how studies of ribosomal RNA produced family trees:
Woese, C.R. 1987. Microbiol. Rev. 51. 221.
Walter Gilbert. 1986. “The RNA World.” Nature. 319:618.
Leslie Orgel and James Joyce postulate:
Leslie Orgel. 1973. The Origins of Life: Molecules and Natural Selection. N.Y.: John Wiley and
Sons.
Leslie Orgel publications on life as a molecular system with capacity to grow and evolve
according to Darwinian principles include
_______. 1963. “The Maintenance of the Accuracy of Protein Synthesis and its Relevance to
Ageing.” Proc Natl. Acad. Sci. USA. 49:517 – 521.
_______. 1973. The Origins of Life: Molecules and Natural Selection. N.Y: John Wiley and
Sons.
_______. 1979. Selection in vitro. Proceedings of the Royal Society of London. B205: 435 – 442.
_______. 1994. The Origin of Life on Earth. Scientific American. October. 53 – 61.
Gerald Joyce discusses the RNA World in 1989. “RNA evolution and the Origins of Life.”
Nature 338:217 – 224.
_______. 1991. “The Rise and Fall of the RNA World.” The New Biologist. 3. 399 – 407.
_______. 1992. “Directed Molecular Evolution.” Scientific American. December. 90 – 97. and
_______. 2002. “The Antiquity of RNA-based Evolution.” Nature. 418 (6894): 214 – 221.
p. 61. Christian de Duve questioned the RNA World and chose to focus on metabolism, 1995.
Vital Dust: The Origin and Evolution of Life on Earth. N.Y.: Basic Books.
196
R.L. Folk.1997. “Nanobacteria: Size limits and evidence. Response.” Science 276:1777. Robert
Folk’s research on nanobacteria has entered them as candidates for possible precursors for life.
Summary of the history of the Murchison meteorite analyses:
Dermot A. Henry. 2003. ‘Star Dust Memories’ — A Brief History of the Murchison
Carbonaceous Chondrite. CSIOR Publishing. 20. vii – ix.
The first analysis of the Murchison meteorite to detect amino acids is described in
K. Kvenvolden, J. Lawless, K. Pering, E. Peterson, J. Flores, C. Ponnamperuma, I.R. Kaplan. C.
Moore. 1970. Evidence for Extraterrestrial Amino-acids and Hydrocarbons in the Murchison
Meteorite. Nature. 228. 923 – 926.
D. W. Deamer’s analysis of the Murchison meteorite:
_______. 1985. Boundary structures are formed by organic components of the Murchison
carbonaceous chondrite. Nature. 317:792–794 and
D. W. Deamer and R. M. Pashley. 1989. Amphiphilic components of the Murchison
carbonaceous chondrite: surface properties and membrane formation. Orig. Life Evol. Biophys.
19:21–38.
McKay, D.S. et al. 1996. “Search for Past Life on Mars: Possible Relic Biogenic Activity in
Martian Meteorite ALH84001.” Science 273. 924 – 930.
McKay, D.S. et al. 1999. “Possible Bacteria in Nakhla [#1816].” Proceedings of the 30th Lunar
& Planetary Science Conference. http://www.jpl.nasa.gov/snc/alh.html Houston ,Texas. March
15 – 19.
C.P. McKay.1997. “The search for life on Mars.” Origins Life Evol. Biosphere. 27:263 – 289.
See discussion by NASA Planetary Protection Officer John D. Rummel. November/ December
2000 Planetary Report.
p. 62. For the evolution of James Ferris’ ideas on clay as a catalyst:
J.P. Ferris, P.C. Joshi, E.H. Edelson, and J.G. Lawless. 1978. HCN: A plausible source of
purines, pyrimidines and amino acids on the primitive Earth. J. Mol. Evol. 11:293 – 311.
James P. Ferris, Chun-Hsien Huang, and William J. Hagan Jr. 1988. Montmorillonite: A
Multifunctional Mineral Catalyst for the Prebiological Formation of Phosphate Esters. Origins of
Life and Evolution of the Biosphere. 18. 121 – 133.
J.P. Ferris and G. Ertem. 1993. Journal American Chemical Society. 115. 12270-12275.
G. Ertem and J.P. Ferris. 1996. “Synthesis of RNA Oligomers on heterogeneous templates.”
Nature. 379:238 – 240.
For a discussion of his thought process, see Graham Cairns-Smith. 1984. “On the Rocks: the vital
cocktail” in Nash, Sara, Editor. Science and Uncertainty. Proceedings of a Conference held under
the auspices of IBM United Kingdom Ltd. London. March IBM United Kingdom Ltd. 25 – 42.
Cairns-Smith, Graham.1982. Genetic Takeover. Cambridge University Press.
For his latest thoughts on broader implications of his research see Graham Cairns-Smith. 2005.
“Sketches for a Mineral Genetic Material.” Elements. 1. 157 – 161.
For Wächterhäuser wee sources for p. xxx
J.P. Dworkin, D. W. Deamer, S. A. Sandford, L. J. Allamandola. 1998. “Self-Assembling
Amphiphilic Molecules: Synthesis in Simulated Interstellar/ Precometary Ices” Proceedings of
the National Academy of Science, USA. 98: 815 – 819.
Deamer, David and Gail L. Barchfield. 1982. Encapsulation of Macromolecules by Lipid
Vesicles under Simulated Prebiotic Conditions. Journal of Molecular Evolution. 18:203–206.
N.Y.: Springer-Verlag.
Deamer. David. 1997. “The first living systems: A bioenergetic perspective.” Microbiology and
Molecular Biology Review. 61(2): 239-261.
p. 63. Sidney Fox selected particular amino acids (with an extra amino or extra acid group),
heated them above the boiling point of water and observed that the amino acids joined into
chains. He called these synthetic composites “proteinoids” in order not to confuse them with
naturally occurring proteins. He dissolved his proteinoids in warm water. As the solution cooled,
197
microspheres formed. When these microspheres were placed in a solution containing proteinoids,
proteinoid accreted on their surface, forming buds.
S.W. Fox and D.K. Harada. 1958. Thermal Copolymerization of amino acids to a product
resembling protein. Science. 128:1214.
S.W. Fox and C.R. Windsor. 1970. Synthesis of Amino Acids by the Heating of Formaldehyde
and Ammonia. Science. 170:984-986.
S.W. Fox and K. Dose. 1977. Molecular Evolution and the Origin of Life. N.Y.: Marcel Dekker.
S.W. Fox. 1988. The Emergence of Life; Darwinian Evolution From the Inside. NY: Basic
Books.
p. 64. However, using NASA’s Spitzer telescope, Doug Hudgins and a team of scientists from
NASA's Ames Research Center have detected the PAHs containing nitrogen throughout our
Milky Way galaxy and far away galaxies nearly as old as the Universe itself. They have shown
that nitrogen containing aromatic molecules, chemical compounds that could be important for
life’s origin, are widespread throughout space. Combining laboratory experiments with computer
simulations, the team showed that complex organic PAH molecules (polycyclic aromatic
hydrocarbons) are widespread throughout space. These stable, hexagonal molecules made up of
hydrogen and carbon can withstand the hostile radiation environment of interstellar space. The
Ames team showed that PAHs are responsible for the mysterious infrared radiation that
astronomers first called the Unidentified Infrared Emission. The information carrying molecules
in the DNA and RNA that make up all living matter as we know it, which are found in many
biologically important species, have nitrogen containing aromatic hydrocarbons. Their signature
has now been found in space.
L. J. Allamandola, D. M. Hudgins, and S. A. Sandford. 1999. “Modeling the Unidentified
Infrared Emission with Combinations of Polycyclic Aromatic Hydrocarbons.” Astrophys. J.
(Letters) 511: L115 – L119.
E. Peeters, L.J. Allamandola, D. M. Hudgins, S. Hony, and A.G.G.M. Tielens. 2004. The
Unidentified Infrared Bands after ISO. In Astrophysics of Dust. Eds. A.N. Witt, G.C. Clayton and
B. T. Draine. ASP Conference Series. 309: 141 – 162.
Hudgins, Douglas M., Charles Bauschlicher, and L. J. Allamandola. 2005. Variations in the Peak
Position of the 6.2µm Interstellar Emission Feature: A Tracer of n in the Interstellar Polycyclic
Aromatic Hydrocarbon Population. The Astrophysical Journal. 632:316 – 332. October 10.
Skeptics argue that PAHs litter the universe. Carbonate minerals do not require water to form.
Chain-like arrays are unusual but magnetite crystals are common in meteorites and do not prove
that they held life. And finally, that the fossils are too small. Journalists dub this debate, “cradle
of life versus cauldron of crud.”
James P. Ferris, Chun-Hsien Huang, and William J. Hagan Jr. 1988. Montmorillonite: A
Multifunctional Mineral Catalyst for the Prebiological Formation of Phosphate Esters. Origins of
Life and Evolution of the Biosphere. 18. 121-133.
p. 65. Based upon an interview with Jack Szostak, May 12, 2006 and the following references:
Martin M. Hanczyc and Jack W. Szostak. 2004. Replicating vesicles as models of primitive cell
growth and division. Current Opinion in Chemical Biology. 8: 660 – 664.
Irene A. Chen Richard W. Roberts, and Jack W. Szostak. 2004. “The Emergence of Competition
Between Model Protocells. Science. 305. September 3. 1474 – 1476.
Martin M. Hanczyc, Shelly M. Fujikawa, and Jack W. Szostak. 2003. “Experimental Models of
Primitive Cellular Compartments: Encapsulation, Growth, and Division.” Science. 302. October
24. 618 – 621.
J. W. Szostak., D. P. Bartel, and P.L. Luisi. 2001. “Synthesizing Life.” Nature. 409:387 – 390.
Martin M Hanczyc and Jack W Szostak. 2004. Replicating vesicles as models of primitive cell
growth and division. Current Opinion in Chemical Biology. 8:660–664.
Luisi, Pier Luigi. 2006. The Emergence of Life. From Chemical Origins to Synthetic Biology. Cambridge
University Press, Cambridge.
198
Bachmann, P.A., Luisi, P.L., and Lang, J. 1992. Autocatalytic self-replicating micelles as models
for prebiotic structures. Nature. 357:57-59.
p. 66. Martin M Hanczyc, Shelly M. Fujikawa, and Jack W. Szostak. 2003. “Experimental
Models of Primitive Cellular Compartments: Encapsulation, Growth, and Division.” Science.
302. October 24. 618 – 621.
p. 67. David P. Bartel and Szostak, Jack W. 1993. Isolation of new ribozymes from a large pool
of random sequences. Science. 261:1411 – 1418.
p. 68. On montmorillonite experiments:
J. W. Szostak., D. P. Bartel, and P.L. Luisi. 2001. “Synthesizing Life.” Nature. 409:387 – 390.
Hanczyc, Martin M., Shelly M. Fujikawa, and Jack W. Szostak. 2003. “Experimental Models of
Primitive Cellular Compartments: Encapsulation, Growth, and Division.” Science. 302. October
24. 618 – 621.
p. 69. David Sloan Wilson and Elliot Sober argue for restructuring the entire edifice of
evolutionary biology, reintroducing group selection to the human behavioral sciences. Behavioral
and brain sciences. 17 (4): 584-608. See p. 591 for discussion in context.
Chapter 7. who was our first ancestor?
70 – 77
p. 70. Quote;
Christopher Wills and Jeffrey Bada. 2000. The Spark of Life: Darwin and the Primeval Soup.
Cambridge, MA: Perseus Books. p. 15.
Chart: Wanda Davis and Chris McKay. 1996. Origins of Life: A Comparison of Theories and
Application to Mars. Origins of Life and Evolution of the Biosphere. 26:61 – 73.
p. 71. de Duve opposes the panspermia theories and sees the emergence of life as necessary from
initial conditions. He thinks it likely that life emerged and evolved on many other planets in the
universe, so he finds no need to assume that germs of life were seeded on Earth from space and
he summarily dismisses the first option with, “Having agreed to disregard the first possibility.” Hr
turns to the other options, concluding that no other chemistry is possible, though he concedes that
there might be more than one pathway for life’s evolution.
See _______. 1995. Vital Dust.
On Kelvin’s miscalculation of the age of the Earth:
P. J., Nahin. 1988. “Kelvin's Cooling Sphere: Heat Transfer Theory in the 19th Century Debate
over the Age-of-the-Earth” in History of Heat Transfer: Essays in Honor of the 50th Anniversary
of the ASME Heat Transfer Division (E. T. Layton and J. H. Lienhard, eds.). New York: ASME,
1988. 65-85.
Lord Kelvin's address to British scientists, December 23,1871 is excerpted here:
http://zapatopi.net/kelvin/papers/on_the_origin_of_life.html
On the Pasteur – Pouchet debate:
N. Roll-Hansen. 1983. “The death of spontaneous generation and the birth of the gene: two case
studies of relativism.” Social Studies of Science 13:481-519.
Louis Pasteur. [1861]. “On the Organized Corpuscles that Exist in the Atmosphere” Annals de
Sciences naturelles in Oeuvres. Ed. Pasteur Vallery-Radot. Paris: Masson et Cie.
Felix Pouchet. 1859. Heterogenesis, or Treatise on Spontaneous Generation
p. 72. On Liebig and Buchner:
Vaclav Smil. 1997. Cycles of Life: Civilization and the Biosphere. NY: Scientific American
Library. Liebig assumed that nitrogen, because of its “indifference to all other substances,” was
significant. But he thought plants obtained it from the ammonia in precipitation. He overlooked
the immense amount of nitrogen contributed by bacteria. But his incorrect theory, that plants take
all their nitrogen from the atmosphere, led to the world’s longest running series of plant
experiments.
On panspermia:
199
Svante Arrhenius. 1987. [1908] Worlds in the Making. London: Harpers in Earth, Moon and
Planets 37: 187-99.
p. 73. JBS Haldane. 1967 [1929]. The Origin of Life. first published in The Rationalist Annual.
Reprinted in J. D. Bernal. The Origin of Life. London: Weidenfeld & Nicolson. 242-249.
For later accounts of the panspermia debate:
D.T. Wickramasinghe and D.A. Allen. 1981. Nature. 294:239.
D.T. Wickramasinghe and D.A. Allen. 1986. Nature 323:44.
Fred Hoyle and Chandra Wickramasinghe. Life on Mars? The Case for a Cosmic Heritage. 1997.
Clinical Press Limited. Redland Green Farm. Redland, Bristol, UK.
On Becquerel’s attack of 1924:
Panspermia 2000. Astrophysics and Space Science Journal. Springer Netherlands. Volume 268,
Numbers 1-3 October, 1999. 1-17.
Fred Hoyle and Chandra Wickramasinghe. 1978. Lifecloud: the Origin of Life in the Universe.
London: Dent.
p. 74. Crick-Orgel spaceship speculation:
F. Crick and L.E. Orgel. 1973. “Directed Panspermia.” Icarus 19:341 – 346.
For a good overview of Wächterhäuser’s work, see
Iris Fry. 2000. The Emergence of Life on Earth. NJ: Rutgers University Press. 162 – 172.
C. Huber and G. Wächterhäuser. 1997. “Activated acetic acid by carbon fixation on (Fe, Ni)s
under primordial conditions.” Science 276:245 – 247.
C. Huber, W. Eisenreich, and G Wächterhäuser 2003. A possible primordial peptide cycle.
Science. 301:938 – 940.
p. 75. Cairns-Smith experimented with his hypothesis of templating for information transmission
using various mica-type and mixed layer clays. He concluded that, unlike organic polymers,
inorganic crystals offer potential for a variety of primitive, self-organizing genetic materials
before that Jack-of-all-Trades protein could be perfected, which accords with a networked model
for LUCA. A. G. Cairns-Smith and G. L. Walker. 1974. “Primitive Metabolism.” Biosystems. 5.
173 – 186.
Graham Cairns-Smith. 1988. The chemistry of materials for artificial Darwinian systems.
International Revs. Phys. Chem. 7. 209 – 250.
Graham Cairns-Smith. 2005. “Sketches for a Mineral Genetic Material.” Elements. 1. 157 – 161.
Graham Cairns-Smith Interview. June 2002. For Harold Morowitz’s three views, see his 2002
book. Beginnings of Cellular Life: Metabolism Recapitulates Biogenesis. Yale University Press.
p. 3.
Davis, Wanda L. and Chris McKay. 1996. Origins of Life: A Comparison of Theories and
Application to Mars. Origins of Life and Evolution of the Biosphere. 26. 61 –73.
p. 76. Robert Folk and Lynch, F.L. 1997. “Nanobacteria are alive on Earth as well as Mars.” Ed.
R.B. Hoover, Proceedings SPIE, San Diego. 3111:406–419.
W. Thomson (Lord Kelvin). 1904. Baltimore. Lectures on Molecular Dynamics and the Wave
Theory of Light. The formal definition is: Any geometrical figure, or group of points is chiral, or
has chirality, its image in a plane mirror, ideally realized, cannot be brought to coincide with
itself.
Jean Baptiste Biot (1774 – 1862) observed that quartz crystals existed in even fifty-fifty righthanded and left-handed mixtures, while organic solutions had optical rotation.
Louis Pasteur (1822 – 1895) experimented with asparagine, both organic (prepared from
asparagus plants) and synthetic. He showed that in the organic preparation the plane of polarized
light rotated to the left, whereas synthetic asparagine showed no rotation at all because the
synthetic mixture had equal numbers of right- and left-handed crystals. Pasteur wondered about
this difference between living and synthetic preparations and speculated that life might be
characterized by asymmetry, which he ascribed possibly to magnetism. However, the electrons
200
given off during the beta decay of radioactive elements are also asymmetric, with a preferred
handedness. See also Wills and Bada 2002.
F.C. Frank. 1953. Spontaneous asymmetric synthesis. Biochem. Biophys. Acta. 11:249. Frank
assumed autocatalytic reactions, where each left or right-handed form catalyzes its own
replication, so that any imbalance will be amplified. How first life was generated, and how life
might be synthesized today, and whether life’s origin occurred only once or repeatedly, remains a
vexing conundrum, mired in details like the chirality (right- or left-handedness) of molecules.
Some postulate that the weak force in beta decay might exert a selection preference, or that clay
might have a selection effect. On the subject of chirality alone an international congress has been
meeting annually for years. But has this detail enabled us to find our first ancestor? Not yet.
W.A. Bonner. 1999. Chirality amplification — the accumulation principle revisited. Orig. Life
and Evol. Biosphere. 29: 615 – 623.
p. 77. Raphael Plasson, Hughes Bersini, and August Commeyras. 2004. Homochirality as a Fixed
Point of Prebiotic Chemistry. Artificial Life IX.
J.B.S. Haldane, 1929. The Origin of Life, first published in The Rationalist Annual.
Artificial life research teams have sought to demonstrate how a prebiotic system might have
evolved spontaneously away from the racemic attractor and toward homochirality through
mechanisms that amplify asymmetry. Simulations try to explain why there isn’t a racemic
attractor (toward equal distribution of right and left-handed forms):
Chapter 8. searching for “LUCA”
78 – 85
p. 78. Quote: Ricardo Solé, and Brian Goodwin. 2000. Signs of Life: How Complexity Pervades
Biology. N.Y.: Basic Books. p. 234.
p. 79. Günter Wächterhäuser. 1988. Pyrite formation, the first energy source for life: A
hypothesis: Systematics and Applied Microbiology. 10. 207 – 210.
Biophys, Molec. Biol. 58:85 – 201.
Carl Woese. 1967. The Genetic Code – The Molecular Basis for Genetic Expression. N.Y.:
Harper and Row.
p. 80. J.B.S. Haldane. 1947. What is Life? New York: Boni and Gaer; London: Alcuin Press,
Graham Cairns-Smith. 1968. An approach to a blueprint for a primitive organism. In
Waddington, Towards a Theoretical Biology, vol. 1. 57—66.
On how our genetic code became a universal standard:
Patrick N. Forterre, Benachenhou, F. Confalonieri, M. Duguet, C. Elie, and B. Labedan. 1993.
The nature of the last universal ancestor and the root of the tree of life, still open questions.
Biosystem 28:15–32.
O.V. Davydov. 1995. “Problem of the genetic code structure: new data and perspectives.” In
Evolutionary biology and related areas of physiochemical biology. Ed. B. F. Poglazov, B. I.
Kurganov, M. S. Kritsky & K. L. Gladilin. Moscow: Bach Institute of Biochemistry, Russian
Academy of Sciences.
_______. 2002. “Trial Homology of the Genetic Code: Biological Significance.” #125. ISSOL
2002. Davydov thought it would be useless to search for LUCA. He argued that many generations
improved the genetic code. The code emerged and gradually converged (notes p. 61 above). How
might its emergence and gradual convergence have been guided? Was evolution solely guided by
environmental selection? Or did other complementary mechanisms exist? Davydov disagrees
with Francis Crick’s Frozen Mutation Theory that the code is universal because now any change
would be lethal, or at least strongly selected against. In contrast, Crick believed that code design
was produced less by heredity and more by protein infrastructure formation. His hypothesis
assumed that nature’s problem-solving method was less tree-like (hereditary) and more web-like
(integrative and emergent). He stressed the importance of non-visible mutations.
Francis H.C. Crick. 1968. The Origin of the Genetic Code. Journal of Molecular Biology. 38:369
– 370. http://www.evolvingcode.net/uni_code.php3
201
p. 81. Rene Descartes. 1985. [1628, 1701]. Rules for the Direction of the Mind in
The Philosophical Writings of Descartes. 3 vols. Eds. John Cottingham, Robert Stoothoff, Dugald
Murdoc. Cambridge University Press.
p. 82. A.I. Oparin. 1994. [1924]. The Origin of Life. Reprinted in David Deamer, Gail
Fleischaker. Origins of Life: The Central Concepts. Boston: Jones and Bartlett.
p. 83. On gene silencing see Sergei N. Rodin and Arthur D. Riggs. Epigenetic Silencing May Aid
Evolution by Gene Duplication. #123. ISSOL 2002.
Anthony M. Poole, What is the Last Universal Common Ancestor (LUCA)?
http://www.actionbioscience.org/newfrontiers/poolearticle.html
Sherrington on his Recruitment Hypothesis:
Sherrington, Sir Charles. 1951[1937-8]. Man on His Nature. Gifford Lectures. Cambridge
University Press.
Scott Turner. 2002. The Extended Organism: The Physiology of Animal-Built Structures. Harvard
University Press.
p. 84. On collaborative autonomy:
Zann Gill. 2002. Webtank (think tank on the web) and the management of organizational
complexity. New England Complex Systems Institute. 4th International Conference on Complex
Systems (ICCS).
p. 85. Beyond metaphors for the origin of life are metaphors that characterize the problemsolving process of a community of scientists trying to understand the origin of life. Wills and
Bada use the building of the first transcontinental railroad in the United States as their metaphor
to describe how two communities of scientists work from opposite directions on the origin of life.
One easily visualizes a gang of workers building the railroad from east to west and another
building it from west to east. Those two efforts joined in 1869 northwest of Ogden, Utah where
they drove the golden spike to mark the railroad’s completion. Wills and Bada invoke this
railroad-building metaphor to clarify how scientists working “bottom up” to create a selfreplicating entity in the laboratory will meet those working “top down” from the genetic code to
analyze how first life appeared. They’ve simplified the origin of life problem to two lines of
effort that, when they collide, should align. But we need another metaphor to characterize an
emergent web of activity that complements linear process to account for emergence and
convergence, dynamics of multi-threaded problem-solving.
Wills, Christopher and Jeffrey Bada. 2000. The Spark of Life: Darwin and the Primeval Soup.
Cambridge, MA: Perseus Books.
Chapter 9. where did life begin?
86 – 97
p. 86. Quote:
Ward, Peter D. and Donald Brownlee. 2000. Rare Earth: Why Complex Life is Uncommon in the
Universe. NY: Springer-Verlag.
Our Sun is a G type star, as is Alpha Centauri. These are seen as likely stars for extrasolar planets
with life, and for SETI programs. A G star is yellowish, spectral type G, with a surface
temperature ranging from 5,000 to 5,800°C. Mass is 0.8 to 1.1 solar masses. G stars have spectra
with absorption lines of neutral and ionized metals, and some molecular absorption bands. The H
and K lines of ionized calcium are particularly strong. G-type giant stars, such as Capella, are
slightly cooler but more luminous, while G-type supergiants have a mass of 10 to 12 solar masses
and a luminosity of 10,000 to 300,000 times that of the Sun.
A.I. Oparin. 1994 [1924]. The Origin of Life. Reprinted in David Deamer, Gail Fleischaker.
Origins of Life: The Central Concepts. Boston: Jones and Bartlett.
J.B.S. Haldane. 1967 [1929]. The Origin of Life. first published in The Rationalist Annual. 1929.
Reprinted in J.D. Bernal. The Origin of Life. London: Weidenfeld & Nicolson. 242 – 249.
p. 87. On the Miller-Urey experiment see
202
Harold C. Urey.1952. On the early Chemical History of the Earth and the Origin of Life.
Proceedings of the National Academy of Sciences USA. 38. 351 – 363.
S.L. Miller. 1953. A production of amino acids under possible primitive earth conditions. Science
117: 528-529 and
Stanley L. Miller and Harold C. Urey. 1959. Organic Compound Synthesis on the Primitive
Earth. Science. 130. 245 – 251.
p. 88. Chemist Jeffrey Bada carried out experiments at Scripps Institution of Oceanography. In
contrast to Stanley Miller, he maintained that to current models of early Earth suggest an
atmosphere with carbon dioxide and nitrogen that would have created nitrites, destroying amino
acids as fast as they formed.
Kvenvolden, K., J. Lawless, K. Pering, E. Peterson, J. Flores, C. Ponnamperuma, I.R. Kaplan. C.
Moore. 1970. Evidence for Extraterrestrial Amino-acids and Hydrocarbons in the Murchison
Meteorite. Nature. 228. 923 – 926.
Speculation about the nature of Earth’s early atmosphere:
J. F. Kasting. 1993. “Earth’s early atmosphere.” Science 259:920-926 and
_______. 1997. “Habitable zones around low mass stars and the search for extraterrestrial life.”
Origins Life Evol. Biosphere. 27: 291 – 307.
p. 89. On extremophiles:
Christopher Wills and Jeffrey Bada. 2000. The Spark of Life: Darwin and the Primeval Soup.
Cambridge, MA: Perseus Books.
From a biochemical perspective:
Robert M. Hazen. 2005. gen•e•sis: The Scientific Quest for Life’s Origin. Washington, D.C.:
Joseph Henry Press.
From a philosophical perspective:
Iris Fry. 2000. The Emergence of Life on Earth. NJ: Rutgers University Press.
The Miller-Lazcano argument and hypothesis of a cold origin of life see Shin H. Miyakawa,
James Cleaves, and Stanley Miller. 2002. The Cold Origin of Life: Nucleic Acid Bases Produced
from Frozen HCN Solutions. #78. ISSOL 2002.
Lazcano, A. and S. L. Miller. 1994. “How long did it take for life to begin and evolve to
cyanobacteria?” J. Mol. Evol. 39:546 – 554.
Chyba, C. and C. Sagan. 1992. “Endogenous production, exogenous delivery and impact-shock
synthesis of organic molecules: an inventory for the origins of life," Nature. Vol. 355. 125 – 132.
_______. 1997. Science. May 27.
For the Chyba – Sagan argument and their green house effect rationale for their assumption about
a warm temperature for early Earth, see their 1997 article in Science. May 27.
p. 90. Darwin’s Letter to Hooker (1871) is in 1888. Ed. Francis Darwin. The Life and Letters of
Charles Darwin. 2. NY: D. Appleton and Co. reprinted in
1985 [1871]. Correspondence of Charles Darwin. Eds. Frederick Burkhardt and Sydney Smith.
Cambridge University Press.
See references for Oparin and Haldane, p.xxx.
See references for Cairns-Smith, p. xxx
See references for Wächterhäuser p. xxx.
Christian de Duve comments on the unstructured soup in “The Beginnings of Life on Earth.” The
American Scientist. Sept. – Oct. 1995. He assumes that life arose on Earth because there’s no
solid evidence to assume otherwise. How life originated remains the same problem either way, so
. . . . why not?: “Even if life came from elsewhere, we would still have to explain how it started.
So we might as well assume that life started on Earth.”
Others disagree. Because we lack solid evidence that life originated on Earth, they wonder
whether some other context might have been more suited for the origin of life.
p. 91. David, Deamer. 1997. “The first living systems: A bioenergetic perspective.” Microbiology
and Molecular Biology Review. 61(2): 239 – 261.
203
On the fresh water scenario:
P-A. Monnard, C.L. Apel, A. Kanavarioti, D.W. Deamer, 2002. Influence of ionic inorganic
solutes on self-assembly and polymerization processes related to early forms of life: Implications
for a prebiotic aqueous medium, Astrobiology. 2. 139 – 152.
A.I. Oparin. 1964[1924]. The Chemical Origin of Life. Trans. Anne Synge. Fort Lauderdale, FL:
Thomas Books.
p. 92. Peter D. Ward and Donald Brownlee. 2000. Rare Earth: Why Complex Life is Uncommon
in the Universe. NY: Springer-Verlag.
On the planetary habitable zone:
Christopher F. Chyba and Kevin P. Hand. 2005. Astrobiology: The Study of the Living Universe.
Annual Review of Astronomy and Astrophysics. 43:31 – 74.
George W. Wetherill. 1995. How special is Jupiter? Nature. 373: 470.
S. J. Kortenkamp and G. W. Wetherill, 2000. Terrestrial planet and asteroid formation in the
presence of giant planets. I. Relative velocities of planetesimals subject to Jupiter and Saturn
perturbations, Icarus 143: 60 – 73.
p. 93. Peter D. Ward and Donald Brownlee. 2000. Rare Earth: Why Complex Life is Uncommon
in the Universe. NY: Springer-Verlag.
p. 94. On systems of fluxes: David Deamer. 1997. “The first living systems: A bio-energetic
perspective.” Microbiology and Molecular Biology Review. 61(2): 239 – 261.
On fitness landscapes:
Stuart Kauffman, At Home in the Universe: The Search for the Laws of Self-Organization and
Complexity. N. Y.: Oxford University Press. 1995.
p. 95. On random Boolean networks:
Stuart Kauffman. 1969. “Metabolic stability and epigenesis in randomly constructed genetic
nets.” Journal of Theoretical Biology. 22:437– 467.
_______. 1991. “Antichaos and Adaptation.” Scientific American. August. 78 – 84.
_______. 1993. The Origins of Order: Self-Organization and Selection in Evolution. N.Y.:
Oxford University Press.
On concentrating organics:
J.D. Bernal.1951. The Physical Basis for Life. London: Routledge and Kegan Paul.and1967. The
Origin of Life. N.Y.: World Publishing Company.
Ferris xxx
p. 96. Stuart Kauffman. 2000. Investigations. Oxford University Press.
Deamer, David and Gail L. Barchfield. 1982. Encapsulation of Macromolecules by Lipid
Vesicles under Simulated Prebiotic Conditions. Journal of Molecular Evolution. 18. 203 – 206.
N.Y.: Springer-Verlag.
Deamer, David and Gail Fleischaker. 1994. Origins of Life: The Central Concepts. Boston: Jones
and Bartlett.
A.I. Oparin. 1957 [1936]. The Origin of Life on the Earth. Edinbourgh: Oliver & Boyd and 1964
[1924]. The Chemical Origin of Life. Trans. Anne Synge. Fort Lauderdale, FL: Thomas Books.
Hanczyc, Martin M., Shelly M. Fujikawa, and Jack W. Szostak. 2003. “Experimental Models of
Primitive Cellular Compartments: Encapsulation, Growth, and Division.” Science. 302. October
24. 618 – 621.
Bernstein, Max P., Scott A. Sandford and Louis J. Allamandola. 1999. “Life’s Far-Flung Raw
Materials,” Scientific American. July.
Hanczyc, Martin M., Shelly M. Fujikawa, and Jack W. Szostak. 2003. “Experimental Models of
Primitive Cellular Compartments: Encapsulation, Growth, and Division.” Science. 302. October
24. 618 – 621.
Hanczyc, Martin M. and Jack W. Szostak. 2004. Replicating vesicles as models of primitive cell
growth and division. Current Opinion in Chemical Biology. 8: 660 – 664.
Szostak, J. W., D. P. Bartel, and P.L. Luisi. 2001. “Synthesizing Life.” Nature. 409. 387 – 390.
204
Bernstein, Max P., Scott A. Sandford and Louis J. Allamandola. 1999, “Life’s Far-Flung Raw
Materials,” Scientific American. July.
Chapter 10. conflicting hypotheses: which came first?
98 – 113
p. 98. Quote: Graham Cairns-Smith. 1985. Seven Clues to the Origin of Life. Cambridge
University Press. p. 2.
Biochemists search for the components of nucleic acids: sugars (and their precursors), the
phosphate backbone, and nucleobases. Others study the pathways of fatty acids. Some
hypothesize that life started with carbohydrate chemistry, leading to an RNA scenario for its
origin.
p. 99. On Leslie Orgel and the RNA World or “naked gene” hypothesis:
Stanley L. Miller and Leslie E. Orgel. 1974. The Origins of Life on the Earth. NY: Prentice-Hall.
Stephen Day. 1991. The first gene on Earth: How did life begin? Revolutionary discoveries about
the genetic material RNA are helping molecular biologists to piece together replicas of the first
genes. November 9. New Scientist.
D. H. Lee, J. R. Cranja, J. A. Martinez, K. Severin, and M.R. Ghadiri. 1996. “A self-replicating
peptide.” Nature. 382:525 – 528.
Francis Crick.1981. Life Itself: Its Order and Nature. N.Y.: Simon and Schuster.
Stuart Kauffman. 2000. Investigations. Oxford University Press.
p. 100. on RNA “choosing”: In an interview I reminded de Duve that he’d said in a public forum
that “every facet of life depends on molecules that recognize each other” (de Duve 1995a). Use of
the term ‘recognize’ suggests that pattern recognition may be a more basic life skill than
metabolism. When de Duve describes how molecules ‘recognize’ each other, he uses the word
recognition in the sense that a lock ‘recognizes’ a key, by fitting, a rudimentary form of
‘recognition’ based upon morphology.
de Duve, Christian 1995. “The Beginnings of Life on Earth” in The American Scientist. Sept. –
Oct. Those who share de Duve’s hypothesis that metabolism governed by constrained
contingency was the basic process for the origin of life conduct a range of experiments to explore
what kinds of energetic reactions could have created life. Theorists who start by identifying an
energy source must still decide which basic process could have originated life using that energy
source and determine what principles govern that process.
D. Lee, K. Severin, Y. Yokobayashi, and M.R. Ghadiri. 1997. “Emergence of symbiosis in
peptide self-replication through a hypercyclic network.” Nature 390:591 – 594.
p. 101. Harry Noller, Professor of Molecular Biology at UC Santa Cruz, described his work in
Science, Sept. 24, 1999. Ribosomes can synthesize proteins in the cell by using genetic
information to assemble amino acids. Using the Macromolecular Crystallography Facility (MCF)
at the Advanced Light Source (ALS), Noller’s research team collaborated with the Department of
Energy’s Lawrence Berkeley National Laboratory produced the first high-resolution images of a
complete ribosome complex. The crystallographic images showed ribosomal structure. ALS at
Berkeley Lab created an image of the crystal structure of the 70S ribosome of the bacterium
Thermus thermophilus at a resolution of 7.8 angstroms (an angstrom is a ten billionth of a meter).
Although smaller than most viruses, a bacterial ribosome is a very large molecular complex,
consisting of three RNA molecules and more than 50 protein molecules, with a mass of some 2.5
million daltons.
Cate, Jamie H., Marat M. Yusupov, Gulnara Zh. Yusupova, Thomas N. Earnest, and Harry F.
Noller. 1999. “X-ray Crystal Structures of 70S Ribosome Functional Complexes.” Science. Vol
285. Issue 5436. September 24. 2095 – 2104.
p. 102. On how ribozyme-like proto-ribozymes, might be an evolutionary link between presentday ribozymes and ribosomes see Ahsen, U von, J Davies, R Schroeder. 1991. Antibiotic
inhibition of group I ribozyme function. Nature 353: 368 - 370 (26 September).
On the Altman Cech discovery see
205
Grabowski, P. J., A. J. Zaug, & T. R. Cech. 1981. The intervening sequence of the ribosomal
RNA precursor is converted to a circular RNA in isolated nuclei of tetrahymena. Cell. February.
23. 2. 467 – 476.
C Guerrier-Takada, Gardiner, K., Marsh, T., Pace, N. & Altman, S. 1983. Cell. 35: 849 – 57.
C Guerrier-Takada, & Altman, S. 1984. Science. 223:285 –286.
p. 103. On the idea that RNA was too complex and the search for a simpler precursor:
Piet Herdewijn. Private correspondence. 2003. Herdewijn argues against any hypothesis that
proteins and DNA suddenly emerged from RNA and proposes a role for peptides.
_______. 2001. “TNA as a Potential Alternative to Natural Nucleic Acids.” Angew. Chem. Int.
Ed. 40. 12. 2249 – 2251.
_______. 1998. “Peptides by activation of amino acids with CO on (Ni, Fe)S surfaces:
Implications for the origin of life.” Science 281: 626 – 627.
The search for simpler systems than RNA, such as peptides:
Albert Eschenmoser, looking for a simpler form than RNA for first life, proposed TNA, an
isomer of RNA, as a possible template to make RNA (and vice versa). TNA is a simpler,
functionally poorer nucleic acid, but one that “speaks” the same “base-pairing language” as RNA
and DNA. Made from a 4-carbon sugar, rather than a 5-carbon sugar, TNA demonstrates the
possibility of simpler precursors to RNA, though evidence is lacking to prove what those
precursors actually were. See Eschenmoser, A. 1994. “Chemistry of potentially prebiological
natural products.” Origins Life Evol. Biosphere. 24:389 – 423.
N.E. Blair, and W.A. Bonner. 1981. A model for the enantiomeric enrichment of polypeptides on
the primitive earth. Orig. Life. 11(4):331-335.On how ribozyme-like proto-ribozymes, might be
an evolutionary link between present-day ribozymes and ribosomes see Ahsen, U von, J Davies,
R Schroeder. 1991. Antibiotic inhibition of group I ribozyme function. Nature 353: 368 - 370 (26
September).
A. Pohorille and M.A. Wilson. 1993. Molecular dynamics studies of simple membrane — Water
interfaces: Structure and functions in the beginnings of cellular life.
Journal of the Origins
of Life and Evolution of Biospheres. Volume 25, Numbers 1-3 / June, 1995.
_______. Interaction of a model peptide with a water-bilayer system. in Structure and Reactivity
in Aqueous Solution: Characterization of Chemical and Biological Systems, Cramer, C.; Truhlar,
D., Eds., ACS Symposium Series No. 568. ACS, Washington D.C. 1994. 11:395.
Pohorille and M.A. Wilson. 1995. Origins of Life and Evolution of Biosphere 25. 21.p. 91 ff.
p. 104. Graham Cairns-Smith Interview. June 2002. Cairns-Smith experimented with his
hypothesis of templating for information transmission using various mica-type and mixed layer
clays. He concluded that, unlike organic polymers, inorganic crystals offer potential for a variety
of primitive, self-organizing genetic materials before a Jack-of-all-Trades protein could be
perfected. A. G. Cairns-Smith and G. L. Walker. 1974. “Primitive Metabolism.” Biosystems. 5.
173 – 186.
Graham Cairns-Smith. 1988. The chemistry of materials for artificial Darwinian systems.
International Revs. Phys. Chem. 7. 209 – 250.
Graham Cairns-Smith. 2005. “Sketches for a Mineral Genetic Material.” Elements. 1. 157 – 161.
p. 105. A.G. Cairns-Smith. 1966. The origin of life and the nature of the primitive gene. Journal
of Theoretical Biology. 10. 53–88.
Graham Cairns-Smith. 1982. Genetic Takeover. Cambridge University Press.
p. 106. The Sherlock Holmes metaphor is from Graham Cairns-Smith. 1985. Seven Clues to the
Origin of Life. Cambridge University Press.
p. 107. Bernal, J.D. 1951. The Physical Basis for Life. London: Routledge and Kegan Paul and
1967. The Origin of Life. N.Y.: World Publishing Company.
The classic study of the mathematics of biological form that inspired JD Bernal:
206
D’Arcy Thompson. On Growth and Form, first published in 1917, revised by the author for its
1942 publication by Cambridge University Press. Reissued (abridged) 1971 by Dover with a
foreword by Stephen Jay Gould.
JBS Haldane. 1949. What is Life? London: Alcuin Press. 58-62.
Also Haldane. 1986. Edited by John Maynard Smith. On Being the Right Size and other Essays.
“The Origin of Life.” Oxford University Press. 101 – 112.
Ertem, G. and J.P. Ferris. 1996. “Synthesis of RNA Oligomers on heterogeneous templates.”
Nature 379:238 – 240.
James P. Ferris, Chun-Hsien Huang, and William J. Hagan Jr. 1988. Montmorillonite: A
Multifunctional Mineral Catalyst for the Prebiological Formation of Phosphate Esters. Origins of
Life and Evolution of the Biosphere. 18. 121-133.
p. 108..Günter Wächterhäuser 1987. Microbiol. Rev. 51. 221.
_______.1988. Pyrite formation, the first energy source for life: A hypothesis. Systematics and
Applied Microbiology. 10:207 – 210.
_______. 1992. Groundwork for an evolutionary biochemistry: the iron-sulfur world.” Prog.
Biophys, Molec. Biol. 58:85 – 201.
p. 109. Freeman Dyson’s Garbage Bag World Hypothesis:
Freeman Dyson. 2000. “Gravity is Cool, or, Why our Universe is Hospitable to Life.”
Oppenheimer Lecture. University of California, Berkeley, California, March 9. Here Dyson
summarized his “Garbage Bag World” concept. Dysons’s dirty bag would contain a mixture of
many compounds, MCAs with different chain lengths, different ionizable headgroups, short
peptides, aromatic hydrocarbons etc.
See also his 1985. Origins of Life. Cambridge: Cambridge University Press.
p. 110. Graham Cairns-Smith. 1988. The chemistry of materials for artificial Darwinian systems.
International Revs. Phys. Chem. 7. 209 – 250.
J.P. Ferris and G. Ertem. 1993. Journal American Chemical Society. 115. 12270 – 12275.
G. Ertem and J.P. Ferris. 1996. “Synthesis of RNA Oligomers on heterogeneous templates.”
Deamer. David, Jason P. Dworkin, Scott A. Sandford, Max P. Bernstein, and Louis J.
Allamandola. 2003. The First Cell Membranes. Astrobiology 2. 4. © Mary Ann Liebert, Inc.
p. 111. Louis Lerman. 1993. Bubble Genesis of Life. Science. July 9.
http://www.lbl.gov/Science-Articles/Archive/bubble-genesis-of-life.html
p. 112. On Stentor: Harold J. Morowitz. 2002. The Emergence of Everything. Oxford University
Press. p. 102 – 3.
p. 113. I use the terms discrimination, filtering, accepting and integrating, and choice as
“continua words” to describe behavior that lies on continua between mechanism and
consciousness. In Clues in Darwin’s Dilemma in the chapter on “Tolerance: Precisely Using
Imprecision” I argue that distinguishing between analog and digital modes of thinking is a
prerequisite to understand why the line between non-life and life is blurry, like the line between
non-conscious and consciousness. Stretching terms traditionally used to describe consciousness to
describe related mechanistic activity emphasizes the continuity between non-life and life.
Chapter 11. how did life begin?
114 – 131
p. 114. Quote: Charles Darwin. Origin of Species. Chapter XV. “Recapitulation and
Conclusion.”
p. 115. On the limitations of analogies:
Rapoport, Anatol. 1991. Ideological commitments in evolutionary theories. Journal of Social
Issues. Issues in Evolutionary Psychology. 47. 3: 83 – 100. Fall.
For the first perspective, the path, see references for p. xxx
For the second perspective, the frame, see references for p. xxx
For the third perspective, the threshold, see references for p. xxx
p. 116. See the chapter on LUCA for an example of the path, frame, and threshold.
207
For the first strand, delivery of organics from space, see references for p. xxx
For the second strand, laboratory synthesis, see references for p. xxx
For the third strand, analysis of Murchison and other meteorites, see references for p. xxx
p. 117. I am indebted to the following scientists in the Astrochemistry Laboratory for interviews
that helped me to develop a scenario format for this section: Lou Allamandola, Founder/ Director,
Charles Apel, Max Bernstein, Scott Sandford.
Sandford thinks that we may be wrong to look for the origin of life as a sudden tipping point,
threshold, or “turning on the light.” Many agree that the blurry boundary between non-life and
life is reflected in how life gradually came to be alive.
For papers on this work see Louis J. Allamandola and Douglas M. Hudgins. “From Interstellar
Polycyclic Aromatic Hydrocarbons and Ice to Astrobiology.” 2003. Ed. V. Pirronello et al. Solid
State Astrochemistry. Netherlands: Kluwer Academic Publishers. 251 – 316. 2003.
Max P. Bernstein, Scott A. Sandford and Louis J. Allamandola. 1999, “Life’s Far-Flung Raw
Materials,” Scientific American. July.
M. P. Bernstein, S. A. Sandford, L. J Allamandola, J. S. Gillette, S. J. Clemett, & R. N. Zare.
1999. “UV Irradiation of Polycyclic Aromatic Hydrocarbons in Ices: Production of Alcohols,
Quinones, and Ethers.” Science. 283. 1135-1138.
Max P. Bernstein, Jason P. Dworkin, Scott A. Sandford, George W. Cooper and Louis J.
Allamandola. 2002. Racemic Amino Acids from the ultraviolet photolysis of interstellar ice
analogues, Nature. 416. Letters. 28 March.
J.P. Dworkin, D. W. Deamer, S. A. Sandford, L. J. Allamandola. 1998. “Self-Assembling
Amphiphilic Molecules: Synthesis in Simulated Interstellar/Precometary Ices.” Proceedings of
the National Academy of Science, USA. 98: 815-819.
S. A. Sandford, M. P. Bernstein, & J. P. Dworkin, 2001. Assessment of the Interstellar Processes
Leading to Deuterium Enrichment in Meteoritic Organics Meteoritics and Planetary Science. 36.
1117–1133.
p. 118. In the 1940s ices were ignored, except by a handful of astronomers (van de Hulst and Jan
Oort among them), who postulated in the 1940s that the atoms known in space would freeze on
very cold dust grains and form ice mantles, but few listened. Mayo Greenberg joined van de
Hulst, an expert on light scattering, to study the size and composition of dust particles.
Scott Sandford describes two extreme views in the debate about the delivery of organics to Earth
from space. One view is that chemical assembly of organic molecules in space served only to get
raw materials into a form that could reside on a grain for delivery to Earth. After stuff falls out of
the sky, having survived its trip to Earth, this view says it would be completely destroyed —
turned back into carbon, hydrogen, and nitrogen. Then subsequent indigenous processes on Earth
would reassemble these raw materials into life. But Occam’s Razor (preference for the simplest
explanation) suggests that this scenario of assembly, disassembly, and reassembly is too
complicated.
The other extreme view is simpler: researchers at NASA have shown that chemical organization
occurs constantly in space. Analyses of meteorites confirm that they contain organic materials
successfully delivered from space to Earth, which could continue to evolve on Earth.
Certain chemicals may not form vesicles until a stabilizing chemical is added. Vesicles that can
recruit chemicals to enable themselves to remain stable under a wide variety of conditions, or to
allow them to incorporate new amphiphiles from other vesicles, win the evolutionary game and
start to dominate.
The NASA Ames Astrochemistry Laboratory radiated analogs of interstellar ice: The residue
produced was analyzed by infrared spectroscopy and gas chromatography and mass spectrometry
(GC-MS) to determine what kindd of molecules were produced. Before hydrolysis, n-formyl
glycine, cycloserine and glycerol were found in the organic residue. After hydrolysis the
experimenters detected glycine, alanine, serine, urea and ethanolamine. Careful experimental
procedures determined that these amino acids formed as individual species, which were not
208
degradation products of macromolecules. Carbonaceous meteorites have abundant silicates and
organic compounds, such as amino and carbo-oxylic acids, hydrous acids, purine, pyramidine,
and sugar derivatives. Experimenters concluded that amino acids could have formed in the
interstellar medium (ISM) and been delivered by meteorites.
Bernstein, Max P., Scott A. Sandford and Louis J. Allamandola. 1999, “Life’s Far-Flung Raw
Materials,” Scientific American. July.
Bernstein, M. P., S. A. Sandford, L. J Allamandola, J. S. Gillette, S. J. Clemett, & R. N. Zare.
1999. “UV Irradiation of Polycyclic Aromatic Hydrocarbons in Ices: Production of Alcohols,
Quinones, and Ethers.” Science. 283. 1135 – 1138.
Bernstein, Max P., Jason P. Dworkin, Scott A. Sandford, George W. Cooper and Louis J.
Allamandola. 2002. Racemic Amino Acids from the ultraviolet photolysis of interstellar ice
analogues, Nature. 416. Letters. 28 March.
Wills and Bada’s analysis of meteorites confirmed that they could have delivered large quantities
of organics to early Earth.
p. 119. Harry Kroto, Robert Curl, and Richard Smalley, working with students James Heath,
Yuan Liu, and Sean O’Brien, discovered of C60 in 1985, and soon after identified the class of
compounds that Kroto called buckminsterfullerenes, for which Kroto, Curl, and Smalley were
awarded the Nobel Prize in Chemistry (1996).
Kroto, Harold, Richard Smalley, and Robert Curl. 1985. C60: Buckminsterfullerene. Nature. 14
November.
Allamandola, Louis J. and Douglas M. Hudgins. “From Interstellar Polycyclic Aromatic
Hydrocarbons and Ice to Astrobiology.” 2003. Ed. V. Pirronello et al. Solid State Astrochemistry.
Netherlands: Kluwer Academic Publishers. 251 – 316. 2003. Global Spec. 9/17/07.
http://materials.globalspec.com/Industrial-Directory/Buckminster_Fullerene
Kroto, H.W., J.R. Heath, S.C. O'Brien, R.F. Curl, R.E. Smalley. 1985. “C60:
Buckminsterfullerene.” Nature. 318. 162.
Kratschmer, W., L.D. Lamb, K. Fostiropoulos, D.R. Huffman. 1990. "Solid C60: A new form of
Carbon." Nature. 347. 354.
Fuller, R. Buckminster and Applewhite, E. J. 1975. Synergetics. New York: Macmillan.
p. 120. P. Ehrenfreund, M.P. Bernstein, J. P. Dworkin, S. A. Sandford, L. J. Allamandola. 2000.
“The photostability of amino acids in space” The Astrophysical Journal.
Pascale Ehrenfreund and Steven B. Charnley. Organic Molecules in the Interstellar Medium,
Comets, and Meteorites: A Voyage from Dark Clouds to Early Earth. 2000. Annual Review of
Astronomy & Astrophysics. 38. 427-483.
p. 121. Deamer, David and Gail L. Barchfield. 1982. Encapsulation of Macromolecules by Lipid
Vesicles under Simulated Prebiotic Conditions. Journal of Molecular Evolution. 18. 203 – 206.
N.Y.: Springer-Verlag.
For a good survey of the analysis of meteorites:
Christopher Wills and Jeffrey Bada. The Spark of Life: Darwin and the Primeval Soup.
Cambridge, MA: Perseus Books. 2000.
Apel, Charles L. and David W. Deamer, Michael N. Mautner. 2002. Self-assembled vesicles of
monocarboxylic acids and alcohols: conditions for stability and for the encapsulation of
biopolymers. Biochimica et Biophysica Acta. 1559. 1 – 9.
Dworkin, J.P., D. W. Deamer, S. A. Sandford, L. J. Allamandola. 1998. “Self-Assembling
Amphiphilic Molecules: Synthesis in Simulated Interstellar/Precometary Ices.” Proceedings of
the National Academy of Science, USA. 98. 815 – 819.
David Deamer, Jason P. Dworkin, Scott A. Sandford, Max P. Bernstein, and Louis J.
Allamandola. 2002. The First Cell Membranes. Astrobiology. 2. 4. © Mary Ann Liebert Inc. p.
371.
209
Monnard, P-A, C.L Apel, A. Kanavarioti, D.W. Deamer 2002. Influence of ionic inorganic
solutes on self-assembly and polymerization processes related to early forms of life: Implications
for a prebiotic aqueous medium, Astrobiology. 2. 139-152.
Bernstein, Max P., Jason P. Dworkin, Scott A. Sandford, George W. Cooper and Louis J.
Allamandola. 2002. Racemic Amino Acids from the ultraviolet photolysis of interstellar ice
analogues, Nature. 416. Letters. 28 March.
Dworkin, J.P., D. W. Deamer, S. A. Sandford, L. J. Allamandola. 1998. “Self-Assembling
Amphiphilic Molecules: Synthesis in Simulated Interstellar/Precometary Ices.” Proceedings of
the National Academy of Science, USA. 98. 815 – 819.
David Deamer, Jason P. Dworkin, Scott A. Sandford, Max P. Bernstein, and Louis J.
Allamandola. 2002. The First Cell Membranes. Astrobiology. 2. 4. © Mary Ann Liebert Inc. 371.
On Luisi’s experiments:
Szostak, J. W., D. P. Bartel, and P.L. Luisi. 2001. “Synthesizing Life.” Nature. 409:387 – 390.
Luisi, Pier Luigi. 2006. The Emergence of Life. From Chemical Origins to Synthetic Biology.
Cambridge University Press, Cambridge.
Bachmann, P.A., Luisi, P.L., and Lang, J. 1992. Autocatalytic self-replicating micelles as models
for prebiotic structures. Nature. 357:57-59.
Morowitz, Harold J. 1992. The Beginnings of Cellular Life. New Haven, CT: Yale University Press.
p. 122. Gruber, Howard E. 1974. Darwin on Man: A Psychological Study of Scientific Creativity.
N.Y.: E.P. Dutton.
Woese, C.R., 1979. “A proposal concerning the origin of life on the planet Earth.” Journal of
Molecular Evolution. 13. 95 – 101.
Woese, C.R. 1987. “Bacterial Evolution.” Microbiology Reviews. 51. 221 – 271.
Carl Woese. 1967. The Genetic Code – The Molecular Basis for Genetic Expression. N.Y.:
Harper and Row.
Woese, C.R., 1979. A proposal concerning the origin of life on the planet Earth: Journal of
Molecular Evolution. 13:95 – 101.
Hargreaves, W. R. and D. W. Deamer. 1978. “Liposomes from ionic, single-chain amphiphiles.”
Biochemistry. 17. 3759 – 3768.
p. 123. Tanford’s hypothesis:
Charles Tanford. 1978. The hydrophobic effect and the organization of living matter. Science.
4345:1012 – 1018.
p. 124. David Deamer, Jason P. Dworkin, Scott A. Sandford, Max P. Bernstein, and Louis J.
Allamandola. 2002. The First Cell Membranes. Astrobiology. 2. 4. © Mary Ann Liebert Inc. 371.
Hanczyc, Martin M., Shelly M. Fujikawa, and Jack W. Szostak. 2003. “Experimental Models of
Primitive Cellular Compartments: Encapsulation, Growth, and Division.” Science. 302. October
24. 618 – 621.
Luisi, Pier Luigi. 2006. The Emergence of Life. From Chemical Origins to Synthetic Biology.
Cambridge University Press, Cambridge.
p. 125. Morowitz, Harold J. 1992. The Beginnings of Cellular Life. New Haven, CT: Yale
University Press.
Apel, Charles L. and David W. Deamer, Michael N. Mautner. 2002. Self-assembled vesicles of
monocarboxylic acids and alcohols: conditions for stability and for the encapsulation of
biopolymers. Biochimica et Biophysica Acta. 1559. 1 – 9.
Deamer, David. 1997. “The first living systems: A bioenergetic perspective.” Microbiology and
Molecular Biology Review. 61(2): 239-261.
Deamer’s hypothesis of liposome opening and closing raises another question: What about
energy? Their proposed scenario: some of those primitive amphiphiles might have been pigment
molecules that could capture light energy in the form of electrochemical ion gradients and use it
to transform other precursor molecules into amphiphiles. In this early photosynthetic growth
process the protocell interior was a chemical reactor; energy was supplied as high energy
210
phosphate bonds. A logical scenario is proposed without specifying a particular chemistry:
Energy input from photons excites a chromophore. An excited chromophore, plus some type of
converter, produces electrochemically stored energy. That energy, plus some other type of
converter, and a low energy compound, produces a high-energy compound. Finally the high
energy compounds, plus membrane precursors, produce membrane amphiphiles and reaction
products.
Harold J. Morowitz. 1985. Mayonnaise and the Origins of Life: Thoughts of Minds and
Molecules. N.Y.: Charles Scribner’s Sons. 29 – 30.
Dworkin, P., 2001. Assessment of the Interstellar Processes Leading to Deuterium Enrichment in
Meteoritic Organics. Meteoritics and Planetary Science. 36. 1117–1133.
Dworkin, J.P., D. W. Deamer, S. A. Sandford, L. J. Allamandola. 1998. “Self-Assembling
Amphiphilic Molecules: Synthesis in Simulated Interstellar/Precometary Ices.” Proceedings of
the National Academy of Science, USA. 98. 815 – 819.
Summary of the research on how membrane vesicles composed of fatty acids can be made to
grow and divide under laboratory conditions, and provide a model system relevant to the
emergence of cellular life:
Irene A. Chen and Jack W. Szostak. 2004. A Kinetic Study of the Growth of Fatty Acid Vesicles.
Biophysical Journal. 87:988–998. The Biophysical Society. This article categorizes and cites
other major research in this field.
p. 126. Sherrington, Sir Charles. 1951[1937-8]. Man on His Nature. Gifford Lectures. Cambridge
University Press.
Deamer, David and Gail L. Barchfield. 1982. Encapsulation of Macromolecules by Lipid
Vesicles under Simulated Prebiotic Conditions. Journal of Molecular Evolution. 18. 203 – 206.
N.Y.: Springer-Verlag.
Apel, Charles L. and David W. Deamer, Michael N. Mautner. 2002. Self-assembled vesicles of
monocarboxylic acids and alcohols: conditions for stability and for the encapsulation of
biopolymers. Biochimica et Biophysica Acta. 1559. 1 – 9.
p. 127. Chen, Irene A. and Jack W. Szostak. 2004. A Kinetic Study of the Growth of Fatty Acid
Vesicles. Biophysical Journal. 87. 988 – 998. The Biophysical Society.
Hanczyc, Martin M. and Jack W. Szostak. 2004. “Replicating vesicles as models of primitive cell
growth and division.” Current Opinion in Chemical Biology. 8. 660 – 664.
p. 128. Hanczyc, Martin M., Shelly M. Fujikawa, and Jack W. Szostak. 2003. “Experimental
Models of Primitive Cellular Compartments: Encapsulation, Growth, and Division.” Science.
302. October 24. 618 – 621.
Chen, Irene A. Richard W. Roberts, and Jack W. Szostak. 2004. “The Emergence of Competition
Between Model Protocells. Science. 305. September 3. 1474 – 1476.
The principle is the same for vesicles, clay, and all of biological evolution: if a set of polymers or
membranes or clays develops an advantage, it takes over. If there are different ways to make
amphiphiles, or different ways to incorporate compounds into vesicles, or different ways to split
vesicles when they get to a certain size, the most effective way wins out. And if, in the process,
one is able to rob products from another, it gains advantage.
Scientists are still gathering evidence to confirm the Membrane World Hypothesis. Fossil
imprints of round, bubblish forms, which might have been vesicles, have been found on
meteorites. They must have been made when the meteorites were wet. Wherever there was water
in space, the vesicle-forming process could have occurred, producing fossil imprints.
p. 129. Popper, Karl Raimond. [1935] 1959. The Logic of Scientific Discovery. London:
Hutchinson.
P ART III.
W HAT LIFE’S O RIGINS IMPLY
p. 132. Quote: E. O. Wilson. 1998. Consilience. NY: Random House. Vintage Books. xxx
Harold J. Morowitz. 2002. The Emergence of Everything. Oxford University Press. p. 8 – 9.
132
211
On extremophiles:
Christopher Wills and Jeffrey Bada. 2000. The Spark of Life: Darwin and the Primeval Soup.
Cambridge, MA: Perseus Books.
From a biochemical perspective:
Robert M. Hazen. 2005. gen•e•sis: The Scientific Quest for Life’s Origin. Washington, D.C.:
Joseph Henry Press.
From a philosophical perspective:
Iris Fry. 2000. The Emergence of Life on Earth. NJ: Rutgers University Press.
Chapter 12. when scenarios reveal hypotheses
133 – 142
p. 133. Quote:
Robert Rosen. 1998. Essays on Life Itself. Columbia University Press. xxx
Heinz von Foerster. [1973] 1984. “On Constructing a Reality.” Address given on April 17, 1973
to the Fourth International Environmental Design Research Association Conference at the
College of Architecture, Virginia Polytechnic Institute, Blacksburg, VA. Discussed in
Zann Gill. “Origin of Life: Case Studies of Hypothesis Construction.” # 51. ISSOL 2002.
Paul Watzlawick. 1984. The Invented Reality. N.Y.: W.W. Norton Company.
p. 134. History of Dmitri Mendeleev’s Periodic Table:
Andrea Woody and Clark Glymour. 2000. “Autonomy and Anti-reductionism: Missing Elements,
What Might Philosophers of Science Discover in Chemistry? in Of Minds and Molecules: New
Philosophical Perspectives on Chemistry. Ed. Nalini Bhushan and Stuart Rosenfeld. Oxford
University Press and J.W. von. Spronsen. 1969.
The Periodic Table of Elements: A History of the First Hundred Years. Amsterdam: Elsevier.
F.P.Venable.1896. The Development of the Periodic Law. Easton, PA: Chemical Publishing.
p. 135. Principles of problem-solving: harnessing uncertainty, collaborative autonomy, avoiding
choke points, overlapping tolerance windows, forming criteria to accept/ reject interim results. On
applying evolutionary principles to Collaborative Problem-Solving Environments (CPSEs), see
Gill, Zann. December 1999. A Design Method Using Darwinian Principles for Collaborative
Problem-Solving Environments (CPSEs), CSCL99 (Computer-Supported Cooperative Learning),
Stanford University.
_______. 2001. Webtank Design: intranet support for collaborative problem-solving; HCI
International 2001; published in Systems, Social, and Internationalization: Design Aspects of
Human Computer Interaction vol 2. edited by Michael Smith and Gavriel Salvendy. N.J.:
Lawrence Earlbaum Assoc. 2001. p. 292-6.
_______. 2002. Designing a Think Tank to Study Design paper #4941 AIAA Space Architecture
Symposium. Houston, Texas. Section: Design Analysis, Methods, & Theory for Space
Architecture.
On Wallin’s proposal that the eukaryotic cell might be a colony of microbes.
Fausto-Sterling, A. 1993. Is Nature Really Red in Tooth and Claw? Discover 14: 24-27.
Endosymbiosis:
Proceedings of the National Academy of Sciences (PNAS). vol. 97. no. 13. June 20. 6954 – 6959.
Lynn Margulis 2002. Acquiring Genomes: A Theory of the Origins of Species. N.Y.: Basic
Books.
p. 136. Margulis, Lynn. 1981. Symbiosis and Cell Evolution. First Edition. San Francisco:
Freeman. For her description of the community evolving into organelles and description of
spirochetes, see the Second edition. 1993.
Lynn Margulis. [Sagan, Lynn]. 1967, “On the origin of mitosing cells.” J. Theoretical Biology
14(3):255 – 74.Lynn Margulis, Michael F. Dolan, and Ricardo Guerrero. 2000. The chimeric
eukaryote: Origin of the nucleus from the karyomastigont in amitochondriate protists.
p. 137. M. W. Gray and W. F. Doolittle. 1982. Has the endosymbiont hypothesis been proven?
Microbiology Review. March. 46(1): 1–42.
212
Lynn Margulis. 1975. Symbiotic theory of the origin of eukaryotic organelles: criteria for proof.
Symp. Soc. Exp. Biol. 29:21-37.
For an account of how the symbiotic origins of chloroplasts and mitochondria were dismissed by
the scientific community:
Christopher Wills and Jeffrey Bada. 2000. The Spark of Life: Darwin and the Primeval Soup.
Cambridge, MA: Perseus Books. 194.
p. 138. Poole AM. and Penny D. 2007. Evaluating hypotheses for the origin of eukaryotes.
Bioessays 29 (1): 74-84.
On the Hydrogen Hypothesis:
William Martin and Miklós Müller. 1998. The hydrogen hypothesis for the first eukaryote
Nature 392. March 5. 6671: 37-41.
Lynn Margulis. 2002. Acquiring Genomes: A Theory of the Origins of Species. N.Y.: Basic
Books.
p. 139. On John Cairns’ experiments:
Cairns, J., J. Overbaugh, and S. Miller. 1988. The Origin of Mutants. Nature. 335:142 – 145.
Kirschner, Marc W. and John C. Gerhart. 2005. The Plausibility of Life. New Haven: Yale
University Press. 27
J. P. Gogarten, W. F. Doolittle, and J. G. Lawrence. 2002. Prokaryotic Evolution in Light of Gene
Transfer. Molecular Biology and Evolution. 19: 2226 – 2238.p. 156. López-Garcia P, Moreira D.
1999. Metabolic symbiosis at the origin of eukaryotes. Trends in Biochemical Sciences. 24 (3):
88-93.
R. Watson, T. Reil, J. Pollack. 2000. Mutualism, Parasitism, and Evolutionary Adaptation.
Artificial Life VII.
R.A. Watson and J.B. Pollack. 1999. “How Symbiosis Can Guide Evolution.” Proceedings of the
Fifth European Conference on Artificial Life. Ed. D. Floreano, JD Nicoud, F. Mondale. Springer.
p. 140. Michael H. New and Andrew Pohorille. 1999. An Inherited Efficiencies Model of Nongenomic Evolution. DIMACS Workshop on Evolution as Computation. January 11–12. Princeton.
A. Pohorille and M.A. Wilson. 1993. Reaction Dynamics in Clusters and Condensed Phases —
The Jerusalem Symposia on Quantum Chemistry and Biochemistry, Jortner, J.; Levine, R. and
Pullman, B., Eds. vol. 26. Kluwer, Dordrecht. 207.
_______. 1994. Interaction of a model peptide with a water-bilayer system. in Structure and
Reactivity in Aqueous Solution: Characterization of Chemical and Biological Systems, Cramer,
C.; Truhlar, D., Eds., ACS Symposium Series No. 568. ACS, Washington D.C. ch. 11, p. 395.
_______. 1995. Origins of Life and Evolution of Biosphere. 25, 21.
p. 141. Research by Chris Henze at NASA Ames Research Center.
Bhushan, Nalini and Stuart Rosenfeld Editors. 2000. Of Minds and Molecules: New
Philosophical Perspectives on Chemistry. Oxford University Press.
p. 142. On webtanks:
Zann Gill. 2002. Webtank (think tank on the web) and the management of organizational
complexity. New England Complex Systems Institute. 4th International Conference on Complex
Systems (ICCS 2002).
Zann Gill. 2001. Webtanks: Tools for Learning by Design. Siggraph. Los Angeles.
Werner Heisenberg. 1958. Physics and Philosophy N.Y.: Harper and Row, Harper Torchbooks.
Chapter 13. when evidence runs scarce
143 – 151
p. 143. Quote;
Richard Dawkins. 1995. River of Eden: A Darwinian View of Life. NY: Basic Books. Science
Masters Series.
A plausible hypothesis may wait many years to become a theory because of lack of evidence. For
example, although Cairns-Smith at first worked with kaolinite clay (an aluminum silicate), though
213
kaolinite could promote condensation reactions in a watery context, it is thought to have been rare
in Precambrian times. More evidence is needed.
p. 144. On sampling:
Daniel Dennett.1984. Elbow Room. Cambridge, MA: Bradford Books Division: M.I.T. Press.
For estimated comet water, see C.B. Cosmovici, et al. 1996. Planet. Space. Sci. 44. 735.
C. Chyba, P. Thomas, L. Brookshaw, and C. Sagan. 1990. Cometary Delivery of Organic
Molecules to the early Earth. Science. 249. 366-373.
On astrobiological criteria for space exploration:
David Des Marais. 2001. Current Earth Environments as Analogues for Extraterrestrial
Environments. Astrobiology. Sept. Vol. 1. 3:317 – 349.
p. 145. C. Chyba and C. Sagan. 1992. Nature. 355. 125-132.
On the Freund hypothesis:
Minoru M. Freund and Friedemann T. Freund. 2006. Solid Solution Model for Interstellar Dust
Grains and Their Organics. The Astrophysical Journal. 639:210 – 226. March 1. The American
Astronomical Society. Their dust grain model is based on a basic principle of solid solutions
applicable to the mineral (silicate) component of the dust in the interstellar medium (ISM). They
show that nanometer-sized mineral grains, which condense in the gas-rich outflow of late-stage
stars or expanding gas shells of supernova explosions, do not consist of just high melting point
oxides or silicates. Instead they form solid solutions with gas-phase components H2O, CO, and
CO2 that are omnipresent in environments where the grains condense.
p. 146. Jennifer Blank. 2002. “Processing of Organic Material During Cometary Impacts.” #14.
ISSOL 2002.
Analysis of the zircon crystal:
Simon A. Wilde, John W. Valley, William H. Peck and Colin M. Graham. 2001. Evidence from
detrital zircons for the existence of continental crust and oceans on the Earth 4.4 Gyr ago. Nature.
January 11. 175.
Chamberlin and Chamberlin on the parallel between life’s carbon cycle and non-living cycles:
TC Chamberlin and RT Chamberlin. 1908. Early Terrestrial conditions that may have favored
Organic Synthesis. Science. 28. 897 – 911.
p. 147. Analysis of a Martian dust storm:
H. Abadi and N.C. Wickramasinghe. 1977. Nature. 267:687 – 688.
Hoyle speculated about the rod-shaped bacteria and panspermia: Fred Hoyle. 1984. Intelligent
Universe. NY: Holt Rinehart, Winston. Some argue that a bit of ethanol and a bit of e-coli have
similar spectral readings. Whether Hoyle and Wickramasinghe were right or not their reasoning
shows hypothesis construction in process.
p. 148. A. Lazcano and S. L. Miller. 1994. “How long did it take for life to begin and evolve to
cyanobacteria?” J. Mol. Evol. 39:546-554.
Christopher House, Nils Holm et. al. 2002. Exploration of Subsurface Pacific Microbial
Ecosystems. #45. ISSOL 2002.
J.W. Schopf, and B.M. Packer. 1987. Early Archean (3.3-billion to 3.5-billion-year old)
microfossils from the Warrawoona Group, Australia. Science. 237: 70 – 73.
J.W. Schopf. Ed. 1983. Earth’s Earliest Biosphere. Princeton University Press. 240 – 259.
_______. 1992. The oldest fossils and what they mean. In Schopf, J.W., ed., Major events in the
history of life. Jones and Bartlett, Boston.
_______. “Life.” 2002. The New Encyclopedia Britannica. vol 22. Macropaedia. 15th edition. and
in Nature, March 7.73 – 81.
_______. 2002. Ed. The Beginnings of Biological Organization. Berkeley, California. University
of California Press.
Martin Brasier. 2002. Nature 416:76 – 81.
Howard Armstrong and Martin Brasier. 2005. Microfossils. Second Edition. London: Blackwell.
214
Donald R. Lowe. 1994. Abiological origin of described stromatolites older than 3.2 Ga. Geology.
May. 22. 5. 387-390.
Donald Lowe. Private Correspondence. September 2005.
David Tenenbaum. 2003. “Earth’s Oldest Fossils Reverse Course.” Astrobiology Magazine. April
7.
Zzz
Lazcano-Miller estimate of when cyanobacteria might have evolved:
p. 149. On extremophiles:
Joseph Cone. 1991. Fire Under the Sea: The Discovery of the Most Extraordinary Environment
on Earth — Volcanic Hot Springs on the Ocean Floor. New York: William Morrow & Company.
NeMO, New Millennium Observatory — http://www.pmel.noaa.gov/vents/nemo/index.html
Some researchers study the Isua Supracrustal Belt in southwestern Greenland, which contains
banded iron formations and pillow laval basalt that may have been deposited in a low-energy
marine environment after the period of bombardment of early Earth. Others study the Tinto River
(southwestern Spain), an extreme environment with a constant acidic pH (near 2.3), a high
concentration of heavy metals, a high level of microbial diversity, and a system where sulfur
metabolism prevails. Geologists also study Barberton and Pilbara greenstone belts in South
Africa and Australia, remains of hydrothermal activity where there might have been habitable
niches. Alchichica Lake at the borders of the Mexican states of Puebla, Tlaxcala and Veracruz
contains both free-floating and stromatolite-forming cyanobacteria. Negative evidence is also
useful. Researchers determined that the Atacama Desert in Chile is almost devoid of life.
Amils, House, Westall, Escobar, Navarro-Gonzalez, and Zuilen. Estremophiles. ISSOL 2002.
Proceedings of the 13th International Conference on the Origin of Life. June 30 – July 5, 2002.
Oaxaca, Mexico.
Extremophiles known as thermophiles, live in hot springs (>50˚C); they are metabolically
“frozen” when they are cooled to what we consider a comfortable temperature. Extremophiles
known as psychrophiles grow at temperatures below 20˚C and are able to grow at 0˚C; they are
“cooked” at our body temperature (37˚C). Extremophiles, known as piezophiles or barophiles live
at the bottom of the deepest parts of the ocean at >1,000 atmospheres pressure. They die rapidly
when decompressed to one atmosphere. Extremophiles known as halophiles live in waters
saturated with salts. When the salt concentration changes from 25% to 15% they burst; they
cannot live in fresh water. Acidophiles thrive in concentrated acid (pH 0.5) and are destroyed at
neutral pH. Other extremophiles are specifically adapted to live in areas with high levels of
radiation, concentrated toxic chemicals, a paucity of nutrients, or a scarcity of water. Viewed
together, extremophiles represent evolution’s ingenuity and versatility to exploit energy sources
and adapt to harsh conditions.
Evidence can be interpreted in contradictory ways. Some argue that extremophiles support the
claim of panspermia that first life came to Earth from space by proving that some microbes can
endure the harsh conditions of space travel. Others claim that the existence of extremophiles
proves that autotrophic organisms (engaging in chemosynthesis without need for light or organic
nutrients) were the first life on Earth. Extremophiles show that life can exist quite successfully in
extremely hot, cold or dry environments where such conditions are found on Earth, such as
boiling waters of volcanic springs and high pressures of deep ocean thermal vents (where
temperatures reach 110°C. or 230° F.). So it’s logical to conclude that extremophiles would be
well adapted to the harsh conditions of space. But despite the seeming fit with observations, there
are barriers to accepting that life’s genetics came as particles from space, not the least of which is
the flaky-sounding name panspermia. Those who espouse the “life is everywhere” version of
panspermia proposed to change the name to cosmicrobia, but the old name stuck. See discussion
in Hoyle, Fred and Chandra Wickramasinghe. 1997. Life on Mars? The Case for a Cosmic
Heritage. Clinical Press Limited. Redland Green Farm. Redland, Bristol, UK. In 1890
Vinogradsky, who studied one extremophile species, the aquatic bacteria Beggiatoa,
215
hypothesized that these bacteria might oxidize sulfur into sulfuric acid. Colleagues congratulated
him on having found a new mode of life. Soon after, he found that Nitrosomonas and Nitrobacter
derived energy by oxidizing ammonia to nitrite, and nitrite to nitrate.
p. 150. “SLiME” (Subsurface Lithoautotrophic Microbial System): Science 270:450 – 454. 20
October, 1995. Stevens, T.O. and J.P. McKinley, two researchers from Pacific Northwest
Laboratory discovered a microbial ecosystem not dependent on photosynthesis. Its microbes
appear to thrive on chemical energy in basalt, a rock common to Earth and Mars. But this basalt
contains little organic carbon, which usually feeds microorganisms. Their research focuses on
microbial populations deep within the Earth, but suggests potential for life on Mars. Microbes
found in groundwater samples taken more than 1,000 meters (3,300 feet) below the surface at the
Department of Energy’s Hanford site on the Columbia Basin basalt flows in southeastern
Washington State include communities of hydrogen–eating bacteria that seem to obtain hydrogen
in an unusual way. Where other microbes depend on organic carbon or hydrogen from decaying
plant matter originally generated from photosynthesis, SLiME consume hydrogen from the
reaction of basalt with groundwater. Methanobacterium thermoautotrophicum has been
sequenced by the Archaeal Proteomics Project, which aims to identify archaeal proteins and
regulatory pathways for bioremediation and energy technology, processes that interest the U.S.
Department of Energy.
Christopher Wills and Jeffrey Bada. 2000. The Spark of Life: Darwin and the Primeval Soup.
Cambridge, MA: Perseus Books.
For the Kelvin analysis, see notes p. xxx
p. 151. Hoyle xxx
Chapter 14. what if?. . .
152 – 164
p. 152. Quote:
Jacob Bronowski. 1974. The Ascent of Man. Chapter 4. Boston: Little Brown.
For background on Otto Butschli, Stephane Le Duc:
Vaclav Smil. 1997. Cycles of Life: Civilization and the Biosphere. NY: Scientific American
Library.
The 1977 discovery of marine hot springs at the Galapagos Rift revealed new species of tubeworms and other species never seen before. Hot springs (known as black smokers) were up to 45
feet tall with water spewing from them up to 600 degrees Fahrenheit. Clouds of bacterial clumps
in the water and on the ocean floor made scientists estimate that the life density at the Hot Springs
exceeded that of any land based systems.
p. 153. On ice in space; history and discussion of experiments at NASA Ames Research Center:
David F. Blake and Peter Jenniskens. 2001. “The Ice of Life.” Scientific American. August.
Bernstein, Max P., Scott A. Sandford and Louis J. Allamandola. 1999. “Life’s Far-Flung Raw
Materials,” Scientific American. July.
Speculating about the role of the moon:
Crick, Francis. 1994. The Astonishing Hypothesis: The Scientific Search for the Soul. New York:
Charles Scribner’s Sons.
Francis Crick. 1981. Life Itself: Its Order and Nature. N.Y.: Simon and Schuster.
On gravity and the origin of life see Paul Davies. The Fifth Miracle. N.Y.: Simon and Schuster
1999 and The Origin of Life. Penguin. 2005.
On plate tectonics:
Ward, Peter D. and Donald Brownlee. 2000. Rare Earth: Why Complex Life is Uncommon in the
Universe. NY: Springer-Verlag.
On gravity as a life-shaping force:
On the need to link the dynamics of matter with the dynamics of information: Paul Davies. 1999.
The Fifth Miracle. N.Y.: Simon and Schuster.
216
Morey-Holton, E. 2002. Gravity shapes life in Evolution on Planet Earth: Impact of the Physical
Environment. Ed. L. Rothschild and A. Lister. NY: Academic Press.
p. 154. On photosynthesis:
Kenneth M. Towe and David J. Des Marais. 2001. On the Origins of Photosynthesis. Science.
January. 19: 436 – 437.
Light-driven energy transfers play a role in photosynthesis. Researchers explore the evolutionary
link between nitrogen fixation and bacterial photosynthesis, asking how fragile early life
protected itself against ultraviolet radiation. Bettina Heinz studies how a protein (nitrogenase)
uses the metal molybdenum to produce atmospheric nitrogen. Though the genes involved in the
metabolic process of nitrogen fixation are known, we know little about its origin and evolution.
Experiments show that amino acids form protective agents against ionizing radiation.
Bettina Heinz. 2002. Origins of Nitrogen Fixation – The Importance of Molybdenum and
Pteridines. #163. ISSOL 2002. If methane-oxidizing micro-organisms could be candidates for
first life, how did they get started?
Each basic questions raises detail questions: nitrogen fixation entails splitting nitrogen molecules
into atoms used to build other molecules, such as nitrates or ammonia compounds, which in turn
are used by plants to build protein, one of the main components of life. So the origin of life spins
off a number of other origin questions: How did nitrogen fixation originate?
On the carbon cycle:
Smil, Vaclav. 1997. Cycles of Life: Civilization and the Biosphere. NY: Scientific American
Library.
On Kenneth Snelson’s tensegrity structures: http://www.kennethsnelson.net/
My reserch for Buckminster Fuller’s Cambridge, MA office, Fuller and Sadao Architects Inc.,
focused on tensegrity structures, developing collapsible configurations for rapid assembly.
p. 155. Donald Ingber explored the tensegrity metaphor for cellular structure and dynamic
loading: Donald E. Ingber, 1993. Cellular tensegrity: defining new rules of biological design that
govern the cytoskeleton. Journal of Cell Science. 104: 613 – 627.
_______. 2003. Tensegrity I. Cell structure and hierarchical systems biology. Journal of Cell
Science. 116: (7)1157 – 1173.and. 2003. Mechanosensation through integrins: Cells act locally
but think globally. PNAS. February 18. vol. 100 no. 4 :1472 – 1474.
http://www.pnas.org/cgi/doi/10.1073/pnas.0530201100
p. 156. Donald Ingber. 2000. Problems and paradigms: The origin of cellular life. Bioessays
22:1160 – 1170. John Wiley & Sons Inc.
p. 157. Donald E. Ingber. 1993. Cellular tensegrity: defining new rules of biological design that
govern the cytoskeleton. Journal of Cell Science 104. 613 – 627.
_______. 1998. The Architecture of Life: A universal set of building rules seems to guide the
design of organic structures — from simple carbon compounds to complex cells and tissues.
Scientific American. January.
p. 158. Ingber, Donald E. 2003. Tensegrity I. Cell structure and hierarchical systems biology.
Journal of Cell Science. 116 (7)1157 – 1173.
_______. 2003. Mechanosensation through integrins: Cells act locally but think globally. PNAS.
http://www.pnas.org/cgi/doi/10.1073/pnas.0530201100 February 18. vol. 100 no. 4. 1472
– 1474.
p. 159. Donald E. Ingber. 2000. Problems and paradigms: The origin of cellular life. Bioessays
22:1160 – 1170. John Wiley & Sons Inc.
p. 160. On the debates about tensegrity as ametaphor for cell behavior:
Ingber, Donald E., Steven R. Heidemann, Phillip Lamoureux, and Robert E. Buxbaum. 2000.
Controversies in physiology: opposing views on tensegrity as a structural framework for
understanding cell mechanics. J. Appl. Physiol. 89. 1663 – 1668.
On nano-robotics.
Goldstein, Alan H. 2006. “I, Nanobot.” Salon.com. March 9.
217
Nano-robotics is a still largely theoretical technology proposed for space, medical, manufacturing
and other applications. Some research groups are working on Nucleic Acid Robots
(Nubots).Discovering other life-filled planets, and especially intelligent life, is the mission of the
SETI Institute.
p. 161. The Drake Equation applies to the search for extraterrestrial intelligence. It was devised
by Dr. Frank Drake (with Carl Sagan) in 1961 a way to estimate the number of extraterrestrial
civilizations in our galaxy so scientists could quantify the uncertainty of the factors that determine
the number of extraterrestrial civilizations. Gene Roddenberry used it to justify the star-faring
civilizations shown in his television show Star Trek. The Drake equation states that:
N = R^{*} ~ \times ~ f_{p} ~ \times ~ n_{e} ~ \times ~ f_{l} ~ \times ~ f_{i} ~ \times ~ f_{c} ~
\times ~ L
where:
N = the number of extraterrestrial civilizations in our galaxy with which we might expect to be
able to communicate and
R* = the rate of star formation in our galaxy
fp = the fraction of those stars which have planets
ne = average number of planets which can potentially support life per star that has planets
fl = the fraction of the above which actually go on to develop life
fi = the fraction of the above which actually go on to develop intelligent life
fc = the fraction of the above which are willing and able to communicate
L = the expected lifetime of such a civilization
The real value of the Drake Equation lies not in the answer itself, but in the questions raised in
trying to figure out the data needed to calculate an answer. Clearly there is huge range in
estimating values for these variables. For example, the number of stars in the Milky Way Galaxy
has been roughly estimated at about 100 billion. Fp, the fraction of stars that have planets around
them estimated range from 20% and 50%. Ne, the number of planets per star that are capable of
sustaining life estimates range from 1 to 5. fl, the fraction of planets in ne where life evolves
estimates range from 0 – 100%. Fi, the fraction of fl where intelligent life evolves estimates also
range from 0% – 100%. Fc, the fraction of fi that communicate estimates range from 10% to
20%. FL, fraction of the planet's life during which the communicating civilizations live starts
from the expected total lifetime of our Sun and Earth, about 10 billion years. We have had radio
communication for less than 100 years. So estimates of the age of civilizations and number of
communicating civilizations in the galaxy could very enormously.
p. 162. The Hoyle/ Wickramasinghe formula:
Fred Hoyle and Chandra Wickramasinghe 1997. Life on Mars? The Case for a Cosmic Heritage.
Clinical Press Limited. Redland Green Farm. Redland, Bristol, UK.
p. 163. The Crick/ Orgel scenario:
F. Crick and L.E. Orgel. 1973. “Directed Panspermia.” Icarus 19:341-346 and revisited in
Francis Crick. 1981. Life Itself: Its Order and Nature. N.Y.: Simon and Schuster.
Not enough time vs plenty of time xxx
p. 164. The Zubrin scenario:
Robert Zubrin. 1999. Entering Space. N.Y.: Jeremy Tarcher/ Putnam.
For a summary of the debate: S.J. Dicke. 1998. Life on Other Worlds: The 20th Century
Extraterrestrial Debate. Cambridge University Press.
Chapter 15. logic loops — the paradox of prediction
165 – 177
p. 165. Quote:
Konrad Lorenz. 1977. Behind the Mirror: a search for the natural history of human knowledge,
translated by Ronald Taylor, London: Methuen and Company Ltd.
218
The four steps of this paradox were originally described in S (Zann) Gill. 1986. “The Paradox of
Prediction” Daedalus: Journal of the American Academy of Arts and Sciences. 115.3: 17 – 49,
republished by Academic Press.
I thank the late Ernst Mayr for his review of this article and for his helpful comments on my early
draft for this book, more than twenty years ago.
Douglas R. Hofstadter. 1979. Gødel, Escher, Bach: an Eternal Golden Braid. N.Y.: Basic Books.
See also his description of the 1995 work of his Fluid Analogies Research Group described in
Fluid Concepts and Creative Analogies: Computer Models of Fundamental Mechanisms of
Thought. N.Y.: Basic Books.
Leslie Orgel’s postulate:
Leslie Orgel. 1973. The Origins of Life: Molecules and Natural Selection. N.Y.: John Wiley &
Sons.
p. 166. M. Eigen and P. Schuster. 1979. The Hypercycle: A Principle of Natural SelfOrganization. N.Y.: Springer-Verlag.
p. 167. Eigen, Manfred. 1992. Steps towards Life. N.Y.: Oxford University Press.
Eigen, M. Lindemann, B.F. Tietze, M., Winkler-Oswatitsch, R, Dress, A. and von Haesler, A.
1989. Science. 244. 673.
D. Lee, K. Severin, Y. Yokobayashi, and M.R. Ghadiri. 1997. “Emergence of symbiosis in
peptide self-replication through a hypercyclic network.” Nature. 390:591 – 594.
p. 168. Eigen, Manfred and Ruthild Winkler. 1981. Laws of the Game: How the Principles of
Nature Govern Chance. N.Y.: Knopf.
M Eigen and P. Schuster. 1979. The Hypercycle: A Principle of Natural Self-Organization. N.Y.:
Springer-Verlag.
p. 169. Ganti, T. 2003. The Principles of Life. Oxford University Press.
Sol Spiegelman developed the technique of nucleic acid hybridization and conducted an
experiment with self reproducing RNA structures, which evolved shorter and shorter segments,
which reproduced faster and faster, known as “Spiegelman’s monster” and further studied by
Manfred Eigen.
D. Gillespie; S. Spiegelman. 1965. A quantitative assay for DNA-RNA hybrids with DNA
immobilized on a membrane. Journal of Molecular Biology 12 (3): 829 – 42.
p. 170. Harold J. Morowitz. 2002. Beginnings of Cellular Life: Metabolism Recapitulates
Biogenesis. Yale University Press. p. 117
Robert Rosen on Metabolic Networks:
Robert Rosen. 1958. A relational theory of biological systems. Bull. Math. Biophys. 20:245 – 317
_______. 1958. The representation of biological systems from the standpoint of the theory of
categories. Bull. Math. Biophys. 20:317 – 341.
_______. 1959. A relational theory of biological systems II. Bull. Math. Biophys. 21:109 – 128.
_______. 1972. Some relational cell models: The metabolism-repair system. In Rosen, R. Editor.
Foundations of Mathematical Biology. New York: Academic Press.
_______. 1991. Life Itself. New York: Columbia University Press.
_______. 2000. Essays on Life Itself. New York: Columbia University Press.
Rosen’s work is assessed from an Alife perspective:
Juan-Carlos Letelier Jorge Soto-Andrade, Flavio Guîñez-Abarzua, Athel Cornish-Bowden and
Marîa Luz Cårednas. 2004. “Metabolic Closure in (M,R) systems.” Artificial Life IX.
p. 171. On recruitment:
Sherrington, Sir Charles. 1951 [1937-8]. Man on His Nature. Gifford Lectures. Cambridge
University Press.
On autopoiesis:
Gail Fleischaker. 1988. Autopoiesis: the System, Logic, and Origin of Life. Boston, MA. Boston
University Professors Program, The Graduate School.
219
Humberto R. Maturana.1970. Biology of Cognition. University of Illinois, Urbana, Illinois and
Francisco Varela. 1979. Principles of Biological Autonomy. N.Y.: McGraw Hill/ Appleton Lange
p. 172. The barber who shaved everyone in town who did not shave himself is a paradox of selfreference attributed to Bertrand Russell.
On probability in the biological sciences:
Ernst Mayr. 1962. Accident or Design: The Paradox of Evolution. Science 134:1501 – 1506;
_______. 1976. Evolution and the Diversity of Life: Selected Essays. Cambridge, MA: Belknap
Division of Harvard University Press.
_______. 1982. The Growth of Biological Thought: Diversity, Evolution, and Inheritance.
Cambridge, MA: Belknap Division of Harvard University Press.
Israel Scheffler. 1963. The Anatomy of Inquiry: Philosophical Studies in the Theory of Science,
N.Y.: Alfred A. Knopf.
Carl. G. Hempel.1965. Aspects of Scientific Explanation and Other Essays in the Philosophy of
Science. N.Y.: Collier-Macmillan Ltd.
p. 173. Other sources on the logic of loops:
Douglas R. Hofstadter. 1979. Gødel, Escher, Bach: an Eternal Golden Braid. N.Y.: Basic Books.
Also 1985. Metamagical Themas: Questing for the Essence of Mind and Pattern. N.Y.: Bantam
Books.
p. 174. On symmetric rules of engagement:
Chris Salzberg, Hiroki Sayama and Takashi Ikegami. 2004. “A Tangled Hierarchy of GraphConstructing Graphs.” Artificial Life IX.
p. 175. Nelson Goodman. 1983. Fact, Fiction, and Forecast. Cambridge, MA: Harvard
University Press.
p. 176. Rene Descartes. 1985. [1628, 1701]). The Philosophical Writings of Descartes. 3 vols.
Eds. John Cottingham, Robert Stoothoff, Dugald Murdoc. Cambridge University Press. Rules for
the Direction of the Mind.
Erich Harth. 2005. The Creative Loop: How the Brain Makes a Mind. N.Y.: Helix Books.
Chapter 16. emerging, converging toward “it”
177 – 181
p. 177. Quote:
Hans Zinsser. 1940. As I Remember Him: The Biography of R.S. Boston: Little Brown.
Economist Frank Knight is known for his distinction between “risk” (randomness with knowable
probabilities) and “uncertainty” (randomness with unknowable probabilities).
p. 178. Dictionary of Philosophy of Mind.
http://www.artsci.wustl.edu/~philos/MindDict/emergence.html
On the implicit:
Michael Polanyi. 1966. The Tacit Dimension. NY: Doubleday.
The buttons and thread metaphor used by Kauffman to describe Random Boolean Networks:
Implications of this scientific research for theories of problem-solving:
David Deamer and Stuart Kauffman. 2003. “Ontological Emergence and the Failure of
Reductionism” presented at the Evolutionary Theory conference at Esalen, October 5 – 10.
http://www.esalenctr.org/display/confpage.cfm?confid=18&pageid=133&pgtype=1
p. 179. Lee Smolin. 1997. The Life of the Cosmos. Oxford University Press.
Elisabet Sahtouris.. 1999. Earthdance: Living Systems in Transition. Web-published at
http://www.ratical.org/LifeWeb/Erthdnce/erthdnce.html
p. 180. On CS Peirce, Jean Piaget, and Stuart Kauffman, three triggers for this book:
Charles Sanders Peirce. 1934. Collected Papers of Charles Sanders Peirce, vol. 5. Ed. Charles
Hartshorne and Paul Weiss. Harvard University Press.
_______. 1955. Philosophical Writings of Peirce. Ed. Justus Buchler. N.Y.: Dover.
220
Jean Piaget raises the question of how the implicit becomes explicit in his introduction to Howard
E. Gruber. 1974. Darwin on Man: A Psychological Study of Scientific Creativity. N.Y.: E.P.
Dutton.
Charles Darwin. 1959 [1872]. Origin of Species. Sixth edition. Chapter XV. “Recapitulation and
conclusion.” For reference to changes in the various editions, see The Origin of Species: A
Variorum Text, edited by Morse Peckham. Philadelphia: University of Pennsylvania Press. 1959.
To say that abstract concepts precede and help to generate hypotheses requires defining the term
“concept.” Not easy. A six hundred-page tome on this subject shows how hard it is to pin down
this term. Whether a concept is a bundle of features, a theory, a mental representation, an abstract
entity, an object or a behavior makes considerable difference in deciding what conceptual
approach to take.
p. 181. Stuart Kauffman. 2000. Investigations. Oxford University Press. p. 35, is based on the
theory of random graphs developed by mathematicians Erdös and Rényi in 1959 to describe
complex networks. Also described in
Ricardo Solé, and Brian Goodwin. 2000. Signs of Life: How Complexity Pervades Biology. N.Y.:
Basic Books. p. 234.
AFTERWORD
182 – 183
p. 182. Quote:
André Gide. Les Nourritures Terrestres. Paris: Société du Mercure de France. 1897.
S (Zann). Gill.1986. “The Paradox of Prediction.” Daedalus: Journal of the American Academy
of Arts and Sciences. 115.3: 17 – 49. Republished by Academic Press.
Peter D. Ward and Donald Brownlee. 2000. Rare Earth: Why Complex Life is Uncommon in the
Universe. NY: Springer-Verlag.
p. 183. “pinnacle of evolution, terminal twig. . .” refers to de Duve, Christian. 1995. Vital Dust:
The Origin and Evolution of Life on Earth. N.Y.: Basic Books.
Robert Zubrin. 1999. Entering Space. N.Y.: Jeremy Tarcher/ Putnam.
221