The Mystery Box Lab
Science as a Process1
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In this laboratory, you will learn about the basic elements of scientific investigation and how to
apply this process to solving problems.
After this lab, you should be able to:
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Explain the scientific method and apply it to various examples
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Identify and characterize questions that can (and cannot) be answered scientifically
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Explain what characterizes a good scientific hypothesis
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Define, give examples of, and identify dependent, independent, and standardized variables
•
Explain the importance of control treatments and replication
•
Design a simple experiment incorporating the essentials of scientific methodology
1 Laboratory Investigations for Biology, 2nd ed., by Jean Dickey. Copyright © 2003, pp. 1–2 and 1–4. Reprinted by permission of Pearson Education, Inc., Upper Saddle River, NJ.
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[materials and procedure]
M ate r i al s
Per group (3 students per group):
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1 sealed box containing 2–3 unidentified items
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1 container with an array of possible items
Per room:
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Empty boxes identical to the sealed boxes
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Double-pan balances
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Magnets
Part A: The mystery box
You have been given a sealed plastic box that contains 2–3 everyday objects. You have
also been given a container of objects that may have been used to fill your box. The goal
of today’s activity is to determine, with your lab partners, what objects are in your box
without opening it.
1. Initial observations
a. Make observations. Use any means you like and have available to you (except
opening your container) to investigate your box. Record your observations.
b. Why is it important to begin solving problems by making observations?
c. When you have an initial idea of what may be in your box, make a guess about
its contents. Record this guess in your lab notebook and write it on the board.
d. What techniques did you use to make this guess?
e. Discuss the process of coming to this initial guess with your lab instructor and
classmates. What other methods or materials (currently unavailable) would be
helpful to you in determining the contents of your box?
2. Additional “technology”
a. Your lab instructor will provide you with empty boxes and magnets. Use these
along with the double-pan balances on your lab benches to refine your initial
guess.
b. Make and record further observations and the results of tests you design to
make a second guess as to what is in your box.
c. Does your new guess agree with your initial guess?
d. Record your new guess in your lab notebook and write it on the board.
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Lab 1: The Mystery Box Lab
3. The big reveal
The Mystery Box Lab
a. Your instructor will gather a member from each group and allow you to open
your boxes in front of the class. Do not open your box until you are advised
to do so. Each group will announce the contents of the box and whether their
guesses were correct.
b. Were any groups wrong about both their guesses? What may have led the
groups to incorrect conclusions about what was in the boxes?
c. As a class, summarize the process you used to determine the contents of your
box.
4. Scientists investigate questions using a process called the scientific method.
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a. After making an observation, a problem or question is posed by the investigator. What was the problem or question you sought to solve or answer about the
mystery box?
b. Next, the investigator makes preliminary observations that lead to an educated
guess or hypothesis. What was your hypothesis?
c. Once a hypothesis is posed, the investigator designs and performs an experiment to test the hypothesis. What experiment(s) did your group perform?
d. Based on the results of the experiment, the investigator draws conclusions that
support, refute, or lead to the revision of the initial hypothesis. What did your
results lead you to conclude?
e. This process may repeat until the point that the investigator is confident of the
conclusions. Assuming you were unable to open your box, what would you
have wanted to do to refine your results and bolster your conclusions?
The Scientific Method
Make Observations
Ask Questions
Check Accumulated Scientific Data
Formulate Hypothesis
Run Controlled Experiments
Make Conclusions
Accept or Reject Original Hypothesis
©Hayden-McNeil, LLC
Make Predictions
Report Findings
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Part B: Scientific questions and hypotheses
How do you test a hypothesis? Generally, a hypothesis leads to very specific scientific
predictions that are testable. For example, based on your observations (sound, weight,
feel), you may have hypothesized that your box contained a paper clip and a roll of
tape. You could have tested this hypothesis by opening the box, but this sort of direct
observation is not always, and one might even say is rarely, possible. Instead, based on
your hypothesis, you predicted what these objects might sound like or weigh in another
similar box. The prediction you made with your initial hypothesis is testable.
In order to investigate a problem scientifically it is essential that the investigation be
based on observations and testable hypotheses. This is the basis of scientific research.
Unless a question leads to testable hypotheses of observable phenomena, it cannot be
answered scientifically. Some hypotheses that start out as untestable can be modified or
expanded on to make them clearly testable.
Discuss one of the following questions (assigned by your lab instructor) with your lab
partners. Can your question be answered with a scientific inquiry?
a. Do blonds make better dance partners?
b. What is the cause of polio?
c. When will your plum tree produce ripe fruit?
d. Why do bad things sometimes happen to good people?
e. When will Mount St. Helens erupt again?
f.
How many bass should you put in your friend’s pond to obtain the maximal sustainable fishing yield?
g. Does eating candy cause children to get more cavities?
h. Who is the better painter, Picasso or Monet?
You will go over these questions as a class. For those that cannot be answered scientifically, record why not in your lab notebook. Can you modify or expand the untestable
hypothesis to make it scientifically testable? For those that can, rewrite them as a testable hypothesis, not as a question.
You could test almost any hypothesis you made about the mystery box, but there are a
few hypotheses that our methods were inadequate to test. As a class, discuss some hypotheses that could not be tested with our methods. (Hint: Look at the list of potential
and actual box contents.) Are these hypotheses scientifically testable? If so, how?
Part C: Experimental components and design
Once you have identified your hypothesis, the next stage of the scientific method is to
design an experiment to test the hypothesis. There are several important factors to keep
in mind when designing a scientific experiment: variables to be tested, measured, and
held constant; controls to be run; and how many times to replicate the experiment.
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Lab 1: The Mystery Box Lab
1. Variables
The Mystery Box Lab
Variables are the things that can be expected to vary in an experiment. There are variables
that the investigator wishes to manipulate (vary) in order to test their effect. These are
known as independent variables. The results of most experiments are measurements
of dependent variables As a result of changing an independent variable, there may be
some effect. Things that are expected to change in response to variation in independent
variables are called dependent variables. The results of most experiments are measurements of dependent variables. In order to make absolutely certain that changes observed
in dependent variables are due to changes in the independent variables and not other
factors, it is critical to keep standardized variables constant.
Read the following description of an experimental question (Figure 1-1) and answer
the following questions with your lab partners.
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An investigator wishes to test the effect of population density on mouse reproduction. She sets up a series of cages with different numbers of mice in them and
records the number of litters in one month and the number of offspring per litter.
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1
0
0
2
4
6
Cage density
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10
8
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©Hayden-McNeil, LLC
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Number of surviving
offspring per litter
Number of litters per year
©Hayden-McNeil, LLC
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2
0
0
2
4
6
Cage density
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Figure 1-1. The basic setup and predicted results of the proposed experiment.
a. What is the independent variable in this experiment?
b. What is the dependent variable?
c. Name two additional factors that might affect mouse reproduction and that could
be used as independent variables in future investigations with the same dependent
variables.
d. Since more than one factor can be an independent variable that could affect mouse
reproduction, it is typical to test only one at a time. Why is this critical?
e. What would you do with the other possible independent variables you came up
with while you examine the effects of population density?
f.
What are some independent variables someone might want to investigate that cannot be directly manipulated? Can these sorts of variables be used in experiments?
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g. What are two additional dependent variables you could measure?
h. Name at least one variable you would want to standardize in this experiment that
could not be considered a potential independent variable.
i.
Identify the independent and dependent variables in the mystery box experiment.
What are the independent and dependent variables for the following experiments?
a. Lizard running speeds are measured at three different temperatures.
b. Corn plant height one month after planting is measured for plants with and without added nitrogen.
c. Bean plant seed production is measured at various frequencies of pesticide spraying.
d. Penguins from the same clutch (group of eggs laid at the same time) are split between two rooms. In one room the temperature is 10°C, while in the other it is 5°C.
Their weights are measured at the end of one year.
2. Controls
Control treatments are a necessary part of a well-designed experiment. A control treatment is a condition where the independent variable is either eliminated or set to a standard value. The measurements of the dependent variables in the control condition (the
control treatment) are compared to the measurements of the dependent variables in
the experimental conditions (the experimental treatments). In the above examples, the
corn plants without added nitrogen would serve as control plants to those with added
nitrogen. However, in the lizard running speed experiment, it would be impossible to
have a treatment with no temperature. Thus, the investigator would need to choose
a standard temperature (perhaps the average temperature where the lizards live) as a
basis for comparisons of running speed.
Indicate the appropriate control for each of the following examples of experiments to
test:
a. the dose of penicillin that is most effective at combating strep throat.
b. the effect of carbohydrate loading on running performance.
c. the effect of antibacterial soap on hand washing.
d. the growth rate of dogs as a function of food brand.
3. Replication and Sample Size
Replication is another important part of a good experimental design. Because biological systems are inherently variable, each time an experiment is done, the results may be
slightly different. A scientist should repeat an experiment many times, keeping the conditions as identical as possible, in order to draw conclusions from the experimental results.
a. Why might you get different average running speeds from your experimental lizards on different days?
b. Do you think a scientist should replicate her own experiments, or should multiple
scientists be involved in replication?
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Lab 1: The Mystery Box Lab
The Mystery Box Lab
Sample size is another aspect of replication. Repeating an experiment is one way to
replicate, but another is to collect data on a large number of test cases (a large sample
size) at one time. Testing the running speed of one lizard at three different temperatures
gives us far less information about running speed in lizards than testing the running
speed of fifteen lizards at three different temperatures. The most convincing experiments are done with both replication and adequate sample size.
a. What, other than temperature, could affect the running speed of a single lizard at
different temperatures?
b. Since we won’t be repeating experiments in our lab, how do we replicate our experiments?
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[Post-Laboratory Questions 1]
Read the following short article and answer the questions that follow it before your
next lab.
The Nature of Scientific Hypothesis and Investigation
Scientific knowledge gained through the process of scientific investigation is based on
generalizations and conclusions drawn from specific observations and experiments, a
process known as inductive reasoning. Of necessity, any information gathered through
inductive reasoning has a level of uncertainty. In the inductive process, generalizations
are made based on specific observations. Since it is never possible to observe every
possible case or scenario in an investigation, we must rely on observations of a sample
of all possible observations. For this reason, scientific “facts” are always regarded with
a certain level of skepticism rather than as absolute truth. In fact, statistics are a formal
way of quantifying an investigator’s uncertainty when experimentally testing a scientific
hypothesis.
New knowledge is actually an accumulation of evidence in support of hypotheses.
When we accept a hypothesis as “true,” we do so on a conditional basis, recognizing that
some future technology, experiment, or other information may falsify it. The scientific
method itself facilitates this.
When we examine the method of scientific inquiry closely, it is clear then that a single
experiment can prove a hypothesis false, but it takes many investigations before we
believe a hypothesis to be true. When we prove a hypothesis false, we say that we
falsify or refute it. Scientists avoid saying that an investigation proves a hypothesis
true, recognizing the level of uncertainty involved in inductive reasoning. Instead, they
say that the data support the hypothesis. Thus, new scientific knowledge is often seen as
tentative, and it is only after much data has been gathered from many experiments and
observations that the knowledge is generally accepted as the “facts” you read in your
textbooks. Many of these “facts” were once very controversial. An excellent example
was the discovery of DNA as the hereditary material by Avery in 1944. Until then, DNA
was a weak candidate for the genetic material and most geneticists favored protein as
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the likely molecule. It wasn’t until the unique structure of DNA was clearly elucidated
by Watson, Crick, and Franklin in 1953 that the last of the skeptics was convinced.
We have focused here on the scientific method, which only applies to hypotheses that
can be proven false through experimentation. There are also other types of scientific investigation, such as observation and comparison, that do not involve hypothesis testing.
However, even nonhypothesis-based investigation depends on observable phenomena
and inductive reasoning. Thus, scientific knowledge gained in this manner is also subject to the same constraints we have discussed for hypothesis testing. By its nature,
scientific knowledge is knowledge that can be proven false. This is not a requirement
for other forms of knowledge (e.g., aesthetic, philosophical, ethical, religious, etc.). Understanding this is critical to understanding the limitations of scientific inquiry. There
are certain things it is simply not possible to learn through science.
For example, consider the following hypothesis: The most beautiful paintings were
those done in France during the Impressionist Era. It is possible to define and measure which art work came from France during this era, but beauty is not scientifically
measurable. (To quote a well-known proverb: “Beauty is in the eye of the beholder.”)
Thus, there is no experiment that can be performed or observations made to test and
potentially falsify the hypothesis.
Answer the following two questions in your lab notebook.
1. What would be a testable hypothesis for artwork from Impressionist-era France?
2. Which of the following hypotheses are testable by scientific inquiry? Explain your
answers.
a. Typed lab reports receive better grades than do handwritten papers.
b. Human behavior is determined by the position of the stars on the day a person
is born.
c. Cats purr when they are happy.
d. Vitamin C prevents sore throats.
3. Use what you have just learned to complete the “Generating Hypotheses” exercise
below on a separate sheet of paper. This will be turned in to your TA as homework.
Generating hypotheses2
One of the very important things that comes from a laboratory course is the knowledge
that you can do “scientific inquiry” in your everyday life. Sometime before your next
lab meeting, make an observation that is related to some sort of process. (Note: This
must be your own observation—the following is just an example.) It can be about any
2 Modified from material at Understanding Science. 2010. University of California Museum of Paleontology.
8 January 2010 <http://www.understandingscience.org>.
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Lab 1: The Mystery Box Lab
The Mystery Box Lab
process, but the key to a decent observation is to be able to ask “Why is it like that?” or
“How does this happen?”
For instance, while sitting in the dentist chair yesterday I noticed a big curved scrape
in the drywall on the wall in front of the chair, about 2 feet long, ¼ inch deep. See the
drawing below.
1. Ask a question about your observation. This question will usually include the words
“how” or “why.” For example, “How did that scrape get there?” If you have trouble
forming a decent question, you might want to consider a different observation.
2. Make at least three more observations that help you answer that question. For example:
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“There are no other marks on the wall.”
“The part of the chair that sticks out the most is the elbow on the rotating arm
the light is attached to.”
“The scrape is higher on the wall than any other part of the chair or other instrument in the room, including the elbow of the light arm.”
“There is some drywall stuck to the back side of the elbow of the light arm, and
it has some paint on it that is the same color as the paint on the wall.” (I had to
get up out of the chair and look around to find this data.)
3. Using your additional observations, try to answer your question. Keep in mind that
the answer to your question is a hypothesis—it should come in the form of a confident statement. Then you should justify your hypothesis with your observations.
For example:
“The scrape on the wall happened when they moved the chair into the office
and the light arm rubbed against the wall. The evidence I see for this is the
paint and drywall stuck on the back of the elbow of the light arm, and that the
light arm is not high enough for this to happen while it is sitting in its current
position. Also, it only happened once because there is only one scrape. It must
have happened when the chair was higher than it is now, and that would be
when people were moving it into the office.”
4. Make two additional hypotheses based on your conclusions that attempt to increase
your understanding of the process or the objects involved. These should ideally be
testable!
“It is difficult to move a dental chair into position.”
“These people really don’t care about what this place looks like since they
haven’t fixed or painted the wall; they haven’t even hung a picture over the
scrape, and the crud is still on the light arm.”
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Lab 1: The Mystery Box Lab
Tree Building
and “Prokaryotes”
2
Describing evolution is dependent on being able to describe and discuss the relationships
among the diversity of organisms on our planet. This diversity is currently represented in multiple ways—through taxonomy and classification of organisms and also through phylogenetic
trees, graphical representations of historical relationships between organisms. In this lab, we will
discuss the merits of various methods of organizing and representing diversity and also show
how phylogenies can be used as tools to better understand the evolutionary history of diversity.
After this lab, you should be able to:
•
Discuss the importance of biological classification
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Identify and make phenograms, with and without dichotomous branching
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Differentiate between phenograms and phylogenies
•
Define and understand the differences between homologies and homoplasies (including
convergent evolution and reversals)
•
Describe the three domains of life
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Understand the rationale for the three domain model
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BAC KG R OU N D M AT E R IA L
Why classify?
Part of being able to discuss the diversity of life is being able to relate species to one
another. A lot of biology is focused on making generalizations about groups of organisms, such as:
•
Birds that feed on nectar from flowers have long, thin beaks to help them retrieve
the nectar.
•
Mammals have hair to keep warm.
•
Plants that grow in hot, dry habitats have very thick leaf coverings and often bear
spines, both being traits that prevent water loss.
Simply by making these types of observations we are grouping organisms, and these
groups inform our understanding of the diversity around us.
Classification is not a new field. One of the earliest well-known classifiers of nature
was Carolus Linnaeus (1707–1778), a Swedish medical doctor and botanist (the two
fields were then tightly joined). Linnaeus was a devout Christian and connected his
religious and professional life through the field of natural theology, which posits that it
is possible to understand the wisdom of God through creation. In following this path,
Linnaeus published the most influential classification scheme ever written: his book
Systema Naturae. This book, which classified all known organisms and created a system
for classifying any yet to be discovered organisms, still forms the basis for the classification system modern biologists use today. Linnaeus believed that it was the naturalist’s
job to reveal the order in the universe by discerning God’s “natural classification.” Linnaeus realized that humans had limited insight into the relationships among organisms and differentiated between artificial classifications based on human observation
and God’s natural perfect order. Modern biologists also realize that species groups that
are solely designated based on our interpretations of the similarities among organisms
are not always natural classifications, which should strictly be based on evolutionary
relationships. Thus, Linnaeus’s quest continues as we work to determine the exact and
correct relationships among the organisms in our world.
Diagramming relationships
A logical place to start a classification, and where Linnaeus started, is to look for similarities among organisms. Interestingly, this is not a skill limited to biology. You can
form a group of any type of item—living or nonliving—and classify it into smaller
groups. Once established, your classification should ideally help you categorize novel
items into your classification system.
Let’s walk through an example, creating a classification scheme you might design to
organize the following items in your closet:
Red wool sweater
Orange trench coat
Red cotton shorts
Green swimsuit
Purple silk turtleneck
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Lab 2: Tree Building and “Prokaryotes”
Orange wool hat
Blue fleece pajamas
Orange leather sandals
Green cotton knit mittens
An easy way to classify is to separate things into two groups. For instance given your
clothing items, you might divide them first by whether you wear the items in fall/winter
or in spring/summer. This leaves you with:
Fall/Winter:
Red wool sweater
Orange trench coat
Orange wool hat
Blue fleece pajamas
Green cotton knit mittens
Purple silk turtleneck
Tree Building and “Prokaryotes”
Spring/Summer:
Red cotton shorts
Green swimsuit
Orange leather sandals
Once one division is made, you can continue dividing the items within one group. Fall/
Winter clothes could be further divided into knit vs. not knit and knit items can be
divided into outerwear vs. non-outerwear. Eventually you could end up with a classification diagram like this (Figure 2-1):
Items
Fall/winter
Knit
Outerwear
For hands
Spring/summer
Not knit
2
Not swim
Innerwear
For feet
Green
swimsuit
For heads
Red sweater
Sleepwear
Green
mittens
Swim
Orange hat
For legs
Orange sandals
Red shorts
Non-sleepwear
Full body
Not full body
LC
eil, L
-McN
yden
©Ha
Purple turtleneck
Blue pajamas
Orange coat
Figure 2-1. Diagram of a classification to help you organize clothing items in your closet.
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You’ll note that the resulting diagram is a series of branches or “decisions” about which
of two categories something fits into until each item is independently categorized
(only one item on a tip). The basis for the “decision” is written above the branch. Some
branches end with an item and then no further branches are needed. The tree diagram
above (Figure 2-1) is called a dichotomous tree (or dichotomous key) because each
branch is split between two groups and each branch ends with a single unique item.
Suppose someone gave you a pair of wool gloves. You could easily place them into your
classification; under the “For hands” branch you could simply add a branch for “Mittens”
and another for “Gloves.” The above classification might be extremely useful for organizing your closet and would allow you to easily organize new clothing acquisitions.
But say you found the same clothing items at a photographic studio working on a photo
shoot where the models were wearing clothes of only one color. In that case, the above
classification wouldn’t be helpful at all. Instead, you would probably organize the same
items into a system like this (Figure 2-2):
Items
Warm colors
Red
Cool colors
Orange
Green
Blue
Purple
Orange hat
Orange sandals
Red sweater
Green
swimsuit
Purple turtleneck
, LLC
cNeil
den-M
©Hay
Red shorts
Blue pajamas
Green
mittens
Orange coat
Figure 2-2. Diagram of a classification to help you organize
clothing items for the photo shoot.
You’ll note that in the new classification, the organization is completely different. Also,
this organization is not a dichotomous key; as one branch divides into more than two
categories and the branches do not all end with an individual item. Several of them end
in item “groups.” For the purpose of the photo shoot, though, further organization is
unnecessary.
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Lab 2: Tree Building and “Prokaryotes”
Tree Building and “Prokaryotes”
These are both valid and helpful classifications for their given purpose. Similar methods
are often used to identify or organize groups of disparate items. Tree diagrams like both
of these are called phenograms. They are based on superficial or arbitrary attributes
that the classified items have in common. The traits used are chosen based on what is
most useful to the phenogram maker. The most scientific phenograms use dichotomous branching (like Figure 2-1), because that method gives a specific and unique
classification to each item. When a phenogram is made of a group of organisms it may
or may not reflect a natural classification, depending on whether the attributes selected
reflect shared ancestry or not.
Let’s go back to some of the basic groupings of organisms we made early in this section.
1. Birds that feed on nectar from flowers have long, thin beaks to help them retrieve
the nectar.
2. Mammals have hair to keep warm.
3. Plants that grow in hot, dry habitats have very thick leaf coverings and often bear
spines, both traits that prevent water loss.
It turns out that only number two (mammals) is a “natural” grouping. Mammals all
have hair because a shared ancestor of all mammals had hair and passed it on to all the
descendent mammals.1 Multiple groups of nectar-feeding birds have developed long
bills independently. Similarly, several plant groups that live in hot, dry habitats have
evolved thick leaf coverings and spines—again independently.
2
Making natural classifications
Because we do not have access to genetic data on all organisms and no one has been
alive for long enough to actually observe all living things evolve, there is no perfect
account of species relationships. Given the data we do have (some genetic, some morphological), we have to make the best estimate of the relationships among organisms.
Most of the time even modern biologists interested in species classification (called systematists) have to start at the same basic place Linnaeus did. We observe organisms and
we judge their apparent degree of similarity or dissimilarity to other organisms. There is
an inherent assumption in doing this: organisms that are more similar are more closely
related than organisms that are less similar.
Systematists presented with a novel organism often focus on physical structures or behaviors that have similar functions to those in other organisms. The tough part is to determine if those features are similar because a shared ancestor had the feature (common
ancestry and thus a closer relationship) or because of independent evolution (no shared
ancestry and a less close relationship). The big question facing a systematist, who is only
interested in traits that indicate shared ancestry, is how do you determine which traits
are from a common ancestor?
To answer that, it might help to think about all the ways a similar trait (be it a physical
structure, a behavior, or whatever) could come into being in multiple organisms.
1 Cetaceans (the order containing whales, dolphins, and porpoises) are mammals who have lost the majority of
their hair and use thick layers of fat (blubber) to keep warm. Even these mammals, though, have retained stiff
hairs on their snouts that are used for sensing the world around them—much like the whiskers of a cat. These
sensory hairs have been modified from the hair of a common mammalian ancestor.
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Homologies are traits that appear in different organisms because they were inherited
from a common ancestor. For example, lizards, birds, and bears have the same functional types of bones in their forelimbs (the most forward part of their front limbs).
These similar forelimbs are homologous because an ancestor of lizards, birds, and bears
had the same types of bones and passed them on to her descendents. While homologous traits can have similar functions, they do not have to have similar functions in the
modern organism. Bears and lizards use their forelimbs to support their weight, while
birds use them to fly. The homologous nature of the limbs is shown when comparing
the similar bones, developmental patterns, and genes associated with forelimb growth
in these organisms.
Homologies are exactly what systematists are looking for when they classify organisms,
because the more homologies two organisms have, the more closely related they are.
Tree diagrams made based on homologous traits are called phylogenies and are the
only trees that are considered to show the path of evolution.
It’s probably unsurprising that there can be trait similarities between organisms that are
not homologous. In these cases, like the nectar-feeding birds or desert plants, the similarities are due to independent development. All the ways that such nonhomologous
traits can arise are called homoplasies (or sometimes analogies). Homoplasies can develop because of convergent evolution (convergence) or reverse evolution (reversal).
Convergent evolution is when a novel (derived) trait evolves independently in two lineages. The derived trait usually appears via different pathways in the two species and
close examination of the trait (or of a correct phylogeny of the organisms involved)
will show that convergence, not homology, is at work. A perfect example of convergent
evolution is the development of vertebrate and cephalopod (the family containing octopi and squid) eyes. The two eye types share many similarities but were developed and
inherited due to completely separate events.
Reversals lead to homoplasies when a group of organisms develops a novel trait (“Circle”
trait in Figure 2-3), but a member of that group reverts to the ancestral trait (“Square”
trait in Figure 2-3).
Reversal to “square” trait
“Circle” trait evolves
Figure 2-3. Evolutionary tree showing a reversion from a novel (derived) trait
to an ancestral trait.
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Lab 2: Tree Building and “Prokaryotes”
Tree Building and “Prokaryotes”
In cases of reversal, the organism that shows the reverted trait does not share it with
other organisms because a common ancestor had the trait. Such is the case in the single
species of frogs that have teeth. Frogs evolved from a species that had teeth, but an early
ancestor to the frog lineage lost its teeth. In a single case though, a frog species has redeveloped teeth due to reversal.
While phylogenies can only be made using homologous traits, phenograms can be
made using either homologies or homoplasies. In fact, sometimes a phenogram designer may not even know if the traits used are homologous or homoplasious. This
implies that while all phylogenies are phenograms, all phenograms are not phylogenies.
Since homoplasies don’t help systematists make natural classifications, a critical question is how you distinguish a homoplasious trait from a homologous one. The answer is
that it’s very difficult. Extremely close examination of the structure or its development
can give you clues or the distribution of the trait on an evolutionary tree can inform you
of patterns of inheritance. Sadly, both of these methods can be misleading. Homoplasious structures can be very similar and evolutionary trees can be incorrect, leading to
erroneous conclusions. Thus, the safest way to determine if structures are homologous
is through genetic comparisons. Genetic comparisons can be made by comparing the
protein or DNA sequences of different organisms.
2
So why does anyone ever make phenograms? There can be several reasons. Genetic data
may not be available (as in the case of extinct organisms) and very newly developing
traits may not be visible in genetic data. Also, physical trait data may be more useful for
the task at hand—identifying a species in the wild is a perfect scenario when genetic
techniques wouldn’t be especially helpful.
[Pre-Laboratory Questions 2]
1. Make a new phenogram of the clothing items listed in the Background Material
section. Use any classification system you would like other than the ones shown
above.
2. Is your diagram from question 1 a dichotomous tree or not? How do you know?
3. Could you make a phylogeny of the clothing items listed in the Background Material section? Explain why or why not.
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4. Can you make a phenogram, a phylogeny, or either using homoplasies? What about
homologies? Is the tree diagram you will make in Part B of this lab a phenogram, a
phylogeny or both?
5. If you have a laptop, bring it to lab with you to start the lab activity.
M at eri als
[materials and procedure]
•
Cards showing species for classification
•
Chalk and paper
•
Character table
•
3D model of mammal phylogeny
•
Drawings and descriptions of unidentified unicellular organisms (all
from a group called “Prokaryotes,” page 20)
•
Mesquite software for comparative analysis of organisms—available
for download at our UBlearns site
•
Computer and internet connection
IMPORTANT NOTE: This lab occurs in three stages. Part A will be done in lab with
your TA and labmates. You will then complete Part B on your own time and e-mail a
classification diagram to your TA. You must submit Part B to your TA within 48 hours
of the end of your lab time. We strongly urge you to e-mail yourself a copy of Part B
at the same time as a record of completing that portion of the lab. Materials necessary
for Part C of the lab will be posted to your LAB UBlearns site 48 hours after your lab
ends. You will need to download those materials to complete Part C and be ready to
participate in Lab 3.
Part A: Clarifying phenograms and phylogenies
We start this lab with a very basic exercise to help understand the difference between
phylogenies and phenograms, as well as how scientists actually build phylogenies.
1. You and your lab partner will receive cards showing pictures of real animals. Based
on the pictures (and anything you know about the organisms pictured), make a
dichotomous diagram of the organisms by drawing a branching diagram on the
provided surface. You may use any classification scheme you would like so long as
you form a dichotomous tree. Write a couple sentences explaining the organization
of your tree in your lab notebook. Is your tree the same as the lab group’s next to
you? Have you made a phenogram or a phylogeny?
2. Your TA will give you a character table and show you how to make a tree using the
listed character traits for the same group of animals.
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Lab 2: Tree Building and “Prokaryotes”
3. Make a new tree using the character table. Is your tree the same as the lab group’s
next to you? Have you made a phenogram or a phylogeny?
Tree Building and “Prokaryotes”
4. Pay attention as your TA shows you the different parts of your tree and demonstrates how to manipulate your tree.
Part B: Relationships among unicellular organisms
1. You’re going to create a phenogram to classify the 10 unicellular organisms in the
table on page 20. You will not know if you are making a phylogeny because you do
not know if these traits are homologous or not. Look at the drawings and descriptions of these organisms and then create a classification system that will help you
make a tree diagram of the organisms. The only criteria for an acceptable diagram
are that 1) you must be able to explain your groupings, 2) you must make a dichotomous tree (the diagram should look like Figure 2-1 in the “Background Material,”
not Figure 2-2), and 3) you must use all the organisms.
2. Once you have a classification system planned, download Mesquite (software that
will allow you to make tree diagrams), the Mesquite instructions for Lab 2, and the
Lab2Phenogram.nex file from your LECTURE UBlearns site.
3. Follow the directions to drag the branches in the Lab2Phenogram tree until it looks
like your phenogram. Do not label your branches with traits or change the numerical taxa labels on your tree. Save your diagram as a pdf and e-mail it to your TA.
Print out the pdf of your tree and attach it to your lab notebook, labeled “Tree #1.”
Write a short paragraph accompanying your tree diagram that explains the rationale
you used to make your classification. Remember Tree #1 is due 48 hours after your lab
session ends. If you have not e-mailed it to your TA by then, you will not receive credit.
2
Part C: A new species and DNA data
1. Forty-eight hours after the end of your lab, two files will become available on your
LAB UBlearns site:
•
a picture and description of a new unicellular organism
•
a DNA-based character file for all the unicellular organisms, including the new
one (Lab2Phylogeny.nex)
2. Look at the new organism and decide where to place it in your classification. Add it
to Tree #1. You can simply draw a new branch on the printout of Tree #1 in your lab
notebook. Please use a colored marker or pencil. Label the new tip Taxon #11. Write
a sentence or two describing whether the new organism made you question your
classification strategy or if it made you feel like your classification worked well.
3. Following the directions from UBlearns, open Lab2Phylogeny.nex in Mesquite and
make a new DNA-based tree. Do not change the numerical taxa labels on your tree.
Save this tree as a pdf file.
4. Print out the pdf of your new tree and attach it to your lab notebook, labeled “Tree
#2.” How are trees 1 and 2 different? How closely does your first tree reflect the
evolutionary relationships in this group of organisms?
5. Label which trees are phenograms and which are phylogenies.
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Shape
Feeding
Style*
Mobile?
Amount of
Peptidoglycan**
Toxic to
Humans
Notes
1
Spirals
Heterotrophic
Yes
Low
Yes
Causes syphilis
2
Tiny circles
Heterotrophic
No
Low
Yes
Causes eye
infections
3
Rods
Heterotrophic
No
High
Yes
Causes
diphtheria
4
Circles
Autotrophic
Some
Low
No
Can form
chains of cells
(filaments)
5
Rods
Heterotrophic
No
High
Yes
Causes anthrax
6
Spirals
Autotrophic
Yes
Low
No
Can live with or
without oxygen
7
Regular or
irregular
circles
Autotrophic
Yes
Low/None
No
Thrives at high
temperatures
#
8
Circles (can
aggregate)
Heterotrophic
Yes
Low/None
No
Thrive in high
temperatures
and high
concentrations
of sulfur
9
Rods
Heterotrophic
No
Low/None
No
Survives in high
concentrations
of saline
10
Irregular
circles
Heterotrophic
No
Low/None
No
Produces
methane
*
**
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Picture
Autotrophs make their own nutrients (via photosynthesis or chemosynthesis), while heterotrophs gain nutrients from other organisms.
Peptidoglycan is a component of the cellular membrane of some of the organisms listed and, as it is easy to observe, is a common way these
organisms are categorized.
Lab 2: Tree Building and “Prokaryotes”
Part D: The three domain model
Read the article handed out in class on the Three Domain Model of life (Frontiers in
Microbiology: Microbes and the Three Domains) and then answer the following questions.
Tree Building and “Prokaryotes”
1. Circle the Archaea on the DNA-based phylogeny you made in Mesquite (Tree #2).
Circle the Bacteria. Add a branch to your phylogeny to represent the Eukaryotes.
2. List traits you used to make your phenogram that are likely homoplasious. Did you
use any traits that seem likely to be homologous?
[Post-Laboratory Questions 2]
1. Most people diagram the three-domain tree of life like this:
Bacteria
Archaea
Eukarya
2
The tree below shows the same evolutionary relationships in a different arrangement.
Archaea
Eukarya
Bacteria
What aspects of the three domains and their relationship to one another does each
tree highlight? Which do you prefer and/or find more intuitive? Is there another
way you could draw this tree?
2. Do you see any problems with diagramming the tree of life this way? Would you
make a different phylogeny?
3. For many years all unnucleated organisms were grouped together and called the
“Prokaryotes.” Many scientists don’t like to use that term anymore. Why do you
think the grouping “Prokaryotes” may be falling out of favor?
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Lab 2: Tree Building and “Prokaryotes”