The Scientific Method, Research Tools, and Techniques.

Objectives
In this lab you will learn:
How to utilize the scientific method
How to make observations and collect data
How to test an hypothesis using simple statistics
Welcome to Life Sciences 1! In this class, we will explore various aspects of
biology focusing particularly on evolution, ecology, and biodiversity. The lab is
designed to illustrate some of the important concepts from lecture. It is also your
chance to explore some aspects of biology in further depth through inclass
exercises and observation of living and preserved organisms. Many of you will
see organisms you have never seen before. Hopefully, all of you will learn much
more about biology. Above all, be enthusiastic and have fun!
Scientific Method
Modern science began during the Age of Enlightenment, which swept through
Europe in the late 16th and early 17th centuries. Although science itself was
performed in all parts of the world and in various manners long before then, the
philosophical advancements that were brought about in the Age of Enlightenment
codified a logically sound methodology that is the basis for all modern scientific
knowledge. The methodology, naturally, is referred to as the scientific
method.
The scientific method is a process that starts with careful observation of the
natural world. From these observations, a hypothesis is formulated to explain the
observation. The hypothesis is used to make predictions, and these are tested
through experimentation. The experimental results are then interpreted to either
support or reject the hypothesis. This process repeats, until the hypothesis is
either highly supported or rejected.
The scientific method is based on deductive reasoning championed by Francis
Bacon (15611626), a philosopher and scientist from the Age of Enlightenment.
Deduction is a philosophical process in which you can conclude that something is
true because it is a logical extension of other things you know to be true. For
instance, because you know that there are two sides to a coin, you can deduce
that the odds of attaining a head is 50%. Induction, on the other hand, is a form
of reasoning in which multiple, consistent observations yield a conclusion. In our
coin example, if you were to flip a coin 10 times and attained 10 heads, you
might inductively conclude that a flipped coin always lands on heads. A
conclusion based on inductive reasoning, however, is easily negated: a single tail
in our example would disprove our conclusion. Often induction is used to develop

hypotheses, because hypothesis development is based on observations. These

hypotheses are in turn tested through experimentation and rejected or supported
through deductive reasoning.

More specifically, the scientific method employs what is known as a hypothetico

deductive (or hypothesisprediction) approach. In this logical method, a specific
hypothesis is formulated to explain a particular phenomenon. The hypothesis is
designed to make predictions about the phenomenon you observed. This
hypothesis is tested with an experiment designed to permit deduction about that
phenomenon. The experimental results will either support or refute your
hypothesis, allowing you to draw conclusions about the truth or accuracy of your
hypothesis. This process can be ongoing ad infinitum, allowing you to learn a
great deal about a single phenomenon.
The formulation of a good hypothesis is an important part of the scientific
method. A hypothesis must give a testable explanation of the observations you
have made of a particular phenomenon. For example, perhaps you have noticed

that your dog is fond of chasing some of your neighborhood cats. You may make
a hypothesis to test, for example, whether your dog chases neighborhood cats
more than outoftown cats, black cats more than tabby cats, more cats in
the morning than in the afternoon, etc. All of these can be tested experimentally
and will provide information about your dog and its relationship to cats. However,
it is important to realize that there are hypotheses that cannot be tested, that are
outside the scope of scientific inquiry. It would be impossible to test, for example,
whether your dog chases cats because it hates them or if it chases cats because
it likes them.
It is much easier to reject a hypothesis than it is to accept one. Recall our
discussion on deductive vs. inductive reasoning. A single observation that
disproves a hypothesis nullifies the validity of that hypothesis, whereas multiple
observations that support it may not be sufficient to demonstrate that it is true.
You might hypothesize that all crows are black, because every crow you have
ever seen has been all black. But take a journey to Europe and you will observe
a crow with a white stripe around its neck and shoulders. Your idea that all crows
are black can be nullified with a single observation of blackandwhite crow.
This is why it is common in the scientific method to try to deductively refute
competing hypotheses rather than gathering inductive support for your
hypothesis. The competing hypothesis states that the factor you are testing
experimentally has no effect. For example, if you hypothesize that birds prefer
red berries, your competing hypothesis should be that berry color has no effect.
This competing hypothesis is called the null hypothesis, and very often
experiments are designed to reject the null. By rejecting the null hypothesis, you
are in fact supporting your own hypothesis. Say you were to hypothesize that
drug abuse during pregnancy causes low fetal birth weight. It would be easier to
disprove the null hypothesis: that drug abuse during pregnancy has no effect on
fetal birth weight. You could then experimentally sample birth weights of drug
abusers and nondrug abusers. If, based on your experimental data, you were
able to reject the null hypothesis that drug abuse has no effect on birth weight,
then your alternative hypothesis is supported. You were able to deductively reject
the null hypothesis (no effect).
An important thing to remember about science is that it is an ongoing enterprise,
where hypotheses are constantly tested and retested. The field of scientific
knowledge therefore is always changing as new ideas are supported and old
ideas are rejected. A hypothesis that withstands a high degree of scrutiny
through many experiments can be called a theory a hypothesis that has
withstood a great deal of scrutiny and has great predictive power but even
theories can be overthrown with a single observation. In 1919, for example,
Einsteins theory of relativity disproved the physics of Isaac Newton that had
robustly explained so many natural phenomena regarding the movement of
heavenly objects for over 200 years. Einsteins

hypothesis was that space and time were curved, whereas in Newtonian physics
(the kind you may have learned in high school), space was flat and time linear. In
1919, an expedition was conducted by the British Royal Society to Brazil and the
island of Principe off the western coast of Africa to observe a total solar eclipse.
Einsteins hypothesis predicted that in those two places, astronomers would be
able to observe stars that were located directly behind the sun because the light
from those stars would curve around the mass of the sun. The Royal Society
astronomers undertook the expedition and were able to observe light from the
stars behind the sun. That single observation was sufficient to disprove Newtons
theory of physics. Such is the nature of science: nothing can ever be proven.
Even the most robust of theories must be revised in light of new evidence.
However, this is also the strength of science. It is not dogmatic in its beliefs; it
constantly evolves so that our level of knowledge only improves with each
experiment that is performed.
Next time you are walking to school, sitting outside studying, or walking to class take a
look around and try to watch some of the animals you see on campus (trust me there are
more than just hungry squirrels). Formulate a hypothesis regarding something you have
seen. State your null hypothesis, and try to design a simple experiment to address this
hypothesis. While you dont have to turn this in, you may be asked to present your
hypothesis in lab this week, so make sure to take some time to look around and think
about what you see.

Observing and Quantifying Animal Behavior

Making an interesting Observation
Most investigations of scientific questions begin with an interesting observation.
People have noticed that some species of ground squirrels exhibit a very peculiar
behavior when they encounter anything that is saturated in snake scent. For
example, California ground squirrels and rock squirrels will chew on shed snake
skins and apply it to their fur by licking their bodies. This behavior has been
called snake scent application (SSA), and is also found in other rodents (e.g.,
chipmunks and mice). Have a quick look at this behavior now.
In this lab exercise you will make observations, record data, quantify observed
behavioral patterns, and learn a simple statistical test to evaluate your
hypothesis. You will watch videos of a behavior exhibited by two species of
ground squirrels to determine if the SSA behavior to various regions of the body
is random.
Asking a Question and Developing a Testable Hypothesis
Intriguing observations about behaviors often lead to questions about how or why
they occur. For instance, we may wonder how rodents apply snake scent do
they apply the scent to the different parts of their bodies in a particular order, or is

the sequence random? Do they apply scent to one region of their body more than
others, or do they cover all regions of the body equally?
We also may wonder about the function of applying the scent. Rattlesnakes have
been a major predator of ground squirrels for millions of years and this
coexistence has led to the evolution of several unique anti-predator strategies in
ground squirrels. For instance, in some species of ground squirrels adults are
resistant to rattlesnake venom and will actively harass and attack these
predators.
Group Exercise
A) Rodents are a major prey source for snakes why do you think rodents
apply their predators scent? Tentative explanations to your question are
called hypotheses. Within your group, brainstorm as many hypotheses as
possible to answer the question about function above. List your
hypotheses. Are all of them testable? Give at least one example of a non
testable hypothesis.
B) Choose one testable hypothesis and suggest specific ways to test the
hypothesis. What predictions would you make to support or refute the
hypothesis?
In this lab we will focus on the SSA behavior. We will address the question: is
SSA applied randomly over the squirrels bodies? We will be making
observations of two different Spermophilus species (S. beecheyi and S.
variegatus). Write your hypothesis and null hypothesis below.

Why might you expect SSA to be non-random? While you are thinking about this
consider some things about the ecology of squirrels: where do they live, where
are they likely to be found in their environment (i.e. on the ground, rocks, in
trees), could there be a benefit of applying snake scent to some regions versus
others on the body?

You will be collecting data on more than one species, do you expect different
patterns between species? What other things did you consider when trying to
address this question?

Testing Your Hypothesis

In this section, you will test the hypothesis that SSA behavior is random with
respect to areas of the body. That is, whether the squirrels simply apply the
snake scent or whether they apply the scent to specific areas of their bodies.
You will watch videos of SSA behavior from two species of ground squirrel,
California ground squirrels (S. beecheyi) and rock squirrels (S. variegatus). To
obtain the videos, a researcher staked out a shed skin of a sympatric rattlesnake
species (Crotalus atrox for rock squirrels, Crotalus oreganos for California ground
squirrels) and surrounded it with a minimal bait trail (sunflower seeds) to attract
the squirrels to the skin. The squirrels were marked with numbers (fur dye) to
identify individuals. Each video represents a different individual. The study sites
were in Winters, CA (California ground squirrels) and Caballo, NM (rock
squirrels) in county or state parks where squirrels were used to cars. The
squirrels were videotaped from a car, ~2030 m away.
Observations and Data Collection
The behavior you will be scoring is what body regions ground squirrels apply
snake scent to after chewing shed skins. You will be tallying snake scent
application on the following body regions:
Head

Tail

Front Legs

Flank

Hind legs

Figure 1: Ground squirrel body sections

http://pad1.whstatic.com/images/thumb/d/d3/Draw-a-Squirrel-Step-19.jpg/550px-Draw-a-Squirrel-Step-19.jpg

You will record the frequency of application behavior for both species. Make
observations for four individuals of each species. You will find the video clips on
the desktop of the computer (labeled SSA video clips). Choose four from each
species (labeled Clip b# for S. beecheyi, and Clip v# for S. variegatus), watch
each of these and record your data for each focal animal in the table above (or
you can make one of your own). Record the total frequency, from all four
individuals for each species, on the table below. At the end, you should have
data collected for four different individuals of each species, eight individuals total.
Species

Ind

Flank

Head

Front
Leg

Hind
Leg

Tail

Row
Total

S. beecheyi

1
2
3
4
Total
S. variegatus 1
2
3
4
Total
Interpreting Your Results
The data collected from the videos allows us to statistically test whether SSA
behavior is random or not. The statistical method employed is the chi-square
test. The chi-square (X2) test compares the observed behaviors to what would be
expected if the behaviors were randomly distributed. The basic Chi-square
formula used to compute the statistic is:

where: o = observed frequency, and e = an expected frequency, asserted by the

null hypothesis
For example, let us say we were to observe 100 SSA behaviors, divided into 4
groups: the flank, the tail base, the middle tail, and the tail tip. If the behavior
were truly random, we would expect those 100 behaviors to be distributed evenly
among our 4 body parts, 25 each. This gives us our expected values for our chi
square calculations. These expected values represent our null hypothesis; in this

case, our null hypothesis is that squirrel snake scent application behavior is
randomly distributed over the body (hence 25 expected touches to each of the 4
body parts). If our statistical analysis allows us to reject this hypothesis, we may
conclude that SSA behavior is nonrandom. (NOTE: Your data is divided into 5
body regions, not 4. The expected number of touches to a particular body region
therefore would be your total number of observations divided by 5.)
In our 100 SSA observations, let us say we see squirrels lick their flanks 21
times, their front legs 22 times, their hind legs 29 times, and their tail 28 times.
We would see that there is some variation between our observed and expected
values. Although a chisquare calculation is simple enough to do as a singleline
equation, some might find it helpful to organize your data into a table like the
ones below. (You will need to do these calculations for both species).
Expected
Observed

Flank
25
21

Front Leg
25
22

Hind Leg
25
29

Tail
25
28

Total
100
100

To begin our chi-square calculations, we subtract the observed values from our
expected values and then square them:
Expected
Observed
o-e
(o-e)2

Flank
25
21
-4
16

Front Leg
25
22
-3
9

Hind Leg
25
29
4
16

Tail
25
28
3
9

Total
100
100

Next, we divide the squares of our expected-observed observations by the

expected value:
Expected
Observed
o-e
(o-e)2
(o-e)2/e

Flank
25
21
-4
16
0.64

Front Leg
25
22
-3
9
0.36

Hind Leg
25
29
4
16
0.64

Tail
25
28
3
9
0.36

Total
100
100

Finally these values are summed giving a chi-square value of 2.

By itself, a 2 value of 2 is quite meaningless. We need to determine whether or
not this indicates a significant deviation from our expected distribution. Therefore,
once our 2 value is obtained, we need to compare it to a table of critical values
(like that shown below) which will allow us to determine whether our observed
data deviates significantly from our expectations due to random chance. The first
step in this process is determining the degrees of freedom we have in our sample
data. Degrees of freedom refer to how many independent pieces of data are

assembled in our final data set. In our case, there are 4 body parts in our data
set. Only three of these are independent, because if we were given three pieces
of the data table, we would be able to determine what the fourth was. As such,
the fourth value is not independent and cannot be included in our degrees of
freedom, leaving us with a df of 3. Generally speaking for simple data sets, the
degree of freedom is one less than the number of observed classes of data.
Table of Chi-squared Critical Values:
Degrees of
Freedom
1
2
3
4
6

0.10

0.05

0.025

0.01

0.001

2.706
4.605
6.251
7.779
9.236

3.841
5.991
7.815
9.488
11.070

5.024
7.378
9.348
11.143
12.833

6.635
9.210
11.345
13.277
15.086

10.828
13.816
16.266
18.467
20.515

In our table of critical values, we see that the critical 2 value to reject our null
hypothesis is 7.815 at a confidence of 0.05 (an arbitrary standard cutoff, although
others are sometimes used) with 3 degrees of freedom. This means that our 2
score would have to exceed 7.815 in order for us to reject our null hypothesis
(that SSA body application is random). In our case, a chisquare value of 2 does
not allow us to reject this hypothesis. Our data therefore cannot be said to be
significantly different from random.
Discussion
Given the data example worked in the lab manual, do you accept or reject your
hypothesis for each of the species observed?
Based on your raw data do you see any differences between species? What
might explain these differences, if any, that you observed?
How might you test hypotheses about different species?