Foundation of Biological Sciences I Scientific Method - 1

BioSci 150 Foundation of Biological Sciences I

1st Lab

I. The Process of Science

What is Science?

A good definition of science for biological research is the orderly process of posing and answering questions about
the natural world through repeated and unbiased experiments and observations.

The way most scientists evaluate ideas and information has come to be know as the scientific method. The
scientific method is a way of gaining information (facts) about the natural world by forming possible solutions to
questions followed by rigorous testing to determine if the proposed solution is valid. Many scientific activities begin
with an observation of a problem or pattern.
The second step is hypothesis formation. A hypothesis (hypothesis is singular, and hypotheses are plural) is a
statement that provides a possible explanation for an observation. Hypotheses are always phrased as statements, not
questions. A good hypothesis has two characteristics: 1) it can account for all the available data, and 2) it is testable.
It is important to note that hypotheses must be falsifiable. In other words, based on the results of the data collected, a
hypothesis is either retained or rejected. Once a hypothesis is formed, predictions need to be formulated that go
along with the hypothesis. The next step is to test the hypothesis. A hypothesis may be tested by collecting
additional observational data, or by designing and carrying out an experiment. After the data is collected and
analyzed, conclusions are drawn from that data that support or refute the hypothesis. It is important to remember
that an experiment or observational study that supports an hypothesis is not inherently better than one that disproves
the hypothesis. Either way our knowledge of the natural world has increased.

Typical steps in the process of science are:

1) Make Observations: The scientific method starts with making a careful observation. Observations can be
made from nature, or from written notes of other investigators collected in books or journals.

2) Formulate a Hypothesis: The next step is to construct a hypothesis – use reasoning to derive a possible
answer to the observation.

3) Formulate a Prediction: Then, formulate a prediction. What would you expect to see if your hypothesis is
supported? What if it is refuted? Often predictions can be constructed as “if-then” statements.

4) Conduct and experiment and/or gather observational data: Perform an experiment or make additional
observations to test the prediction. Experiments need to be carefully planned to make sure the correct
experimental variables are noted (see below). Careful observation and recording of data is critical.

5) Analyze data: After performing the experiment or collecting observational data, you analyze the data.

6) Formulate conclusion: Depending on the results you conclude to support or reject the hypothesis you set
out to test.
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II. Designing Experiments

An important component of the scientific method are thoughtfully planned experiments. Experiments are not as easy
to conduct as you might think, and several crucial components have to be considered during the planning stage of.

The first step is to identify the pertinent variables. A variable is anything (factor, trait or condition) that is
controlled, manipulated or measured. There are three kinds of variables: Dependent, independent, and standardized.

1) Independent (experimental) variable: this variable is changed

for the purpose of the experiment, and as the independent
variable is changed, the changes in other variables are observed.
Independent variables are chosen because the experimenter
thinks that they will affect the dependent variable. There may be
multiple independent variables, but it is best to manipulate each
one independently, so that the defect of each independent
variable can be determined. Independent variables are the ones Fig. 1: Graphing independent
that are changed by the experimenter. and dependent variables

2) Dependent (response) variable: this is the variable that is

closely observed during the experiment to see how it responds to the change made to the independent
variable. The new value of the dependent variable is caused by and depends on the value of the independent
variable. Dependent variables are the ones that are observed by the experimenter.

3) Standardized variables: these variable need to remain constant during the experiment, so that change in
the dependent variable can be attributed to change in the independent variable alone. Controlled variables
need to be monitored as closely as the other variables, to be sure that they did not change. Standardized
variables are the ones that are kept the same by the experimenter.

Two other factors are important to consider when planning experiments. Whenever possible, a control treatment
should be included, and there should be replicates.

Control treatment: This is an experiment in which the independent variable is either eliminated or set to a standard
value. This allows comparison between results obtained during the control and the experimental treatments.

Replicates: Replicating (repeating) the experiment, and getting similar result, increases the confidence in the results
of the experiment. Replicates do not have to give the exact same result each time, because a certain amount of
variation in nature is normal.
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III. Hypothesis Testing &

Graphing in Excel Exercise
In this exercise you will develop hypotheses and predictions,
conduct an experiment, gather data, and use Excel to analyze
the data.

What makes a champion thumb wrestler? Does anatomy (e.g.,

thumb length) have an effect on the chances of winning a thumb
wrestling match?

Turn to one of your lab partners and have a couple of thumb wrestling matches. Observe the movements and think
about what might determine the outcome of the matches.

Write a hypothesis about what determines thumb wrestling matches in your lab notebook.

Then think about which prediction(s) your hypothesis makes. Write the prediction(s) into your lab notebook.

Next, run an experiment testing your hypothesis.

Which is the dependent variable in your experiment? Which are the independent variables? Thumb length might be
one independent variable that can affect the outcomes of the matches. Can you think of others? Discuss in class
which other independent variables might be important. Then, measure thumb length and 2-3 other variables you
decided on as a class. Add your own values of the independent variables to the table below. Conduct a series of
thumb wrestling matches with your lab partners (students from your lab table). Add the data on how often you won
to the table below. Then, assemble a master data table on the board, and add the table to your lab notebook for future
reference. Next, go to the computer lab to analyze the data you just collected. Your TA will show you how to make
graphs in Excel. Pay attention – you will need to be able to make graphs for assignments throughout the semester.

Raw data table (for each student): Right or left hand

Thumb length [cm]
Parameter 1
Parameter 2
Parameter 3
% wins (wins/total x 100)

The Master Data Table assembled for the whole class (and copied into your lab notebook) should include the
following information:
Student Thumb length Parameter 1 Parameter 2 Parameter 3 % Wins
(write in what (write in what (write in what
parameter you parameter you parameter you
chose) chose) chose)
G.H. 53mm 100mm 57mm 35mm 50

Data Analysis (graph your results):

After graphing the data, sketch the graphs in your lab notebook (as shown in
the example to the right). Do the same for all parameters you measured.

What conclusion(s) can you draw from each graph? In your own words,
describe the relationship between the measured anatomical parameter and
the success of winning thumb war matches. Write this in your notebook next
to each graph.

Compare your results with your hypothesis. What conclusions can you draw
from the experiment. End your lab notebook entry for this part of today’s lab
by writing your final conclusion.
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IV. Elements of Scientific Publications

Science does not stop with the conclusion of an experiment. Scientific findings are shared; there are several avenues
for this, the most common one are scientific publications.

Scientists communicate their research findings in scholarly journals. A paper in one of these journals will have a
layout designed to make it easy for readers to follow the content of the paper. Scientific papers often deal with
highly technical subjects, and the idea is to allow people from diverse fields to understand the paper, while
maintaining a high degree of thoroughness. Another goal is to be explicit about the methods that were used. Any
adequately trained person should be able to replicate the observations or experiments and verify the findings.

An example of the structure of a scientific paper is the following:

TITLE – ABSTRACT – INTRODUCTION – METHODS – RESULTS – DISCUSSION – LITERATURE CITED

The TITLE is a concise description of the content of the paper.

The ABSTRACT is a brief summary of the paper. It gives an overview of the conceptual background, hypotheses,
predictions, and interpretation and relevance of the findings. All of these subjects are dealt with in more detail in the
subsequent sections of the paper, but a casual reader can use the abstract to decide if the paper is of interest.

The INTRODUCTION provides the reader with a general framework about the significance of the subject before
leading to the specific hypotheses and predictions that are dealt with in the paper.

The METHODS section provides all the necessary details about the observations or experiments that were conducted,
and about how the data were collected and analyzed. The information presented should be detailed enough to allow
other interested scientists to replicate the study.

The RESULTS section presents the findings and analyses. To facilitate interpretation, results are often presented as
figures and tables, with text being used to provide a general overview and refer to specific illustrations. To make it
even easier to interpret the findings, each table and figure comes with a short legend that clearly describes its
content.

The DISCUSSION section presents an interpretation of the findings, in terms of the framework and hypotheses
outlined in the introduction. Here, the paper takes a step back and describes the big-picture significance of its
contents.

Throughout the paper, and especially in the Introduction and Discussion, scientific publications refer to other papers
that are relevant to the concepts and methods dealt with. Therefore, the last section is a list of LITERATURE CITED,
which allows the reader to refer to those sources of information.
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V. Citations
In scientific writing, it is very important to cite the sources that you use. Citations tell the reader where you found
the information, and give enough information that the reader can go find the source you used. Both in-text citations
and a Literature Cited section at the end of the paper are required. In-text citations give an abbreviated version of
information about the source(s) you used. This abbreviated information allows the reader to look for the full citation
in the Literature Cited section at the end of your paper.

In this class, you will be required to correctly cite all the sources you use, both in-text and in the Literature Cited.
Note that citations follow an exact format (see below). Correct order of information and correct use of punctuation
will be required for full credit. Note also that citations in scientific papers are likely to be different from those you
have used in other classes. You must use the citation method outlined below; you will not get credit for citation done
in other formats (English, Psychology, etc). If you have more than one source in your Literature Cited, the citations
should be listed alphabetically by the last name of the first author.

In-Text Citations:

For one author: ….they occasionally build nests on platforms of vegetation (Vermeer 1973)

For two authors: … died following swallowing lead sinkers (Scheuhammer and Norris 1996).

For three and more authors: …selenium can form a complex with mercury that could have an impact on the
degree of poisoning (O’Brien et al. 1995).

NOTE: Placement of periods and commas is important!

Literature Cited:

For journal articles:

O’Brien, D. J., R. H. Poppenga, and C. W. Ramm. 1995. An exploratory analysis of liver element relationships in a
case series of common loons (Gavia immer). Preventive Veterinary Medicine 25:37-49.

Scheuhammer, A. M. and S. L. Norris. 1996. The ecotoxicology of lead shot and lead fishing weight. Ecotoxicology
5:279-295.

Vermeer, K. 1973. Some aspects of the nesting requirements of common loons in Alberta. Wilson Bulletin 85:429-
435.

For books:

Hickman, C. P., L. S. Roberts, and A. Larson. 1998. Biology of Animals (Seventh Edition). WCB McGraw-Hill,
Madison, WI.
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VI. Literature Searches

Imagine that you are preparing to write a research paper on some topic of interest in biology. In order to learn more
about your topic, you will first need to learn how to access the information pertaining to it. Sometimes, a google
search is a good place to start if you know nothing about a topic, but many websites contain erroneous or misleading
information because they are not subject to the peer review process.

Publications which use peer-review send submitted manuscripts to experts in that particular field to fact-check and
edit them. Then they are sent back to the author for revision, after which they are re-submitted. There are usually
several revisions before an item is allowed to be published. This ensures that the information presented is very
accurate. So, in order to get correct information, you will need to search through scholarly, peer-reviewed sources
using a college library database. This may seem like a simple task, but using library resources like BIOSIS and
MEDLINE can be overwhelming and frustrating the first few times.

To get to the Biological Sciences/Health databases:

1. Go the UWM library homepage

2. Under “Research” click on “Resources by Subject/Major”
3. On the “Resources by Subject/Major” page, click on “Biology” or “Medicine”
4. Both links will take you to a page with a listing of Library Databases for Bio Sci and health topics.
5. Depending on your topic, choose the database that sounds most appropriate for a search. BIOSIS
(Biological Abstracts), Web of Sciences, and MEDLINE are popular for Bio Sci.
6. Be careful when using Academic Search and other databases. Be sure to use the option to search in only
scholarly, peer-reviewed journals or only those articles with abstracts.

Some examples of scholarly, peer-reviewed journals:

JAMA (Journal of the American Medical Association) American Midland Naturalist

Ecology Journal of Heredity
TREE (Trends in Ecology and Evolution) Genetics
Proceedings of the Royal Society of London, Series B: Biological Sciences Nature
Molecular Ecology PNAS (Proceedings of the National Academy of
Evolution Science)
Animal Behaviour Science Magazine (American Association for the
Condor Advancement of Science)

Some examples of non-scholarly or non-peer reviewed publications:

Popular Mechanics National Enquirer

Discover Magazine Mother Earth News
Scientific American Smithsonian Magazine
Reader’s Digest Popular Science
Field & Stream National Geographic
Time Any newspaper, newsletters, or bulletins
Newsweek

A good rule of thumb for weeding out the non-scholarly or non-peer reviewed publications is to ask yourself the
following question: could I find this magazine at my local bookstore (B&N, Border’s, Harry W. Schwartz)? If
the answer is yes, it probably is not a scholarly, peer-reviewed journal. Also, peer-reviewed journals usually do not
contain many color photos or advertisements. They’re mostly text and graphs.
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Literature Searches (homework assignment)

The goals of this assignment are to:

• Introduce you to the databases available through the UWM Golda Meir Library, which are similar to ones
at other college libraries.

• Guide you through the processes that biology students and professionals use to find information relevant to
their research topics.

• Help you become comfortable with performing literature searches and help you to use your time more
effectively.

Instructions for the Literature Search Assignment

1. Choose a topic of interest from some area of biology. You may find it useful to look through your textbook for
ideas, or go to the Biology Department homepage to see what the faculty members are researching. Or you can
choose a topic you heard or read about in the recent news.

2. Perform a literature search for your topic on one of the Biological Sciences databases (BIOSIS, etc.) available
through the library’s website. Make sure you are searching for articles in scholarly, peer-reviewed journals. If
necessary, narrow your search to 100 or fewer articles. At this point, be sure that the topic you chose is not beyond
your understanding. For example, if you get a lot of citations that read like the following title you should probably
perform a new search: “Type I polyketide synthase requiring a discrete acyltransferase for polyketide biosynthesis.”

Once you’re satisfied with your search results, print out the first ten (10) citations from your search. It is not
necessary to print out the abstracts, but it may help in steps four and five.

3. For each of those citations you printed out, go to the library catalog on the library’s website and find out if: 1)
our library has access to the journal and 2) if they have the year, volume, and issue you need. Be sure to write down
the call numbers of the journals our library has in order to proceed. If the item is available as “Full Text” from an
electronic resource online, be sure to indicate that in lieu of a call number.

4. Go to the stacks/electronic resource and retrieve three articles from your database search. The three articles must
be included in the citations you printed out. Photocopy/print-out only the first page of each article you chose. This
should contain the title, authors, and the abstract (summary) of the research article. You need the actual first page
of the article, NOT the expanded citation with abstract that the database provides.

5. In your own words, summarize one of the research articles in a short paragraph.

Hand in the following before class next week:

A. A copy of the results from your search (first 10 citations) with call numbers written next to journals the library
has. If the item is available as “Full Text” from an electronic resource online, indicate that in lieu of a call
number. [10 pts]

B. The first page from each of 3 of the articles [3 pts.].

C. Your summary of one of the articles [7 pts.].