Philosophy of Introductory Biology 151-152 Laboratory

What makes biology a quantitative science? 
This one week lab introduces students to interpretation of scientific data represented as percents, proportions and actual numbers. In addition it is designed to refresh their understanding of probability, measures of means and central tendencies. Students are introduced to how data distributions can differ for small versus large data sets/populations. Students are taught how to use Excel for data management, statistical analysis and graphing. Skills learned in this lab will be used throughout the first and second semesters.

In this one-week lab, students will learn:

• How to make decisions about the validity of data presented in the news and in scientific papers
• How to determine theoretical probabilities
• How to develop a testable question
• How to most efficiently organize and conduct a data collection activity
• How to analyze the data collected statistically to determine mean, standard deviation, type of distribution (e.g. normal vs skewed)
• How to interpret the results of the statistical analysis relative to the question asked
• How population size can affect the outcome

Assessment: Powerpoint presentation of results in graphical format

What can we learn about life using some basic biological techniques? ©JG Heitz

Our current understanding of the structure and function of biological organisms and systems was derived over many years of observation, study and experimentation. In this lab, you will review/learn some of the most basic techniques of biological research. For example, you will determine wet versus dry weights and organic versus inorganic composition of various animal and plant tissues (muscle, root, stem, leaf and fruit). You will investigate factors that affect rates of osmosis and diffusion in a model cell system and learn to do simple biochemical tests for major types of organic compounds.

In this one-week lab, students will learn:

• How much of living tissue is free water
• What types of chemicals make up life forms
• Which chemical characteristics are similar among life forms
• What types of molecules are more likely to cause a change in the osmotic potential of a cell
• What characteristics of molecules determine whether or not they can move readily across membranes
• Why organisms use starch and fats as storage compounds instead of sugars
• Basic laboratory techniques including:
  1. Pipetting and the use of Pipumps and repipets
  2. Density determination using water displacement
  3. Determination of organic vs inorganic content using Bunsen burners for ashing
  4. A variety of biochemical tests, e.g.:
     1. Biuret’s reaction for protein
     2. Benedict’s reaction for reducing sugars
     3. Feulgen/Schiff’s reagent for DNA
     4. Tetrazolium for redox reactions
     5. Iodine test for starch

Assessment = Quiz

What can we learn from a microscopic study of the cell structure and behavior of single-celled organisms? ©JG Heitz

That all living things are composed of cells is one of the most fundamental of all biological generalizations or principles. The two major cell types, prokaryotic and eukaryotic differ greatly. However, both carry out all of the functions of life. In this lab, you will review/learn some of the basics of microscopy in order to study these cell types in more detail. You will determine object orientation, field diameter and resolution for both compound and dissecting microscopes. Using these tools and others, you will investigate the structure and behavior of prokaryotes and eukaryotes. .

In this one to two-week lab, students will learn:

• Basic physics and operation of light microscopes, both compound and dissecting. This includes being able to:
  1. Demonstrate proper handling of the microscopes and proper methods for focusing.
  2. Demonstrate proper methods for cleaning the microscopes, replacing bulbs and fuses.
  3. Discuss the functions of the substage condenser and phase rings, why these are useful and how they should be used.
  4. Describe how the field diameter for an objective lens is measured, show the values of field diameter for the compound and dissecting scopes at different magnifications, and explain how knowledge of the field diameter can be used in practical applications
  5. Describe the differences in actual versus observed specimen orientation using the compound and the dissecting scopes and explain why it is useful to know this.
  6. Explain why good resolution power is more like a good score in golf than a good score in basketball.
  7. Explain how the resolution of a light microscope can be improved.
• The differences and similarities in prokaryote and eukaryote structure and behavior using direct observations
  1. Which structures of each cell type are visible using a simple compound microscope
  2. How do their cell sizes compare.
  3. How their behavior changes when exposed to specific environmental conditions.
  4. What stimuli each responds to and how they respond.

Assessment = Usually a quiz or worksheet

A preliminary analysis of unknowns for evidence of life forms ©JG Heitz
This lab is designed to give you some experience with the overall research process. Research costs time and money. Often preliminary data must be collected to establish trends and define the experimental system. In this particular lab, you are asked to determine which samples collected from various areas in a deep oceanic trench, are most likely to contain evidence of life forms. You are not asked to definitively identify each sample. The exercise involves developing operational definitions of alive, dead, organic and inorganic to use in developing your protocol, writing a grant proposal and developing a budget for the proposed research.

In the scenario presented, each lab is “competing” for the government contract to analyze the thousands of grab samples that were taken from the different areas of the deep trench. To determine which lab will receive the contract (and the funding) the government has provided each of the labs which have applied with a small subset of the samples. The contract will go to the lab that develops the most cost effective and accurate methodology to determine which of the samples contain evidence of life.

In this three-week lab, students will learn how to:

• Develop practical working definitions (and how these differ from absolute definitions), e.g. how do you define alive, dead, organic and inorganic for purposes of an experiment
• Apply these definitions as criteria for analyzing samples
• Design and implement an original research project
• Use the Internet appropriately to obtain scientifically accurate information relating to their research topic
• Write a research proposal including background literature, preliminary results, proposed methodology and budget.

In addition, students are expected to apply the skills and abilities they gained in the previous weeks of lab.

Assessment = Oral presentation of preliminary results and a proposal to NSF in final scientific format

©JG Heitz
This lab was developed using the Classical Genetics Simulator (CGS), a computer simulation of classical genetics laboratory exercises using either Arabidopsis or the fruit fly, Drosophila melanogaster. The program provides you with sets of organisms with unknown patterns of inheritance and gives you the tools to design and perform experiments to discover these inheritance patterns. You will be able to mate or cross the unknown organisms and analyze your crosses in ways similar to those used by practicing geneticists and genetics counselors.
In this two- to three-week lab, students will learn how to:

• Solve standard Mendelian genetics problems
  Use their understanding of Mendelian genetics to:
  1. Determine if a phenotypic trait is inherited genetically or not by both pedigree analysis and use of controlled crosses.
  2. Set up a logical series of crosses to determine the genetics behind phenotypes by doing specific crosses and analyzing the ratios of offspring.
• Use Chi square analysis to determine if observed results are statistically different from expected
• Present evidence supporting their findings in both oral and written forms.

Assessment = Formal journal style paper or poster presentation /oral presentation plus worksheet/quiz. .

Gel electrophoresis is a technique used in separating biological molecules that are charged, such as proteins and nucleic acids. Before DNA sequencing became readily available, gel electrophoresis and restriction mapping were common techniques used in characterizing DNA. Today, among other uses, gel electrophoresis is performed to verify presence/absence of specific DNA segments and to purify DNA.

In this lab you will be given the known DNA sequence of a gene and will be asked to determine its restriction sites using restriction analysis software available on the Web. Following this, you will test a colleague’s construct (plasmid plus insert) to verify that only the desired gene sequence has been ligated (inserted) into the plasmid vector.

In this two- to three-week lab, students will learn:

• What restriction enzymes are and how they can be used to determine size of DNA inserts into plasmids
• How to pour, run and read agarose gels of DNA fragments undergoing electrophoresis
• How to load DNA onto a gel using 10µl pipettes
• How to construct restriction maps of DNA using the data from the electrophoresis run.
• How to use “Webcutter” software to determine where restriction sites exist in a known sequence of DNA
• How to determine what differences exist (if any) between the known “Webcutter” results and the observed (gel) results

Assessment = Restriction mapping exercises and a formal business letter to client explaining results

The overall goal of this lab is to give you practice in developing well-defined and testable hypotheses, and in coming up with appropriate experimental designs to test your hypotheses. In this case, you will concentrate on some aspect of the behavior of Physarum, an acellular slime mold or planaria (fresh water free-living flatworms). By doing this lab you will discover that you begin by setting up experiments designed to eliminate possibilities in order to determine how something works.

In this three-week lab, students will learn how to:

• • Use the Web to find appropriate scientific background information on their organism, etc.
  • Form a testable hypothesis
  • Design and understand what a control is
  • Develop and conduct protocols for experiments in general and for behavior experiments in particular
  • Analyze data statistically and graphically
  • Report results in standard journal format

Assessment = Proposal followed by final paper in scientific journal style format which is reviewed by students and modified based on review.

• ©JG Heitz, J Breschak and D. Abbott

Overview In this study, you will investigate a number of the many factors that affect human energy budgets. You will be asked to use data you gather from the literature and data you obtain from a subset of student volunteers date to determine the effects of diet and activity level on energy homeostasis. This will include being able to explain the factors that affect energy balance in humans.

In this 3-week lab students will learn how to:

1. Extract, interpret and critically analyze both data from the literature and data collected during the course of the lab. As a pre-lab assignment, we have posted a number of news articles and scientific research papers on L@UW. Each student in your lab will be assigned to read and analyze a few of these before coming to lab week 1. Your goal in doing this will be to:
   1. determine the factors affecting the obesity epidemic.
   2. develop an explanation of the factors that affect energy balance in humans.
   3. indicate which of these are factors over which individuals have control.
2. Conduct a baseline study to collect normal diet and activity level data from a group of volunteers. This includes collecting and comparing self-reported data and data collected using an activity meter.
3. Use the base-line date to determine the effects of diet and activity level on energy homeostasis. This will include being able to explain the factors that affect energy balance in humans.

Students’ ultimate goal as a group will be to develop a scientifically-based and workable plan for a patient (or yourself) to use to track energy balance. The emphasis here is on the words “scientifically-based” and “workable”. Many plans can be developed to lose or gain weight. Many of these do not take the science into account. Those that do often fail to recognize that how effective or workable a plan is depends not only on the quality of the plan but also on how easy it is for individuals to follow.

Assessment = Proposal followed by final paper in scientific journal style format which is reviewed by students and modified based on review.

©JG Heitz
I. A Very Short Course in Mammalian Anatomy
II. Experiments in Human Physiology – An Overview

Part I of this module is a designed to help students develop dissection techniques. More importantly, it serves to help students discover and understand the structural and functional relationships among organ systems within a mammalian model organism. In Part II, students conduct simple physiological experiments on respiratory volume, blood pressure, etc. to determine how the functions of these systems are affected by exercise or other activity.

In this two-week lab, students will learn:

• How to dissect a rat (as a representative mammal)
• Basic structure/function relationships among the major organs and organ systems of the mammalian body
• The overall structure and function of the major organ systems: respiratory, digestive, circulatory and urogenital including:
  1. The flow of blood from the body, through the mammalian heart and back to the body
  2. The mechanisms involved in inhalation and exhalation
  3. The functions of each of the major parts of the digestive system
  4. The major roles of the pancreas and hepatic portal vein in digestion and homeostasis
  5. Comparison of musculature as it relates to function of major organs
  6. How surface area to volume ratios affect structure and function of most major organ systems
• The differences in structure and function of the digestive system that accompany herbivory vs carnivory
• How to measure changes in blood pressure and/or pulse rate
• How to measure lung volume
• How to conduct simple experiments in human physiology including:
  1. What factors influence respiratory rate?
  2. How much carbon dioxide do we exhale per unit time and how is this influenced by exercise?
  3. How do blood pressure and pulse rate change following exercise, eating, or other activities?
  4. How is lung volume related to sex, height, activity levels, existing conditions, e.g. asthma?
  5. How does sample size affect analysis and interpretation of our data?
• How to analyze data using Excel to produce means, standard deviations, data distributions, regression analyses and associated graphical representations

Assessment = Worksheet, quiz or formal journal style article.

©JG Heitz

Overview: One of the best ways to study the results of the adaptive radiation that occurred among the different groups of vertebrates is to study their skeletons. Limb structures in the terrestrial vertebrates that exist today evolved from the basic pentadactyl (5 digit) form of the primitive tetrapods (4-footed animals, also called quadrupeds). In the primitive condition, each limb is supported by a girdle (pelvic in the hip region and pectoral in the shoulder region). The pelvic girdle is attached to the vertebral column; while the pectoral girdle is unattached. The limbs consist of a single upper bone in the upper fore or hind limb (the humerus or femur respectively) and two parallel bones in the lower region (radius and ulna in the forelimb or fibula and tibia in the hind limb). A series of small bones (the carpals or tarsals) made up the wrist or ankle. Five longer bones, the metacarpals or metatarsals, made up the hand or foot proper. The fingers and toes (or digits) were each composed of several smaller bones, the phalanges.

Throughout the evolution of the various species of vertebrates this basic form has been much modified. Such modification has resulted in:

1. changes in the position of limbs in relation to the long axis of the body.
2. reduction in the kinds and number of bones in the lower limb regions.
3. elaboration of some structures and total elimination of others.

This lab exercise is designed to give you experience in:

1. developing procedures to make quantitative measures of how parts of the skeletal structure vary among vertebrates
2. determining whether the variation evident can be correlated with particular life habits, e.g. type of diet, habitat, locomotion, mass of animal, etc.

In this two- to three-week lab, students will learn:

Major bone/muscle systems in the vertebrate body
• How change in one aspect (e.g. weight of an organism) requires numerous compensations in structure and function.
• Basic biomechanical concepts (e.g. differences in first, second and third class lever systems and their mechanical advantages)
• Use of quantitative measurements to do comparative study of vertebrate skeletons. Measurements include: proportional measurements, e.g. length vs. cross sectional area, length of limb bones vs overall length of body or overall mass; analysis of digital imagery, comparison of the positioning of limbs under the body , the positioning of the vertebral column and neck in different animals relative to function, lifestyle, feeding habits, etc.
• How to:
  1. collect and analyze data and graphically depict a linear relationship between two variables (using Excel)
  2. use the data to develop a reasonable testable hypothesis about possible trends in evolution and/or structure function relationships evident among the species analyzed
  3. write a formal paper or poster presentation to explain how the hypothesis is supported by the results

Assessment = Formal proposal or poster presentation or oral presentation and possibly a worksheet or quiz.

A phylogenetic analysis of HIV transmission © D. Baum and J. Heitz In this study, you take on the role of Center for Disease Control (CDC) epidemiologists attempting to understand a large number of HIV cases among patients in an isolated community who have no known risk factors. The names and places are fictionalized, but the molecular data and the basic situation are real.

You will be asked to use data you gather from the literature and the phylogenetic data you obtain using PAUP to develop a final CDC report. In writing the report, you will indicate whether your data support one or multiple sources of HIV infection and present a solid scientific argument to support your assertion.

In this three-week lab, students will learn:

• How to find and analyze the literature to determine:
  1. What HIV is and how it is transmitted.
  2. The modes and rates of mutation of the HIV virus (rates of evolution) AND what effects these changes have on the immune system’s ability to fight off the virus.
  3. The current treatments for HIV, survival rates and relative costs of treatment.
• How to interpret phylogenetic trees including:
  1. What a phylogenetic tree represents and how to read it
  2. How to determine how closely related two species are relative to other species
  3. How to determine if a group of species are monophyletic, paraphyletic or polyphyletic
  4. What “root”, “nodes” and “terminals” on a phylogenetic tree represent
  5. The definition of a clade and of cladistic analysis
  6. How to infer character evolution using phylogenetic trees
• How PAUP analysis of DNA sequences can be used to determine phylogenetic relationships. For our students this includes requirements to:
  1. State the scientific arguments they will use to support their hypotheses.
  2. Indicate what scientific data they need to support those arguments. To do this they must have a very good understanding of both how the virus can be transmitted and how it cannot be transmitted.
  3. They also need to understand the basic structure of the virus, how it infects cells and how changes in the viral RNA (or DNA) can occur.
• Explain:
  1. why (for what reasons) they selected their data
  2. what their PAUP phylogenetic analyses and bootstrap trees imply
  3. any problems or limitations they feel might arise by using the hypotheses or data proposed

Assessment = A quiz on “Tree thinking”, a Powerpoint presentation of the literature analysis and a mock CDC Report

When working with a new or unknown system or organism, scientists usually begin by gathering baseline data and testing their own biases by making objective observations of the behavior, etc. of the system or organism under study. The initial exercises in this lab are designed to provide you with some baseline data on the behavior of the hypocotyl of Brassica oleraceae (broccoli) and to allow you to begin developing hypotheses and the rationale for these. Such experiments can also help you determine if you have any biases or “preconceived” notions of how the system or organism “should act”. Based on these preliminary observations you will propose, develop and test a hypothesis concerning the mechanism(s) affecting the gravitropic response of the hypocotyl in Brassica. (Note: In some years we have students investigate phototropic response.)

In this three-week lab, students will learn how to:

• Approach a complex question, i.e. what causes the gravitropic response, by asking smaller questions designed to eliminate possible factors involved
• Develop testable hypotheses that align with methodology
• Develop adequate controls and methods for quantitative measurements
• Set up adequate replicates of both experimental and control treatments
• Use basic scientific tools and techniques, e.g.:
  1. Serial dilution
  2. Pipetting
  3. Capture and analysis of digital images
  4. Cell staining and microscopy
• Use Excel to analyze and interpret data collected in statistical and graphic formats
• Present data in scientific format either as a journal article or poster/Powerpoint presentation.

Assessment = Formal paper or poster/Powerpoint presentation.

In this 3-week module on environmental sensing and signal-transduction pathways, students investigate the use of mutant screens as a tool for genetic dissection of biochemical/biophysical pathways in living organisms. All known organisms utilize an enormous number of separate and/or interwoven biochemical/biophysical pathways to mediate various processes of physiology, metabolism, synthesis & replication, and environmental response necessary for life. Specific examples of any of these general processes can be viewed as a connected series of biochemical and/or biophysical steps that form various types of pathways. Two simple examples are Glycolysis and the Krebs Cycle. Both are metabolic pathways consisting of multiple, ordered biochemical reactions to form a linear sequence in the case of Glycolysis and a cyclical pathway in the case of the Krebs Cycle. Although still being studied today, these two pathways are generally well-established in the literature and the classroom. But how are these pathways (and others) discovered?

One particularly useful method involves the use of genetic selection/screening for mutant phenotypes. This laboratory is designed to demonstrate how a genetic screening strategy can be employed to help understand the pathway(s) by which a plant responds to environmental stimuli such as gravity or light.

In this 3-week lab module the students will:

1. Learn that life processes can be explained in terms of interactions of complex pathways.
2. Learn that plants’ tropic responses are mediated by signal-transduction pathways.
3. Recognize the advantages and limitations of conducting genetic screens to facilitate understanding of complex, biological pathways.
4. Design and execute novel genetic screens to extend understanding of gravitropism and phototropism.
5. Further develop their skills in scientific questioning, reasoning, and modeling.
6. Experience science as a collaborative, human endeavor.
7. Learn the characteristics and importance of effective model systems.

Assessment = A formal journal style article or a synopsis of the research

©JG Heitz

This lab uses Bioquest’s BIRDD computer data base program to investigate evidence for evolution in the finch populations on the Galapagos Islands. Much of the data that has already been collected on the islands is included in the BIRDD program. You will use these data as a basis for writing a grant proposal to do further research in the Galapagos. The first step in writing any grant proposal is to examine data that already exist. Using the information from existing studies, you can develop new questions and propose ideas for further research.

Two categories of data are included in the BIRDD program: general island data and bird data. Green and blue booklets have been developed to help show you what types of information are contained in BIRDD.

In this three-week lab, students will learn how to:

• Design and implement an original and testable research question using existing real data sets. The data sets include: e.g. finch morphology data, song data, DNA data, geographic data for the islands
• Conduct the experiment using Excel to sort and subset data, do statistical analysis (ANOVA) and graphing
• Use the results of the analysis as a basis for proposing continued study
• Write a research proposal including background literature, preliminary results, proposed methodology and budget.

Assessment = Oral presentation of preliminary results and proposal to NSF in final scientific format.

When organisms live together, or occupy the same living space, they inevitably compete for a variety of resources. In the animal world, undoubtedly one of the most limiting resources is food. Organisms also compete for physical space or habitat, sunlight (in the case of photosynthetic organisms) and even mates in order to ensure reproductive success. Competition between individuals of a single species is termed intra-specific competition, while any competitive interaction between individuals of different species is termed inter-specific competition.

The primary goals of this lab are to (1) introduce you to the concepts underlying competition ecology and (2) allow you to test a hypothesis and make conclusions using actual data collected during the laboratory. To do this you will test the effects of intra- and inter-specific competition on Wisconsin Fast Plants (Rapid-cycling Brassica rapa or RcBR) under different environmental conditions in a laboratory setting.

Guided by your lab instructor, each lab section will collectively develop a hypothesis and design the experiments necessary to test the hypothesis. Each of the student groups in the lab section will conduct a subset of the proposed experiments. The data gathered by all groups will be compiled. Each of the student groups will analyze the compiled data, develop graphs summarizing the results and submit a final report in the form of a journal-style article, worksheet or Powerpoint presentation.

In this four-week lab, students will learn:

• The concepts of ecological competition, including symbiotic, commensalistic, parasitic and neutral interactions among organisms; of fundamental versus realized ecological niche
• What a model organism is and why models are used
• The life cycles of the plants to be used including the Wisconsin fast plant model organism (Rapid-cycling Brassica rapa), three grass species (cheatgrass, bent grass, annual rye grass) and three species with symbiotic nitrogen fixers (birdsfoot trefoil, clover, alfalfa)
• How to research peer-reviewed literature
• How to develop a testable hypothesis and design an experiment to test the effects of intra – and/or interspecies competition on RcBr
• How to record, compile and analyze the data from all student groups and develop graphs using Microsoft Excel
• How to write up and present your experiment and results in the format of a scientific paper, worksheet, or Powerpoint presentation.
• Basic laboratory skills used include:
  1. Basic plant growth methods and how growth is affected by:
     1. Temperature
     2. Moisture
     3. Light conditions
     4. Nutrition (nitrogen in particular)
     5. Soil type
  2. Serial dilution (e.g. of fertilizer concentrations)
  3. Quantitative measurements of plant growth in size and/or biomass

Assessment = Journal style article, worksheet or Powerpoint presentation of research plan and results.

© Stanley Dodson Adapted by Brian Parks and Kerry Martin

Ecological principles apply to nature across a broad range of scales and biomes. Even urban and agricultural biomes can be studied as ecological systems. Given the constraints and trade-offs of large introductory courses, it makes sense to study ecology in an urban microcosm. The most available and easily-recognized habitat is the mowed lawn. On the UW campus, mowed lawns are dominated by narrow-leaf grasses, such as Kentucky blue grass (Poa pratensis). There are at least a score of other common species that live within the matrix of the blue grass – these species, which can be thought of as either biodiversity or weeds, are the focus of this exercise. The lawn community is frequently disturbed. The vegetation is regularly mowed, frequently walked on (which is a challenge for the plant, and which compacts soil), and in some locations, treated with herbicides about once every year or two. The community is especially disturbed near cement walks by foot traffic, vehicular traffic (trucks) and snow management (salt and sweeping). Dozens of species are able to live with the dominant grass in the disturbed habitat. Many of these species have a similar life form, and thus are members of the same ecological guild.

This field laboratory experience spans population, community, and landscape ecology, with a focus on community concepts. A goal in population and community ecology is to characterize the relative abundance of different species, and to use environmental and biological variables to explain why some communities (or locations) differ from others. Typical questions include:

1. Why are there more species in one place than another?
2. Do big patches have more or different species than small patches?
3. Do some species show preferences for specific environmental conditions?
4. Do species differ in their environmental preferences — as indicated by abundance, population growth rate, or spatial distribution?

The Goals of this 3-week lab module are:

1. Provide an opportunity for research outdoors.
2. Look at plants in their environment.
3. Collect typical ecological data using standard (and simple) field techniques.
4. Analyze the data using ecological concepts presented in lecture.
5. Practice thinking like an ecologist, and using statistical analysis.
6. Explore the ecological concepts related to community ecology, adaptation, plant morphology, and statistical analysis.

Assessment = Worksheet of data analysis and graphical representation of the data including: niche diagrams, species area curves, Spearman Rank correlations.