1. Module 1: Science, Biology and Evolution 1. Studio Biology - What is it? 1. Studio Biology - What is it? 2. Science as a way of knowing 1. Science as a way of knowing 3. Evolution 1. Evolution 4. Taxonomy and phylogeny 2. Module 2: Ecology 1. Introduction to Ecology and Ecosystems 1. The Scope of Ecology . Ecology of Ecosystems . The Laws of Thermodynamics . Energy Flow . Biogeochemical Cycles . Biogeography Biomes 8. Aquatic Biomes 2. Population Ecology 1. Population 2. Population Growth 3. Population Regulation 4. Human Population Growth 3. Community Ecology 1. Community Ecology 4. Ecological Research 1. Ecosystem Experimentation and Modeling 2. Nitrogen and Phosphorus Cycles 3. Freshwater Biomes 4. Population Growth Curves

NOU RWN

5. Introduction to Water Pollution 3. Module 3: Cell Biology 1. Introduction to Cell Biology 1. Introduction to Cells . Prokaryotic Cells . Eukaryotic Cells . Protists . Fungi 6. Eukaryotic Origins 2. Tour of the Cell: Water, Carbohydrates and Lipids

ui BR WN

1. Atoms, Isotopes, Ions, and Molecules: The Building

Blocks . Water: the Molecule of Life . Introduction to Biological Molecules

. Carbohydrates . Lipids

AuBRWN

. Chemical Reactions of Biological Macromolecules

7. Components and Structure of Plasmal Membranes

3. Tour of the Cell: Proteins and Enzyme Function 1. Proteins 2. Enzymes 3. Buffers and Enzymes 4. Tour of the Cell: Nucleic Acids and Cell Cycle 1. Nucleic Acids and Nucleotides . Cell Reproduction . DNA Replication . Prokaryotic Cell Division . Eukaryotic Cell Cycle 6. Cancer and the Cell Cycle 4. Module 4: Genetics 1. Molecular Genetics: DNA to Protein to Phenotype 1. ‘Transcription

ui BW N

2. Translation 3. Connection Between DNA and Phenotype 2. Meiosis and Mendelian Genetics 1. Sexual Reproduction 2. Meiosis 3. Mendel’s Experiments 4. Laws of Inheritance 3. Variations on Mendelian Genetics 1. Extensions of the Laws of Inheritance 4. Population Genetics 1. Population Evolution 2. Population Genetics 3. Formation of New Species 5. Module 5: Energetics 1. Cellular Energetics 1. Energy and Metabolism . Thermodynamics . Potential, Kinetic, and Free Energy . Energy in Living Systems . Cell Membranes and Passive Transport 6. Energy Requiring ‘Transport 2. Photosynthesis 1. Overview of Photosynthesis 2. The Light-Dependent Reactions 3. Calvin Cycle 3. Cellular Respiration 1. Overview of Cellular Respiration 2. Glycolysis 3. Oxidation of Pyruvate and the Krebs Cycle 4. Oxidative Phosphorylation 5. Metabolism Without Oxygen 4. Bacteria and Fungi: Using Alternative Energy Sources

ui BW N

—_ -. a] =) = ig?) QD ld fmie oO =) 1p) oO — Cd) = oO ie) a

< Cu = jab) os

1D a=) om oO aaa a>) —

=) jab) =) an ay fmie

=) fae (ae

Metabolic Pathways 2. Prokaryote Structure 3. Prokaryotic diversity 4. Kingdom Fungi 6. Module 6: Plant Biology 1. Evolution and Diversity of Plants 1. Lichens, Protists and Green Algae . Early Plant Life . Bryophytes . Seedless Vascular Plants . Evolution of Seed Plants . Gymnosperms . Angiosperms 8. Asexual Reproduction 2. Plant Reproduction; Structure and Function of Plant Tissues 1. The Plant Body 2. Plant Sensory Systems and Responses 3. Reproductive Development and Structure 4. Pollination and Fertilization 3. Interactions of Plants With Their Environment 1. Root and Leaf Structure 2. ‘Transport of Water and Solutes in Plants 3. Nutritional Requirements of Plants 4. Nutritional Adaptations of Plants 4. Photosynthesis, Global Climate Change, and Food Production 1. Photosynthetic Pathways 2. Climate and the Effects of Global Climate Change 3. Human Population Continues to Grow 7. Module 7: Animal Biology

NID OB WN

1. Introduction to Animals 1. Features of the Animal Kingdom 2. Animal Tissue Types 3. Sponges and Cnidarians 4. Flatworms, Nematodes, and Arthropods 5. Mollusks and Annelids 6. Echinoderms and Chordates 7. Vertebrates 8. Homeostasis 2. Material Acquisition and Transport 1. Digestive Systems 2. Digestive System Processes 3. Nutrition 4. The Circulatory System 5. Systems of Gas Exchange 3. Internal Communication and Coordination 1. Nervous System 2. Endocrine System 3. Digestive System Regulation 4. How Animals Reproduce 4. External Communication and Coordination 1. The Integumentary System . Sensory Systems . Reflexes and Homeostasis . Viruses . Innate Immunity 6. Adaptive Immunity 5. Adaptations to Land 1. Urinary System 2. Musculoskeletal System

wu BW N

Studio Biology - What is it? An introduction to the format of Biology 198 - Principles of Biology, taught at Kansas State University

The Studio Format

Introduction

"The first principle is that you must not fool yourself - and you are the easiest person to fool." Richard Feynman, American physicist and Nobel Prize winner, delivering the Caltech commencement address, 1974

Welcome to Principles of Biology, Kansas State University’s innovative introductory biology course. Because this course is almost certainly unlike any course you have taken before, we need to spend a little time to introduce it, and tell you why this course is a great way to learn about biology.

Unlike the traditional lecture & lab introductory biology courses at most universities, Biology 198 at K-State is a studio-format course, combining lecture and lab into the same class period. There are some unique things about studio courses, and especially this one. Our studio model involves 2 separate 2-hour sessions per week, with a maximum of 78 students in the studio; thus you will spend about 4 hours per week in the studio classroom. So it is important to understand that you are in a studio course, which is not a lecture, and not a lab, but is actually a hybrid of lecture and lab. Although it is an introductory course, it was developed with input from all the faculty members in the Division of Biology. There are usually two faculty members, two GTAs and one or more undergraduate practicum student instructors per 80 students in each section.

Why do we teach this course this way? Because we believe in education, and also in giving KSU students a lot of education for their tuition dollars. The studio format has been shown to be a very effective way for us to help you learn about biology. In fact, it is about twice as effective as the traditional lecture/lab course in terms of your learning and retention of the material. So that’s why we teach it this way.

It is also unique in that the faculty members teaching this course can include anyone in the department, including full professors. Introductory science courses, in particular, tend to be taught by graduate teaching assistants here, and at other institutions. If they are taught by a full professor in Biology 198, many freshman students will not have another course taught by a full professor until their junior or senior year. At many of our peer institutions, introductory biology courses are taught with a single instructor lecturing to 500-800 students, accompanied by a lab taught solely with graduate students. That’s a relatively inexpensive way to teach introductory science courses, but also a relatively ineffective way. If you take advantage of the significant resources (both personnel and material) that the Division of Biology devotes to this course, you will learn a lot of biology. Equally importantly, you will learn how to study and be successful in a university environment. That’s another advantage of the studio format!

Course materials

Two items are essential to your successful learning in this course, both of which are designed to maximize learning in the studio environment. The first is the free electronic textbook, which you are reading now. The second is the Principles of Biology Studio Manual, which must be purchased from the KSU Biology Graduate Student Association. It may look like a lab notebook, but is actually something quite different. The studio manual is analogous to your lecture notes in a standard lecture class; it is simply YOUR record of what you do in the studio. What you see, do and hear during your time in class will be recorded in your Principles of Biology Studio Manual. More importantly, it is not analogous to a lab notebook ina lab class. You do not need to turn it in to be graded (just like nobody grades your lecture notes in a lecture class!). So please treat that studio manual, which is a required text for this course, like you would your lecture notes in any other class. Read it over before the next class, mark down any questions you might have, and make sure you get a copy of the notes from another student if you have to miss a studio class.

Course and testing structure

The course is divided into 7 units, each with four or five class periods that are devoted to those units. There are tests on all 7 units, and the dates for those tests can be found on your course syllabus (link). You will start with an Introduction to Science and Biology (including two classes on Evolution), then go immediately into the study of Ecology and Ecosystems. After gaining this large-scale perspective, you will move to the study of living things at the smallest scale (molecules and cells), and then move up to the organism level (Genetics, Energetics). The final two units are more traditional (Plant Biology, Animal Biology). The final exam, at the end of the semester, is not a comprehensive exam; it covers only the last unit (Animal Biology). But all of the learning that you have done in prior units will be very important in your understanding of the concepts covered in that final exam

The test questions are all written to evaluate your knowledge of the unit Objectives. More importantly, the objectives for each class period are provided to you at the very beginning of each section of the studio manual. So if you want to know “What do I have to know for the tests?”, the simple answer would be “the Objectives for that unit”. You will gain an understanding of these objectives in many ways, not only from this electronic textbook, but from the studio exercises, the web pages for this class, and from discussions with your fellow students both inside and outside the classroom. In addition we have prepared Study Guides that are also based on the Objectives. For each of the day’s Objectives, we provide a detailed listing of all the places (e.g. textbook, studio exercise, web page, or some combination of those) where you can get the information needed to master that Objective. If you spend your time in the studio wisely, and study with those Study Guides regularly (not just the day before the exam!), you should have a very clear understanding of the material that we think you should be learning in this class. Each question on each exam is written with one of those Objectives in mind, so it should be obvious that the Objectives are the key item on which to focus your efforts.

Your responsibilities

There will be readings in the textbook for every class day (except for the very first day of class); those reading assignments are listed in the Studio

Manual, right after the Objectives for every class period. The textbook readings are an introduction to the topics for the studio exercises that day, so you need to read them BEFORE coming to class each day. In order to assure that you do the reading, there will be a short quiz over the reading material for every class period. By the end of the semester, the points for these quizzes add up to approximately the same value as a unit exam. The points should provide some incentive, but as you learn more about this course you should also figure out that learning in the studio classroom is more efficient if you have a good understanding of the material covered in the reading for that day. And more efficient learning in the classroom translates to better scores on the unit exams!

In addition, your instructors will track your attendance in the studio; attendance is strongly recommended for this class. Interacting with your instructors and fellow students is an important component of the class, and we have excellent data which prove that missing multiple classes is highly correlated with lower exam scores, and lesser learning and retention. We really want you to learn biology, but you can’t do that if you are not in class. So to make sure that you take full advantage of the learning opportunities in the studio, we give an attendance bonus at the end of the semester. Please see the syllabus for more details.

Your success in this course, both in terms of amount learned and in terms of a good grade, is assured if you understand the format of the course, do the assigned readings and attend the studio sessions faithfully, and spend at least as much time studying outside the classroom as you spend inside the classroom. You are responsible for learning, just as you are responsible in every class you take. But the difference in this class is that we do everything we can to provide the resources and the environment where learning is maximized.

Instructor responsibilities

Your studio instructors will deliver a brief (10-15 minute) introductory lecture at the start of each class day, and an equally brief wrap-up session at the end. In between those two lectures, you will be working with your fellow students on the studio exercises for that day. During that time the

instructors will circulate in the studio, asking questions, answering questions, and generally helping you learn the material. Please take advantage of this incredible opportunity to interact, one on one, with your faculty and GTA instructors. If you have a question, don’t be shy. If you want to know if your class notes (i.e., the stuff you are writing in the Studio Manual) are accurate, ask an instructor. Their job is to help you learn the material, and they can help a lot more if they know what your questions and concerns might be.

Your studio instructors will also be responsible for grading the daily quizzes and recording those grades, usually in a course that they set up on K-State Online. If you are not familiar with K-State Online, don’t worry. It is our course Management system, and it is very easy to navigate. Your studio instructors will not be responsible for writing the biweekly unit exams. Since there are 10 sections of this course each semester, it is better (and more fair) if all students in all sections take the same exams. So those exams are written by the course coordinator, and all exam questions are vetted by faculty members who are teaching in one or more sections in a semester. The first 6 unit exams are administered on Monday evenings (see syllabus for the exact dates), and the final unit exam is administered on Thursday morning during finals week. Grades for these exams will be recorded on K-State Online as well, so that you have ready access to your grade information.

Helpful hints

¢ Read the assigned material before coming to class.

e Don’t skip class.

e Take advantage of the learning opportunities afforded in the studio (your fellow students, the instructors, the practicum students, the studio exercises, etc.) every time you are in class.

e Take good notes and read over your notes in the studio manual within 24 hours after every class.

e Use the study guides and concentrate on the Objectives when you study for the unit exams.

e Study a little bit every day rather than cramming the day before the exams.

e Ask lots of questions, and be prepared to answer lots of questions. ¢ Don’t fall behind, but if you do, make every effort to catch up as soon as possible.

Science as a way of knowing The scientific method as it applies to biology

Science as a way of knowing

"We absolutely must leave room for doubt or there is no progress and no learning. There is no learning without having to pose a question. And a question requires doubt. People search for certainty. But there is no certainty." — physicist Richard Feynman, in a lecture at the Galileo Symposium, 1964.

Introduction

What is “Science”? Everyone probably has some idea of what the word means, but have you ever really thought about it? If so, here are some questions to consider.

e Is science a body of knowledge?

e Is it the same thing as “truth”?

e Is it a way to understand everything, or just a few things?

e Is it a process, and if so, can everyone do it? Or do you have to be highly intelligent, highly trained, or both, if you want to understand science?

Hopefully by the end of this course, or even by the end of this first module, you will have some good answers to those questions, and will be well on your way to thinking like a scientist (at least for this class!). Let’s start with the title of this chapter — Science as a Way of Knowing. That description is from the title of a great little book by biologist John A. Moore, and is actually a pretty good answer to the question of “What is Science?” Science is both a body of knowledge, and an evidence-based process for generating that knowledge. The word itself comes from a Latin term, scientia, which means knowledge. But science is also about a particular kind of knowledge - knowledge about the natural world. In addition, the process of “doing science” can only help us gain additional understanding about the natural world. It is of no use to us if we want to understand the supernatural. For that we need other ways of knowing.

There are also some other aspects of science which you need to know, as you move toward a better understanding of both the scientific knowledge base and the scientific process.

Science

e requires interaction with the natural world in terms of observation, detection, or measurement.

e is objective, or evidence-based; that evidence, or a repeated demonstration of the evidence, must be available to everyone. Scientists generally don’t just “take your word for it.”

e requires independent evaluation and replication by others.

e leads to conclusions that are always provisional, i.e., they will be rejected or modified if new observations or measurements show that they are false.

There are, of course, other "ways of knowing". How do we know what we know? People who study knowledge (yes, there are such people, and they are in the branch of philosophy known as epistemology) often classify that knowledge based on the source of the knowledge. In mathematics and logic, for example, we can point to things that we know are "rationally true". In science, we focus on things that are "empirically true", i.e., based on evidence that we can see, hear, touch, etc. In religion, and, to a lesser extent, in history, we focus on "revelational truth", or knowledge that comes from another source that we accept as true, based on our assessment of the reliability of the source. So the subjects that you might study at this university can depend on different sources for the knowledge that you will be gaining. In this class we will focus, as noted above, on objective evidence obtained from observations of the natural world, and we will use some very specific terms to describe how those empirical observations form the basis for scientific knowledge and understanding.

The process of science

So how does this process work? The processes that generate scientific knowledge are known as the scientific method. But even as you learn this method, it is important to realize that this is not a set recipe or process that

MUST be followed in all cases. The scientific method is best understood as a statement of the core logical principles underlying how science works. The process of science always uses these core logical principles, but any individual scientific enterprise might not adhere exactly to the method outlined below ([link]).

The Basic Scientific Method

Formulate Hypotheses

I

Observation & Experimentation

Accumulated Data or observations i" =

— => Theory

The Scientific Method — 1) Observations are used to formulate the 2) hypothesis, which is then 3) tested with experiments or new observations. The 4) new data contribute to the pool of observations, and also are used to refine the hypothesis as needed. Eventually the accumulated data allow one to make a 5) conclusion, which can contribute support for an existing 6) theory, or in some cases, support for a new theory. In all cases theories can be used to generate new testable hypotheses, which is why we say theories are both explanatory and predictive.

All science starts with an observation, or set of observations, about the natural world. You might observe a pair of male elk fighting in a high- country meadow in Colorado, for example. The next step, if you want to think about this scientifically, is to formulate some hypothesis to explain that observation. A hypothesis is a statement that is simply an educated guess about the cause(s) of the observed phenomenon. In order for that hypothesis to be useful in a scientific sense, however, it must have some additional characters. A scientific hypothesis must be testable, and it must be falsifiable. It does no good to generate a hypothesis that you cannot test in the real world. Thus it would not be a scientific hypothesis if you stated that the elk were fighting because invisible men in an invisible spaceship parked on the far side of the moon were controlling these elk with undetectable brain waves. That might be the actual explanation, but you can’t test it, and you can’t falsify it.

A good scientific hypothesis lends itself to making testable predictions; if the hypothesis is true, then X must be true. In this case you might state generate this hypothesis — these are male elk, and they are fighting for control of a herd of female elk. Immediately some predictions come to mind. If this hypothesis is true, you should be able to detect that these are male elk. Without getting too close, you can see that they have antlers, and previous work by other scientists (part of the set of accumulated observations that you are relying on) has shown that only male elk have antlers. Prediction confirmed. Another prediction might be that there should be one or more female elk nearby, and that these females would eventually go with the male who wins the fight or drives off the other male. You look around, and you see a herd of 10 or so female (antlerless) elk watching the spectacle. Another prediction confirmed. You will have to wait until the fight is over before you know if the prediction about the females staying with the winner is confirmed. But you have two predictions confirmed, and so far your hypothesis is supported by the evidence. More importantly, it has not been falsified. All of the data so far support it.

This brings up another important aspect of the process of science. In this case you made predictions and confirmed them with additional

observations. You didn’t do anything to the subjects; you merely observed them more closely. That is a valid approach. An equally valid approach would be to test your hypothesis by means of experiments. Experiments are manipulations of the experimental system, followed by additional observations. In this case, for example, you might hypothesize that the male hormone testosterone is causing the elk to fight. One prediction from that hypothesis would be that injection of testosterone into female elk (which don’t normally produce testosterone) would lead to aggressive behaviors in the female elk. You would also predict that male elk, deprived of testosterone, would be less aggressive. You might be able to come up with some other predictions from this hypothesis that could be tested with other experiments. You would have to capture some elk (male and female) to do the experiments needed to test these predictions, of course. That could be tricky, or dangerous, and you might need to hire and train help. Or you could look for similar behaviors in smaller, more easily handled animals such as mice or rats, and do the same experiments with those creatures. Both of these approaches, using observations or using experiments, are scientifically valid, as long as your hypothesis is testable and falsifiable. Furthermore, as you will learn many times in this course, there are other aspects of the experimental approach, involving concepts like sample size, variables, and controls, which you will need to consider as well. We’ |l save the discussion of those until a bit later, after we conclude our consideration of the general scientific method.

If you look at ({link]), you will see that multiple tests of the predictions lead to an increase in the number of observations. Any test of the hypothesis, no matter if it confirms or disconfirms the hypothesis, adds to our knowledge base. Generating new knowledge is one of the exciting parts of doing science, in fact. All of these observations can be used by future generations of scientists to test future hypotheses.

You’ll also find another important word in ({link]), and that is the word theory. In regular conversations, people outside of science often use this word to mean an unproven or unsupported explanation, a wild guess. As you learned above, in science that description would be more appropriate for the word hypothesis. In science, a theory means something quite different. A theory is a statement or set of statements that explains some

aspect of the natural world that is supported by substantial amounts of data from diverse lines of investigation. The statements that form a theory are NOT "wild Guesses" but are often hypotheses that have been tested many times. Therefore, a theory has predictive power and those predictions can be tested. If a prediction is falsified, it does not mean the theory is false, it means the hypothesis needs to be reworked. There are many theories in science; examples relevant to the study of biology include the germ theory, the cell theory, plate-tectonic theory, and of course the grand unifying theory of evolution. All of them are well supported by incredible numbers of observations; all of them are considered the best available explanation for a diverse set of observations.

In addition, as shown in ({link]), you can see that just as observations lead to predictive hypotheses, theories can lead to predictive hypotheses as well. In fact, one of the hallmarks of a theory is that it provides a solid framework for generating hypotheses and making predictions. Scientists are confident in the explanatory power of theories, and thus are comfortable in using them to construct hypotheses, design experiments, and frame the interpretation of the data generated by those experiments. Just as a scientific hypothesis is useless if it cannot generate predictive hypotheses, a theory must serve as a framework for hypothesis building and testing. And just as the predictions of the hypothesis must be borne out by new observations if the hypothesis is going to be accepted, predictions from a theory must be supported by the observations if the theory is to continue to serve as the best available explanation for a vast set of observations.

Not shown in that figure, but implied nonetheless, is the fact that the observations must be repeatable. Other scientists, working in other locations, need to be able to do similar experiments and get the same results. That is what is meant by the statement that science is objective, not subjective. Another scientist has to be able to get the same results as you, and vice versa. Again, the history of science has thousands of examples where a new and exciting result was announced, but eventually forgotten when other scientists could not get the same result. Recent ones include the phenomenon known as “cold fusion”, or the identification of a virus that was thought to cause Chronic Fatigue Syndrome (CFS). In all of these cases the original observation was found to be flawed in some way, and

subsequent work, either by the original observers or by others, revealed the flaws and debunked the explanation.

Finally, it is important to remember that all scientific conclusions are provisional. In other words, a scientific conclusion is accepted as the current best explanation, but with the understanding that future investigators could make observations that might negate or modify the conclusion. So it is likely that some of the things that you will learn in this class are wrong, or at least incomplete. We still expect you to learn them, since they are the current best explanation, but it is almost certain that something in this textbook, or in the other materials for this course, will be shown by future scientists to be erroneous or incomplete. Who knows, you might be the scientist who does the work that reveals the error. Scientists actually dream about being the person who overturns a long-established notion, since that often means that their work will be remembered, and may even appear in future biology textbooks. One example of overturning a long-established concept, and ensuring a place in future textbooks, can be found in Louis Pasteur’s experiments, described below

Experiments and controls

As mentioned above, a common approach to generate new scientific knowledge is to perform experiments, where the scientist changes the situation and then observes the effects of these changes. In keeping with the scientific method, this starts with an observation, from which the scientist generates a hypothesis. The hypothesis leads to a testable prediction, followed by experiments based on that testable prediction. Let’s look at one of the most famous experiments in all of biology as an example.

¢

| Broth without contamination without contamination

‘

‘Grgenismagrew | grew

Pasteur's test of the hypothesis of spontaneous generation [By Carmel830 (Own work) [Public domain], via Wikimedia Commons]. Pasteur attempted to explain the observation that organisms (molds and bacteria) appeared in meat broth that had been boiled. His hypothesis was that these organisms came from the air, rather than from spontaneous generation. That hypothesis would predict that organisms would not appear if the meat broth was not exposed to air. He boiled the broth in flasks with long necks; air could not enter past the fluid that was left in a U-shaped section of the neck of the flask. As a control he boiled broth in other long-necked flasks, but then broke the necks off so that room air (and any microbes in that air) could fall on the broth. No organisms grew in the flasks with intact necks; organisms were found in abundance in the flasks with the broken necks.

It was widely believed in ancient times that living things arose spontaneously if conditions were right. One of the observations that led to this belief was that molds, bacteria, maggots and other life forms appeared if one left a piece of meat out in the air for a while. This concept of spontaneous generation was tested in 1860 by Louis Pasteur, using an experimental setup diagrammed above ((link]). Pasteur heated meat broth, in glass flasks, to a temperature where he imagined that no living things were left alive in the broth. If he left this broth out in the open, it developed active bacterial and mold growth, an observation which was consistent with the notion of spontaneous generation. But Pasteur, having recently learned about microbes, suspected that the mold and bacteria arose not from spontaneous generation, but from microbes present in the air. So he devised a set of experiments to test this hypothesis: Living microbial cells present on dust particles in the air are the source of the living cells growing in the heated meat broth.

What prediction could one make with this hypothesis? You can probably think of a couple, but the one that Pasteur came up with was that if the meat broth was in a vessel which excluded cells dropping into it from the air above, there would be no bacterial or mold growth in the broth. So he heated batches of broth in long-necked glass flasks until he thought the broth was sterilized, and also heated the necks of the flask to allow him to bend them into an “S” shape. The ends of the flasks remained open to the outside air, but dust settled in the trap in the neck of the flask and did not reach the surface of the meat broth. In other experiments, he broke off the neck after heating the flasks, allowing dust particles to settle on the broth, or waited a few days and then tilted the flasks so that the broth came into contact with the dust trapped in the bottom of the trap in the neck of the flask. Then he observed the results. Just as importantly, he repeated the experiments several times to make sure that his observations were correct.

We’ve already discussed the hypothesis, and one prediction, above. But what are some other important aspects of this experimental approach? One is the concept of a variable. A variable is some condition of the experimental setup that can be manipulated by the experimenter. Ideally, the experimenter should change only one variable at a time (keeping all other conditions identical); this makes interpretation of the results a lot more

straightforward. What was the variable in Pasteur’s experimental setup? In this case, the variable was access of dust to the surface of the broth. In flasks that were left open, access was allowed. In the flasks that had an intact S-shaped trap in the neck, access was not allowed. Pasteur also manipulated this variable by tilting the S-shaped flasks so that accumulated dust could contact the broth.

The other important part of this experimental approach is the concept of control experiments, also known by a shorter term as just controls. A control experiment is a setup where the variable is not introduced, so that it can be directly compared to the experimental situation where the variable (access of dust particles to the broth) is included. So a control experiment for Pasteur's incubation of broth in an open-necked flask would be incubation of broth in the S-necked flasks. If the variable is introduced by tilting the flasks, the control would again be the S-necked flasks. All other conditions (heating temperature, amount of broth, size of flasks, etc.) were the same in the experimental and control situations. The only thing that was different was a single variable (access of dust particles to the meat broth), because that was the hypothesized source of the living cells that grow in meat broth left out in the open. A single control experiment is usually all that is needed if there is only a single experimental variable being manipulated.

But it is not always possible to simplify a system so that there is only one variable. In those cases, as you will learn in the studio exercises for this class, you might need multiple control experiments. Experiments and controls will also be repeated before the investigator reports the results. It will be described in a way such that other investigators can readily repeat it as well. In some situations the results will be subjected to statistical analysis, although this was not necessary in Pasteur’s experiment. Statistical analysis is critical in many scientific approaches, particularly in studies involving hypotheses about human subjects (e.g., the hypothesis that smoking causes lung cancer), where experimental manipulation of the subjects is difficult or impossible. A scientific experiment, no matter how the results are analyzed, should lead to a conclusion that either supports, or fails to support, the hypothesis. Finally, the experimental results should lead to additional hypotheses, and additional predictions, that can generate

further support (or lack of support) for the hypothesis. Try to think of a few additional experiments that you might have suggested to Louis Pasteur if you were alive in 1860, and if you could speak French!

Other aspects of science

The characteristics inherent in the scientific process lead to another property of science, and that is that science is self-correcting. By that we mean that errors can be made, but that continued application of the tools and processes of science will usually lead to elimination of the errors and a more accurate understanding of the natural world. Science never really and finally proves anything to be true; it can, however, prove things to be untrue. To some people, in fact, that characteristic of science, its fluid and changing nature, is maddening. If you require solid ground to stand on, and immutable truth in all aspects of your life, you probably shouldn’t become a scientist. If you find excitement in being part of an enterprise that is constantly changing the extent, and even the nature, of knowledge, then you have some of what it takes to be a scientist. But even if you don’t become a scientist, a bit on scientific knowledge, and a bit of practice with the scientific process, will help you understand the things you need to understand in order to make intelligent decisions about many things, such as health care, climate change, or other concepts that are in your future.

Science is also a curious mix of intuitive and counter-intuitive behaviors. You practice the scientific method intuitively every day, whether you realize it or not. If you flip on the light switch in your bathroom in the morning, and the light doesn’t come on, you probably take a scientific approach to solving that problem. You might hypothesize that the bulb is burnt out, and if that hypothesis is correct, replacing the bulb should solve the problem. So you do that experiment, and replace the bulb, and the light goes on, and you can continue with your daily activities blissfully unaware of the fact that you acted scientifically already that day. Intuitive science in action!

But some aspects of science, and particularly the scientific process, are not intuitive. All of us have the ability to think that our explanation of some phenomenon is correct, even if there are other observations that contradict that explanation. In fact, we often search for additional evidence to confirm

our conclusion, and ignore any evidence that we might find that casts doubt on the conclusion. This is known as confirmation bias, and is particularly strong in situations where we have an large emotional or financial stake in the conclusion. For example, you might consider yourself a pretty good basketball player. So when you have missed 10 shots in a row, you keep shooting until you make a shot, and then you feel better about your belief that you are a good basketball player, even if those shooting percentages contradict that belief. Or you might make a visit to the chiropractor when your neck hurts, and the chiropractor might make your neck feel better. But a few days later, when it hurts again, you might not take this as a sign that chiropractic manipulation is not a cure. You might go back to that chiropractor, to have the same manipulation, because you have already invested money there, and you’d like to think that you are not wasting your money. Confirmation bias, of the active sort rather than the passive version in the previous examples, is particularly evident in people who buy into conspiracy theories. They seek out others with the same beliefs, or they only look at websites that are dedicated to that belief. It’s only human nature that people like to hear what they think they already know. As a character in Terry Pratchett’s Discworld series observes, “...what people think they want is news, but what they really crave is olds...Not news but olds, telling people that what they think they already know is true.” We all like to think that we know everything that we need to know, and scientists are no exception.

So scientists have to actively guard against confirmation bias. If a scientist has an hypothesis, she has to come up with predictions and experiments that will disprove that hypothesis. If the experiments indicate that the hypothesis is wrong, the scientist has to abandon that hypothesis and generate a new one, and it has to include the results of those disconfirming experiments. This is a very difficult assignment, and certainly goes against lots of human impulses. As the physicist Richard Feynman wrote, “The first principle is that you must not foolyourself, and you are the easiest person to fool.” Every good scientist has abandoned many more hypotheses than he or she has confirmed; science teaches humility that way, for certain. Scientists must be able to change their minds if observations warrant it; there is no shame for a scientist who admits being wrong. Exactly the opposite, in fact. There are many sad examples of individuals who hung on to a hypothesis

too long, and ended up with a tarnished reputation. But as we all know, admitting you are wrong is difficult for most people, and scientists are human too.

The science of biology

It’s now time to shift from a discussion of science in general to the specific scientific discipline that you will be learning about, biology. Biology is the study of life. that naturally leads to the question — What is life? Suprisingly, that has proven to be a difficult question to answer in just a few words! Most textbook-level definitions of life are merely a list of characteristics; anything that exhibits all of those characteristics is said to be alive. Here’s a typical list.

Living things:

e Respond to the environment.

e Assimilate and use energy from their environment.

e Maintain a relatively constant internal environment, even as the external environment changes (homeostasis).

e Reproduce (at the level of organisms) and can evolve (at the level of populations).

e Are highly organized, relative to their environment.

These are general characteristics, and might describe all organisms, even those which have not yet been discovered yet (e.g., those on other planets or solar systems). Until those organisms are discovered and studied, however, that statement is provisional. In addition, scientists have discovered that all living things discovered to date (i.e., the ones on this planet).are composed of one or more cells, and have DNA as their hereditary/genetic material. Some textbooks include these characteristics in their definition of life as well. More importantly, the commonality of DNA as the genetic molecule in all known life forms is strong evidence that all living things on this planet are related, i.e., they have a common ancestor. A putative common ancestor was a prediction made by Charles Darwin when he elucidated his theories about evolution and natural selection. The fact that his prediction

proved to be correct is one (of many) pieces of evidence that support that theory. You’ll learn about some of the other evidence later in this course.

One productive way to study and understand living things is to recognize that there is a biological hierarchy, which is basically an organizational concept map that allows us to focus on various levels of life.

Biosphere Life on Earth

=

All the organisms plus

Ecosystem = bees ‘ ate i | physical components

cy

All the organisms of a prairie: animal, plant, fungus, etc.

Community

=

Population Bison population

=

Organism A bull bison Organ System ‘ J Circulatory system Heart

>is

Tissue Cardiac Muscle tissue

cs

Cell Cardiac Muscle cell