ZOOL 304, Class Notes
Introduction, Week 1
304 index page
- Most important: Record this address where you will not lose it:
At this website you can find all class materials (syllabus, policies, assignments, class notes, etc.)
Below are some introductory comments on this course, on evolution's place in biology, and on sources of scientific information.
- Philosophical preface
- Status of evolutionary biology
- Reliability of information sources
Look over the syllabus and course description. Skim through the textbook. Determine whether this is really the course you expected. Contrary to the SIUC catalog description, this course will NOT examine "prebiotic evolution" (i.e., the origin of life). Nor will we devote much class time to "defending" evolution against the creationist arguments that arise from [misguided] religious apologetics, although we will occasionally discuss the historical sources and philosophical underpinnings of evolutionary concepts.
Ideas and facts (Questioning and understanding vs. memorization.)
Most of you have probably had several biology courses in which you were expected simply to remember a very large number of facts. This course will be different. There will be remarkably few straightforward facts but a lot of ideas. Many of the ideas will be challenging, and some of the ideas involve competing explanations. Understanding what the ideas are about will be at least as important as remembering the associated facts.
The facts of evolutionary biology are all of the facts of all of the other areas of biology. Evolutionary biology is a discipline that tries to provide an explanatory framework for all those facts. Evolutionary biology deals with questions and hypotheses, and with tests of those hypotheses. You have had other biology courses, and hopefully you are already familiar with lots of biology information -- from systematics to comparative anatomy to genetics to ecology. You'll be expected to recall and apply that information in this course. While it might be possible to learn about evolution as an abstract concept, you will find the experience much richer if you bring to this course a lot of information about real, factual living things, how they are constructed and how they work.
In evolutionary biology, understanding the questions that are being asked can be as important, and as challenging, as understanding the various explanations. In many biology courses, the questions are obvious. Given any organism, whether beetle or begonia or bacterium, What is its name? What group does it belong to? Where does it live? How does it survive and reproduce? Given any part of an organism, whether bone or molecule, What is it called? What does it do in the organism? How does it work?
In evolutionary biology, the questions are often rather subtle. And the answers are seldom simple facts but are rather a mixture of several different explanations. Sometimes the various explanations are complementary, sometimes supplementary, sometimes contradictory (more).
Evolutionary questions often take the form of, How did this situation come to be? What events and processes led to this set of species, with this set of characteristics, in this ecosystem? And evolutionary theory generally gives several possible answers. So, important issues in evolutionary biology often involve appreciating what the questions are, why the questions matter, and how many differing explanations may be available to provide answers.
It also matters whether those explanations are mutually exclusive, complementary, or supplementary (more). In a number of areas, we will NOT be emphasizing nice pat answers to obvious questions. Rather, we shall be considering what types of questions should be asked, what types of data are relevant to answering the questions, and what problems must be addressed in any attempt to interpret the data.
In short, this course may be quite different from any you have had before. You will actually need to think. Rote memorization will NOT serve you well. Last minute cramming will NOT be a reliable study strategy. You will need to be exerting yourself day by day, week by week. If you do not understand what is going on or why it matters, you need to ask questions. To do that effectively, you need to come to class, and you need to come prepared by reading the text ahead of time.
Here is a simple study aid: As you are reading every chapter, ask yourself "What questions about nature led scientists to the ideas related in this chapter?" Then ask, "What problems, or what evidence, provoked the questions?" Only when you have answered such questions will you be prepared to appreciate the ideas in the chapter. You might usefully repeat this process for each section of the chapter.
For example: Chapter 1 is titled "The Nature of Evolution". You might ask yourself the question, How many different meanings does the word "evolution" encompass? Indeed, What is evolution? (more) Then try stepping back and asking, Where did the idea of evolution come from? What could explain the diversity and adaptation of life on earth? Several general observations suggest further questions: Why can species be classified into nested sets of taxa? Why do organisms alive at the present time differ from those revealed in fossils? If those seem too easy, Are any patterns of evolution predictable? Is evolution inevitable? Under what circumstances could evolution cease?
If you appreciate the evidence for descent with modification (which quite a few scientists had already interpreted as evidence for evolution, decades before Charles Darwin came along), you might ask "What mechanism could possibly drive evolutionary change and produce adaptation?" Then, "What must be the necessary consequences of reproductive excess in combination with hereditary variation?" "What might happen if observable small changes over short spans of time were extended over indefinitely long ages?" In other words, don't begin by presuming the answers that science has already discovered (answers that have already been handed to you in previous classes). Instead, learn to ask yourselves where those answers came from, and (especially!) why the questions were asked in the first place. By doing so, you will be recreating in your own mind the process of scientific discovery. And in the process you will understand current answers much better than if you had never wondered why the original questions had been asked.
Uncertainty, multiplicity of viewpoints, and controversy
Implicit in this emphasis on questions and explanatory principles rather than simple facts is the complexity of evolution as a process and the often insurmountable difficulty of acquiring appropriate information to explain specific cases.
Providing evolutionary explanations for particular biological phenomena (as opposed to understanding explanatory principles) is in some ways like predicting the weather. For weather, even though we understand most of the underlying causal principles with great precision, it is simply not possible to acquire data sufficient for predicting chaotic dynamics with long-term accuracy. Chaotic dynamics may also govern many evolutionary processes, but in any case too much depends on specific details which are not available for scientific analysis.
Examples of unknowable information which can be critical for precise understanding of specific evolutionary events may be grouped into at least three categories.
- Data which are available in principle but wildly impractical to obtain, such as DNA sequence data for the entire genome of every member of a population.
- Data which are fundamentally unobtainable, like a precise genotype for every organism in the ancestral genealogy of a living species, and all environmental conditions for in which those ancestors lived. Most of this information is irretrievably lost in the depths of time, although inferring significant bits of it (e.g., global conditions during ice ages, or major branches of life's phylogenetic tree) is the principal goal for some branches of geology and evolutionary biology.
- Concepts which are currently unavailable but avidly sought, like the relationship between genetic information and adaptive morphology, or between genetic differences and differences in selective advantage, or between ecosystem parameters and population dynamics. Advances in any of these fields could move evolutionary biology forward immensely. Meanwhile, hopefully, data from evolutionary studies may contribute to advances in these other domains of biology.
Evolutionary processes are multifaceted. That is, there are often many different explanations that compete for our attention. (See definitions of evolution.) Competing definitions and/or explanations may be mutually exclusive (at most, only one can be true), complementary (more than one are necessarily true), or supplementary (more than one might be true, in various possible proportions). Yet multiple explanations are often presented (and learned) one at a time, rather than in concert. Recall the famous Hindu fable of "The Blind Men and the Elephant", excerpted here from the verse form by John Godfrey Saxe:
It was six men of Indostan
To learning much inclined,
Who went to see the Elephant
(Though all of them were blind).
That each by observation
Might satisfy his mind.
The six men encounter in turn various parts of the animal -- and then each announces enthusiastically what the elephant is like. The one who feels the elephant's side proclaims that "the Elephant is very like a wall." Similarly, those who feel the tusk, trunk, ear, tail or leg each proclaims that the Elephant is very like a spear, snake, fan, rope, or tree.
And so these men of Indostan
Disputed loud and long,
Each in his own opinion
Exceeding stiff and strong,
Though each was partly in the right,
And all were in the wrong.
Note that the proffered descriptions (wall, spear, snake, etc.) all appear to be mutually exclusive, when they are actually supplementary (i.e., each is but part of a complete description).
Remember, much information in evolutionary biology is partial and limited, revealing at best only one aspect of the "elephant" of evolutionary processes.
STATUS OF EVOLUTIONARY BIOLOGY
Centrality of evolution to biology (in principle)
Books on evolution commonly quote Theodosius Dobzhansky: "Nothing in biology makes sense except in the light of evolution". However, you may have noticed that evolution is not mentioned nearly as often as such declarations might lead one to expect, and much (most?) modern biology pays only lip service to evolution. For example, here at SIU, evolutionary biology is neither a required course for any major nor a prerequisite for any other course. What's going on here?
I would rephrase Dobzhansky: "In our modern understanding of physics and chemistry and natural laws, the mere existence of biological phenomena only makes sense in light of evolution." In other words, we can quite happily study many things in biology without reference to evolution, but we cannot explain how those things exist in the first place without evolution.
Marginality of evolution (in recent practice)
"For all its formal elegance, however, [the genetical theory of natural selection] has provided very limited guidance in the work of biologists."
George Williams, Adaptation and Natural Selection, 1966, p. 20.
Much of modern biology consists of efforts to explain how organisms work, whether in terms of protein function, cellular organization, developmental gene regulation, organismal physiology, population behavior and genetics, or ecological relationships. Evolutionary questions cannot even be asked until such phenomena are understood in some detail at this level of proximate mechanism. Therefore, much research in biology has proceeded apace without much regard for evolution. This is true even in areas like systematics where evolutionary considerations might seem essential.
By way of analogy, people can manufacture, buy, and use automobiles or refrigerators with little appreciation for the profound laws of thermodynamics upon which the operations of those machines are based. However, the better one understands underlying principles, the more intelligently one can choose and care for a machine. No one with a basic understanding of physics could be fooled by claims that you can keep your kitchen cool by leaving open your refrigerator's door, or that water offers an inexhaustible source of hydrogen fuel. Similarly, a basic understanding of evolution can help guide intelligent investigations in many areas of biology.
Renewed relevance of evolution (in current practice)
Recently, many areas of modern biology have become newly dependent on evolutionary principles. Examples will not be developed here, but you might wish to read a recent editorial in Science 281:1959 (25 Sept. 1998), "A Revolution in Evolution", by Jim Bull and Holly Wichman or a longer article "Applied Evolution" by the same authors in the Annual Review of Ecology and Systematics 23:183-217 (2001). "Today, the study of evolution ... has become socially and economically relevant", in medicine, agriculture, and even criminal law, as well as basic research. A recent article in Scientific American presents the relevance of evolution to problems in medicine: "Evolution and the Origins of Disease", by Randolph M. Nesse and George C. Williams, Sci. Am., November 1998, pp. 86-93.
Furthermore, it is becoming ever more evident that evolutionary analysis may illuminate some of the deepest problems of biology, such as the genetic basis for development or the cellular organization of the human brain.
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RELIABILITY OF INFORMATION SOURCES
By the time you are taking upper-division courses, you ought to have some concern for the source and quality of information you receive. That is, you shouldn't just automatically trust the authority of the textbook or the professor but should look for independent validation.
Primary and secondary sources.
You should be familiar with the basic "rules" governing scientific literature, both the primary literature and the secondary literature.
- Primary literature consists of journal articles that report first-hand observations and experimental results.
- Secondary literature consists of review articles or books which bring together, summarize, and sometimes interpret, information from many primary articles. Some textbooks also fall into the "secondary" literature category, to the extent that they are written by practitioners in the field who are directly familiar with the primary literature and include extensive citations of the primary sources.
In science, ONLY the primary literature is totally respectable. (Of course, this doesn't mean that the primary literature is all correct, or even minimally competent. It just means that nothing else is taken seriously.) This respectability is founded on two traditions.
- The first of these traditions is the fundamental structure of scientific reports, which provides the reader with the basis for independent assessment of the report's validity. With a well-written research report:
- The introduction should place the work in context of relevant ideas and previous studies.
- The procedure section should enable the well-prepared reader to determine whether or not the methods are sufficient to sustain the purpose of the study.
- The results described should be adequate to sustain any conclusions reached in the discussion.
- The discussion should help the reader to explore all the various doubts and reservations which attend the work.
- Any significant omission from any of these sections, whether of experimental control, statistical test, counterargument or alternative interpretation, should cue the alert reader to be suspicious of the report.
- The second tradition is the requirement for "peer review", wherein independent expert referees must approve a report prior to acceptance for publication. Peer review is an essential element in respectable scientific publication. The referees bear heavy responsibility for enforcing the highest standards of thorough and proper scientific analysis.
Before leaving this brief consideration of the primary literature, we should note that even the primary literature of science is susceptible (just like all other human endeavors) to laziness, incompetence, sloppiness, and even fraud.
Some scientists perform their research less carefully than others. Some do not know how to design adequate experiments or perform appropriate analyses. Some referees take their responsibility quite casually. Some have very low standards, some enforce rigid standards for trivialities while ignoring issues of substance, some are simply not qualified to perform adequate review. Some will even accept manuscripts from friends or like-minded colleagues while rejecting papers from competitors or those who disagree with them, without regard for scientific merit. Some journals are scrupulous about choosing well-qualified, competent, and honorable referees; others are not. Even apart from such ethical failings, some reports err simply because the foundations for the study entail unrecognized conceptual or technical limitations.
An important part of professional training consists of learning how to discern the good from the bad. Among sources of published information; reputation does matter. Nevertheless, the respectable options in science are generally either to trust (and cite) the primary literature or to perform (and publish) the study yourself. And, of course, your own reputation will depend not only on the quality of your own experiments but also on the quality of the papers you choose to cite. If you fail to cite important papers, or if you base significant conclusions on poor work done by others, your own credibility will suffer.
Secondary literature is generally only as good as (1) the primary literature cited, and (2) the expertise of the review writer. If the reviewer knows the primary literature well, and understands how to interpret it, then the secondary literature can be quite solid and respectable. But the formal safeguards of detailed "Materials and Methods" and "Results" are no longer presented right up front. It becomes the responsibility of the reader either to trust the authority of the reviewer (which is often risky) or to check out the primary literature. Secondary citations are most properly used as convenient resources for accessing the primary literature. That is, instead of citing all the relevant primary literature, an author can simply cite one substantial review and the reader will thereby gain access to the primary literature.
Evolution is a multidisciplinary field. Articles with an evolutionary theme may be found in many life sciences journals as well as in multidisciplinary journals like Science and Nature. Some journals are entirely devoted to evolution.
To learn something about currently active research topics, you are encouraged to examine the monthly journal, Trends in Ecology and Evolution (TREE). TREE is an excellent secondary source for up-to-date reviews of current developments and controversies. Most articles have a fairly accessible introduction. You are also encouraged to scan the table of contents (at least) for a primary journal such as Evolution, published by the Society for the Study of Evolution.
Textbooks and their limitations.
Textbooks can be quite various, from those which are reliable secondary sources to those which are thoroughly unreliable muddles. Most textbooks are more-or-less idiosyncratic, reflecting the viewpoint of a particular author. Good texts can differ greatly in style. The extent to which style matters depends individually on each reader.
Textbooks can be judged by standards comparable to those for the secondary literature. What is the reputation of the author? Of the publisher? (Some textbook publishers will publish anything to make a buck. Others have high academic standards.) Has the text been reviewed by other professionals (both content experts and educators) prior to publication? That's one standard for a quality publisher. Where has the textbook been adopted? (There may be significant differences between texts adopted by strong research institutions and those adopted by junior colleges.) Have reviews of the book been published? Noteworthy texts are generally reviewed in professional journals, and their strong and weak points noted. Are there citations to primary or secondary literature for important facts and ideas? A textbook without citations may be a helpful learning aid, but without some external validation it should NOT be used as a source for reliable information.
In the opinion of your professor, the chosen textbook for this course (S.C. Stearns and R.F. Hoekstra, EVOLUTION, an introduction) is both readable and reasonably reliable.
Professors and other "expert" professionals
Professors are a source of information comparable to textbooks. It would be nice if they were all reliable sources of information. But some are quite conspicuously better than others. Students may have little opportunity to choose professors for their courses. However, in any case, you can (and should!) decide how much confidence you can place in the information each of your professors provides. Was the professor trained at reputable institutions? Is the professor currently employed by a respectable institution? In what field has the professor published? Is the expertise implied by this publication relevant to the content of the professor's course? Are the professor's published ideas treated with respect by other professionals (as indicated by citations)? Does the professor use citations appropriately, and show respect for skeptical inquiry?
Here I invite you to check out my own credentials. My professional background is outlined at my personal web page: http://www.science.siu.edu/zoology/king/index.htm. This site includes my educational experience (you might note that I was trained not as an evolutionary biologist but as a neuroscientist), a list of my research publications, summaries of current research projects (e.g., "evolutionary tuning knobs"), and links to other sites related to evolution and to neuroscience. You may find a citation to my theoretical work in Scientific American (January 1999, pp. 94-99; "DNA Microsatellites: Agents of Evolution?", by Richard Moxon and Chris Wills).
Remember, ultimately YOU are responsible for the quality of your own education and for the reliability of any information you choose to make your own. Make sure that any information that you choose to believe comes from reliable sources, and remember that reliability is never absolute.
References cited above
"A Revolution in Evolution", by Jim Bull and Holly Wichman, Science 281:1959 (25 Sept. 1998).
"Evolution and the Origins of Disease", by Randolph M. Nesse and George C. Williams, Scientific American, November 1998, pp. 86-93.
"DNA Microsatellites: Agents of Evolution?", by Richard Moxon and Chris Wills, Scientific American January 1999, pp. 94-99.
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Last updated: 8 September 2009 / dgk