ZOOL 510, Class Notes
Introduction, Week 1

• Most important:  Record this address where you will not lose it:
  http://www.science.siu.edu/zoology/king/510/index.htm
• At this website you can find all class materials (syllabus, policies, assignments, lecture notes, etc.)

  BRIEF OUTLINE (Hyperlinks to expanded outline; use "back" button to return here.)

• Course content and policies.
  • Course content
  • Classroom participation
  • Papers
• Introductory comments
  • Ideas and facts
  • Multiplicity of viewpoints, and controversy
• Status of evolutionary biology
  • Centrality of evolution to biology (in principle)
  • Marginality of evolution (in recent practice)
  • Renewed relevance of evolution (in current practice)
• Reliability of information sources
  • Primary and secondary sourcess
  • Textbooks (and their limitations)
    • Text by Ridley
  • Professors and other "expert" professionals
• References

Class participation
     Most importantly, please, discipline yourself to read each chapter before coming to class.  I shall not be leading you by the hand through the text, but will be speaking on the presumption that you have already read the text once and will do so again after class.
     Class participation matters.  That means, most importantly, asking questions.  I am not going to recite the textbook to you.  I am going to try to help you out by offering background information and interpretation.  Occasionally that may be enough.  But I cannot address the confusion that YOU feel or help fill the gaps in YOUR background unless you ask questions.  REMEMBER:  The only dumb question is the one that is not asked.  Note again, you will be ill-prepared to ask questions that make a difference if you do not come to class having already read the text assignment.

Papers
     Two papers are required for grade in this course, in addition to midterm and final exams.  You may also prepare papers as a substitute for exam scores.  

Introductory comments.
Ideas and facts (or, 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 may 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 subject 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 bug or begonia, 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 tend to be a bit more subtle.  And the answers are seldom simple facts but rather a mixture of several different explanations.  Sometimes the various explanations are complementary, sometimes supplementary, sometimes contradictory.
     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.  In a number of areas, we will be emphasizing NOT nice pat answers to obvious questions, but rather 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 prepare for class 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 3 is titled "The Evidence for Evolution".  Instead of asking the obvious but not especially imaginative question, "What is the evidence for evolution?", try stepping back asking something more like, "Where did the idea of evolution come from?", or "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 is present life different from past life?  What might happen if observable small changes over short spans of time were extended over indefinitely long ages?"
     Once you have grappled with those questions, you may be ready for Chapter 4, "Natural Selection and Variation".  If you accept evidence for descent with modification, 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?"  In other words, don't begin by presuming the answers that science has already discovered.  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 never appreciated 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 specific evolutionary events may be grouped into at least three categories.  In one category would be data which are available in principle but wildly impractical to obtain, such as DNA sequence data for the entire genome of all members of a population.  In a second category would be data which are fundamentally unobtainable, like a precise genealogy and genotype for every organism that has ever lived, and all environmental conditions for all locations since life began.  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 following asteroid impact; major branches of life's phylogenetic tree) is the principal goal for some branches of geology and evolutionary biology.  In the third category are concepts 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 complementary (i.e., each an essential 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" (e.g., Ridley, on the first page of chapter 1).  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 prodeeds apace with little or no regard for 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)
     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 the level of immediate 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 operation of those machines is 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 scammed by claims that a new model car could use water for fuel or that a refrigerator could keep milk cold while producing rather than consuming energy.  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.  "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.

RELIABILITY OF INFORMATION SOURCES
     By the time you are taking graduate-level courses, you ought to have some professonal 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.  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 well-educated reader should be able to determine whether or not the methods are sufficient to sustain the purpose of the study, and whether or not the results are adequate to sustain any conclusion.  The introduction should present all the relevant ideas and previous studies, while the discussion should help the reader to explore all the various doubts and reservations which attend the study.  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 responsbility 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.
     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.  It is highly worthwhile to examine at least the table of contents of such journals, just to see what general topics are currently active.  One good example is the journal Evolution, published by the Society for the Study of Evolution.  Typically much more readable are the review articles in Trends in Ecology and Evolution, an excellent secondary source for up-to-date views on current developments and controversies.

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; how much this 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 a significant difference 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 primary or secondary citations for important 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 is both readable and reasonably reliable.  One significant caution:  The author tends to be quite casual about the nature of argument -- if you read carefully and think about what you are reading, you will realize he often pulls conclusions out of his hat.  They may be good, sound conclusions, but they often do not follow logically from what has gone before.
     NOTE:  The first edition of your textbook (Evolution, by Mark Ridley) is reviewed in Trends in Ecology and Evolution, Vol. 9, No. 4 (April 1994), pp. 153-154.  The strengths noted for the first edition remain strong in the second edition (the one required for this course).  The second edition also successfully addresses several of the weaknesses noted for the first edition.  It's still not a perfect text (does such a thing exist?), but we'll save further comment for classtime.  The CD that accompanies the second edition is reviewed in Trends in Ecology and Evolution, Vol. 12, No. 11 (April 1997), pp. 455-456.
     The main competition for serious upper-division evolutionary biology texts is Evolutionary Biology, 3rd edition, 1998, by Douglas J. Futuyma, published by Sinauer.  Futuyma's text is also quite appropriate for a graduate-level introduction to evolution.  His style is vastly different Ridley's, but the content is comparable.  If you would like to read an alternative to Ridley, this text is highly recommended.

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, as a graduate student, your future career may depend on your wisdom in choosing a major professor.  In any case, you can (and should!) decide how much confidence you can place in the information your professors provide.  Was the professor trained at reputable institutions?  Is the professor currently employed by a respectable institution?  Where and what 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.  You might note that I was trained neuroscientist, not as an evolutionary biologist.  This site includes my educational experience, a list publications, summaries of current research projects, and links to other sites related to evolution and to neuroscience.  You can find my most recent work cited in a recent issue of 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

"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.

Review of the first edition of Evolution, by Mark Ridley, Trends in Ecology and Evolution, Vol. 9, No. 4 (April 1994), pp. 153-154.

Review of the CD that accompanies the second edition of Ridley's text, Trends in Ecology and Evolution, Vol. 12, No. 11 (April 1997), pp. 455-456.

Evolutionary Biology, 3rd edition, 1998, by Douglas J. Futuyma, published by Sinauer.

"DNA Microsatellites: Agents of Evolution?", by Richard Moxon and Chris Wills, Scientific American January 1999, pp. 94-99.

510 index page

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