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January 6th, 2010
BIOE 109
Winter 2010
Lecture 1
Introduction
Textbook
- Evolutionary Analysis, 4th Edition by Scott Freeman and Jon Herron.
- this is a new edition (2007) that differs somewhat from the 3rd edition (2003).
Websites
- the class web site will be in place early next week.
- here, you’ll be able to access section papers, weekly assignments, past exams, and abridged versions
of lecture notes.
- its URL is http://bio.classes.ucsc.edu/bioe109/
- there is also a website for the textbook: : http://wps.prenhall.com/esm_freeman_evol_4/
Overview of Grading System
Discussion sections: 20%
Midterm exam:
40%
Final exam:
40%
Discussion sections
- attendance at section is mandatory.
- please attend the session that you have enrolled for next week.
- two things will be happening in section.
- first, it will provide you with the chance to question the TA about lectures.
- it is not meant, however, to be a review of the material covered in lecture.
- instead, it will allow you to explore concepts covered in class (or the textbook) in more depth.
- this will be accomplished by reading assignments that will typically be articles appearing in the
primary scientific literature.
- these will be available online through the bioe 109 web site.
- assignments will be short essay type questions.
- a small number of assignments will involve solving problems.
- papers from the primary literature will be made available for students to be discussed each week.
- participation in weekly discussion (14 pts) and performance on 4 assignments (4 pts each, 16 pts
total) will count for 20% of final grade.
Scope and outline of the course:
- scope of the course will be very broad - will cover all facets of evolutionary biology and include
examples of plants, animals, fungi and bacterial groups.
- unlike many other courses you may have taken in biology, the course is conceptual in its focus.
- evolutionary biology is a field ripe with controversy and uncertainty unlike many other areas of
biology where issues are known with greater certainty.
- the organization of lectures will follow the textbook.
- I will not simply review the material covered in the book.
- most of the themes, concepts and definitions will be similar to those outlined in specific chapters.
- however, I will supplement this material with different examples and incorporate many molecular
approaches to evolutionary studies that are not in the textbook.
- evolutionary biology can be divided into two main areas: microevolution and macroevolution.
- microevolution refers to the processes responsible for directing evolutionary change within
populations over relatively short periods of time.
- these include natural selection, migration (gene flow), mutation, and random genetic drift.
- macroevolution usually refers to evolution above the species level.
- it also differs from microevolution in its time reference.
- it is concerned with processes and patterns of evolutionary change over long periods of time - 10’s to
100’s of millions of years.
What is Evolution?
- the Oxford Concise Dictionary lists eight definitions for “evolution”.
- these include (i) a gradual development from a simple to a more complex form, (ii) the process by
which species develop from earlier forms, (iii) the appearance or presentation of events in due
succession, (iv) the giving off of gas or heat, or (v) the unfolding of a curve.
- this is obviously not a complete list. It is common to use the word evolution to describe in general
terms any process of change. For example, languages, ideas and culture are all said to “evolve”. The
style of an artist may be said to “evolve” over his or her career. Used in these contexts, “evolution”
describes change that occurs over relatively short periods of time.
- biological evolution has a much more restrictive definition.
- the origin of the word is from the Latin infinitive “evolvere” which means “to unfold or disclose”. evolutio, its substantive form, refers to the unfolding or reading of a scroll.
- it is therefore not surprising that the first use of the term “evolution” was by scientists studying
embryogenesis in the 18th century such as Haller (1708-1777) and Charles Bonnet (1720-1793).
- the term “evolution” slowly grew to have a broader meaning, particularly among English-speaking
scientists, to refer to both the transformation of embryos and to the transformation of species.
- Darwin himself never used the term “evolution” in his 1859 book “On the origin of species”.
- this course will concern itself only with biological evolution.
Definition 1 (from Mayr): change in a population over time of the proportions of individual
organisms that differ in one, or more, genetically-determined traits.
- the key features of this definition are the elements of time and of genetic change
- changes in phenotypes of individuals without any accompanying genetic change in the population is
not biological evolution.
- an excellent example of this is the change in average height of human populations in developed
countries over the past few centuries.
- this is entirely attributable to improved nutrition, not to any underlying genetic change.
Definition 2 (from Dobzhansky): the transformation of genetic variation originally present within
populations into variation between populations in both space and time.
- note that the focus in both definitions is on populations of organisms.
- individual organisms do not evolve.
- biological evolution occurs at the population level by the differential survival and fecundities of
individual organisms that result in the replacement of one genetic character for another.
How does the study of evolution differ from other areas of biology?
1. Method of study: inference based on the “comparative” versus “experimental” method.
- Greek philosophers such as Aristotle thought that they could solve scientific problems by reasoning
alone, a process we now call “deduction”.
- this tradition continued up to the 19th century.
- this has gradually been replaced by a less dogmatic stance.
- modern scientists now accept that it is impossible to absolutely “prove” anything.
- scientists are content to consider as “true” something that appears consistent with available evidence,
or more consistent than some competing hypothesis.
- the burden of the argument has thus shifted to the opponent of a scientific principle.
- now, the extent to which a scientific theory is accepted as fact is related to the number of times that it
has withstood attempts to refute it.
- in other words, falsification has become the critical issue deciding the acceptance of a scientific
theory.
- this is the case with the “theory of evolution”.
- that biological evolution has occurred, and is continuing to occur, is a fact that has not been disputed
among reputable scientists since Darwin published the Origin back in 1859.
- Darwin used what is now called the hypothetico-deductive method.
- the method proceeds as follows:
1. gather a series of facts or observations and then generate a hypothesis to explain the observations or
facts.
2. conduct experiments, or gather additional evidence, that permit a testing of the hypothesis.
- if the experiments or new observations do not mesh with the original hypothesis, then modify the
hypothesis and proceed to test it again by another round of experiments or gathering of observations.
- the strengths of this method are that it encourages a continuous interplay between the establishment of
new theories, more observations, and new types of experiments.
- the so-called “comparative method” that has developed from this tradition is now widely used in
evolutionary biology and has become recognized as a valid scientific method of inquiry.
- experimentation is generally not possible for the majority of questions pursued by evolutionary
biologists.
- we cannot “rewind” the clock and allow an evolutionary lineage to evolve a second time under, under
say different conditions.
- this does not mean, however, that we cannot perform experiments that provide evidence favoring an
evolutionary hypothesis.
- we will be examining many studies that test evolutionary hypotheses by experimental approaches
throughout the class.
2. Types of questions asked: “proximate” versus “ultimate” causations (Mayr 1961).
- “proximate” questions are the realm of what may be called “functional biology”, i.e., physiology,
biochemistry, molecular biology.
- the most common question posed begins with “how”.
- how are ions pumped into a mitochondrion against a concentration gradient?
- how are proteins transcribed from mature mRNA?
- how does a receptor bind a certain ligand?
- these are all “proximate” questions and the experimental method is used to answer this type of
question.
- “ultimate” questions are the norm of evolutionary biology and usually begin with “why”.
- “why” may mean either “how come” or “what for”.
- in posing questions concerned with “ultimate” causation, the evolutionary biologist has implicitly in
mind the fact that organisms are the products of long evolutionary histories and thus there is hardly a
structure or function that cannot be fully understood unless it is interpreted against this historical
background.
- consider the subject of bird migration.
- when we consider the question “why do birds migrate south for the winter?” we can identify both
proximate and ultimate answers.
- the proximate answers are typically a combination of photoperiod and temperature changes.
- the ultimate causation is that this behavior has evolved in these species because individuals that
undertook these migrations survived and reproduced better than those that did not.
- both proximate causes and ultimate causes of migration, or any other trait, are apparent.
- with few exceptions, in most biological studies there will be both proximate and ultimate causes.
- one type of question is not “superior” to the other - both are required for a complete understanding of
any biological phenomenon.
Objectives of the Course:
1. To foster “evolutionary thinking”.
- this aims to have the class understand the fundamental role that genetic variation in natural
populations has in determining evolution, and to appreciate the fundamental importance of biological
diversity in nature.
2. To foster an understanding of organisms in the context of their evolutionary histories.
- this objective aims to have you appreciate that the evolution of characters occurs over time scales that
you may not be used to considering (over hundreds of millions of years rather than over a few
generations).
3. To realize the potential and the limits of evolutionary change within species.
- an appropriate metaphor, developed by the great French geneticist Francois Jacob, is to think of
evolution as a “tinkerer” rather than an engineer.
- rather than developing structures from a blueprint (as an engineer would), evolution as a tinkerer
works with odds and ends.
- it takes whatever materials are available and fashioning them into new, functional objects. It may
form a wing from a leg, feathers from scales, a part of the ear from a piece of a jaw.
- unlike an engineer who can obtain materials from wherever he or she chooses, evolution is
constrained to work from the existing form of the organism.
- this imposes important limitations, or “constraints”, on the ability of evolution to operate, as we’ll
see.
4. To appreciate that like a tinkerer, evolution has no ultimate goal in mind.
- evolutionary change responds to demands or whims of its immediate time and has no ability to
foresee, or plan for, the future.
- because of this fact, the notion that evolution always leads to “progress” or “advancement” is not
correct.
- evolution resulting in the loss of functions and/or structures occurs as often, or even more often, than
it leads to production of novel characters.