Open Questions: Evolutionary Theory

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See also: Molecular evolution -- Evolutionary psychology -- Evolutionary history of animals -- Evolutionary milestones -- Human evolution

Nothing in biology makes sense except in the light of evolution.

Theodosius Dobzhansky


There is not a single Why? question in biology that can be answered adequately without a consideration of evolution.

Ernst Mayr


Introduction

Levels of selection

Advantages of sexual reproduction

Punctuated equilibrium

Adaptation

Randomness and chance in evolution

Speciation

Genetic variability within species

Diversity

Evolutionary developmental biology

Phenotype plasticity and evolution

Phylogenetics


Recommended references: Web sites

Recommended references: Magazine/journal articles

Recommended references: Books

Introduction

Ever since Darwin's Origin of Species was published in 1859, his theory of evolution has generated vigorous controversy -- not because it was obviously wrong, but, certainly, because for all of its originality and power, it left so many tantalizing questions unanswered.

The theory of evolution is a prime example of an "emergent" sort of theory, in which the phenomena it describes and explains are treated on the basis of principles which are formulated directly in terms of the phenomena which are to be explained, in this case, the historical origins of living things on Earth.

Although this seems like a reasonable and proper way to proceed, and the theory of evolution itself was a brilliant and successful development, it has suffered from one nagging weakness: Insofar as the theory is founded on observation of the available evidence, many key facts will be forever outside our reach, simply because they relate to events in the distant past which we can never actually observe. All we have to work with are the living things which we can observe today, and a few haphazard fossil remains of living things which flourished millions or billions of years ago.

In short, although we can often make shrewd guesses as to why things have turned out the way they seem to have, our conclusions often remain just guesses. We frequently find ourselves wanting key pieces of evidence which would confirm or disconfirm the guesses. As a result, controversies remain, for lack of the evidence which could settle them conclusively beyond a reasonable doubt.

For example: Is evolution generally a smooth and continuous process, with one animal species changing slowly and almost imperceptibly into one or more descendent species? Or does it, instead, more often involve sudden, discontinuous changes -- perhaps provoked by radical environmental changes -- with species otherwise remaining essentially unchanged for millions of years? It's usually difficult to determine this from the fossil record, given the few samples we frequently must deal with, where the distances between their origins in time and space are both large and not very certain. Given only a few bones, how much can we really say about the relationship between the animals they were once a part of?

It would be a tremendous help in resolving such questions if we had available entirely different sorts of evidence to work with. And now, half a century after the determination of the structure and function of DNA in cells, we do.

It should be cause for serious reflection that Darwin was as successful as he was in formulating his theory, given that he knew almost nothing of the actual science of genetics which controls how living creatures pass on their characteristics from one generation to the next. And yet, the fact that this inheritance takes place is absolutely key to the theory. Astonishingly enough, Darwin knew nothing of Mendelian genetics, and in fact he believed in the Lamarckian idea of the inheritance of acquired characteristics.

This is a tribute to what can be done with a non-reductionistic theory in the hands of someone as brilliant as Darwin. And yet, there is so much more that can be done, so many unresolved puzzles which can be solved, once we have learned enough to reduce many of the known facts of evolution to the more fundamental insights painstakingly acquired through the science of molecular biology.


Levels of selection


Advantages of sexual reproduction


Punctuated equilibrium


Adaptation


Randomness and chance in evolution


Speciation


Genetic variability within species


Diversity



Recommended references: Web sites

Site indexes

Open Directory Project: Evolution
Categorized and annotated links. A version of this list is at Google, with entries sorted in "page rank" order. May also be found at Netscape.
Unoficial Stephen Jay Gould Archive: Links
Relatively short but carefully selected list of links related to Gould and evolution.
Evolution and Behavior
Many external links on evolutionary theory in general, by Jie Yin.
Sites of Interest to Botanists, Ecologists, and Evolutionary Biologists
External links collected by Kent Holsinger.
Biology Links: Evolution
From the Harvard Department of Molecular and Cellular Biology.
Evolutionary Biology Resources
Good list, orgainized into ten categories.
Galaxy: Evolution
Categorized site directory. Entries usually include descriptive annotations.

Sites with general resources

UCMP Exhibit Halls: Evolution
Information on the theory of evolution and history of evolutionary thought. Part of the University of California at Berkeley's Museum of Paleontology
The Talk.Origins Archive
Excellent general collection of resources on evolutionary theory.
New Scientist Special Report on Evolution
Primarily offers links to many news articles from the past several years of New Scientist magazine. But there are also other features, including facts and figures, external links, frequently-asked questions, and a short bibliography.
EvoWiki
Also known as the Evolution Education Wiki -- "a free, reader-built encyclopedia of evolution, biology, and origins. It is inspired by the Talk.Origins Archive and the Wikipedia project."
Evolution Resources From the National Academies
"This Web page is designed to provide easy access to books, position statements, and additional resources on evolution education and research."
The World of Richard Dawkins
An unofficial Web site dealing with the work of evolutionary theorist Richard Dawkins. It contains a great deal of information and external links for many controversial topics in evolutionary theory.
The Unofficial Stephen Jay Gould Archive
Site contains a wide variety of material related to Gould. This includes an extensive online library of articles and papers on evolution by Gould and others, a bibliography of books and papers by Gould, and a very good list of selected external links on evolution.
Niles Eldredge Evolutionist
Site contains a wide variety of material related to Eldredge. This includes a "Library of Evolution", consisting of many of Eldredge's papers on evolution, and information on books by Eldredge.
Evolution and ecology@nature.com
A portal to relevant Nature Publishing Group resouces in the field of evolution and ecology.
BBC Evolution Website
Large collection of educational material related to the history and content of evolutionary theory. Includes a very good bibliography of both print and online reference material.
Understanding Evolution
The site is intended for science teachers, to explain some of the common misconceptions about evolution in order to help students understand it more easily. Provides a good basic introduction to the subject, including good external readings and resources.
Evolution
Material from a PBS series. Includes a large number of articles, interviews, videos, recommended readings, and links. Best accessed through the site map or the library page. Good glossary. Answers to frequently asked questions.

Surveys, overviews, tutorials

Category: Evolutionary biology
Topic category from Wikipedia.
Evolution
Article from Wikipedia. See also Evolutionary biology, Natural selection, Modern evolutionary synthesis, List of evolutionary biology topics.
Species
Article from Wikipedia. See also Speciation.
Nothing in Biology Makes Sense Except in the Light of Evolution
An important and well-known article published in 1973 by Theodosius Dobzhansky. It provides both a concise overview of evolutionary theory, and the facts and reasoning which make it so compelling.
Genetics and Evolution Tutorial
Good tutotrial, covering genetics as well as evolutionary theory, located at the Biology Online site.
Evolution
Good overview lecture by Eugenie Scott, at the BioForum site.
Speciation
Single-page overview from Kimball's Biology Pages.
Evolution: Fact AND Theory
General page on evidence for evolution. Includes Notes on Evolution -- class notes from a course.
Why Sex?
April 2006 online article in Seed Magazine - an interview with Ricardo Azevedo, who has developed computer models of evolution, about the evolutionary importance of sex.
The Woodstock of Evolution
June 2005 Scientific American In Focus article, subtitled "The World Summit on Evolution, held in the Galapagos Islands, revealed a science rich in history and tradition, data and theory, as well as controversy and debate."
High-Speed Speciation
October 2000 Scientific American news article about an example of very rapid speciation.
Sex and Speciation
September 2000 Scientific American news article about how different mating systems in insects affect the rate of speciation.
Score One for Punk Eek
July 1996 Scientific American Explore article about an experiment involving the evolution of bacteria which claims to provide support for the theory of punctuated equilibrium.
Sexual conflict pushes species making
September 2000 news article in Science News, about speciation in inssects due to sexual conflict.


Recommended references: Magazine/journal articles

Should Evolutionary Theory Evolve?
Bob Grant
The Scientist, January 2010
Some biologists are calling for a rethink of the rules of evolution.
A Most Private Evolution
Susan Milius
Science News, February 14, 2009
Dumb designs for sex: Evolutionary biology walks on the weird side.
Computing Evolution
Patrick Barry
Science News, January 16, 2009
Scientists sift through genetic data sets to better map twisting branches in the tree of life.
Darwin's Living Legacy--Evolutionary Theory 150 Years Later
Gary Stix
Scientific American, January 2009
Evolutionary theory has broadened and changed as Darwin's ideas have been melded with genetics. Evolutionary biology still must contend with some of the same questions that preoccupied Darwin: What, for one, is a species?
Testing Natural Selection with Genetics
H. Allen Orr
Scientific American, January 2009
Biologists working with the most sophisticated genetic tools are demonstrating that natural selection plays a greater role in the evolution of genes than even most evolutionists had thought.
What Is a Species?
Carl Zimmer
Scientific American, June 2008
Formal taxonomic systems first identified species based on visual traits such as fins or fur. Later, the species concept changed, specifying that two organisms should be capable of breeding.
Founder Mutations
Dennis Drayna
Scientific American, October 2005
Was Darwin Wrong?
David Quammen
National Geographic, November 2004, pp. 2-35
Shows and explains, with many illustrations, that the evidence for evolution is overwhelming.
[Additional resources]
Evolutionary Shocker?
John Travis
Science News, June 22, 2002, pp. 394-396
The protein known as heat shock protein 90 may assist evolution by allowing genetic changes to remain unexpressed until an organism experieces stress, such as elevated temperature.
[References]
Alarming Butterflies and Go-Getter Fish
Susan Milius
Science News, July 21, 2001, pp. 42-44
Additional conditions that lead to the emergence of new species continue to be discovered.
[References]
Evolution: A Lizard's Tale
Jonathan B. Losos
Scientific American, March 2001
The Mother of Mass Extinctions
Douglas H. Erwin
Scientific American, July 1996, pp. 72-78
Catastrophic changes in the Earth's environment 250 million years ago caused the largest episode of mass biological extinction in history. About 90% of ocean-dwelling species, for example, disappeared, but the exact evolutionary factors that account for which species survived and which didn't is not clear.


Recommended references: Books

Ernst Mayr -- What Evolution Is
Basic Books, 2001
Mayr is one of the 20th century's most outstanding contributors to evolutionary theory and began publishing (on ornithology) in 1923. The present book is a detailed introduction to evolution for general readers. Topics include how evolutionary change and adaptation occur, speciation, and macroevolution. The final part of the book deals with human evolution.
Menno Schilthuizen -- Frogs, Flies, and Danelions: The Making of Species
Oxford University Press, 2001
Although Darwin called his book The Origin of Species, and his ideas were a giant leap forward, he never really answered the question of what causes new species to appear, or even exactly what a "species" is. Biologists today are still very actively investigating these difficult questions. Schilthuizen's relatively brief book provides a good snapshot of where things stand today.
Kim Sterelny -- Dawkins vs. Gould: Survival of the Fittest
Icon Books, Ltd., 2001
The author, a professor of philosophy, presents key points of controversy in the modern theory of evolution, especially with respect to the well-publicized diasgreements between Richard Dawkins and Stephen Jay Gould. The book provides a good introduction to modern evolutionary theory and its main issues in a brief compass.
Richard Morris -- The Evolutionists: The Struggle for Darwin's Soul
Henry Holt and Company, 2001
The theme is the ongoing controversy within evolutionary theory between "orthodox" interpreations and dissenting opinions offered by scientists such as Stephen Gould. In the course of an even-handed and relatively brief discussion of the controversy, Morris is able to impart a useful understanding of topics such as the content of Darwin's theory, the evidence for it, complexity theory, and evolutionary psychology.
Steve Jones -- Darwin's Ghost: The Origin of Species Updated
Ballantine Books, 2001
Jones, a distinguished geneticist, rewrites Darwin's classic to reflect the vast quantity of findings in biology since 1859. The outline of Darwin's work, and some of the original passages, are retained. The result is a very good introduction to modern evolutionary theory.
Jeffrey H. Schwartz -- Sudden Origins: Fossils, Genes, and the Emergence of Species
John Wiley and Sons, 1999
Schwartz tackles head-on the problem of speciation in evolution. There is a long review of the history of evolutionary theory, followed by arguments regarding the importance for speciation of recent findings in developmental biology -- especially the role of gene regulatory mechanisms and the homeobox genes.
Henry Gee -- In Search of Deep Time: Beyond the Fossil Record to a New History of Life
Cornell University Press, 1999
"Deep time" refers to the geological time scale, measured in millions of years. The author presents a view of evolutionary theory for general readers which is based on the idea that in "deep time" it is not possible to make testable hypotheses about ancestry relationships between species, but only more general statements about degree of relatedness. He explains this using the tools of "cladistics", for which this is a good introduction.
Laurent Keller, ed. -- Levels of Selection in Evolution
Princeton University Press, 1999
This is a volume of contributed papers addressing many issues in the controversies over "levels of selection". The goal is to synthesize divergent views and move beyond old arguments. Many of the papers are technical, but well worth reading to understand the complexities of the overall problem.
Michael Ruse -- Mystery of Mysteries: Is Evolution a Social Construciton?
Harvard University Press, 1999
The author has held professorships in both philosophy and biology. Although this book has the explicit purpose of enquiring into the nature of science using evolutionary theory as a case study, it is as valuable for the presentation of the theory as for the philosophy. It examines the work of a number of the leading thinkers about evolution, from Darwin (both Erasmus and Charles) to contemporary scietists like Edward Wilson and Stephen Jay Gould. It's a good introduction to many of the current controversies in the field.
Michael R. Rose -- Darwin's Spectre: Evolutionary Biology in the Modern World
Princeton University Press, 1998
Rose, a professor of evolutionary biology, presents a history of the theory of evolution from its origins to the present. The history includes a brief explanation of the theory, how it has itself evolved over time, and some of its effects on society and the way we view ourselves and the world. This short book makes a good introduction for general readers to many aspects of the theory.
John Maynard Smith -- Evolutionary Genetics
Oxford University Press, 1998
Here is an understandable textbook by a master of the subject, on the genetic mechanisms that underlie evolutionary theory. Simple mathematical models help illuminate otherwise difficult issues such as natural selection, population biology, genetic drift, evolutionary strategies, sexual reproduction, speciation, and macroevolution.
Richard Dawkins -- Climbing Mount Improbable
W. W. Norton & Company, 1996
Dawkins shows, through many examples, the ways in which long evolutionary processes have succeeded in producing very complex and seemingly improbable biological structures. An especially interesting example is the numerous independent evolutions of "eyes" (light-collecting devices) in various species.
Richard Dawkins -- The Blind Watchmaker
W. W. Norton & Company, 1996
The author provides an account of the theory of evolution for a general audience, with special emphasis on how is is possible for complex biological forms to arise without the need for a pre-conceived "design".
Daniel C. Dennett -- Darwin's Dangerous Idea: Evolution and the Meanings of Life
Simon and Schuster, 1995
This is a superb work by a philosopher who is scientifically informed. It considers the arguments that have been made, pro and con, about evolution over the years, and it show how the general model of biological evolution applies in other areas of scientific interest as well.
Richard Dawkins -- River Out of Eden: A Darwinian View of Life
Basic Books, 1995
A short overview of the theory of evolution from the author's customary perspective. Dawkins focuses on "utility functions" -- the maximization of which is in some sense the "purpose" of evolution, another way of referring to the "good" that evolution is metaphorically directed towards.
Richard Dawkins -- The Selfish Gene
Oxford University Press, 1989
This is a revised edition of the first of the author's series of books on evolutionary theory for a general audience. It explains the theory in the light of Dawkins' emphasis on the central role individual genes play in the unending marathon race for survival.
Richard Dawkins -- The Extended Phenotype
Oxford University Press, 1983
In this volume, Dawkins provides a sequel to The Selfish Gene aimed at an audience with more background in biology. The theme remains not a new variation of the theory of evolution so much as a new way of looking at it where the focus is on "replicators" such as the individual gene, instead of organisms, which are merely vehicles for the replicators.

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