THE EVOLUTION LIST

Fox News Polling Data Shows Support for Evolution Increasing Exponentially

2011-09-10T05:55:00.008-04:00

There's a new poll out on the percentage of Americans who agree with the scientific evidence in favor of the theory of evolution. The new poll was conducted by Anderson Robbins Research and Shaw & Company Research for Fox News (polling data are here). The questions asked in the poll are very similar to those in the periodic polls on this question conducted by the Gallup organization (their polling data are here).

As a professional evolutionary biologist and someone who has followed this debate for decades, I find the Fox News poll results surprisingly encouraging. Although the fraction of the American public that agrees with the Young Earth Creationist position hasn't changed significantly for almost half a century, the fraction that agrees with the position taken by evolutionary biologists has increased very significantly since the Gallup organization first polled Americans on this question in 1982.

Here are the data, in chronological order:

Percent of Americans agreeing with evolutionary theory:

GALLUP:
1982 9%
1994 11%
2002 12%
2006 14%

FOX NEWS:
2011 21%

From 9% to 21% in only twenty-nine years (i.e. less than two generations)! If you plot the data, the increase is clearly exponential, with the inflection point at around 2006 (i.e. following the Kitzmiller-Dover decision). At the current exponential rate of increase, the "evolutionary biology" position should be the majority position within another generation. This is why we need to keep presenting the science, and why creationists (including the "intelligent design" variety) are their own worst enemies.

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

Teleological Explanations in Biology

2011-06-08T10:21:00.012-04:00

Biologists tend to use teleological language in explaining the origin and evolution of living organisms and their characteristics. As John Reiss has pointed out (Reis, J. Not by Design: Retiring Darwin's Watchmaker, University of California Press, 2009), this entails the idea that evolution is necessarily a teleological process. This entails the idea that evolution is not a "natural" process, like gravity or oxidation, and that therefore there is some "non-natural" component (i.e. "magic") in biology that fundamentally distinguishes it from the other natural sciences.

Evolutionary biologists like Richard Dawkins try to make this distinction when referring to the problem of human free will (see "Let's all stop beating Basil's car"), but unless they are careful about how they talk about evolution (especially natural selection) they revert to the same teleological descriptions and explanations that Reiss so decries. What is the problem, here?

I believe that the underlying problem is the tendency by most evolutionary biologists to think of natural selection as a "force" or "mechanism". As John Endler has pointed out (Endler, J. Natural Selection in the Wild, Princeton University Press, 1986), natural selection is not a "force" or "mechanism", it is an outcome. To be precise, it is the outcome of four separate, but related processes:

• Variety: structural and functional differences between individuals in populations,

• Heredity : the inheritance of structures and functions from parents to offspring (either genetically or epigenetically),

• Fecundity : the ability to reproduce, especially (but not necessarily) at a rate that exceeds replacement, and

• Demography : some individuals survive and reproduce more often than others.

As a result of these four processes, the heritable characteristics of some individuals become more common in populations over time.

Notice that the same list of processes can be used to explain non-adaptive evolutionary change (e.g. genetic drift). Also notice that the only source of new phenotypic variations is what I have called the "engines of variation": all of those processes that produce heritable phenotypic changes in phylogenetic lines of organisms in populations. There are at least fifty such processes (you can see a summary list here). While it is the case that "random mutation" is included in this list, there are many other processes in this list that do not involve "mutation" (in the genetic sense) and which also are not "random" (at least insofar as that term is often used).

Is there a real distinction between non-teleological and teleological processes, or are all processes either teleological or not? If all processes (i.e. changes over time) are teleological, as asserted by Aristotle (and some of the commentators), then there is no point in talking about it. However, if some processes are teleological and some are not (as most people, including presumably most of the commentators here, now believe), then the question becomes "how can one distinguish between teleological and non-teleological processes, and what explains the differences between them?"

In his comprehensive analysis of teleology, Andrew Woodfield (Woodfield, A. Teleology, Cambridge University Press, 1976) pointed out that all teleological descriptions can be reformulated to conform to the linguistic formula " x happens in order to/for y outcome." He also asserted that such linguistic formulations describe metaphysically real processes. That is, some processes are genuinely teleological – they involve pre-existing designs or plans that cause processes to tend toward particular outcomes, regardless of perturbations or outside interference – while other processes only seem teleological – they involve laws of nature, such as gravity, that result in particular outcomes, without responding actively to perturbations or outside interference.

This distinction is essential when considering whether "genuine" teleology exists. To be precise, teleological descriptions sound "reasonable" when they are applied to genuinely teleological processes, but sound ridiculous if they are applied to non-teleological processes. For example, does it sound reasonable to say that when you drop a rock, it falls "in order to" reach the ground? By contrast, does it sound reasonable to say that birds have wings "in order to" fly? Is there a difference between the "reasonableness" of the first teleological explanation and the second?

When I pose this question to my students, almost all of them say yes: the first is ridiculous and the second isn't. I then point out that this implies that the origin of the wings of birds therefore seems to be the result of a teleological process. I then point out (reprising Aristotle) that there are at least four ways of explaining the presence of wings:
• "this bird has wings because it is composed of materials that are assembled and operated as wings" (Aristotle's "material" cause);
• "this bird has wings because its parents had wings" (Aristotle's "efficient" cause);
• "this bird has wings because birds have wings" (Aristotle's "formal" cause); and
• "this bird has wings in order to fly" (Aristotle's "final" cause).

Since at least the 17th century (and mostly because of Newton), natural scientists have stopped using formal or final causes to explain natural phenomena...except in biology. This was first pointed out by Colin Pittendrigh (Pittendrigh, C. S. Behavior and Evolution) (ed. by A. Rose and G. G. Simpson), Yale University Press, 1958), who coined the term "teleonomy" to refer to the kind of teleological phenomena observed in biological processes. Francisco Ayala modified and extended Pittendrigh's analysis (Ayala, F. J. 'Teleological Explanations in Evolutionary Biology', Philosophy of Science, vol. 37 pp. 1-15, 1970). Ernst Mayr finally sorted the whole thing out in 1974 in "Teleological and teleonomic: A new analysis" (Boston Studies in the Philosophy of Science, vol. XIV, pp. 91 -117). According to Mayr, the difference between the "behavior" of dropped rocks and genuinely purposeful processes is the presence or operation of a pre-existing information-containing program in the latter. Rocks do not fall because there is an encoded program in nature that makes them fall. They fall because there is a force (i.e. a law of nature) that causes them to fall. However, a bird has wings because there is a program encoded within its genome which, as the result of interactions between the "phenome" of the bird and its environment, causes the construction and operation of wings.

To say that natural selection is teleological would therefore require that there be a pre-existing encoded program somewhere that would cause natural selection to bring about its effects. This is ridiculous for at least two reasons:
• there is no such program as far as we can tell (where would it be encoded?), and
• this would require that natural selection be a process in and of itself, rather than the outcome of the four processes listed above.

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

The Metaphysical Foundations of Modern Science

2011-05-29T21:35:00.017-04:00

I started attending the weekly meetings of the Ithaca Friends Meeting in September, 1969. One of the people who made an immediate and lasting impression on me was an older gentlemen, always impeccably dressed, who sometimes spoke in meeting in a quavery, but very determined voice. His "messages" were always very literate, but not necessarily complicated. I was eventually introduced to him, and learned that his name was "Ned" Burtt, and that he was one of the founders of the Ithaca meeting.

After several years we became good friends, but only in the context of the Friends Meeting. I got to know his wife, Marjory, with whom I had many very engaging conversations. She was a retired psychotherapist with an interest in Eastern philosophy, especially Buddhism. I didn't have as many conversations with Ned, not because he wasn't willing, but because he was almost completely deaf. Indeed, after a few years I noticed that Marjory and some of his older friends took turns sitting next to him in meeting, and when someone rose to speak, would write down what they said on a slip of paper and pass it to Ned.

Year later I was co-teaching a course on the history and philosophy of science, for which the teaching staff had chosen as one of the required readings a "classic" in the history of science, The Metaphysical Foundations of Modern Science, by Professor Edwin Arthur Burtt, the Susan Lynn Sage Professor of Philosophy at Cornell University. Translated into dozens of languages and continuously in print since 1924, Burtt's Metaphysical Foundations was often mentioned as the precursor to Thomas Kuhn's The Structure of Scientific Revolutions, and one of the seminal texts in the history of science.

Imagine my surprise (and chagrin) when I discovered that "Ned" Burtt of the Ithaca Friends Meeting was Prof. Edwin Arthur Burtt himself, author of the Metaphysical Foundations and perhaps the most famous historian of science in the first half of the 20th century. Characteristically, he never mentioned it in any of our conversations (brief and halting as they were), and no one else in meeting seemed to think it important enough to mention either.

Ned died in 1989 at the age of 97, and was memorialized at the Ithaca Meeting in our usual way – a silent meeting, punctuated by a few heart-felt "messages" from his friends. I think of him now as I am re-reading once again his Metaphysical Foundations, and am once again struck by his keen insight and masterful use of language. Here's just one sample:

"The glorious romantic universe of Dante and Milton, that set no bounds to the imagination of man as it played over space and time, had now been swept away. Space was identified with the realm of geometry, time with the continuity of number. The world that people had thought themselves living in – a world rich with colour and sound, redolent with fragrance, filled with gladness, love and beauty, speaking everywhere of purposive harmony and creative ideals – was crowded now into minute corners in the brains of scattered organic beings. The really important world outside was a world hard, cold, colourless, silent, and dead, a world of quantity, a world of mathematically computable motions in mechanical regularity. The word of qualities as immediately perceived by man became just a curious and quaint minor effect of that infinite machine beyond. In Newton the Cartesian metaphysics, ambiguously interpreted and stripped of its distinctive claim for serious philosophical consideration, finally overthrew Aristotelianism and became the predominant world-view of modern times.

*Whew* - talk about a splash of cold water in the face. It is this world-view – the one that forms the basis of all of modern science, including biology – that depresses and terrifies those who cannot live without the "old magic" and motivates those who want to tear down "modern" science and go back to the pre-scientific world-view, what Carl Sagan called "the demon-haunted world." But, just like the magic realm of childhood, there is no going back now, not to the innocent and often terrifying universe of the childhood of our cultures. In the words of Bertrand Russell (one of Ned Burtt's contemporaries):

"That Man is the product of causes which had no prevision of the end they were achieving; that his origin, his growth, his hopes and fears, his loves and beliefs, are the outcome of accidental collections of atoms...that all the labours of the ages, all the devotion, all the inspiration, all the noonday brightness of human genius, are destined to extinction in the vast death of the solar system, and that the whole temple of Man's achievement must inevitably be buried beneath the debris of a universe in ruins...only on the firm foundation of unyielding despair can the soul's habitation henceforth be safely built." – A Free Man's Worship [1923]

And so tomorrow (it's Memorial Day once again), I will go walking through the little grave yard out behind the Hector Meeting House where Ned and Marjory are buried, and think once again about the old, deaf gentleman whose messages were so eloquent and whose view of reality so unflinching.

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

Evolutionary Psychology: The Science of Human Nature

2011-03-17T07:54:00.017-04:00

Having been tickled by Google Alert that my name had been mentioned in the comments at Pharyngula (P. Z. Myer's blog), I took a quick look. Just a few comments for now:

1) I became an evolutionary psychologist when studying the behavioral ecology of Microtus pennsylvanicus got boring. Those cute little field voles got boring because their ethology is relatively simple. Human ethology is a lot more interesting, mostly because it is a lot more complex. Should we not try to study it because it is more complex? Or because it might not jibe with some people's political preconceptions?

2) I assign Gould & Lewontin's "spandrels" paper to my students in evolutionary biology, along with various criticisms of it. I also assign Eldredge & Gould's "punk eek" paper and Gould and Vrba's "exaptation" paper (along with close to three dozen others, not to mention the entire Origin of Species, 1st. ed.). I also give them chunks of George William's 1966 classic, Adaptation and Natural Selection, so that they will know exactly how "onerous" the concept of "adaptation" actually is.

3) Here's the definition of "adaptation" I use:

An evolutionary adaptation is any heritable phenotypic character whose frequency of appearance in a population is the result of increased reproductive success relative to alternative versions of that heritable phenotypic character.

4) Here are the criteria I believe are most useful when one is attempting to determine if one is dealing with an "adaptation":

Qualification 1: An evolutionary adaptation will be expressed by most of the members of a given population, in a pattern that approximates a normal distribution;

Qualification 2: An evolutionary adaptation can be correlated with underlying anatomical and physiological structures, which constitute the efficient (or proximate) cause of the evolution of the adaptation;

Qualification 3: An evolutionary adaptation can be correlated with a pre-existing evolutionary environment of adaptation (EEA), the circumstances of which can then be correlated with differential survival and reproduction; and

Qualification 4: An evolutionary adaptation can be correlated with the presence and expression of an underlying gene or gene complex, which directly or indirectly causes and influences the expression of the phenotypic trait that constitutes the adaptation.

To me, it seems reasonable that if one can apply those to a specific human behavior, one can make arguments about its evolutionary derivation. Would anyone disagree?

As for the ridiculous idea that evolutionary psychology only deals with sex, has anyone making such a claim actually read a textbook on the subject? Here are several:

Human Evolutionary Psychology

Evolutionary Psychology: The New Science of the Mind (4th Edition)

Evolution and Human Behavior, 2nd Edition: Darwinian Perspectives on Human Nature

Evolutionary Psychology: The Science of Human Nature

[Full Disclosure Notice: The fourth title is indeed by Yours Truly.]

If you haven't, then please do so, and then we can discuss these questions.

While we're on the subject, Part II of Evolutionary Psychology: The Science of Human Nature (on the ethology of between-group behavior in humans) is coming out in May. My next project is an introductory textbook in evolutionary biology, entitled Evolutionary Biology: The Darwinian Revolutions, again in two parts. Part I (due out in September) is The Modern Synthesis and Part II (due out next May) is The Evolving Synthesis.

After that (if I live that long) will be On Purpose: The Evolution of Design by Means of Natural Selection (won't there be some fireworks when that comes out?), in which I present one of the core arguments for The Metaphysical Foundations of the Biological Sciences, in the spirit of E. A. Burtt's The Metaphysical Foundations of Modern Physical Science. Should be fun!

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

Is Science True?

2010-12-09T10:04:00.005-05:00

In my experience, everyone bases their "arguments on certain metaphysical suppositions, scientists and non-scientists included. As a good friend and student of E. A. Burtt, I have found his Metaphysical Foundations of Modern Physical Science to be extraordinarily useful in this regard. In fact, I have begun work on what I hope will be a companion volume: Metaphysical Foundations of Modern Biological Science, in which I will examine the assumptions that underlie the science of biology as it is practiced today.

One of the bedrock assumptions underlying both modern physics and modern biology is non-teleology: the assumption that natural processes do not include any teleological input. I personally think that this is wrong, and base my objection to this idea on Ernst Mayr's monumental book, Toward a New Philosophy of Biology, published in 1988. Mayr argued very persuasively that teleological explanations are entirely appropriate in biology insofar as they refer to the development and maintenance of living organisms. According to Mayr, both of these processes (and indeed all biological processes) are directed by programs (i.e. genomes, etc.) that pre-exist the entities and processes that they specify and regulate. In the jargon of the current debate, genomes and other developmental programs are "designs" for the assembly and operation of living organisms.

However, Mayr also argued very strongly that the origin of biological programs – that is, the various mechanisms of biological evolution – need not (and apparently do not) include any teleological component. Like all physical processes, there is no detectable "grand design" (much less a Grand Designer) which/Who has formulated beforehand the programs that regulate life. In other words, teleology is entirely appropriate when applied to life and the operation of living programs, but not when applied to the origin of life or the origin of living programs.

So, what does this say about the question of whose opinions to trust when considering these issues? My first criterion is skepticism: if someone claims to know the truth about anything at all (including, of course, the contents of their own mind), my immediate reaction is intense skepticism. Science (at least that version of it that has been practiced since the 17th century) isn't about truth. It's about reasonable confidence in explanatory models, all of which are grounded on a metaphysical assumption of the usefulness of methodological naturalism. Notice I wrote "usefulness", not "truth", because as far as I can tell the only "truth" that exists on either side of the evolution/ID divide is a version of Colbert's "truthiness". It feels like "truth", but isn't really. In my opinion, "experts" are people who keep these distinctions in mind at all times, and do not easily (if ever) use absolute statements when talking about nature.

For example, I have an immediate, knee-jerk negative reaction to the title of Jerry Coyne's book, Why Evolution is True, and indeed to much of what he writes for the general public. Consider a similar title, Why Quantum Mechanics is True, or if you prefer Why the Gas Laws are True. How would a physicist react to titles such as these? I hope (and my general experience has been) that they would object to the word "true", and also perhaps to the question "why". Physics isn't about "truth" and doesn't usually ask about "why" things happen. Physics is about "useful" and "consistent" and "empirically testable" models of reality, and it's about "how" things happen, not "why" they happen.

Indeed, in the natural sciences (including biology) the answer to the question "how" is the same as the answer to the question "why". How do birds come to have wings? They inherit a genetic and developmental program that, via interactions with their environment, produces those structures we call "wings". Why do birds come to have wings? Same answer. How have birds acquired these genetic and developmental programs? They evolved by natural selection and other evolutionary mechanisms. Why have birds acquired these genetic and developmental programs? Again, same answer.

Speculating as to whether the biological processes by which the programs that specify and regulate living organisms and processes are somehow externally/supernaturally directed seems to me to be metaphysical arguments, rather than scientific ones. Interesting, compelling even, but not part of science, at least as it has been practiced for a very long time.

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

Many Metabolisms, Many Origins?

2010-12-04T09:21:00.018-05:00

An unspoken but widely held belief among both evolutionary biologists (and some "intelligent design" supporters) is the idea that life (or, to be more specific, living organisms and/or metabolic processes) originated once a very long time ago. Along with my fellow biology majors, I was taught this by William T. Keeton in introductory biology at Cornell, where we also were told that if life (or biomolecules) somehow spontaneously started again today, it would immediately be scarfed up by already living organisms.

This idea ultimately derives from the last paragraph of Darwin's Origin of Species, in which he proposed that

"There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved." [Origin of Species, 1st edition, 1859]

Darwin asserted this partly to contrast his theory of evolution from that of Lamarck's, which included the idea that life was continuously arising spontaneously, generating new phylogenetic lines of organisms throughout deep evolutionary time. The discovery of the (almost) "universal" genetic code in the 1950s by Crick, Nirenberg, Holley, Khorana, et al provided strong evidence for the "one origin" hypothesis.

However, the fact that there is currently no evidence for an alternative "many origins" hypothesis doesn't necessarily support the conclusion that this hypothesis has been falsified. On the contrary, as the recent discovery by Felisa Wolfe-Simon of a "shadow arsenic metabolism" indicates, this lack of evidence is the result of lack of investigation, rather than actual lack of such origins. It is, in other words, quite possible that life (or at least biochemical processes similar to metabolic processes and molecules similar to "standard" biomolecules, and even cell-like structures incorporating both) is "originating" spontaneously all the time, but that we haven't noticed it because we haven't been looking. After all, nobody suspected the existence of an entire domain of living organisms (i.e. the Archaea) until Carl Woese starting looking two decades ago.

As J. B. S. Haldane — who formulated an early hypothesis for the origin of life — once quipped,

"[T]he Universe is not only queerer than we suppose, but queerer than we can suppose." [Haldane, J. B. S. (1927) Possible Worlds and Other Papers, page 227]

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

What is "Darwinism" and am I a "Darwinist"?

2010-11-10T22:56:00.004-05:00

I don’t use the term “Darwinism” at all, any more than I would use the term “Newtonism” when referring to classical physical mechanics, “Einsteinism” to refer to relativity theory, “Bohr/Feinman/Heisenberg/Schroedingerism” to refer to quantum mechanics, or “Mendeleevianism” to refer to chemistry. What I and my colleagues (and friends) do is probably best described as “evolutionary biology”, and includes (at a bare minimum) the following:

1) the formulation and testing of a set of interconnected theories explaining the origin of biological diversity, consisting of descent with modification from common ancestors over deep geological time, describable via cladistic analysis, and supported by inference from multiple sources of empirical evidence, including comparative anatomy, biogeography, developmental biology, genomics, historical geology, and paleontology; and

2) the formulation and testing of a separate but related set of interconnected theories explaining the origin and modification of the phenotypic characteristics of living organisms, consisting (at a bare minumum) of the mechanisms of natural selection, sexual selection, genetic drift, and neutral molecular evolution in deep geological time, grounded (at least in part) in theoretical mathematical models of population genetics, depending on multiple sources of heritable phenotypic variation, and supported by inference from multiple sources of empirical evidence, including field and laboratory research in the fields of biochemistry, cell biology, comparative physiology, developmental biology, ecology, ethology, genetics, neurobiology, and physiological ecology.

Note that these two definitions of the principle domains of evolutionary biology correspond roughly to what are sometimes referred to as “macroevolutionary theory” and “microevolutionary theory” (in that order) and do not explicitly mention:

• theories of the origin of life from non-living materials, which are properly the purview of astrophysics, chemistry, and geology, not biology;

• the concept of “adaptation”, which has had a checkered past in evolutionary biology and is facing increasing challenges within the field; and

• teleology, which is almost never mentioned, except for those evolutionary biologists who have thought about it (which, in my experience, are relatively few), who generally assume that resort to teleological explanations in evolutionary biology is unnecessary. Not wrong, just unnecessary (not to mention unproductive as an empirical research hypothesis).

As philosophical concepts, both adaptation and teleology have a very long history, stretching back at least to Plato and Aristotle. However, recent developments in evolutionary theory, including (but not limited to) theories of epigenetics, exaptation, genetic drift/draft, neutral and nearly neutral molecular “drift” in deep evolutionary time, and punctuated equilibrium, have rendered the concept of “adaptation” as an increasingly marginal diversion rather than a central topic in evolutionary biology.

And teleology, rather than being considered “wrong” (when it is considered at all, which is seldom) is now increasingly being incorporated into new theories of “evolved agency”, especially in evolutionary psychology (my own field). I am currently working on a treatise on this latter subject, which I hope to finish before departing this veil of tears and laughter for that undiscovered country from whose bourn no traveller returns.

The Annotated Origin of Species

2010-06-06T09:54:00.015-04:00

In November of 1859, the
London publishing house of John Murray brought out the first edition of what would become the most famous and important work of science of the 19th century: Charles Darwin's On the Origin of Species. The first edition of 1,250 copies sold out in one afternoon (first edition copies today fetch over a hundred thousand dollars on the rare book market) and was eventually reprinted over the next fifteen years in five increasingly popular editions. The success of the Origin catapulted Darwin from a relatively unknown specialist in the taxonomy of barnacles to the most famous naturalist of the 19th century and became the most widely read (and most controversial) science text of all time.

Many historians of biology credit the Origin with founding the modern science of biology. Hence, it is very curious that the first edition of the Origin lacks what most scholars expect to find in such influential and widely respected works. Unlike most other books of its kind — including Darwin's other famous books, The Voyage of the Beagle (first published in 1839) and The Descent of Man (first published in 1871) — the Origin has virtually none of the usual "machinery" of a scholarly work. Although Darwin cites the findings and opinions of hundreds of naturalists worldwide in the Origin, he does not provide any footnotes or written citations to their published works. The first edition of the Origin also does not include a bibliography nor any listing of published references. And, despite focusing on the most visual of the natural sciences, the Origin contains only one illustration, a hand–drawn diagram of the branching pattern of descent that Darwin proposed for his theory of descent with modification (his term for what we now refer to as "evolution").

The reason for this surprising lack of documentation is well known: Darwin had been scooped on his theory of natural selection by a fellow English naturalist, Alfred Russel Wallace. In April of 1858, Wallace sent Darwin a letter that included a brief essay "On the Tendency for Varieties to Depart Indefinitely from the Original Type", in which Wallace anticipated virtually all of the major concepts of Darwin's theory of evolution by natural selection. Darwin had been working on his theory for over two decades, and had been writing the book that would eventually be published as the Origin for at least five years when he received Wallace's letter. Anxious to preserve his priority as the discoverer of natural selection and urged on to do so by his friends and fellow naturalists, Darwin rushed what he considered to be an "abstract" of his ideas into print in November of 1859. This "brief abstract", published without footnotes, illustrations, or bibliography, was the first edition of the Origin of Species by Means of Natural Selection.

The first edition of the Origin was a masterwork and is still published in its original form, without footnotes, illustrations, and bibliography. Reading it, one can still get a taste of the overwhelming scholarship with which Darwin supported what he called his "long argument" for descent with modification. However, to really appreciate how much of the science of natural history Darwin wove into his argument, one really needs to know what Darwin's sources were and how they were related to each other.

Presenting these sources and showing how Darwin marshaled them in his defense of his theory is the heart of James Costa's brilliant annotation of Darwin's classic, The Annotated Origin, published by Belknap Press of Harvard University Press. Brought out in celebration of the 150th anniversary of the publication of first edition of the Origin, Costa's annotated version more than compensates for the "missing" material in Darwin's original. The introduction to The Annotated Origin alone is worth the price of the book. In it, Costa presents a lightning biography of Darwin and a nuanced exploration of the reasons for his rush to publish in 1859. It also contains a reader's guide to the Origin, a book that is often difficult for modern readers who are unaccustomed to the density of Victorian prose. Costa then analyzes and annotates virtually every page of the Origin, including the title page, in which he provides a brief history of Darwin's illustrious publisher, John Murray, and his decision to print only 1,250 copies of what would eventually become his best-selling and most famous publication.

Costa's annotations run the gamut from personal anecdotes to hard-science references. He weaves together Darwin's own telegraphic notes in his unpublished notebooks, his correspondence, his other published works, and his autobiography, providing the reader with a wealth of information and insight. Tracking down each line of evidence becomes a kind of "exploration" in itself. One can follow threads of evidence that elucidate Darwin's views about nature, science, his fellow naturalists, and even such "taboo" subjects (at least in the Victorian era) as sex and the intimate details of family life.

Costa's annotations also provide a detailed framework for Darwin's argument, showing how the various explanations and examples are marshaled in such a way as to support Darwin's underlying argument for "descent with modification by means of natural selection." As just one example, consider Costa's annotations to the section of pigeon breeding in the first chapter of the Origin ("Variation Under Domestication"). Naïve readers of this chapter are sometimes puzzled by Darwin's emphasis on pigeon breeding and its relationship to his theory. But, as Costa points out, "[p]igeons provided a microcosm of Darwin's model of selection, as well as valuable data on development, correlation of traits, and reversion." Like so many of his Victorian contemporaries, Darwin raised pigeons at his country estate at Down House in Kent, and conducted dozens of breeding experiments to test his theories. Darwin pointed out that all of the various breeds of pigeons could be shown to have descended from the wild rock pigeon (Columba livia) by a process that we now refer to as artificial selection. Darwin constructed an argument by analogy that natural selection followed the same rules as artificial selection. And, since so many of his contemporaries (and potential readers) were also pigeon fanciers, he could be reasonably confident that they would be able to follow his argument without extensive explanation or citations of obscure references to the scientific literature.

Reading the first edition of Darwin's Origin of Species is a revelation. One catches the threads of Darwin's argument and follows his reasoning through to his startling (and sometimes troubling) conclusions. James Costa's masterful annotation of the Origin does much more. It supplies the scholarly apparatus that the first edition lacked and provides a coherent and comprehensive background for Darwin's arguments, as well as many fascinating insights into Darwin's personality, thought processes and research methods. No other scientist has been as exhaustively analyzed as Darwin, and no other published work of science has been as widely criticized or praised as the Origin of Species. Reading James Costa's Annotated Origin provides an even deeper appreciation for Darwin's achievement and its impact on science and society.

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

More on Evolution and Human Free Will

2010-04-16T20:55:00.003-04:00

Every summer I teach a seminar course at Cornell in which we examine the historical, philosophical, religious, and scientific implications of evolutionary theory. This summer our seminar course will once again consider the question: Is free will an illusion?

On the 15th of July, 1838, Charles Darwin began a notebook which he labeled as “M”, in which he intended to write down his correspondence, discoveries, musings, and speculations on “Metaphysics on Morals and Speculations on Expression”. On page 27 of that notebook, he wrote

“…one doubts existence of free will every action determined by hereditary constitution, example of others or teaching of others. (…man…probably the only [animal] affected by various knowledge which is not heredetary & instinctive) & the others are learnt, what they teach by the same means & therefore properly no free will. [Emphasis added]

In his private musing on the question of free will, Darwin came to the conclusion that human free will is an illusion, and that all of our actions (and, by extension, our thoughts and intentions) are the result of our “hereditary constitution” and “the example…or teaching of others.”

Some evolutionary biologists, notably William Provine of Cornell University, have followed Darwin’s lead and asserted that human free will is an illusion. Most philosophers disagree, asserting that free will is the principle difference between humans and non-human animals. Many Christian theologians go further, asserting that free will is the foundation of all human action, without which no rational ethics or theology is possible.

In our seminar course this summer we will take up this debate by considering two alternative hypotheses: (1) that human free will is real and can provide a basis for our morals and ethics, or (2) that human free will is an illusion, the capacity for which is a product of the same evolutionary processes that have shaped our anatomical and behavioral adaptations. Included in this debate will be an extended consideration of the hypothesis that the capacity for ethical decision making is an evolutionary adaptation that has evolved by natural selection. We will read from some of the leading authors on both sides of the subject, including George Ainslie, Daniel Dennett, Robert Kane, William Provine, Daniel Wegner, and Edward O. Wilson. Our intent will be to sort out the various issues at play, and to come to clarity on how those issues can be integrated into a perspective of the interplay between philosophy and the natural sciences.

Here are some particulars for the course:

INTENDED AUDIENCE: This course is intended primarily for students in biology, history, philosophy, religious studies, and science & technology studies. The approach will be interdisciplinary, and the format will consist of in-depth readings across the disciplines and discussion of the issues raised by such readings.

PREREQUISITES: None, although a knowledge of general evolutionary theory, evolutionary psychology, sociobiology, and the philosophy of human free will would be useful.

DAYS, TIMES, & PLACES: The course will meet on Tuesday and Thursday evenings from 6:00 to 9:00 PM in Mudd Hall, Room 409 (The Whittaker Seminar Room), beginning on Tuesday 29 June 2010 and ending on Thursday 5 August 2010.

CREDIT & GRADES: The course will be offered for 4 hours of credit, regardless of which course listing students choose to register for. Unless otherwise noted, course credit in BIOEE 4670 / BSOC 4471 can be used to fulfill biology/science distribution requirements and HIST 4150 / STS 4471 can be used to fulfill humanities distribution requirements (check with your college registrar's office for more information). Letter grades for this course will be based on the quality of written work on original research papers written by students, plus participation in class discussion. All participants must be registered in the Cornell Six-Week Summer Session to attend class meetings and receive credit for the course (click here for for more information and to enroll for this course). Registration will be limited to the first 18 students who enroll for credit.

REQUIRED TEXTS:

Ainslie, G. (2008) Breakdown of Will, Cambridge University Press, ISBN: 0521596947 (paperback: $34.99), 272 pages.

Dennett, D. (2004) Freedom Evolves, Penguin Books, ISBN: 0142003840 (paperback: $17.00), 368 pages.

Kane, R. (2005) A Contemporary Introduction to Free Will, Oxford University Press (USA), ISBN: 019514970X (paperback: $19.95), 208 pages.

Wegner, D. (2003) The Illusion of Conscious Will, MIT Press, ISBN-10: 0262731622 (paperback: $21.95), 419 pages.

Wilson, E. O. (2004) On Human Nature (Revised Edition), Harvard University Press, ISBN: 0674016386 (paperback: $22.00), 284 pages.

OPTIONAL TEXTS:

Darwin, Charles (E. O. Wilson, ed.) (2006) From So Simple a Beginning: Darwin's Four Great Books. W. W. Norton, ISBN-10: 0393061345 (hardcover, $39.95), 1,706 pages. Available online here.

Fisher, J., Kane, R., Pereboom, D., & Vargas, M. (2007) Four Views on Free Will, Wiley-Blackwell, ISBN: 1405134860 (paperback: $33.95), 240 pages.

Kane, R. (2001) Free Will (Blackwell Readings in Philosophy), Wiley-Blackwell, ISBN: 0631221026 (paperback: $33.95), 328 pages.

Wilson, E. O. (2000) Sociobiology: The New Synthesis (25th Anniversary Edition), Belknap Press, ISBN: 0674002350 (paperback: $44.00), 720 pages

Our summer seminar course is always fascinating, and often quite controversial (see this and this). Over the years we have explored many of the implications of Darwin's theory, and the participants have always found our discussions (perhaps they should be called "debates") enlightening. As always, the intent is not necessarily to reach unanimity, but rather for each participant to come to clarity on where they stand on the issues and to be able to defend that stance using evidence and rational argument.

So, please consider taking our seminar on free will this summer - the choice is yours!

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

More on "Meaningful" Information

2010-03-22T21:15:00.009-04:00

In the ongoing debate about meaningful information at Uncommon Descent, one of the commentators asked:

"Does an of arrangement of nucleobases ‘adenine-cytosine-adenine’ in DNA mean anything?"

This is a surprisingly interesting and revealing question. To attempt to answer it, I would first like to put a limit on the question: let us consider the answer if the nucleotide sequence "adenine-cytosine-adenine" is in DNA (i.e. not RNA). If "meaningful" information is necessarily analogical, as I have suggested in the previous post on "Evolution, Information, and Teleology", then the answer to this question depends upon the circumstances in which the nucleotide sequence ACA is a part. If, for example, this sequence is part of a longer sequence of nucleotides in a longer DNA molecule, then there are several possible answers:

1) the DNA nucleotide sequence ACA could be located in a single strand of DNA that is suspended in a test tube (i.e. not in a living cell) and is therefore completely biologically inert (i.e. it is not binding to a complementary strand of DNA, nor being replicated, nor transcribed, nor translated);

2) the DNA nucleotide sequence ACA could be hydrogen bonded to the complementary sequence TGT (i.e. "thymine-guanine-thymine") in another strand of nucleotides that is anti-parallel with it and close enough to form hydrogen bonds between the nitrogenous bases;

3) the DNA nucleotide sequence ACA could be in a strand that is being replicated by DNA polymerase, which can synthesize the complementary sequence TGT in a newly synthesized strand of DNA;

4) the DNA sequence ACA could be in a strand of DNA that is being transcribed by RNA polymerase, which can synthesize the complementary sequence UGU in a newly synthesized strand of RNA;

5) the DNA sequence ACA could be in a strand of DNA that has already been transcribed by RNA polymerase into the complementary sequence UGU in a strand of mRNA that is bound to a ribosome and can be actively translated into an amino acid sequence in a polypeptide; or

6) the DNA sequence ACA could be in a strand of DNA that has already been transcribed by RNA polymerase into the complementary sequence UGU in a strand of mRNA that is bound to a ribosome and is being actively translated into an amino acid sequence in a polypeptide inside a living cell, within which the polypeptide has a biological function (i.e. participates in those biochemical reactions that maintain the cell alive/against the depredations of the second law of thermodynamics).

In case #1 the DNA nucleotide sequence ACA has no "meaning", in that it is not analogically related to anything. It also has no Shannon information nor Kolmogorov information nor Orgel information either, as it is not in the process of being transmitted or compressed, nor is it "specifying" anything.

In case #2 the DNA nucleotide sequence ACA has no "meaning" because its bonding with its complementary sequence is purely chemical, not analogical. Like the bonding together of water molecules in a snowflake (i.e. the regular crystalline solid form of water), the hydrogen bonding of the nitrogenous bases in complementary DNA sequences is wholly determined by "natural laws", and is therefore neither analogical nor meaningful.

Cases 3 and 4 appear to be the same as in case 2; the relationships between the nucleotide sequences and the bonding patterns therein are entirely the result of chemistry, with no analogical nor meaningful information involved.

However, in cases 5 and 6 we seem to come to a radical discontinuity. In both of these cases, there can be an analogical (and therefore "meaningful") relationship between the nucleotide sequence ACA in DNA and the corresponding amino acid sequence in a translated polypeptide, either in vitro or in a cell. What makes this difference possible (and what may make it necessary) is the analogical relationship between the nucleotide sequence and the corresponding amino acid sequence (if one exists). If the DNA sequence ACA is located in the template strand of an actively transcribed DNA sequence (i.e. a DNA sequence beginning with a promoter to which RNA polymerase can bind) and furthermore its complementary RNA analog is located in an mRNA molecule following the "start" codon AUG but not following a "stop" codon (either UAA, UAG, or UGA, assuming a three-base reading frame), then that the DNA sequence does indeed contain "meaningful" information: it is encoded in one medium, is translated into another medium, and has a function in the system of which it is a part.

It is not yet clear from current research whether or not the amino acid that is "translated" from the DNA sequence ACA (i.e. from the mRNA sequence UGU, assuming that the DNA sequence ACA is in a template strand) is necessarily related to that mRNA sequence. That is, we do not know with confidence whether the relationship between mRNA codons and the amino acids for which they code is purely arbitrary (i.e. the result of a "frozen accident") or if there is some as-yet-undetected necessary (i.e. "natural") relationship between them.

What we can say with reasonable assurance is that what distinguishes "meaningful" information from any other kind of information is not the material into which it is encoded, but rather the relationship between the information encoded in one physical medium and its decoded complement in a related physical medium. As Gregory Bateson pointed out many years ago, meaning is entirely in the relationship between material things; it is not the things themselves. Or, as Alfred Korzybski pointed out,

"The map is not the territory"

In the same way, meaningful information is not the medium in which it is encoded, transmitted, and decoded.

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

Evolution, Information, and Teleology in Biology

2010-03-22T10:56:00.015-04:00

I am currently in the middle of a debate at Uncommon Descent, the leading "intelligent design" website. The debate focuses on the concept of "information": what it is, where it comes from, and what its properties are. In thinking about these questions, I have been struck by how central they are to biology in general and evolutionary biology in particular.

When one uses the term "information", one can be referring to at least four different phenomena: Shannon information, Kolmogorov information,complex specified ("Orgel") information[1], and meaningful information. To me, it appears that the first three types of information – Shannon, Kolmogorov, and complex specified information – are fundamentally different from meaningful information.

What do we "mean" when we say that something is "meaningful"? To me, "meaningful" information is encoded information in which the "bits" of information "encode" (or "stand for") other bits of information via analogy. A meaningful "bit" therefore "stands for" some other bit.

Furthermore, two bits of information that stand for each other necessarily not identical, even if they are written (i.e. symbolized) using exactly the same symbols. That is, two copies of the same symbol may "mean" the same thing, but they are not the "same" symbol, except via analogy. To be the "same" symbol, there could only be one symbol which "stands for itself". This is simply a reinterpretation of Aristotle's law of non-contradiction.

Moreover, it seems to me that not only is meaningful information necessarily analogical, it is also necessarily arbitrary, in the sense that the analogical relationship between the bits of a message and the concept with which those bits is associated is not "natural" (i.e. it is not the result of physical necessity), but rather "non-natural" (i.e. the result of arbitrary semantic association).

For example, consider the meaningful word "two". I can substitute the numeral "2" for the English word "two" without changing the meaning of the word. Indeed, the following words all "mean" the same thing: 2, ii, II, 10 (binary), dué, deux, duo, twa, zwei, etc. [see http://en.wikipedia.org/wiki/2_%28number%29 ] This list can be infinitely extended: 0 + 2, 1 + 1, 2 + 0, 3 - 1, 4 - 2, etc. (and, of course, zero plus two, one plus one, two plus zero, three minus one, four divided by two, ten divided by five, etc.). All of these words and phrases "mean" exactly the same thing: that which we refer to with the English word "two" (or, if you prefer, the Arabic numeral "2").

In the previous example, all of the words and phrases are encoded analogies of the concept of "twoness", none of them are more or less "twoish" than any other (You're twoish? That's funny, you don't look twoish), and indeed none of them are necessarily "twoish" at all. That is, the meaningful relationship between the various words and phrases and "twoishness" is arbitrary or, more precisely, non-natural. We may refer to such meaningful (and ultimately arbitrary) relationships between the "name" and "the thing named" as semantic associations, to distinguish them from non-arbitrary natural relationships.

It appears to me that arbitrary semantic associations such as those symbolized by the numeral "2" are fundamentally different from the natural relationship between the number of protons in an atomic nucleus and its chemical properties. Regardless of what one "calls" a nucleus with two protons ("helium" is the most common name for it, but there are others), and no matter which of the words or phrases one chooses to refer to the number of protons in the nucleus, the chemical and physical properties of the nucleus remains the same [see helium for more about the properties of this element]. Ergo, the "twoness" of the protons in the nucleus of helium is a non-arbitrary, "natural" property of such nuclei, and is therefore not a form of meaningful information.

By contrast, saying that the number of protons in the nucleus of an atom of helium has no more effect on the natural properties of such a nucleus than if one says that there are deux (or twa or zwei) protons in such a nucleus. No matter what you call it nor how you refer to the number of protons in its nucleus, helium is helium is helium (pacé Gertrude Stein).

Given the foregoing, it should be clear that the first three types of information I listed at the beginning of this comment are not necessarily meaningful. That this is the case for Shannon and Kolmogorov information is widely accepted. However, it is also the case for some (but not all) forms of complex specified ("Orgel") information. For example, if one constructs a string of random nucleotides (or any random string of bits), if that string does not subtend a promoter sequence, it will not "code" for the amino acid sequence of a polypeptide. Furthermore, unless such a string subtends a "binding region" (i.e. a sequence to which a protein or RNA molecule may bind via hydrogen bonding) it will also not have a regulatory function in a larger biochemical/cellular system. Under these circumstances, such a random string will not "encode" for any structure or function, but still possesses what Leslie Orgel [1] referred to as "complex specified information".

Ergo, "meaningful information" is analogical information; it "stands for" something else. Furthermore, the relationship between a bit of meaningful information and the thing it stands for is a functional relationship. That is, the meaningful bit specifies the function of the thing for which it stands (i.e. not "Richard Stans"). This means that meaningful information is necessarily teleological, as "functions" are semantically equivalent to "goals" which are semantically equivalent to "ends".

So, teleology must exist in any functional relationship, including those in biology. The question is not "is there teleology in biology"; no less an authority on evolutionary biology than the late Ernst Mayr (not to mention Franciso Ayala) emphatically stated "yes"! The real question (and the real focus of the dispute between EBers and IDers) is the answer to the question, "where does the teleology manifest in biology come from"? EBers such as Ernst Mayr assert that it is an
emergent property of natural selection, whereas IDers assert that it comes from an "intelligent designer". It has never been clear to me how one would distinguish between these two assertions, at least insofar as they can be empirically tested. Rather, the choice of one or the other seems to me to be a choice between incommensurate metaphysical world views, which are not empirically verifiable by definition.

This is not, however, to say that the distinction between evolutionary and non-evolutionary models of reality is purely and solely a matter of choice of metaphysics. On the contrary, the empirical evidence for evolution is overwhelming, as is the evidence for at least some of the characteristics of living organisms having arisen as the result of natural selection. What is still a matter of dispute is where meaningful information "comes from": does it arise as an emergent property of natural processes (such as natural selection), or must it be "read into nature" from some non-natural source?

That is the question...

REFERENCE CITED:

[1] Orgel, L. (1973) The origins of life, Chapman & Hall, London, UK, pg. 189:

"...living organisms are distinguished by their specified complexity. Crystals are usually taken as the prototypes of simple well-specified structures, because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures that are complex but not specified. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity."

P.S. Shannon information, Kolomogorov information, and Orgel information need not be perceived to exist, but meaningful information does.

P.P.S. As for the second law of thermodynamics, it seems clear to me from what I know about biology (the only natural science that deals with meaningful information) that both encoding and decoding meaningful information requires the transformation of energy from a condition of lower to higher entropy. This is always the case when meaningful information is “transformed”, whether one is referring to the replication of DNA, the transcription of DNA into RNA, the translation of mRNA into polypeptides, the catalysis of biochemical reactions via enzymes, the transduction of changes in the physical environment into action potentials in the sensory nervous system, the transduction of action potentials in the motor nervous and musculoskeletal systems into behaviors, or the playing of a game of chess (regardless of whether one uses a board and pieces).

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

Gauss, ID, and the Red Queen Hypothesis

2010-03-17T22:38:00.032-04:00

Robert Sheldon has posted a blog entry at Uncommon Descent that is a masterpiece of misdirection, misunderstanding, and mendacity. His post is linked to a longer post at TownHall.com, which I would like to analyze in some detail, as it represents a paradigm of the kind of twisted "logic" that passes for "science" among supporters of "intelligent design". Let's start at the beginning:

First of all, Sheldon asserts that

"a "Gaussian" or "normal" distribution...is the result of a random process in which small steps are taken in any direction."

This is a gross distortion of the definition of a Gaussian distribution. To be specific, a Gaussian distribution is not "the result of a random process in which small steps are taken in any direction". On the contrary, a Gaussian distribution is "a continuous probability distribution that often gives a good description of data that cluster around [a] mean (see http://en.wikipedia.org/wiki/Gaussian_distribution). There is a huge difference between these two "definitions".

• The first – the one invented by Robert Sheldon – completely leaves out any reference to a mean value or the concept of variation from a mean value, and makes it sound like a Gaussian distribution is the result of purely random processes.

• The second – the one defined by Gauss and used by virtually all statisticians and probability theorists – assumes that there is a non-random mean value for a particular measured variable, and illustrates the deviation from this mean value.

Typically, a researcher counts or measures a particular environmental variable (e.g. height in humans), collates this data into discrete cohorts (e.g. meters), and then constructs a histogram in which the abscissa/x axis is the counted/measured variable (e.g. meters) and the ordinate/y axis is the number of individual data points per cohort (e.g. the number of people tallied at each height in meters). Depending on how broad the data cohort, the resulting histogram may be very smooth (i.e. exhibiting “continuous variation”) or “stepped” (i.e. exhibiting “discontinuous variation”).

Graphs of variables exhibiting continuous variation approximate what is often referred to as a “normal distribution” (also called a “bell-shaped curve”). This distribution is formally referred to as a Gaussian distribution, in honor of its discoverer, Carl Friedrich Gauss (this, by the way, is one of only three accurate statements conveyed by Sheldon in the post at TownHall.com). While it is the case that Gaussian distributions are the result of random deviations, they are random deviations from a mean value, which is assumed to be the result of a determinative process.

In the example above, height in humans is not random the way Sheldon defines “random”. If it were, there would be no detectible pattern in human height at all, and we would observe a purely random distribution of human heights from about 0.57 meters to about 2.5 meters. Indeed, we would see no pattern at all in human height, and every possible height would be approximately equally likely.

Instead, we see a bell-shaped (i.e. “normal” or “Gaussian”) distribution of heights centered on a mean value (around 1.6 meters for adults, disregarding gender). The “tightness” of the normal distribution around this mean value can be expressed as either the variance or (more typically) as the standard deviation, both of which are a measure of the deviation from the mean value, and therefore of the variation between the measured values.

Sheldon goes on to state in the post at TownHall.com that “[s]o universal is the "Gaussian" in all areas of life that it is taken to be prima facie evidence of a random process.” This is simply wrong; very, very wrong – in fact, profoundly wrong and deeply misleading. A Gaussian distribution is evidence of random deviation from a determined value (i.e. a value that is the result of a determinative process). Indeed, discovering that a set of measured values exhibits a Gaussian distribution indicates that there is indeed some non-random process determining the mean value, but that there is some non-determined (i.e. “random”) deviation from that determined value.

Why does Sheldon so profoundly misrepresent the definitions and implications of Gaussian distributions? He says so himself:

“Because many people predict that Darwinian evolution is driven by random processes of small steps. This implies that there must be some Gaussians there if we knew where to look.”

This is only the second accurate statement conveyed in the OP, but Sheldon goes on to grossly misrepresent it. It is the case that the “modern evolutionary synthesis” is grounded upon R. A. Fisher’s mathematical model for the population genetics of natural selection, in which the traits of living organisms are both assumed and shown to exhibit exactly the kind of “continuous variation” that is reflected in Gaussian distributions. Fisher showed mathematically that such variation is necessary for evolution by natural selection to occur. In fact, he showed mathematically that there is a necessary (i.e. determinative) relationship between the amount of variation present in a population and the rate of change due to natural selection, which he called
the fundamental theorem of natural selection.

But in his post at TownHall.com Sheldon goes on to strongly imply that such Gaussian distributions are not found in nature, and that instead most or all variation in nature is “discontinuous”. Along the way, Sheldon also drops a standard creationist canard: “Darwin didn't seem to produce any new species, or even any remarkable cultivars.” Let’s consider these one at a time.

First, most of the characteristics of living organisms exhibit exactly the kind of variation recognized by Gauss and depicted in “normal” (i.e. “bell-shaped”) distributions. There are exceptions: the traits that Mendel studied in his experiments on garden peas are superficially discontinuous (this is Sheldon’s third and only other accurate statement in his post). However, almost any other characteristic (i.e. “trait”) that one chooses to quantify in biology exhibits Fisherian “continuous variation”.

I have already given the example of height in humans. To this one could add weight, skin color, density of hair follicles, strength, hematocrit, bone density, life span, number of children, intelligence (as measured by IQ tests), visual acuity, aural acuity, number of point mutations in the amino acid sequence for virtually all enzymes...the list for humans is almost endless, and is similar for everything from the smallest viruses to the largest biotic entities in the biosphere.

Furthermore, Darwin did indeed produce some important results from his domestic breeding programs. For example, he showed empirically that, contrary to the common belief among Victorian pigeon breeders, all of the domesticated breeds of pigeons are derived from the wild rock dove (Columba livia). He used this demonstration as an analogy for the "descent with modification" of species in the wild. Indeed, much of his argument in the first four chapters of the Origin of Species was precisely to this point: that artificial selection could produce the same patterns of species differences found in nature. No, Darwin didn’t produce any new “species” as the result of his breeding experiments, but he did provide empirical support for his theory that “descent with modification” (his term for “evolution”) could indeed be caused by unequal, non-random survival and reproduction; that is, natural selection.

To return to the main line of argument, by asserting that Mendel’s discovery of “discontinuous variation” undermined Darwin’s assumption that variation was “continuous”, Sheldon has revived the “mutationist” theory of evolution of the first decade of the 20th century. In doing so, he has (deliberately?) misrepresented both evolutionary biology and population genetics. He admits that the “modern evolutionary synthesis” did indeed show that there is a rigorously mathematical way to reconcile Mendelian genetics with population genetics, but he then states

”…finding Gaussians in the spatial distribution of Mendel's genes would restore the "randomness" Darwin predicted….But are Gaussians present in the genes themselves? Neo-Darwinists would say "Yes", because that is the way new information should be discovered by evolution. After all, if the information were not random, then we would have to say it was "put" there, or (shudder) "designed".

And then he makes a spectacular misrepresentation, one so spectacular that one is strongly tempted toward the conclusion that this massive and obvious error is not accidental, but rather is a deliberate misrepresentation. What is this egregious error? He equates the “spatial distribution of Mendel's genes” (i.e. the Gaussian distribution of “continuous variation” of the heritable traits of organisms) with “the distribution of ‘forks’ (i.e. random genetic changes, or “mutations”) in time (i.e. in a phylogenetic sequence).

He does so in the context of Venditti, Meade, and Pagel’s recent letter to Nature on phylogenies and Van Valen’s “red queen hypothesis”. Venditti, Meade, and Pagel’s letter outlined the results of a meta-analysis of speciation events in 101 species of metacellular eukaryotes (animals, fungi, and plants). Van Valen’s “red queen hypothesis” states (among other things) that speciation is a continuous process in evolutionary lineages as the result of “coevolutionary arms races”.

Van Valen suggested (but did not explicitly state) that the rate of speciation would therefore be continuous. Most evolutionary biologists have assumed that this also meant that the rate of formation of new species would not only be continuous, but that it would also be regular, with new species forming at regular, widely spaced intervals as the result of the accumulation of relatively small genetic differences that eventually resulted in reproductive incompatibility. This assumption was neither rigorously derived from first principles nor empirically derived, but rather was based on the assumption that “continuous variation” is the overwhelming rule in both traits and the genes that produce them.

What Venditti, Meade, and Pagel’s analysis showed was that

“… the hypotheses that speciation follows the accumulation of many small events that act either multiplicatively or additively found support in 8% and none of the trees, respectively. A further 8% of trees hinted that the probability of speciation changes according to the amount of divergence from the ancestral species, and 6% suggested speciation rates vary among taxa. “

That is, the original hypothesis that speciation rates are regular (i.e. “clock-like”) as the result of the accumulation of small genetic changes was not supported.

Instead, Venditti, Meade, and Pagel’s analysis showed that

“…78% of the trees fit the simplest model in which new species emerge from single events, each rare but individually sufficient to cause speciation.”

In other words, the genetic events that cause reproductive isolation (and hence splitting of lineages, or “cladogenesis”) are not cumulative, but rather occur at random intervals throughout evolving lineages, thereby producing “…a constant rate of speciation”. Let me emphasize that conclusion again:

The genetic events that cause reproductive isolation…occur at random intervals throughout evolving lineages, thereby producing “…a constant rate of speciation”.

In other words (and in direct and complete contradiction to Sheldon’s assertions in his blog post), Venditti, Meade, and Pagel’s fully support the assumption that the events that cause speciation (i.e. macroevolution) are random:

“…speciation [is the result of] rare stochastic events that cause reproductive isolation.

But it’s worse than that, if (like Sheldon) one is a supporter of “intelligent design”. The underlying implications of the work of Venditti, Meade, and Pagel is not that the events that result in speciation are “designed”, nor even that they are the result of a determinative process like natural selection. Like Einstein’s anathema, a God who “plays dice” with nature, the events that result in speciation are, like the spontaneous decay of the nucleus of a radioactive isotope, completely random and unpredictable. Not only is there no “design” detectible in the events that result in speciation, there is no regular pattern either. Given enough time, such purely random events eventually happen within evolving phylogenies, causing them to branch into reproductively isolated clades, but there is no deterministic process (such as natural selection) that causes them.

Here is Venditti, Meade, and Pagel's conclusion in a nutshell:

Speciation is not the result of natural selection or any other “regular” determinative process. Rather, speciation is the result of “rare stochastic events that cause reproductive isolation.”

And stochastic events are not what Sheldon tried (and failed) to assert they are: they are not regular, determinative events resulting from either the deliberate intervention in nature by a supernatural “designer” nor are they the result of a regular, determinative process such as “natural selection”. No, they are the result of genuinely random, unpredictable, unrepeatable, and irregular “accidents”. Einstein’s God may not “play dice” with nature (although a century of discoveries in quantum mechanics all point to the opposite conclusion), but Darwin’s most emphatically does.

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

Darwin Day Petition Drive

2010-02-05T10:31:00.011-05:00

Darwin Day is a global celebration of science and reason held on or around Feb. 12, the anniversary of the birthday of evolutionary biologist Charles Darwin. This year (2010) marks the 201st anniversary of the birth of Charles Darwin and the 151st anniversary of the publication of his most famous book, the Origin of Species.

As part of this year's commemoration of Darwin's birthday, the International Darwin Day Foundation has launched a petition drive to have President Obama issue a proclamation recognizing Darwin Day and the importance of Darwin's work to the science of biology.

Here's what the International Darwin Day Foundation has to say about this petition drive:

Please sign our petition urging President Obama to recognize Darwin Day!

We need our elected leaders to speak out about the importance of scientific knowledge and its contribution to the advancement of humanity, and send a signal that religious infiltration into our science classrooms will not be tolerated. That's why we're asking you to sign our petition urging President Obama to recognize Darwin Day.

Far-right extremists are using every trick in the book to keep the teaching of evolution out of science classes, and to the degree they are successful they are undermining American values of scientific inquiry and integrity.

Their thinly-veiled religious agenda will have negative effects on our society. Incomplete education about evolution in our classrooms sends the message that not only can the theory of natural selection be sidestepped, but all science can be muzzled if it doesn't neatly fit within a particular ideology. Failure to provide our children with a first rate science education will create future generations who are scientifically illiterate and unable to compete in the global market of ideas.

We need our elected leaders to speak out about the importance of scientific knowledge and its contribution to the advancement of humanity, and send a signal that religious infiltration into our science classrooms will not be tolerated. That's why we're asking you to sign our petition urging President Obama to recognize Darwin Day.

Darwin Day, celebrated every year on February 12, is a day in which people gather together to commemorate the life and work of Charles Darwin, who was born this day in 1809. Charles Darwin was the first to propose the scientific theory of evolution by natural selection—a theory that has done more to unify and bring understanding to the life sciences than any other. Darwin Day is a celebration of this discovery and of scientific progress.

Our petition asks President Obama to issue a proclamation on Darwin Day that honors Charles Darwin and his theory of evolution by natural selection and that calls on all Americans to preserve scientific discovery as a bedrock of our society. It also asks Americans to commemorate the day with appropriate events and activities.

Sign our petition today to let Obama know that you're on the side of science and you need him to be, too. If President Obama will issue a Darwin Day proclamation, it will send a strong signal to our elected officials in Congress and in the school boards that the American people want scientific integrity to be preserved.

So please sign our petition today and let your voice be heard!

Sincerely,
Roy Speckhardt
Executive Director
International Darwin Day Foundation
The International Darwin Day Foundation promotes public education about science and encourages the celebration of Science and Humanity throughout the global community.

Here is the text of a message to President Obama, urging him to proclaim February 12th as Darwin Day:

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Dear President Obama,

As an American who values scientific inquiry and integrity, I urge you to issue a presidential proclamation recognizing Darwin Day on February 12. Darwin Day is celebrated every year on the anniversary of Charles Darwin’s birthday in 1809, and is a day in which people gather together to commemorate his life and work. Charles Darwin was the first to propose the ground-breaking scientific theory of evolution by natural selection—a theory that has done more to unify and bring understanding to the life sciences than any other—and Darwin Day is a celebration of this discovery and of scientific progress.

I believe that issuing this proclamation will send a powerful message that scientific discovery and integrity in our society are top priorities—priorities that are needed now more than ever as extremists with narrow ideological agendas are attempting to undermine science in our schools.

Please stand with me and countless others who value science and discovery by issuing the following or a similar proclamation on Darwin Day.

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And here is the text of the proposed proclamation:

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A PROCLAMATION

Charles Darwin was the first to propose the scientific theory of evolution by natural selection. On Darwin Day, celebrated on the anniversary of Darwin’s birth on February 12, 1809, we celebrate the life and discoveries of Charles Darwin and express gratitude for the enormous benefits that scientific knowledge, acquired through human curiosity and ingenuity, has contributed to the advancement of humanity.

It is sobering to imagine where the human race would be today without advances in science. Science has helped us to live longer by enabling us to find cures for diseases and alleviating pain and suffering. It has allowed us to travel before unimaginable distances, to interact with and understand people of other cultures and recognize what makes us similar as well as what makes us unique. It has allowed us to understand and maneuver in our world and has provided us insight into the complexities of life.

Charles Darwin recognized the importance and power of scientific discovery, and perhaps no one has influenced our understanding about life on earth as much as he. Darwin was an English naturalist, who on his legendary five-year voyage on the HMS Beagle made important observations about the geological and zoological diversity of the lands he visited, which helped spark his theory of evolution by natural selection. Most of what we understand about the diversity of life and the process by which it has adapted and changed has come from his profound insights, and his contribution to the canons of science cannot be overstated.

On this anniversary of Darwin’s birthday, it is important to recognize the contributions he has made to the advancement of science. It is also important that we continue to educate future generations about evolution by natural selection in our science classrooms. We must not water down the significance of Darwin’s theory, nor the breadth of evidence supporting it, and we must at every turn challenge efforts to undermine science so that we can keep alive in our children and grandchildren the wonder of discovery and the eagerness to obtain knowledge.

Now, Therefore, I, Barack Obama, President of the United States of America, by virtue of the authority vested in me by the Constitution and laws of the United States, do hereby proclaim February 12, 2010, as Darwin Day. I call on all Americans to recognize the importance of Charles Darwin and his theory of evolution by natural selection, to endeavor to preserve scientific discovery and human curiosity as bedrocks of American society, and to commemorate this day with appropriate events and activities.

In Witness Whereof, I have hereunto set my hand this twelfth day of February, two thousand ten, and of the Independence of the United States of America the two hundred and thirty-fourth.

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I personally think that this petition drive is a good idea, and that if it succeeds it will add significantly to both the status of evolutionary biology in America and to President Obama's reputation as a staunch supporter of science. I hope you will to go to the International Darwin Day Foundation's website and sign their petition.

And have a great Darwin Day!

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

John S. MacNeill, Jr.

2010-01-21T23:22:00.011-05:00

John S. MacNeill Jr. passed away on January 19, 2010, at Cortland Regional Medical Center, Cortland, New York, just five days short of his 83rd birthday. During his last years, he persevered through increasing complications of diabetes.

John was born on January 24, 1927, in Weehawken, New Jersey, the son of John S. MacNeill Sr. and Margaret Stalee MacNeill. After attending a number of different schools growing up, he graduated from Homer Academy, Homer, New York, in 1944. Upon graduation, he enlisted in the U.S. Navy at the age of 17 and served his tour of duty during the remaining months of World War II in the Pacific theater. Following the war, he earned a bachelor’s degree in civil engineering from Cornell University in 1950 and married “the girl next door,” Elizabeth “Betty” Hazzard.

After living and working in several locations throughout New York State, John and his growing family settled in Homer, New York. He then started his own civil engineering and surveying firm and subsequently joined a number of professional organizations. Participation in Cortland Rotary Club led to many rewarding years working with international exchange students, who knew him affectionately as “Papa John.” He and his wife, Betty, traveled all around the world visiting former exchange students and their families. John was proud of his Scottish heritage and took pleasure in being the drum major for the Mohawk Valley Frasers Bagpipe Band for many years, along with his wife Betty (tenor drum), son Allen (announcer), daughters Billie Jean (snare drum) and Claudia (tenor drum), and grandchildren (Aurora, Conall, and Adam MacNeill, highland dancers).

John is survived by his wife of nearly 60 years, Elizabeth Hazzard MacNeill, their son, Allen (Leah) MacNeill of Ithaca, NY; their daughters, Billie MacNeill of Homer, and Claudia (Jerome) Caretti of Morrisville, NY; a brother, Robert (Sue) MacNeill of Walton, NY; a sister-in-law, Joyce MacNeill of Homer; ten grandchildren, three great-grandchildren, and many nieces and nephews. He was predeceased by a brother, Arthur MacNeill, of Homer.

Contributions in John MacNeill’s memory may be made to the Cortland Rotary Club, P.O. Box 5248, Cortland, NY 13045, or the charity of one’s choice. Email to: CNY MacNeills

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Evolution: The First Four Billion Years

2010-01-03T14:15:00.022-05:00

A REVIEW OF:
Michael Ruse and Joseph Travis, editors (2009)
Evolution: The First Four Billion Years
Belknap Press of Harvard University Press, Cambridge, MA
ISBN #9780674031753 (hardcover, $39.95), 979 pages

In 2009 scientists worldwide celebrated the 200th anniversary of the birth of Charles Darwin and the 150th anniversary of the publication of his most important book, On the Origin of Species. There have been "Darwin Day" observances at hundreds of colleges, universities, and museums, and scientific conferences and meetings devoted to Darwin and evolution. Many books have also been published to mark the Darwin bicentennial, reviewing Darwin's work and its impact on the science of biology and on society in general. However, relatively few of these books have attempted to place Darwin's theory of evolution in its modern context.

A brilliant exception is Michael Ruse and Joseph Travis's anthology, Evolution: The First Four Billion Years, published by Belknap Press of
Harvard University Press. Released on 12 February 2009, to correspond with the 200th anniversary of Darwin's birth, Evolution: The First Four Billion Years, is really two books in one: a collection of original essays on the major aspects of evolutionary theory today, followed by a comprehensive biographical and historical encyclopedia of evolutionary theory and related scientific and philosophical concepts and terms.

In the first half of the book, Ruse and Travis have gathered together a collection of sixteen essays, written by noted evolutionary biologists, historians, and philosophers of science and covering most of the major topics in evolutionary biology and philosophy today. The essays begin with a historical overview by Michael Ruse of the development of evolutionary thought in western science and philosophy, followed by essays on the origin of life, paleontology, adaptation, molecular evolution, genomics, speciation, evolutionary developmental biology ("evo-dev"), sociobiology, human evolution, and Darwinian medicine. The last five essays cover the major philosophical issues related to evolution, including the relationship between form and function, the impact of evolution on society and religion, and concluding with an essay by Eugenie C. Scott on anti-evolutionism and creationism in America.

The second half of Evolution: The First Four Billion Years is a detailed biographical, historical, and scientific encyclopedia of evolution in all of its dimensions. As far as I am aware, it is the only compendium of its kind available in book form, and for that reason alone is worth the price of the book. Although there are a few missing concepts/topics (for example, "microevolution" and "macroevolution" are not defined nor covered as concepts in their own right), the coverage is generally as good as one would find anywhere. Furthermore, detailed biographies of nearly every important evolutionary biologist, historian, or philosopher of the 19th and 20th centuries are included, and bibliographical references are cited for every article and entry. Once again there are a few curious lacunae (for example, George R. Price is not mentioned, despite the importance of his mathematical analyses to current theories of multi-level selection), but I was impressed with some of the biographies of scientists less well known to most people, such as Russian population geneticist, Sergei Chetverikov, and American paleontologist and fossil hunter, Edward Drinker Cope.

Overall, therefore, Evolution: The First Four Billion Years is a fascinating compendium of modern evolutionary thought, which nearly anyone interested in the current state of evolutionary biology will find both interesting and valuable. Readers interested in a review of the most important aspects of evolution today will find it useful, and those who want to get deeper into the various topics included can follow them up using the bibliographical citations following every essay and encyclopedia entry. The only thing more useful than this book might be an online version with links to related concepts and references, but I suspect that this will not be long in coming. Until then, I recommend you pick up a copy of Evolution: The First Four Billion Years and set it somewhere you will be frequently tempted to open it up and browse!

Here is a link to Evolution: The First Four Billion Years at Amazon.com, where it can be purchased in hardcover for $13.58 less than the cover price. You can also browse readers' reviews at Amazon.com here.

And a Happy New Year to you all!

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

I WON the game!

2009-12-08T09:42:00.014-05:00

Weird things have been happening lately. In my entire life I have never won any kind of contest, lottery, or sweepstakes. Indeed, as I pointed out here, the only game that I have consistently played is one that I have consistently lost simply by remembering that I'm playing it (see here for more).

But now, this has happened:

REPORT ON THE MAGAZINE OF FANTASY AND SCIENCE FICTION'S 1980 30TH ANNIVERSARY CONTEST:

AS GREAT AS it is for contemplating the future, science fiction is also valuable for reminding us that we are living in someone else's future.

This little truism came to mind when our last publisher, Ed Ferman, sent word that a winner from our 1980 contest has been decided a few months early. (If the contest doesn't sound familiar to you longtime readers, don't go searching through your back issues—the contest was conducted by mail as part of a subscription drive.)

In 1980, F&SF sponsored a 30th Anniversary Contest called "Win $2,010 in the year 2010." It asked readers to choose one science fiction concept which will have been realized by the year 2010 and which will have had the most significant impact (good or bad) on your life.

As promised, the approximately 2,700 entries were held securely and recently opened in order to select a winner. I read through all of them over several days, and here are some comments:

• Only a tiny minority chose something bad, typically, "thermonuclear war; I'll be dead."

• The vast majority chose concepts that seemed—in hindsight at least—wildly optimistic. Most frequent entries of this sort included:
- World government, world peace
- Colonies or factories in space
- Robots in the home
- Tourist travel in space

• Most frequent of all: medical advances that would extend life span to 200 years or more.

So many entries projected a sense of confidence and hope that it was somewhat distressing to see how badly we fell short in realizing these predictions.

• More realistic predictions occurred in two areas: genetic research and alternative sources of energy. But even here, the only concept we came across that has come close to being realized is the electric car.

• The winner was chosen from a fairly large group who saw that computer technology and communication would have the greatest impact. In 1980 personal computers had only been available for a few years (Apple was founded in 1976), and wide use of the Internet was more than a decade in the future.

It was hard to select a winner from this group. What tipped Allen MacNeill's entry into the winner's circle was his prediction of hand-held computers, though he admits that he never thought they would be the size of a pack of cigarettes.

—Ed Ferman, former publisher, The Magazine of Fantasy and Science Fiction

On hearing the news, the contest winner, Allen MacNeill, sent a note that's worth reprinting in its entirety:
Greetings, Ed:

Please forgive my skepticism, but I receive about a hundred "phishing" invitations a day and so am very leery of the kind of notification contained in your email. However, it is indeed the case that I was a very loyal subscriber to F&SF from the 1970s through the late 1980s. As a senior lecturer in biology at Cornell, I eventually let my subscription lapse, mostly because I no longer had the luxury of spending time reading a lot of science fiction (more's the pity). I still glance through a copy now and then (usually in the library) and find it to still have the best short fiction in the genre.

Anyway, yes I did indeed enter the contest, and remember the premise well. I believe that I entered several times, with several predictions. I came up with the one about "home computer terminals with interactive access to other home, business and academic terminals, and including hand-held terminals" mostly because I had been using the PLATO terminals in Uris Hall at Cornell and wished very, very much that I could have one of my own (and especially one that I could carry around with me). Of course, the fact that you are reading this email on precisely the kind of "home computer terminal" that I originally predicted would come about is evidence that this prediction was pretty accurate.

However, I never would have predicted either spam or viruses/worms (although David Gerrold did in When HARLIE was One, which first appeared in Galaxy magazine, another sf mag I read with devotion in those days). I have owned at least one "home computer terminal" since 1982 (it was a Commodore 64), only two years after I made the prediction for your contest. My first real desktop (i.e. the fulfillment of the prediction) was an Epson QX-10, which I bought in 1983 when I landed a contract to write an introductory biology textbook for Prentice-Hall. When it died suddenly in 1987 I bought a Mac Plus, and have stuck with Macs ever since. Right now I have three 24" 2.4 GHz Intel Core 2 Duo iMacs, running simultaneously as WIntel machines using Parallels, one at home and one in my office at Cornell, plus a 15" MacBook G-4 that is now starting to show its age (it's almost five years old, and so a virtual antique).

If pressed today, I would say that thirty years from now it is most likely that we will be using some version of a "cloudbook", for which most of the processing and hard memory/data storage will be located somewhere else. This will, of course, depend on the Moore's Law-enhanced capabilities of the descendants of today's cell phones, which I suspect will be incorporated into our clothing, with something like a virtually invisible BlueTooth earbud/jaw mike interface. I don't think we will have implants, however, as they would need to be surgically replaced too often as technology changes—fun as it was at the time, I certainly would not have wanted to have the equivalent of my old C-64 implanted in me!

Anyway, my very brief bio is this: In 1980 when I entered the contest I had just recently finished graduate school and begun teaching introductory biology at Cornell. I have been doing so ever since, with a brief sabbatical leave as Chief Academic Officer for a Web 1.0 startup in 1999-2000. I am about to be taped for a series of online lectures on evolution for Cornell's CyberTower "study rooms" and am currently writing several books and maintaining four active blogs. I couldn't do any of this without my trusty home computer terminals with interactive access to other home, business and academic terminals, and including hand-held terminals, and indeed cannot imagine what life today would be without them. Very different, and much less interesting in many ways.

By the way, I wish that back in 1980 you had bought $2,010 worth of Apple stock (or any kind of stock, for that matter) and held on to it for the winner of your contest. Now that I think of it, could I have my grand prize winnings in 1980 dollars? ;-)

My sincerest thanks for a terrific magazine, a terrific contest, and for making my day! Please let me know where the announcement of the contest and the fact that I am the grand prize winner will appear, so I can blog it!

Still in Ithaca/Utopia and still crazy after all these years, I remain…
As always.
—Allen MacNeill

So, congratulations to Allen MacNeill, and for anyone who is reading this editorial in the year 2040, I hope you're making the most of our future.
—Gordon Van Gelder, current publisher, The Magazine of Fantasy and Science Fiction

And, it gets weirder yet:

As of yesterday (Monday 7 December 2009), The Evolution List is currently #63 in the Top 100 Science Blogs list at Wikio.com. Furthermore, it is currently #12 among science blogs that regularly cover evolutionary biology:

1. Pharyngula
2. The Panda's Thumb
3. Greg Laden's Blog
4. Gene Expression
5. A Blog Around the Clock
6. Thoughts from Kansas
7. EvolutionBlog
8. Mike the Mad Biologist
9. Laelaps
10. Aetiology
11. The Evolving Mind
12. The Evolution List

What's next, I wonder?

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

The Searchers

2009-12-07T20:51:00.017-05:00

AUTHORS: William A. Dembski and Robert J. Marks II

SOURCE: Proceedings of the 2009 IEEE International Conference on Systems, Man, and Cybernetics. San Antonio, TX, USA – October 2009, pp. 2647-2652

COMMENTARY: Allen MacNeill

First, congratulations to Drs. Dembski & Marks! Publication is the life blood of all career academics and the living heart of the intellectual process. It takes courage and hard work (and a little bit of luck) to get your original work published, and more of the same to weather the criticism that inevitably ensues. But, just as one cannot have a fencing match without an opponent, real progress in any intellectual endeavor cannot come from consensus, but only from the clash of ideas and evidence.

And so, to specifics:

I have no quibble with most of the mathematical analysis presented. Indeed, given the assumptions upon which the authors' Conservation of Information (COI) theory is based (with which I do not necessarily agree, but which are clearly presented in their paper), the analysis presented is apparently not completely outside the domain of No Free Lunch (NFL) theorems in general.

However, the same cannot be said for the application of these ideas to biological evolution. To be specific, consider the following quote [Dembski & Marks (2009) pg. 2651, lines 2-5]:

"From the perspective of COI, these limited number of endpoints on which evolution converges constitute intrinsic targets, crafted in part by initial conditions and the environment." [emphasis added]

This is indeed the crux of the issue vis-a-vis biological evolution. While it is clearly the case that Simon Conway-Morris asserts that there is an apparently limited number of biological "endpoints", it is neither the case that Morris' viewpoint represents the core of evolutionary theory, nor that his point is relevant to the analysis of COI presented in Dr. Dembski and Marks' paper.

To be specific, the highlighted qualifier from the quote above – crafted in part by initial conditions and the environment – is precisely the issue under debate between evolutionary biologists and supports of intelligent design (ID).

Taken at face value, this qualifying simply phrase means that, given specific starting conditions and a specific time-varying environmental context, the various mechanisms of evolution (e.g. mutation, natural selection, genetic drift, inbreeding, etc.) tend to converge on a relatively limited set of genotypic and phenotypic "endstates" (i.e. what could be loosely referred to as "evolutionary adaptations").

This is simply another way of defining evolutionary convergence, and in no way constitutes evidence for intrinsic evolutionary teleology. On the contrary, it simply provides support for the hypothesis that, given similar conditions, similar outcomes result.

Furthermore, it assumes that virtually all characteristics of living organisms are adaptations (that is, genotypic/phenotypic characteristics that fulfill some necessary function in the lives of organisms). However, this is manifestly not the case, nor is it an absolutely necessary component of current evolutionary theory. On the contrary, many (perhaps the majority) of the characteristics of living organisms are not adaptive. This is certainly the case at the level of the genome, as evidenced by the neutral and nearly neutral theories of molecular evolution.

Finally, Morris' (and, by extension, Dembski and Marks') position completely omits any role for historical contingency, which both the fossil and genomic record indicate are of extraordinary importance in macroevolution. As Dembski and Marks state, the "endpoints" (perhaps it would be more precise to refer to them as "way stations") of macroevolution depend fundamentally on initial conditions and the environment. But this is not fundamentally different from Darwin's position in the Origin of Species:

"The complex and little known laws governing variation are the same, as far as we can see, with the laws which have governed the production of so-called specific forms. In both cases physical conditions seem to have produced but little direct effect; yet when varieties enter any zone, they occasionally assume some of the characters of the species proper to that zone." [Darwin, C. (1859) Origin of Species, pg. 472, emphasis added]

Moreover, Dembski and Marks' analysis completely ignores the appearance (or non-appearance) of new genotypic and phenotypic variations, and on the accidental disappearance of such characteristics (via extinction), without regard to the adaptive value of such characteristics, or the lack thereof.

In other words, Dembski and Marks' analysis, while interesting from the standpoint of what could be called "abstract" search algorithms, completely fails to address the central issues of evolutionary biology: the source of evolutionary novelty (i.e. the "engines of variation"), the effects of changing environmental conditions on the actual forms and functions of living organisms, and the fundamental importance of historical contingency in the ongoing evolution of genotypes and phenotypes.

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

A New Species of Finch in the Galapagos: So What?

2009-11-28T10:22:00.023-05:00

Since the first reports of the origin of a new species of finch on the island of Daphne Major in the Galapagos archipelago appeared, there has been a flood of questions about just what exactly it was that Peter and Rosemary Grant observed, and how their observations relate to the larger question of macroevolution. As many evolutionary biologists (including me) anticipated, creationists and intelligent design ("ID") supporters have moved the goalposts, arguing that they have always accepted that speciation occurs, but that it does not necessarily mean anything for macroevolution, especially if one defines "macroevolution" as the origin of higher taxa (i.e. taxonomic categories above the level of species). So, what did the Grants observe, and how are their observations related to the larger question of the origin of higher taxa (i.e. macroevolution)?

The answer is that this long-term research project has provided direct evidence for the initial stages of macroevolution in the field. To be precise, what is at issue in the research reported by the Grants is what is known as “secondary contact”. This is what happens after a sub-population has become reproductively isolated from the population from which it was derived. According to Theodosius Dobzhansky and Ernst Mayr (two of the founders of the “modern evolutionary synthesis”), speciation is the result of genetic isolation resulting from geographic isolation: the members of two geographically separated populations of organisms no longer interbreed, and therefore genetic differences between the two populations accumulate over time.

This process, commonly known as allopatric speciation, can be considered to consist of six discrete, successive stages:

1) Vicariance: A subpopulation (in this case, a couple of finches) becomes geographically isolated (on Isla Daphne Major) from its former panmictic conspecifics (i.e. the species Geospiza fortis on Isla Santa Cruz, a neighboring island);

2) Divergence: The genomes of the members of the vicariant subpopulation diverge from the genomes of the members of the panmictic source population as the result of various genetic mechanisms (for a list of such mechanisms, click here);

3) Reproductive Isolation: The reproductive anatomy, physiology, and behavior of the members of the vicariant subpopulation diverge from the reproductive anatomy, physiology, and behavior of the members of the original source population, resulting in reproductive isolation and (eventually...at least sometimes) reproductive incompatibility;

4) Secondary Contact: Successful hybridization between members of the diverging sub-population and the original source population decreases in frequency as the result of pre-zygotic and post-zygotic isolating mechanisms (for more, click here);

5) Reinforcement: Hybrids continue to decrease in frequency as non-hybrids increase in frequency as the result of microevolutionary mechanisms (i.e. mutation,natural selection, gene flow, genetic drift, and inbreeding depression), resulting in reinforcement of reproductive isolation and species boundaries; and

6) Maintenance: Species incompatibility is continuously reinforced via pre-zygotic and post-zygotic isolating mechanisms, resulting in continued genotypic and phenotypic divergence.

This is why Alfred Russell Wallace entitled his paper (which he mailed to Darwin in April 1858), “On the Tendency for Varieties to Depart Indefinitely from the Original Type”.

Note that none of these stages is absolutely defined; rather, they integrade in what Darwin characterized as an “insensible series”. Also note that stages 4 through 6 can be condensed into one stage (i.e. “reinforcement”), in which reproductive incompatibility increases steadily over time. Finally, some evolutionary biologists (most notably C. H. Waddington, Mary Jane West-Eberhard, Eva Jablonka and Marion Lamb) have proposed that stages 2 and 3 probably happen in reverse order (a process known as genetic assimilation).

This is the theoretical model; what actual empirical studies have shown is that diverging phylogenetic lines frequently become reintegrated, separating and then re-integrating more than once. Sometimes they become sufficiently reinforced that they remain separate and diverge continuously, and sometimes they “collapse” back into a single, panmictic “species”.

The importance of all of this to the theory of macroevolution is that divergence is divergence: phylogenetic divergence via reproductive isolation is macroevolution. Speciation is simply the first stage in the origin of all higher taxa.

Therefore, what is ultimately at issue between evolutionary biologists and creationists (including most ID supporters) is not speciation per se nor the mechanisms by which it occurs or is reinforced, but rather whether there are “natural” limits to the degree of divergence that can take place as a result of the mechanisms that comprise the “engines of variation”.

Despite much posturing on both sides, this is not a question that can be answered via pure theoretical (i.e. mathematical) speculation. However compelling a theoretical model may appear, it must be tested empirically to see if it conforms to the evidence from nature. This is what evolutionary biologists do all the time, and what ID theorists seem either unable or unwilling to do. Until this situation changes (if it ever does), no reputable empirical scientist anywhere will ever take ID seriously.

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

The Longest Running Failed Prediction in Creationism

2009-11-24T09:08:00.010-05:00

AUTHOR: G.R. Morton

SOURCE: Answers in Science

COMMENTARY: Allen MacNeill

First, today is the 150th anniversary of the original publication of Charles Darwin's Origin of Species. So many people have written about this event that it would be superfluous for me to write about it here. However, some of what has been written about the Origin lately, mostly by creationists and supporters of "intelligent design", is that Darwin's theory of evolution by natural selection is "crumbling" and will soon be "dead".

Admittedly, I have written recently that the "modern evolutionary synthesis" is dead (see here for more), but in doing so I have taken pains to point out that the theory of evolution itself is most assuredly not dead. On the contrary, it is very much alive. Indeed, it has never been more vigorous than it is today.

But that's not what the creationists are saying. What they're saying (or trying to say) is that the whole concept of evolution itself is dead: the Earth and everything on it was created a relatively short time ago, and even if life on Earth has changed (a little), all of that change has been guided by the deity of the Abrahamic religions (Judaism, Christianity, Islam, Mormonism, etc.) Indeed, just this morning a new podcast was launched at the website of the Discovery Institute, in which neo-Paleyist and ID creationist John West asserts once again that "Darwinism is dead".

Is this news? And is it new? How long have creationists been predicting the demise of Darwin's theory of evolution? Apparently, they've been doing so since a few decades before Darwin published it. G. R. Morton has compiled a short list of quote from creationists predicting the impending overthrow of the theory of evolution (you can read it here). He introduces his anthology of science denialism with this:

In recent reading of [Dr. William] Dembski and other ID proponents I saw them make a claim which has been made for over 40 years. This claim is one that the young-earthers have been making. The claim is that evolution (or major supporting concepts for it) is increasingly being abandoned by scientists, or is about to fall. This claim has many forms and has been made for over 162 years. This is a compilation of the claims over time. The purpose of this compilation is two-fold. First, it is to show that the claim has been made for a long, long time. Secondly, it is to show that entire careers have passed without seeing any of this movement away from evolution. Third, it is to show that the creationists are merely making these statements for the purpose of keeping hope alive that they are making progress towards their goal. In point of fact, no such progress is being made as anyone who has watched this area for the last 40 years can testify. The claim is false as history and present-day events show, yet that doesn't stop anyone wanting to sell books from making that claim.

Morton's quotations from creationists begins with a quote dating to 1825, 34 years before Darwin published the Origin of Species. Apparently, what many historians have asserted was true: that the idea of evolution was "in the air" in the mid-19th century, and that Darwin simply codified and provided evidence for an idea that was already becoming generally well-known and at least partially accepted. The fact that Alfred Russell Wallace came up with the same mechanism that Darwin did for descent with modification — natural selection — is further evidence for the idea that evolution was "in the air" at the time.

It still is, and even moreso. Not only has the theory of evolution not "crumbled", it is currently undergoing its most rapid expansion since 1859. Darwin's original theory was limited strictly to biological evolution, but now his theory is being extended into astrophysics, geology, economics, psychology, sociology, and even literature and art history. It is this tremendous success that upsets the opponents of Darwin's theory, and that impels them (in the face of overwhelming evidence to the contrary) that the most widely accepted, most generally applicable, and most analytically powerful theory in all of science is on its way out.

In other words (and true to their creationist roots), they stare reality in the face and deny it.

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

Comfortable Creationists Wimp Out at Cornell

2009-11-20T09:52:00.018-05:00

Many people have recently heard about how creationist and televangelist Ray Comfort has been planning to distribute 170,000 copies of Charles Darwin's Origin of Species at the 100 top colleges and universities in America.

Well, the appointed day (19 November) for Ray's distribution of the Origin came and went, but apparently no creationists showed up at Cornell to pass out Ray's "abridged" copy of the Origin of Species with Ray's laughably mendacious introduction. I really wanted to get a copy, eagerly pressed into my grasp by the hot little hands of a freshly scrubbed creationist, but after checking every likely location — from Ho Plaza in front of the Straight (where there were a few empty folding tables, sitting forlornly in the rain) to the plaza between Olin and Uris libraries (where a few damp smokers contemplated "The Song of the Vowels") to Trillium (where Cornell's elite meet to eat) to Mann Library (the second largest agriculture and biology library in the world...where is the first, exactly?) to Appell Commons (where you can work up a sweat before downing your stir fry)...nada, nobody, zip, just grey sky and freezing rain. And so my quest for another artifact from the culture wars went unsatisfied...

Apparently, Ray got worried that people like me would make things "unComfortable" for his minions, so he secretly ordered them to go out a day early. But, this is the Age of Twitter, and so a lot of Godless Evilutionists were out in force on Wednesday...but, no Comfortable creationists then either. Looks like I picked up that bunch of bananas for nothing — *sigh*

By the way, Ray Comfort has apparently been making a career out of lying lately, asserting that his version of the Origin would be passed out at Cornell yesterday, and that his bastardized version would be available in its entirety. Although I didn't get my copy, I have been informed by people at other academic institutions who did that, on the contrary, he's apparently cut out precisely those chapters that have proven most inconvenient for creationists in the past. And, he's added a fifty-page "introduction" that's filled with laughably inaccurate so-called "arguments" against the content of Darwin's masterpiece.

Furthermore, his apparently false claim that he was printing 170,000 copies of his version of the Origin was apparently intended to push his version to the top of Amazon.com's search results for the Origin of Species, where members of the uninformed public who were interested in reading Darwin's masterpiece during this bicentennial year (it's the 200th anniversary of Darwin's birth and the 150th anniversary of the first publication of the Origin of Species) would innocently buy his bastardized version with his mendacious introduction. A clever public relations gambit — gaming Amazon.com's popularity algorithm — but I guess he forgot about the reviewer's comments at Amazon, where his lying and propaganda techniques and public relations tricks have been exposed by people more interested in the truth than making money by shilling for Jesus (who would have been horrified by Ray's tactics, and probably by his theology as well).

So, why did Ray's minions wimp out at Cornell? Maybe because Cornell is well-known for being the Ivy League university most dedicated to the principles of modern science, including evolutionary biology — we've got the best department of ecology and evolutionary biology in the world, and Cornellians (including our presidents) have been well-known for speaking out against bad science since the beginning.

Or maybe because Ray's followers were "discomfited" by our ever-present November drizzle...

...whatever.

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

The Modern Synthesis is Dead - Long Live the Evolving Synthesis!

2009-11-19T21:47:00.014-05:00

It has been almost exactly a century and a half since Darwin's Origin of Species was first published, and half a century since the conference at the University of Chicago where the "triumph" of the "modern evolutionary synthesis" was celebrated. So, isn't it a little odd that some well-respected scientists and historians of science are proclaiming in this celebratory year that the modern evolutionary synthesis is dead?

For example, Eugene Koonin, senior investigator at the National Center for Biotechnology Information, National Library of Medicine, and National Institutes of Health in Bethesda, Maryland, has published two essays on the current status of the "modern evolutionary synthesis":

The Origin at 150: Is a new evolutionary synthesis in sight?
Trends in Genetics, 25(11), November 2009, pp. 473-475.

Abstract: The 200th anniversary of Charles Darwin and the 150th jubilee of the On the Origin of Species could prompt a new look at evolutionary biology. The 1959 Origin centennial was marked by the consolidation of the modern synthesis. The edifice of the modern synthesis has crumbled, apparently, beyond repair. The hallmark of the Darwinian discourse of 2009 is the plurality of evolutionary processes and patterns. Nevertheless, glimpses of a new synthesis might be discernible in emerging universals of evolution.

and

Darwinian evolution in the light of genomics.
Nucleic Acids Research, 37(4), 2009, pp. 1011-1034.

ABSTRACT: Comparative genomics and systems biology offer unprecedented opportunities for testing central tenets of evolutionary biology formulated by Darwin in the Origin of Species in 1859 and expanded in the Modern Synthesis 100 years later. Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected. Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept. An adequate depiction of evolution requires the more complex concept of a network or 'forest' of life. There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a nonadaptive consequence of evolution under weak purifying selection rather than an adaptation. Several universals of genome evolution were discovered including the invariant distributions of evolutionary rates among orthologous genes from diverse genomes and of paralogous gene family sizes, and the negative correlation between gene expression level and sequence evolution rate. Simple, non-adaptive models of evolution explain some of these universals, suggesting that a new synthesis of evolutionary biology might become feasible in a not so remote future.

A big deal, right? Well, not really. Will Provine and I have been saying that “the modern evolutionary synthesis is dead” for years. Indeed, Will Provine coined the phrase “the hardening of the synthesis” to describe the narrowing of focus in evolutionary theory during the first half of the 20th century to concepts entirely reducible to mathematical models, especially theoretical population genetics.

Ironically, Dr. John Sanford and Dr. William Dembski (among others in the ID camp) have not moved beyond this narrow focus on theoretical population genetics, and so have apparently missed the fact that evolutionary biology has evolved far beyond the narrow theoretical focus of the mid-20th century. Some ID supporters have also suggested that Dr. Koonin might be taking a “big career risk” in stating the obvious. I don't think so. On the contrary, what Dr. Koonin has pointed out is that evolutionary biology today is broader, more generally applicable, and less narrowly focused than at any time since the publication of the Origin of Species 150 years ago. Being an evolutionary biologist today is like being a physicist in 1905 — a whole new world of theoretical and practical empirical research is opening up, with new discoveries being made every day.

As just one example, Kyoto-prize-winning evolutionary biologists Peter and Rosemary Grant have reported on something that Darwin could only speculate about: the systematic empirical documentation of the “origin” of a new species (reported here yesterday). Creationists have of course moved the goalposts, arguing that they accepted all along that new species could arise from existing ones, it’s just microevolution, which of course everyone accepts. This, despite the fact that speciation has always been considered to be the first (and perhaps most important) stage in macroevolution, and that less than two decades ago creationists were confidently stating that “true” speciation had not only never been observed, it couldn’t ever be observed because it can’t happen.

Now the leaders of the ID movement — people like Dr. Michael Behe and Dr. William Dembski — publicly state that they fully accept that descent with modification from common ancestors (i.e. evolution) has happened, that microevolution (i.e. natural selection, sexual selection, and genetic drift) are also fully supported by the evidence, and that the “real” focus of disagreement is over the “engines of variation” that produce the raw material upon which the “engines of evolution” operate. They’ve come a long way, but they’ve missed the parade by a couple of decades. So it goes…

I would say that Dr. Koonin's essays on where evolutionary biology is today are quite close to the the mark. The concept of natural selection as the foundation of evolutionary change has been largely superseded, mostly through the work of Motoo Kimura, Tomoko Ohta, and others, who have shown both theoretically and empirically that natural selection has little or no effect on the vast majority of the genomes of most living organisms.

However, ID supporters should find this sea change in evolutionary biology to be cold comfort. The overall effect of the advances in our understanding of how genomes and phenotypes change over time has had the same effect on evolutionary theory that the rise of quantum mechanics had on classical physics. Einstein famously asserted that “God does not play dice”, but a century of physics research has shown him to be more wrong about how the universe works at the quantum level than ever.

The same is true for the “evolving synthesis”. Rather than revert to a neo-Paleyan paradigm (as proposed by Behe, Dembski, and their supporters), evolutionary biology has gone in the opposite direction, the same direction that quantum mechanics has taken. According to the “modern synthesis” of the last century, the genome was “homeostatic”, “organized”, and “regulated” primarily by natural selection. Sure there were purely random processes also going on (such as genetic drift), but most evolutionary change was both adaptive and coherent over time.

Here's what Dr. Koonin writes (see above):

"There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a nonadaptive consequence of evolution under weak purifying selection rather than an adaptation."

Kimura, Ohta, Jukes, and Crow dropped a monkey wrench into the "engine" at the heart of the modern synthesis — natural selection — and then Gould and Lewontin finished the job with their famous paper on “the spandrels of San Marco and the Panglossian paradigm”. The rise of evo-devo over the past two decades has laid the groundwork for a completely new and empirically testable theory of macroevolution, a theory that is currently facilitating exponential progress in our understanding of how major evolutionary transitions happen. And iconoclasts like Lynn Margulis, Eva Jablonka, Marian Lamb, Mary Jane West-Eberhard, and David Sloan Wilson are rapidly overturning our understanding of how evolutionary change happens at all levels, and how it is inherited.

So, as I have said many times before, when ID supporters set their sights on “neo-Darwinism” as a target for criticism, they set their sights on a model that has been all but abandoned. The carnival has moved on and ID supporters are fighting battles that evolutionary biologists left behind a half century and more ago.

And so, on this 150th anniversary of the publication of Darwin's Origin of Species, evolutionary biologists can raise a frosty glass and say

The modern synthesis is dead — long live the evolving synthesis!

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

The Darwinian Revolution To Be Shown at Cornell

2009-11-19T10:48:00.008-05:00

There will be a free public showing of The Darwinian Revolution video series at 4 PM on Tuesday 24 November 2009 in the large classroom (room 3330) of the Tatkon Center in Balch Hall. This presentation will take place on the 150th anniversary of the publication of Charles Darwin's Origin of Species, and is part of Cornell's celebration of the Darwin Bicentennial. The host of the video series, Cornell evolutionary biologist Allen MacNeill, will be on hand at the presentation to discuss the videos and answer questions about evolutionary biology in general, and about The Darwinian Revolution video series in particular.

The Darwinian Revolution is a series of six videos addressing the content and history of the theory of evolution. Produced by Cornell's CyberTower program and hosted by evolutionary biologist Allen MacNeill, the six-part series includes an overview of evolutionary biology, a history of the concept of evolution in western civilization, a brief consideration of Lamarck's theory of evolution via the inheritance of acquired characteristics, a detailed look at Darwin's theory of evolution by natural selection, a brief exploration of Mendel's theory of particulate inheritance and its role in the origins of the "modern evolutionary synthesis", and a look forward at the future prospects for evolutionary biology. The series was videotaped at the Museum of the Earth in Ithaca, New York, and features interviews with museum director and paleontologist Warren Allman and Cornell historian of science William Provine.

This public showing of The Darwinian Revolution is free and open to the general public. It is cosponsored by Cornell's CyberTower program, in cooperation with the Museum of the Earth and Cornell's Tatkon Center as part of this year's celebration of the 200th anniversary of the birth of Charles Darwin and the 150th anniversary of the publication of Darwin's Origin of Species.

The Darwinian Revolution video series can also be viewed online here. For more information about the video series, go here.

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

A New Species of Finch may have Evolved in the Galapagos

2009-11-18T09:49:00.006-05:00

AUTHOR: Daniel Cressey

SOURCE: Nature.com News

COMMENTARY: Allen MacNeill

As I have noted in several recent blogposts, Charles Darwin's Origin of Species was published 150 years ago this month. One of Darwin's crucial examples of descent with modification in the Origin was the evolutionary diversification of a group of finches now usually referred to as "Darwin's finches". In the Origin Darwin did not speculate as to how long this evolutionary diversification took place, except to suggest that it would require "the passage of long ages". However, in a private letter to one of his correspondents, Darwin suggested that it would take at least fifty years to see unambiguous effects of natural selection.

A recent publication in the Proceedings of the National Academy of Sciences lends empirical support to Darwin's suggestion. Peter and Rosemary Grant have been studying the finches of Daphne Major, a small island in the Galapagos archipelago since 1973. In PNAS, they have proposed that a population of finches on Daphne Major may be on the verge of becoming a new species of finch. Here's how their proposal was reported at Nature.com News:

"It was in 1981, that the Grants spotted an unusually heavy medium ground-finch (Geospiza fortis). At 29.7 grams, the male was more than 5 grams heavier than any they had seen on Daphne Major before. Genetic analysis showed that it probably came from the neighbouring island of Santa Cruz.

The Grants numbered the bird 5110 and followed it and all its known descendants over seven generations. Many of its descendants stuck out from the other G. fortis on Daphne Major: they had unusually shaped beaks and their songs differed from those of the other finches.

...

In the fourth generation, a severe drought hit the island and 5110's descendants were reduced to one male and one female — a brother and sister. From then on the immigrant lineage isolated itself, breeding with no other G. fortis on the island....

"No study of this sort has been done before, and it shows one way in which speciation can get started," say the Grants from Japan, where they are receiving the Kyoto Prize for basic science for their life work."

Several further points from the Grants' report are significant. Many evolutionary biologists (including Tijs Goldschmidt) have speculated that sexual selection may be a significant cause of evolutionary diversification, including the origin of new species as the result of female choice. It appears that sexual selection has played an important part in the differentiation of the incipient species of finch on Daphne Major:

"The fact that 5110's descendants haven't mixed could be because they differ from the natives. The Grants note that the descendants have a differently shaped beak from those native to Daphne Major. As finch beaks are vital in identifying potential mates, this could serve to keep them reproductively isolated.

5110's offspring also have the avian equivalent of a strange accent. These finches learn their songs from their father, and the Grants suggest that 5110 sang the songs from his birth home of Santa Cruz then modified his come-hither ballad by roughly copying the Daphne Major birds'. This imperfect copying, they suggest, has over time acted as a barrier to interbreeding.

Also, the Grants' research has illustrated an important point concerning Darwinian speciation. As Darwin pointed out in the Origin, the distinction between varieties, subspecies, and species are "entirely arbitrary", and ultimately depend on reproductive isolation:

"The Grant's aren't yet ready to call 5110's lineage a new species, a term fraught with difficulty for evolutionary biologists. "There is no non-arbitrary answer to the question of how many generations should elapse before we declare the reproductively isolated lineage to be a new species," they say. "For the present it is functioning as a [separate] species because its members are breeding only with each other."

The Grants think there is only a small chance that 5110's descendants will remain isolated long enough to speciate. If they do, the new species will have to be named: "When discussing these birds we call them 'big birds'," the Grants say. "That could be translated into Latin."

According to the biological species concept, since 5110's descendants are not interbreeding with the other finch species on Daphne Major, they should already be considered to be a separate species. If at some point in the future they do interbreed with the other species of finches, this would not violate their status as a distinct species, any more than the hybridization between blue-winged warblers (Vermivora pinus) and golden-winged warblers (Vermivora chrysoptera) indicates that these two species are not "genuine" biological species.

Finally, the observation that this incipient species of finch resulted from the consanquineous mating of a pair of full siblings lends support to my proposal that speciation can be facilitated by first degree inbreeding. Here's what I wrote about this proposal on Thanksgiving in 2006:

"Wouldn't [the genetic rearrangements usually accompany reproductive isolation] have to occur within at least two members- one male, one female- of the same population in order for it to have any chance of getting passed on? And therefore, wouldn't this make such genetic rearrangements difficult, if not impossible to pass on?"

To which I answered:

No. All that would need to happen to make this possible would be for two first-degree relatives carrying the genetic rearrangement to mate and have offspring. First degree relatives (i.e. parents and offspring or full siblings) can easily have the same chromosomal mutation (i.e. a fusion, fission, translocation, or inversion), as they would inherit it from a single parent. If they were to mate with each other (a not uncommon event among non-humans...and even among some humans), they would be able to produce fertile offspring carrying the same chromosomal mutation.

Yes, it is true that first degree mating carries with it the possibility of reinforcement of recessive lethal alleles. However, as many geneticists and evolutionary biologists have repeatedly pointed out, this is actually beneficial to the population within which such reinforcement happens, as the alleles are "purged" from the population as a result.

In other words, mating between first degree genetic relatives within a small, isolated population would have the effect of both removing deleterious alleles from the population and allowing chromosomal mutations to spread throughout the population, especially if such mutations were at all beneficial (although they would diffuse almost as well if they were selectively neutral, as would probably be the case given that no change in overall genetic information would have occurred).

Furthermore, the hypothesis that I have presented above squares very well with the currently prevailing theory of speciation: that of peripatric speciation, as first proposed by Ernst Mayr. According to Mayr's theory, speciation occurs most often in small, isolated populations on the periphery of large, panmictic populations. There is abundant natual history evidence that this is the case, especially in animals.

However, to my knowledge no one has yet proposed a mechanism explaining how peripatric speciation would come to be associated with the kinds of chromosomal changes that are commonly associated with reproductive isolation and speciation. My hypothesis – that first-degree inbreeding facilitates chromosomal speciation – is an attempt to reconcile those two observations.

In a large, panmictic population, selection would tend to eliminate individuals who mate with first-degree relatives as a result of decreased viability due to inbreeding depression and the increased frequency of expression of homozygous lethal alleles.

However, in very small, isolated populations individuals who occasionally mate with first degree relatives (i.e. "facultative first degree inbreeders") could easily have a selective advantage of individuals who avoid mating with first degree relatives (i.e. "obligate outbreeders").

Males in particular would tend to loose less as the result of mating with first degree relatives, as their parental investment in offspring is lower (i.e. they can waste gametes and even zygotes by mating with their first degree relatives, without significantly decreasing their reproductive success).

However, even females can cut their losses by mating with first degree relatives if the likely alternative is failure to mate at all due to unavailability of non-relatives. This would especially be the case in small, isolated populations, which are exactly the kind of populations in which speciation is most likely to occur.

The effects described above would be facilitated by increased genomic homogeneity, such as would result from genetic bottlenecks and founder effects. This is because close inbreeding intensifies genomic homogeneity and decreases genetic variation, especially in isolated populations with decreased gene flow from other populations.

This hypothesis – that first degree inbreeding facilitates chromosomal speciation – immediately suggests a series of predictions, all of which are empirically testable:

• The frequency of mating between first degree relatives should be inversely correlated with effective breeding population size. That is, the smaller the effective breeding population, the greater the frequency of mating between first degree relatives (i.e. “first degree inbreeding”).

• The increased frequency of “first degree inbreeding” in such populations should be more pronounced in males. That is, males should be more likely to attempt mating with first degree relatives, especially in small, isolated populations.

• The frequency of “chromolocal mutations” (that is, chromosomal fission/fusion/inversion/translocation mutations) should also be inversely correlated with effective breeding population size. That is, the smaller the effective breeding population, the greater the frequency of viable “chromolocal mutations.”

• Peripatric speciation events should be correlated with small population size, chromolocal mutations, and first degree inbreeding.

• Speciation resulting from chromolocal mutations should be much less common in large, panmictic populations.

• First degree inbreeding should also be much less common in large, panmictic populations.

• The success rate of artificial (i.e. facilitated/forced) first degree mating should be directly correlated with the degree of inbreeding. That is, the more inbred a population, the more successful artificial first degree inbreeding should be.

• Paleogenomic analysis should find close correlations between genetic bottlenecks, founder events, and peripatric speciation events and the frequency of chromolocal mutations and genetic homogeneity (resulting from first degree inbreeding).

• Relatively large changes in phenotype resulting from chromolocal effects should be more common in small, isolated populations.

• Speciation should be easier (and therefore more frequent) among asexually reproducing eukaryotes, such as plants and parthenogenic animals (among whom aneuploidy is largely irrelevant).

Let me stress two things about the foregoing:

• What I am suggesting is, at this stage, merely a hypothesis, but one that generates a series of immediately testable predictions.

• The hypothesis is, of course, based on the idea that incest (i.e. first degree inbreeding) is the most likely explanation for the diffusion of chromolocal mutations throughout small, isolated populations of animals. Let me stress as strongly as possible that I am NOT advocating incest, I am simply pointing out that first degree inbreeding would facilitate the kind of chromolocal mutations that are often correlated with species differences in animals. The same is also true for plants, of course, but in plants we don't call it "incest," we call it "self-pollination."

At the time that I proposed this hypothesis in November, 2006, I was a little perplexed at why no one has yet proposed this mechanism, given the fact that it is already used as the explanation for speciation in plants via polyploidy. The only explanation that seems reasonable to me is that most evolutionary biologists assume that animals will always avoid mating with first-degree relatives as a result of the increased frequency of inbreeding depression and expression of homozygous lethal alleles that result from it.

However, the Grants' observation of incipient speciation among the finches of Daphne Major, which was apparently facilitated by first-degree inbreeding lends support to my hypothesis.

And that's a reason for me to give thanks next week — Happy Thanksgiving, one and all!

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

The ID Cookie Crumbles...

2009-11-16T21:50:00.009-05:00

During this year of celebration of Darwin and evolutionary biology, Intelligent Design (ID) supporters are fond of asserting that a branch of the biological sciences that currently accounts for over 100 regularly published journals (containing over 1000 peer-reviewed scientific reports) per year, over 1000 books published by reputable scientific publishers per year, and involving grant and foundation support amounting to several billion dollars per year is "crumbling", while ID, which accounts for not one peer-reviewed scientific journal and one peer-reviewed book (published over a decade ago) is replacing it.

I can go to Mann Library here at Cornell (the second largest library of biology in the world, comprising over a million books and bound periodicals) and find the equivalent of an entire floor devoted to evolutionary biology. I couldn't carry this month's issues of the various journals devoted to evolutionary biology to the loan desk, even if I used a large laundry basket and made several trips. I have a paltry selection of the most current books on the subject of evolution in my personal library: only 1000+ volumes published in the past ten years or so. If I had unlimited funds, I could buy ten times as many, and still could not keep up with the field.

Virtually every large university in the world has a department of ecology and evolutionary biology. Here at Cornell we have such a department, with almost two dozen professors and dozens of graduate students, and there are at least five other departments at Cornell who number evolutionary biologists among their members. There are almost half a dozen undergraduate and graduate organizations devoted to the scientific aspects of evolutionary biology at Cornell; branches of such societies are found worldwide.

By contrast, there are two tenured professors in the entire world who explicitly support ID, only one of whom is in a department devoted to an empirical science (the other teaches at a theological seminary). Neither of them is currently engaged in empirical research intended to validate ID.

Of the 35+ undergraduate IDEA clubs (a very liberal estimate) that were founded during the heyday of ID (the late 1990s and early 2000s), not one is currently maintaining a website or apparently meeting regularly. And according to Google Trends, interest by the news media in ID has fallen almost to zero since the Kitzmiller v. Dover trial in late 2005, while interest in evolutionary biology is at an all-time high and still increasing with no end in sight.

So, based on the empirical evidence, which is "crumbling", evolutionary biology or ID?

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

Books in Celebration of the 150th Anniversary of the Origin of Species

2009-11-11T10:55:00.069-05:00

2009 marks several important anniversaries in the science of evolutionary biology. Perhaps the two most important are the 200th anniversary of the birth of Charles Darwin and the 150th anniversary of the publication of his most important book, On the Origin of Species, originally published in November of 1859. Scientific societies around the world are celebrating these two events, with “Darwin Day” observances at hundreds of colleges, universities, and museums, including Cornell University and the Museum of the Earth at the Paleontological Research Institution in Ithaca, New York.

Publishers are also celebrating these two anniversaries, bringing out a flood of books on Darwin and evolution. There isn’t space in this blogpost to note all of these publications, but we can mention some of the most noteworthy and relevant of these publications. Here is an annotated list of some of the best and most comprehensive publications that have come out recently, celebrating the life and work of Charles Darwin and his theory of evolution by natural selection. The full publication information for each work is included in this list, followed by a brief paragraph describing its contents.

DARWIN'S BOOKS (in print)
Darwin, Charles (Edward O. Wilson, editor) (2005) From So Simple a Beginning: Darwin's Four Great Books. W.W. Norton & Co.: New York, NY, ISBN 0393061345 (hardcover, $39.95), 1706 pages. Available here.

Perhaps the best way to celebrate Darwin’s life and work is to read his most important and influential books. In preparation for the Darwin bicentennial several publishers have brought out various versions of his books. This one is the best, not only because it includes his four most influential publications, but also because the editor, evolutionary biologist Edward O. Wilson, provides a brief but illuminating introduction to each one. Wilson places Darwin’s work in its historical and scientific context, and shows how each of his four great books laid the groundwork for the modern science of biology. If you only have time for one of these books, let this compendium be the one you read this year.

Darwin, Charles (James T. Costa, editor) (2009) The Annotated Origin: A Facsimile of the First Edition of On the Origin of Species. Belknap Press of Harvard University Press: Cambridge, MA, ISBN 0674032810 (hardcover, $35.00), 576 pages. Available here.

Darwin didn’t originally intend to publish the book we now know as the Origin of Species. He was working on a much longer multi-volume work that he intended to call Natural Selection, and rushed to publish an “abstract” of this work in 1859 to forestall losing his priority for the idea to Alfred Russell Wallace. As a consequence, the Origin of Species has no footnotes, endnotes, nor bibliography. This version of the Origin makes up for that lack. Ably edited by James Costa, The Annotated Origin contains many of the annotations that the original Origin of Species lacked, and provides the reader with a comprehensive grounding in the natural history that Darwin marshaled in support of his revolutionary theory.

Darwin, Charles (David Quammen, editor) (2008) On the Origin of Species: The Illustrated Edition. Sterling Publishers: New York, NY, ISBN 1402756399 (hardcover, $35.00), 560 pages. Available here.

Darwin rushed to publish the Origin of Species, and included only one technical illustration in the first edition. This lack of illustrations has been rectified in David Quammen’s beautifully illustrated version of the Origin. Perhaps best known for his masterful book on island biogeography and extinction, The Song of the Dodo, Quammen has chosen a huge selection of images that illuminate Darwin’s theory in ways that Darwin himself would have found both fascinating and extremely valuable for a deeper understanding of his theory.

DARWIN'S BOOKS (online)

The Internet has provided readers and scholars today with an unparalleled opportunity to study the works of Darwin online. By far the best of these electronic resources is a website initiated and maintained by John Van Whye and his colleagues in England. Available online at http://darwin-online.org.uk/, The Complete Works of Charles Darwin includes not only all of Darwin’s books (available in all of their various editions), but also photographic facsimiles of these works side-by-side with searchable full text versions, plus all of Darwin’s scientific publications and a massive and growing collection of his voluminous correspondence. Here is a sampling:

Darwin, Charles (1845) Journal of Researches into the Natural History and Geology of the Countries Visited During the Voyage of H.M.S. Beagle Round the World, Under the Command of Capt. Fitz Roy, R.N. 2d edition. John Murray: London, UK, 536 pages. Text and images available here.

This was Darwin’s first and most popular book for the general public, establishing him as the premier naturalist in England at the time of its publication. Continuously in print since 1845, the Voyage of the Beagle (as it is most often referred to) is both a marvelous compendium of natural history and a fascinating journal of a voyage of discovery almost unparalleled in the literature of science.

Darwin, Charles (1859) On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. John Murray: London, UK, 522 pages. Text and images available here.

Darwin’s most important book, and perhaps the most important book ever published in the science of biology. Indeed, a strong argument could be made that this book single-handedly founded the modern science of biology. This online edition juxtaposes the text of the Origin with photographs of the corresponding pages from the first edition.

Darwin, Charles (1871) The Descent of Man, and Selection in Relation to Sex. John Murray: London, UK, 424 pages. Text and images available here.

Darwin’s second most important book, and perhaps the most controversial of his published works, the Descent of Man (as it is most often referred to) contains Darwin’s proposal that humans have evolved from “lower” primates, and a detailed exploration of what Darwin believed to be the most important mechanism in the evolution of humans: sexual selection. Darwin also speculates on the evolutionary origin of such uniquely human traits as art, language, and morality.

Darwin, Charles (1871) The Expression of the Emotions in Man and Animals. John Murray: London, UK, 374 pages. Text and images available here.

One of Darwin’s lesser-known books, but no less important in its own way, The Expression of the Emotions in Man and Animals is often credited with founding the modern science of animal behavior. In it, Darwin explored the biological basis for the expression of emotions in humans and other animals, with detailed examples (many with accompanying photographs) that show how human emotions are most probably derived from the emotions of other “lower” animals, including dogs as well as monkeys and other primates.

DARWIN'S LIFE AND WORK (adults/general)

Many people (including many evolutionary biologists) not only have never read Darwin's books, but also do not know how Darwin came to write them. Furthermore, opponents of Darwin's theories often portray Darwin's life and personal beliefs in as negative a light as possible, in an attempt to discredit his theories. Perhaps the best antidotes to both of these deficiencies are the books listed here, which together provide a comprehensive view of Darwin's life and work. Most of them are written for non-scientists, and all of them provide a fascinating glimpse into the work of the founder of the science of biology.

Browne, Janet (1996) Charles Darwin: A Biography, Volume 1: Voyaging. Princeton University Press: Princeton, NJ, ISBN 0691026068 (paperback, $25.95), 622 pages. Available here.

Although not explicitly published in celebration of the Darwin bicentennial, Janet Browne’s two-volume biography of Darwin is widely recognized as the premier biography of the founder of evolutionary biology. This first volume covers Darwin’s youth and early career, up to the completion of the voyage of HMS Beagle and the germination of his theory of evolution by natural selection. Using the extensive collection of Darwin’s correspondence along with personal papers and those of his family and scientific associates, Browne draws a detailed and sometimes surprising portrait of the founder of the most comprehensive and controversial theory in the natural sciences.

Browne, Janet (2003) Charles Darwin: A Biography, Volume 2: The Power of Place. Princeton University Press: Princeton, NJ, ISBN 0691114390 (paperback, $25.95), 600 pages. Available here.

In this second volume of Janet Browne’s two-volume biography of Darwin, Janet Browne explores the origin of the Origin of Species and Darwin’s other ground breaking and revolutionary works. Unlike some of Darwin’s other biographers, Browne gets most of the science right in her biography, and illuminates Darwin’s ideas in light of his detailed work in natural history. She also provides insights into Darwin’s personality, including his much-noted reclusive nature, and shows how his scientific work and ideas were influenced by events in his private life.

Darwin, Charles (Nora Barlow, editor) (1993) The Autobiography of Charles Darwin: 1809-1882. W.W. Norton & Co.: New York, NY, ISBN 0393310698 (paperback, $14.95), 224 pages. Available here.

Although Darwin wrote an autobiography, he never intended it to be a comprehensive history of his life or his ideas. Rather, he did it almost on a lark, as a kind of “gift” to the members of his family and closest friends. Despite this, his autobiography provides some fascinating insights into his personality, and especially his views on art, literature, religion, ethics, and philosophy. This edition includes autobiographical material that was suppressed by Darwin’s widow and son, and should be considered to be the definitive edition.

Darwin, Charles (Gordon Chancellor & John Van Wyhe, editors) (2009) Charles Darwin’s Notebooks from the Voyage of the Beagle. Cambridge University Press: New York, NY, ISBN 0521517575 (hardcover, $150.00), 650 pages. Available here.

This is an expensive, but absolutely invaluable publication, brought out by Cambridge University Press as part of this year’s bicentennial celebration and edited by Gordon Chancellor and John Van Whye (the same John Whye who maintains the complete works of Darwin online). It contains the entirety of Darwin’s handwritten journals of the voyage of HMS Beagle, written during the voyage. In it one can trace the development of Darwin’s revolutionary ideas as they first occurred to him, and see how the events of the voyage laid the groundwork for his revolutionary theories. This is a must-have edition for anyone who wants to understand how and when the Darwinian revolution began.

Desmond, Adrian & Moore, James (2009) Darwin's Sacred Cause: How a Hatred of Slavery Shaped Darwin's Views on Human Evolution. Houghton Mifflin Harcourt: New York, NY, ISBN 0547055269 (hardcover, $14.95), 448 pages. Available here.

Charles Darwin was born on February 12, 1809, the same day as Abraham Lincoln. This propinquity of origins is all the more notable when one realizes that Darwin and his family were staunch abolitionists. Darwin himself tells how he became horrified by the institution of slavery while on the voyage of HMS Beagle.

Desmond and Moore, whose 1994 biography of Darwin (Darwin: The Life of a Tormented Evolutionist, available here) is widely recognized as one of the best biographies of Darwin, have in this volume dug deeper into Darwin’s personal history, showing how his views on slavery and its abolition helped shape his views on the evolution of humans, as outlined in his Descent of Man.

McCalman, Iain (2009) Darwin's Armada: Four Voyages and the Battle for the Theory of Evolution. W.W. Norton & Co.: New York, NY, ISBN 0393068145 (hardcover, $29.95), 432 pages. Available here.

Although perhaps the best known, Darwin’s round-the-world voyage aboard HMS Beagle was not by any means the only such voyage of discovery in the 19th century. Three of Darwin’s closest friends and collaborators in evolutionary biology — botanist Joseph Hooker, zoologist Thomas Henry Huxley, and professional collector and naturalist Alfred Russell Wallace — all participated in similar voyages, and all contributed to Darwin’s theories. McCalman describes all four voyages, and shows how the insights and information about natural history gained by these four great naturalists provided the foundation for the science of evolutionary biology in the 19th and early 20th centuries.

Quammen, David) (2007) The Reluctant Mr. Darwin: An Intimate Portrait of Charles Darwin and the Making of His Theory of Evolution. Atlas Books: New York, NY, ISBN 039332995X (paperback, $35.00), 304 pages. Available here.

Quammen’s biography of Darwin’s personal origin of the Origin is a perfect companion to Janet Browne’s two-volume biography of Darwin. Focusing on the period in Darwin’s life leading up to the original publication of the Origin, Quammen shows how Darwin’s personality and early education predisposed him to the intellectual and emotional labor that resulted in the publication of the Origin and its reception by the scientific community.

DARWIN'S LIFE AND WORK (children/school)

All too often people think that the work of great scientists such as Charles Darwin is only accessible to adults, especially scientists. Here is a brief selection of books for children, all published during this bicentennial year, which present Darwin and his work in a way that anyone, including young children, can understand and appreciate.

Heiligman, Deborah (2009) Charles and Emma: The Darwins' Leap of Faith. Henry Holt and Co.: New York, NY, ISBN 0805087214 (hardcover, $18.95), 272 pages. Available here.

Heiligman’s biography of Charles and Emma Darwin begins with Charles drawing up a list of the pros and cons of marriage to his first cousin, Emma. His decision to marry her set in motion an emotional odyssey for Charles and Emma, who had very different views of religion. Charles’ theory of evolution threatened Emma’s deep religious belief, and forced Darwin to thoroughly document his views before publishing them. This sympathetic rendering of their happy, though sometimes turbulent, marriage is a wonderful introduction to the real life of a famous scientist, one that young adults will find particularly relevant to their own lives.

Lasky, Kathryn (2009) One Beetle Too Many: The Extraordinary Adventures of Charles Darwin. Candlewick Press: Somerville, MA, ISBN 076361436X (hardcover, $17.99), 48 pages. Available here.

Lasky’s copiously illustrated account of Darwin’s life and work, focusing especially on his adventures while on the voyage of HMS Beagle, gives younger readers an engaging look at the work of the founder of the theory of evolution by natural selection. Lasky does not shy away from Darwin’s views on evolution and religion, presenting them in Darwin’s own words. The illustrations are particularly charming, rendered in various media in a quirky and engaging style.

McGinty, Alice B. & Azarian, Mary (2009) Darwin, with Glimpses into his Private Journal and Letters. Houghton Mifflin Books for Children: New York, NY, ISBN 0618995315 (hardcover, $18.00), 48 pages. Available here.

Another illustrated account of Darwin’s life and work, this time covering his childhood, his adventures while on the voyage of HMS Beagle, and the subsequent development of his theory of evolution by natural selection. gives younger readers an engaging look at the work of the founder of the theory of evolution by natural selection. Illustrated with woodcuts and watercolor, McGinty and Azarian’s biographical history also touches on Darwin’s views on religion and philosophy in a way that is accessible to younger readers.

Schanzer, Rosalyn (2009) What Darwin Saw: The Journey That Changed the World. National Geographic Children's Books: Des Moines, IA, ISBN 1426303963 (hardcover, $18.00), 48 pages. Available here.

Schanzer’s illustrated account of Darwin’s voyage of HMS Beagle is more limited in scope than the others in this list, but succeeds in presenting Darwin’s natural history investigations in an engaging (and sometimes humorous) way. More like a graphic novel than a standard biography (complete with cartoon-like illustrations and speech balloons), Schanzer presents selected observations that led Darwin to his theory of evolution. Unlike the other three books for younger readers in this list, Schanzer avoids discussion of Darwin’s views on religion and philosophy, sticky strictly to the natural history of his historic voyage and the science that it inspired.

In addition to the books listed and reviewed here, those who are interested in the life and works of Charles Darwin can search Amazon.com, where most of the books listed above can be browsed, along with many others published in connection with the Darwin bicentennial. Books on the subject of evolution are listed here, including books both supportive of Darwin’s theory and critical of it.

I hope this list provides you with some ideas of how to celebrate Darwin's life and work by learning more about it.

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

Macroevolution: What Were the Evolutionary Ancestors of Whales?

2009-11-09T22:53:00.004-05:00

ID supporters often assert that, although there is abundant empirical evidence for microevolution, there is no such evidence for macroevolution. One of the macroevolutionary transitions that they often cite is the evolution of whales from a land-dwelling ancestor. Which leads me to ask the following question:

What empirical evidence would verify (i.e. support) or falsify (i.e. undermine) the hypothesis that whales had evolved from a land-dwelling mammal? Please note that this is a hypothesis about macroevolution, not microevolution.

A basic principle of hypothesis validation in the natural sciences is that if one can find multiple lines of evidence, all of which support the hypothesis, then such evidence is much stronger than if there were only a single line of evidence. This is especially the case if the different lines of evidence are from very widely separated fields.

Until recently the main line of evidence for the evolution of whales (i.e. members of the mammalian order Cetacea) from even-toed ungulates (i.e. members of the mammalian order Artiodactyla) was anatomical. This anatomical evidence was derived from two sources:

1) similarities between the anatomy (especially skeletal anatomy) of living (i.e. "extant") Artiodactyls and Cetacea, and

2) an evolutionary phylogeny of the transition from terrestrial Artiodactyls to aquatic Cetacea, based on fossils.

Rather than summarize this comparative anatomical evidence here, I recommend that interested readers follow this link. What you will find is a fairly detailed summary of the evidence from comparative anatomy, all of it pointing to the conclusion that whales (i.e. Cetaceans) evolved from even-toed ungulates (i.e. Artiodactyls). It is this evidence that most evolutionary biologists have until recently cited as support for the macroevolutionary derivation of Cetaceans from Artiodactyl ancestors.

However, one can also ask the question Does the comparative genomics of Artiodactyls and Cetaceans support the same hypothesis? That is, are there observable DNA sequence similarities and differences that are similar in both scope and timing to the similarities and differences in the fossil record (and as reflected in the comparative anatomy of Artiodactyls and Cetaceans)?

This is an easily falsified hypothesis: If the genomic evidence does not support the Artiodactyl into Cetacean hypothesis — e.g. that Cetaceans evolved from some other clade, or that they had not evolved at all, but rather sprang into existence fully-formed and without genetic evidence of a macroevolutionary transition — then this evidence would not support the evidence from comparative anatomy and the macroevolutionary hypothesis based on comparative anatomy would be called into question.

So, what does the comparative genomic evidence indicate about the macroevolutionary relationships between the Artiodactyla and the Cetacea? Here’s a summary of the findings from comparative genomics:

The idea that whales evolved from within the Artiodactyla was based on analysis of DNA sequences. In the initial molecular analyses, whales were shown to be more closely related to ruminants (such as cattle and deer) than ruminants are to pigs. In order for the order name to reflect a real evolutionary unit, the term Cetartiodactyla was coined.

Later molecular analyses included a wider sampling of artiodactyls and produced a more complete tale. Hippos were determined to be the closest relative of whales, ruminants were related to a whale/hippo clade, and pigs were more distant. In addition to producing the controversial whale/hippo clade, these analyses debunked the idea that hippos and pigs are closely related. This had been a popular taxonomic hypothesis (Suiformes) based on similarities in morphological (physical) characteristics.

In addition to DNA and protein sequences, researchers tracked the movement of transposons called SINEs in the genome. A transposon is a DNA sequence that will occasionally make a copy of itself and insert that copy into another part of the genome. It is considered highly unlikely that SINEs will insert themselves into the exact same part of a genome by chance. The data indicate that several transposons inserted themselves at the same point in the genomes of whales, ruminants and hippos (sometimes referred to as "pseudoruminants" because although they have four-chambered stomachs like true ruminants, they do not chew the cud). This insertion point is not shared with camels and pigs.

This hypothesis has been tested with DNA sequences from a host of genes: the complete mitochondrial genome (as well as several of its genes independently), beta-casein, kappa-casein, von Willebrand factor, breast cancer 1, recombination activating genes 1 and 2, cannabinoid receptor 1, and several others. These sequence data and the transposons converge on the same conclusion that hippos and whales are more closely related to one another than either is to other artiodactyls.

Sequences analyzed in combined analyses with morphological characters have also produced the same results as sequences alone. Some have argued that the sheer number of characters (one for each nucleotide) in sequences swamps out the effects of morphology. There have been a few morphology-based studies that have suggested (weakly) the same results as the molecular results, but overall most morphological studies have conflicted with the whale/hippo hypothesis of Cetartiodactyla.

An important exception is a recent conducted by Boisserie et al. (2005). They examined 80 hard morphological characters of fossil and extant cetartiodactylan taxa. Their results suggest that hippopotamids evolved from within a clade of anthracotheres. That anthracothere/hippopotamid clade appears to be sister to the Cetacea and supports the molecular results.

[sources: http://en.wikipedia.org/wiki/Cetartiodactyla (summary article), where you can find links to many primary references]

Note that much of the genomic data (especially from transposon sequences) supporting the macroevolutionary hypothesis is based on non-adaptive DNA sequences. That is, DNA sequences that do not code for adaptive characteristics, and in many cases that do not code for anything at all. This is like figuring out which students have been copying the answers to test questions from other students by comparing their wrong answers. The right answers are the same for everybody, but wrong answers vary from student to student in virtually random ways. If two students have the same wrong answers, you can be reasonably confident that one of them copied the wrong answers from the other. You can then test this hypothesis by looking at seating charts, past test performance (cheaters are often identified by sudden increases in test scores without apparent increases in effort), and – often the last resort – asking them if they copied answers.

Conclusion: The empirical evidence from comparative genomics closely matches the empirical evidence from (both extant and fossil) comparative anatomy.

Is that all, or is there yet another line of evidence that might be pursued to verify or falsify the Artiodactyl into Cetacean hypothesis? Yes, there is. Consider the observable fact that whales reproduce much more slowly than even-toed ungulates (such as deer and hippos). Indeed, there is a general principle in zoology that the larger the members of a species are (on the average) the fewer offspring they have, the more widely spaced those offspring are in time, the fewer offspring they can have over their lifetime, and the longer the average lifespan of individuals.

For example, deer can have offspring every year, and under good conditions can sometimes have twins or even triplets in one reproductive cycle. By comparison, baleen whales can only have offspring every few years (it can take up to two years for one pregnancy in large baleen whales), they virtually never have more than one calf at a time, they have only a few reproductive life cycles per lifetime, and they have much longer lifespans than deer.

This means that, if Cetaceans evolved from Artiodactyls, one might be able to find empirical evidence that the rate of the macroevolutionary transition from Artiodactyl ancestors into Cetacean descendants had slowed down as the result of the increase in size, decrease in number of offspring per reproductive cycle, decrease in total number of offspring per lifetime, and increase in average lifespan. In brief, there might be evidence that the macroevolutionary “clock” slowed down as Cetaceans evolved larger and larger size.

Here’s the latest genomic evidence vis-a-vis this hypothesis:

Big and slow: phylogenetic estimates of molecular evolution in baleen whales (suborder mysticeti).
Molecular Biology and Evolution. 2009 Nov;26(11):2427-40. Epub 2009 Jul 31.
Jackson JA, Baker CS, Vant M, Steel DJ, Medrano-González L, Palumbi SR.
Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, OR, USA.

ABSTRACT: Baleen whales are the largest animals that have ever lived. To develop an improved estimation of substitution rate for nuclear and mitochondrial DNA for this taxon, we implemented a relaxed-clock phylogenetic approach using three fossil calibration dates: the divergence between odontocetes and mysticetes approximately 34 million years ago (Ma), between the balaenids and balaenopterids approximately 28 Ma, and the time to most recent common ancestor within the Balaenopteridae approximately 12 Ma. We examined seven mitochondrial genomes, a large number of mitochondrial control region sequences (219 haplotypes for 465 bp) and nine nuclear introns representing five species of whales, within which multiple species-specific alleles were sequenced to account for within-species diversity (1-15 for each locus). The total data set represents >1.65 Mbp of mitogenome and nuclear genomic sequence. The estimated substitution rate for the humpback whale control region (3.9%/million years, My) was higher than previous estimates for baleen whales but slow relative to other mammal species with similar generation times (e.g., human-chimp mean rate > 20%/My). The mitogenomic third codon position rate was also slow relative to other mammals (mean estimate 1%/My compared with a mammalian average of 9.8%/My for the cytochrome b gene). The mean nuclear genomic substitution rate (0.05%/My) was substantially slower than average synonymous estimates for other mammals (0.21-0.37%/My across a range of studies).

CONCLUSION: The nuclear and mitogenome rate estimates for baleen whales were thus roughly consistent with an 8- to 10-fold slowing due to a combination of large body size and long generation times. Surprisingly, despite the large data set of nuclear intron sequences, there was only weak and conflicting support for alternate hypotheses about the phylogeny of balaenopterid whales, suggesting that interspecies introgressions or a rapid radiation has obscured species relationships in the nuclear genome. [emphasis added]

So, there are indeed empirically falsifiable hypotheses for the macroevolution of whales from land-dwelling ancestors. If whales (Cetacea) evolved from even-toed ungulates (Artiodactyla), then the following predictions should be supported by the observable data:
• that there should be anatomical similarities between extant Artiodactyls and Cetaceans,
• that there should also be anatomical similarities between fossil Artiodactyls and Cetaceans,
• that there should be shared similarities and differences between the genomes of extant clades of Artiodactyls and Cetaceans, and that the overwhelming majority of these similarities and differences would mirror the comparative anatomical evidence for the macroevolutionary origin of the various clades of the Cetartiodactyla, and
• that the inferred slowing of macroevolutionary change during the transition from Artiodactyl ancestors to Cetacean descendants should also be consistent with the hypothesis that the rate of this transition would have slowed as the result of increasing body size, increasing reproductive spacing, decreasing numbers of offspring per life cycle, and increasing longevity.

And it is.

Clearly, an ID supporter might then ask for specific empirical evidence on how the various transitions occurred at the genetic and developmental level, and if these details could unambiguously distinguish between natural and supernatural causes for such genetic mechanisms. Evolutionary developmental biologists are currently working on answers to the first part, but I personally cannot imagine how one could empirically test the second part. Furthermore, it seems to me that invoking a supernatural cause for the macroevolutionary transition from Artiodactyls to Cetaceans would be unnecessary, and would add nothing whatsoever to our understanding of the mechanisms by which this transition occurred.

Ergo, if I were doing this research and publishing my results I wouldn’t mention it, as it would be completely unnecessary for a scientific explanation of this phenomenon.

Just out of curiosity, ask yourself how one might use any of the foregoing as positive or negative empirical evidence for the existence of God. I mention this because some evolutionary biologists believe they can use the data of evolutionary biology to disprove the existence of God, and some ID supporters believe they can use the data of evolutionary biology to prove the existence of God. Personally, I believe both attempts are misguided, pointless, and ultimately futile. That’s why I don’t make such attempts, and wonder why anyone would.

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

The Darwinian Revolutions Video Series

2009-11-08T19:21:00.033-05:00

The Darwinian Revolutions

An online video lecture series
in honor of the 150th anniversary
of the original publication of
Charles Darwin's Origin of Species

Produced by:
The Cybertower at Cornell University

Written, directed and narrated by:
Allen MacNeill, Senior Lecturer
The Biology Learning Skills Center
Ecology & Evolutionary Biology

Videography by:
Dina Banning

Sound Engineering by:
Colbert McClennan

Technical Direction by:
Becky Lane

Videotaped at:
The Museum of the Earth
The Paleontological Research Institution
Ithaca, New York

Voiceover Narration Recorded at:
Fall Creek Studios
1201 North Tioga Street
Ithaca, New York

Images Obtained at:
WikiMedia Commons
Stebbins/Simpson/Dobzhanky photo credit: Martin Tracey

Galapagos Video Credit:
Prof. William Provine

It's finally done! After more than a year of meetings, writing, image acquisition, videotaping, sound recording, editing, revising, captioning, and (most of all) thinking, our video series on the Darwinian revolutions is now online!

This series of six online videos is a brief introduction to Darwin's theory of evolution by natural selection and its implications. Here is a brief synopsis of the six episodes (click on each episode title to go to the linked video):

Episode One: Darwinian Revolutions
We begin with an overview of the series, which has been released to coincide with the 150th anniversary of the publication of Darwin's Origin of Species. Darwin's theory of evolution by natural selection revolutionized both the biological sciences and our understanding of ourselves and the world around us. In this episode we learn that Darwin's theory has itself evolved in the 150 years since it was published. We also learn that Darwin actually presented two theories:
• a theory of descent with modification from common ancestors, and
• the theory of natural selection, Darwin's mechanism for evolution.

Episode Two: Evolutionary Ancestors
Beginning with an overview of Darwin's predecessors, we learn how the idea of evolution by natural means alone goes back more than two thousand years, to ancient Greece and Rome. Democritus of Abdera first proposed the "ground rules" for naturalist evolution, which were later extended by the Roman poet and philosopher, Lucretius. However, these early naturalistic theories were eclipsed for almost two millennia by the ideas of Plato and Aristotle.

Episode Three: Lamarck's Theory
In the 19th century, Jean Baptiste Lamarck set the stage for Darwin's monumental achievement with his Philosophie Zoologique (published in 1809), which advanced a theory of evolution by means of the inheritance of acquired characteristics. Lamarck's theory was the first theory of evolution to include a testable mechanism for evolutionary change — the inheritance of acquired characteristics — and provides a useful comparison with Darwin's theory.

Episode Four: One Long Argument
Darwin, whose academic training at Cambridge University was in Anglican theology, became an acclaimed naturalist and science writer following the five-year voyage of HMS Beagle. Using the notes and specimens that he had collected during the voyage, Darwin spent twenty years refining his theory, first published in 1859, of evolution by natural selection.

Episode Five: Mendel and the Eclipse of Darwin
Darwin's theory of descent with modification was accepted by most scientists worldwide within ten years of its publication in 1859. However, his theory of natural selection was widely criticized, and by the turn of the 20th century was widely considered to be dead. However, the work of Gregor Mendel, who discovered the foundations of what we now call genetics, provided a mechanism by which Darwin's theory could be revived and expanded.

Episode Six: The Evolving Synthesis
In the final segment of this series, we visit the The Museum of the Earth in Ithaca, New York, whose director, Dr. Warren Allman, discusses the importance of such museums to the science of evolutionary biology. We also hear from Cornell professor William Provine, who discusses Darwin's work and its importance to the history and philosophy of biology. He tells us how Darwin's original theory of natural selection was integrated into the sciences of population genetics, ecology, physiology, paleontology, embryology, and botany, to produce a "modern synthesis" of evolutionary theory. Prof. Provine also tells us how the "modern synthesis" has continued to evolve, and that today is the most exciting time yet in the history of Darwin's scientific revolution.

This has been an exciting year: the 200th anniversary of the publication of Lamarck's Philosophy Zoologique, the 200th anniversary of the birth of Charles Darwin, and the 150th anniversary of the publication of Darwin's Origin of Species. There have been many events marking these anniversaries, and there will be many more. As Will Provine says, the theory of evolution is more dynamic, more exciting, more widely accepted, and more widely applied than at any time in the past century and a half. With the accelerating pace of discoveries in evolutionary biology and their applications in biology, medicine, psychology, economics, and even literature and art, the 21st century shows all indications of being what the founders of the "modern synthesis" called it back in 1959: the "century of Darwin" and his theory of evolution by natural selection.

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

Why I Post Comments on Creationist and ID Blogs

2009-11-07T19:29:00.016-05:00

A fellow blogger asked me recently "Why waste your time posting [at creationist and ID blogs] at all? You do not seem to have a receptive audience." Other people ask me why I generally treat creationists and ID supporters with respect, rather than taking every opportunity to heap scorn and ridicule upon them. Here's what I hope is an adequate explanation to both of these questions.

I post comments at creationist and ID blogs (when I have the time, which is definitely not all the time) because I expect that there are a lot of people who read these comments without participating directly in such debates. This is why I try to keep as civil a tone as possible, especially when my opponents use ad hominem arguments, character assassination, insults, and ridicule. The contrast between their tactics and mine undermines their credibility (and, by extension, that of their soi dissant “science”). Indeed, some commentator’s comments are so insulting that I refuse to respond to them, and I believe that this does not pass unnoticed by readers who are not yet irrationally committed to one side or the other.

Also, as a teacher (currently in my 35th year of teaching at Cornell University), I feel a professional responsibility to correct some of the more egregious misrepresentations and misunderstandings of the science of evolutionary biology which are promulgated at creationist and ID blogs. Some of these misrepresentations clearly stem from ignorance, and in a gratifying number of cases some the commentators whom I have corrected have thanked me for the information and references I have provided.

However, other misrepresentations are apparently part of a deliberate and ongoing effort to distort the public record and deliberately misrepresent the relevant scientific information for political and religious purposes. I strongly believe that this kind of mendacity should be exposed for what it is, and for what it isn’t (i.e. it isn’t science).

Furthermore, I have always tried to emulate the long-standing Quaker tradition of “speaking truth to power”, which is the opposite of “preaching to the choir”. It means confronting directly what I perceive to be misunderstanding (and what I perceive to be deliberate mendacity), rather than limiting my interactions to people with whom I already agree. I agree with Charles Darwin, who said that he paid much more attention to the criticisms of people who disagreed with him than the praise of people who agreed with him. Like Darwin, I find that debating with people with whom I disagree helps me greatly to clarify my own position on the relevant issues, and to help my opponents clarify theirs. I believe that it would be a terribly boring (and non-progressive) world in which everyone agreed upon every subject, and so I am grateful to some of the commentators here for helping me improve my understanding of the relevant issues and my ability to argue persuasively for what I perceive to be the best supported position.

Like Hegel, I believe that genuine synthesis usually arises out of the clash between thesis and antithesis, and that progress in human understanding is almost always gained at the price of diligence, honesty, and honor. As my fencing master often says, “a gentleman is always gracious and dignified in defeat, humble and gentle in victory”. I have to the best of my ability tried to account myself according to this standard of conduct, and believe that the world would be a better place if everyone tried to do so.

Finally, to the best of my ability, I try to “fight the good fight” in defense of what I understand to be an accurate description of reality. I expect my opponents to do the same. When they do, I tell them so. Indeed, if they do a good job, I congratulate them, especially if they persuade me to change my mind, as the result of sufficiently convincing arguments. However, when my opponents depart from honorable and honest argumentation and stoop to ad hominem attacks, character assassination, insults, and ridicule, I call them on it and I inform them in no uncertain terms that I will no longer respond to them.

The same principles apply to this blog, and can be read here.

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

Rescuing Darwin from His Detractors (and Supporters)

2009-11-04T14:02:00.025-05:00

TITLE: Rescuing Darwin

AUTHOR: Paul Fayter

SOURCE: The United Church Observer

SUMMARY: Ever since the Origin of Species was first published 150 years ago, scientists and creationists have tried to spin the religious views of Charles Darwin their way.

COMMENTARY: This article by Paul Fayter (appearing on a website sponsored by The United Church Observer, a Christian organization) directly contradicts many of the assertions made by some evolutionary biologists and most ID supporters, including most of the egregious distortions in Benjamin Wiker's recent book,
The Darwin Myth: The Life and Lies of Charles Darwin.

Unlike Wiker and most ID supporters, Paul Fayter has spent a significant fraction of his professional life studying Charles Darwin and his work. Here's what he found:

- Darwin was not an atheist when he wrote the Origin of Species and therefore could not possibly have written it as an "apology" for his atheism;

- the most important factors in his eventual agnosticism were 1) the death of his daughter, Annie, and 2) his view that a benevolent deity would not have created a world with such horrors as parasites (and the indiscriminate death of innocents);

- that despite his agnosticism, Darwin remained a "practicing" member of both the Church of England and his local parish church;

- that despite his embrace of the science of evolutionary theory, he did not descend into a life of libertinism and immorality, nor did he distort his theory to support any political position (including eugenics or "social darwinism");

- he remained a dedicated scientist, a loving husband, a doting father, a devoted member of his parish, and an unwavering opponent of slavery and its concomitant evils; and

- he also remained what would now be considered to be a "theistic evolutionist" until his death.

Here is Faytor's conclusion:

Darwin was able to reconcile the power and glory of a good and loving God with nature's cold indifference and manifest cruelty - the infamous and pitiless "survival of the fittest" - by viewing struggle, pain, suffering and death not as the direct will of God but as the result of the impersonal operation of universal laws. The process of evolution by means of natural selection was deadly and wasteful, and yet, as Darwin concluded in The Origin, it had a higher, nobler purpose. Higher species would evolve. The Creator - the God of scientific theism - lawfully drew good out of evil and progress out of pain.

Near the end of his life, Darwin thought it impossible to conceive that "this immense and wonderful universe" was "the result of blind chance or necessity." No, it still seemed that the world had been willed into being. "I feel compelled to look to a First Cause having an intelligent mind in some degree analogous to that of man," he wrote in his autobiography, "and I deserve to be called a Theist." At the same time, Darwin believed that "the mystery of the beginning of all things" was simply unsolvable; and so he also declared, "I for one must be content to remain an agnostic."

All of this directly contradicts Wiker's biography of Darwin and the opinions of most ID supporters. Demonizing Darwin, especially when there are very good (and unbiased) biographies of Darwin (not to mention his own, very candid autobiography) does nothing to harm Darwin's scientific reputation. By contrast, the fundamental misunderstanding among many ID supporters of how real science is done does quite a bit to harm ID's scientific reputation.

Neither evolutionary biology nor ID will be advanced or forestalled as scientific enterprises by pro- or anti-hagiographies of Charles Darwin (or any other individual scientist or ID supporter). This will happen only when sufficient field and laboratory work has been done and the results published in reputable scientific journals to decide between them. So far ID supporters have chosen to pursue a political program and the vilification of world-renowned scientists, rather than do the requisite science. Until they decide to abandon ad hominem arguments and actually focus on the science, they will remain (like "scientific creationism") a cautionary footnote to the history of the triumph of evolutionary biology.

In closing, I find it quite significant that only ID supporters refer to Darwin as a "little God". Like all evolutionary biologists, I consider him to have been a dedicated and talented observer of nature and a genuinely good person, but (like all of us) a plain and simple (and, of course, fallible) human.

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

Evolution, Intelligent Design, and the Banana Diet

2009-11-02T09:54:00.041-05:00

There has been a lot of speculation lately about the status of "intelligent design". Last December, I posted an essay on the demise of the Intelligent Design and Evolution Awareness clubs. At that time it was clear that the IDEA club movement at American colleges and universities was dead. Despite protestations to the contrary, the available data indicate that this is still the case.

Which leads to a more interesting question: what is the current status of the intelligent design "movement"? This question is even more significant this month, as November 24th marks the 150th anniversary of the original publication of Charles Darwin's Origin of Species, the founding document of the science of biology and the most influential book ever published in the natural sciences. Although some ID supporters assert that ID is compatible with evolutionary theory, it is clear from even a cursory examination of their views that the majority of ID supporters are opposed to the idea of evolution in virtually all of its versions.

Which brings me to the point of this blogpost: what impact has ID had on mainstream evolutionary theory, and which of these alternative explanations for the origin of adaptations and the diversity of life is gaining in veracity and which is losing? One way to answer this question is to analyze the frequency with which the terms "evolution" and "intelligent design" appear in internet searches and in news stories in the mainstream media. To assess this, Google has a marvelous tool: Google Trends. The following two graphs were produced using Google Trends. I have copied the graphs directly from the relevant web pages, adding only the red line at 1.5 (on the Y axis) to make possible comparison of relative values.

The first graph (above) shows the frequency of the term "evolution" as it appeared in Google searches and in news articles on the web over the past six years. What the upper graph shows is that Google search volume for the term "evolution" has fluctuated over the past six years, but held relatively steady. The lower graph shows that there has been a steady increase in news articles about evolution over the past six years.

The second graph (above) shows the frequency of the term "intelligent design" as it appeared in Google searches and in news articles on the web over the same six years. As you can see, these graphs are markedly different than those for "evolution". These graphs show that prior to 2005 there were very few searches and almost no news stories for "intelligent design". In 2005 this pattern changed abruptly: by the end of the year, there were over ten times as many Google searches for the term "intelligent design", and a concomitant spike in news articles on the same subject. This spike corresponds to the Kitzmiller vs. Dover Area School District trialin Dover, Pennsylvania, in the course of which the ID movement gained national attention. The decision in that trial, issued by Judge John E. Jones (a Republican, appointed by President George W. Bush), was widely hailed as a massive defeat for the ID movement.

This assessment is borne out by the remainder of the graph. As you can see, both internet searches and news articles on ID have declined precipitously since December of 2005, falling to almost unmeasurably low levels.

This graph (above), comparing the search volume and news article frequency of the terms "evolution" (in blue) and "intelligent design" (in red) is even more revealing. Here it can easily be seen that both search volume and news articles on "evolution" have consistently dwarfed those for "intelligent design", even during the period covering the Kitzmiller v. Dover trial. Furthermore, there is a steady upward trend in the frequency of news articles on evolution, while the frequency of news articles on intelligent design has fallen to almost unmeasurable levels.

So, what are we to make of these trends? Clearly, interest in evolution is on a steady upward course, which just as clearly reflects its importance in the sciences. As I have written elsewhere, the fundamental concepts of the theory of evolution by natural selection have been steadily spreading into all of the branches of biology, and have recently begun to transform such disparate fields as psychology, literature, and even diets and nutrition and art.

By contrast, interest in intelligent design exploded in 2005 and has crashed since then. What other phenomena exhibit this same "boom and bust" pattern? One such transitory phenomenon is the explosion in fad diets. For example, this graph shows the Google search volume and news article frequency for the term "banana diet" (the choice of this term was at least partly in honor of young Earth creationist and ID supporter, Ray Comfort):

The similarity between this graph (above) and the graph for "intelligent design" is striking, and is probably no accident. As many critics of ID have asserted, the ID movement has essentially consisted of a public relations campaign, rather than a scientific research program. Public relations campaigns, like advertising campaigns in general, often show the "boom and bust" pattern shown in the "intelligent design" and "banana diet" graphs. This is because public relations campaigns do not depend on veracity, but rather on appearance. The supporters of ID (such as the Discovery Institute in Seattle, WA) have consistently promoted ID as a scientific research program, but even a cursory examination shows that, while there is abundant evidence that ID is a quasi-religious movement, there is virtually no empirical research being conducted by its supporters.

And so, as we approach the 150th anniversary of the founding of the rapidly expanding science of evolutionary biology, we may note in passing that this anniversary can also be used to mark the demise of the ID movement, a phenomenon with all of the earmarks of a passing fad and all of the scientific content of the banana diet.

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

Memento mori: The Metaphysics of The Game

2009-10-14T16:24:00.022-04:00

I just lost the game. And so have you, especially if you know what I'm talking about.

Some background: my eldest son, Conall, attended a highland dance camp this past summer. While he was there, he learned about The Game. Being obsessed with games in general and mind games in particular (like his dad), he came home and told us all about it, and has since reveled in telling us every time he loses the game. Since learning about The Game, I have myself announced the same to several of my classes at Cornell, each time to a chorus of groans.

So, how does The Game work?

The Game has only three rules:

1) Everyone is always playing The Game.

2) Whenever you think of The Game, you lose.

3) Having lost The Game, you must announce this to at least one other person (usually by saying or writing "I just lost The Game").

Some active players of The Game also assert that there are two corollaries:

4) You can lose The Game multiple times.

5) You can only lose The Game once every half hour.

That is, The Game "resets" after half an hour, so that having forgotten that you are playing, you can lose again and again and again...

Having lost The Game many, many times since Conall told me the rules, it has occurred to me that there is a metaphysical dimension to The Game. Thinking about The Game is essentially the same thing as thinking about one's own death. That is, The Game is a kind of memento mori. Most of us go through most of our lives without often thinking about the incontrovertible fact that all of us will, at some point in the indefinite future, cease to exist. We will all, in other words, "lose The Game".

There have been several times in my life when I have become bemused by the thought of my own mortality. The first time it happened I was four years old. We were living in an old farmhouse on Scott Road, east of Homer, New York, and I was walking up the stairs to my bedroom. Between one step and the next, it occurred to me that I would someday die - that I would cease to exist. This realization was very shocking to me, and came back into my mind steadily for some time.

But then, I forgot about it...for a while. Since then, I have gotten caught in the same "becoming aware of mortality loop" several times, and each time it has had the same quality as losing The Game. That is, it comes with a sense of "doubled consciousness", in which I have become conscious of my own stream of consciousness, and its eventual termination.

Many theologians (and some evolutionary biologists) have speculated that the origin of religion is grounded in the realization of personal mortality. From an evolutionary standpoint, the argument is as follows:

1) Individuals who avoid situations in which their lives are threatened survive (and can therefore reproduce) more often than individuals who do not avoid such situations.

2) Individuals who are aware of their own mortality are more likely to avoid situations in which their lives are potentially threatened.

3) Ergo, the cognitive operation in which one becomes conscious of one's mortality has adaptive value; that is, it can increase in frequency among the individuals that make up a population as the result of natural selection.

Some evolutionary psychologists (myself among them) have argued that the capacity for such cognitive operations is the basis for our evolved psychology, and that there is a positive feedback relationship between ideas like "mortality" (and The Game) and the underlying neurological wiring that facilitates the acquisition and transmission of such ideas. This idea, known as "gene-meme coevolution", was first and most rigorously explored by Charles Lumsden and Edward O. Wilson in their 1983 book, Genes, Mind, and Culture: The Coevolutionary Process. The underlying ideas in their work were summarized in non-technical language in Promethean Fire: Reflections on the Origin of Mind.

Having pondered both The Game and mortality, it seems quite plausible to me that our minds are indeed adapted to the kind of mental operation that results in both "losing The Game" and recalling our personal mortality. And so, I expect to go on losing The Game until I lose The Game...and now, having read this, so will you.

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

What's So "Intelligent" About "Intelligent Design"?

2009-06-02T10:16:00.020-04:00

Many of the debates about "intelligent design" (ID) that I have read online have focused on the defintion of "intelligent". This is not necessarily because we all agree what "design" means, but rather because we know even less about that quality we refer to with the term "intelligent". If one cannot define what one means by "intelligent", then any attempt to define or investigate "intelligent design" would seem to me to be a futile exercise.

Some ID supporters have suggested substituting the term "purposeful design" for the term "intelligent design". To me, this sounds almost redundant; after all, design is all about "purpose", isn't it? And if that's the case, then "purposeful design" reduces to "purposeful purpose" or "designed design". Furthermore, it's not clear to me that the terms "intelligent" and "purposeful" are necessarily interchangeable, or mean even similar things.

Many ID supporters seem most upset about the implication that evolutionary theory is "random". That is, the processes by which new characteristics of living organisms come into being are not necessarily the result of intentional design. To many of them, this would eliminate a supernatural force or deity as the causal factor in biological evolution. Ergo, if one is committed to the intervention in nature of a supernatural force or deity, one must deny a priori the possibility that new characteristics of living organisms can come into being without "intention".

However, it is not necessarily the case that "purposeful" (i.e. teleological) objects and processes are necessarily non-random. First of all, it seems to me that "purposeful" is not an antonym for "random". For example, consider a falling rock: its movement as it falls is most definitely not random. Neither its trajectory nor its acceleration are "random" at all. On the contrary, they are predictable to such a degree that we call the mathematical description by which we can predict the movement of falling objects a "law" - the "law of gravity".

Ergo, it seems to me that the best antonym for "random" is "predictable", in the sense of being able to predict successive states in a dynamically changing system.

Given the foregoing, what is the best antonym for "purposeful"? Forgive me, but I think the only reasonable answer is "non-purposeful". This then forces one to define what one means by "purposeful". To me, the best definition of a "purposeful" (or "teleological", if you prefer the more technical term) object or process is "a dynamical process (or component of a dynamical process) in which the dynamical entity's actions are actively and homeotelically regulated by a cybernetic process that functions according to a pre-existing program, the outcome of which is a specified end state.

A homeotelic process is one in which a dynamical entity reacts to external perturbations from its original trajectory in such a way as to regain its original goal orientation. For example, an arrow fired from a bow is not homeotelic, whereas a heat-seeking missile is. By the same logic, a snowflake growing in a supercooled cloud is not homeotelic, whereas a virus replicating in a host cell is.

In my opinion, most of the arguments about "intelligent design" founder, not on the definition of "intelligent" but rather on the definition of "design". If one focuses not on "design" but rather on "purpose" (i.e. teleology), much of the disagreement (like a boojum) vanishes softly and silently away.

Indeed, I think the qualifier "intelligent" is unnecessary, and quite possibly redundant. Why argue over something – that is, "intelligence" – that is indefinable without self-reference?

That is to say, "purpose" is very clearly and unambiguously defined in cybernetics, as Gregory Bateson and Norbert Weiner pointed out a half a century ago. "Purpose" (aka "teleology") are what this argument is really about, and so it would help immensely if all of the participants on both sides of the debate would define it in such a way as to render its presence or absence empirically verifiable.

The same could also be wished about "intelligence", but I see no real hope for this, given that virtually every definition of "intelligence" given in this thread (and all previous threads) is neither empirically verifiable nor applicable to simple systems such as those found in viruses or very simple cells. How "intelligent" is the lambda bacteriophage? Compared to a human, not much; compared to a crystal of sodium chloride, tremendously so. Indeed, what separates crystallized viruses from crystallized salts is precisely the "quality" that separates life from non-life and "purposeful" from "non-purposeful" things.

Termites build termite mounds using a surprisingly simple set of "decision rules". For example, one decision rule (which is clearly "wired in" to the nervous system of worker termites) is the rule to stack particles of sand on top of each other and glue them together using a material like saliva in such a way as to produce an arch (this is beautifully illustrated in E. O. Wilson's masterpiece, The Insect Societies). In Höldobler and Wilson's new book, Superorganism, they explain in detail how insect societies produce astonishingly complex, adaptive, functional dwelling places, "highways" (army and driver ants), "farms" and "pharmacies" (leaf-cutter ants), etc. without anything that remotely resembles what we would call "intelligence" or "consciousness" (remember, their brains are smaller than a poppy seed and their life spans are measured in days).

Furthermore, none of the instructions for doing all of this "design" is encoded directly into the DNA of any given social insect. Rather, the instructions are "compiled" from the individual activities of thousands of individual insects performing very simple, stereotyped actions (mostly coordinated by chemical pheromones). In other words, the "intelligence" that produces the marvelous structures and functions of insect societies is a collective "intelligence" consisting of a small set of "decision rules" hard-wired into the nervous systems of individual insects.

Might it not be the case that this same process is the paradigm for all biological complexity? This would not only explain where the "designer" is (it's all around / inside us) and who the "designer" is (it's everyone, interacting collectively in producing the "superorganism"), it would also present what ID has so far completely lacked: an empirical research program. That is, one could search for the "decision rules" that produce biological complexity, in viruses, cells, insect societies, primate societies, and human societies, and figure out how the interaction of such rules produces biological complexity. And when you did that, you would have recreated the already-existing field of biology known as sociobiology, which is a branch of evolutionary biology.

Termites do not have "goals and foresight". Rather, they are quite literally programmed (i.e. "hard wired") to perform a surprisingly simple set of simple behaviors. They are born with this capability and do not have to learn it. Furthermore, their behaviors are extremely stereotyped and subject to quite a bit of essentially "random" variation. Despite this, and because there are so many of them (literally millions in some large hives), they collectively produce structures and functions that rival the most complex "artificial" factories and dwelling places designed by humans.

The point here is that "intelligence" is not being defined well at all, if it is restricted to humans and higher vertebrates, but not to insect societies. Each insect is definitely not "intelligent" (any more than each of our individual cells is), but collectively both the insect societies and our multicellular selves are intelligent. "Intelligence" is therefore an emergent property, rather than a pre-existing attribute. And evolution, of course, is all about emergent properties.

One of the points I tried to make earlier is that using human "intelligence" as a yardstick for intelligence in general is like using a Cray XMT as your yardstick for evaluating the "intelligence" of an abacus. In virtually every discussion I have read about "intelligence" at ID blogs, there seems to be an unspoken yet universal assumption that "intelligence" is an either/or phenomenon: either something is at least as intelligent as a human (or the Intelligent Designer aka God) or it isn't intelligent at all.

How "intelligent" a virus like the lambda bacteriophage? If "intelligence" is to be a useful (not to mention empirically measurable) phenomenon, it seems to me that it should fall somewhere along a spectrum, from the "intelligence" manifested by simple viruses up through the "intelligence" manifested by complex animal societies such as ours.

The latter point - that "intelligence" must somehow be massively multiplied as the result of social/collective interactions - is also non-trivial. As I pointed out earlier, an individual termite is extraordinarily "stupid", especially by human standards. Indeed, taken out of their social contexts, the behaviors of most social organisms seem pointless and almost random. However, what appear to be pointless and virtually random behaviors when viewed at the individual level become extraordinarily complex and "hyper-intelligent" when one moves up in organizational levels in animal societies.

How "intelligent" would each of us be, if we were forced to live in complete isolation from all other humans? If we were forced to do so from birth, our "intelligence" would be so limited as to result in almost instant death. Ergo, if one uses "able to live independently" as one's criterion for "intelligence", one would have to conclude that oak trees are immensely more intelligent than humans.

In my opinion, until ID theory comes to grips with the concept of "intelligence" in such a way as to make it both empirically verifiable and quantifiable, ID "theory" will continue to be not much more than unsupported speculation.

As a first approach to an operational definition of intelligence, consider whether learning is a necessary component of intelligence. Several commentators have strongly implied that this is the case. That is, the more an entity is capable of "learning", the more intelligent it is.

However, using the ability to learn as a criterion for intelligence is fraught with difficulties. For example, termites do not learn to build termite mounds, yet virtually everyone in this thread has agreed that mound-building behavior in termites indicates that termites (at least as a group) are indeed intelligent. Ergo, it is quite clear that an entity that is utterly incapable of "learning" can still qualify as being highly "intelligent".

This would also apply to some ID supporter's assertion that the Intelligent Designer is the God of the Abrahamic religions. This entity is universally recognized as being a "4-O deity": that is, He is omnibenevolent, omnipotent, omnipresent, and omniscient. However, this last quality also strongly implies that the ID/God does not learn from His actions, as to do so would be directly contradictory with His being forever omniscient (i.e. from the beginning to the end of time, assuming that time does indeed end). Ergo, the ability to learn is quite clearly not a criterion for determining intelligence, if one assumes that the Intelligent Designer of ID theory is the God of the Abrahamic religions.

If one is familiar with so-called "expert systems" in computing, the same would be the case. Expert systems (ESs) do not "learn" to do anything in the sense that animals with "wet" minds do. On the contrary, an ES performs a complex (sometimes recursive) calculation using data embedded in one or more "truth tables", producing a calculated outcome. This outcome is sometimes hedged with statistical error calculations, but it is a calculated (i.e. not learned) outcome nonetheless. While the final calculation produced by an ES can be modified, this happens only when the values in the "truth tables" are modified. Otherwise, the outcome is simply a calculation. Ergo, expert systems do not actually "learn" anything, at least in the same way that animals (and some other living organisms) do.

So, I believe that it is fair to conclude that the ability to "learn" is quite clearly not a necessary criterion for intelligence. Some highly intelligent entities (such as termite colonies and the God of Abraham) are clearly incapable of true "learning". Conversely, some very unintelligent entities, such as bacteria, are nonetheless capable of changing their behavior over time in response to changes in their environment (the standard operational definition of "learning" in the cognitive sciences).

CONCLUSION: Intelligence is fundamentally unrelated to the ability to learn.

Which brings us back once again to the fundamental question: what is "intelligence", how can it be observed, and can it be quantified in any way? If not, then ID is quite literally a "science" without an empirically definable subject, and therefore a pointless exercise in mental masturbation.

One might also be tempted to define "intelligence" as "adaptability". That is, an "intelligent" entity has the ability to adapt its behavior (and, presumably, its underlying cognitive machinery by means of which its behavior is generated and regulated) in response to changes in its environment. However, this presents two serious problems to an ID supporter:

1) "Adaptability" is what natural selection is all about. Why posit the existence of an "intelligent" entity that is capable of "adapting" to changes in the environment, when this is precisely what natural selection is supposed to be able to do?

2) Since ID is supposed to be a theory that explains adaptation, then saying that the Intelligent Designer (i.e. the entity that moulds adaptations) is adaptable is essentially defining "intelligence" via constructing a tautology:

• "intelligence" = "ability to produce adaptations"

• "intelligent design" = the process by which adaptations are created

Ergo, "intelligent design" reduces to "adaptability producing adaptations".

This is what is sometimes referred to in logic as the "dormative principle" argument, from Moliere's "The Imaginary invalid". When asked how or why opium produces sleep, the learned doctor replies "because it contains a 'dormative principle'"; that is, it causes sleep because it contains a material that causes sleep. In the same way, defining "intelligence" as "the ability to adapt to changes in the environment" (including changes that have not yet happened, i.e. foresight) reduces to "design that is 'adaptable' because it is 'adaptable'".

Where does this leave us in a search for an empirically quantifiable definition of "intelligence"? And if the answer is, "nowhere", then where does this leave "intelligent design"?

In the same line of argument, one clearly cannot define "intelligence" as "that principle/process/quality by which complex specified information is produced". To do so would once more be arguing via tautology:

Question: What produces "complex specified information"?

Answer: Intelligence.

Question: What is "intelligence"?

Answer: That principle/process/quality that produces complex specified information.

Ergo, "the principle/process/quality that produces complex specified information" is what produces "complex specified information".

Again, a pointless exercise in semantic gymnastics.

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

How Not To Fight A "Culture War"

2009-05-02T15:01:00.013-04:00

There has been an interesting and often heated discussion about "methodological naturalism" taking place at Uncommon Descent. After more than 350 comments, the dispute about what "methodological naturalism" was, and how long scientists have been practicing it was resolved in the way that most such discussions are resolved: with the participants agreeing to disagree.

I think it would be interesting for both sides in the debate around methodological naturalism (MN) to consider why this term has become so widely used in recent times. For the sake of argument, let us assume that the entire concept of MN only became "solidified" following Paul de Vries' coinage of the term in 1983. Also for the sake of argument, let us concede that prior to that time the use of "non-natural" assumptions was indeed legitimate for at least inspiring scientific research (as, indeed, history shows us was clearly the case). Let us then further assume that the current application of MN does indeed exclude any reference to "non-natural causes", either in the design of experimental tests of hypotheses or in their interpretation.

One might then reasonably ask, "What happened in the early 1980s that prompted such a dramatic shift in the perception of scientists, so dramatic that it led most scientists to reject what had previously been allowable: that is, the use of "non-natural" hypotheses as an inspiration for scientific research (if not necessarily also in the interpretation of the results of such research)?

I believe that if one examines what was happening the early 1980s vis-a-vis evolutionary biology, the answer to this question is obvious: the rise of "scientific creationism" (especially of the "young Earth" variety) as a political force in the U.S., culminating in the Supreme Court of the United States (SCOTUS)'s decision in Edwards v. Aguillard (
482 U.S. 578) in 1987. During the 1960s, American science was promoted very vigorously, both by the U.S. government and by scientists themselves, as a reaction to scientific advances by the Soviet Union (particularly the launching of Sputnik, the first artificial satellite). Part of this promotion involved the formulation of the Biological Sciences Curriculum Study (BSCS) protocol and its associated textbooks (the "blue", "green", and "yellow" versions). All three versions stressed evolutionary theory as providing a foundation for the biological sciences. This was virtually the first time since 1925 (and the conviction of John T. Scopes for having violated Tennessee's Butler Act by teaching evolution in a public school classroom) that evolutionary theory had been so prominently featured in biology textbooks that were widely promoted in the American public school system.

This caused an immediate negative reaction among American evangelical Christian groups. Legislative bans on the teaching of evolution similar to the Butler Act were either reinstated or promoted in several states. At the same time, Henry Morris and other "scientific creationists" founded and promoted the "scientific creationism" movement, which sought to provide scientific evidence for their version of "young Earth creationism" (YEC). Not much actual science was done by these self-described YECs, but strenuous political efforts were undertaken to have their YEC reinterpretations of existing scientific information incorporated into public school curricula in several states (most notably Arkansas and Louisiana).

In reaction to these efforts by YECs, the scientific community partnered with the American Civil Liberties Union (ACLU) and allied organizations to bring such efforts to the attention of the SCOTUS, with the intention of having them outlawed as violating the first amendment to the US constitution. These efforts were ultimately successful, as both laws banning evolution from public school science classes and the attempts to insert YEC in public school science classes were struck down as unconstitutional by the SCOTUS. These events, and not the subsequent rise of Intelligent Design (ID), are the context within which the adoption of MN by the scientific community in the 1980s can most effectively be viewed.

From my interactions with them, I have found that some ID supporters are very strongly in sympathy with the YECs, and view ID as a way of getting their version of YEC back in the public schools. This was clearly the case in the Dover Area school board's 2005 attempt to provide students with alternative biology textbooks incorporating ID, as shown by the sworn testimony by several of the members of that school board and other members of the board who were present at meetings at which this plan was discussed and approved.

However, in my interactions with other ID supporters (and especially the members of the Cornell IDEA Club and some commentators at Uncommon Descent), I have come to understand that a significant fraction of ID supporters do not accept that YEC is a legitimate empirical science, nor support it's incorporation in public school science curricula.

The dispute that has occurred in this thread (and similar recent disputes elsewhere) seem to me to be examples of people "fighting the last war" rather than dealing with the situation as it exists today. ID supporters who are not YECs need to understand that most evolutionary biologists lump the two together, partly because of the behavior of the Dover Area school board and similar, more local situations in which YECs have persisted in pushing their views into the public schools. At the same time, evolutionary biologists and their political supporters need to understand that there is no necessary connection between YEC and ID, nor are they united in their conviction that YEC and ID must be incorporated into the public school curriculum today.

A recognition of the political contexts within which both evolutionary biologists and Intelligent Design supporters have come to their positions, and what these contexts imply about the value of possible further actions would be valuable for both sides in this debate. I have had many ID supporters say privately to me that Dover was a disaster for ID, and especially for its quest to be accepted as a legitimate empirical science. I have also had many evolutionary biologists express to me their opinion that there is essentially no difference between YEC and ID, a viewpoint that I have learned through experience is clearly in error.

Ergo, I have concluded that the most effective way to move forward in this debate is the way I have been conducting it since the mid-1990s. That is, to invite supporters of both sides of the debate to make presentations in my evolution courses and seminars at Cornell and to conduct such debates in public forums such as this website. Ironically, I find this venue to be much more congenial to such debates than places like AtBC, in which character assassination is the order of the day, rather than the last resort of people who are either confused about their own position or uncertain about its logical force.

And so, I recommend that all participants in this debate avoid name-calling and ad hominem arguments. For each committed commentator on both sides of this issue, there are many thousands of quiet observers who are trying to come to their own conclusions about the issues being debated. While mud-slinging is fun, it's fun in the same way that smoking or drinking heavily is fun; it provides short-term personal gratification, but in the long term it undermines everything one is trying to accomplish.

I believe that clarity should be our goal, not necessarily agreement. If we come to clarity about our positions and agree to disagree, then we have accomplished a great deal more than we would have accomplished if our goal was simply to attack our opponents' characters or to question their personal motives. Going forward I will do my best to pursue this course of action, and recommend that all who genuinely wish to come to clarity on these issues and, by doing so, help the "silent watchers" of this forum to do so as well, treat each other as colleagues (in the "collegiate" sense of that word) in their pursuit of what they perceive to be the truth, rather than as enemies in a culture war.

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

More on Teleology in Evolutionary Biology

2009-04-29T14:16:00.012-04:00

I’ve been corresponding via email with a fellow evolutionary biologist (who shall remain nameless). I thought that some of her/his comments might be useful or interesting to those who read this blog, as they have a direct bearing on the "problem" of purpose (i.e. teleology) in evolutionary biology.

My correspondent's comments and questions are in block quotes:

I’ve been following the ‘Survival of the Sickest’ thread at Uncommon Descent, and have some comments on it and on your essay on the (un)reality of adaptations.

First, a major area of agreement between us is that the original post is fatally flawed by:

1) the assumption that “Darwinism” implies “constant progress”, and

2) failure to understand that fitness is always defined relative to a particular environment, and that environments change over time.

Now, on to some points of disagreement:

You mentioned Gould and Vrba’s 1982 paper on exaptation, and wrote:

"The reason is quite simple: if (as Gould, Lewontin, and Vrba argue) adaptation isn’t legitimately part of what evolutionary theory is about, then the whole idea of “design” and “function” is read completely out of evolution, leaving only descent with modification."

I have been very strongly influenced on this topic by Warren Allman, director of the Paleontological Research Institute here in Ithaca. He asserted that all adaptations should be considered to be exaptations. His rationale for this assertion was that the term “adaptation” has built into it an assumption of teleology. Literally translated, the word "adaptation" means “toward usefulness”. It’s the “toward” part that is the problem. As you and I both understand it, evolution (including natural selection, but not artificial selection) does not tend toward anything. It has no goal as far as we can tell. Ergo, it builds on what has gone before, but without any specific goal “in mind”.

This is why “exaptation” expresses better how we understand natural selection. It builds “away from” non-functionality (or even away from previous functionality), but never really “toward” anything at all as far as we can tell. And, if Sewall Wright’s “shifting balance” theory is a reasonable model of evolution, then it never really “arrives” anywhere at all, since the “goal” is constantly shifting anyway.

I’m wondering why you think that Gould and Vrba regard adaptation as being outside the legitimate scope of evolutionary theory. My take on the paper is not that they regard the concept of adaptation as illegitimate, but just that it has been typically construed too broadly and should be broken down into the categories of true ‘adaptation’ and ‘exaptation’, where they define a true adaptation thusly:

“Following Williams, we may designate as an adaptation any feature that promotes fitness and was built by selection for its current role.”

The problem I have with this definition is the inclusion of the words “promotes” and “for”. “Promotion” means exactly what it says: “motion towards” something. Ergo, using this word immediately suggests teleology, and as I have pointed out above, teleology cannot be a valid assumption in the origin of the products of evolution at any level. This is not because including teleology allows for “a divine foot in the door” (c.f. Lewontin, 1997), but rather because it requires that the “plan” for the teleological process must exist prior to the coming into being of that process. When we do things, this assumption is perfectly valid, but when something happens in nature, such an assumption is entirely unwarranted. Where, in nature, could such a pre-existing plan exist?

As for the word “for, I always point out to my students that teleological explanations virtually always reduce to sentences that include the phrase “in order to”. This can be shortened even further to “to” (leaving out the “in order”). However, the entire phrase “in order to” can be replaced with the word “for” without changing its meaning. Ergo, the definition quoted above is still irreducibly teleological, and therefore includes an assumption that we should not make in evolutionary biology.

In my paper on the evolution of the capacity for religious experience, I began with a succinct definition of “adaptation”, from which I lay out four criteria that a characteristic (i.e. a “trait”) must meet to be considered a genuine adaptation.

An evolutionary adaptation is any heritable phenotypic character whose frequency of appearance in a population is the result of increased reproductive success relative to alternative versions of that heritable phenotypic character.

Here are the four criteria that I believe must be met for a characteristic to be considered to be an adaptation:

1) An evolutionary adaptation will be expressed by most of the members of a given population, in a pattern that approximates a normal distribution;

2) An evolutionary adaptation can be correlated with underlying anatomical and physiological structures, which constitute the efficient (or proximate) cause of the evolution of the adaptation;

3) An evolutionary adaptation can be correlated with a pre-existing evolutionary environment of adaptation (EEA), the circumstances of which can then be correlated with differential survival and reproduction; and

4) An evolutionary adaptation can be correlated with the presence and expression of an underlying gene or gene complex, which directly or indirectly causes and influences the expression of the phenotypic trait that constitutes the adaptation.

I would now modify criterion #4 to state that such genes/gene complexes must be shown to have been conserved, relative to other sequences in the genome. However, one must keep in mind that such conservation, while necessary, is not sufficient. As we know now, some sequences are conserved, but can be knocked out, with no discernible effect on phenotype. Ergo, to fully satisfy criterion #4, a characteristic must be shown to be associated with a particular gene or gene complex, the knocking out of which can be shown to have significant negative effects on fitness.

Obviously, this means that a great many characteristics that we observe in living organisms will not qualify as adaptations. I believe that this is fully justified, following Williams’ assertion that the concept of adaptation is “onerous” and should only be resorted to “in the last resort”. It is only by doing so that we may avoid the otherwise almost inevitable pitfall of appealing to teleology in our explanations.

Gould and Vrba close their paper with this:

“The argument is not anti-selectionist, and we view this paper as a contribution to Darwinism, not as a skirmish in a nihilistic vendetta. The main theme is, after all, cooptability for fitness. Exaptations are vital components of any organism’s success.”

There’s that nasty little word “for” again! Fitness is immediately measurable as relative differential reproductive success, but “adaptation” can only be legitimately inferred retrospectively. We can’t say that something is a genuine adaptation until it already is, and this seems to me the kind of logical circularity that has also plagued Herbert Spencer’s phrase “survival of the fittest”. If we stick to the four criteria listed above, we will rarely fall into the trap that teleological thinking always sets for us.

Also, you later wrote the following, which seems to acknowledge that Gould and Vrba did regard adapation as a legitimate part of evolutionary theory:

“Yes, indeed, except that I believe that Gould, Lewontin (and later, Vrba) were, like Darwin, unwilling to take their principles to their logical conclusion: that adaptations (like species) are a figment of the human imagination, and do not actually exist in nature (or, to be even more precise, do not have to exist in nature).”

What I meant by this is that the only way we can actually “detect” the presence of adaptation is by inferring it. In that sense, adaptations are not “primary” characteristics; that is, characteristics that can be directly observed (such as differential reproductive success). Rather, such “secondary” characteristics must be indirectly inferred. In that sense, they are indeed “imaginary”; we must “imagine” that they exist (as the result of our application of inferential logic), as we cannot observe them directly.

Am I missing something? Are you trying to say that although Gould and Vrba regarded adaptations as real, they nevertheless thought they should be excluded from evolutionary theory?

No, I’m saying what Williams was saying, only I’m saying it more strongly and consistently: that we should never include any hint of teleology in our explanations, as such inclusion includes the biological equivalent of that old bugaboo of physics: “action at a distance” in physics is the equivalent of “goals preceding causes” in biology.

When I reread Williams’ famous 1966 book, Adaptation and Natural Selection, which supposedly reads teleology out of evolutionary biology, I was astonished to find it shot through with the same kind of teleological reasoning that he was supposedly trying to eliminate. I think I could find all the “hidden teleology” in Williams because I have spent so much time debating with ID supporters. They are the ultimate teleologists, and can always find where we have subtly woven teleological assumptions into our biology.

Finally, you wrote:

“To be as clear as I can, I believe that asserting a position of “metaphysical materialism” is just that: a metaphysical, not a scientific assertion. Confusing metaphysics with science is nearly as pernicious as confusing “ought” and “is”. The former makes for questionable science and the latter makes for questionable ethics.”

I would agree that science has no say on metaphysical questions that don’t have observable consequences (although I would argue that even then, Ockham’s razor should cause us to prefer simpler metaphysical systems to needlessly complex ones). However, some metaphysical assertions do have observable consequences. For example, I consider the existence of the Young Earth Creationists' God to be a metaphysical assertion that has nevertheless been decisively falsified by science.

I agree, but the same cannot be said for the more subtle versions of teleology found in Michael Behe or William Dembski's works. Their books (especially Dembski’s) present a much more subtle and less easily refuted version of teleological explanation, one that is easily reinforced by our own unwitting resort to teleological explanations.

Evolutionary adaptation is where the rubber of both evolutionary theory and ID hit the road.

Now on to your essay “Are Adaptations ‘Real’?”

You wrote:

“...although there are characteristics of organisms that are correlated with relatively high reproductive success (and would therefore be considered by most evolutionary biologists to qualify as “adaptations”), it becomes problematic to decide exactly which of those characteristics are the “real” adaptations and which are merely ‘accidental’”.

The problem, of course, is the words “real” and “accidental”. If we are genuinely dedicated to rooting out teleology in all of our explanations of the origins of biological objects and processes, then all adaptations are “accidental”, in the sense that they are all unplanned. We perceive them as having “functions” because our naive viewpoint of reality is always teleological. We can think non-teleologically only with very great difficulty. It’s like special relativity or quantum mechanics. We have to twist our minds to be able to even begin to conceive of them, and even then we constantly slide back into our naive (and unwarranted) views of reality.

True, if by “accidental” adaptations you mean exaptations. But while it may sometimes be difficult to tell whether an adaptation is “real” or “accidental”, that is not evidence that “real” adaptations don’t exist. Indeed, the only scenario I can envision in which “real” adaptations would not exist would be one in which every fitness-enhancing feature was an exaptation.

Exactly!

But that would mean, among other things, that every incremental improvement to the eye would have to have been the accidental result of changes that were selected for some reason other than improved vision. That seems far-fetched to me. Am I misunderstanding your position?

It’s not that that every incremental improvement to the eye would have to have been the accidental result of something, it’s that every incremental change to the eye would have had to originate accidentally, but then increase in frequency as the result of differential survival and reproduction. If we think the way you worded it (and we almost always think that way), then the teleological trap is that all of the incremental changes are somehow “predestined” and that complex eyes must be the inevitable result.

But this just plays into the hands of intelligent Design supporters. When we argue that “half an eye is still adaptive” we unwittingly include the assumption that “half an eye” is just that: half of what will ultimately evolve by natural selection. But our knowledge of the natural history of vision has shown us over and over again that “half an eye” is the whole thing in many cases. We can only say that the eyes of, say, flatworms, are “half an eye” because we already know that such a thing as a “whole eye” exists in cephalopods and vertebrates. We have to disabuse ourselves of the idea that any characteristic is only partially the whole deal. All characteristics of all organisms are the whole deal for those organisms, period, end of story, that’s all She wrote. Anything else contains the beginnings of teleology, and that way lies error, endlessly compounded.

We now have the ability to selectively delete individual characteristics from many different organisms. This makes possible something that natural selection does not: the precise determination of the selective “value” of particular characteristics. This has already been done, and the surprising outcome has been that even some gene sequences that were thought to have been very important in selection (due to having been “conserved” over deep evolutionary time) are apparently insignificant or useless. We know this because knocking them out of the genome has no discernible effect on the survival or reproduction of the “knock-out” progeny.

Precisely my point, above.

That interpretation seems to depend on the hidden assumption that the environment hasn’t changed significantly in the recent history of the organism, and that the experimental environment is fully representative of the historical environment over the entire time during which the features in question evolved. In the case of knocked-out sequences that have no apparent effect on fitness, how sure are we that the experimental environment is fully representative in this way?

No, but to assume that we are making the opposite mistake - assuming that some characteristic really has some function, even if that function is entirely unobservable - is once again to fall into the “teleology trap”. This is essentially the same argument that ID people make about “junk DNA”. Just because we haven’t found any function for it, doesn’t mean that all of it has no function. They argue that all of it must have some function. They are, like the evolutionary biologists for whom Williams, Gould and Lewontin, and Gould and Vrba wrote their warnings about, assuming teleology in evolution: they are, in a word, “pan-adaptationists”.

As a hypothetical example, imagine a bacterial DNA sequence that is expressed only during the formation of spores to protect the organism during periods of extreme environmental conditions. Knock out the sequence and test the viability of the resulting variant. If the experimental environment doesn’t include the extreme conditions that induce spore formation, the organism will never attempt to express the knocked-out sequence, and so its absence will not be noticed. If the experimenter concludes that the sequence is insignificant or useless, she is mistaken.

True, but I would strongly prefer that adaptation be considered a “diagnosis by exclusion” rather than our first and most important resort. By focusing on adaptation and natural selection, we teeter on the edge of the “teleology trap” and often (maybe even usually) fall in, despite our best efforts to avoid doing so.

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

Why Intelligent Design Supporters Insist That ID Must Be True

2009-04-22T22:28:00.009-04:00

It has taken me a very long while, but I think I finally understand why Intelligent Design (ID) exists, why websites like Uncommon Descent exist, and why the regular commentators who support ID at those websites are so determined to assert the absolute reality of ID, in spite of a complete lack of empirical evidence.

It’s all right here in this quote about the ultimate justification for morality:

“Of course [the validity of an objective moral code] is all dependent upon the truth of the existence of God and the truthfulness of scripture - most of us here are aware of that.”

I believe that this is the crux of the whole science versus ID debate: if there is no empirical evidence for the existence of God, then it all comes down entirely to pure, unsupported supposition. Yes, one can assert that God exists, and can assert that therefore whatever God asserts must, by definition, be the absolute objective truth, but by the standards of scientific logic (which are now almost universally accepted as providing the most reliable evidence for descriptions of reality), arguments based purely and solely on assertion are no longer considered valid.

Ergo, without some independent source of evidence – independent of the original assertion, that is – then it all comes down to dueling assertions, which means that eventually it all comes down to force majeure: whoever can make the most forceful assertion gets to define the Truth.

Therefore, there must be some kind of empirical evidence for the existence of God. The fact that no one has ever found any is completely irrelevant, and will remain so indefinitely. It also explains why it is perfectly legitimate to deliberately distort, misinterpret, omit, or otherwise alter empirical evidence if it does not support the otherwise unsupportable assertion that God exists. [1]

Here is the way it looks to me:

Condition #1:

• If a moral code is not objective, it is ipso facto invalid.

• The moral code asserted by God is the only objective moral code. [2]

• If God does not exist, then there is no basis for the assertion that there is an objective moral code.

• Therefore, if God does not exist, anything is permitted.

Condition #2:

• An argument supported purely by assertion(s) is invalid. [3]

• Ever since Francis Bacon’s Novum Organum, it has generally been considered necessary that there should be empirical evidence (either direct or indirect) in support of arguments.

• Ergo, there must be empirical evidence in support of the assertion that God exists. Otherwise, there can be no objective morals, and therefore anything is permitted.

Conclusion:

Since God must exist (otherwise there are no morals and anything is permitted), then there must be empirical evidence for His existence. Finding none, it is therefore necessary to pretend that some exists, or to make some up. Otherwise there can be no objective basis for morals, society will necessarily collapse into chaos, and we will all inevitably become insatiable, maniacal, cannibalistic, orgiastic mass murderers, rapists, and thieves.

It also seems to me that this is the reason why ethical philosophers now virtually unanimously agree that ethical prescriptions cannot be derived from statements derived from empirical science (i.e. "ought" cannot be derived from "is"). To do so not only conflates two separate domains of logic (i.e. deductive versus inductive), but also requires that there be empirical evidence for something (i.e. ethical prescriptions) that are not and cannot be justified by empirical analysis (i.e. the workings of nature). Yes, we can use empirical analysis to determine if our ethical prescriptions have brought about the goals which we have decided to pursue, but we cannot use empirical analysis to formulate those goals.

Notes:

[1] Unsupportable on the basis of empirical evidence, that is.

[2] An obvious corollary to this is that each and every one of God’s moral prescriptions is both objective and absolutely True, by definition. Hence the argument that anything God prescribes (such as the massacre of the Canaanites) is morally right, simply by virtue of His saying so.

[3] To be specific, arguments based purely on deductive (i.e. Aristotelian) logic have been largely superseded by arguments based on inductive logic.

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

Evolution: Is Free Will An Illusion?

2009-04-20T11:16:00.013-04:00

Every summer I teach a seminar course at Cornell in which we examine the historical, philosophical, religious, and scientific implications of evolutionary theory. This summer our seminar course will consider the question: Is free will an illusion?

On the 15th of July, 1838, Charles Darwin began a notebook which he labeled as “M”, in which he intended to write down his correspondence, discoveries, musings, and speculations on “Metaphysics on Morals and Speculations on Expression”. On page 27 of that notebook, he wrote

“…one doubts existence of free will every action determined by hereditary constitution, example of others or teaching of others. (…man…probably the only [animal] affected by various knowledge which is not heredetary & instinctive) & the others are learnt, what they teach by the same means & therefore properly no free will. [Emphasis added]

In his private musing on the question of free will, Darwin came to the conclusion that human free will is an illusion, and that all of our actions (and, by extension, our thoughts and intentions) are the result of our “hereditary constitution” and “the example…or teaching of others.”

Some evolutionary biologists, notably William Provine of Cornell University, have followed Darwin’s lead and asserted that human free will is an illusion. Most philosophers disagree, asserting that free will is the principle difference between humans and non-human animals. Many Christian theologians go further, asserting that free will is the foundation of all human action, without which no rational ethics or theology is possible.

In our seminar course this summer we will take up this debate by considering two alternative hypotheses: (1) that human free will is real and forms the basis for our morals and ethics, or (2) that human free will is an illusion, the capacity for which is a product of the same evolutionary processes that have shaped our anatomical and behavioral adaptations. Included in this debate will be an extended consideration of the hypothesis that the capacity for ethical decision making is an evolutionary adaptation that has evolved by natural selection. We will read from some of the leading authors on both sides of the subject, including George Ainslie, Daniel Dennett, Robert Kane, Daniel Wegner, and Edward O. Wilson. Our intent will be to sort out the various issues at play, and to come to clarity on how those issues can be integrated into a perspective of the interplay between philosophy and the natural sciences.

Here are some particulars for the course:

INTENDED AUDIENCE: This course is intended primarily for students in biology, history, philosophy, religious studies, and science & technology studies. The approach will be interdisciplinary, and the format will consist of in-depth readings across the disciplines and discussion of the issues raised by such readings.

PREREQUISITES: None, although a knowledge of general evolutionary theory, evolutionary psychology, sociobiology, and the philosophy of human free will would be useful.

DAYS, TIMES, & PLACES: The course will meet on Tuesday and Thursday evenings from 6:00 to 9:00 PM in Mudd Hall, Room 409 (The Whittaker Seminar Room), beginning on Tuesday 23 June 2009 and ending on Thursday 30 July 2009.

CREDIT & GRADES: The course will be offered for 4 hours of credit, regardless of which course listing students choose to register for. Unless otherwise noted, course credit in BIOEE 4670 / BSOC 4471 can be used to fulfill biology/science distribution requirements and HIST 4150 / STS 4471 can be used to fulfill humanities distribution requirements (check with your college registrar's office for more information). Letter grades for this course will be based on the quality of written work on original research papers written by students, plus participation in class discussion. All participants must be registered in the Cornell Six-Week Summer Session to attend class meetings and receive credit for the course (click here for for more information and to enroll for this course). Registration will be limited to the first 18 students who enroll for credit.

REQUIRED TEXTS:

Ainslie, G. (2008) Breakdown of Will, Cambridge University Press, ISBN: 0521596947 (paperback: $34.99), 272 pages.

Dennett, D. (2004) Freedom Evolves, Penguin Books, ISBN: 0142003840 (paperback: $17.00), 368 pages.

Kane, R. (2005) A Contemporary Introduction to Free Will, Oxford University Press (USA), ISBN: 019514970X (paperback: $19.95), 208 pages.

Wegner, D. (2003) The Illusion of Conscious Will, MIT Press, ISBN-10: 0262731622 (paperback: $21.95), 419 pages.

Wilson, E. O. (2004) On Human Nature (Revised Edition), Harvard University Press, ISBN: 0674016386 (paperback: $22.00), 284 pages.

OPTIONAL TEXTS:

Darwin, Charles (E. O. Wilson, ed.) (2006) From So Simple a Beginning: Darwin's Four Great Books. W. W. Norton, ISBN-10: 0393061345 (hardcover, $39.95), 1,706 pages. Available online here.

Fisher, J., Kane, R., Pereboom, D., & Vargas, M. (2007) Four Views on Free Will, Wiley-Blackwell, ISBN: 1405134860 (paperback: $33.95), 240 pages.

Kane, R. (2001) Free Will (Blackwell Readings in Philosophy), Wiley-Blackwell, ISBN: 0631221026 (paperback: $33.95), 328 pages.

Wilson, E. O. (2000) Sociobiology: The New Synthesis (25th Anniversary Edition), Belknap Press, ISBN: 0674002350 (paperback: $44.00), 720 pages

Our summer seminar course is always fascinating, and often quite controversial (see this and this). Over the years we have explored many of the implications of Darwin's theory, and the participants have always found our discussions (perhaps they should be called "debates") enlightening. As always, the intent is not necessarily to reach unanimity, but rather for each participant to come to clarity on where they stand on the issues and to be able to defend that stance using evidence and rational argument.

So, please consider taking our seminar on free will this summer - the choice is yours!

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

Evolution: The Darwinian Revolutions

2009-04-14T11:49:00.009-04:00

Long-time readers of this blog will know that every summer I teach an introductory evolution course for non-scientists at Cornell. This year the focus of the course will be somewhat different. In honor of the bicentennial of the birth of Charles Darwin and the 150th anniversary of the publication of his monumental book, On the Origin of Species..., we will be focusing on the impact of Darwin's concept of evolution by natural selection, both on the sciences and on society as a whole.

Darwin's theory of evolution is the most revolutionary idea ever entertained by the human mind. It fundamentally alters our perception of reality. In profound and unsettling ways the theory of evolution changes our understanding of who we are, where we come from, why we do the things we do, and where we might be going. It does this by making us look carefully and dispassionately at the world around us, asking questions and seeking answers in the things we can observe.

This summer we will explore Darwin's theory and the impact that it has had on the sciences and on human society. Here is the syllabus for the course:

EVOLUTION: THE DARWINIAN REVOLUTIONS
BIOEE 2070 / HIST 2870 / STS 2871
Cornell University Six-Week Summer Session – Summer 2009

PREREQUISITES: None - Intended for non-science majors with an interest in evolutionary theory

CREDIT HOURS: 3 (does not count toward evolution distribution requirement in biological sciences)

CLASS TIMES: Mondays and Wednesdays 6-9 PM, Monday 22 June 2009 to Wednesday 29 July 2009

CLASS LOCATION: Lectures in Morrison Room, Corson-Mudd Atrium. Discussions TBA in class.

COURSE FORMAT: The format for each class will be a two-hour interactive lecture/discussion, in which the professor outlines the major concepts, followed by a one-hour discussion section in which all participants present their interpretations and opinions of the concepts and readings under consideration. Participants will also have the opportunity to make full-length presentations of their original work. Grades will be based on the quality of three essays, due at the end of each two-week segment. Students may also opt to do one essay and a research paper (see description and point scores, below).

GRADE BASED ON: Attendance and participation in lecture and section, plus combined letter grade on three essays (suggested length = 4 to 8 pages) or one essay and one research paper (maximum length = 20 pages), for a total of 100 points (electronic/email submission encouraged, but not required)

COURSE DESCRIPTION: Evolution is the founding concept of the science of biology. This course examines evolution in historical and cultural contexts. Aims of the course include understanding the major issues in the history and current status of evolutionary theory and exploring the implications of evolution for culture and human psychology. Issues range from controversies over mechanisms of evolution in natural populations to the philosophical implications of evolutionary theory.

REQUIRED TEXTS:

Darwin, Charles (E. O. Wilson, ed.) (2006) From So Simple a Beginning: Darwin's Four Great Books. W. W. Norton, ISBN: 0393061345 (hardcover, $39.95), 1,706 pages. Available online here

Goldschmidt, Tijs (1998) Darwin's dreampond: Drama in Lake Victoria, MIT Press, ISBN: 0262571218 (paperback, $27.00), 274 pages.

Jabloka, Eva & Lamb, Marion J. (2006) Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life, MIT Press, ISBN: 0262600692 (paperback, $19.95), 474 pages.

Raup, David M. (1991) Extinction: Bad genes or bad luck? W.W. Norton, ISBN: 0393309274 (paperback, $14.95), 228 pages.

Ruse, Michael (2004) Darwin and design: Does evolution have a purpose? Harvard University Press, ISBN: 0674016319 (paperback, $19.50), 371 pages.

OPTIONAL TEXTS:

Darwin, Charles (1892) The autobiography of Charles Darwin (Nora Barlow, ed.), W.W. Norton, ISBN: 0393310698 (paperback, $14.95), 365 pages. Available online here

COURSE PACKET:

All of the course packet readings listed below are available from the course website. The password to access the course packet is “evolutioncp” (without the quotation marks). Alternate weblinks are provided for your convenience.

NOTE: Students will not be required to read all of these articles. Your instructor and/or TA will tell you which articles you are responsible for.

Ayala, F. (1970). Teleological explanations in evolutionary biology. Philosophy of Science, vol. 37, pp. 1–7.

Behe, M. (2002) Intelligent design as an alternative explanation for the existence of biomolecular machines. Unpublished manuscript.

Cosmides, L. & Tooby, J. (1997) Evolutionary psychology: A primer. Center for Evolutionary Psychology. Available online here

Dembski, W. (2005) What every theologian should know about creation, evolution, and design. Orthodoxy Today. Available online
here

Dobzhansky, T. (1973) Nothing in biology makes sense except in the light of evolution. The American Biology Teacher, vol. 35 (March 1973), pp. 125–129. Available online
here

Eldredge, N. and Gould, S. J. (1972) Punctuated equilibria: An alternative to phyletic gradualism. In Schopf, T. J. M. (1972) Models in Paleobiology, Freeman, Cooper, & Co., pp. 82–115. Available online here

Gould, S. J. And Lewontin, R. C. (1979) The spandrels of San Marco and the Panglossian paradigm: A critique of the adaptationist programme. Proceedings Of The Royal Society of London, Series B, vol. 205, no. 1161, pp. 581-598. Available online here

Huxley, T. H. (1860) Letter to Charles Kingsley, Available online
here

Jenkin, F. (1867) Review of Origin of Species. The North British Review, June 1867, vol. 46, pp. 277-318.
Available online here

Kaviar, B. (2003) A history of the eugenics movement at Cornell. Unpublished manuscript.

MacNeill, A. (2004) The capacity for religious experience is an evolutionary adaptation for warfare. Evolution and Cognition 10:1, pages 43 to 60.

MacNeill, A. (2005) Natural selection, sparrows, and a stochastic God. Available online here

MacNeill, A. (2006) Vertical polygyny in modern America: An evolutionary perspective. Available online here

Mayr, E. (1974) Telological and teleonomic: A new analysis. Boston Studies in the Philosophy of Science, XIV, pages 91 to 117.

Mayr, E. (1982) The growth of biological thought. Harvard University Press. Chapters 12 & 13, pages 535 to 627.

Pinker, S. (2004) The evolutionary psychology of religion. Freedom From Religion Foundation. Available online here

Wegner, D. (2002) The illusion of conscious will. MIT Press: Cambridge. Chapter 3, pages 63 to 98.

PART ONE: THE ORIGIN OF EVOLUTIONARY THEORY
The science of evolutionary biology began with the publication of Charles Darwin's On the Origin of Species. It is one of the most important books ever written and should be read by any person who wants to understand who we are, where we come from, and why we are here (and how we know).

PART TWO: THE MODERN SYNTHESIS
Darwin's theory was accepted by most scientists of his generation within a surprisingly short time. Then, within just one more generation, it fell out of favor, replaced by genetic theories of evolution suggested by the rediscovered work of Gregor Mendel. Then, in another generation, the pendulum swung the other way, and Darwin's ideas were integrated with Mendel's and codified in the "modern synthesis."

PART THREE: MACROEVOLUTION, EVO-DEVO, AND BEYOND
Evolutionary theory has exploded in the fifty years since the "modern synthesis" was proclaimed. Sociobiology, punctuated equilibrium and new ideas about evolutionary psychology, genetic engineering, macroevolution, speciation…these are just a few of the directions that evolutionary theory and biology have expanded in the second half of the 20th century and the beginning of the 21st.

I would like to invite anyone who has found this blog interesting to take this course, or follow along with us by keeping up with the course materials posted at the course website. Either way, you will find your mind being stretched and your view of reality challenged. What better way could one spend a few summer evenings?

See you this summer!

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

Platonic Ideal Forms Versus Evolutionary Developmental Biology

2009-04-08T10:59:00.032-04:00

In a recent thread at Uncommon Descent,
Salvador Cordova wrote:

"[The existence of] platonic forms would strongly suggest that [evolutionary] transitional [form]s don’t exist. And if there are only lawful morphological forms, transitional forms, even in principle, couldn’t exist. Transitional forms and Platonic Forms don’t fit well together in any theory. It appears the two are mutually exculsive.

In engineering we have many platonic forms. As engineers we are taught to recognize and implement certain canned architectures. A lot of systems biology is mapping biological forms to the forms engineers recognize.

[The] quest for “correct designs” ... makes sense in a world of ideal forms, platonic forms. We instinctively have platonic forms in our mind. We have a sense that a defect is a defect, that an error is an error.

In the Darwinian world, it’s all about selective advantage. A blind cave fish is “selectively advantaged”. Defect is only a relative term. However in the eyes of plato, a blind cave fish is less than the ideal, it is a broken form. In such case, natural seleciton helped to infuse the defect in the population and thus introduce a defect that is not consistent with the ideal pattern.

The notion of platonic forms does not seem to be compatible with Darwinian evolution. [Emphasis added]

The idea of Platonic ideal forms in biology is an old one. The now mostly defunct tradition of orthogenesis is essentially a version of Platonic ideal forms applied to biology (and an argument can also be made that Lamarck’s progressive theory of evolution by means of the inheritance of acquired characteristics is as well). However, and contrary to what some might expect, applying the concepts of orthogenesis to "intelligent design theory" ("ID") is problematic, because in its early 20th century form, orthogenesis was considered to be progressive, but not goal oriented (i.e. teleological).

In addition to the early orthogenesists, two other names stand out in this tradition: D’Arcy Thompson and Stephen Jay Gould. Both were primarily concerned with the origin and evolution of form, and both developed theories of evolution based on this. Even J.B.S. Haldane (one of the founders of the “modern evolutionary synthesis”) wrote in this tradition in his essay "On Being the Right Size". Haldane’s musings on the relationship between size and constraints on form have become known as “Haldane’s Principle”, and have recently been applied to urban planning.

The newly emerging science of evolutionary developmental biology (”evo-devo”) has some similarities to orthogenesis, especially insofar as both are attempts to explain why the evolution of overall form (i.e. phenotype) appears to be constrained to certain types of forms, rather than all possible forms. The orthogenesists asserted that there are certain forms that are much more likely than others. These forms are similar in some ways to Platonic forms, in that there is no necessarily materialistic explanation for the predominance of certain forms, at least according to the theory of orthogenesis.

Evo-devo explains the similarities within “formal types” with reference to shared developmental programs, especially among eukaryotes. This shared developmental programming is based on the hierarchical gene regulation systems, most of which are based on homeotic gene regulatory mechanisms. Similar developmental constrains appear to exist among plants and fungi, but not so much among prokaryotes and multicellular protists. So, looking for things that resemble Platonic ideal forms in biology will probably involve identifying and categorizing the various developmental “channels” which are produced by these homeotic gene regulatory systems.

None of this, of course, says how the various hierarchical gene regulation systems originally evolved. This is another of those “deep time” problems, such as the origin of life and the origin of the genetic code. As I have commented repeatedly in the past, I believe that questions about such origins are almost certainly unanswerable using current empirical methods.

I also personally believe that the question of the origin of Platonic ideal forms (if such things exist and are empirically distinguishable from the various “channels” produced by the action of homeotic gene regulatory mechanisms) is both an open question and one that is almost certainly not answerable using empirical methods.

For more on the question of Platonic forms in biology, see this and this.

For a critique of my analysis of Platonic ideal forms in biology, see this.

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen