Fox News Polling Data Shows Support for Evolution Increasing Exponentially

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

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

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

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?

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?

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"?

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

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

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

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

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

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