THE EVOLUTION LIST

Far Above Cayuga's Waters...

noreply@blogger.com (Allen MacNeill) — Fri, 24 Jan 2014 15:40:00 +0000

Another week of sub-zero weather here in Utopia, NY, and still Cayuga's waters (the ones we are far above) stubbornly remain waters, not ice. Yes, there's about 100 yards of crumbling rime ice drifted up against the shore at Stewart Park, but the rest of the lake is open water. COLD open water, but water nonetheless.

By contrast, when I first started teaching at Cornell (back in the Pleistocene, or the 1970s, I forget - it was so long ago), Cayuga's waters routinely froze over end-to-end, sometimes so thick that a truck could drive across it. Indeed, back in the late 1800s, there was a thriving winter industry in Ithaca, whereby guys in heavy clothing would drive teams of horses and wagons out onto the ice, which they cut with big saws into two-foot-thick blocks and shipped to New York City in boxcars full of sawdust, to supply the ice boxes and ice houses of the Big Apple. Even as late as the 1980s, hardy Ithaca folk would drag their ice fishing shacks (some were more like mini-resorts) out onto the ice, where they would remain until just before breakup in March.

But now, despite two bone-chilling "polar vortices" (which are genuine meteorological phenomena, despite the rantings of Rush Windbag), Cayuga's waters remain...water. Why? Could it be that a few decades of increased atmospheric heat has warmed those billions of gallons of lake water to the point that a few days of sub-zero cold won't freeze them any more? And could this foreshadow what will happen as the immensely larger oceans of the world absorb more and more heat from the warming atmosphere? And could that have something to do with the fact (and yes, it is a FACT) that the atmosphere hasn't had this much carbon dioxide in it since the Jurassic? And could that be due to the fact that since the 1800s we have released an almost incomprehensible quantity of carbon dioxide into the atmosphere, while cutting down millions of acres of forest that used to take it up and turn it into wood? Damn good question...

And an even better question: if this keeps up, what will the world be like in a few more decades, much less a few more centuries?

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

Myths in Biology: Mendel's Pea Flowers

noreply@blogger.com (Allen MacNeill) — Mon, 04 Nov 2013 13:35:00 +0000

At P.Z. Myers' blog, Pharyngula, he has a post on the subject of "myths" in biology, using the number of cell types in humans as an example. He cites Stephen J. Gould's famous article on fox terriers as an example of such myths and how they get incorporated in the science of biology.

You want myths in biology? Pick up any introductory biology textbook and look up Mendel’s original experiments with garden pea plants. Look at the color illustration of the seven phenotypic characters Mendel supposedly tested. Is purple versus white flower color in the figure? Now, read Mendel’s paper describing the seven different characters in garden peas that he studied (you can find the original paper here, in the original German and in English translation). Is purple versus white flower color in the list of characters tested? Interesting…

Toward the end of the paper, Mendel mentions that in a later set of experiments he tested flower color and found the same ratios that he found with the original seven traits he tested. According to the paper, he tested “violett-rothe und weiss Blüthenfarbe” (i.e. “violet-red and white blossom color”), but this test was NOT in his original set of seven experiments, which are the ones always illustrated in biology textbooks.

So, when did biology textbooks start this particular myth? As far as I can tell it was in the first biology textbook with full color illustrations: William T. Keeton’s Biological Science, 2nd ed. The illustrator thought he could kill two birds with one stone by illustrating the technique used to ensure controlled fertilization (i.e. removing the stamens from the flowers using iris scissors) and purple and white flower color. Except that Mendel didn’t study purple versus white flower color in his original series of seven crosses.

Which pair of traits did Mendel actually study, but were replaced by purple versus white flowers in all introductory biology textbooks? The color of the seed-coat, in which gray-brown is dominant and white is recessive. According to Mendel’s original paper, gray-brown seed coats are associated with (what we would now refer to as linked with) “violet-red blossoms and reddish spots in the leaf axils,” but once again Mendel did NOT explicitly test purple versus white flower color in the experiments for which he is remembered, and for which the science of “Mendelian genetics” is named.

And why is the clearly incorrect list (and colored figure) of the seven traits Mendel supposedly studied included in every introductory biology textbook today? Because Keeton’s textbook was the most widely used textbook in biology for decades, so all of the other publishers simply copied what was in his textbook as a way of gaining market share.

Can this myth be corrected now? How many professors’ sets of lecture notes and PowerPoint slides would have to be changed to correct this mistake, and how many textbooks would need new illustrations that included the correct list of the seven traits, and how many people would complain about these changes, or (even worse) suggest that Mendel really did study purple and white flower color in his original series of seven experiments?

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

--Allen

Why vaccinate your children?

noreply@blogger.com (Allen MacNeill) — Sun, 31 Mar 2013 14:43:00 +0000

QUESTION: Not immunizing does not expose someone to a disease, only actual exposure to the disease does so. If a vaccine is effective and your children are vaccinated, how does an unvaccinated person put them at risk? Especially if that person has not been exposed to the disease in question?

ANSWER: It has to do with herd immunity (also known as "community immunity"). With the exception of the smallpox vaccination (reaction to which is easily observed), none of the vaccinations we give our children are tested individually to see if they "took". This is difficult at best and next to impossible in many cases. Instead, the effectiveness of a vaccination program is measured by the prevalence of the disease before, during, and after vaccination of a target population. If the prevalence of the disease goes down as more people are vaccinated (this is verified using statistical analysis), then the vaccination is assumed to work even if it doesn't in some cases.

In fact, no vaccination (including the smallpox vaccination) works in every single case. There is a small, but non-zero fraction of any vaccinated population in which the vaccination doesn't "take" (this again is statistically testable). What this means is that in any population that has been vaccinated, there is a small residual fraction that is still susceptible to the infection.

The rate at which an infection is transmitted depends upon the "infection triangle": (1) virulence (how easily the infectious agent enters a potential host), (2) resistance (how easily the host fights off the infection), and (3) prevalence (how many carriers/potential spreaders there are in the population). Herd immunity depends on 2 and 3, and is defined as that percentage of a vaccinated population that is high enough to stop further transmission of the infection. For example, epidemiologists (doctors who study how infectious diseases spread through populations) define the "herd immunity threshold" for diptheria as 85% (see here). This means that in a population in which at least 85% of the individuals have been vaccinated against diptheria, the probability of an infectious individual spreading the disease to an unprotected member of the population (i.e. the 15% who have not been vaccinated or in whom the vaccination hasn't "taken") is sufficiently low that unprotected individuals probably won't be exposed.

The problem here is that "unprotected" doesn't necessarily mean "unvaccinated". Like any real process in the real world, not all vaccinations "take". A small but non-zero fraction of vaccinations don't cause the vaccinated individual to develop permanent resistance to the disease. This can happen from a number of factors, including the immune status of the vaccinated individual and variations in the potency of the vaccine. This means that, like the actual rate of resistance following vaccination, the probability that a vaccinated individual is actually resistant to the infection is not 100%, but usually somewhere between 80% and 95%. What this means is that the actual level of herd immunity is lower than the rate of vaccination, sometimes by quite a bit (this is a function of both individual variations and group variability - some people are more likely to develop resistance than others).

Therefore, if people in a population don't get vaccinated, then the size of the susceptible carrier population is larger, and if it's large enough (i.e. greater than the "herd immunity threshold"), then the probability that the infectious agent will be spread is high enough that susceptible individuals (i.e. those that have not been vaccinated AND those whose vaccinations didn't "take") will be exposed to the infectious agent, get the disease, and spread it to other susceptible individuals.

This is why there have recently been mini-epidemics of pertussis (whooping cough), measles, and other infectious diseases that were formally almost completely eliminated. Badly educated people (including, but not limited to people who have a visceral anti-science/anti-government bias) don't vaccinated their children, who become part of the susceptible population who, if they are numerous enough, can spread the disease to others, including those whose vaccinations didn't "take".

So, how do you know if your vaccination (or your kid's vaccination) "took" or not? Simple answer: you don't (indeed, in most cases, even with the old smallpox vaccination, you can't). Therefore those of us who don't want our children sickened, crippled, or killed by a preventable infectious disease are counting on everyone else getting their children vaccinated to the point at which the "herd immunity" of our community is above the "transmissibility threshold" and therefore won't be exposed to the infectious agent.

The same kind of reasoning that underlies the concept of "herd immunity" can be used to see if the argument that increased vaccinations cause autism is valid. If there is a causative relationship between increased vaccinations and autism, and if the underlying causative agent is thimerosol in the vaccinations, then there should be a decrease in autism since thimerosol was removed from the vaccinations. No such correlation has been found; ergo, thimerosol in vaccinations was not the causative agent for the perceived increase in frequency of autism.

Another potential test of this hypothesis is to see if those children who, for whatever reason (e.g. immune dysfunctions, religious prohibitions, lack of access to vaccines, etc.) have NOT been vaccinated have lower rates of autism. This is also not the case, so once again the hypothesis that vaccinations (and specifically vaccinations with serum that has been preserved with thimerosol) cause autism is unfounded. This is precisely the kind of statistical correlation testing that is the basis for every single one of the peer-reviewed epidemiological studies that have been done to determine if there is a causative link between vaccinations and autism (or ADHD, or your choice of mental disorder for which we do not yet know the underlying cause). And every single one of these studies (and there have now been many, including several meta-analyses of multiple studies) have shown no statistically significant (i.e. real) correlation between rates of vaccination and the observed rate of increase in autism, ADHD, and some other developmental disorders?.

So, what is causing the statistically detectable increase in the rate of autism, ADHD, and some other developmental disorders? There are plenty of candidates. People (both men and women) are having children at older ages, which has been shown to be causally related to some of these disorders. People are exposed to increasing levels of artificial chemicals and heavy metals in the environment, which again have been shown to be causally related to some of these disorders. Perhaps most significantly, the diagnostic criteria for some of these disorders have changed, especially for ADHD and autism, which are now considered to be "spectrum" disorders, rather than single pathologies that one either has or does not have. Had the current criteria for these developmental disorders been used when I was a kid, I would almost certainly have been diagnosed with ADHD and also probably mild Aspergers' syndrome (i.e. autism spectrum disorder). When you change the definition of a disease, you change your perception of its prevalence.

The same is not the case for the demonstrated decline in crippling and potentially fatal diseases, however. There is very strong statistical evidence that this dramatic decline over the past century and a half has been due to two factors: vaccination and public health. Both of these were and are developed by medical scientists, implemented by health professionals, and supported (and in some cases legally mandated) by governments, usually at the state level.

I believe that it is the case that in New York State you can refuse to have your children vaccinated for religious reasons, yet the public schools are still required to let those children attend classes and therefore expose all of their classmates to an increased possibility of contracting a potentially crippling or fatal disease. In my opinion this is wrong: children who have not been vaccinated should not be allowed to even enter a public building, much less attend public school. Sure, their parents can exercise their right to endanger their children's health (whether their children have a right to not be endangered by their parents is another question), but that right should not take precedence over the rights of other parents (and their children) to not be exposed to the threat of contracting the diseases that such parents have exposed their children to.

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

--Allen

The Evolution of Cooperation – Three Theories or One (or None)?

noreply@blogger.com (Allen MacNeill) — Fri, 01 Feb 2013 05:09:00 +0000

Ever since Darwin, evolutionary biologists have thought and written (and argued about) the evolution of cooperation. In the 20th century, at least three different major theories were proposed to explain how cooperation (and especially unselfish altruism) could evolve by natural selection. Several attempts to unify these theories have been made and are currently a topic of intense debate.

Now, as part of Cornell's Darwin Days celebration, you are invited to come to a dinner discussion to hear about, think about, talk about, and (hopefully) argue about these theories and their implications for human behavior, ethics, and philosophy.

PRESENTER: Allen MacNeill, Senior Lecturer in Biology and Evolution at Cornell and author of Evolutionary Biology and Evolutionary Psychology

SPONSORS: Liebermania! and the Cornell Human Ethology Forum (this will also be the organizational meeting for CHEF)

DAY, TIME, & LOCATION: Thursday 14 February 2013 at 6:00 PM at Risley Dining/Tammany at Cornell University. This event is part of Cornell and PRI/MOTE's Darwin Day 2013 celebration.

Please contact Allen MacNeill at adm6@cornell.edu by Tuesday 12 February 2013 if you plan to attend this event. Hope to see you there!

Fox News Polling Data Shows Support for Evolution Increasing Exponentially

noreply@blogger.com (Allen MacNeill) — Sat, 10 Sep 2011 09:55:00 +0000

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

noreply@blogger.com (Allen MacNeill) — Wed, 08 Jun 2011 14:21:00 +0000

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

noreply@blogger.com (Allen MacNeill) — Mon, 30 May 2011 01:35:00 +0000

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

noreply@blogger.com (Allen MacNeill) — Thu, 17 Mar 2011 11:54:00 +0000

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?

noreply@blogger.com (Allen MacNeill) — Thu, 09 Dec 2010 15:04:00 +0000

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?

noreply@blogger.com (Allen MacNeill) — Sat, 04 Dec 2010 14:21:00 +0000

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"?

noreply@blogger.com (Allen MacNeill) — Thu, 11 Nov 2010 03:56:00 +0000

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

noreply@blogger.com (Allen MacNeill) — Sun, 06 Jun 2010 13:54:00 +0000

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

noreply@blogger.com (Allen MacNeill) — Sat, 17 Apr 2010 00:55:00 +0000

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

noreply@blogger.com (Allen MacNeill) — Tue, 23 Mar 2010 01:15:00 +0000

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

noreply@blogger.com (Allen MacNeill) — Mon, 22 Mar 2010 14:56:00 +0000

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

noreply@blogger.com (Allen MacNeill) — Thu, 18 Mar 2010 02:38:00 +0000

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

noreply@blogger.com (Allen MacNeill) — Fri, 05 Feb 2010 15:31:00 +0000

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.

noreply@blogger.com (Allen MacNeill) — Fri, 22 Jan 2010 04:22:00 +0000

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

noreply@blogger.com (Allen MacNeill) — Sun, 03 Jan 2010 19:15:00 +0000

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!

noreply@blogger.com (Allen MacNeill) — Tue, 08 Dec 2009 14:42:00 +0000

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

noreply@blogger.com (Allen MacNeill) — Tue, 08 Dec 2009 01:51:00 +0000

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?

noreply@blogger.com (Allen MacNeill) — Sat, 28 Nov 2009 15:22:00 +0000

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

noreply@blogger.com (Allen MacNeill) — Tue, 24 Nov 2009 14:08:00 +0000

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

noreply@blogger.com (Allen MacNeill) — Fri, 20 Nov 2009 14:52:00 +0000

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!

noreply@blogger.com (Allen MacNeill) — Fri, 20 Nov 2009 02:47:00 +0000

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