Tuesday, August 31, 2010

Is Glenn Beck an IDiot?

 
Watch this video right to the end and hear Glenn Beck say, "Charles Darwin, the father of modern day racism." That's the standard creationist line—one that's especially prominent on the IDiot blogs. Beck's statement is factually incorrect. It's actually the Christian God of the old testament who's the father of modern day racism.




The Mutationism Myth, VI: Back to the Future

This is the eighth in a series of postings by guest blogger, Arlin Stoltzfus. You can read the introduction to the series at: Introduction to "The Curious Disconnect". The first part is at: The "Mutationism" Myth I. The Monk's Lost Code and the Great Confusion. The second installment is: Theory vs Theory. The third part is: The Mutationism Myth, II. Revolution. The fourth installment is: The Mutationism Myth: III Foundations of Evolutionary Genetics. Part five is The Mutationism Myth, IV: Mendelian Heterodoxies. The sixth installment was The Mutationism Myth, V: The response to Mendelian heterodoxies.

This is Arlin's last contribution. The entire series has been an excellent introduction to the history of evolutionary theory and the concept of mutationism. There are many ways in which the so-called "Modern" Synthesis has to be revised and extended. One of them is to reinstate the concept of mutationism which was purged from evolutionary theory in the 1940s. If you want to understand why this is important then these articles are the place to start.



The Curious Disconnect

Today on The Curious Disconnect (credits), we wrap up our 6-part series on the Mutationism Myth, and set the stage for the future by locating the primary weakness of the 20th century neo-Darwinian consensus in its theory of variation.

I'd like to thank Larry Moran for hosting this series of posts on Sandwalk. If it still seems like a good idea later in the year, I will continue the Curious Disconnect on my own blog site (to be announced).

The Mutationism Myth, part 6. Back to the Future

The Mutationism Myth, a story about how the discovery of genetics affected evolutionary thought, continues to be part of modern neo-Darwinism's monologue with itself (e.g., Charlesworth and Charlesworth, 2009), being used even by leading thinkers calling for an "Extended" Synthesis (e.g., Pigliucci, 2010 1). Since April, we've been deconstructing the Mutationism Myth by exploring what the early Mendelians actually thought, and how their view was replaced by the Modern Synthesis (MS).

Today we'll take the opportunity to review what we've learned and start unpacking its relevance for the future of evolutionary biology.

Review

In the Mutationism Myth (see part 1 for examples), the founders of genetics misinterpret their discovery, concluding that evolution takes place by large mutational jumps, without selection. The false gospel of these "mutationists" brings on a dark period of confusion and error that lasts until the 1930s, when theoretical population geneticists (Fisher, Haldane and Wright) prove that Mendelian genetics is not only compatible with selection, but provides the missing link that completes Darwin's theory and unites all the biological disciplines. The "Modern Synthesis" combining genetics and selection becomes the foundation for all subsequent evolutionary thought.

As we discovered, the Mutationism Myth isn't very accurate. Heredity is not missing from Darwin's theory; selection is not missing from the Mendelian view. Darwin had a theory of heredity both in the sense of a set of phenomenological laws, and in the sense of a mechanism to account for them (part 2). Both were wrong. The Mendelians synthesized genetics and selection, rejecting Darwin's "Natural Selection" theory due to its dependence on fluctuations or "indefinite variability" (defined by Darwin as the subtle variations that arise anew each generation in response to conditions of life). As we know today, such enrivonment-induced fluctuations are non-heritable.

In part 3, we found that the Mendelians laid the conceptual foundations of evolutionary genetics (later formalized mathematically), while part 4 addressed how their view diverged from Darwinian orthodoxy. The Mendelians assumed that new hereditary variants arise rarely and discretely, by mutations whose effects may be large or small. Each new mutation is likely to be rejected, but it may be accepted by chance, especially if it improves fitness. Because, in this view, change depends on discrete events of mutation, the Mendelians (part 4) considered the process of mutation to be a source of initiative, discontinuity, creativity and direction in evolution (Stoltzfus, 2006). This view expanded the role of variation well beyond the subordinate role of raw materials that Darwin had imagined.

The Mendelians were unable to convince naturalists (the majority of their biologist peers) to accept their new view of evolution, nor even a new view of inheritance. Many naturalists remained wedded to Lamarckian and Darwinian views of "soft inheritance".

As we found out in part 5, the "Modern Synthesis" (modern neo-Darwinism) claimed to reconcile Darwin's own view with genetics, though it quietly ignored Darwin's errors while depicting the Mendelians as foolish "saltationists", dismissing their "lucky mutant" view and their ideas about the role of mutation in evolution. In the MS view, each species has a "gene pool" that automatically soaks up and "maintains" hereditary variation, providing abundant "raw materials" for adaptation. The key innovations of this view were to define "evolution" as "shifting gene frequencies" in the "gene pool", to erase the link between "Darwinism" and Darwin's own theory of soft inheritance, and to develop a theory of causation in terms of population-genetic "forces", in which continuous shifts in allele frequencies are the common currency of causation. The new theory put mutation in a subordinate position of supplying infinitesimal "raw materials" for selection. As a result, the MS created a consensus where the Mendelians had failed: naturalists such as Ernst Mayr found that they could accept Mendelian genetics without giving up adaptationist preconceptions.

A bright line

The backdrop for this whole discussion (in case you missed it) is that the MS is strikingly wrong in its neo-Darwinian departures from the Mendelian view. I've implied this several times, and perhaps I've waved my hands and pointed vaguely to mountains of molecular evidence contradicting the MS, but I haven't made this point perfectly clear.

In a moment, I will do that, but first I want to make clear what is at stake.

The Mendelians allowed that evolutionary change could be initiated by an event of mutation, and they interpreted this to mean that mutation was (to an unknown degree) a source of initiative, discontinuity, creativity and direction in evolution. The MS represents a very deliberate rejection of this view, and proposes instead that evolution is a complex sorting out of available variation to achieve a new multi-locus equilibrium, literally by "shifting gene frequencies" in the "gene pool". The rate of evolution, in this view, does not depend on mutation, which merely supplies the "gene pool" with variation; evolution is not shaped by mutation, which is the "ultimate" source of variation, but not the proximate source.

When I made this distinction at a 2007 symposium in honor of W. Ford Doolittle, Joe Felsenstein was in the audience and pointed out that, while Fisher may have looked at things in this way, Wright's stochastic view took into account random events, like new mutations. It's true that Wright's "shifting balance" model assigns a prominent role to random genetic drift, while Fisher's view was deterministic. However, these are just two different flavors of the same "shifting gene frequencies" paradigm: neither view incorporates new mutations. The absence of new mutations from Wright's shifting balance process is apparent from the fact that Patrick Phillips (1996) extended it to include a new starting phase ("phase 0") of "waiting for a compensatory mutation".

The fact that contemporary evolutionary biologists, for the most part, don't understand this aspect of their intellectual heritage is not evidence of a cover-up. Scientists don't get much chance to learn history. The history that they absorb is mainly from stories that appear in scientific writings, like the Mutationism Myth and the Essentialism Story, stories that represent Synthesis Historiography (Amundsen, 2005), the discipline of telling history in ways that make things turn out right for the Modern Synthesis. Synthesis Historiography teaches us that "saltationism" (Mayr's pejorative term for the Mendelian view) and other alternatives to neo-Darwinism are nonsensical, "doomed rivals", supported only by "typologists", creationists, vitalists and other crazies. That is, Synthesis Historiography teaches the TINA doctrine: There Is No Alternative.

As contemporary research drifts away from the "gene pool" theory and the Darwinian doctrines of the MS, each evolutionary biologist remains confident that, due to the TINA doctrine, his own view must be "neo-Darwinian". In reality, alternatives are being explored with increasing vigor in molecular evolution, evo-devo, and evolutionary genetics.

A few folks today are in the reverse situation of being familiar with MS orthodoxy, but not with recent research. Dawkins (2007) stakes his critique of a book by "intelligent design" creationist Michael Behe entirely on his faith in the gene pool theory. Behe claims, in effect, that there was not sufficient time for all the mutations needed to account for evolution. Dawkins responds by attacking the premise that evolutionary rates depend on mutation rates:

"If correct, Behe's calculations would at a stroke confound generations of mathematical geneticists, who have repeatedly shown that evolutionary rates are not limited by mutation. Single-handedly, Behe is taking on Ronald Fisher, Sewall Wright, J.B.S. Haldane, Theodosius Dobzhansky, Richard Lewontin, John Maynard Smith and hundreds of their talented co-workers and intellectual descendants. Notwithstanding the inconvenient existence of dogs, cabbages and pouter pigeons, the entire corpus of mathematical genetics, from 1930 to today, is flat wrong. Michael Behe, the disowned biochemist of Lehigh University, is the only one who has done his sums right. You think? The best way to find out is for Behe to submit a mathematical paper to The Journal of Theoretical Biology, say, or The American Naturalist, whose editors would send it to qualified referees."

With his signature over-the-top rhetoric, Dawkins insists that "mathematical genetics" has proven that evolutionary rates are not limited by mutation. Allowing for some exaggeration, this is an accurate representation of MS orthodoxy ca. 1959, the approximate vintage of Dawkins's views. If Mayr had been alive, he might have said the same thing.

Meanwhile, no one who has been active in evolutionary genetics research in the past 15 years would represent the current state of knowledge in this way. If you want to know what a contemporary researcher would say, take a look at the most recent issue of Evolution in which the article by Douglas Futuyma (famous for his evolution textbook) gives many examples of how evolutionists (including himself) repeated the doctrine that mutation does not "limit" evolution, but argues that we are no longer making this dubious assumption. Another example would be the piece by Ronny Woodruff and James Thompson (1998) that introduces their symposium volume on Mutation and Evolution.2

Yet the MS and its "gene pool" theory have left their mark on evolutionary biology, even if the MS itself has largely disappeared from the collective memory of researchers. One indelible mark is what Gillespie calls "The Great Obsession" of population genetics to understand the "maintenance of variation", but that's a story for another day.

Another indelible mark is the long absence of mutationist models of "adaptation", a topic that has blossomed just in the last dozen years. Allen Orr has achieved well deserved fame for his innovations in this area, and we'll discuss his work briefly in the next section. For now, let us note how other researchers have pointed out the absence of such models:

"Almost every theoretical model in population genetics can be classified into one of two major types. In one type of model, mutations with stipulated selective effects are assumed to be present in the population as an initial condition . . . The second major type of models does allow mutations to occur at random intervals of time, but the mutations are assumed to be selectively neutral or nearly neutral." (Hartl & Taubes, 1998)

"The process of adaptation occurs on two timescales. In the short term, natural selection merely sorts the variation already present in a population, whereas in the longer term genotypes quite different from any that were initially present evolve through the cumulation of new mutations. The first process is described by the mathematical theory of population genetics. However, this theory begins by defining a fixed set of genotypes and cannot provide a satisfactory analysis of the second process because it does not permit any genuinely new type to arise. " (Yedid and Bell, 2002)

These authors are not trying to make a point about history or about the Modern Synthesis: they are simply claiming the novelty of their own models of adaptation that incorporate new mutations. And what they are saying is that the paradigm of 20th-century population genetics is "shifting gene frequencies": overwhelmingly, it's a body of theory about what happens to the variation that is present in a population as an initial condition, not about a larger-scale process in which there are new beneficial mutations.3

One small step for a phage, one giant leap for evolutionary biology

The actual role of mutation in evolution is not what is theorized in the MS. Many arguments could be made to support this contention, but I'm going to make just one argument drawing on one source, namely Rokyta, et al., 2005. I choose this argument because it is particularly compelling and concise. My argument addresses the lucky mutant view of initiative or (to put it another way) dynamics.

Rokyta, et al. is a study of parallel evolution in an experimental population of the bacteriophage phiX174, published in Nature Genetics. It was hailed as "the first empirical test of an evolutionary theory" (Bull & Otto, 2005), where the theory in question is Orr's (2002) ingenious extension of Gillespie's (1984) "mutational landscape" model to take into account predictions of extreme value theory.4

In spite of the fancy name, the "mutational landscape" model of sequence evolution is simple. Rather than considering all conceivable evolutionary changes from a starting sequence, we simplify the problem by considering only changes that occur via 1-bp mutations. That set of possibilities, by definition, is the "mutational landscape" or (my preferred term) the "evolutionary horizon". Each change will shift the evolutionary horizon, but it's easy to recompute the horizon, because it's easy to enumerate (theoretically) all the alternative sequences.

We are going to make this a model of beneficial changes ("adaptation"). A beneficial mutation is introduced into the population of N individuals at some total rate Nu, and faces acceptance with a probability of 2s, based on the classic formula p = 2s for the probability of fixation of a new beneficial mutation.5 For beneficial substitution i with selection coefficient si, the probability6 is just Nu*2si. If we divide an individual Nu*2si by the sum of all such values on the horizon, we get a normalized probability: the probability that the next step in our evolving system is step i. The factor Nu*2 is the same for every step, so it cancels out: only the si values matter. To evolve our sequence, we just sample from this probability distribution of possible steps, then recompute the new evolutionary horizon in preparation for the next step. Easy! 7

From past experiments, Rokyta, et al. know which steps on the horizon are beneficial, and they even know the selection coefficients. They know that sometimes, the same evolutionary steps happen in parallel, in replicate phage populations. They can compare the observed pattern of parallel evolution with the pattern predicted from theory.

Now, the preceding description suggests something fascinating: the cutting edge of evolutionary genetics today, with papers that get published in Nature Genetics with commentaries, uses experimental systems to explore the "lucky mutant" view of parallel evolution.

But the story gets even better. Rokyta, et al actually reject Orr's model, in its original version. They find more parallel evolution than expected. Why? Because the model treats all mutation rates equally. Note above that we canceled out mutation rates on the grounds that they are all the same. But that's not realistic. Some mutations are more likely than others, and this will affect the rate at which they are introduced into the population and subjected to acceptance or rejection. The more heterogeneity in rates of mutation, the more parallel evolution. Rokyta, et al. found that if they revised the model to take into account transition:transversion bias (I think it's about 5-or 6-fold under the experimental conditions), then the predicted amount of parallelism matched the observed amount.

Just let that soak in for a moment. We have an experimental study and a precise model. Evolution in this model is characterized by origin-fixation dynamics, dependent on the rate of mutational introduction of new alleles, and on their probability of fixation. Both factors affect the outcome of evolution; both factors affect the chance of parallelism. The experimental study eliminates (statistically) a model that lacks mutational bias in the introduction of new alleles. Thus the study clearly illustrates the dual causation of evolutionary change, in regard to its dynamics.

Back to the future

The MS is wrong, and not in a small way: it's wrong because reality just looks too much like the antithesis of the MS, i.e., the mutationist view. For instance, as we found out in part 4, Vavilov (1922; see Stoltzfus, 2006) understood the dual causation of parallel evolution, including the role of parallel variation. By contrast, Mayr famously said that the search for homologous genes or homologous mutations was foolish.

This mistaken prediction is repeated ad nauseam in the evo-devo literature. If you have been following along, you now understand why Mayr would make such a prediction. The MS makes substantive claims about evolution, among which are the claim that, while mutation is ultimately necessary to keep the "gene pool" from drying up, selection doesn't need to wait for a new mutation, but draws together a multi-locus optimum from the abundance of raw materials in the gene pool; "evolution" is so far removed from the process of mutation, with so many complex dynamic processes interceding, that the outcome of evolution does not depend on specific events of mutation. If evolution really were like that, parallel mutation would be unimportant. That is, Mayr's prediction accurately reflects the logic of the MS. But as the Rokyta, et al study (and many others) show, the prediction is not fulfilled.

According to Dawkins, "the entire corpus of mathematical genetics" from 1930 to "today" (i.e., about 1959, for Dawkins) would be "flat wrong" if one accepts the premise that evolution depends on new mutations, or that it is limited by the mutation rate. While this view is not often defended, that isn't because it's Dawkins's own personal opinion. Dawkins is accurately characterizing a theory that makes substantive claims about the world, a theory that most of us have forgotten. One of these claims is that "evolution" can be represented mathematically as a process of shifting the frequencies of alleles already present in an initial population, without new mutation; sometimes this doctrine is invoked by saying that "macroevolution" can be extrapolated from "microevolution".

If evolution actually worked like this, then evolutionary change would not exhibit a dependence on the rate of mutation, and Dawkins would be right in his criticism of Behe. But this is wrong. In fact, the dependence is so sensitive that effects of only a few-fold are noticeable, as the Rokyta, et al study (and many others) shows.

I'm not going to mince words. The MS is wrong, and not in a small way: reality looks too much like the mutationist view that we (the scientific community) rejected when we bought into the MS. We need another theory1, perhaps several others.

The road less traveled

What's wrong about the MS, and what its replacement(s) must replace, is its theory of the role of variation in evolution. In future posts on the Curious Disconnect, I intend to focus on this issue. The Mutationism Myth suggests a lesson about how to develop (or rather, how not to develop) a theory of variation.

Darwin knew that hereditary variation played a vital role in evolution. He studied the subject intensely. He found that organisms vary in many different ways, and on many scales, but the evidence on heredity was bewildering and inconclusive. Lacking the means to derive a mechanism of evolution by reasoning upward from genetics, Darwin reasoned downwards from his premises that 1) organisms are exquisitely and pervasively adapted to their niches, 2) selection must have played some role in this, and 3) Mother Nature never makes a jump. Gould argues that Darwin's willingness to posit precise restrictions on variation was a stroke of genius.8 Darwin knew that discrete "sports" (mutants) could be heritable, but he discounted them: they could not make his theory work as desired. Instead, he staked his "natural selection" theory on the heritability of fluctuations, because they were infinitesimal, indefinite (unbiased), and "everywhere present", being induced in abundance whenever organisms encountered altered "conditions of life". Inferring the heritability of fluctuations completed his theory and made it work.

But it was wrong: the fluctuations that made Darwin's theory work are non-heritable, as the Mendelians discovered.

The architects of the MS tried again, with advantages unavailable to Darwin. Not only did they know genetics, they had some mathematical tools to work out unforeseeable implications of genetic concepts. However, they didn't have the knowledge to distinguish among different, genetically consistent modes of evolution. They had to fill in this gap somehow. Their downwards Darwinian reasoning and their upwards Mendelian reasoning met in the middle with the "gene pool": a theory of population genetics that would supply abundant, infinitesimal, "random" variations, in order to rationalize their commitment to the same premises Darwin accepted. That was the genius of the MS.

But again, it was wrong.

If we look at Darwinism in Popperian terms, as a theory1 that takes risks and generates potentially falsifiable claims, then (counterintuitively) it is largely a theory of the role of variation in evolution. The claims that selection is "important", and that it has some inalienable role in adaptation, carry little risk and have been widely accepted for 150 years. By contrast, the restrictions that Darwinism places on variation, in order to make it a subordinate factor that supplies "raw material" to selection, are risky and controversial, e.g., the claim that variation is random with respect to the direction of evolution, or that the rate of evolution does not depend on the rate of mutation, or the "gradualist" claim that variation is not a source of discontinuity. The architects of the MS invested the "gene pool" with nearly magical properties in order to improve the prospects for adaptation. Problematic claims about the role of variation are, and have been for 150 years, the overwhelming basis for scientific criticism of Darwinism.

And this problematic view of variation is based on reasoning from the premise that organisms are exquisitely and pervasively adapted to their niches, to the conclusion that variation must play just the right role of supplying abundant raw materials to make this possible. I believe that there is something fundamentally wrong with this mode of reasoning. Perhaps it betrays a kind of subconscious Panglossian agenda. Every time I give a lecture on mutation-biased evolution, someone suggests that perhaps the mutation biases themselves are adaptive, as though this inference could restore one's faith that everything turns out for the best, and that "the ultimate source of explanation in biology is the principle of natural selection" (Ayala, 1970). Remarkably, the evo-devo-inspired view that seems destined for inclusion in the emerging "Extended Synthesis" is headed down much the same path, with a focus on the idea that the process of variation has been jiggered to make things turn out right for adaptation. What's revealing about this new view is how little attention its proponents have paid to understanding precisely, in terms of population-genetic causation, how the process of variation shapes evolution, before jumping ahead to the shadowy inference that the process of variation itself was shaped by selection for this very role.

We are not going to go down that same road here on the Curious Disconnect, which should make things all the more interesting.

References

Ayala, F. J. 1970. Teleological Explanations in Evolutionary Biology. Philosophy of Science 37:1-15.

Bull, J. J., and S. P. Otto. 2005. The first steps in adaptive evolution. Nat Genet 37:342-343.

Charlesworth, B., and D. Charlesworth. 2009. Darwin and genetics. Genetics 183:757-766.

Dawkins, R. 2007. Review: The Edge of Evolution. Pp. 2. International Herald Tribune, Paris.

Gould, S. J. 2002. The Structure of Evolutionary Theory. Harvard University Press, Cambridge, Massachusetts.

Hartl, D. L., and C. H. Taubes. 1998. Towards a theory of evolutionary adaptation. Genetica 103:525-533.

Medawar, P. B. 1967. The Art of the Soluble. Methuen and Co., London.

Nei, M. 2007. The new mutation theory of phenotypic evolution. Proc Natl Acad Sci U S A 104:12235-12242.

Orr, H. A. 2002. The population genetics of adaptation: the adaptation of DNA sequences. Evolution Int J Org Evolution 56:1317-1330.

Phillips, P.C. 1996. Waiting for a compensatory mutation: phase zero of the shifting-balance process. Genetical Research, Cambridge 67:271-283.

Rokyta, D. R., P. Joyce, S. B. Caudle, and H. A. Wichman. 2005. An empirical test of the mutational landscape model of adaptation using a single-stranded DNA virus. Nat Genet 37:441-444.

Woodruff, R. C., and J. D. Thompson. 1998. Preface in R. C. Woodruff, and J. D. Thompson, eds. Mutation and Evolution. Kluwer, Dordrecht, The Netherlands.

Yedid, G., and G. Bell. 2002. Macroevolution simulated with autonomously replicating computer programs. Nature 420:810-812.


Notes

1 Pigliucci, along with Gerd Muller, edited a book on "the extended Synthesis" with papers from a select group of thinkers who were invited in July, 2008 to a special meeting in Altenberg, Austria. The book is now available in paperback: http://www.amazon.com/Evolution-Extended-Synthesis-Massimo-Pigliucci/dp/0262513676

2 from p. 1 "Although mutation is a key parameter in the genetics of populations, the role of mutation as an evolutionary factor has been debated since the time of Darwin. Early geneticists, who held to the 'classical' view of the genome as being homogeneous with occasional mutant alleles, saw new mutation as a major determining force in adaptive change. When the classical view was replaced with the 'balance' view of the genome, i.e., highly heterogeneous, pre-existing variation became more important as the resource on which selection would act. Many, therefore, began to disregard new mutation as a significant force in evolution, since the level of genetic diversity is already so high that new mutants would generally be expected to add little to that resource . . . Mechanisms responsible for maintaining levels of genetic diversity became the focus of attention, and mutation pressure is now thought by many to have only minor significance, especially when compared to selection, recombination, gene flow, and similar factors. We think this position, like the classical view, is too extreme. While there can be little doubt that mutation per se is not the principle driving force it was once believed to be for phenotypic evolution, we see growing evidence that its role is under-appreciated in important situations. The rate and pattern of mutation can be influenctial variables in adaptive responses, and the role of mutation in evolution deserves to be reexamined."

3 Orr (2002) notes the absence of such models by making a far more sweeping claim that population genetics has ignored, not just new-mutations models of adaptation, but all models of adaptation, and instead has focused on neutral and deleterious alleles. That is an odd thing to say, given that the quantitative genetics of adaptation have been a topic for a long time. In any case, here is what Orr says: "Evolutionary biologists are nearly unanimous in thinking that adaptation by natural selection explains most phenotypic evolution within species as well as most morphological, physiological, and behavioral differences between species. But until recently, the mathematical theory of population genetics has had suprisingly little to say about adaptation. Instead, population genetics has, for both historical and technical resasons, focussed on the fates of neutral and deleterious alleles. The result is a curious disconnect between the verbal theory that sits at the heart of neo-Darwinism and the mathematical content of most evolutionary genetics. "

4 Also known as the theory of records—"record" in the sense of "pinnacle of achievement". Given a series of records, such as the world record in the long-jump, what's the interval of time to the next record, and by how much will it break the previous record? The theory of records addresses such questions. Can you see how this would be useful to make a predictive theory of adaptation?

5 Rokyta, et al. used a different formula for the probability of fixation, because the classic approximation only works for s << 1, whereas the phiX174 populations experience very large s, sometimes s > 1.

6 Formally Nu*2si is not a probability but a steady-state rate (e.g., for an infinite-alleles model). If we treat it as an instantaneous rate, and then compare it to all other instantaneous rates, this makes it a relative probability of choosing step i over a short interval.

7 For our present purposes, we don't need to explain Orr's addition to this model, which was a theory of the distribution of the favorable s values under generalized assumptions (oddly, the commentators on Rokyta, et al. did not mention that Orr's theory wasn't really needed, and that the study really was a test of the mutational landscape model itself).

8 Gould (2002, p. 140) is not endorsing Darwin's error about fluctuation. Darwin's followers think of that mistake as a trivial detail. Instead Gould is endorsing a more general inference. Here is what he writes. "Darwin reasoned that natural selection can only play such a role [as exclusive source of creativity and direction] if evolution obeys two crucial conditions: (1) if nothing about the provision of raw materials—that is, the sources of variation—imparts direction to evolutionary change; and (2) if change occurs by a long and insensible series of intermediary steps, each superintended by natural selection—so that "creativity" or "direction" can arise by the summation of increments.


Under these provisos, variation becomes raw material only—an isotropic sphere of potential about the modal form of a species. Natural selection, by superintending the differential preservation of a biased region from this sphere in each generation, and by summing up (over countless repetitions) the tiny changes thus produced in each episode, can manufacture substantial, directional change. What else but natural selection could be called 'creative,' or direction-giving, in such a process? As long as variation only supplies raw material; as long as change accretes in an insensibly gradual manner; and as long as the reproductive advantages of certain individuals provide the statistical source of change; then natural selection must be construed as the directional cause of evolutionary modification.


These conditions are stringent; and they cannot be construed as vague, unconstraining, or too far in the distance to matter. In fact, I would argue that the single most brilliant (and daring) stroke in Darwin's entire theory lay in his willingness to assert a set of precise and stringent requirements for variation—all in complete ignorance of the mechanics of heredity. Darwin understood that if any of these claims failed, natural selection could not be a creative force, and the theory of natural selection would collapse. "



Credits: The Curious Disconnect is the blog of evolutionary biologist Arlin Stoltzfus, available at www.molevol.org/cdblog. An updated version of the post below will be maintained at www.molevol.org/cdblog/mutationism_myth6 (Arlin Stoltzfus, ©2010)


Sunday, August 29, 2010

Center for Inquiry Doublespeak

 
On August 27th, the Center for Inquiry USA issued a statement on the controversy surrounding the renovation of the Islamic Cultural Center in New York City [CFI Releases Statement in Response to the Proposed Islamic Religious Center in Lower Manhattan]. Here's the last paragraph.
CFI maintains that a mosque near Ground Zero, in and of itself, is no worse than a church, temple, or synagogue. It is undeniable that the 9/11 terrorists were inspired by their understanding of Islam, and that currently there are far more Islamic terrorists in the world than terrorists of other faiths, but the deeper threat confronting humanity is not confined to Islam. To the contrary, it is presented by all religions. Religious morality is based on faith and authority, with the authority often being a sacred text cobbled together long ago that readily lends itself to contradictory interpretations. The Bible and the Koran have been used to justify almost everything, from mass slaughter of those with other beliefs, to slavery, to oppression of women and gays and lesbians, to the throttling of scientific research—as evidenced by the recent halt to stem-cell research. Faith will continue to harm and kill, whether it is in Oklahoma City or New York City, until people stop basing their conduct on imaginary divine commands and accept their responsibility to reason together. To honor those killed by faith fanatics, Ground Zero and its immediate vicinity should be kept free of any newly constructed house of worship — of any religion.
This statement triggered a storm of controversy in the blogosphere. The main objection was that CFI is adopting an anti-religious stance that sounds intolerant. I agree.

I'm a proud member of the Centre for Inquiry Canada but I'm less than pleased with the American version. The people speaking and writing for CFI USA don't speak for me. This included Paul Kurtz, founder of CFI, before he was ousted.

CFI USA soon realized they had goofed. Today they sent out a revised statement [CFI Releases a Clarification and Revision of Statement on Ground Zero Controversy]. Here's the last paragraph of today's (August 29th) statement.
CFI’s unequivocal support for the legal right of Muslims to place a community center near Ground Zero does not imply that CFI views the new center as an event to be celebrated. To the contrary, CFI is committed to the position that reason and science, not faith, are needed to address and resolve humanity’s problems. All religions share a fundamental flaw: they reflect a mistaken understanding of reality. On balance, CFI does not consider houses of worship to be beneficial to humanity, whether they are built at Ground Zero or elsewhere.
Yeah, right. It's better but it's still silly. I look forward to a time when nobody wants to built houses of worship but until that time they are free to build them wherever they want, as far as I'm concerned. The "revised" (i.e. backpedeling) statement is better but it still sounds like CFI USA is against building of houses of worship when they should be advocating rationality and skepticism.

I wish there was a way to give up my membership in the international organization but retain my membership in the Centre for Inquiry Canada.


Saturday, August 28, 2010

The Scientific Method

 
Over at Respectful Insolence, Orac picked up on a comment by Dr. R.W. and said [Some excellent questions for medical reporters] ....
An excellent idea, and Dr. R.W. has a list of some things that every medical journalist should know. My favorites? These:
  • Outline the scientific method. (I'm betting there are a lot of journalists out there reporting on medicine who can't outline the scientific method.)
  • Explain why consideration of biologic plausibility is important in the evaluation of health claims and why evidence based medicine often fails when biologic plausibility is not taken into account. (This one is hard, but knowing the answer would eliminate a lot of truly ignorant articles like the one Parker-Pope wrote yesterday.)
I was surprised that Orac picked teaching the scientific method as one of his favorites. I don't think there's any such thing as a "scientifc method" that garners majority support among scientists and/or philosophers. This led to a discussion in the comments section of his post.

What do you think? Is there a "scientific method"? If so, what is it?


Wednesday, August 25, 2010

Bated Breath

 
Jonathan Wells made an announcement that sets my heart all aflutter. I just can't wait for his new book to appear Zombie Genes?.
Richard Dawkins, Douglas Futuyma, Michael Shermer, Philip Kitcher, Kenneth Miller, Jerry Coyne and John Avise have also written recent books in which they argue that much of the human genome consists of "junk DNA" that provides evidence for Darwinian evolution--and evidence against intelligent design.

But the notion of "junk DNA" owes more to the historical contortions of neo-Darwinian theory than to biological evidence. In fact, there is now a large and growing body of evidence that Collins, Dawkins, Futuyma, Shermer, Kitcher, Miller, Coyne and Avise are dead wrong on this point--as I will show in my forthcoming book, The Myth of Junk DNA.
I teach a course that analyzes the "science" behind Intelligent Design Creationism and the book we use is Icons of Evolution. Problem is, the students have already written over 100 essays on this book and there's little more they can say. The book has been thoroughly trashed.

Next year we'll have an entirely new Jonathan Wells book to kick around. Yeah!


[Photo Credit: Jonathan Wells from Conservapedia]

Tell Me Something I Don't Know

 
Chad Orzel is bored so he asked his readers to Tell him something he doesn't know. It's lot's of fun reading the comments on his blog so I though I'd ask for more.

Can you tell me something I don't know? I can assure you that there's plenty of opportunities.

Saturday, August 21, 2010

Six Professors

 
Chad Orzel thinks you can get a good undergraduate education in physics from only six different professors [How Many Physics Professors Does It Take?].

That got me thinking about how many professors our students need. It depends on which courses they take but a typical biochemistry student encounters lots more professors in their required biochemistry/molecular biology courses. How many? ....about 25-30!!!

Is that because biological sciences are so much harder than physics? :-)


You Can Skip This One

 
Some people are enamored with the idea of collecting blogs together into some kind of consortium. Several of these people, Anton Zuiker, Bora Zivkovic and Dave Munger, were so traumatized by the defections from ScienceBlogs they decided to create a new site bringing together all the science blog groups [scienceblogging].
Summer of 2010 saw a rapid reorganization of the science blogging community. Where once ScienceBlogs reigned as the most important network of science bloggers, in the wake of many noted bloggers’ departure from ScienceBlogs, a new ecosystem arose in which many different networks were founded, or grew, and became much more visible and prominent.

While the change from a system in which a single network dominates to a system in which many networks, aggregators, and services are somewhat equally represented is a positive one, leading to a healthier overall ecosystem, this development posed a new difficulty for readers: how to keep track of all of these networks and blogs?

There is now no one-stop-shopping place for a daily fill of science and culture – instead, there are dozens of such places. Thus a need arose to aggregate all these networks in a single web page as a starting point leading to all of the diverse places where science is discussed online.
Is your blog part of a "network"? Mine isn't. If you don't belong to a group of science bloggers then you don't count as far as scienceblogging is concerned. Isn't that strange?

Don't bother with scienceblogging unless you share their opinion that independent science blogs aren't worth reading.


Thursday, August 19, 2010

Sometimes School Trustees Make You Proud

 
In Ontario there's been a bit of a kerfflufle lately over WiFi in public schools. It started when some parents in a town north of here claimed that their kids were getting sick in school because of radiation from WiFi networks. One parent (Patricia Naylor) claimed the she and one of her children were very sensitive to radiation. She formed the "Safe School Committee" to lobby for a ban on WiFi.

The claims have received considerable media attention leading to the inevitable spread of the problem as more and more parents "recognize" that their children suffer from nausea and lethargy in school and it must be due to radiation. A group of teachers almost supported a ban on WiFi in response to these parents.

The latest round occurred at a conference of The Ontario Elementary Teachers Federation where they voted down a resolution banning WiFi [Teachers not joining Wi-Fi fight].

The money quote comes from a trustee ...
Collingwood/Clearview Trustee Caroline Smith said the board must balance free speech with science, education and access to technology.

"In this case, a very small group of people came forward and actually one person brought forward a concern. Normally a school board can say ‘thank you’ (and stop at that). We said thank you and asked staff to do additional research. We brought in a scientist," she said.

"We allowed a second series of deputations (including Naylor in April) to come forward and we listened again," she said, adding she then put forward a motion asking for the education and health ministers for advice.

"We want our children to have the most modern pathways to education. We don’t want to tie their hands (by not giving them access to the technology that’s available)," she said.

The board’s program committee chairman, Trustee Rob North called the Safe School Committee’s stance "bizarre" in a blog, and criticized the group for relying on studies by a botanist which have not been peer-reviewed.

"It’s time to shut this down, folks. Junk science simply cannot be allowed to influence public policy decisions. Wireless technology, installed and operated correctly, is perfectly safe. The World Health Organization, Industry Canada, Health Canada, the Ontario Ministry of Health and countless others who have access to people who are experts in the fields of biology, electrical engineering and so on have deemed it to be safe," said North.

"I can tolerate people’s eccentricities for a while. I can wait while people vent about perceived injustices for hours on end. I can sit by and let some folks try to salvage their long lost credibility for a bit. But at the end of the day, sometimes you just have to look people squarely in the eyes and tell them, ‘I’m sorry, you’re wrong.’"
Let's hope that puts an end to this silliness.


Wednesday, August 18, 2010

Socrates and His Method

 
Socrates (~469 BC - 399 BC) was a teacher in Athens. Most of what we know about him comes from the writings of his students and contemporaries. Let's assume that Plato's depiction of his methods are accurate.

Here's a brief description of the Socratic Method from Wikipedia,
The Socratic method (or Method of Elenchus or Socratic Debate), named after the Classical Greek philosopher Socrates, is a form of inquiry and debate between individuals with opposing viewpoints based on asking and answering questions to stimulate critical thinking and to illuminate ideas.[1] It is a dialectical method, often involving an oppositional discussion in which the defence of one point of view is pitted against the defence of another; one participant may lead another to contradict him in some way, strengthening the inquirer's own point. (Think about the question before you speak.)

The Socratic method is a negative method of hypothesis elimination, in that better hypotheses are found by steadily identifying and eliminating those that lead to contradictions. The Socratic method searches for general, commonly held truths that shape opinion, and scrutinizes them to determine their consistency with other beliefs. The basic form is a series of questions formulated as tests of logic and fact intended to help a person or group discover their beliefs about some topic, exploring the definitions or logoi (singular logos), seeking to characterize the general characteristics shared by various particular instances. To the extent to which this method is designed to bring out definitions implicit in the interlocutors' beliefs, or to help them further their understanding, it was called the method of maieutics. Aristotle attributed to Socrates the discovery of the method of definition and induction, which he regarded as the essence of the scientific method. Perhaps oddly, however, Aristotle also claimed that this method is not suitable for ethics.
The only good is knowledge and the only evil is ignorance.

—attributed to
    Socrates
Why is this relevant? It's relevant because we've been discussing university education and whether it can be replaced by surfing the net. Whenever we talk about university education I want you to imagine what it SHOULD be like and not what it IS like. Imagine that university education actually focused on critical thinking. Imagine that students could learn like the pupils of Socrates.

Raise your hand if you actually think that modern students of Socrates could learn just as much on the internet as they could by engaging in dialogue? Everyone with their hand in the air is part of the problem and not part of the solution to what's wrong with university education.



Tuesday, August 17, 2010

Are University Professors Ignorant Luddites?

 
Here's an interview with Don Tapscott where he tells us what's wrong with universities and why they need to become more student focused [The future of education: reboot required]. The main theme is that today's students are wise in the ways of the internet and that will force universities to change.
I think the net generation will be a key driver for change. They have the knowledge and tools to challenge the existing model, and I see a growing generational clash.

I also think some administrations will recognize that the writing is on the wall.

If students can pass a course by never attending class and watching the lectures online, why should the student be restricted to only those courses available at that university? If it's online, why not choose from the courses offered at other universities. I also see a lot of the old guard faculty retiring soon. That will help generate fresh thinking.
There are several issues in this debate. They need to be sorted and clarified. First, many of the "old guard" faculty are among those who are most upset with the current system. At my university, they are the ones who are advocating change. Younger faculty in science departments just don't care about undergraduate education. They have much more important things on their minds. The situation isn't much different in the humanities except that there's a somewhat higher percentage of younger faculty calling for change. Many of them are postmodernists and the changes they're advocating aren't necessarily desirable.

Who is Don Tapscott and why is he an expert on university education? Here's what Wikipedia says [Don Tapscott].
Don Tapscott (born 1947) is a Canadian business executive, author, consultant and speaker based in Toronto, Ontario, specializing in business strategy, organizational transformation and the role of technology in business and society. Tapscott is chairman of business strategy think tank New Paradigm (now nGenera Insight), which he founded in 1993. Tapscott is also Adjunct Professor of Management at the Joseph L. Rotman School of Management, University of Toronto.
This brings me to a second point that needs clarification. People whose main concern is business and management aren't necessarily qualified to have an informed opinion on university education. That includes 99% of the faculty at the Rotman School of Management, here at the University of Toronto.

The third point that needs to be made is that there is widespread agreement that current university education is in bad shape. It should not be possible to skip lectures and still get an "A" in a course. It should not be possible to graduate with a degree when you have never physically attended a university. The fact that we are doing a bad job of teaching students how to think does not mean that we should abandon that goal and make it even easier for students to avoid intellectual challenges. We need to fix the problem, not surrender.

The fourth point concerns technological change. Tapscott is apparently one of the true believers when it comes to the internet and how it's going to change everything. I think he's wrong but that's not the point I want to make. The thing that annoys me the most is the assumption that universities are behind the times when it comes to technological change and that professors are luddites who don't know anything about computers and the internet.

There may be professors like that, but not in science or engineering departments. I suspect that they're rare in the humanities as well. This may come as a bit of a shock to Don Tapscott but some of us old fogies have been using computers for over forty years. We've been on the internet for thirty years. We know about electronic databases, listserves, social networks, webpages, and blogs. Some of us even have cellphones, iPads, and GPS—and we know how to use them. We have HD televisions, stereo systems that will blow your socks off, laptops, and—believe it or not—power windows in our cars.

We've been incorporating these technologies into our courses for over two decades. (That's before our entering class of students was born.) Our children, and the current crop of students, may be the first generation to grow up with personal computers and the internet but when they come to university they will be meeting the generation that invented those technologies.

Give us a bit of credit. We've been experimenting with new technologies long enough to know how they are affecting university education. We are not stupid. If they were capable of totally transforming university education then we would have discovered that by now. Fact is, these technologies have been around for decades and, while they are very useful supplements to education, they are not a panacea and they cannot replace everything that happens on a university campus.

Students need to be provoked, challenged, and stimulated. They need to be thrust into an environment that's outside of their comfort zone. They need to hear things they don't want to hear, even if it makes them angry. They need to see for themselves what kind of scholarship goes on at a university. They need to do a research project and that requires a mentor.

They need to meet graduate students and postdocs and professors who aren't teaching one of their courses. They need to play varsity sports, join the debating team, attend meetings of the student Secular Alliance, meet students from different cultures, protest, volunteer at the local hostel, play in the school orchestra.

This is all part of a university education and you can't do it by sitting in your bedroom at home staring at your monitor.

The article on the CBC News site makes reference to two videos. I'm including them here in order to provoke discussion. The first one is a classic example of the kind of superficial thinking that passes for knowledge among today's generation of students. Although that's not its intent, it illustrates perfectly what's wrong with university education. There's no evidence of critical thinking. The students are holding up sound bites of meaningless phrases.

The second one is similar except that the students are much younger. It's an example of brainwashing. They are "digital learners"—but what the heck does that mean? It doesn't mean a damn thing.






Sunday, August 15, 2010

Learning About America

 
Jim Lippard posted this video on his blog [Gun-toting, Scientology-supporting, Bible-thumping, climate change-denying Pamela Gorman wants to be elected to Congress].

I lived in America for six years and I'm passionately interested in American politics and culture. But I don't think I'll ever understand America. If a commercial like this were ever shown in a Western European country, the candidate would be doomed. I'm not sure it would work even in Alberta or the conservative parts of Australia.



University vs Fundamentalist Christian

 
Timothy Larsen writes for Times Higher Education [Opinion: Stop turning the other cheek].
I had lunch this summer with a prospective graduate student at the evangelical college where I teach. I will call him John, because that happens to be his name. John has done well academically at a public university. Nevertheless, as often happens, he said that he was looking forward to coming to a Christian university, and then launched into a story of religious discrimination.

John had been a straight-A student until he enrolled in English writing. The assignment was an “opinion” piece and the required theme was “traditional marriage”. John is a Southern Baptist and he felt it was his duty to give his honest opinion and explain how it was grounded in his faith. The professor was annoyed that John claimed the support of the Bible for his views, scribbling in the margin, “Which Bible would that be?” On the very same page, John’s phrase, “Christians who read the Bible,” provoked the same retort, “Would that be the Aramaic Bible, the Greek Bible, or the Hebrew Bible?” (What could the point of this be? Did the professor want John to imagine that while the Greek text might support his view of traditional marriage, the Aramaic version did not?) The paper was rejected as a “sermon” and given an F, with the words “I reject your dogmatism” written at the bottom by way of explanation.
It's religious discrimination. John didn't get an "F" because he was incapable of presenting a rational argument. He failed because he's a Christian.

This is a serious problem for IDiots and fundamentalists. They are, for the most part, incapable of learning how to think without abandoning their dogmatic religious views. In an ideal world, that would make it very difficult to graduate from university while maintaining their faith. (Unless they can fake it by pretending to be tolerant and rational.)

Fortunately John has found the solution—he's going to an evangelical college for his graduate degree. Now he won't have to deal with the problem of being challenged to think rationally.


Thursday, August 12, 2010

AAAS Accommodationism

 
The American Association for the Advancement of Science (AAAS) sponsors a program called DoSER (Dialogue on Science, Ethics, and Religion). As you might imagine, it's basically a cover for presenting the accommodationist position. There's very little "dialogue" going on.

On June 16th they held a forum to honor the new director, Jennifer Wiseman, an astronomer, a Christian, and a member of the American Scientific Affiliation. In order to belong to this group you must agree to the following statement ...
I believe in the whole Bible as originally given, to be the inspired word of God, the only unerring guide to faith and conduct. Since God is the Author of this Book, as well as the Creator and sustainer of the physical world about us, I cannot conceive of discrepancies between statements in the Bible and the real facts of science.
William Phillips was awarded the 1997 Nobel Prize in Physics. Here's his talk from the June 16th meeting.



The main theme is civility. A good example of civility is when Phillips accuses New Atheist of saying that Francis Collins was unfit to be director of NIH solely because he believes in God. Like many accommodationists, Phillips is confused about the difference between civility and dialogue. If you oppose religion, then you are uncivil. If you are religious, then you can say anything you damn well please about atheists without being uncivil, as long as you say it with a gentle, soothing, voice.


Stephen Meyer Explains the Origin of Information

 
Intelligent Design Creationism is struggling to maintain scientific credibility. The movement claims to be scientific, not religious, and it's strongest defense is that it offers credible scientific explanations of biological phenomena.

Most of us don't see it that way. All we see is a bunch of people who attack science in general and evolution in particular. They publish lots and lots of stuff that raises questions about standard scientific explanations—some of the criticisms are valid but most are nothing more than wishful thinking. What we never, ever, see is a true explanation of how intelligent design creationism actually works.

This video was published on the Evolution News & Views (sic) blog [Stephen Meyer on Intelligent Design: What is the origin of the digital information found in DNA?]. Watch it to see if Meyer1 explains the origin of information according to the Intelligent Design Creationism Model. Wait right 'till the end to make sure you don't miss the explanation of how an intelligent creator put information into DNA. Learn who the creators(s) is/are and why they did it. Find out when she did it. Wait to see how this accounts for life as we know it today.

Folks, this is the best they have to offer. It's why we call them IDiots. There's nothing there but obtuse rhetoric about the origin of life and information. They have nothing to offer but criticism of evolution.



1. Stephen Meyer is one of the founders of the Discovery Institute in Seattle. He has a Ph.D. in the History and Philosophy of Science from Cambridge University (UK).

Tuesday, August 10, 2010

The Death of Universities

 
Bill Gates thinks that universities are about to become obsolete [Bill Gates: In Five Years The Best Education Will Come From The Web].
"Five years from now on the web for free you’ll be able to find the best lectures in the world," Gates said at the Techonomy conference in Lake Tahoe, CA today. "It will be better than any single university," he continued.
This is nonsense on many levels. First, who's going to determine whether any given lecture is the "best lecture in the world?" Second, why will it be online? (Most professors don't want to put their lectures online.) Third, who says that listening to a lecture is the only thing that a university has to offer?
One particular problem with the education system according to Gates is text books. Even in grade schools, they can be 300 pages for a book about math. "They’re giant, intimidating books," he said. "I look at them and think: what on Earth is in there?"

According to Gates, our text books are three times longer than the equivalents in Asia. And yet they’re beating us in many ways with education. The problem is that these things are built by committee, and more things are simply added on top of what’s already in there.
In the interests of full disclosure, I am a textbook author. That means I have more of a stake in this debate than Bill Gates. (Of course, it also means that as a textbook author and a university professor, I'm probably more of an expert than the former chairman of a software company.(1))

When they are well done, a textbook is like the best lecture you could ever get. If you want to learn about evolution, for example, then you could hardly do better than reading EVOLUTION by Douglas Futuyma. I can't imagine any series of online lectures that could compete with a such a good textbook.

Textbooks are collaborative affairs that undergo considerable review by experts before publication. Most online lectures are the work of a single individual and they have not been reviewed for accuracy.

The most important goal of a university education is to teach student how to think and a major component of that process is critical thinking. Unfortunately, sitting in front of your monitor reading a lecture is not the best way to learn how to think and it doesn't give you any practice in critical thinking. There's a reason why students need to interact with other students and scholars in a university setting and it's very sad that people like Bill Gates don't get it.

On the other hand, if Gates is correct then it might be a really good thing for universities. The standing joke among professors is that universities would be wonderful places if only we could get rid of the students!


John Hawks seems to be quite sympathetic to the Gates stupidity [Bubbling through college].

1. How did we ever get ourselves into the situation where executives from for-profit companies are thought to be experts on education? They are not. They are just about the last people on Earth I would ask for advice on university education.