Lyon, France

 
I'm in Lyon for the evolution meeting and this was our day to see the city. We haven't been here for over 30 years.

I love European cities. They are simultaneously more modern and more ancient than cities in Canada and the USA. I love the cafes and bistros and I love the old buildings and the history.

Lyon was an ancient hill top Celtic fort when it was captured by the Romans in 43 BC. Under the Romans it grew rapidly on the hill overlooking the Rhône and Saône rivers. Lugdunum, the Roman city, was the capital of Gaul and its most important city.

Here's an example of a bistro from Pixdaus.


And here's a photo taken today by Ms. Sandwalk. This is the Roman amphitheater built in about 15AD under the reign of Augustus. Today it's known as Théâtres Romains de Fourvièreand it's still in use as an outdoor theater, although part of it is in ruins and the capacity is much less than it was 1800 years ago after it was expanded.


Tomorrow we're going to the flea market.

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Evolutionary Psychology as Maladapted Psychology

I just bought Evolutionary Psychology as Maladapted Psychology by Robert C. Richardson ($13 CDN). I couldn't resist after reading the blurb.

Human beings, like other organisms, are the products of evolution. Like other organisms, we exhibit traits that are the product of natural selection. Our psychological capacities are evolved traits as much as are our gait and posture. This much few would dispute. Evolutionary psychology goes further than this, claiming that our psychological traits—including a wide variety of traits, from mate preference and jealousy to language and reason—can be understood as specific adaptations to ancestral Pleistocene conditions. In Evolutionary Psychology as Maladapted Psychology, Robert Richardson takes a critical look at evolutionary psychology by subjecting its ambitious and controversial claims to the same sorts of methodological and evidential constraints that are broadly accepted within evolutionary biology.

The claims of evolutionary psychology may pass muster as psychology; but what are their evolutionary credentials? Richardson considers three ways adaptive hypotheses can be evaluated, using examples from the biological literature to illustrate what sorts of evidence and methodology would be necessary to establish specific evolutionary and adaptive explanations of human psychological traits. He shows that existing explanations within evolutionary psychology fall woefully short of accepted biological standards. The theories offered by evolutionary psychologists may identify traits that are, or were, beneficial to humans. But gauged by biological standards, there is inadequate evidence: evolutionary psychologists are largely silent on the evolutionary evidence relevant to assessing their claims, including such matters as variation in ancestral populations, heritability, and the advantage offered to our ancestors. As evolutionary claims they are unsubstantiated. Evolutionary psychology, Richardson concludes, may offer a program of research, but it lacks the kind of evidence that is generally expected within evolutionary biology. It is speculation rather than sound science—and we should treat its claims with skepticism.

Thanks to Denyse O'Leary for finding this book [Evolutionary psychology racket alert: Serious news, not just more embarrassment for science]. This is one issue that we agree on.

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The Dunning-Kruger Effect

 
Bora alerted me to something called the Dunning_Kruger Effect. Here's the Wikipedia definition and description [Dunning–Kruger effect].

The Dunning–Kruger effect is a cognitive bias in which "people reach erroneous conclusions and make unfortunate choices but their incompetence robs them of the metacognitive ability to realize it."[1] The unskilled therefore suffer from illusory superiority, rating their own ability as above average, much higher than it actually is, while the highly skilled underrate their abilities, suffering from illusory inferiority. This leads to the perverse situation in which less competent people rate their own ability higher than more competent people. It also explains why actual competence may weaken self-confidence: because competent individuals falsely assume that others have an equivalent understanding.

...

The phenomenon was demonstrated in a series of experiments performed by Justin Kruger and David Dunning, then both of Cornell University.[1][4] However, the phenomenon had been assumed by many philosophers for nearly a century prior to Kruger and Dunning's study (see Russell quote above).

Kruger and Dunning noted a number of previous studies which tend to suggest that in skills as diverse as reading comprehension, operating a motor vehicle, and playing chess or tennis, "ignorance more frequently begets confidence than does knowledge" (as Charles Darwin put it).[5] They hypothesized that with a typical skill which humans may possess in greater or lesser degree:

1. Incompetent individuals tend to overestimate their own level of skill.
2. Incompetent individuals fail to recognize genuine skill in others.
3. Incompetent individuals fail to recognize the extremity of their inadequacy.
4. If they can be trained to substantially improve their own skill level, these individuals can recognize and acknowledge their own previous lack of skill.

That last point is interesting. Perhaps we should focus our attention on teaching Intelligent Design Creationists about evolution? It's worth a try.

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The Mutationism Myth, V: The response to Mendelian heterodoxies

This is the seventh 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.

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.

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Deconstructing The Mutationism Myth erodes the conventional wisdom about the early Mendelians, and also exposes the incompatibility with genetics that led the Mendelians to reject Darwin's theory. As we will see today on the Curious Disconnect (credits), unraveling the Mutationism Myth also puts the Modern Synthesis in a new light.

The Mutationism Myth, part 5. The Restoration

In the Mutationism Myth (see part 1), the Modern Synthesis (MS) rescues evolutionary biology from the Mendelian heresy, by showing that genetics is consistent with selection. In reality, the Mendelians had already synthesized genetics and selection (part 3), but rejected Darwin's errant views of heredity (part 2) and rejected, to varying degrees, the Darwinian doctrines that subordinated the role of variation so as to render selection the ruling principle in evolution. How, then, did the Modern Synthesis restore Darwinism?

The response to Mendelian heterodoxies

As recounted previously (part 4), the Mendelians recognized mutation as a source of discontinuity, initiative, direction and creativity in evolution. In this section, we will look at the MS (Modern Synthesis) as a Darwinian response to these Mendelian heterodoxies ¹.

Initiative

Darwin knew that spontaneously arising "sports" (mutants) occurred in nature, but denied them any meaningful role in evolution. Hereditary fluctuation, induced by altered "conditions of life", would produce subtle variations in bulk, providing suitable material for selection. Evolution, in this view, is a process of automatic adjustment to altered "conditions of life".

The Mendelians frequently invoked a quite different view of evolution as a causal sequence initiated by a new mutation. This made the impetus for change internal rather than external, and suggested that, to understand evolution, it would be important to understand the rates and propensities of mutations.

The architects of the MS rejected this view and asserted that evolution begins, not with a new mutation, but with the abundance of variation in the "gene pool"

"evolution is not primarily a genetic event. Mutation merely supplies the gene pool with genetic variation; it is selection that induces evolutionary change" (Mayr 1963, p. 613).

Rates and propensities of mutation are rendered irrelevant, because the "gene pool" serves as a dynamic buffer that insulates evolution from mutational effects:

"mutations are rarely if ever the direct source of variation upon which evolutionary change is based. Instead, they replenish the supply of variability in the gene pool . . . . Consequently, we should not expect to find any relationship between rate of mutation and rate of evolution. There is no evidence that such a relationship exists." (Stebbins, 1966, p. 29)

"The large number of variants arising in each generation by mutation represents only a small fraction of the total amount of genetic variability present in natural populations. ... It follows that rates of evolution are not likely to be closely correlated with rates of mutation. Besides mutation, natural selection and migration help maintain high levels of genetic variation in natural populations. Even if mutation rates would increase by a factor of 10, newly introduced mutations would represent only a very small fraction of the variation present at any one time in populations of outcrossing, sexually reproducing organisms." (Dobzhansky, et al., 1977, p. 72) ²

"Those authors who thought that mutations alone supplied the variability on which selection can act, often called natural selection a chance theory. They said that evolution had to wait for the lucky accident of a favorable mutation before natural selection could become active. This is now known to be completely wrong. Recombination provides in every generation abundant variation on which the selection of the relatively better adapted members of a population can work." (Mayr, 1994, p. 38)

Thus, Darwin's view of a process initiated by a change in conditions is restored: the source of initiative is not the occurrence of mutations, which are individually insignificant (Dobzhansky et al. 1977, p. 72) and merely "replenish the supply of variability in the gene pool" (Stebbins 1966, p. 29), but the change in conditions that brings on selection of variation already present (e.g., Dobzhansky 1955, p. 282; Dobzhansky et al. 1977, p. 6; e.g., Stebbins 1982, p. 160).

Infinitesimalism ("gradualism")

Darwin believed that evolution always proceeds by "infinitesimal" or "insensible" steps, and he stated this clear commitment in various ways, e.g., he said that "Natural selection can act only by the preservation and accumulation of infinitesimally small inherited modifications" (Origin of Species, Ch. 4) and that

If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. (Darwin, Ch. 6, Origin)

The "saltationist" alternative typically offered to this doctrine, as stated by Huxley in his 1860 review of the Origin of Species (online source), is merely that evolution takes some jumps:

Mr. Darwin's position might, we think, have been even stronger than it is if he had not embarrassed himself with the aphorism, "Natura non facit saltum," which turns up so often in his pages. We believe, as we have said above, that Nature does make jumps now and then, and a recognition of the fact is of no small importance in disposing of many minor objections to the doctrine of transmutation.

As we found out in part 4, the Mendelians sided with Huxley on this issue, and did not share Darwin's commitment to infinitesimalism.

Fisher (1930) and Dobzhansky (1937) played a significant role in restoring a "Darwinian" view, at least superficially. Fisher argued on theoretical grounds that evolution was more likely to take place by arbitrarily small modifications. He considered the evolutionary prospects of a phenotypic form represented by a point located somewhere near a point in geometric space that represents a global fitness optimum. Under this condition, the chance that a shift in location will be beneficial approaches an upper limit of 50 % as the size of the shift becomes arbitrarily small, i.e., infinitesimal. This argument was influential with MS authors in spite of the fact that the model was geometrical rather than biological (Orr and Coyne, 1992).

The architects of the MS developed a second line of argument based on the genetics of differences between species or sub-specific races, to the effect that the analysis of such differences showed a predominance of "small" or "slight" effects. Dobzhansky (1937) tied these arguments together:

"The high frequency of mutations producing small changes in the phenotype raises a strong presumption in favor of supposing that such mutations play a greater role in evolutionary processes than mutations with grosser effects. Fisher (1930) has given an interesting mathematical argument in favor of this view. These considerations agree very well with the results of the genetic analysis of the interracial and interspecific differences (Chapter III), showing these differences to be caused in a majority of cases by cooperation of numerous genes, each of which taken separately has only slight effects on the phenotype." (p. 26)

I think this aspect of the MS is familiar and uncontroversial, so I won't bore the reader with more quotations from original sources, several of which are given in the review by Orr and Coyne (1992). In general, the architects of the MS emphasized the importance of "slight" or "small" differences, and they claimed that this position was borne out by theoretical considerations, as well as by experimental studies.

Orr and Coyne took issue— rather audaciously— with the latter claim. They argue that the architects of the MS "seem to have based their support of micromutationism on almost no data at all", claiming that the studies reviewed by Dobzhansky above did not justify Dobzhansky's own stated conclusions.

Another interpretation of this apparent discrepancy is that Orr and Coyne are taking Darwin literally, while the MS architects did not.³ That is, the architects of the MS aligned themselves rhetorically with Darwin, and against the mythic saltationists-who-believe-in-evolution-by-large-jumps-without-selection. By doing so, they leveraged loyalty to the Darwin brand, but in reality, their scientific product was not the same as Darwin's. Darwin says that the fraction of saltations in evolution is zero, whereas Dobzhansky, in the passage quoted above, says merely that mutations producing "small changes" play a "greater role" than those with "grosser effects", and that evidence for this view is seen, not universally, but merely in "the majority of cases". Orr and Coyne (1992) conclude that large effects are common, which contradicts Darwin's extreme view but not the fuzzier claims made by MS advocates.

Creativity (novelty)

The Darwinian claim that natural selection is "creative" ⁴ was disputed initially (see Beatty, 2010) and continues to be questioned by critics (e.g., Kirschner and Gerhardt, 2005) and defended by Darwin's followers (e.g., Charlesworth, 2005).

The critics always make the same objection, namely that creativity resides somehow in the process of variation, which accounts for "the arrival of the fittest", rather than selection ("the survival of the fittest"), which merely decides what will live and what will die. The Mendelians, in particular, argued that the discovery of genetics had clarified the previously fuzzy line between selection and hereditary variation, which is not induced but arises spontaneously by mutation, making clear that, in Punnett's words, "the function of natural selection is selection and not creation" (see part 4).

The architects of the MS responded by renewing the claim for the creativity of selection. However, its also interesting to note that, early in the "Synthesis" period, some of the architects (to my knowledge, only Huxley and Dobzhansky) appeared to offer a compromise, to the effect that creativity was shared by selection and mutation, e.g., Huxley wrote that "Neither mutation nor selection alone is creative of anything important in evolution; but the two in conjunction are creative" (Huxley, 1942, p. 28).

The more prominent argument, which eventually became orthodox, was to attribute creativity to selection by depicting it as a craftsman or artist using "raw materials" supplied by variation. Gould (1977) has analyzed this pattern extensively, and I will simply repeat a passage that he offers in explanation:

"But why was natural selection compared to a composer by Dobzhansky; to a poet by Simpson; to a sculptor by Mayr; and to, of all people, Mr. Shakespeare by Julian Huxley? I won't defend the choice of metaphors, but I will uphold the intent, namely, to illustrate the essence of Darwinism— the creativity of natural selection. Natural selection has a place in all anti-Darwinian theories that I know. It is cast in a negative role as an executioner, a headsman for the unfit . . . The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies the raw material only. Natural selection directs the course of evolutionary change. It preserves favorable variants and builds fitness gradually. In fact, since artists fashion their creations from the raw material of notes, words, and stone, the metaphors do not strike me as inappropriate."

Dobzhansky also invokes the same "raw materials" metaphor, but in the context of a factory rather than an artist:

"the objection [that natural selection cannot be the guiding agent in evolution because it produces nothing new] became invalid in the light of modern biological knowledge . . .We should clearly distinguish the two basic evolutionary processes: that of the origin of the raw materials from which evolutionary changes can be constructed, and that of building and perfecting the organic form and function. Evolution can be compared to a factory: any factory needs a supply of raw materials to work with, but when the materials are available they must be transformed into a finished product by means of some manufacturing process. " (Dobzhansky, 1955, p. 131)

That is, selection is understood to be the builder or artist or manufacturing process, while mutation supplies "raw" materials. Note that Gould ultimately endorses the creativity claim precisely on the grounds that variation supplies raw material only. It might seem surprising that the metaphor of "raw materials" should play such an important role in evolutionary reasoning.

However, as we will learn later, metaphors are vital for causal reasoning, filling a gap that mathematics (which is not itself a language of causation) cannot cover. In the context of an argument about causation, to designate something as "raw material" is to reference the classic distinction ⁵ between material causes (stuff, material) and efficient causes (forces, agents). The architects of the MS had a theory of "forces", and they believed that population genetics had proven that mutation (variation), though it contributes stuff or material to evolution, is not an effective force. This claim is explained further below.

Directionality

Many authors have suggested that the essence of Darwin's "Natural Selection" theory is that evolution emerges by combining a random process of variation and a non-random process of selection, with selection directing the outcome, adding a previously absent component of direction:

"Darwin assumed in the Origin of Species that the evolution of living organisms depended on the origin of new forms which varied from old forms by continuous differences in no constant or predictable direction. Crossed together the new and the old showed blending inheritance. To these variations direction was given by a process of natural selection which, like artificial selection, preserved some while it destroyed others. A direction, an adaptive direction, was thus given to variations after they arose. This view was intended by Darwin to supplant the alternative view that direction was given to variations before they arose." (Darlington, 1958, p. 231)

"The idea that evolution comes about from the interaction of a stochastic and a directed process was the essence of Darwin's theory. The stochastic process that he invoked was the occurrence of small random variations which he supposed, provided the raw material for natural selection, a process directed by the requirements of the environment and one that builds up, step by step, changes that would be inconceivably improbable at a single step . . .The meaning of 'random' . . . is that the variations are, as a group, not correlated with the course subsequently taken by evolution (which is determined by selection)." (Wright, 1967, p. 117)

As noted in part 4, the Mendelians were ready to challenge this assumption, though their alternative view was not well developed. Some Mendelians noted that the repeated occurrence of a mutation improved its chance of being established in evolution (part 4), and that "in the deal out of mutations, the cards are stacked" (Shull, 1936). Vavilov (1922) applied this line of thinking at length in his explication of a possible role for parallel variations in parallel evolution.

The architects of the Modern Synthesis returned to the Darwinian view expressed in the statements of Wright and Darlington above. Frequently in MS writings, mutation is contrasted with selection and described as a "random" process. ⁶ In Mayr's 1980 reflection on the Modern Synthesis, he defines "Darwinism" as "the theory that selection is the only direction-giving factor in evolution." In the passage below, Dobzhansky refers to selection as "the directional force of evolution":

"Each unitary random variation is therefore of little consequence, and may be compared to random movements of molecules within a gas or liquid. Directional movements of air or water can be produced only by forces that act at a much broader level than the movements of individual molecules, e.g., differences in air pressure, which produce wind, or differences in slope, which produce stream currents. In an analogous fashion, the directional force of evolution, natural selection, acts on the basis of conditions existing at the broad level of the environment as it affects populations." (Dobzhansky, et al., 1977, p. 6)

Note that Dobzhansky uses an analogy with statistical physics to argue that selection's unique role is due to its status as a high-level "force", whereas a "random variation" is not a force, but is like the movement of a single particle.

Dobzhansky's comment suggests that the MS position on direction is tied to "gene pool" thinking. Indeed, in the passage below, Stebbins ⁷ makes clear that selection "directs evolution" by choosing from among the abundance of offerings in the "gene pool":

"Natural selection directs evolution not by accepting or rejecting mutations as they occur, but by sorting new adaptive combinations out of a gene pool of variability which has been built up through the combined action of mutation, gene recombination, and selection over many generations" (p. 31 Stebbins, 1966, Processes of Organic Evolution)

Finally, given this position, its not surprising that Vavilov's hypothesis about the role of parallel variation in parallel evolution was not taken seriously. Given the abundance of variation in the "gene pool", and the ability of selection to shape this gene pool to fit circumstances, it was not safe to assume that shared characters had a shared genetic basis, as Mayr (1963) argued in one of his more famous erroneous claims ⁸:

"In the early days of Mendelism there was much search for homologous genes that would account for such similarities. Much that has been learned about gene physiology makes it evident that the search for homologous genes is quite futile except in very close relatives (Dobzhansky, 1955). If there is only one efficient solution for a certain functional demand, very different gene complexes will come up with the same solution, no matter how different the pathway by which it is achieved." (p. 609)

Defining "forces" and re-defining "evolution"

The previous section suggested the central importance of the "gene pool" view, which argues that evolution begins, not with a new mutation, but with the abundance of variation "maintained" in the "gene pool". On the basis of this view, "evolution" was redefined so as to exclude the mutationist alternative:

"The theory of evolution by natural selection is a theory that relates the variation between individuals within a population to variation of populations in time and space. The theory amounts, in short, to the realization that intrapopulation variation is converted into spatial and temporal differentiation. The process of this conversion is the process of evolution." (Lewontin, 1965, p. 67)

That is, "the process of evolution" ("evolution by natural selection") literally does not include the introduction of new alleles, but instead corresponds to the sorting out of available variation.

Given that "evolution" (redefined) is all about "shifting gene frequencies", the causes of evolution may be presented as "pressures" or "forces" that shift frequencies. Lets suppose we have two alleles, A1 and A2, with frequencies f(A1) = f(A2) = 0.5. If A1 improves fitness relative to A2, then "selection" can be seen as a "force" that shifts its frequency over some period of time to f(A1) = 0.5 + d, and ultimately to fixation, f(A1) = 1. Likewise, there is some rate of mutation from A1 to A2, and another rate for the reverse pathway, and this rate can be understood to shift the relative frequencies to the point where f(A1) = 0.5 + d.

The key innovation in this view is its identification of mathematically continuous shifts in allele frequency as the common currency underlying a theory of causal agency. In classical physics, the displacement of a particle in continuous space (over continuous time) plays a similar role as the common currency of causal effects: multiple forces can cause such displacement, and their effects can be combined or decomposed. Likewise, in the MS, selection, drift, and mutation are identified as "forces" because they can cause shifts in frequencies.

Accordingly, the founders of population genetics looked at mutation as a "force" or "pressure" that, if powerful enough, could cause or "drive" evolution. From the mutation-selection balance equation and available data on mutation rates, Fisher (1930) and Haldane (1932) argue that, because mutation rates are so small, the opposing "force" of selection rules and mutation "pressure" cannot drive an allele to fixation. The conclusion of this "opposing pressures" argument ⁹ is that mutation is not an effective evolutionary force. Thus, in classical population-genetics modeling, its quite common to simply leave out mutation rates, on the grounds that they don't have substantial effects on the behavior of the model (e.g., as in the seminal analysis of 2-locus models by Lewontin & Kojima, 1960).

Having ruled out mutation as a "force", this left the idea of mutation as a source of "raw materials". That is, the architects of the MS looked at mutation in two ways, as a material cause, and as an efficient cause (agent, force). As just noted, the schematization of mutation as a "force" led to its rejection as an important "force", while its role as a material cause was addressed with the metaphor of "raw materials", as in several quotation given above, and in the following:

"The process of mutation supplies the raw materials of evolution, but the tempo of evolution is determined at the populational levels, by natural selection in conjunction with the ecology and the reproductive biology of the group of organisms" (Dobzhansky, 1955, p. 282)

"Mutation as an evolutionary force. In the early days of genetics it was believed that evolutionary trends are directed by mutation, or, as Dobzhansky (1959) recently phrased this view, 'that evolution is due to occasional lucky mutants which happen to be useful rather than harmful.' In contrast, it is held by contemporary geneticists that mutation pressure as such is of small immediate evolutionary consequence in sexual organisms, in view of the relatively far greater contribution of recombination and gene flow to the production of new genotypes and of the overwhelming role of selection in determining the change in the genetic composition of populations from generation to generation." (p. 101 of Mayr, 1963)

In this way, following the arguments of Fisher (1930), population genetics was believed to undermine any and all non-Darwinian theories of "evolution worked by mutation".

The keys to the kingdom

As we have seen, the restoration of "Darwinism" depended on several key innovations.

The first innovation was the change in attitude that inaugurated the process of redefining "Darwinism" that, for better or worse, continues today. For literally decades after the re-discovery of Mendelian genetics in 1900, the generality of Mendelian inheritance was disputed by biologists who, loyal to 19th century views of Darwin and Lamarck, reacted to genetics as though it must be some kind of misleading laboratory artefact, inapplicable in "nature".

Nevertheless, by 1930, Mendelian inheritance had been shown in a wide variety of macroscopic organisms, while experimental support for the hereditary laws of Darwin and Lamarck was trivial in comparison. The architects of the MS took Mendelian genetics as a given and simply ignored Darwin's laws of heredity, or treated them as an unimportant detail. In a sense, Darwin's followers had switched their allegiance from Darwin's specific theory₁ to a more abstract view, which we might call Darwinian selectionism, in which selection has a kind of causal pre-eminence, and all other issues are negotiable. Darwin's followers quietly backed away from his risky position of natura non facit salta, and ignored the fact that their new idea of the maintenance of abundant variation in the gene pool was not isomorphic with Darwin's concept of indefinite variability (hereditary fluctuation).

The second key innovation was this "gene pool". Even if one deletes from the Origin of Species all the details that are obviously contrary to genetics, the resulting view still makes strenuous and non-arbitrary demands on a theory of variation, as Gould (2002) persuasively argues. Regardless of any other mechanistic details, Darwinian selectionism (the pre-eminence of selection) demands that variation be "copious, undirected, and small in effect" (in Gould's formulation). Darwin's view of evolution as an automatic process of smooth adaptation to altered conditions seemed to require abundant, uniform, and infinitesimal variation, yet the new science of Mendelian genetics seemed to suggest the kind of rare, idiosyncratic, and discrete variants that Darwin rejected.

The key to reconciling the two— at least, rhetorically— is the notional "gene pool". According to an idea first articulated in 1926 by Chetverikov, every species has a "gene pool" that soaks up variation like a "sponge" (Chetverikov 1997), "maintaining" it for later use by selection, and ensuring an abundance of minute heritable variations in every trait, in every generation, as Darwin had conjectured. Thus, in Darwinism 1.0, fluctuation provides fuel "on demand" for selection, which is seen as the engine of evolution; in Darwinism 2.0, the engine has a tank of fuel, the "gene pool", that automagically keeps itself full. Though not equivalent, both views represent variation as merely an abundant source of fuel, with no influence on where evolution goes.

The crowning innovation of the Modern Synthesis was to invoke "population genetics" as a framework of causation that excluded all alternatives to Darwinism (redefined). Viewing evolution from a distance, as a paleontologist or systematist, one sees patterns that might be explained by various modes of evolution: Darwinian, Lamarckian, Buffonian, orthogenetic, saltational, and so on. While Darwinism seems to have been the dominant interpretation, the range of interpretations remained wide at the turn of the century when Mendelism burst onto the scene. While Mendelism revolutionized the evolutionary thinking of those who accepted it, most doubted its relevance to evolution. As late as 1930, one could read in the pages of Nature the view that "a gene is germ damage of which the outward manifestation is a mutation . . In my opinion, mutations and adaptations have nothing to do with one another" (MacBride, 1930).

The architects of the MS, following the original arguments of Fisher (1930), claimed that they could reduce evolution to a causal mechanism based on population genetics, and that this causal mechanism ruled out all modes of evolution but the "Darwinian" one. By the Origin of Species centennial in 1959, the architects of the MS had declared that the debate over evolutionary theory was over, and that they— and Darwin— had won. "Mutationism" came to be seen as discredited:

The genetic work of the last four decades has refuted mutationism (saltationism) so thoroughly that it is not necessary to repeat once more all the genetic evidence against it. (Mayr 1960, p. 355)

if ever it could have been thought that mutation is important in the control of evolution, it is impossible to think so now (Ford 1971, p. 361)

As late as 1932 T.H. Morgan was asserting that 'natural selection does not play the role of a creative principle in evolution', but ten years later all but a very few biologists were agreed on an evolutionary theory based firmly on Darwin's own ideas knitted with subsequent developments in genetics. (Berry 1982, p. 14)

for simplicity we speak of mutation as the first stage in the Darwinian process, natural selection as the second stage. But this is misleading if it suggests that natural selection hangs about waiting for a mutation which is then either rejected or snapped up and the waiting begins again. It could have been like that: natural selection of that kind would probably work, and maybe does work somewhere in the universe. But as a matter of fact on this planet it usually isn't like that. (Dawkins 1996, p. 87)

Looking ahead

Thanks for your forbearance in plowing through all of this history. Ultimately, though, we want to move on to other things. The Curious Disconnect is not a blog about scientific history: its about the current muddle in evolutionary thinking. I'm only explaining the history so that we can take a critical look at the MS and the view of causation that we have inherited from it.

Here is an example of what I mean. Rates of evolution, including adaptive evolution as in Rokyta, et al, 2005, are sensitively dependent on rates of mutation, directly contradicting the MS doctrine that the buffering capacity of the "gene pool" insulates evolution from mutational dynamics ¹⁰.

Because the MS is a coherent and integrated view (not just an extendible list of stuff that happens in evolution), and because reality is cohesive as well, fixing the failure of the MS to recognize this dependence is not an arbitrary or isolated error. We can't fix the MS by going through all the works of Mayr, Dobzhansky, Fisher, et al and 1) deleting every explicit claim that the rate or direction of evolution does not depend on mutation and 2) adding the words "And, we think the rate of evolution depends on the rate of mutation". That would not be enough.

For instance, the Gillespie-Orr "mutational landscape" model underlying the analysis of Rokyta, et al, which accounts for the aforementioned rate dependence, is based on a mutationist conception of evolution as a 2-step mutation-fixatioon process. The author of the model writes (Orr, 2003):

Adaptation is a two-step process: (i) alleles having different effects on fitness arise by mutation and (ii) those alleles that improve fitness tend to increase in frequency by natural selection.

thus directly contradicting what Dawkins says (above) about evolution "on this planet" (which, I suppose, raises a question about where Dawkins was when he wrote that statement).

Thus, the problem is not just the specific issue of a rate correlation, but its also the 2-step mutationist view.

To accomodate the observation that the rate of evolution depends sensitively on the rate of mutation, then, we would need to fix the MS view of causation, changing the common currency of causation so that an effect of biases in the origination process can be recognized ¹¹. In turn, to allow a bias in the origination process to affect "evolution" would require us to put the origination process back into "evolution", i.e., we would have to toss out the "shifting gene frequencies" definition. After that, we would have to delete all of the statements rejecting the 2-step "mutationist" view, including all the claims that "selection" never "waits" for a new mutation due to the magical maintenance of variation in the "gene pool". In addition, the effect of mutation biases violates the Darwinian and MS rule that variation is "random" in the sense that the tendencies of variation are unrelated to the realized direction of evolutionary change (this is the sense used in the quotation from Wright given above; see Beatty, 2010 for the analysis of Darwin's view).

The reason that so many changes would be required is that the exclusion of any important formative or directional role for mutation in the MS was not unforeseen or incidental, but utterly deliberate and essential. Real theories make commitments and take risks. Our analysis of the Mutationism Myth shows what these commitments were: the MS represents a commitment to the pre-eminence of selection and the subordination of variation, rejecting Mendelian ideas on mutation as a cause of discontinuity, initiative, creativity, and direction.

Because of this, its rather foolish to talk about "extending", "finishing", or "updating" the Modern Synthesis. We can't "revise" the MS to repudiate Mayr's understanding of evolutionary causation and endorse Morgan's mutationist view instead. To "revise" the MS in that way would be to repudiate the MS itself. Real theories make commitments and take risks. What's wrong about the Modern Synthesis is not a minor detail, but its essential and definitive subordination of the role of variation, and all that comes with it. The MS represents a wager, a bet, that reality would turn out to be a certain way. It didn't. The architects of the MS bet on the wrong horse. End of story.

So, its time to place a new bet, but on what? Just tossing out the MS will not give us that new theory of causation, the one that allows us to compare causal effects across different types of causes. With that, we might be able to address some of the big questions of evolution and confront contemporary challenges relating to "evo-devo". Our goal on the Curious Disconnect is to define issues like this, and to consider what are some of the possible bets. But thats getting ahead of ourselves.

Summary

Darwin's 20th-century followers responded to the Mendelian threat— which (at least partially) called for a stochastic, non-infinitesimal, mutation-driven view of evolution and adaptation— by developing the Modern Synthesis (aka "modern neo-Darwinism" or the "New Synthesis"), a new theory that purported to be consistent both with genetics and with Darwin's 19th-century view of evolution as a process of infinitesimal change controlled, initiated and directed by selection.

The development of this theory, which went on to dominate the 20th century, was based on 3 innovations. The first innovation was to redefine Darwinism. The version of "Darwinism" that the MS restored was not the one that the Mendelians rejected. Instead, Darwinism 2.0 was "Darwinian" in emphasizing the pre-eminence of selection, leaving out the Darwin's non-Mendelian laws of heredity. The second innovation was the notional "gene pool", a populational buffer that insulates ÇevolutionÈ from effects of mutation by churning and mixing and "maintaining" abundant variation. The "gene pool" concept provided a foundation to reject the "lucky mutant" view and argue against Mendelian heterodoxies, e.g., given that evolution begins with the "gene pool", selection (not mutation) initiates evolution, and chooses its direction from the abundance of possibilities.

Finally, the MS included an integrated view of causation in which continuous shifts in allele frequencies are seen as the common currency of causal effects. That is, a factor is identifiable as an evolutionary "force" to the extent that it is capable of causing mass-action shifts in allele frequencies. This view appeared to justify the claim that selection is the driving force in evolution, and that mutation is not a potent force, but merely serves to supply "raw materials" to the "gene pool".

Thus, while the Mutationism Myth wrongly suggests that the MS reconciled genetics and selection (instead, the Mendelians accomplished this), it correctly suggests that the MS restored a "Darwinian" view, and that arguments from population genetics were the key to this restoration, though (as we'll find out later) the crucial arguments from population genetics were based less on mathematics than on metaphors and metaphysics.

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References

Beatty, J. 2010. Reconsidering the Importance of Chance Variation in M. Pigliucci, and G. MŸller, eds. Evolution: The Extended Synthesis.

Berry, R. J. 1982. Neo-Darwinism. Edward Arnold, Ltd., London.

Charlesworth, B. 2005. On the Origins of Novelty and Variation. Science 310:1619-1620.

Chetverikov, S. S. 1997. On Certain Aspects of the Evolutionary Process from the Standpoint of Modern Genetics. Genetics Heritage Press, Placitas, New Mexico.

Darlington, C. D. 1958. The Evolution of Genetic Systems. Basic Books, New York.

Dawkins, R. 1996. Climbing Mount Improbable. W.W. Norton and Company, New York.

Dobzhansky, T. 1937. Genetics and the Origin of Species. Columbia University Press, New York.

Dobzhansky, T. 1955. Genetics and the Origin of Species. Wiley & Sons, Inc., New York.

Dobzhansky, T., F. J. Ayala, G. L. Stebbins, and J. W. Valentine. 1977. Evolution. W.H. Freeman.

Fisher, R. A. 1930. The Genetical Theory of Natural Selection. Oxford University Press, London.

Ford, E. B. 1971. Ecological Genetics. Chapman & Hall, London.

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

Gould, S. J. 1977. Ever Since Darwin. W.W. Norton & Co., New York.

Huxley, J. S. 1942. Evolution: The Modern Synthesis. George Allen & Unwin, London.

Kirschner, M. W., and J. C. Gerhart. 2005. The Plausibility of Life: Resolving Darwin's Dilemma. Yale University Press, New Haven.

Lewontin, R. C. 1965. The Gene and Evolution. Pp. 67-75 in R. M. Nardone, ed. Mendel Centenary: Genetics, Development and Evolution. Catholic University of America Press, Washington, DC.

Lewontin, R. C., and K. Kojima. 1960. The evolutionary dynamics of complex polymorphisms. Evolution 14:458-472.

MacBride, E. W. 1930. Embryology and Evolution. Nature 126:918-919.

Maynard Smith, J. 1976. What determines the rate of evolution? American Naturalist 110:331-338.

Mayr, E. 1963. Animal Species and Evolution. Harvard University Press, Cambridge, Massachusetts.

Mayr, E. 1980. Some Thoughts on the History of the Evolutionary Synthesis. Pp. 1-48 in E. Mayr, and W. Provine, eds. The Evolutionary Synthesis. Harvard University Mayr, E. 1994. The Resistance to Darwinism and the Misconceptions on which it was Based. Pp. 35-46 in J. H. Campbell, and J. W. Schopf, eds. Creative Evolution?! Jones & Bartlett, Inc., London.

Orr, H. A. 2003. The distribution of fitness effects among beneficial mutations. Genetics 163:1519-1526.

Orr, H. A., and J. A. Coyne. 1992. The Genetics of Adaptation: A Reassessment. American Naturalist 140:725-742.

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.

Shull, A. F. 1936. Evolution. McGraw-Hill, New York.

Stebbins, G. L. 1966. Processes of Organic Evolution. Prentice Hall, Englewood Cliffs, NJ.

Stoltzfus, A., and L. Y. Yampolsky. 2009. Climbing mount probable: mutation as a cause of nonrandomness in evolution. J Hered 100:637-647.

Vavilov, N. I. 1922. The Law of Homologous Series in Variation. J. Heredity 12:47-89.

Wright, S. 1967. Comments on the preliminary working papers of Eden and Waddington. Pp. 117-120 in P. S. Moorehead, and M. M. Kaplan, eds. Mathematical challenges to the neo-Darwinian interpretation of evolution. Wistar Institutional Press, Philadelphia.

Yampolsky, L. Y., and A. Stoltzfus. 2001. Bias in the introduction of variation as an orienting factor in evolution. Evol Dev 3:73-83.

Notes

¹ The point of this comment is that I don't claim to be presenting the MS in a comprehensive way. This view of the MS is one view. In particular, it represents a kind of dialectic perspective on the MS as a response to Mendelism, focusing on what seems to be a characteristically Darwinian view of the role of variation, and focusing on evolutionary causation.

² Note that Dobzhansky, in particular, started out as a bit of a heretic on the importance of mutation. In his 1937 book he speculated that different rates of mutation might explain different rates of evolution (p. 37), an idea that later was mocked by Simpson and others, lending credence to Gould's idea of a "hardening" of the Synthesis.

³ Orr and Coyne write "the micromutational view of Darwin, Fisher and others is clear: adaptations arise by allelic substitutions of slight effect at many loci, and no single substitution constitutes a major portion of an adaptation." I think they are right about Fisher and Darwin (ignoring the flagrant anachronism linking Darwin to a position on "allelic substitutions"), but who are the "others"? I can't put Dobzhansky in the same category. He only emphasizes that "small" or "slight" differences predominate in "the majority of cases".

⁴ Some present-day biologists have an adverse reaction to the term "creativity". Perhaps this is similar to my own adverse reaction to "design": I'd rather that biologists not use the term "design", which smacks of teleology. A similar objection might be made to the term "creativity". Nevertheless, in some sense, a theory of evolution must explain how new things come into existence (creativity) and how they appear to be adapted (design). So, if you are having an adverse reaction to "creativity", then please bear in mind the possibility that there might be ways to re-frame the issues at stake, but that for now, we are going to continue to use the old language of "creativity" because that is what's historically important.

⁵ This distinction is from Aristotle. His 4-fold taxonomy of causes includes material, efficient, formal (plans, archetypes), and final (goals, intentions) causes.

⁶ Its hardly ever clear what "random" means in such contexts. This is a topic that we will take up in a future post. The definition that is perhaps the most defensible historically is the one given by Wright, which also corresponds to Darwin's view as discussed in Beatty, 2010. By this definition, "randomness" is not a property of mutation per se, but of its role in evolution.

⁷ In passing, note how this argument obscures where "new" things come from. In reality, new combinations of pre-existing alleles arise by sexual mixis, by the reassortment of chromosomes, and by intra-chromosomal recombination. These processes, and not future selection, bring the new combinations into existence (and may break it apart again).

⁸ This passage has been singled out by Gould, 2002 and others. Amundsen (2005) gives a brief explanation of the thinking that underlies this (in his Ch. 11).

⁹ The "opposing pressures" argument is analyzed in more detail in Yampolsky and Stoltzfus (2001).

¹⁰ In the genesis of the MS, this doctrine had no clear basis in theory or experiment. It was not considered in a rigorous way until Maynard Smith tried (and, in my opinion, failed) to justify it in 1976, long after it had become an established orthodoxy.

¹¹ This is explained in more detail in Stoltzfus (2009; see also Yampolsky and Stoltzfus, 2001).

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_myth5 (Arlin Stoltzfus, ©2010)

Chris Mooney Asks a Hard Question

 
Chris Mooney was at the AAAS meeting in Washington and he attended the session on Re-Envisioning the Science and Religion Dialogue. Most of you are familiar with what went on at that session—a bunch of religious people declared that science and religion are perfectly compatible.¹

Chris wrote up something on his blog ... [Science and Religion Dialogue at the AAAS].

At the close of the session, I rose and posed a question. One can never remember exact words, but in essence, it was this: “I’m glad you’re trying to foster dialogue between scientists and the religious community, and I’m sure you’ll succeed. But here is a harder question–how will you foster dialogue with the New Atheists?”

I can understand why Chris wants to know the answer to this question. After several years of trying to have an intelligent discussion with New Atheists he is no closer to succeeding than when he first started. It's a tough problem for him.

Allow me to suggest an answer. The first thing you have to realize is that atheists do not accept the premise that supernatural beings actually exist. You aren't going to get anywhere in a discussion with an atheist if you base your arguments on that premise.

Let's say you're a religious person—like those on the panel—and you want to have a productive dialogue with an atheist about whether science and religion are compatible. The first thing you do is admit up front that most religions have beliefs that are in direct conflict with science. The second thing you do is either admit that you hold those beliefs, and therefore your religion is in conflict with science, or that you disavow all those beliefs, in which case your version of non-conflicting religion that's left needs to be explained.

At that point you can have a dialogue by describing your remaining religious beliefs and explaining why they don't conflict with science.

William Phillips, a Nobel Laureate in Physics, answered the question.

Phillips, the Methodist Nobel Laureate, had a very interesting answer. He essentially replied that if the New Atheists would get to know serious religious people–people who do not in any way represent the parody version of religion that is so frequently attacked–they could no longer maintain their point of view.

Other Bloggers
Same Topic

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Jerry Coyne
Ophelia Benson
Eric MacDonald
Nonsense. That's extremely insulting and it's no way to have a dialogue with people who disagree with you. I know lots of serious religious people and I've read lots of books and articles by "serious" religious people like Francis Collins, Ken Miller, Keith Ward, and Alister McGrath. I've also read a great deal of literature by accommodationsts (atheists) like Michael Ruse and Eugenie Scott. My point of view remains the same: aside from strict deism, all other religious viewpoints conflict with science.

My question to William Phillips would be based on his description of himself as a Methodist. What are the basic tenets of Methodism that you subscribe to and how are they compatible with science as a way of knowing? We could then have a productive dialogue.

Mooney continues ...

I’m not so sure, though. I think the New Atheists have a ready and built-in answer to this appeal to the significance of so-called “religious moderates.” They claim–in an argument that I for one find weak–that the moderates enable extremists, and so are part of the problem. (Even, I suppose, if they are perfectly lovely human beings.)

I can see why Chris Mooney is having so much difficulty engaging in productive dialogue with atheists. It's because he doesn't listen.

I'm perfectly happy to discuss the compatibility of science and religion with any religious moderate. All I ask is that they stop pointing the finger at Christian fundamentalists and start describing what they, themselves, actually believe. They may have fooled Chris Mooney by employing this diversionary tactic but they don't fool most other atheists.

Still, surely the New Atheists must on some level recognize the critical importance religion plays in many people’s lives–which implies that we can hardly expect believers to discard their faith based on philosophical considerations, no matter how persuasive these may seem to many secularists or scientists.

What nonsense! People believe all kinds of things that play an important role in their lives. If those beliefs provide them with a great deal of comfort then, of course, they are going to be reluctant to abandon them. What does that prove?

It proves that we have a lot of work to do if we want people to abandon superstition and base their lives on evidence, rationality, and skepticism. That applies to homeopathy, astrology, the belief that climate change isn't happening, and the belief that universal health care is a communist plot. Would Chris prefer that we simply abandon those efforts because it's going to be difficult?²

I, for one, do expect societies to abandon religion in spite of the fact that many individuals will find this extremely difficult. It's working in Europe and in other nations throughout the world. Chris' point, I think, is that we should avoid talking about the possible conflict between science and religion because it makes religious people very nervous. Since religion plays such an important role in their lives, we should tip-toe around the topic and pretend that science and religion aren't in conflict, especially with "religious moderates." This is no way to have a productive dialogue. It's the exact opposite of a productive dialogue.

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1. Imagine that!

2. The conservative mindset is extremely important in the lives of many Americans. Would Chris avoid criticizing Republicans because it might hurt their feelings? Or is it because he isn't likely to change their minds?

Making a Fool of Yourself

There are many ways of making a fool of yourself. I know, because I've successfully attempted every one of them over the past few decades. I've even repeated some of the easier ones. Several Dozens of times.

Michael Shermer reminds us how easy it is by quoting a physicist. [When Scientists Sin: Fraud, deception and lies in research reveal how science is (mostly) self-correcting]

In his 1974 commencement speech at the California Institute of Technology, Nobel laureate physicist Richard P. Feynman articulated the foundation of scientific integrity: “The first principle is that you must not fool yourself—and you are the easiest person to fool.... After you’ve not fooled yourself, it’s easy not to fool other scientists. You just have to be honest in a conventional way after that.”

This reminds me of an even earlier quotation from Peter Medawar in 1961. It's from a review of The Phenomenon of Man by Pierre Teilhard de Chardin.

It is a book widely held to be of the utmost profundity and significance; it created something like a sensation upon its publication in France, and some reviewers hearabouts called it the Book of the Year—one, the Book of the Century. Yet the greater part of it, I shall show, is nonsense, tricked out with a variety of metaphysical conceits, and its author can be excused of dishonesty only on the grounds that before deceiving others he has taken great pains to deceive himself.

It's much easier to fool yourself these days, in part because Peter Medawar and Richard Feynman aren't around to keep us honest.

That's one of the problems with modern science.

It's worth noting that Medawar was an atheist and he had little use for those who attempt to bolster religious beliefs with scientific arguments. It's also worth noting that forty years after Medawar's review you can still find people defending Teilhard as in Prophets without honour?, an essay published in Nature in 2000.

Teilhard's books were published posthumously: his religious superiors forbade him publishing his views on human evolution in his lifetime. He thus shared with Galileo the distinction, if that is the right word, of having his work suppressed by the Roman Catholic Church. Just because Galileo was right does not, of course, give everyone else whose work is proscribed the stamp of scientific rectitude, but Teilhard was doubly distinguished in his second martyrdom at the hands of scientific orthodoxy. But apart from its religious streak, Teilhard's approach is not so different from that of the modern field of evolutionary psychology, and he anticipated the explosive growth of mass communication. For a book written in the late 1930s, The Phenomenon of Man seems remarkably prescient.

Teilhard is not alone in being tried by the scientific establishment while experiencing popular success. A good deal of hostility has been directed at the concept of the biosphere as an intelligent organism — James Lovelock's Gaia — and at astronomer Fred Hoyle's ideas on the extraterrestrial origin of life. Both met with popular enthusiasm before the scientific establishment would admit that they were candidate hypotheses. The evolutionary biologist John Maynard Smith castigated Hoyle recently in this very journal ( Nature 403, 594–595; 2000).

Teilhard's books must have far outsold Medawar's Reith Lectures, and therein lies a dilemma for scientists in their relationship with the public. Should they, like Medawar, stick to the facts, satisfying the dictates of scientific conscience but, with a limited horizon, reaching a limited audience? Or should they throw caution to the winds as Teilhard did, appeal to a large audience, but risk disapprobation by the scientific community? There is a psychological issue, too, which is that the public may have twigged that not only do orthodox scientists restrict their enquiries to the physical world, but also that many of them believe in their hearts that there is nothing beyond it.

Speaking of phenomena, how often do you see someone's work compared to evolutionary psychology where the comparison is meant to be a compliment?

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On the Origin of the Double Membrane in Mitochondria and Chloroplasts

I've just finished revising my chapter on lipids and membranes for the 5th edition of my textbook. I decided to insert a short explanation about double membranes in order to clear up some common misconceptions.

Eukaryotic cells are surrounded by a single membrane—the familiar lipid bilayer we learned about in high school. Prokaryotic cells come in two varieties, those that have a single membrane like the gram positive bacteria, and those that have a double membrane, like the gram negative bacteria. A double membrane consists of two lipid bilayers (plasma membrane and outer membrane) with an enclosed intermembrane compartment.¹

There are membrane bound compartments within eukaryotic cells. Many of them are surrounded by a single lipid bilayer. Some have a double membrane. The nucleus, for example, is surrounded by a complex double membrane that completely breaks down and is reformed during mitosis and meiosis. Mitochondria and chloroplasts also have double membranes.

Mitochondria and chloroplasts are derived from ancient gram negative bacteria that entered into a symbiotic relationship with primitive eukaryotic cells. The bacteria entered the cytoplasm of the much larger eukaryotic cell where they continued to generate energy by creating a proton gradient across their inner membranes. The protons were temporarily stored in the intermembrane space until they were used to drive ATP synthesis during their return to the cytoplasm. According to chemiosmotic theory, the generation of this protonmotive force in primitive bacterial cells required an intermembrane compartment bounded by two membranes [Ode to Peter Mitchell, Ubiquinone and the Proton Pump].

It's no surprise that mitochondria and chloroplast have a double membrane because their ancestral bacterial cells also had double membranes.

The fact that gram negative bacteria have a double membrane has been known for over half a century. The fact that mitochondria and chloroplasts descend from bacteria has been accepted for almost forty years. The fact that the ancestral bacteria are gram negative bacteria became well established 25 years ago.

In spite of all this evidence, there's still a persistent mythology about the origin of the double membrane in mitochondria and chloroplasts. I was reminded of this when I read the article that won third place in the 3 Quarks Daily 2010 prize for best blog posting about science [The Winners of the 3 Quarks Daily 2010 Prize in Science]. The judge was Richard Dawkins.

First prize was won by Ed Young of Not Exactly Rocket Science for his article on Gut bacteria in Japanese people borrowed sushi-digesting genes from ocean bacteria. Second prize went to Carl Zimmer for Skull Caps and Genomes. Third prize was for an article by Margaret Morgan on The Evolution of Chloroplasts: endosymbiosis and horizontal gene transfer.

Morgan repeats the common myth ...

About 2.7 billion years ago, another remarkable change was occurring: the evolution of eukaryotic cells. This entailed the process of endosymbiosis [Gk: endon "within", syn "together" and biosis "living".] In endosymbiosis, one organism engulfs another and incorporates it into its own body or cells. It's important to remember that this takes place by invagination: think of pushing your finger into the side of an inflated balloon. Your finger is surrounded by both its own external membrane (your skin) as well as the membrane of the balloon itself. Now imagine (and sorry, the metaphor gets a bit gross at this point!) that your finger falls off and the balloon seals itself up again. Now your finger is inside the balloon, wrapped in a double membrane. That endosymbionts evolved by this process is evidenced by the fact that they have a double membrane, including their own original form that resembles the ancestral bacterial surface.

This is very wrong. The original bacteria had a double membrane and that double membrane was an integral part of the energy producing pathway that became so important for the eukaryotic cell. It's simply not true that the double membranes of bacteria and chloroplasts were the result of endocytosis.

Unfortunately, there are a lot of other things about this article that are wrong or misleading. I suppose it's further evidence that Richard Dawkins is not a biochemist!

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1. I don't mean to imply that a membrane consists only of lipids. Proteins make up a substantial percentage of all membranes.

Ogura, M. (1963) High resolution electron microscopy on the surface structure of Escherichia coli. Journal of Ultrastructure Research 8:251-263 [doi:10.1016/S0022-5320(63)90006-6 ]

Stephen Meyer Explains Intelligent Design Creationism

 
Here's Stephen Meyer on The 700 Club explaining why Intelligent Design Creationism is likely to be true. This is about as good an explanation as you're ever going to get.

Keep in mind that Intelligent Design Creationism is a strictly scientific theory. It is not religious. It just so happens that an evangelical Christian television show has an audience that's very interested in science.

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PZ's Radical Tree of Life

 
Check out PZ Myer's "radical" tree of life [Radial tree of life].



Why is this tree "radical"¹? Because it completely misrepresents the relative importance of animals. Bacteria are relegated to insignificant status when, in fact, the diversity among bacteria is every bit as great as the diversity within eukarotes. Protists are grossly underrepresented as well.

This is a tree for those people who think that humans and other animals should be much more important than they are. One word for that is "radical" but I can think of many others. I'm surprised at PZ for using this tree. That's not at all like him.

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1. PZ says it's a "radial" tree, not a "radical" tree.

[Tree Source: David M. Hillis, Derrick Zwickl, and Robin Gutell, University of Texas]

AAAS Supports Accommodationism, Illogically

 
Alan I. Leshner is the CEO of the American Association for the Advancement of Science (AAAS) and Executive Publisher of Science. He has written an article for the Huffington Post [Science, Religion and Civil Dialogue]. As usual, this type of accommodationist focuses on the fact that there are religious scientists. In this case, the recent study by Elaine Ecklund gets a prominent mention.

Let's hope that Ecklund's unusually comprehensive assessment will help overturn the myth that scientists reject spirituality, or that science and religion are inherently incompatible.

That myth persists among scientists and religious believers alike. In 2009 study by the Pew Research Center, 61% of Americans said that science poses no conflict with their own faith. Nonetheless, 55% of those same respondents said they view religion and science generally as "often in conflict." Evolution, for instance, has divided Americans since 1859, when Charles Darwin published "On the Origin of Species."

There is a better way, which will be demonstrated June 16 when leading scientists and a respected Christian minister engage in a free, public dialogue at the American Association for the Advancement of Science (AAAS).

There may be a myth that all scientists reject spirituality. I really can't comment on that except to note that I have never, ever, heard anyone make this claim.

The real issue is whether science and religion are inherently incompatible and that issue is not a "myth" by any stretch of the imagination. It's a perfectly reasonable position, whether you agree with it or not. The existence of scientists who are religious does nothing to decide the issue one way or another. After all, there are scientists who believe in homeopathy but that doesn't mean homeopathy is compatible with science. What Leshner says is illogical and logic is supposed to be one of the hallmarks of good science.¹

If the CEO of AAAS can't distinguish real philosophical issues from "myth" then I suggest that Americans need a new CEO—one who will keep the organization out of domains where it has no mandate to speak for all scientists. If Alan I. Leshner can't keep religion out of the organization then he should resign.²

As you might expect, Jerry Coyne restates the position that many of us hold [The AAAS goes all accommodationist]. Scientific organizations like AAAS have no business making claims about whether science and religion are compatible or not. When they cow-tow to religion they are separating themselves from a great many scientists who hold contrary points of view. The organization does not, cannot, and should not speak for scientists on subjects outside of science.

What Should Scientific Organizations Say about Religion?

How Should Scientific Societies Treat Religion?

Are Science and Religion Compatible? AAAS Says Yes.

AAAS Panel: Communicating Science in a Religious America

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1. I haven't mentioned the other illogical part of the argument; namely, that criticism of religion is "uncivil."

2. Please, let's not have any silly debate over whether Leshner is expressing a personal opinion or speaking for AAAS. Read his article and note how he identifies himself as author.

Richard Dawkins Talks About the Human Genome

Richard Dawkins is hosting a four part series on the human genome to be broadcast on BBC radio [The Age of the Genome]. Here's part of the summary for episode 1.

In spite of the advances, there have been some surprises and deepened mysteries. One of the greatest shocks was the finding that we have far fewer genes than scientists had assumed before they read out our genetic instructions. It takes no more genes to make a person than it does to make a simple microscopic worm. What makes a man different from a worm lies more in what researchers now calling the Dark Matter of the genome - 300 million letters of genetic code which work in currently mysterious ways.

Richard Dawkins is an evolutionary biologist at Oxford University and the author of numerous books on evolution and genetics such as 'The Selfish Gene'. In interviews with scientists who led the initial effort to decode the genome and those who are now at the forefront of genetic research, Richard brings his evolutionary insights and fascination with the universal genetic code of life to illuminate how far we've come, and where we are heading in the Age of the Genome.

Note to Richard,

Many scientists, including the experts in the subject, expected there to be about 30,000 genes in our genome. They were pretty close to being right. No surprises there.

What makes a man different from a worm is that we have a smallish number of different genes and the genes we have in common are regulated differently. This conclusion comes from studies in developmental biology that were completed before the Human Genome Project began. Differences in regulating gene expression can be easily accomplished by changing a few base pairs in the promoter/enhancer region of the gene. No mystery there. The field is called evolutionary developmental biology and it's based on an understanding of evolution.

The "dark matter" is junk. The sequence of the human genome goes a long way toward proving what was suspected back in 1970. That's not a surprise. It's a prediction confirmed. Everything we know about the evolution of genomes in diverse species is consistent with the idea that much of our genome has no function. Evolution explains pseudogenes, it explains the so-called C-value paradox, it explains transposons and selfish DNA, it explains highly repetitive sequences. The "dark matter" has been exposed to the light of day and it looks like junk.

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False History and the Number of Genes 2010

Mihaela Pertea and Steven L Salzberg have just published a paper in Genome Biology with an interesting title: Between a chicken and a grape: estimating the number of human genes. Part of their paper covers the history of gene number estimates and it includes the figure shown here.

Figure 2. The trend of human gene number counts together with human genome-related milestones. Individual estimates of the human gene count are shown as blue diamonds. The range of estimates at different times is shown by the two vertical blue dotted lines. Note how this range has narrowed in recent years.

This is really annoying because it perpetuates a myth that needs to be debunked. I've addressed it in an earlier posting [Facts and Myths Concerning the Historical Estimates of the Number of Genes in the Human Genome].

Mihaela Pertea and Steven L Salzberg have completely ignored a substantial literature on the subject. First, there's the genetic load arguments of King and Jukes from 1969. They estimated that there had to be fewer that 40,000 genes in our genome. Ohno summarized the estimates in a 1972 paper and came up with an estimate based on current knowledge of 30,000 genes (Ohno 1972).

Then there's the substantive literature on expressed sequences from the 1970's These were mostly hybridization experiments showing that human tissues had a core of about 10,000 genes expressed in the most complex tissues. The estimate was that there were probably no more than double that number of genes in total. Benjamin Lewin was the expert on this subject and his early books (especially Gene Expression II) covered all the bases. By 1983, Lewin was able to conclude in Genes II ...

Given some uncertainties about estimating the numbers of genes present in multiple copies, we might say that the mammalian genome looks to be of the order of 30,000 - 40,000 gene functions.

He published the same estimate in Genes IV in 1990.

Lewin was not alone. Most textbooks contained similar estimates in the 1980s. In Molecular Biology of the Cell by Alberts et al. (1983) the estimate was also 30,000 genes (p. 406). These estimates were not dismissed as unreliable. Quite the contrary. In my circles, the general impression was that humans had to have fewer than 50,000 genes and the number was likely to be less than 30,000.

It's true that Walter Gilbert had "guesstimated" 100,000 genes and it's true that the early estimates from the Human Genome Project used a number like this (based on a false assumption). But that doesn't mean that everyone agreed. Indeed, among those who had really studied the problem, a much lower number was preferred.

During the 1990s, the preliminary results from EST cloning and sequencing started to come in and it looked like there were at least 100,000 genes based on this data. However, this was a controversial estimate precisely because so many people knew that it conflicted with a lot of data. Sure, there were those who believed the EST data over everything else but they did not represent everyone who was interested in gene numbers. It is very misleading to suggest that there was a consensus in favor of more than 50,000 genes as the figure implies.

That's false history and it does a great disservice to those who turned out to be correct.

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[HatTip: Carl Zimmer]

King,J.L. and Jukes,T.H. (1969) Non-Darwinian evolution. Science 164; 788-798.

Ohno, S. (1972) So much "junk" in our genome. Brookhaven Symp. Biol. 23:366-310.

Nicholas Wade Writes about Genomes and Evolution

His fellow science writers often think that Nicholas Wade is among the best of their ilk. Wade writes for the New York Times and his latest article is: A Decade Later, Genetic Map Yields Few New Cures. A couple of paragraphs from that article deserve some kind of award.

But while 10 years of the genome may have produced little for medicine, the story for basic science has been quite different. Research on the genome has transformed biology, producing a steady string of surprises. First was the discovery that the number of human genes is astonishingly small compared with those of lower animals like the laboratory roundworm and fruit fly. The barely visible roundworm needs 20,000 genes that make proteins, the working parts of cells, whereas humans, apparently so much higher on the evolutionary scale, seem to have only 21,000 protein-coding genes.

The slowly emerging explanation is that humans and other animals have much the same set of protein-coding genes, but the human set is regulated in a much more complicated way, through elaborate use of DNA’s companion molecule, RNA.

Thanks to Jonathan Eisen at The Tree of Life, Nicholas Wade can now add the "Twisted Tree of Life Award" to his many others [Twisted tree of life award #5: Nicholas Wade & use of higher, lower, ladders, etc].

You see, Wade makes one of the most fundamental errors of evolutionary thinking when he writes about "higher" and "lower" on the "evolutionary scale."

There are two other flaws in his quoted excerpt. First, it did not come as a big surprise to all scientists that humans had about the same number of genes as other animals. That's a myth based on overemphasizing the opinions of some people and underemphasizing the opinions of the experts [Facts and Myths Concerning the Historical Estimates of the Number of Genes in the Human Genome]. This is part of what I call The Deflated Ego Problem and it's not endemic. It can be cured by reason.

Second, the explanations for similar numbers of genes in animals come from genetics and developmental biology over the past fifty years. It may have been "slowly emerging" back when I first started teaching but it's now fully emerged and has been for twenty years. Long before the human genome was sequenced we knew that major morphological changes could be caused by small mutations in regulatory sequences. During the 1980s and 1990s it became apparent that animals such as Drosohila and humans shared many important development genes¹ and even more of the genes involved in basic metabolism. This was not a surprise.

It may be true that RNA places a much more important role in regulating gene expression than we thought. The jury is still out on that one. However, even if RNA is part of the regulation picture that fact does not change the basic principle that molecular biologist developed over the past thirty years; namely, that the same basic gene set is just regulated differently in different animals. This is the contribution of Evo-Devo.

There's one other logical flaw made by those with deflated egos. What they're looking for is some specific mechanism that explains the marvelous complexity of humans relative to the "lowly" fruit fly or nematode. What they need in order to satisfy this longing is a mechanism that we have and they don't. As far as I know, there isn't (hardly) anyone who claims that regulatory RNAs have only evolved in humans. The genome sequences of all animals is pointing in the same direction. If there are abundant regulatory RNAs then there are lots in nematodes and fruit flies as well. It's not going to solve the pseudoproblem that Nicholas Wade imagines.

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1. Perhaps you've heard of homeotic genes and HOX genes?

Nature Opens Mouth—Inserts Foot

 
Nature Publishing Group has responded to the potential boycott of its products by the Universities of California [Nature vs. The University of California]. Here's what they have to say for themselves ... [Public statement from Nature Publishing Group regarding subscription renewals at California Digital Library (CDL)].

The implication that NPG is increasing its list prices by massive amounts is entirely untrue. We have been publishing our academic site licence pricing for several years on our librarian gateway. Dollar list price increases have been reasonable (averaging roughly 7 % over 4 years), and publicly available throughout. A 7% cap on annual list price increases is currently in place.

The complication with CDL is that they have been on a very large, unsustainable discount for many years, to the point where other subscribers, both in the US and around the world, are subsidising them. The origins of this discount can be found in the lack of clear definitions around consortia and 'single institute, multisite' subscribers, as well as previous accommodations of CDL's budget limitations.

If we regard CDL as a consortium of multiple libraries (not least suggested by CDL's membership of International Coalition of Library Consortia (ICOLC), and the libraries' ARL listings), the CDL discount on list price is 88%. By their own figures, CDL receives average discounts of 55% from publishers. After several attempts, we are now trying to bring them close to a 50% discount (although this leaves CDL on better terms than many other consortia). We do recognise the situation can be viewed from different perspectives, and we remained committed to ongoing discussions.

Translation: It's completely untrue that NPG is increasing its prices. It's only massively increasing prices for the Universities of California. Price increases for other schools are "only" 7%.

Question: Is it true that the prices to other universities have increased because CDL has been getting a bargain? That's the only way to interpret the statement that, "... other subscribers, both in the US and around the world, are subsidising them"? If so, then if the new contract with CDL results in a huge price increase, doesn't it follow that the prices for all other subscribers should go down? That means the University of Toronto will get a price reduction when CDL and NPG reach agreement, right? Or am I missing something?

Our own projections show CDL will be paying roughly $0.56 per download under the new prices. This represents incredible value for money across any publisher's range of titles. We now call on CDL to reveal how much it spends with all the major publishers, and how this translates into cost per use, and/or other indicators of value. If NPG represents poor value for money, we will work with CDL to readjust their pricing. If, as we expect, NPG represents good value for money compared with other publishers, even at the new proposed pricing, we want to work with CDL to have this reflected in our agreement. We sincerely hope that no boycotts will occur, not least because it is detrimental to the advance of science, but we will not be bullied into continuing CDL's subsidy by our other customers.

Translation: We're embarrassed and we probably will be bullied into making a much lower offer to CDL. Furthermore, we equate the advance of science with the business of publishing. It's it reduces our profits then it must be bad for science.

The one good thing that will come of this is that it will stimulate many universities to get together and form bargaining groups. That will give them a lot more clout. I'm sure all the other publishers will be thanking NGP for making this such a prominent issue.

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