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Showing posts sorted by relevance for query curious disconnect. Sort by date Show all posts
Showing posts sorted by relevance for query curious disconnect. Sort by date Show all posts

Thursday, January 31, 2013

Theme: Mutation

This is a collection of Sandwalk posts on mutation starting in 2007. The latest ones are at the bottom of the list.

March 27, 2007
Silent Mutations and Neutral Theory
Neutral Theory and random genetic drift explains variation and it also explains molecular evolution and the (approximate) molecular clock. There are no other explanations that make sense and nobody has offered a competing explanation since Motoo Kimura (1968) or Jack King and Thomas Jukes (1969) published their papers almost fifty years ago. (Aside from occasional nitpicks, of course. There are always scientists who like to show that some mutations that were thought to be neutral are actually beneficial or deleterious. None of them have mounted a serious claim that most variation or most of molecular evolution can be explained by natural selection.)

April 19, 2007
Haldane's Dilemma
This is very interesting. Dembski has teamed up with Walter ReMine, demonstrating once again that the old addage "opposites attract" does not apply to kooks.

ReMine has an article on Uncommon Descent where he pushes his usual whine about evil scientists and how their world-wide conspiracy has kept him from revealing the fatal flaw in evolution [Evolutionist withholds evidence on Haldane’s Dilemma]. I can see how similar this is to Intelligent Design Creationism.


Tuesday, May 04, 2010

The Mutationism Myth, II. Revolution

This is the fourth 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.

Arlin is going to explain to you why everything you thought you knew about mutationism is wrong. You may even be a supporter of mutationism without even being aware of it!


The Curious Disconnect

Our journey to map out the Curious Disconnect— the gap between how we think about evolution and how we might think if we were freed from historical baggage— began with The Mutationism Myth, part 1. Then, in Theory vs Theory, we took a brief detour to distinguish theory1 (grand conjecture) from theory2 (body of abstract principles). Today we are back to the Mutationism Myth and our goal is to probe its claim that the scientific community rejected Darwin's ideas on erroneous grounds.1


The Mutationism Myth, II. Revolution

The Mutationism Myth is a story told in the literature of neo-Darwinism, regarding the impact of the (re)discovery of Mendelian genetics a century ago. In this story, the discoverers of genetics (characterized as laboratory-bound geeks) misinterpret their discovery, thinking it incompatible with natural selection; the false gospel of these "mutationists" brings on a dark period that lasts until the 1930s, when theoretical population geneticists prove that genetics is the missing key to Darwinism; Darwinism is restored, and there is peace and unity in the land.

In typical versions of the mutationism story that we reviewed in part 1, the Mendelians cast a spell on the scientific community, convincing it of a false belief that either

  • Mendelian genetics is inconsistent with the concept of natural selection or
  • selection is irrelevant because mutational jumps alone explain evolution

For instance, Eldredge (2001) writes:

Many early geneticists at the dawn of the 20th century, thought their discoveries of the fundamental principles of genetics somehow cast doubt [on], or rendered obsolete, the concept of natural selection

As noted earlier, a myth is not necessarily false. Some parts of the Mutationism Myth reflect history accurately, and others do not. An underlying truth in the Mutationism Myth is that, as a direct result of the re-discovery of Mendelian genetics, leading geneticists— Bateson, Johannsen, de Vries, Morgan, Punnett, and others— rejected Darwin's theory for how evolution works.

Our goal is to understand why. We must begin with heredity, the heart of the issue.


Re-discovering a lost theory

The re-discovery of Mendel's principles of heredity was nothing short of a revolution, and if you were trained in 19th-century views of heredity, this would be obvious, and there would be no need for me to explain it.

Unfortunately, the chances are good that you, dear reader, have been trained in the principles of Mendelism, and that puts us at a disadvantage. Once we can imagine the purity of hereditary factors, and we learn Johannsen's genotype-phenotype distinction, these principles seem to change our view of the world irreversibly, and its hard to understand what came before. Johannsen's quantitative-genetics experiments on seed weights of the Princess bean, conducted in the first decade of the 20th century, appear to have had more impact on evolutionary thinking than any single study conducted before or since. In the figure below, Johanssen (1903) shows the distribution of weights of beans from a plot planted with a mixture of seeds from pure self-fertilizing lines (the legend says "The variation of the weight of 5494 beans from the 1902 harvest, descendants of all weight classes in 1901") (online source):


The beans from the mixed plot show a nice bell-shaped distribution (figure). Similarly, the beans harvested from pure lines grown in separate garden plots also show nice bell-shaped distributions, though the means differ for each pure line. The key difference is in the results of selective breeding for heavier (or lighter) beans, i.e., planting a new crop using only the heaviest (or lightest) beans: selection shifts the distribution of seed weights in the mixed plot, but has no significant effect on the distribution of seed weights produced by a pure line.

Within just a few decades, neo-Darwinians such as Ford (1938) dismissed Johannsen's results as a logical necessity, as though the experiments proved nothing. Johannsen's studies had changed our understanding so profoundly that Ford was unable to imagine how scientists (mis)understood the world before.

I won't ask you to do what Ford could not, which is to forget genetics.

Instead, I would like to ask you to join me in imagining a different world— one in which particulate inheritance of pure hereditary factors does not apply.

We have been sent to this alien world as evolutionary experts, to consult with its scientists about how evolution might work on their planet. The alien scientists explain that, in their world, the bodies of organisms have differentiated organs composed of diverse cell-like units (CLUs), which swell, fuse, split and exchange material. The CLUs don't seem to have nuclei or central control centers. Instead, they are composed of substances that interact productively and grow, crystal-like (possibly some kind of prion-like protein, we think to ourselves). Different CLUs have different compositions, and thus have different developmental tendencies, e.g., some CLUs have a tendency to aggregate and interact to form a differentiated organ.

We are skeptical of the alleged lack of nuclei, so we explain the "nucleus" concept to the aliens and propose that CLUs actually have a spatially localized store of information that controls growth and development. The aliens listen carefully and ask clarifying questions in order to understand our hypothesis. Then they tell us that they know we are wrong. Alien scientists long ago developed a method of splitting CLUs which showed that the separated parts of CLUs largely retain their potential for growth and development, even if the CLUs are cut in multiple pieces. Thus, the alien scientists had demonstrated that CLUs and their substances have a hereditary aspect, but the potential for heredity seems to be dispersed in the substances, not centralized in a nucleus.

During the life of an organ, CLUs may come and go. CLUs circulating in the body are harvested continually in the reproductive organs, where substances are extracted to form minute reproductive corpuscles, RCs, whose role in reproduction is similar to gametes. However, the RCs or reproductive corpuscles don't have the 1-copy-of-each-factor neatness of earthly Mendelian gametes. The growable substances in the RCs are variable in amount, thus RCs vary in hereditary potencies. Furthermore, the composition of CLUs circulating in the body reflects the totality of what is happening in the body: because the body is continually growing and reacting and changing, the RCs are changing, too. In particular, the composition of the RCs tends to deviate more strongly when the organisms are stressed or face unusual conditions.

While some of the alien organisms are asexual, others have tri-parental reproduction that involves mixing of RCs from different parents. Each of the 3 parents makes a contribution of RCs, typically equal in size, though in some species, one type of parent contributes much more than the other two. When the parental RCs come together, the substances in them seem to mix or blend.


A different kind of evolution

The alien scientists have outlined the basis of heredity on their planet, and they are looking to us expectantly for ideas about how evolution is going to work. We were hoping to gather more facts, and particularly to hear from other experts about the diversity of life, and so on, but the aliens are eager for our ideas right away. What can we infer about evolution in a bottom-up manner, from an understanding of heredity?

We see immediately that it will be possible to apply some concept of "selection" in this world, but its going to be awfully slippery. We reach into our conceptual toolbox, and the first thing we find is the concept of "selection coefficient". But thats not useful on the alien planet, because there is no stable genetic entity to which one may apply the selection coefficient— everything in the alien world with a bearing on heredity seems to be variable in potency and to be subject to blending. Heredity depends on the differential growth of continuous substances, modulated by their differential incorporation into RCs due to conditions of life, and so on. The alien world lacks the algebraic neatness of pairwise combinations and pure factors.

In fact, our hearts sink as we realize that, because of this blending-together, it might be impossible for evolution to start from a single hereditary variant, as would be possible on earth starting with a single Mendelian mutant. The distinctive features of the individual variant would simply diffuse and blend.

But our discouragement is only temporarily. Yes, it would have been simple and easy if hereditary factors emerged discretely, combined in simple ratios, and maintained their purity during reproduction— but who said science was supposed to be simple and easy?

We are undaunted. We are determined to discover some way to apply the principle of selection. In fact, given that the RCs deviate more strongly under unusual conditions, we note with enthusiasm that extra hereditary variation will emerge just when it would be helpful to provide fuel for adaptation to new conditions! Due to hereditary blending, one variant individual, with a variation in a favorable direction, would not be enough.

But thats not a problem. In fact, to treat it as a "problem" is wrong-headed, because this alien world is not a world of discrete heredity anyway! Instead, on the alien planet, heredity is a bulk process, like the flow and mixing of liquids. The hereditary substances flow (metaphorically) in new directions every generation, and selection can get some leverage from these fluctuations of hereditary potency, even if there is not any single discrete particle to grasp. Selection would guide these fluctuations, building them smoothly from generation to generation. Possibly we could develop a mathematical formalism for this process by adapting the breeder's equation of quantitative genetics, although the shifting of hereditary potencies from one generation to the next would be problematic. An even more radical thought occurs to us: Lamarckian evolution can't happen in our world, but in the alien world, it just might be possible due to the way the RCs reflect what is going on in the body as it experiences its environment.

If you have followed me thus far, congratulations! You are one of the re-discoverers of Darwin's lost theory of evolution!


Evolution without mutation

Sadly, when I refer to a "lost theory", its not a joke, because Darwin's "Natural Selection Theory" (not to be confused with the principle of natural selection2) is largely unknown to contemporary scientists. During the Darwin bicentennial last year, I lost track of how many times "Darwin's theory" was explained by reference to "selection and random mutation" or some such anachronism.

Darwin had no such theory. Given Darwin's assumptions that inheritance is blending (not particulate), that the germ-line is responsive to external conditions (not isolated), and that hereditary potencies shift gradually every generation (not rarely and abruptly, from one pure, stable state to another), it is physically impossible for a rare trait, having arisen by some process, and conferring a fitness advantage of (for example) 2 %, to be passed on to offspring by a stable non-blended hereditary factor, thus conferring on the offspring a 2 % advantage, and for such a process to continue for thousands of generations until the previously rare trait prevails. We may think of evolution in this way: Darwin did not.

Instead, Darwinism 1.0 (Darwin's conception of evolution) is an automatic process of adjustment to altered conditions, dependent on a rampant process of "fluctuation" yielding abundant "infinitesimally small inherited modifications" in response to the effect of altered "conditions of life" on the "sexual organs" (Chs. 1, 2, 4 and 5 of Darwin 1859). Fluctuation was not rare and discrete, but shifted hereditary factors continuously and cumulatively each generation, producing visible effects in "several generations" (Ch. 1 of Darwin 1859). Muller (1956) referred to Darwinian fluctuation as "creeping variation". I have called it "variation on demand", and I also think that, to understand Darwin's view, its helpful to think of heredity and variation as processes mediated by fluids (liquids or gases). Darwin's critics, and quite a few of his friends such as Huxley and Galton, believed that individual "sports" (mutants) could be the start of something new in evolution, but this was not part of Darwin's theory, which invoked blending inheritance and held fast to natura non facit salta.

For those who would like to get more of a flavor of Darwin's view from his own writings, I have included a few passages below in an appendix. Readers may wish to go further by browsing online sources via the links provided. Others may wish to take a colorful look at Darwin's laws of variation from the Virtual Museum of the Origin of Species.

To account for his principles or "laws"3 of variation, Darwin proposed a "gemmule" theory for the mechanism of heredity, where "gemmules" are somewhat like the RCs or "reproductive corpuscles" in the fictional alien world described above.

Although Darwin's "Natural Selection" theory invoked Lamarckian effects, the fluctuation-selection process that Darwin called "Natural Selection" was recognized immediately as its mechanistic core. Only this core mechanism remains in the reformed view of Weismann and Wallace— "Darwinism 1.2" for our purposes—, which expunged Lamarckism and relied on selection of ever-present fluctuations, a process understood (in Darwinism 1.2) as the exclusive and all-powerful driving force of evolution.


Developing a new view of evolution

In fact, the "Mendelians" did not reject the principle of selection. Instead, they rejected "fluctuation" as the basis of evolutionary change for exactly the reason we would expect, namely that these fluctuations are not heritable. Johannsen's experiments were influential because they suggested that the fluctuations that emerge reliably every generation, i.e., Darwin's "endless slight peculiarities which distinguish the individuals of the same species and which cannot be accounted for by inheritance from either parent or from some more remote ancestor", are non-heritable and cannot be the basis for evolution by natural selection.

This is precisely the reason that geneticists gave, explicitly, for rejecting Darwin's view. For instance, in his 1911 book Mendelism, Punnett (of the "Punnett square" one studies in Genetics 101) explains the new "basis of evolution":

"The distinction between these two kinds of variation, so entirely different in their causation, renders it possible to obtain a clearer view of the process of evolution than that recently prevalent. . . Evolution only comes about throught the survival of certain variations and the elimination of others. But to be of any moment in evolutionary change a variation must be inherited. And to be inherited it must be represented in the gametes. This, as we have seen, is the case for those variations which we have termed mutations. For the inheritance of fluctuations, on the other hand, of the variations which result from the direct action of the environment upon the individual, there is no indisputable evidence. Consequently we have no reason for regarding them as playing any part in the production of that succession of temporarily stable forms which we term evolution. In the light of our present knowledge we must regard the mutation as the basis of evolution— as the material upon which natural selection works. For it is the only form of variation of whose heredity we have any certain knowledge.

It is evident that this view of the process of evolution is in some respects at variance with that generally held during the past half century. " (Punnett, 1911, p. 139-140; online source)

Punnett rejects "fluctuations", defined as "the variations which result from the direct action of the environment upon the individual".

It wasn't about rejecting natural selection: Punnett identifies mutation as the "basis" of evolution precisely on the grounds that it provides "the material on which selection works". While TH Morgan (1916) often avoided the phrase "natural selection", as in the following passage, he clearly is not rejecting a role for differential effects of fitness

"evolution has taken place by the incorporation into the race of those mutations that are beneficial to the life and reproduction of the organism" (p. 194) (online source)

This "mutationist" view was merely the start of a new way of looking at evolution. In the next installment, we'll find out what sort of understanding of evolution emerged among this new generation of evolutionists inspired by Mendelian principles. We'll see that, contrary to the Mutationism Myth, the period between the discovery of genetics and the origin of the Modern Synthesis in the 1930s was not a dark period of confusion at all, but a period of innovation that gave rise to key elements of the genetics-based understanding of evolution that persists today, including new ways of understanding selection.


Looking ahead

This post raises several issues that will receive attention in future posts of The Curious Disconnect. For instance, the mutationists rejected "Natural Selection", the theory1 of Darwin, but not the "concept of selection" (as mistakenly asserted by Eldredge, above). In a later post, we will explore how the ambiguity in "natural selection" covers a multitude of sins (e.g., Charlesworth, 2005), and we'll consider ways to speak (and think) more clearly.

A second issue is the cult of personality that has developed around Darwin, which instills in so many scientists the desire to align themselves with Darwin and label themselves "Darwinists" while ignoring Darwin's actual views. Rather than reject or defend Darwin's actual theory, the cultists make personal excuses for Darwin ("he couldn't have known!"), as though science were about judging persons rather than evaluating theories. In a future post, we'll explore the distorting influence of the Darwin Fetish.

A third issue has to do with the structure of Darwin's theory, and more generally, how we determine the structure of a theory, and how the parts fit together. This will become important when we evaluate the deeply problematic claim of the Modern Synthesis to have reconciled Darwin's view with genetics. In essence, the architects of the Modern Synthesis will claim that "the maintenance of abundant infinitesimal variation in the gene pool" replaces "fluctuation" while leaving the rest of Darwin's theory unchanged.


Summary

Darwin espoused a theory of evolution, not merely a principle of selection. If this theory merely asserted the principle of selection, then no possible finding in genetics could contradict it. In fact, Darwin's theory invoked the principle of selection, in the context of a mechanism he called "fluctuation", to account for most of the actual facts of evolution, leaving a residue to be explained by other means (Lamarckian and Buffonian effects)— other means that Darwin's followers soon rejected as untenable, leaving only the fluctuation-selection process.

Thus, prior to the discovery of genetics, Darwin's theory was understood correctly to rely on continuous hereditary variation that Darwin called "fluctuation", and that was induced by environmental conditions, not inherited from parents. The Mendelians argued that, if we wish to understand the "the basis of evolution— the material on which selection works", we must look to mutation, not to Darwin's "fluctuations", because variations induced by conditions are not heritable.

Little of this is understood today, because "Darwinism" or "Darwin's theory" has been redefined, and the original meaning of "Darwin's theory" has gone done the proverbial memory hole.


References

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

Darwin, C. 1859. On the Origin of Species. John Murray, London.

Darwin, C. 1883. Variation of Animals and Plants under Domestication. D. Appleton & Co., New York.

Eldredge, N. 2001. The Triumph of Evolution and the Failure of Creationism. W H Freeman & Co.

Ford, E. B. 1938. The Genetic Basis of Adaptation. Pp. 43-56 in G. R. de Beer, ed. Evolution. Clarendon Press, Oxford.

Johannsen, W. L. 1903. Erblichkeit in Populationen und in reinen Linien. Gustav Fischer, Jena.

Morgan, T. H. 1916. A Critique of the Theory of Evolution. Princeton University Press, Princeton, NJ.

Muller, H. J. 1956. On the Relation between Chromosome Changes and Gene Mutation. Brookhaven Symposia in Biology 8:126-147.

Punnett, R. C. 1911. Mendelism. MacMillan.


Appendix: Darwin's principles of heredity

Three passages below illustrate Darwin's view of the emergence of hereditary variation. The first indicates that the emergence of hereditary variation occurs on the scale of a few generations— no waiting around for mutations— and that the fluctuations build up cumulatively:

"It seems clear that organic beings must be exposed during several generations to new conditions to cause any great amount of variation; and that, when the organisation has once begun to vary, it generally continues varying for many generations." (Darwin, 1859, Ch. 1; online source

Darwin knew that "sports" (mutants) could have heritable effects, but he imagined that infinitesimal fluctuations were even more likely to be heritable:

"If strange and rare deviations of structure are really inherited, less strange and commoner deviations may be freely admitted to be heritable. Perhaps the correct way of viewing the whole subject would be, to look at the inheritance of every character whatever as the rule, and non-inheritance as the anomaly" (Darwin, 1859, Ch. 1; online source).

Darwin learned about heredity the hard way: by exchanging hand-written letters with hobbyists and stockmen who bred pigeons, sheep, dogs, and so on. Below he is describing an experiment in domestication of ducks from wild eggs, based on information provided by Mr. Hewitt, a source referenced by Darwin many times in his works:

"Mr. Hewitt found that his young birds always changed and deteriorated in character in the course of two or three generations; notwithstanding that great care was taken to prevent their crossing with tame ducks. After the third generation his birds lost the elegant carriage of the wild species, and began to acquire the gait of the common duck. They increased in size in each generation, and their legs became less fine. The white collar round the neck of the mallard became broader and less regular, and some of the longer primary wing-feathers became more or less white. When this occurred, Mr. Hewitt destroyed nearly the whole of his stock and procured fresh eggs from wild nests; so that he never bred the same family for more than five or six generations. His birds continued to pair together, and never became polygamous like the common domestic duck. I have given these details, because no other case, as far as I know, has been so carefully recorded by a competent observer of the progress of change in wild birds reared for several generations in a domestic condition. "(Darwin, 1883, p. 293; online source)

Thus, Darwin is describing subtle variations that emerge in response to new conditions, and that emerge immediately or, at least, within a few generations. He saw hereditary fluctuation as an effectively continuous process, i.e., a process that can be subdivided arbitrarily in time and in outcome because it is the summation of infinitesimal increments. Adaptation can happen rapidly and reliably because organisms start to vary immediately upon encountering new conditions. Similar variations will be manifested in many individuals (as in the case of the ducks above), so that multiple members of a "race" may emerge and interbreed simultaneously with, or prior to, selection. This avoids the problems posed by the swamping effect of blending inheritance (Darwin did not believe that a solitary variant could begin an evolutionary change). Darwin's principles of variation are roughly that

  • hereditary variation emerges in response to "altered conditions of life" (e.g., domestication);
  • the process is so rapid and productive that visible effects appear in one or a few generations;
  • continuous ("infinitesimal", "insensible") fluctuations occur in virtually all characters;
  • some effects are definite or reliable ("all or nearly all the offspring of individuals exposed to certain coditions during several generations are modified in the same manner"), while others are "indefinite" (isotropic);
  • definite effects reflect mainly internal (developmental) causes, but also external (environmental) and Lamarckian causes ("effects of use and disuse").

Notes

1 An updated version of this post will be available at http://www.molevol.org/cdblog/mutationism_myth2

2 Don't blame me for this egregious ambiguity, which we will address in a future post.

3 Today we would call these laws "principles" or "generalizations". "Laws" in 19th century science are empirical generalizations, reached by the method of Baconian induction: collect lots of facts and distill them into generalizations.




Thursday, May 20, 2010

The Mutationism Myth: III Foundations of Evolutionary Genetics

 
This is the fifth 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 Curious Disconnect


Today in the Curious Disconnect we continue with our series on the Mutationism Myth. In this oft-told story (see part 1), the discovery of genetics in 1900 leads to rejection of Darwin's theory and the rise of "mutationism", a laughable1 theory that imagines evolution by mutation alone, without selection. "Mutationism" prevails for a generation, until Fisher, Haldane and Wright show that genetics is the missing key to Darwinism. In the conclusion to the story, the world is set right again when the "Modern Synthesis", combining selection with Mendelian genetics, shoulders aside the mutationist heresy, which ends up in the dustbin of history with the other "doomed rivals" of Darwin's great theory.2

Thats the story, at least. In reality- as we found out in part 2-, the Mendelians rejected Darwin's errant principles of heredity, not his principle of selection. What kind of view did the Mendelians develop? Addressing this question is our next challenge. Today, in part 3, we'll consider aspects of the Mendelian view that became the foundations of mainstream 20th-century thinking. In part 4, we'll delve into some "non-Darwinian" or "anti-Darwinian" aspects that were rejected, or merely ignored.

The Mutationism Myth. 3. Foundations of evolutionary genetics


Darwin's "Natural Selection" theory posited a smooth and automatic process of adaptation to altered conditions, dependent on infinitesimal hereditary fluctuations ("indefinite variability", in Darwin's terminology) induced by the effect of "altered conditions of life" on the "sexual organs". As we discovered in part 2, geneticists rejected fluctuation because it is incompatible with the assumption of exclusively Mendelian inheritance, an assumption embraced eagerly by geneticists, and held in suspicion by others for many years. As Bateson wrote:
"To Darwin the question, What is a variation? presented no difficulties. Any difference between parent and offspring was a variation. Now we have to be more precise. First we must, as de Vries has shown, distinguish real, genetic, variation from fluctuational variations, due to environmental and other accidents, which cannot be transmitted." (p. 95)
and as Morgan wrote:
"As has been explained, the kind of variability on which Darwin based his theory of natural selection can no longer be used in support of that theory, because, in the first place, in so far as fluctuating variations are due to environmental effect, these differences are now known not to be inherited, and because, in the second place, selection of the differences between individuals, due to the then existing genetic variants, while changing the number of individuals of a given kind, will not introduce anything new. The essential [feature] of the evolutionary process is the occurrence of new characteristics." p. 148-149 of Morgan (1932) 3

Because heredity and variation did not behave in the manner assumed by Darwin and his followers, it was up to a new generation of evolutionists to develop a new understanding of evolution. Thus, at a time when naturalists were dismissing genetics and clinging to 19th-century views of heredity, including Darwinism and Lamarckism, a group of Young Turks4 was laying the foundations of the genetics-based understanding of evolution that dominated the 20th century.

The concept of population genetics


To understand these foundations, I need to say a few words about the theoretical side of evolutionary genetics, often referred to as "population genetics". Please recall from Theory vs. Theory that when we talk about population genetics theory or music theory, thats a different sense of "theory" from Lamarck's theory or the prion theory of disease. Previously, we called them theory2 (body of abstract principles) and theory1 (grand conjecture).

Population genetics theory2 (roughly speaking) works out the implications of transmission genetics in populations of reproducing organisms, focusing on implications of such Mendelian phenomena as biparental inheritance, chromosome assortment, mutation, recombination, sex-linked inheritance, and so on.

As it exists today, population genetics theory2 covers a wide range of possible worlds, and thus a wide range of possible theories1. For instance, it provides classic equations to treat allele frequencies continuously and deterministically (e.g., Hardy-Weinberg), and at the same time, it provides another framework for addressing probabilistic changes with random drift. Is evolution deterministic or probabilistic? Population genetics theory2 doesn't say- it allows us to consider both possibilities. Is evolutionary change smooth or does it come in chunks? Population genetics theory2 doesn't say: it provides a quantitative genetics framework for continuous changes in quantitative characters, and a completely different framework for molecular evolutionists examining discrete characters. There are limiting cases where these different frameworks converge in some respects, but there is not any single realizable world in which all of population genetics theory2 applies, thus theoretical population genetics can't be understood as a theory1.

Crudely speaking, three frameworks of population genetics theory have been important in the 20th century: the stability analysis5 of systems of continuous allele frequencies, initially deterministic a la Hardy-Weinberg (or Lewontin-Kojima and so on) and later stochastic; the "quantitative genetics" theory of generational change in continuous-valued phenotypic characters (with implicit genetics) subject to selection; and the dynamics of the steady-state origin-fixation process, which was not an important paradigm until Kimura proposed the neutral theory.

The Bateson-Saunders equilibrium


In a landmark 1902 report to the Evolution committee of the Royal Society, Bateson and Saunders report some of their own findings and, more generally, try to explain the new science of Mendelian genetics, and the implications of Mendel's rules for evolution. In one of many fascinating comments, Bateson and Saunders suggeest that:
"It will be of great interest to study the statistics of such a population [with recognizable Mendelian characters] in nature. If the degree of dominance can be experimentally determined, or the heterozygote recognised, and we can suppose that all forms mate together with equal freedom and fertility, and that there is no natural selection in respect of the allelomorphs, it should be possible to predict the proportions of the several components of the population with some accuracy. Conversely, departures from the calculated result would then throw no little light on the influence of disturbing factors, selection, and the like.
Those of you who know your population genetics will recognize, in this passage, a paradigm that continues to play a key role in contemporary research as a "zero-force" model, describing the case of an unperturbed system, i.e., a system at rest. Deviations from this resting state indicate the perturbing effect of some factor or force.

In 1908, Hardy and Weinberg independently derived solutions for the frequencies of genotypes and alleles in the zero-force model of Bateson and Saunders. The mathematical solution to the Hardy-Weinberg equilibrium, as it came to be called, is sufficiently trivial that publishing it was nearly beneath the dignity of G.H. Hardy, the archetypal pure mathematician. In his paper, Hardy seems to sneer at biologists, saying "I should have expected the very simple point which I wish to make to have been familiar to biologists". Legend has it that Hardy learned of this problem while playing cricket with Punnett, the Mendelian, providing an early example of how interdisciplinary work is done.

The research program that eventually developed around this model was exactly as Bateson and Saunders imagined: compute the Hardy-Weinberg equilibrium, compare this to the observed frequencies, then interpret any deviations in terms of "the influence of disturbing factors". Researchers continue to use it, as one may find by searching PubMed with "hardy-weinberg AND 2009 [date]", which yields 532 publications for 2009. Contemporary philosophers discussing causation in evolutionary theory make frequent reference to Hardy-Weinberg as a zero-force law (see Stephens, 2001).

Given the crystal-clear statement of the problem by Bateson and Saunders, including the assumptions and the interpretive framework, should we not call it the Bateson-Saunders-Hardy-Weinberg equilibrium (or the Bateson-Saunders-Weinberg equilibrium, saving Hardy the embarrassment of receiving credit for something practical 6)?

Morgan's origin-fixation process


An entirely different, but similarly prescient, model is found in T.H. Morgan's 1916 book:
"If through a mutation a character appears that is neither advantageous nor disadvantageous, but indifferent, the chance that it may become established in the race is extremely small, although by good luck such a thing may occur rarely. It makes no difference whether the character in question is a dominant or a recessive one, the chance of its becoming established is exactly the same. If through a mutation a character appears that has an injurious effect, however slight this may be, it has practically no chance of becoming established.
If through a mutation a character appears that has a beneficial influence on the individual, the chance that the individual will survive is increased, not only for itself, but for all of its descendants that come to inherit this character. It is this increase in the number of individuals possessing a particular character, that might have an influence on the course of evolution." (187-189)
This is an abbreviated framework for understanding evolution under the "new mutations" or "mutation-limited" view that is now commonplace in molecular evolution. A new mutation arises and may "become established- we would say "become fixed" or "reach fixation" in population-genetics jargon- with a probability (not a certainty) that depends on its effects. If its effects are injurious, is has practically no chance of being established, and so on.

Morgan's verbal description is remarkably accurate. Later, in the 1920s, Haldane, Wright, and Fisher began to work out some approximations for the probability of fixation of a new mutant allele. For newly introduced neutral alleles,  (substitute 2N for diploids), where N is the population size, and this value is not affected by recessivity or dominance, just as Morgan says; for a newly introduced beneficial allele, , where s is the selective advantage; for a significantly deleterious allele, the probability of fixation is vanishingly small. Later, diffusion theory was used to derive a more general expression for the probability of fixation (e.g., Gillespie, 1998, p. 82)

where the starting frequency p would be 1/N for a new mutation in the haploid case (and 1/2N for the diploid case).

To the extent that there was a distinctive "mutationist" perspective on evolutionary genetics that was rejected for its non-Darwinian implications, this was it. While Haldane, Fisher and Wright worked out the theory2 for the probability of fixation of a new mutation, they didn't use this knowledge for anything important, because evolution by new mutations was not part of their theory1 of evolution. Instead, Morgan's view of evolution as a series of mutation-fixation events was rejected by the Modern Synthesis as the "lucky mutant" view, and was ignored for nearly 50 years; Kimura popularized a neutral version of this view, which remained associated with neutral evolution for another 30 years; and in the past 10 years, Morgan's perspective is emerging as a more general view that may serve as the basis for models of adaptation (e.g., Orr, 2002).

The Mendelian interpretation of continuous variation


The advocates of Darwin's view of blending inheritance and fluctuation fought hard against Mendelism early in the 20th century, leading to the infamous biometrician-Mendelian debate. Thus, a century ago, it was necessary to defend Mendelian principles from attack by those who- disparaging Mendelism's simplistic rules and suspecting its experimental foundations in "artificial" breeding- held out hopes for a fuzzier, more organic conception of heredity and variation that would fit better with Darwin's view. In Bateson's 1902 "defense" of Mendelism, he provides a Mendelian interpretation of continuous variation:
"In the case of a population presenting continuous variation in regard to say, stature, it is easy to see how purity of the gametes in respect of any intensities of that character might not in ordinary circumstances be capable of detection. There are doubtless more than two pure gametic forms of this character, but there may quite conceivably be six or eight. When it is remembered that each heterozygous combination of any two may have its own appropriate stature, and that such a character is distinctly dependent on external conditions, the mere fact that the observed curves of stature give 'chance distributions' is not surprising and may still be compatible with purity of gametes in respect of certain pure types." (p. 31)
By "chance distribution", Bateson is invoking what we now call a "normal distribution". Such a distribution "may still be compatible with the purity of the gametes", i.e., compatible with Mendelian inheritance, because it can result by the combined effects of a multiplicity of Mendelian loci (6 or 8, he imagines), each with 2 homozygotes and 1 heterozygote, with environmental variation due to "external conditions".

Thus, Bateson interpreted quantitative characters precisely as we do today, as the result of overlaying environmental fluctuation on a discrete distribution of genetic types. This interpretation is not due to little Ronny Fisher, the 12-year-old boy who would grow up to be a founder of mathematical population genetics and would declare that genetics was the key to Darwin's theory7, but to Bateson and other geneticists, including Danish botanist Wilhelm Johannsen and the Swedish geneticist Herman Nilsson-Ehle.

The Mendelian interpretation was bolstered by a series of precise quantitative experiments conducted by Johannsen with the Princess bean. Johannsen isolated 19 stable self-fertilizing lines, each of which produced seeds with a different average weight. Planting any single variety would produce a smooth distribution of seed weights. Johannsen selected larger beans to plant a new generation, but this had no significant effect on the distribution of seed weights, proving that this newly arising variation was not heritable Darwinian fluctuation, but non-heritable somatic variation. Johannsen coined the terms "genotype" and "phenotype" to help explain this distinction.

By 1909, both Johannsen and Nilsson-Ehle had contrived to generate populations that, at the level of "genotype", were known mixtures of discrete Mendelian types, but which- at the level of "phenotype"- produced a nice smooth bell-shaped distribution. Johannsen's distributions of beans are reproduced in the figure below (right) from Morgan (1916; online source). 

The evolution of quantitative characters


Finally, the Mendelians developed a causal theory for the gradual change in a quantitative character due to selection that negotiated the phenotype-genotype distinction and was appropriately probabilistic.

In the Darwinian view based on fluctuation and blending of hereditary substances, the superficial appearance that the whole population has shifted continuously and homogeneously reflects the underlying reality that hereditary substances have shifted continuously and homogeneously.

The new Mendelian view differed in two respects. First, given the genotype-phenotype distinction, selection of a particular phenotypic range implicates hereditary factors indirectly and probabilistically. For instance, Punnett (1911) constructs a simplified example in which there are just 3 genetically defined types, A, B and C, with mean weights of 10, 12 and 14 grains (a "grain" is a unit of weight equal to 0.065 gram). "A seed that weighs 12 grains may belong to any of these three strains. It may be an average seed of B, or a rather large seed of A, or a rather small seed of C" (p. 162; online source):
"On this view we can understand why selection of the largest seed[s] raises the average weight in the next generation. We are picking out more of C and less of A and B, and as this process is repeated the proportion of C gradually increases and we get the appearance of selection acting on a continuously varying homogenous material and producing a permanent effect."
Second, as the Mendelians stressed repeatedly, the end result of this process is a not a new complement of hereditary factors, but a mixture of old components in new and different proportions. The hereditary factors are not changed by this process (as Darwin and his followers wrongly believed): only their proportions in the population are changed. Without new mutations, the new population would never transcend the genetic limits inherent in the original mix.

Homework


The popular view of history reflected in the Mutationism Myth is that our contemporary understanding of evolution began with Fisher, Haldane and Wright, not with Bateson, Morgan, Johannsen, Punnett and others. I see this as a whitewashed version of history, in which the contributions of the Mendelians have been erased.

But lets consider for a moment that, just as Darwin's followers did not give up on blending inheritance without a nasty fight that created lasting suspicions about geneticists, they are not likely to give up Synthesis Historiography8 without a nasty fight that will leave a stain on critics such as myself. So, how does one convincingly establish a point about influence or credit? How do we know whose views were influential and whose views were purged? Here are some examples of types of information that might be useful:
  • A popular evolution education web site has a timeline listing important contributors to evolutionary thinking. The timeline has a gap of a whole generation between the late-19th-century neo-Darwinians (e.g., Weismann) and the early "Synthesis" architects. Kimura is not listed.
  • Morgan published several books on evolution that went through multiple printings; the Boston Public Library includes his 1916 book in its list of 100 most influential books of the 20th century.
  • The Oxford Encyclopedia of Evolution, which includes biographic entries, does not have an entry for any Mendelian except Morgan, whose evolutionary views are not discussed.
In what other ways might we establish objectively that certain scientists, and not others, receive credit for their work and get included in histories? How could you generate a large amount of data quickly? How could one show an unwarranted or extra-scientific bias for or against certain authors, i.e., excluding the alternative possibility that "the judgment of history" favoring one person over another reflects true scientific merit?

Conclusion


The Mutationism Myth suggests that our contemporary understanding of evolution did not emerge until Fisher, Haldane and Wright combined Darwin's principle of selection with Mendelian genetics; and that a generation was wasted while Mendelians developed a "doomed rival" to Darwin's great theory, in the form of a "mutationist" view that denied selection.

In fact, the Mendelians did not develop such a view. Instead, their interpretations paved the way for the Modern Synthesis and laid the foundations for our contemporary genetics-based understanding of evolution: they developed the Hardy-Weinberg model, interpreted quantitative trait evolution correctly, and even thought ahead to the "new mutations" perspective currently making inroads into evolutionary genetics.

Among the Mendelians, I also would count Nikolai Vavilov, the extraordinary Russian geneticist who started the first global seed bank (which persists today at the Vavilov Institute), leading expeditions that collected some 200,000 seeds. In 1922 he made a fascinating contribution to "mutationist" thinking, proposing parallel variations as a key component of parallel evolution. Vavilov was sent by the Soviets to a prison camp, where he died in 1943.

The Soviets purged Vavilov because of his opposition to Lysenkoism, the non-Mendelian theory of genetics with a Lamarckian theme of improvement-through-effort that fit nicely with Soviet ideology. Why were the contributions of Mendelians purged from our history, leaving the false impression of a generation-long gap in our intellectual history? Why don't we count Bateson, Morgan, Punnett, Johannsen, and others among the "founders" of modern evolutionary thinking? Possible answers to this question will emerge in part 4 of The Mutationism Myth, where we explore the non-Darwinian aspects of Mendelian thinking, and in part 5, where we consider the "Modern Synthesis" as a restoration of Darwinian orthodoxy.


References

Batson, W., and E. R. Saunders. 1902. Experimental Studies in the Physiology of Heredity. Reports to the Evolution Committee. Royal Society. (Bateson%20saunders&pg=PP1#v=onepage&q&f=false">online source)

Bateson, W. 1902. Mendel's Principles of Heredity: A Defense. Cambridge University Press, Cambridge. (online source)

Bateson, W. 1909. Heredity and Variation in Modern Light. Pp. 85-101 in A. C. Seward, ed. Darwin and Modern Science: Essays in Commemoration of the Centenary of the Birgh of Charles Darwin and of the Fiftieth Anniversary of the publication of the Origin of Species. Cambridge, London.

Gillespie, J. H. 1998. Population Genetics: A Concise Guide. Johns Hopkins University Press, Baltimore, MD.

Morgan, T. H. 1932. The Scientific Basis of Evolution. W.W. Norton & Co., New York.

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

Punnett, R. C. 1911. Mendelism. MacMillan. http://www.archive.org/stream/mendelism00punn#page/172

Stephens, C. 2001. Selection, Drift, and the "Forces" of Evolution. Philosophy of Science 71:550-570.

Sturtevant, A. H. 1965. The Early Mendelians. Proceedings of the American Philosophical Society 109:199-208.

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


Notes

1 As quoted in part 1, mutationism is a source of "mirth" for Dawkins.

2 The words "doomed rivals" are also from Dawkins. Back when I was a lad in school, my evolution professor- Dr. Kenneth Christiansen, who has been at Grinnell College for at least 45 years and is still there today- had a slightly gentler way of referring to alternative theories as the "also-rans".

3 Note that Morgan's choice of words leaves some wiggle room that some other kind of variability could be offered "in support of" Darwin's theory. A century ago, admiration for Darwin was nearly universal, as it is today. The meaning of Darwin's theory, and ownership of the "Darwin" brand, were contested by scientists. By 1950, the "Modern Synthesis" school had captured the Darwin brand and began to use it more aggressively than they had dared to do before. However, things might have turned out differently. De Vries labeled himself as a "Darwinian". Bateson and others sometimes cozied up to "Darwinism".

4 Sturtevant (1965) lists 22 Mendelians who published from 1900 to 1905, and notes that all but 5 were under 40 (the older exceptions are de Vries, Garrod, Johannson, Wilson and Lang).

5 "stability analysis" means finding the "attractors" or points of stability in a dynamic system.

6 Hardy reveled in the purity of mathematics and stated that he had no desire to do anything useful. He said that his most important discovery was Srinivasan Ramanujan, a largely self-taught Indian genius who had written to Hardy and others seeking a mentor- only Hardy recognized his genius.

7 Synthesis Historiography attributes the resolution of Darwinism and Mendelism to Fisher (1918). In reality, the problem that Fisher (1918) solved was how to derive Galton's law as a formal consequence of Mendelian principles. Either this is a red herring, or it suggests that as late as 1918, "Darwinism" still implied a rejection of Mendelism in favor of blending. Note that Galton himself lacked the ideological purism of his followers: he believed in discontinuous evolutionary changes and felt that this was a missing element in Darwin's theory.

8 "Synthesis Historiography" is Ron Amundson's term for the industry of writing versions of history in which the Modern Synthesis is presented as the manifest destiny of science, and Mayr, et al are the heroes, while their intellectual opponents are fools and knaves.

*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_myth3 (Arlin Stoltzfus, ©2010)

Thursday, June 03, 2010

The Mutationism Myth, IV: Mendelian Heterodoxies

This is the sixth 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.

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

Last month, we debunked the Mutationism Myth and learned why the discovery of genetics in 1900 led "Mendelians" to reject Darwin's view. These same Mendelians went on to lay the foundations of a genetics-based view of evolution, during a period of rapid innovation from 1900 to 1915. But this begs another question: if the Mendelians invented the 20th-century consensus, and just left it to others to work out the math, why aren't they lauded as "founders" of modern neo-Darwinism, instead of being derided as fools? We'll find out in part 4 (today), and part 5, here on on The Curious Disconnect (credits).

The Mutationism Myth, part 4. Mendelian Heterodoxies

The reader who has been following our story so far may be baffled. As we found out in part 3, the Mendelians understood how to conceptualize a population as a dynamic system of allele and genotype frequencies (the Bateson-Saunders equilibrium), how to see evolutionary change as a probabilistic 2-step process of the introduction and acceptance-or-rejection of mutations, and how to think about selection-driven changes in a quantitative trait.

Why don't the Mendelians get credit for laying the foundations of the 20th-century consensus?

As we will learn today and in part 5, the Mendelian view is not the 20th-century "neo-Darwinian" consensus. The Mendelians combined genetics with selection. By contrast, the 20th-century consensus combines genetics with Darwinism, i.e., the Modern Synthesis invokes the principles of genetics to prop up 19-century doctrines of Darwin and his followers, such as natura non facit salta, the creativity of selection, the idea of evolution as a process of adaptive adjustment initiated by changed conditions, and the notion that the course or direction of evolution is determined by selection but not by "random" variation.

When I mock the Modern Synthesis for its Darwinian excesses, I don't want to give the impression that its wrong for a theory1 to go beyond what is demanded by the facts. All theories1 must go beyond the facts, taking risks. While most theories, it seems, take risks in the service of conceptual simplicity, the Modern Synthesis takes risks in the service of 19th-century Darwinian doctrines. On the basis of these commitments, e.g., its rejection of the "lucky mutant" view necessary to understand molecular evolution, the Modern Synthesis later failed.

But that's getting ahead of ourselves. Our task right now is to begin sorting out why the Modern Synthesis is Darwinian, while the Mendelian view it replaced was not.

"Mutationism" vs the Mendelian "view"

My understanding of the evolutionary views of "Mendelians" is based on the works of Bateson (1894, 1900, 1902, 1909), Johannsen (1903, 1909), de Vries (1905), Morgan (1903, 1916, 1925, 1932), Punnett (1911), Vavilov (1922), Shull (1936) and, with some reservations, Goldschmidt (1940). Every time I research the Mendelians, I find new material and revise my views, e.g., I am resolving more and more to avoid the label "mutationism", which I see increasingly as a pejorative term preferred by opponents rather than supporters.

I also have come to understand more confidently that, while the Mendelians had much to say about evolution— indeed, many of them were motivated to study heredity precisely because of their interest in evolution—, they didn't have a unified "view". With the exception of de Vries, the Mendelians did not propose what we would call "a theory of evolution", i.e., a Grand Unified Theory1 of Evolution (GUTE) that purports to be comprehensive. Instead they argued that we need to rethink how evolution works, and follow the implications of genetics wherever they led— typically away from a more Darwinian view emphasizing infinitesimalism, determinism, and selective control.

Thus, while "Mendelism" (in contrast to "mutationism") does not sound like a very good name for a theory of evolution, that's ok, because it's not: Mendelism is a theory of genetics, and the "Mendelian view of evolution" is simply what the early Mendelian geneticists thought about evolution.

Recognizing the lack of a Mendelian GUTE helps us to appreciate more fully the role of the "Modern Synthesis" in the development of evolutionary thinking, and in the Mutationism Story. In the 19th century, before the discovery of genetics, scientists divided their allegiance among multiple GUTEs, most importantly, Darwinism and Lamarckism. By 1910, it was clear to leading thinkers that genetics had undermined all 19th-century GUTEs (including de Vries's "MutationsTheorie" 1). The geneticists (for whatever reason) did not fill this gap by proposing a new GUTE. Thus, while the Mendelian era from 1900 to 1930 was not a stagnant period, it may be seen as a GUTE-less period that ended with the rise of the Modern Synthesis.2

Initiative

The view that events of mutation initiate evolutionary change contrasts with the view that evolutionary change is a series of adjustments or responses to external stimuli, as in the views of Buffon or Darwin. Punnett writes:
"With the advent of heredity as a definite science we have been led to revise our views as to the nature of variation, and consequently in some respects as to the trend of evolution. Heritable variation has a definite basis in the gamete, and it is to the gamete, therefore, not to the individual, that we must look for the initiation of this process. Somewhere or other in the course of their production is added or removed the factor upon whose removal or addition the new variation owes its existence." (p. 141)

Variation (mutation) is the locale of evolutionary initiative, to the extent that both 1) the possibilities or directions of future evolutionary change are established at the moment of the mutation (i.e., mutation as a source of creativity or direction, as addressed below); and 2) the dynamics of evolutionary change depend on the times of appearance of mutations. This second sense depends somewhat on the "new mutations" conception of evolution as a 2-step process of the introduction of a variant followed by its acceptance or rejection.

In this view, one may expect that the dynamics of evolution (adaptive or not) will depend on mutation rates. In fact, the Mendelians sometimes recognized this kinetic dependence, as when Shull (1936, p. 140) argues, "a gene produced twice by mutation has twice as good a chance to survive as if produced only once" (see also Morgan 1925, p. 142). This non-Darwinian idea that propensities of variation could make an evolutionary change more or less likely was not a new thought (indeed it was understood as the potential mechanistic basis of "orthogenesis"), but now it could be given a more precise interpretation.

The architects of the Modern Synthesis later ridiculed what they called the "lucky mutant" view (Mayr 1963, p. 101), but it was hardly an unsophisticated appeal to chance, as we saw in part 3 with the quotation illustrating Morgan's stunning grasp of the probability of acceptance of new mutations. Punnett made a similar statement in his 1911 book (online source):

"The new variation springs into being by a sudden step, not by a process of gradual and almost imperceptible augmentation. It is not continuous but discontinuous, because it is based upon the presence or absence of some definite factor or factors— upon discontinuity in the gametes from which it sprang. Once formed, its continued existence is subject to the arbitrament of natural selection. If of value in the struggle for existence[,] natural selection will decide that those who possess it shall have a better chance of survival and of leaving offspring than those who do not possess it. If it is harmful to the individual[,] natural selection will soon bring about its elimination. But if the new variation is neither harmful nor useful[,] there seems no reason why it should not persist."

By rejecting this component of the Mendelian view of evolution, the Modern Synthesis disallowed a direct link between the rate of mutation and the rate of evolution, making the theory incompatible with the results of studies of "molecular evolution" that began to emerge a half-century after the insights of Punnett and Morgan.

Discontinuity

To understand the issue of discontinuity or discreteness, again we must distinguish 2 senses. In the passage quoted above from Punnett, it's clear that Punnett is talking about what we might call a "mechanistically" discontinuous change in the sense that the mutant factor comes into existence at a specific point in time, due to an event of mutation, rather than gradually, due to an ongoing process of "imperceptible augmentation".

Mayr and others frequently misinterpret the Mendelian commitment to mechanistic discontinuity as a commitment to dramatic phenotypic saltations, but this is a different issue entirely.

In fact, the Mendelians entertained a range of views on the sizes of evolutionary changes important in evolution, excluding only the Darwinian extreme of relying wholly on "insensible" or "infinitesimal" changes. De Vries adopted an antithetical position emphasizing dramatic changes that create new species (with intra-specific variation and selection playing only a minor role). Bateson challenged

"the crude belief that living beings are plastic conglomerates of miscellaneous attributes . . . and that by Variation any of these attributes may be subtracted or any other attribute added in indefinite proportion" (Bateson 1894, p. 80)
Bateson's view was that, if we wish to understand evolution, we must move beyond speculative reconstructions of past events based on assuming variability and then assuming some adaptive rationale, and start studying what variations actually tend to occur. In pursuit of a less speculative approach to evolution, Bateson traveled the world to catalog 886 cases of discontinuous variation, published in his volume "Materials for the Study of Variation" (Bateson 1894); he planned a second volume on continuous variation but never completed it. Morgan argued that "even the smallest changes that add to or subtract from a part in the smallest measurable degree" may arise by mutation, and these are "the most probable variants that make a theory of evolution possible" (Morgan 1925, p. 129).

Both senses of "discontinuity" represent departures from late-19th-century and 20th-century versions of Darwinism. The mechanistically discretized view of the mutationists clashed with the incipient Modern Synthesis view in Punnett's (1930) Nature review of Fisher's The Genetical Theory of Natural Selection:

Throughout the book one gets the impression that Dr. Fisher views the evolutionary process as a very gradual, almost impalpable one, in spite of the discontinuous basis upon which it works. Perhaps this is because he regards a given population as an entity with its own peculiar properties as such, whereas for the geneticist it is a collection of individuals.
Much of the neo-Darwinian antipathy to "mutationists" was based on a negative reaction to the "saltationism" of de Vries and Goldschmidt, even though their views do not represent a shared commitment of the Mendelians. However, the mere fact that the Mendelians allowed some large changes distinguished them from the Darwinian view that "Natural selection can act only by the preservation and accumulation of infinitesimally small inherited modifications" (Darwin, Ch. 4, Origin of Species).

Creativity

The mutationists held that "the function of natural selection is selection and not creation. It has nothing to do with the formation of new variation" (Punnett 1911). Likewise, Bateson (1909) writes:

"we must relegate Selection to its proper place. Selection permits the viable to continue and decides that the nonviable shall perish; just as the temperature of our atmosphere decides that no liquid carbon shall be found on the face of the earth: but we do not suppose that the form of the diamond has been gradually achieved by a process of Selection. So again, as the course of descent branches in the successive generations, Selection determines along which branch Evolution shall proceed, but it does not decide what novelties that branch shall bring forth."
The creativity of mutation or, more properly, of mutation-and-altered-development (Stoltzfus, 2006), may be illustrated (in the extreme case) by Goldschmidt's concept of a "macromutation", akin to Galton's concept (invoked repeatedly by Bateson, 1894) of a shift between "positions of organic stability". If a variant toad arises with fully formed eyes in the roof of its mouth, such that it must open its mouth to see— as in the actual toad pictured on p. 97 of Dawkins (1996)— this is an extreme yet coordinated change, and a "macromutation" if it is heritable. If such a variant supplants the parental form or becomes a separate species, this is a non-Darwinian, saltational change in which creativity is due largely to mutation-and-altered-development. In the case of less dramatic transformations, the creative role of mutation-and-altered-development is correspondingly less dramatic.

In spite of Goldschmidt's notorious belief that distinctive phenotypic transformations suggested major genetic reorganizations ("systemic mutations"), he insisted that the complexity of the underlying genetic change is not the decisive issue:

It does not make any difference whether a single macroevolutionary step is caused by a major change within the chromosomal pattern, [that is,] a systemic mutation, or by a special kind of gene mutation with generalized effect, if such is imaginable. The decisive point is the single change which affects the entire reaction system of the developing organism simultaneously, as opposed to a slow accumulation of small additive changes. (Goldschmidt 1940, p. 251)
The claim that selection is creative is one of the key claims of Darwinism, advanced and defended by supporters of Darwinism, and rejected by its critics, as Gould (1977) documents extensively. We see this argument arising again and again up to the present day, e.g., the authors of a recent "evo-devo" book echo the century-old rhetoric of Mendelians, claiming that selection is not creative and is merely a "sieve" (Kirschner and Gerhardt, 2005), and in response (in the Nature review of this book), a dyed-in-the-wool Darwinist defends the ancient orthodoxy that selection is creative (Charlesworth, 2005). Later on, we will devote an entire post (probably more than one) to the Darwinian doctrine of selective creativity, and its relation to the Darwinian doctrine known as "gradualism".

Directionality

On a one-dimensional scale of fitness or adaptedness, every change is either "up" (beneficial) or "down" (deleterious), but in a multi-dimensional space of phenotypes, every change has a distinctive direction.

Punnett invoked mutation as a source of direction in considering features such as lepidopteran wing patterns (Punnett 1911, p. 145). A more typical statement was to draw a contrast with the views of Weissman, Fisher, and others who imagine variation in all directions. For instance, in the book review cited earlier, Punnett (1930) chides Fisher for denying to mutations "any importance in determining the direction of evolutionary change"; likewise Shull takes aim at Fisher's view:

"To assert, as Fisher does, that mutation has nothing to do with the direction of evolution is like assuming that a tetrahedron may fall, at different times, with ten or a hundred points uppermost. The ten points and ten opposite sides to fall upon do not exist. How great a restriction is placed upon the course of evolution by the inability of genes to mutate in certain ways it is impossible to tell; but it may easily be much greater than any of us suppose." (Shull, 1936, p. 448)

A clearer Mendelian concept of the influence of mutation emerges in regard to parallel evolution, which was assumed to indicate non-random tendencies of variation, since "it strains one's faith in the laws of chance to imagine that identical changes should crop out again and again if the possibilities are endless and the probabilities equal" (Shull 1935, p. 448). Vavilov noted that the same varieties or polymorphisms often occur in parallel, even in distantly related species in the same genus or family, and he argued for a causal role of this "law of homologous variation" (Vavilov 1922) in parallel evolution. As an example, Vavilov reports that lentils (Ervum lens), a food crop, and vetch (Vicia sativa), a weed, have many homologous variations, and notes that vetches sometimes mimic lentils so closely in cultivated fields that their seeds cannot be separated by mechanical sorters:

the role of natural selection in this case is quite clear. Man unconsciously, year after year, by his sorting machines separated varieties of vetches similar to lentils in size and form of seeds, and ripening simultaneously with lentils. The same varieties certainly existed long before selection itself, and the appearance of their series, irrespective of any selection, was in accordance with the laws of variation. (Vavilov 1922, p. 85)

Darwin preceded Vavilov in recognizing a principle of "analogous variation" due to a similar "inherited constitution", but denied it any influence on evolutionary change:

But characters thus gained [by analogous variation] would probably be of an unimportant nature, for the presence of all important characters will be governed by natural selection, in accordance with the diverse habits of the species, and will not be left to the mutual action of the conditions of life and of a similar inherited constitution. (ch. 5, Darwin 1859)

That is, while we might recognize a kind of dualism in Darwin's view, in the sense that both fluctuation and selection are required for change as opposed to non-change, Darwin insists that selection "governs" the course of evolution, over-ruling variation. Darwin's followers, likewise, emphasize that selection, while not sufficient to cause change by itself, is the proper cause of the manner of change (that is, its directionality, dynamics, creativity, and so on). Darwin's followers have an ideological commitment to giving selection a power to control or dominate "random" mutation, and a commitment to denying internal causes of direction in evolution (if you have these commitments, you are probably a Darwinian; if you don't, you are not— or maybe you're just confused). The Mendelians did not share these ideological commitments.

Nonetheless, the Mendelians were a long way, as we still are, from having a clear view of this issue. Shull once remarked "What the world most needs, then, is not a good five-cent cigar, but a workable— and correct— theory of orthogenesis" (p. 449), "orthogenesis" being the idea of a trend or direction due to intrinsic tendencies of variation. The Mendelians did not develop such a theory. In spite of knowing that some variations occur more often than others, they often spoke as though any conceivable variation were either possible or impossible, which I see— and I see it almost everywhere— as a sign of immature thinking on this topic.

Of course, we are not much better off today. The evo-devo field clearly needs an idea of developmental tendencies in variation as a source of direction, and leading thinkers have called (vaguely) for such an idea for 30 years, but the evo-devo field still has no theory and instead is schlepping around its clunky old "toolbox" metaphor. Apparently, this toolbox contains the tools that selection uses to build structures, revealing that evo-devoists remain Darwinians who personify selection as a craftsman. Elsewhere (Stoltzfus, 2006; Stoltzfus and Yampolsky, 2009; online source), I have argued that we manifestly need a causal theory of orthogenesis, linking tendencies of variation to tendencies of evolution, and I have outlined the conceptual and mechanistic basis for such a theory, including population-genetics modeling.

In a series of later posts, we will take up the issue of "source laws and consequence laws" of variation, i.e., source laws governing the emergence of variation, and consequence laws governing its influence on evolutionary change.

Synopsis

Upon the discovery of genetics in 1900, a new breed of scientists rejected Darwin's theory and began developing a new understanding of evolutionary change based on Mendelian principles. They combined genetics with Darwin's principle of selection, but departed from Darwin's view in arguing that evolutionary change is not composed entirely of infinitesimal increments, and in representing mutation as a source of discontinuity, directionality, creativity and initiative.

Yet, somehow, "Darwinism" returned in the form of the Modern Synthesis. This new view included all the principles of Mendelian genetics, yet rejected all the non-Darwinian innovations of the Mendelians. The restoration of Darwinism in the Modern Synthesis— an accomplishment based more on rhetorical sleight-of-hand than on population genetics theory— will be our topic next time.

References

Bateson, W. 1894. Materials for the Study of Variation, Treated with Especial Regard to Discontinuity in the Origin of Species. Macmillan, London.

Bateson, W. 1900. Problems of Heredity as a Subject for Horticultural Investigation. Journal of the Royal Horticultural Society 25:54-61.

Bateson, W. 1902. Mendel's Principles of Heredity: A Defense. Cambridge University Press, Cambridge.

Bateson, W. 1909. Heredity and Variation in Modern Light. Pp. 85-101 in A. C. Seward, ed. Darwin and Modern Science: Essays in Commemoration of the Centenary of the Birgh of Charles Darwin and of the Fiftieth Anniversary of the publication of the Origin of Species. Cambridge, London.

Bateson, W., and E. R. Saunders. 1902. Experimental Studies in the Physiology of Heredity. Reports to the Evolution Committee. Royal Society.

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

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

De Vries, H. 1905. Species and Varieties: Their Origin by Mutation. The Open Court Publishing Company, Chicago.

Goldschmidt, R. 1940. The Material Basis of Evolution. Yale University Press, New Haven.

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

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

Johannsen, W. L. 1903. Erblichkeit in Populationen und in reinen Linien. Gustav Fischer, Jena.

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

Morgan, T. H. 1903. Evolution and Adaptation. Macmillan, New York.

Morgan, T. H. 1916. A Critique of the Theory of Evolution. Princeton University Press, Princeton, NJ.

Morgan, T. H. 1925. Evolution and Genetics. Princeton University Press, Princeton.

Morgan, T. H. 1932. The Scientific Basis of Evolution. W.W. Norton & Co., New York.

Punnett, R. C. 1911. Mendelism. MacMillan.

Punnett, R. C. 1915. Mimicry in Butterflies.

Punnett, R. C. 1930. Genetics, Mathematics, and Natural Selection. Nature 126:595-597.

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

Stoltzfus, A. 2006. Mutationism and the Dual Causation of Evolutionary Change. Evol Dev 8:304-317.

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

Footnotes

1 Although de Vries continued to promote his "MutationsTheorie" for some years after 1900, it actually was a 19th-century theory of species-selection based on his work on Oenothera varieties, not on his work as one of the 3 re-discoverers of Mendel's principles.
2 The perceived need for a dominant GUTE, and the ideological immunity that develops around a dominant GUTE, are issues that we will address in a future post.

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_myth4 (Arlin Stoltzfus, ©2010)


Tuesday, June 22, 2010

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.




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.


References

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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)