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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.




Shoddy But Not "Junk"?

Philip Ball is a freelance science writer based in London (UK). He frequently writes for Nature. His latest article is a review of a recently published paper by John Avise [What a shoddy piece of work is man]. Apparently Avise has just published a paper in PNAS where he points out that our genome does not look like it was designed. It's an attack on Intelligent Design Creationism and Adaptationism.

I can't find the paper but I have read Avise's book, Inside the Human Genome so I'm familiar with his thesis—and I agree with it.

The purpose of this posting is not to review the points that John Avise makes but to comment on one of the points made by Philip Ball. At the end of his Nature review he says,
However — although heaven forbid that this should seem to let ID off the hook — it is worth pointing out that some of the genomic inefficiencies Avise lists are still imperfectly understood. We should be cautious about writing them off as 'flaws', lest we make the same mistake evident in the labelling as 'junk DNA' genomic material that seems increasingly to play a biological role. There seems little prospect that the genome will ever emerge as a paragon of good engineering, but we shouldn't too quickly derogate that which we do not yet understand.
THEME

Genomes & Junk DNA

I just gave a talk on junk DNA where I explained to my audience the nature of the scientific controversy. We know for a fact that our genome is littered with pseudogenes of all sorts and we know for a fact that more than 50% of our genome is repetitive DNA of one kind or another. A good hunk of that is degenerative transposons and fragements of transposons [Junk in your Genome: LINEs]. Another large hunk is Alu sequences: fragments of an ancient primate transposon derived from 7SL RNA [Transcription of the 7SL Gene].

We also know a great deal about introns and that knowledge leads to the conclusion that most intron sequences are dispensable. it's part of the junk in our genome. We know about the genetic load argument [Genetic Load, Neutral Theory, and Junk DNA] and we know about the C-Value Paradox. Most scientists who study the problem of junk DNA know about The Onion Test.

My point is that it's extremely misleading to suggest that our identification of junk DNA is based on a lack of understanding. That's simply not true. There are some very good scientific reasons for maintaining that most of our DNA is junk based on over 40 years of work on genome organization.

Yes, it's true that there have been some scientific challenges questioning the conclusion of those studies. There is a group of scientists who claim that vast amounts of our genome serve some mysterious purpose that's only vaguely defined. It could be regulation of some sort or even an entire new class of RNA-encoding genes that make us human.

These claims make the debate over junk DNA a scientific controversy but they certainly haven't succeeded in disproving the hypothesis. None of the recent claimants can explain pseudogenes and degenerative transposons, which make up more than half of our genome. None of the opponents can refute the genetic load argument.

Science writers like Philip Ball can be forgiven for not delving into the problem. It's easy to fall for the latest articles that purport to show function for a large part of what we call junk DNA. After all, those anti-junk proponents don't do their homework either and they gloss over all the data that contradicts their "new" hypothesis.

My point is that the idea of junk DNA is alive and well in spite of what modern science writers seem to think. It's just not true that today's scientists think we made a big mistake in the past by calling it junk DNA. This is still very much a scientific controversy and it's too soon to tell how it will pan out.

Personally, I think the evidence in favor of a large amount of junk in our genome is persuasive and I'd be very, very surprised if a significant amount of it turns out to be functional. I wish science writers would stop behaving as though the issue had been resolved and junk DNA is dead.


Wednesday, April 28, 2010

The Toronto Star Gets Suckered!

At least they weren't the only ones. The Toronto Star is a perfectly respectable newspaper. It's not one of those tabloids that publish anything in order to pander to the lowest common denominator.

But even a "respectable" newspaper can get taken in when it comes to religion. For some reason, the editors of this newspaper thought it was legitimate to publish a story on the latest announcement about the discovery of Noah's Ark [Noah’s Ark found, researchers claim]. They picked up on a story in a Chinese newspaper.

Anyone with an IQ over 100 knows there was no such thing as a world-wide deluge in 2800 BCE and there's no such thing as a giant ark built by some shepherd in Israel.

Science disproved that particular Biblical myth a long time ago. Whenever you see a story like this there are only two possibilities; either the "researchers" are making it up, or they were the victims of a hoax (or a bit of both). In this case, it seems to be mostly a hoax perpetrated on a gullible group who were only too willing to fall for it.

PZ Myers has the details: Latest Ark finding is a fake.

What about when a presumably respectable newspaper publishes something silly that flies in the face of everything we know about science and history? There's no excuse for that. Shame on The Toronto Star. Maybe they should hire a science journalist to save them from future embarrassment?




I Am Not a Crook

Sometimes you discover that you're related to people you'd rather not be related to. Here's a valid relationship between me and Richard Nixon.

Deborah Lockwood and her husband William Ward are my great9 grandparents. Deborah was born in Watertown Massachusetts in 1636 [see The Hanging of Goodwife Knapp in 1653]. William Ward was born in Fairfield Connecticut in 1631. Deborah's mother was Susanna Norman. There must be a million descendants of the Norman, Ward and Lockwood families. They're all related to Richard Nixon so I'm in good company.




Friday, April 23, 2010

What Is Evolutionary Theory? Futuyma vs Coyne

I've been under the impression that the distinction between the fact of evolution and evolutionary theory is not controversial—at least among evolutionary biologists. Ever since Gould, the point has been that the facts of evolution include things like common descent and the history of life on Earth. Evolutionary theory attempts to provide a mechanism that accounts for those fact and observations.

Richard Dawkins makes this clear in his book The Greatest Show on Earth (p. 17).
Biologists often make a distinction between the fact of evolution (all living things are cousins) and the theory of what drives it (they usually mean natural selection, and they may contrast it with rival theories such as Lamarck's theory of 'use and disuse' and 'the inheritance of acquired characteristics'). ... Nowadays it is no longer possible to dispute the fact of evolution itself—it has graduated to become a theorum or obviously supported fact—but it could still bedoubted (just) that natural selection is its major driving force.
The distinction is important. Things like common descent and the history of life are the facts that demonstrate evolution. Evolutionary theory offers a solid, widely-accepted, explanation of how evolution happens.

Douglas Futuyma has written one of the most respected textbooks on evolution. He agrees with this distinction—as do all other textbook authors that I know of. Here's what Futuyma says in Evolution 2nd ed. p. 4.
The explanation of how modification occurs and how ancestors gave rise to diverse descendants constitutes the theory of evolution. We now know that Darwin's hypothesis of natural selection on hereditary variation was correct, but we also know that there are more causes of evolution than Darwin realized, and that natural selection and hereditary variation themselves are more complex than he imagined. A body of ideas about the causes of evolution, including mutation, recombination, gene flow, isolation, random genetic drift, the many forms of natural selection, and other factors, constitute our current theory of evolution or "evolutionary theory." Like all theories in science, it is a work in progress, for we do not yet know the causes of all of evolution, or all the biological phenomena that evolutionary biology will have to explain. Indeed, some details may turn out to be wrong. But the main tenets of the theory, as far as it goes, are so well supported that most biologists confidently accept evolutionary theory as the foundation of the science of life.
No doubt you're puzzled about the purpose of this posting. You are probably saying to yourself. "So what? We all know that, already."

Apparently, not all of us agree. In an otherwise excellent review of Richard Dawkin's book, Jerry Coyne says the following [see: The Improbability Pump].
Demonstrating the truth of natural selection is just one of Dawkins's aims, for the theory of evolution is composed of several more or less independent parts, which I like to describe in one longish sentence: "Life on earth evolved gradually, beginning with one primitive species; it then branched out over time, throwing off many new and diverse species--and the process producing the illusion of design in organisms is natural selection." This sentence constitutes a scientific theory, which is not just a guess but an informed statement about the general principles that explain many observations about nature.
I think that's very wrong. First, it's wrong because it states that the history of life is a theory. Second, it's wrong because it states that the "illusion of design" is part of modern evolutionary theory (it isn't). Third, it's wrong because it only mentions natural selection and modern evolutionary theory is much more than that.

I hope this was just an attempt to (over-)simplify evolution for the readers of The Nation. In that case it might be (just) excusable. But I can't wait until the creationists get a hold of this review. They'll be delighted to learn that, according to Jerry Coyne, the gradual descent and diversification of life is only a theory.

They'll also be happy to learn from a prominent evolutionary biologist that design is part of modern evolutionary theory.


Prepare for a "Boobquake" on Monday, April 26, 2010

 
I don't know what I'm going to do on Monday. On the one hand, I should stay home in case there's a massive earthquake. On the other hand, I may miss all the fun if I stay home [Blogger: Show cleavage to test cleric’s quake theory].

I think I'll take my chances on the university campus.


Wednesday, April 21, 2010

Francis Collins on Compatibility

 
Many of us struggle with the controversy between science and religion. As one who argues that science and religion are not compatible (with minor exceptions), I try hard to understand the views of my opponents. One of the greatest challenges is to understand why Francis Collins sees his position as an argument in favor of compatibility.

Here's a video of a talk he gave last October at The Veritas Forum in California. All of it is really interesting but the punchline comes at 50 minutes when he gives a short summary of his beliefs.
[First Slide] Almighty God, who is not limited in space and time, created a universe 13.7 billion years ago with its parameters precisely tuned to allow the development of complexity over long periods of time.

[Second Slide] God's plan included the mechanism of evolution to create the marvelous diversity of living things on our planet. Most especially, that plan included human beings.

[Third Slide] After evolution, in the fullness of time, had prepared a sufficiently advanced neurological "house" (the brain), God gifted humanity with free will and with a soul. Thus humans received a special status, "made in God's image."

[Fourth Slide] We humans used our free will to disobey God, leading to our realization of being in violation of the Moral Law. Thus we were estranged from God. For Christians, Jesus is the solution to that estrangement.

That's it. A very simple but, I think, entirely compatible view that does no violence either to faith or to science. And puts them in a harmonious position ...
Collins goes on to describe this view as "Theistic Evolution." It could also be called the "New Creationism."

I can think of six, perfectly scientific, questions that could be asked.
  1. Is there any evidence of purposeful "fine tuning"?
  2. Is there any evidence that humans were inevitable?
  3. Is there any evidence of a Moral Law?
  4. Is there any evidence of a soul?
  5. Is there any evidence that humans have something called "free will" that other species lack?
  6. Is there any evidence that such a personal God exists?
I think the answer to all six question is "no," therefore, believing those things conflicts with science. They are supposed to part of the natural, observable, universe and they should all be detectable, if they exist.

The Language of God: A Scientist Presents Evidence for Belief from The Veritas Forum on Vimeo.




Argue Both Sides

 
One of the distinguishing features of a true scientific controversy is that there are good arguments on both sides. In my class on controversies and misconceptions, I teach my students that they have to recognize a real scientific controversy and, when they do, they should be prepared to argue both sides. That's the only way to demonstrate that they understand the issues.

Unfortunately, this simple concept is not widely practiced—even among scientists. Quite often we see a case being made for one side without even acknowledging that there's plenty of evidence for the opposing view. I'm giving a talk on Monday about "Junk DNA" and that's one of the main points. The current literature is full of claims about the demise of junk DNA. The claim is based on some recent findings but nobody ever mentions the older evidence that has to be refuted. When you're advocating a new model you have to do two things: (1) present evidence in favor of our model, and (2) demonstrate that evidence against your model should be rejected.

You can't do one without the other.

This rule only applies to controversies within science. In many cases, the trick is to recognize a "real" scientific controversy from one that only appears to be a scientific controversy. Take Intelligent Design Creationism for example ....

I was thrilled to see a posting by Granville Sewell on one of the IDiot blogs. The title suggested that he was finally recognizing that science had some valid points in this non-scientific controversy [Acknowledging our opponents’ strong points]. My "thrill" rapidly turned to disgust when I read the posting ....
In any debate, it is always good strategy to acknowledge your opponent’s strongest points, thereby taking them off the table. In the debate over ID, our opponents have two very strong points:

1. We have discovered scientific explanations for so many other previously mysterious phenomena, why not evolution as well? The laws God made are very clever and fine-tuned, and probably are sufficient to explain everything in astronomy, geology, chemistry and atmospheric science, for example, so it is hardly surprising that many would insist that they must be able to explain all of biology as well.

2. There are a lot of things about the development of life that give the appearance of natural causes. “This just doesn’t look like the way God would create things,” is an argument frequently used by Darwin, and by modern day evolutionists. There are also things that don’t suggest natural causes–such as the sudden appearance of nearly all the animal phyla at the beginning of the Cambrian era–but much of the history of life admittedly does leave us with a strong impression of natural causes.

All of the “evidence” for evolution falls into one of these two categories, there is no evidence to support the idea that natural selection of random mutations or any other unintelligent process can explain the major steps of evolution. Once you have acknowledged these two strong points, our opponents have nothing.
Oh, dear. He just doesn't get it.

That's why we call them IDiots.


[Photo Credit: University of Texas El Paso]

Granville Sewell is in the Mathematics Department at the University of Texas El Paso. His major research interest is differential equations.

Tuesday, April 20, 2010

A vestige of the 18th century

 
I belong to the Committee for the Advancement of Scientific Skepticism (CASS) at the Centre for Inquiry—Canada. Members of that group have published an article about homeopathy on the National Post website: A vestige of the 18th century.

Congratulations to Mitchell Gerskup, Ryan Gray, Michael Kruse, Iain Martel and Justin Trottier for a great contribution to homeopathy awareness. And congratulations to the National Post for publishing it.


Monday, April 19, 2010

Charles Darwin Died on this Day in 1882

 
Charles Darwin died at Down house during the afternoon of April 19, 1882. Janet Brown describes the moment in her biography (Charles Darwin: The Power of Place p. 495).
He died on the afternoon of 19, April 1882, after sinking very low for two or three days beforehand and suffering what Emma called "fatal attack" at midnight on the 18th. There was no deathbed conversion, no famous last words. "I am not the least afraid to die," he apparently murmured to Emma. "Remember what a good wife you have been." Allfrey signed the death certificate giving "Angina Pectoris Syncope" as the cause of death, the gradual ceasing of the heart. He was seventy-three.
The subtitle of Janet Browne's book (The power of Place) alludes to the remarkable status that Darwin achieved following publication of On the Origin of Species. Darwin was buried in Westminster Abbey at a huge funeral held on Wednesday, April 26, 1882. He was buried next to Sir John Herschel near the tomb of Sir Isaac Newton, "... an honorable place but not as close to [Charles] Lyell as Emma had hoped" (Browne, p. 497).

Here's a list of the pallbearers from AboutDarwin.com.
George Campbell - The 9th Duke of Argyll
William Cavendish - The 7th Duke of Devonshire
Edward Henry Stanley - The 15th Earl of Derby
James Russell Lowell - The American Ambassador to Britain
William Spottiswoode - Mathematician, physicist, the Queen's Printer, and friend of Darwin
Joseph Dalton Hooker - Darwin's close friend and champion of his Theory of Evolution
Thomas Henry Huxley - Darwin's close friend and champion of his Theory of Evolution
Alfred Russel Wallace - Darwin's friend and the co-founder of Natural Selection
Sir John Lubbock - The 1st Baron of Avebury, Darwin's next door neighbor and close friend
Here's the report of the funeral published in The Times on Thursday, April 27, 1882 [Wikisource].

The Funeral of Mr. Darwin

The mortal remains of Charles Robert Darwin were interred in the Abbey at Westminster yesterday with marks of respect due to one whose name has been for many years familiar as a household word to his countrymen, and whose works have shed so much distinction upon English science. The coffin containing the body was brought to the Abbey late on the previous evening and borne through the cloisters, Mr. Darwin's five sons following, into the Chapel of St. Faith. This is a portion of the Abbey little known to casual visitors. It is a long narrow apartment, with a groined and vaulted roof, situate between the end of the south transept and the vestibule of the Chapter House, and was until a few years ago used as a store room, and for some time was mistakenly called the Chapel of St. Blaize. Sir Gilbert Scott, however, discovered at the east end, where traces of an alter are found, a mural painting of a female figure, evidently a saint, holding in her hands a book and an iron rod — the emblems of St. Faith. The western portion of the room formed of old a revestry. Into this bare chapel, which, to the eyes of of the greatest architect seemed "a picturesque and beautiful room," the coffin was carried on Tuesday night, and, seen by the dim light from two old-fashioned lanterns, the place seemed gloomy and tomb-like in contrast with the lofty, nobly proportioned interior of the Abbey which could be seen through the glass door opening into the south transept. The presence of death was more painfully forced on the mind even than during the solemn ceremonial of yesterday, when the great building was again peopled with the living. Soon after 11 in the morning those who were to follow the body as mourners began to assemble in the Chapter House. The Embassies of France, Germany, Italy, and Spain were represented, and among those invited through Messrs. T, and W. Banting to be present or to send representatives nearly all those who received invitations were present, were:—

The Marquis of Salisbury, K.G., Chancellor of the University of Oxford; Lord Aberdare, President of the Geographical Society; the Speaker of the House of Commons, M.r. Childers, M.P., Sir Stafford Northcote, M.P., Mr. Fawcett, M.P., Mr. Mundella, M.P., Sir T Brassey, M.P., Sir Charles Dilke, M.P., Lord Kensington, M.P., Mr. A. J. Beresford, M.P., and Mr. Spencer Walpole, M.P., the two members of the University of Cambridge; Sir J. R. Mowbray, M.P., and Mr. J. G. Talbot, M.P., the members for the University of Oxford; Mr. J. A. Campbell, M.P. for the Universtiy of Glasgow and Aberdeen; Lord Arthur Russell, M.P., Mr. Plunket, M.P., and Mr. Edward Gibson, Q.C., M.P., the members for the University of Dublin; Dr. Lyon Playfair, M.P., for the Universities for Edinburgh and St. Andrew's; Sir Farrer Herschell, Q.C., M.P., Sir David Wedderburn, M.P., Sir Henry Holland, M.P., Mr Nevil Story Maskelyne, M.P., Mr. H. Broadhurst, M.P., Mr. T,. Burt, M.P., Professor Bryce, M.P.; the vice-Chancellor of the University of Oxford, the Master of Balliol, the Regius Professor of Medicine (Dr. Acland), and the Linacre Professor of Zoology, as representing the University of Oxford; the President of the College of Surgeons, the President of the College of Physicians, the Council of the Royal Society, the Council of the Linnean Society, the Council of the Royal Geographical Society, the council of the Geological Society, the Master of Christ's College, Cambridge, the Head-Master of the Grammar School, Shrewsbury; the Rev. Professor Kennedy, the Rev. Professor Pritchard, F.R.S., Professor Humphry, F.R.S., Professor Max Müller, Professor Henry S. Smith, F.R.S., Professor Prestwick, F.R.S., Professor Hirst, F.R.S., Professor Mosely, F.R.S., Professor Babington, F.R.S., Professor De Chaumont, F.R.S., Sir William Thomson, F.R.S., Sir John Hawkshaw, Dr. W. B. Carpenter, C.B., F.R.S., Mr. Ray Lankester, F.R.S., Sir Henry Maine, Mr. John Simon, C.B., Professor W. Chandler Roberts, F.R.S., Mr. John Murray, Captain Douglas Galton, secretary to the British Association for the Advancement of Science; Mr. W. Onless, R.A., Professor W. B. Richmond, R.A., Mr. George Atherley, Mr. W. Dallas, Mr. H. W. Bates, Mr. Walter White, Mr. J. W. Judd, Mr. G. A. Spottiswoode, Mr. R. C. Hankinson, Mr. John Morley, Mr. R. H. Hutton, Mr. W. C. Leckie, Mr. Frederic Harrison, Captain Abney, R.E., Mr. Frederick Pollock, Mr. W. R. S. Ralston, the Hon. Robert Winthrop, Professor Flower, F.R.S., and Mr. Herbert Spencer, F.R.S.

The Anthropological Institute appointed a deputation to attend, composed of the following members of the Society:— Sir John Lubbock, Mr. John Evans, F.R.S., Mr. E. B. Tylor, F.R.S., Professor Busk, F.R.S., Mr. Hyde Clarke, Professor W. H. Flower, Mr. Francis Galton, F.R.S., Dr. Allen Thomson, F.R.S., Mr. F. W. Rudler, F.G.S., Mr. F. E. W. Brabrook, F.S.A., Mr. J. E. Price, F.S.A., Lieutenant-Colonel H. H. Godwin-Austen, F.R.S., Professor Huxley F.R.S., Mr. R. R. Martin, M.P., Mr. Alfred Tylor, F.G.S., and Mr. George W. Bloxam, M.A., assistant secretary.

At about 20 minutes to 12 the body was brought out of the Chapel of St. Faith, through the Chapter-house vestibule, into the west cloister, and the procession was formed. The coffin was covered with a black velvet pall edged with white silk, On it were laid many wreaths of beautiful white flowers, one of the wreaths having been sent by members of scientific societies in Liverpool, represented by Mr. Isaac C. Thompson, F.R.M.S., honorary secretary of the Microscopical Society of Liverpool. The pall-bearers were the Duke of Devonshire, the Duke of Argyll, the Earl of Derby, Mr. J. Russell Lowell, the American Minister; Mr. W. Spottiswoode, LL.D., President of the Royal Society; Sir Joseph Hooker, Mr. A. R. Wallace, Professor Huxley, Sir John Lubbock, and the Rev. Canon Farrar. Proceeding slowly along the south cloister those heading the procession were met at the west entrance by members of the family and others, whose names follow:—

Mr. William Erasmus Darwin, chief mourner; Mr. George Darwin, F.R.S., Mrs. William Darwin, Miss Darwin, Mrs. Litchfield, Mr Francis Darwin, Mr. Leonard Darwin, Mr. R. B. Litchfield, Mr. Horace Darwin, Mr. Leonard Darwin, R.E., Mr. Darwin of Elston-hall, Mr. F. Alvey Darwin, Captain Charles Darwin, Mr. Reginald Darwin, of Buxton, Mrs. Vaughan Williams, Miss Wedgwood, the Rev. Charles Parker, Mr. Robert Packer, Mr. H. F. Bristowe, Q.C., Mr. Francis Galton, F.R.S., Mr. Ernest Wedgwood, Mr. Hensleigh Wedgwood, Mr. T. H. Farrer, Secretary of the Board of Trade, Mrs. Farrer, Mr. Godfrey Wedgwood, Miss A. Wedgwood, Mrs. Ruck, the Rev. Arthur Wedgwood, Mr. J. C. Hawkshaw, Mrs. Hawkshaw, Mr. George Allen, Mr. Henry Allen, M.P.; servant, Mr. William Jackson, and Mr. Joseph Parslow.

Within the Abbey a large congregation was assembled, filling the seats on the south side of the nave, the seats in the choir and such as were not reserved for the mourners in the transepts, while a large number admitted without tickets stood on the north side of the nave. Among those present were the Baroness Burdett-Boutts and Mr. Burdett-Coutts, the Lord Mayor, and Lady Mayoress and Miss Ellis, Mr. Sheriff Ogg, the Rev. R. C. Billing, Mr. Mark H. Judge, Mr. L. T. D'Eyncourt, and the Head Constable of Westminster. Masters and Queen's scholars of the Westminster School also attended. At the West Cloister door the mourners were met by the Rev. Canon Prothero, as senior canon in the absence of the Dean, who is abroad. Canon Prothero having read the opening sentence of the Service for the Burial of the Dead, the choir changed the other processional sentences to the music of Croft, as the procession moved down the south aisle to the west end of the church and then up the nave into the choir. Following the choristers came the Rev. J. H. Cheadle and the Rev. J. Troutbeck (minor canons of Westminster), Canon Rowsell, Canon Barry, Canon Duckworth, and the Rev. S. Flood Jones (precentor), and near the senior canon the Chapter Clerk, Mr. C. St. C. Bedford. The body was placed in front of the Communion rails during the first portion of the service. The Psalms were chanted to Purcell's music, and after the Lesson, which was read by Canon Duckworth, an anthem composed for the occasion by Mr. Bridge was sung to the words from the Book of Proverbs, "Happy is the man that findeth wisdom. and getteth understanding. She is more precious than rubies, and all the things thou canst desire are not to be compared unto her. Length of days is in her right hand, and in her left hand riches and honour. Her ways are ways of pleasantness, and all her paths are peace." The soft and subdued ending of the composition, which was sung with much feeling by the choir, prepared the mind for the last sad duty that remained to be performed. The body was not removed to the grave, which is at the north-east corner of the nave next to that of Sir John Herschell, Dr. Bridge playing first Beethoven's Funeral March and then a more plaintive march by Franz Schubert in B minor, while the mourners proceeded to the grave, and the rest of the service was impressively read by Canon Prothero, the choir singing their part to Croft and Purcell's music. Near the grave and just beneath the monument to Sir Isaac Newton stood a remarkable and representative crowd of distinguished men, such as only an occasion of deep and general would bring together. Leaders of men and leaders of thought; political opponents, scientific co-workers; eminent discoverers, and practitioners of the arts. To name only a few as representative, there were Lord Spencer, President of the Council, who represented Her Majesty's Ministers at the funeral; the Marquis of Salisbury, Viscount Sherbrooke, Sir William Jenner, Sir Stafford Northcote, Sir Charles Dilke, Mr. Moncure D. Conway, Dr. Siemens, Sir William Gull, Mr. Childers, Professor Marshall, Sir John Hawkshaw, Mr. Ernest Hart, Mr. W. H. Smith, Mr. Herbert Spencer, Dr. Farquharson, Professor Flower, Mr. Robert Winthrop, and Mr. Ellis. The anthem by Handel, "His body is buried in peace, but his name liveth evermore," was sung, and the senior Canon having pronounced the Benediction, the mourners left, and the public were then allowed to pass round the grave. The inscription on the plate of the white, unpolished oak coffin read, "Charles Robert Darwin. Born February 12, 1809. Died April 19th, 1882."

In an article in to-day's Nature on the late Mr,. Darwin, Professor Huxley writes as follows:— "Not only in these islands, where so many have felt the fascination of personal contact with an intellect which had no superior, and with a character which was even nobler than the intellect, but in all parts of the civilized world it would seem that those who business it is to feel the pulse of the nations and to know what interests the masses of mankind were well aware that thousands of their readers would thin the world poorer for Darwin's death, and would dwell with eager interest upon every incident of his history. In France, in Germany, in Austro-Hungary, in Italy, in the United States, writers of all shades of opinion, for once unanimous, have paid a willing tribute to the worth of our great countryman, ignored in life by the official representatives of the kingdom, but laid in death among his peers in Westminster Abbey by the will of the intelligence of the nation. One could not converse with Darwin without being reminded of Socrates. There was the same desire to find some one wiser than himself; the same belief in sovereignty of reason; the same ready humour; the same sympathetic interest in all the ways and works of men. But instead of turning away from the problems of nature as hopelessly insoluble, our modern philosopher devoted his whole life to attacking them in the spirit of Heraclitus and of Democritus, with results which are as the substance of which their speculations were anticipatory shadows. The due appreciation or even enumeration of these results is neither practicable nor desirable at this moment. There is a time for all things—a time for glorying in our ever extended conquests over the realm of nature, and a time mourning over the heroes who have led us to victory. None have fought better, and none have been more fortunate than Charles Darwin. He found a great truth, trodden under foot, reviled by bigots, and ridiculed by all the world; he lived long enough to see it chiefly by his own efforts, irrefragably established in science, inseparably incorporated with the common thoughts of men, and only hated and feared by those who would revile, but dare not. What shall a man desire more than this? Once more the image of Socrates rises unbidden, and the noble peroration of the 'Apology' rings in our ears as if it were Charles Darwin's farewell:—'The hour of departure has arrived, and we go our ways—I to die and you to live. Which is the better God only knows.'"

We are requested to state that the absence of the Vice-Chancellor and members of the Council of the Senate of the University of Cambridge from the funeral of the late Mr. Darwin was occasioned by the circumstance that it was impossible for them to attend in consequence of the approaching election to the Regius Professorship of Hebrew. By the statute regulating the election it is imperative on the Vice-Chancellor and the members of the Council, who are the electors, to be present during the whole time each of the candidates for the Professorship delivers his exposition on the portions of Hebrew books assigned to him. The times for the delivery of these dissertations had been fixed nearly a month ago, and it was impossible to postpone them and to defer the election. Consequently, much to the regret of the Vice-Chancellor and the members of the Council, none of them could attend as representing the University of Cambridge.


[Photo Credit: Funeral of Charles Darwin: The Complete Works of Charles Darwin Online, Invitation: English Heritage Prints]

Sunday, April 18, 2010

Bill O'Reilly "Discusses" European Paganism

 
I don't watch Bill O'Reilly's show very often so I missed this segment. I find it extremely interesting that a major television network could air such a discussion in the 21st century. To me, it says something about popular views in American culture. It doesn't say that a majority of Americans agree with these idiots but it does say that their point of view is an acceptable part of the cultural mix. That's shocking.

The priest's comments are interesting from the perspective of the accommodationist wars. He claims that Roman Catholicism conflicts with all kinds of things, including socialism. Who knew?

[I haven't been keeping up with financial news. Is it true that Europe is in much worse economic shape that the USA? I didn't notice that during recent visits to Europe and the USA.]




[Hat Tip: Pharyngula: A priest, a scientist, and a Communist discuss morality]

The "New Creationism"

 
Jerry Coyne has "coyned" a new term to describe people who accept most of science but still want to have their cake [HuffPo screws up evolution again].
I’m coyneing the term “New Creationism” to describe the body of thought that accepts Darwinian evolution but with the additional caveats that 1) it was all started by God, 2) had God-worshipping humans as its goal, and 3) that the evidence for all this is that life is complex, humans evolved, and the the “fine tuning” of physical constants of the universe testify to the great improbability of our being here—ergo God. New Creationism differs from intelligent design because it rejects God’s constant intervention in the process of evolution in favor of a Big, One-Time Intervention, and because these ideas are espoused by real scientists like Kenneth Miller and Simon Conway Morris. (Note that Miller, though, has floated the possibility that God does sometimes intervene in the physical world by manipulating electrons.) New Creationism is bad because, while operating under the deep cover of real science, it tries to gain traction for dubious claims about the supernatural.
This is pretty good but let's not insist that New Creationists have to postulate humans as the only goal of evolution. Some of them do and some of them are content with any kind of sentient being. The common characteristic is that they envisage some kind of purpose to the way the universe has unfolded.

"New Creationism" is a much better term than "Theistic Evolution" and I think I'll use it from now on. It has the advantage of putting the emphasis on "creationism," where it belongs. (Note, this is small-"c" creationism.)


Friday, April 16, 2010

Theory vs Theory

This is the third 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. Arlin is challenging the status quo in modern evolutionary theory. He's not alone in this challenge but it's important to distinguish between kooks who don't know what they're talking about and serious thinkers who have something to say. Arlin is going to explain to you why everything you thought you knew about mutationism is wrong. In this article we learn about theories.

Please pay attention.

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 last time with part 1 of The Mutationism Myth.

Before continuing with part 2, I would like to take a detour. Issues surrounding "evolutionary theory", and evolutionary theories, are going to be coming up again and again. In fact, I can see these issues emerging already in The Mutationism Myth. So, before we get bogged down in confusion and disagreement, I would like to begin a discussion of "theory" and "theories". We'll return to the Mutationism Myth next time.

An updated version of the post below will be maintained at www.molevol.org/cdblog/theory_vs_theory (Arlin Stoltzfus, ©2010)

Theory1 vs theory2

What does it mean to invoke "evolutionary theory"? Is "neo-Darwinism" (or "Darwinism") a theory, a school of thought, or something else? What gives a theory structure and meaning (e.g., axioms, themes, formulae)? What is the relationship between mathematical formalisms and other statements of "theory" (e.g., what does it mean for a lecturer to show a key equation of quantitative evolutionary genetics and assert "this is neo-Darwinism")? Who decides how a theory is defined, or redefined (e.g., is Ohta's "nearly neutral" theory an alternative to, or a variant of, Kimura's Neutral Theory of Molecular Evolution)?

Confusion regarding "theory" and "theories" is going to be an ongoing topic of attention in The Curious Disconnect. As noted in the Introduction, we're in an enormous muddle. The way to get out of this muddle is to take some time to build common understanding, learn some useful terms, and establish ground rules.

In this post, we'll begin the process of developing a shared framework for productively discussing "theory" and "theories". We will begin by addressing an ambiguity in the use of the word "theory", partly because this particular ambiguity is important, and partly as an exercise in addressing semantics. 0

Definitions

Dictionaries provide definitions that can be helpful to clarify the meanings of words and the complications of their usage. Definitions can be descriptive, telling us how a word is used, or prescriptive, telling us how it ought to be used. But, as most of us don't like to be told what we ought to do, I suspect that you share my belief in studying how words are used, in order to determine their denotations (what the word says) and connotations (what the word hints or implies). The English dictionaries used in America typically agree: the definitions that they provide reflect patterns of common usage, not the decrees of authorities.

A difficulty with dictionaries arises given that, within an isolated community, e.g., a scientific discipline, words can take on special meanings. So, dictionaries can be helpful, with the proviso that we need to be sensitive to the special use of terms within a discipline.

The discipline-specific use of a term can be nailed down by looking at examples of usage. For evolutionary biology, the discipline-specific use of a term is to be found in the research literature, and also in the secondary literature of monographs, textbooks, and other disciplinary writings.

Two meanings of "theory"

A good dictionary will distinguish several different senses of the word "theory", including the following two that I believe are the most relevant for our discourse:

1) a major conjecture or systematic hypothesis to account for observed phenomena, as in "prion theory of disease" or "Lamarck's theory of evolution";

2) the body of abstract principles relevant to some discipline, methodology or problem area, as in "music theory" or "population genetics theory"

That is, a theory1 is a grand hypothesis, a conjecture about the actual world, while a theory2 is a collection of principles or models or other formalisms that might apply only in an imagined world. Fisher (1930) famously said that "No practical biologist interested in sexual reproduction would be led to work out the detailed consequences experienced by organisms having three or more sexes; yet what else should he do if he wishes to understand why the sexes are, in fact, always two?" Theoreticians aren't necessarily good with facts, so we'll ignore that the sexes (in the sense of mating types) are not, in fact, always two. Fisher clearly encourages us to work out formalisms for imagined or hypothetical cases. The collection of all these models or formalisms about sexes would constitute the theory2 of sexes. A theory1 of sexes might propose a causal explanation for the actual historic phenomenon of the origin and maintenance of sexual reproduction in animals, addressing such issues as the heterogametic basis of sex determination. 1

These two meanings are not just recognized in dictionaries, but are established in scientific usage. Gilbert's "Exon Theory of Genes" (Gilbert 1987) is the conjecture that genes evolved from exons (i.e., large protein-coding genes emerged by joining primordial exon-minigenes). The prion theory1 of disease clearly revolves around a conjecture that there are actual diseases caused by actual prions. By contrast, population genetics theory2 is not the conjecture that populations have genetics; likewise, the theory2 of stochastic processes is not a conjecture that stochastic processes occur, but consists of a body of abstract principles that might be applicable to such stochastic processes as might occur in some actual or imagined universe.

The use of the abstract noun, as in "let's talk about theory" as opposed to "let's talk about { a | the | this } theory", often signals the use of theory2. For instance, the title of a report by the National Academy of Sciences on "The Role of Theory in Advancing 21st Century Biology" signals a likely emphasis on theory2, and indeed, the report emphasizes the development of formalisms more than conjectures, and says that "a useful way to define theory in biology is as a collection of models", clearly a reference to theory2. The report also mixes in some references to theories1.

Obviously, there is a connection between scientific theories1 and scientific theory2. One way of thinking about the connection is that the abstract principles of theory2, when suitably limited by measurable or observable quantities from the actual world, can provide the basis of a theory1, and conversely, theories1 draw on theory2 for logical structure. Kimura's Neutral Theory (Kimura 1983) provides a clear example because the theory1 and theory2 were developed separately: Kimura combined pre-existing theory2 (of stochastic population genetics) with the concrete assertion that the values of certain quantities (relating to population sizes and mutant effects) were such that, for DNA and protein sequences, neutral evolution by mutation and random fixation would be far more common than anyone had imagined previously. The definition of effectively neutral alleles (perpetually misunderstood by critics) and the probability of fixation under pure drift were known to the canonical founders of population genetics ((Wright 1931); ch. IV of (Fisher 1930); appendix of (Haldane 1932)). Another indication of the distinctness of theory1 and theory2 is that opponents of the Neutral Theory1, who deny the truth of the theory1, are nonetheless quite happy to make use of its theoretical2 infrastructure (Kreitman 1996).

Development and application of theory1 and theory2

We treat the two kinds of "theory" differently, and rightly so.

A theory1 contains a major supposition or unproved conjecture about the world. Kimura's Neutral Theory is the conjecture that most changes at the "molecular level" represent the random fixation of effectively neutral alleles. Darwin proposed, but could not prove, that all large-scale evolutionary changes were built from infinitesimal increments of change that emerged by a process of hereditary "fluctuation". A theory1 takes risks: in Popperian terms, its subject to empirical refutation; in the words of Huxley, a beautiful theory1 can be "killed by an ugly fact."

The relevant standard of validity for theory2 is not verisimilitude (trueness to life), but consistency: the principles derived in the theory are consistent with its assumptions. Importantly, new principles added to a body of theory2 are consistent with previous principles, except in the sense that a body of theory2 may be subdivided into branches that cover non-overlapping universes. If they are not, a logical error has occurred.

While new theory2 is consistent with existing theory2, theories1 often stimulate interest precisely because they conflict with previous theories1. Of course theories1 strive to be internally consistent, but in biology at least, theories1 are not axiomatic, and often encompass ambiguities that make rigorous analysis difficult. A theory1 can be brought down by a contradiction that arises internally, e.g., one part can be found to contradict another part.

While a theory1 is about the actual world, and thus is judged by verisimilitude, principles of theory2 need not apply to the real world. Indeed, no amount of conflicting data will cause us to discard a principle of theory2 that is properly derived: a beautiful piece of theory2 cannot be killed by an ugly fact. Fisher's fundamental theorem either is logically valid or is not logically valid, independent of any facts.

Digressions

The distinction between theory1 and theory2 is hidden in the ambiguous word "theory", but I think it comes out more clearly in specific word-derivatives and grammatical usages that seem to favor one meaning more than the other. I mentioned above that the abstract noun typically signals theory2. I'm also convinced that when we refer to a "theoretician", we typically do not mean someone like Tom Cavalier-Smith whose scientific output consists of bold conjectures or systematic hypotheses (we might call such people "theorizers"), but instead someone like Joe Felsenstein whose work focuses on mathematical or algorithmic foundations, i.e., theory2. Its a rare scientist, it seems to me, who is productive both as a theoretician and as a theorizer (e.g., Kimura, Hamilton).

Neither meaning of theory would cause us to relinquish the label "theory" for a proposition that lacks verisimilitude. Clearly the propositions of theory2 do not have to apply to the real world. And a theory1 is a conjecture, not necessarily a true conjecture. Thus, even opponents of the Neutral Theory1, who believe that the theory does not fit the actual world, still refer to it as The Neutral Theory (Kreitman 1996).

I mention this because there is an absurd tendency in the literature of evolution advocacy, e.g., NCSE's screeds, to say that, because scientists reserve the word "theory" only for constructions that have been extensively verified and are accepted as true, the use of "theory of evolution" among scientists means that evolution is well supported.

This argument clearly is false, and the proof does not depend on the theory1 vs. theory2 distinction, but only on the fact that scientists habitually choose to refer to Kimura's theory or Lamarck's theory or Gilbert's theory as a "theory", even if its known to be wrong or is considered deeply suspect. This pattern holds, not just in biology, but in other disciplines. In astronomy, the geocentric theory remains a theory though it has been abandoned; in physics, the phlogiston theory, or the aether theory of light propagation (roughly, the theory that space must be substantive in order for waves to propagate in it) remain theories even though they were abandoned. So, write to the NCSE and tell them to stop using this lame argument. Really, we can do better than that.

The NCSE fallacy seems to arise from mixing together the proposed explanation of phenomena aspect of theory1 and the accepted as valid aspect of theory2. This is suggested from the way that NCSE's screed cites the NAS report on theory2 (the same one that I quoted above) as though it provided a definition of theory qua "well substantiated explanation", which definitely is not the same as "collection of models".

Lets try to sort this out in terms of the distinction between theory1 and theory2. Evolutionists have recourse to a body of theory2 (formalisms or models or principles), ranging from purely phenomenological models of branching and character-state change used in phylogenetics, to the breeder's equation used in quantitative genetics, to detailed formulas for population-genetics processes, and so on. We accept the validity of these abstractions in the theory2 sense of validity, i.e., we accept that they are derived without error, so as to be logically consistent with their assumptions. This body of abstractions, principles, or formalisms (in NAS parlance, this collection of models) is evolutionary theory2.

But saying that this theory2 is valid is not at all the same thing as claiming that its true in the sense of verisimilitude; and claiming that it has verisimilitude is not the same as saying that its complete, in the sense of sufficiently accounting for the phenomena of evolution. For instance, the theory2 of quantitative evolutionary genetics is based on the assumption of infinitesimal variation, but the theory2 itself does not claim that all traits, nor even any single trait, evolved in this manner-- that would be a theory1 issue. Kimura's diffusion equations are a part of population genetics theory2 that provides a way to work out the probability of fixation of alleles under ideal conditions, but it doesn't assert that the results are applicable to any particular case. Got it?

Homework

The wikipedia entry on theory (http://en.wikipedia.org/wiki/Theory) has a "List of Notable Theories" that clearly mixes up theories1 or grand conjectures (the cell theory, the phlogiston theory) with theories2 or bodies of abstract principles (music theory, extreme value theory). What are some other clear examples of theory1 and theory2 in this list? Which examples are difficult to classify (and what does one learn from those)?

Who, besides Kimura and Hamilton, was productive as both a theoretician and as a theorizer?

Think of a few theories in science, ideally in life sciences. I'm going to assert that they are not axiomatic, i.e., they are not completely encompassed by precisely stated propositions. Given this, how do we really know what defines the theory? If we know a theory from the verbal statements in a body of literature (i.e., "things people say"), what is the relationship of an individual expression (e.g., a paper, a monograph, a quotation) to the theory? Is it the instantiation of a platonic form or essence? How do we get to the essence? Is the distribution of expressions of a theory its "reaction norm", representing environmental noise in the expression of an underly structure (the theory's "genotype")?

The Modern Synthesis as theory1: into the memory hole

The folks at NCSE and wikipedia are not the only ones blurring the issues. The Modern Synthesis or modern neo-Darwinism 2 was put forth originally as a falsifiable theory1 of evolution, but evolutionists themselves don't treat it that way anymore. For instance, in Maynard Smith's defense of "neo-Darwinism" (Maynard Smith 1969), the only kinds of falsifying observations he can imagine are cases that seem to introduce supernatural forces, e.g., if the spots on a fish always appeared in prime numbers, he says this would contradict neo-Darwinism. He does not imagine variation-induced trends, discontinuous jumps based on individual mutations, or extensive neutral evolution as contradictions of "neo-Darwinism", though these ideas were rejected by the architects of modern neo-Darwinism. Maynard Smith makes the claim in regard to the Neutral Theory that "I have never seen any reason why, as a naive Darwinist, I should reject this theory" (Maynard Smith 1995). It seems that, for Maynard Smith, "neo-Darwinism" is not a theory1 at all, but merely indicates a commitment to scientific materialism, i.e., seeking natural causes through observation and experiment.

Other authoritative sources suggest that the Modern Synthesis is no longer viewed as a falsifiable conjecture. In Hull's Encyclopedia of Evolution article on the history of evolutionary thought (Hull 2002), the Modern Synthesis is presented as an open-ended "theory" that merely assumes the principle of selection and the rules of genetics, and which has swallowed up the neutral theory along with all other useful ideas:

"Any criticism of the synthetic theory that turned out to have some substance was subsumed in a modified version of this theory. Instead of being a weakness, this ability to change is one of the chief strengths of the synthetic theory of evolution. As in the case of species, scientific theories evolve" (p. E16)

Hull's conception of the Modern Synthesis sounds more like an extensible set of principles, theory2, than the theory1 of Mayr, Simpson, Ayala, etc (which is extensible in some ways but closed and falsifiable in others). I'm not necessarily going to say its wrong for scientists to decide that the Modern Synthesis is no longer a theory1, but can someone please tell me when, and on what basis, did we make this decision? Is there a citation for that? And who decided that we wouldn't tell Richard Dawkins, leaving the poor fellow stuck in a time warp defending the original Modern Synthesis? 3

But I'm getting ahead of myself. I started The Curious Disconnect with the The Mutationism Myth because 1) most evolutionists don't understand how the Modern Synthesis came into existence as a theory1 that entails risky conjectures, and 2) the mutationist challenge provides the definitive historical proof that the Modern Synthesis is a theory1 and not just a commitment to selection and the rules of genetics. The historical record will show clearly that the mutationists or "Mendelians" presented a workable synthesis of selection and the rules of genetics, and that their view was rejected by the architects of the Modern Synthesis. Once we find out why, we will understand what makes the Modern Synthesis a theory1.

Literature cited

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

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

Gilbert, W. 1987. The exon theory of genes. Cold Spring Harbor Symp. Quant. Biol. 52:901-905.

Haldane, J. B. S. 1932. The Causes of Evolution. Longmans, Green and Co., New York.

Hull, D. L. 2002. History of Evolutionary Thought. Pp. E7-E16 in M. Pagel, ed. Encyclopedia of Evolution. Oxford University Press, New York.

Kimura, M. 1983. The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge.

Kreitman, M. 1996. The neutral theory is dead. Long live the neutral theory. Bioessays 18:678-683.

Maynard Smith, J. 1969. The Status of Neo-Darwinism. Pp. 82-89 in C. H. Waddington, ed. Towards a Theoretical Biology 2. Sketches. Edinburgh Universeity Press, Edinburgh.

Maynard Smith, J. 1995. Life at the Edge of Chaos? Pp. 28-30. New York Review of Books, New York.

Wright, S. 1931. Evolution in Mendelian populations. Genetics 16:97.

Notes

0 I thank Dr. Mike Coulthart for originally drawing my attention to the importance of this distinction.

1 If we were to propose just that the sexes are always 2 in number, simply because that is what we have seen in the past, I would call this an empirical generalization or "law". Sometimes "theory" is used for such a generalization, but that usage does not correspond to either meaning of "theory" addressed here.

2 I'm using "modern neo-Darwinism" as a synonym for "Modern Synthesis". Neo-Darwinism (for our purposes, Darwinism 1.2) is the pre-Mendelian theory of Weissman and Wallace emphasizing the supreme power of selection and infinitesimal variation to build adaptation (and rejecting Darwin's reliance on Lamarckism). The Modern Synthesis (Darwinism 2.0) comes from this tradition and is often called "neo-Darwinism", though "modern neo-Darwinism" is clearer.

3 Kidding aside, its quite useful to have a scholar still defending the actual Modern Synthesis. For instance, in his attempt to rebut Behe (Dawkins 2007), Dawkins claims that mathematical geneticists "have repeatedly shown that evolutionary rates are not limited by mutation" and that Behe's critique based on the idea that evolution depends on specific mutations would mean that "the entire corpus of mathematical genetics, from 1930 to today, is flat wrong". In making this claim, Dawkins is correctly representing the Modern Synthesis view that (due to the buffering effect of the "gene pool") evolution does not depend on the rate of new mutations, a principle that he believes to be an infallible theoretical result.


Wednesday, April 14, 2010

Chris Mooney vs Atheists: Part XXXIV

 
Chris Mooney is at it again. His latest posting sounds ominous: Are Top Scientists Really So Atheistic? Look at the Data.
Elaine Howard Ecklund is a sociologist at Rice University; we cited her work on the topic of science and religion in Unscientific America. Now, she is out with a book that is going to seriously undercut some widespread assumptions out there concerning the science religion relationship.
Unfortunately, Chris doesn't present any data because he's not a scientist. Data really isn't his thing.

I don't have a copy of the book so I can't check it myself. Fortunately, Razib Khan, one of Chris Mooney's fellow bloggers on the Discover website, was able to find some of the data [Scientists as “spiritual atheists”].

Let's be clear about one thing. This is not a poll of scientists. It's a poll of American scientists. The title of Ecklund's book, Science vs Religion: What Scientists Really Think, is somewhat misleading.1 Here's two charts from the book.



Hmmm ... none of my assumptions have been undercut. How about yours?

I guess what Chris Mooney means is that some of his assumptions will have to be re-evaluated. It's about time.


1. Unless you're an American. Then you probably believe that all scientists live in the USA.

Is Evolution Guided or Unguided?

Michael Ruse has criticized Alvin Plantinga for being critical of evolution. Plantinga defends himself in a letter published in The Chronicle of Higher Eduaction: Evolution, Shibboleths, and Philosophers.

I want to address one particular point that Plantinga makes because it's relevant to the issues that come up in the accommodationist wars.
"Why," asks Ruse, "does Plantinga feel this way?" Because, he says, "In his view, Darwinism implies that there is and can be no direction in life's history." Still another missed distinction. As far as I can see, God certainly could have used Darwinian processes to create the living world and direct it as he wanted to go; hence evolution as such does not imply that there is no direction in the history of life. What does have that implication is not evolutionary theory itself, but unguided evolution, the idea that neither God nor any other person has taken a hand in guiding, directing or orchestrating the course of evolution. But the scientific theory of evolution, sensibly enough, says nothing one way or the other about divine guidance. It doesn't say that evolution is divinely guided; it also doesn't say that it isn't. Like almost any theist, I reject unguided evolution; but the contemporary scientific theory of evolution just as such—apart from philosophical or theological add-ons—doesn't say that evolution is unguided. Like science in general, it makes no pronouncements on the existence or activity of God.
Plantinga is allying himself with Eugenie Scott and other accommodationists who fiercely defend the idea that science can't address issues such as purpose. In fact, Genie fought hard to remove references to "unsupervised, impersonal, unpredictable and natural process" from a statement on evolution by the National Association of Biology Teachers back in 1995 [NCSE v National Association of Biology Teachers].

I disagree with Plantinga, and with the National Center for Science Education. The idea that evolution might be guided by God is a legitimate question for scientists to address. After all, if it's true then parts of evolutionary theory might have to be revised. I do not accept the claim that scientists must avoid this question because it comes from religion.

When you are thinking like a scientist there's only one possible conclusion. There is no scientific evidence to support the hypothesis that the history of life on Earth was guided by God. Everything we know about the history of life is consistent with an entirely natural process—one that's characterized by chance and contingency. It is perfectly reasonable as a scientist to state this position clearly. This is not stepping outside of the boundaries of science.

Let me explain my position by using an analogy. Imagine the claim that aliens visited the Earth 3.5 billion years ago and seeded our planet with cyanobacteria. After much investigation scientists find no support for such a claim. Is it legitimate for them to conclude that aliens are not responsible for life on Earth? Of course it is. All scientists know that you can't prove a negative but that doesn't mean you can't assign probabilities and behave accordingly.

Philosophers aren't likely to get upset if scientists make statements denying that aliens are responsible for life as we know it. That's because belief in alien visitors isn't one of those kooky ideas that demands special status. However, if scientists make the more general claim that life appears to have evolved by purely natural processes then this gets their dander up. All of a sudden science is threatening religion and this is not allowed. It's "philosophical naturalism" and not "methodological naturalism." It's not science according to Plantinga and many accommodationists, including Michael Ruse. Bollocks, I say.

Scientists call it as they see it. If that upsets the theists then they had better learn to deal with it instead of whining about the science being illegitimate.

Science says that evolution is not divinely guided, based on what we know today.