Biological evolution explains both the unity and diversity of species. Biological evolution results from the interactions of (1) the potential for a species to increase its members, (2) the genetic variation of individuals within a species due to mutations and recombinations of genes, (3) a finite supply of the resources required for individuals to survive and reproduce, and (4) the ensuing selection by the environment of those organisms better able to survive and reproduce. Organic evolution, and the net result of speciation minus extinction, has led to the planet’s biodiversity and ecosystem functioning. Sustaining biodiversity is essential for the maintenance and enhancement of the human population’s quality of life.

The fossil record provides evidence of different life forms at different periods of geological history. This evidence supports the idea that newer life forms descended from older life forms, a phenomenon that Darwin aptly called “descent with modification”. DNA provides further evidence for lines of descent from ancestral species to later-appearing species.

Genetic variation of individuals within a species gives some individuals an advantage to survive and reproduce in the conditions of their environment. This leads to the predominance of certain inherited traits within a varied population. When an environment changes, there is a subsequent change in the supply of resources or in the challenges imposed by abiotic and biotic factors of the environment. This results in selective pressures that influence the survival and reproduction of organisms and which lead to adaptations, that is to changes in the traits of survivors within populations, and to extinction of species unable to adapt to such changes. Mutations most often produce non-viable individuals, but, infrequently, can introduce new traits within a population that offer survival advantages. Many such changes, along with reproductive isolation and the selective pressures from the environment can lead to the development of adaptations and, eventually, to distinct new species.

Biodiversity – the diversity of genes, species, and ecosystems – provide humans with renewable resources such as food, fuels, fertile soils, clean water and air, medicines, as well as surroundings (from species to landscapes) of inspirational value. The resources of biological communities can be used within sustainable limits, but in many cases the human impact is exceeding sustainable limits.

1. Evoluion it the leading principle of the biological sciences. Evolutionary biology aims to discover the history of life and the causes of the diversity and characteristics of organisms.

2. Darwin's evolutionary theory, published in The Origin of Species in 1859, consisted of two major hypotheses: first, that all organisms have descended, with modification, from common ancestral forms of life, and second, that a chief agent of modification is natural selection.

3. Darwin's hypothesis that all species have descended with modification from common ancestors is supported by so much evidence that it has become as well established a fact as any in biology. His theory of natural selection as the chief cause of evolution was not broadly supported until the "evolutionary synthesis" that occurred in the 1930 and 1940s.

4. The evolutionary theory developed during and since the evolutionary synthesis consists of a body of principles that explain evolutionary change. Among these principles are (a) that genetic variation in phenotypic characters arises by random mutation and recombination; (b) that changes in the proportions of alleles and genotypes within a population may result in replacement of genotypes over generations; (c) that such changes in the proportions of genotypes may occur either by random fluctuations (genetic drift) or by nonrandom, consistent differences among phenotypes in survival or reproductive rates (natural selection); and (d) that as a result of different histories of genetic drift and natural selection, populations of a species may diverge and become reproductively isolated species.

Many have assumed that humans ceased to evolve in the distant past, perhaps when people first learned to protect themselves against cold, famine and other harsh agents of natural selection. But in the last few years, biologists peering into the human genome sequences now available from around the world have found increasing evidence of natural selection at work in the last few thousand years, leading many to assume that human evolution is still in progress.

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

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

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

...

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

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

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

The Mutationism Myth, part 5. The Restoration

The response to Mendelian heterodoxies

Initiative

"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).

"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)

Infinitesimalism ("gradualism")

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)

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.

"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)

Creativity (novelty)

"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."

"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)

Directionality

"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)

"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)

"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)

"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 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)

"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)

The keys to the kingdom

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

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.

Summary

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

The cringeworthy "dad dancing" witnessed at wedding receptions every weekend may be an unconscious way in which ageing males repel the attention of young women, leaving the field clear for men at their sexual peak.

"The message their dancing sends out is 'stay away, I'm not fertile'," said Dr Peter Lovatt, a psychologist at the University of Hertfordshire who has compared the dancing styles and confidence levels of nearly 14,000 people.

His research has backed up scientific studies showing a connection between dancing, hormones and sexual selection.

Men between the ages of 35 and 60 typically attempt complex moves with limited co-ordination – an observation that will be obvious to anyone who saw George W Bush shake his stuff with a troupe of West African performers in 2007.

Dr Lovatt pointed to research showing that women could gauge the testosterone levels of their dance partners by the style and energy of their moves, and suggested that "dad dancing" may be a way of warning women of child-bearing age that they might be better off looking elsewhere.

"It would seem completely unsurprising to me that since middle-aged men have passed their natural reproductive age, and probably have a family already, evolution would act to ensure they are no longer attractive to 18-year-old girls," Dr Lovatt said.

Keith Yamamoto is a professor of molecular biology and executive vice dean of the School of Medicine at UC-San Francisco. He stands ready to help organize a boycott, if necessary, a tactic he and other researchers used successfully in 2003 when another big commercial publisher, Elsevier, bought Cell Press and tried to raise its journal prices.

After the letter went out on Tuesday, Mr. Yamamoto received an "overwhelmingly positive" response from other university researchers. He said he's confident that there will be broad support for a boycott among the faculty if the Nature Group doesn't negotiate, even if it means some hardships for individual researchers.

"There's a strong feeling that this is an irresponsible action on the part of NPG," he told The Chronicle. That feeling is fueled by what he called "a broad awareness in the scientific community that the world is changing rather rapidly with respect to scholarly publication."

Although researchers still have "a very strong tie to traditional journals" like Nature, he said, scientific publishing has evolved in the seven years since the Elsevier boycott. "In many ways it doesn't matter where the work's published, because scientists will be able to find it," Mr. Yamamoto said.

Boudry, M., Blancke, S., and Braeckman, J. (2010) How Not to Attack Intelligent Design Creationism: Philosophical Misconceptions About Methodological Naturalism. Foundations of Science doi:10.1007/s10699-010-9178-7.

Abstract
In recent controversies about Intelligent Design Creationism (IDC), the principle of methodological naturalism (MN) has played an important role. In this paper, an often neglected distinction is made between two different conceptions of MN, each with its respective rationale and with a different view on the proper role of MN in science. According to one popular conception, MN is a self-imposed or intrinsic limitation of science, which means that science is simply not equipped to deal with claims of the supernatural (Intrinsic MN or IMN). Alternatively, we will defend MN as a provisory and empirically grounded attitude of scientists, which is justified in virtue of the consistent success of naturalistic explanations and the lack of success of supernatural explanations in the history of science (Provisory MN or PMN). Science does have a bearing on supernatural hypotheses, and its verdict is uniformly negative. We will discuss five arguments that have been proposed in support of IMN: the argument from the definition of science, the argument from lawful regularity, the science stopper argument, the argument from procedural necessity, and the testability argument. We conclude that IMN, because of its philosophical flaws, proves to be an ill-advised strategy to counter the claims of IDC. Evolutionary scientists are on firmer ground if they discard supernatural explanations on purely evidential grounds, instead of ruling them out by philosophical fiat.

So why are Matheson and Moran so sure that huge portions of introns don’t have functions? According to Matheson, it’s because “Larry Moran and I clearly know a whole lot more about molecular genetics” than Sternberg.

A more naked appeal to authority would be hard to find. It sounds like an undergraduate trying to score points in a late-night bull session (“I know all about that; I took a course in it…”), not a college professor engaged in a scientific debate.

But Matheson didn’t stop there. He demeaned Sternberg by calling him “poor Richard.” He also claimed that Sternberg is “disastrously clueless” because he doesn’t understand “the important and very basic distinction between a transcript and an intron.” Since every undergraduate biology student learns that an intron is a segment of DNA, while a transcript is a segment of RNA encoded by DNA, this last jibe is on a par with Moran’s insult that Sternberg can’t do elementary arithmetic. And it is equally unjustified.

Internal sequences that are removed from the primary RNA transcript are called introns. Sequences that are present in the primary transcript and in the mature RNA molecule are called exons. The words intron and exon also refer to the regions of the gene (DNA) that encode corresponding RNA introns and exons. Since DNA introns are transcribed, they are considered part of the gene.

A historical drama set in Roman Egypt, concerning a slave who turns to the rising tide of Christianity in the hopes of pursuing freedom while also falling in love with his master, the famous female philosophy professor and atheist Hypatia of Alexandria.

In the field of science/religion studies, there's a consensus statement that's been widely circulated and agreed to, and it states: "in most instances, biology and religion operate at different and non-competing levels… natural theology may be a legitimate enterprise in its own right, but we resist the insistence of intelligent-design advocates that their enterprise be taken as genuine science - just as we oppose efforts of others to elevate science into a comprehensive world view (so-called scientism)." The New Atheists reject this consensus, as they are entitled to do. But they reject it without going through the academic literature of the relevant field, preferring pop-culture books to academic engagement.

1. Atheists don't believe in supernatural beings. They have not been convinced by any of the arguments offered up by religious scholars or passionate friends and relatives. This does not mean they "elevate science into a comprehensive world view (so-called scientism)." Speaking as one of those atheists, if anyone wants to argue for another valid way of knowing (other than science) then I'm more than happy to pay attention. Just don't ask me to make the assumption that supernatural beings exist. You have to convince me of that first.


2. There are perfectly valid, rational, objections to accommodationism. Josh insults all of us by saying that we don't read the academic literature. That's just not true and I expect an apology.

Our central aim is the facilitation of dialogue between the two academic disciplines of science and religion, one of the most important current areas of debate in terms of understanding the nature of humanity. This includes both the enhancement of the profile of the science-religion interface in the public eye, as well as the safeguarding of the quality and rigour of the debate in the more formal, academic arena.

While maintaining rigorous qualifications for membership (membership is through nomination by existing members only) the Society has now grown to over 140 members, including many of the leading scholars in the science and religion field. Indeed the last two presidents, George Ellis, a theoretical cosmologist and Professor of Applied Mathematics at the University of Cape Town, and John Polkinghorne, are both recipients of the Templeton Prize for Progress Toward Research or Discoveries about Spiritual Realities - the world's best-known religion prize, awarded each year to a living person to encourage and honour those who advance spiritual matters.

Membership of the society is truly universal: the society incorporates, and welcomes, representatives from a variety of faith traditions including Buddhism, Hinduism, Judaism, and Islam in addition to Christianity. Membership is also widely distributed geographically, with representatives from countries as diverse as South Korea, India, Australia, New Zealand and South Africa as well as from Europe and America.

Consider the retrotransposons that, in addition to its promoter sequence that helps initiate the copying of its DNA into an single-stranded RNA molecule, carries its own handy reverse transcriptase gene which encodes the protein machine that copies the RNA back into a DNA molecule, for later insertion into the genome. This can certainly cause biological variation, but it is anything but free.

With evolution we must believe that so many of the sophisticated biological variation mechanisms, such as in retrotransposons, were produced by evolution. Do you see the problem? In this circular tale that even Hans Christian Andersen could never have imagined, evolution produces the intricate mechanisms that produce evolution.

Evolutionists insist that there is no problem because none of this is impossible. Why can’t evolution produce mechanisms that produce evolution? Unless one can prove this is impossible, evolution wins (an argument that goes back to the sage of Kent himself). Though the evidence fails to prove evolution, it nonetheless must be a fact. In this Alice-in-Wonderland world, that which is not false is a fact (if it is evolution, that is).

Earlier today I criticized Calvin College biologist Steve Matheson’s incorrect view of “junk” DNA. Matheson had argued in February that the human genome contains about 190,000 introns (stretches of non-protein-coding DNA that interrupt protein-coding genes), of which “only a handful” had important functional roles. “How many? Oh, probably a dozen,” he wrote, “but let's be really generous. Let's say that a hundred introns in the human genome are known to have ‘important functional roles.’ Oh fine, let's make it a thousand.”

On the contrary, I pointed out that at least 90% of genes are alternatively spliced, meaning that 0.9 x 190,000 = 171,000 introns are involved in alternative splicing, an essential process that helps to ensure that the proper proteins are made at the correct developmental stage and in the appropriate cells and tissues.

Along comes University of Toronto biochemist Larry Moran, an outspoken Darwinist who hates the Center for Science and Culture so much he would probably heap abuse on us for saying that the Earth goes around the Sun. Sure enough, Moran wasted no time jumping on me for being an “Intelligent Design Creationist.” He posted the relevant portion of my critique and concluded: “It's up to you, dear readers, to figure out all the things wrong with this explanation. You can start with the math. Arithmetic isn't one of their strong points.”

1. I am not a Darwinist [Why I'm Not a Darwinist]
2. I don't hate the Center for Science and Culture. I mock it. It's a joke.
3. Richard Sternberg supports intelligent design and be believes in a creator who used intelligent design to create life. Therefore, he is an Intelligent Design Creationist.

So let’s do the math. Again. I will make the task easy for everyone—even Moran and Matheson:

Step 1. There are ~25,000 protein-coding genes in the human genome.
Step 2. There are 190,000 introns/25,000 protein-coding genes = 7.6 introns/gene on average.
Step 3. Ninety percent (possibly more) of gene transcripts undergo alternative splicing. Hence, 0.9 x 25,000 = 22,500 genes (actually, their RNAs) undergo alternative splicing.

Therefore, 22,500 genes x 7.6 introns/gene = 171,000 introns involved in alternative splicing.

This is just a rough estimate, of course. And as I wrote in my original critique of Matheson, even if I’m off by a factor of two we are still left with far more functional introns than Matheson acknowledges. This compels me to ask Steve Matheson: How exactly did you come up with your estimates? And what about you, Larry Moran? What sort of arithmetic are you using?

The segments of our DNA that are commonly called "genes" consist of protein-coding exons and non-protein-coding introns. Initially, the entire DNA segment is transcribed into RNA, but between ninety and ninety-five percent of the initial RNAs are "alternatively spliced."

What is alternative splicing? Imagine that the initial RNA derived from its DNA template has the organization A—B—C—D—E—F, where the letters represent blocks that specify amino acid sequences and the dashes in between the letters stand for introns. Alternative splicing enables multiple proteins to be constructed given the same RNA precursor, say, ABCDF, ACDEF, BCDEF, and so forth. In this way, hundreds or thousands of proteins can be derived from a single gene.

There’s more. The messenger RNAs that are produced by this process—and therefore the proteins that are made in a cell—are generated in a way that depends on the stage of development as well as the cell and tissue type. In the above example, a nerve cell may express the ACDEF version of a messenger RNA whereas a pancreatic cell may produce only the BCDE version. The differences are biologically essential.

What does this have to with introns? Everything. It is the presence of introns that makes this permutative expansion of messenger RNAs possible in the first place.

So let’s do the math. At least ninety percent of gene transcripts undergo alternative splicing, and there are at least 190,000 introns in the human genome. That means we have at least 0.90 x 190,000 = 171,000 introns that participate in the alternative-splicing pathway(s) available to a cell.

For all their historical tensions, scientists and religious scholars from a wide variety of faiths ponder many similar questions—how did the universe begin? How might it end? What is the origin of matter, energy, and life? The modes of inquiry and standards for judging progress are, to be sure, very different. But is there a common ground to be found? ABC News’ Bill Blakemore moderates a panel that includes evolutionary geneticist Francisco Ayala, astrobiologist Paul Davies, Biblical scholar Elaine Pagels and Buddhist scholar Thupten Jinpa. These leading thinkers who come at these issues from a range of perspectives will address the evolving relationship between science and faith.

The Curious Disconnect

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

"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)

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.

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."

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)

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

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)

According to the study authors, the addition of water-based prey into early-human diets may have been what boosted brain size in certain hominins—humans plus human ancestral species and their close evolutionary relatives.

That's because reptiles and fish are particularly rich in long-chain polyunsaturated fatty acids. Some experts think this so-called good fat was "part of the package" of human brain evolution, said study leader David Braun, an archaeologist at the University of Cape Town in South Africa.

Discovering evidence for "brain food" in the late Pliocene (about 3 to 1.8 million years ago) may explain how bigger brains—for instance in our likely direct ancestor Homo erectus—arose in humans and their relatives about 1.8 million years ago, Braun said.

The evidence from FwJj 20 indicates that hominins were very effective at securing access to a wider variety of high-quality animal tissues than has been previously documented. Some of these resources would have provided necessary dietary resources without the added predation risks associated with interactions with large mammalian carnivores that are sometimes involved with the acquisition of elements of large mammal carcasses (28, 33). In addition, although animal tissues provide nutrient-rich fuel for a growing brain, aquatic resources (e.g., fish, crocodiles, turtles) are especially rich sources of the long-chain polyunsaturated fatty acids and docosahexaenoic acid that are so critical to human brain growth (2). Therefore, the incorporation of diverse animals, especially those in the lacustrine food chain, provided critical nutritional components to the diets of hominins before the appearance of H. ergaster/erectus that could have fueled the evolution of larger brains in late Pliocene hominins.

Anthony Griffiths (University of British Columbia, Vancouver) places more emphasis on core principles than on specific applications: “The goal is to show how genetic inference is made ... hence overall the emphasis is more on process than the discoveries.”

[Scott] Hawley also places a heavy emphasis on core topics, because he “factor[s] in heavily the concept that so-called facts can be pretty ephemeral in science.” As Hawley explains, “Many of the ‘facts’ I was taught in college are either irrelevant now or wrong. For example, I heard many lectures as an undergrad asserting that a huge part of the genome was useless ‘junk’. We no longer look at things that way.”

Creationists have learned enough scientific terminology to use it in their attempts to disprove evolution. They do this in numerous ways, but the most common example, at least in the mail I receive is the repeated assertion that the second law of thermodynamics demonstrates the evolutionary process to be impossible.

In kindergarten terms, the second law of thermodynamics says that all spontaneous change is in the direction of increasing disorder—that is, in a "downhill" direction. There can be no spontaneous buildup of the complex from the simple, therefore, because that would be moving "uphill." According to the creationists argument, since, by the evolutionary process, complex forms of life evolve from simple forms, that process defies the second law, so creationism must be true.

Such an argument implies that this clearly visible fallacy is somehow invisible to scientists, who must therefore be flying in the face of the second law through sheer perversity. Scientists, however, do know about the second law and they are not blind. It's just that an argument based on kindergarten terms is suitable only for kindergartens. [my emphasis - LAM]

I believe no one can read the history of our country without realizing that the Good Book and the spirit of the savior have from the beginning been our guiding geniuses.

Whether we look to the first charter of Virginia, or the charter of New England...the same objective is present — a Christian land governed by Christian principles.

I like to believe we are living today in the spirit of the Christian religion. I like also to believe that as long as we do so, no great harm can come to our country.

JAMES, by the Grace of God, King of England, Scotland, France and Ireland, Defender of the Faith, etc. WHEREAS our loving and well-disposed Subjects, Sir Thomas Gates, and Sir George Somers, Knights, Richard Hackluit, Clerk, Prebendary of Westminster, and Edward-Maria Wingfield, Thomas Hanham, and Raleigh Gilbert, Esquires William Parker, and George Popham, Gentlemen, and divers others of our loving Subjects, have been humble Suitors unto us, that We would vouchsafe unto them our License, to make Habitation, Plantation, and to deduce a colony of sundry of our people into that part of America commonly called VIRGINIA, and other parts and Territories in America, either appertaining unto us, or which are not now actually possessed by any Christian Prince or People, situate, lies, and being all along the Sea Coasts, between four and thirty Degrees of Northerly Latitude from the Equinoctial Line, and five and forty Degrees of the same Latitude, and in the main Land between the same four and thirty and five and forty Degrees, and the Islands thereunto adjacent, or within one hundred Miles of the Coast thereof;

....

We, greatly commending, and graciously accepting of, their Desires for the Furtherance of so noble a Work, which may, by the Providence of Almighty God, hereafter tend to the Glory of his Divine Majesty, in propagating of Christian Religion to such People, as yet live in Darkness and miserable Ignorance of the true Knowledge and Worship of God, and may in time bring the Infidels and Savages, living in those parts, to human Civility, and to a settled and quiet Government: DO, by these our Letters Patents, graciously accept of, and agree to, their humble and well-intended Desires;

William Thorsell
Director, the Royal Ontario Museum
100 Queen's Park
Toronto, ON
M5S 2C6

Mr. Thorsell,

We at the Committee for the Advancement of Scientific Skepticism (CASS) at the Centre for Inquiry (Canada) and its supporters were dismayed  to learn that the Royal Ontario Museum will be sponsoring a talk by Deepak Chopra at the University of Toronto in connection with the Director's Signature Series: The Warrior Emperor and China's Terracotta Army.

While we fully support the concept of academic freedom, we are baffled by this invitation and wonder how it fits into the mandate of the museum to "serve as an advocate for science in the study of nature," as stated in your message on the ROM website.  Mr. Chopra's new age psycho-babble may be attractive to the general public, but by inviting him to speak at the ROM, you lend undeserved scientific credibility to his pseudo-scientific claims about quantum physics, psychology, chemistry and medicine. These claims are rightly rejected as absurd by the scientific community and by promoting them you tarnish the otherwise excellent scientific reputation of the Royal Ontario Museum.

CASS will be publishing the standard rebuttals of Deepak Chopra's fanciful quackery in order to help the public understand where he goes off the rails. Our hope is to turn this otherwise embarrassing event into a learning opportunity.  We are also contacting the sponsors of the event and the ROM's other private donors in order to voice our concern about Mr. Chopra's presentation. We would like the ROM to clarify how Mr. Chopra's visit fits into this lecture series, as it seems this is just another opportunity for him to promote his new book.  

We look forward to hearing from you.

 
Sincerely,

The Committee for the Advancement of Scientific Skepticism (CASS) at the Centre for Inquiry Canada

The Curious Disconnect

The Mutationism Myth. 3. Foundations of evolutionary genetics

"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)

"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

The concept of population genetics

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

"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.

Morgan's origin-fixation process

"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)

The 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)

The evolution of quantitative characters

"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."

Homework

• 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.

Conclusion

Argument and debate are common in science, yet they are virtually absent from science education. Recent research shows, however, that opportunities for students to engage in collaborative discourse and argumentation offer a means of enhancing student conceptual understanding and students’ skills and capabilities with scientific reasoning. As one of the hallmarks of the scientist is critical, rational skepticism, the lack of opportunities to develop the ability to reason and argue scientifically would appear to be a significant weakness in contemporary educational practice. In short, knowing what is wrong matters as much as knowing what is right. This paper presents a summary of the main features of this body of research and discusses its implications for the teaching and learning of science.

To investigate the extent and nature of transcriptional dark matter, we have analyzed a diverse set of human and mouse tissues and cell lines using tiling microarrays and RNA-Seq. A meta-analysis of single- and paired-end read RNA-Seq data reveals that the proportion of transcripts originating from intergenic and intronic regions is much lower than identified by whole-genome tiling arrays, which appear to suffer from high false-positive rates for transcripts expressed at low levels.

With an eye to the discussion of the previous chapters, I want to pick out four items or claims that are central to Christian belief—four items that the Christian takes on faith. If you do not believe in these, then you should not call yourself a Christian. First, that there is a God who is creator, "maker of heaven and earth." Second, we humans have duties, moral tasks here on earth, in the execution of which we are going to be judged. Hence, God stands behind morality. Third, Jesus Christ came to earth and suffered because we humans are special, we are worth the effort by God. The usual way of expressing this is to say that we are "made in the image of God." We have "souls." Fourth and finally, there is the promise of "life everlasting." We can go to heaven, what ever that means.

Let me spell out carefully what I see as the task in this and the next chapter. It is not to defend Christianity as a true or compelling belief system. I take it that you can enter these chapters as an agnostic or an atheist and depart in the same frame of mind. I do not want to dissuade people from Christianity, nor do I want to convince them of it. I want to explain in a fair manner what is meant by Christianity in terms of the four points introduced in the last paragraph. I also want to show that you could hold these, if you so wish, in the light of modern science—if you prefer, in the face of modern science. In other words, the Christian's claims are not refuted by modern science—or indeed threatened or made less probable by modern science.

Ward effortlessly flows from one fascinating insight to another about the often contentious relationship between diverse religious views and the new scientific knowledge. Writing with both passion and clarity, he masterfully converys the depth, the difficulty, and the importance of the greatest intellectual and existential questions of the modern age.

Mr. Prime Minister and excellent minister Bev Oda:

Please stand firm against the people who will get money from aborting babies in other countries, if you cave in.

This is for a number of non-religious reasons:

1. There is NO reason to believe abortion will even be voluntary. And what can we do if it isn't? It is better if we Canadians just do not fund it. (If people in other countries want to force women to be aborted, to meet grant-based population reduction quotas, we cannot stop them. But at least we had nothing to do with it, right? It's not like the cheque is stamped 'From a grateful CANADA'. Surely, there are some shames we cannot stoop to.)

2. Contrary to population whackos, most of the world is in steep demographic decline. This is bad news for business, pension plans, etc. Why add to the problem? Right now, YOUR government is advertising for healthy young workers from abroad. So we should kill their successors?

3. Abortion clinics are run by people who do not mind killing babies for a living. Even if you didn't agree that that is a problem, a number of other evils result, including: Teachers molest underage girls and ship them to clinics for discreet abortions, unbeknown to their parents. Abortion clinics may also function on the adoption black market. = Would you keep it for a while instead of killing it, if we get you some money?

4. No one should believe anything an abortion clinic operator says about not killing viable babies. If he really cared about stuff like that, he would not likely do what he does now. So you can assume, for practical purposes, it is unreliable.

5. Some babies may be sold for research that should never be done on a human being, but remember that they do not technically exist.

Stand firm! Most of the criticism I hear about your government comes from NOT standing up for traditional Canadian values. Most of the praise I hear is for doing so.

And REPEAL Section 13 and FIRE Jennifer Lynch. Quit fooling around about that too. People are really angry.

Traditional values and civil rights are important to the people who would re-elect you.

Katarin MacLeod is an Assistant Professor in Science Education at St. Francis Xavier University in Antigonish, NS. Her areas of interest include physics educational research (PER), and the incorporation of science, technology, society and environment (STSE) outcomes into science courses at all levels to help students understand the relevancy of science, increase scientific literacy, and to promote citizenship.

Although the text is very good in describing the theory of Evolution, there are points in the book where the author makes comments that could imply that Evolution is more than a theory. For example, “…Charles Darwin revealed the solution to the mystery of evolution” (p. 7). He also makes the comment that Evolution is the most important idea in all of biology (p. 7). Such phrases may lead the reader into thinking that scientists completely understand the theory of Evolution which would be incorrect, else Evolution would be a principle or a law and not a theory. As well, it is a bit bold to claim that evolution is the most important idea in all of biology – biology is a huge field of study with other key discoveries.

An Evening with Deepak Chopra
Wednesday, June 23, 7:00 - 8:00 pm (Doors Open 6:00 pm)

Status: Registration Starts May 14!

Director's Signature Series
The Warrior Emperor and China's Terracotta Army

World renowned teacher, author and philosopher Deepak Chopra presents his latest concepts in the field of mind-body medicine bridging the technological miracles of the West with the wisdom of the East. He will show you how your highest vision of yourself can be turned into physical reality and discuss how you can become a living cell within the body of a living universe. You don't join the cosmic dance - you become the dance. Deepak will address the deeper meaning of our existence including: What is our true nature? What is the meaning and purpose of our existence? How can I transform myself? How can I make a better world? Deepak explains how the greatest spiritual secrets are tied up in this simple answer: You can't change the body without changing the self, and you can't change the self without bringing in the soul. He explains, "It's all one process, and it begins with knowing that your body exists to mirror who you are and who you want to be."

Deepak Chopra is the author of more than 56 books translated into over 35 languages, including numerous New York Times bestsellers in both the fiction and non-fiction categories. He is a fellow of the American College of Physicians, a member of the American Association of Clinical Endocrinologists, Adjunct Professor at Kellogg School of Management and Senior Scientist with The Gallup Organization. Time magazine heralds Deepak Chopra as one of the top 100 heroes and icons of the century and credits him as "the poet-prophet of alternative medicine." For more information visit: www.deepakchopra.com

Location: Convocation Hall, 31 King’s College Circle, University of Toronto

Cost: Price: Ground VIP: $175, Rise Area: $89, 1st Balcony: $69, 2nd Balcony: $49, Behind Stage: $25

Tickets are non-refundable.

Transcripts from approximately 95% of multi-exon human genes are spliced in more than one way, and in most cases the resulting transcripts are variably expressed between different cell and tissue types. This process of alternative splicing shapes how genetic information controls numerous critical cellular processes, and it is estimated that 15% to 50% of human disease mutations affect splice site selection.

Frey compared his computer decoder to the German Enigma encryption device, which helped the Allies defeat the Nazis after it fell into their hands.

“Just like in the old cryptographic systems in World War II, you’d have the Enigma machine…which would take an instruction and encode it in a complicated set of symbols,” he said.

“Well, biology works the same way. It turns out to control genetic messaging it makes use of a complicated set of symbols that are hidden in DNA.”

Given the number of biological activities needed to grow and govern our bodies, scientists had believed humans must have 100,000 genes or more to direct those myriad functions.

But that genomic search of the 3 billion base pairs that make up the rungs of our twisting DNA ladders revealed a meagre 20,000 genes, about the same number as the lowly nematode worm boasts.

“The nematode has about 1,000 cells, and we have at least 1,000 different neuron (cells) in our brains alone,” said Benjamin Blencowe, a U of T biochemist and the study’s co-senior author.

To achieve this huge complexity, our genes must be monumental multi-taskers, with each one having the potential to do dozens or even hundreds of different things in different parts of the body.

And to be such adroit role switchers, each gene must have an immensely complex set of instructions – or a code – to tell them what to do in any of the different tissues they need to perform in.

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.

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.

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.

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 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.

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.

[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 ...

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?

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.

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.

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

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.

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.

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

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

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.

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