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Peer-Reviewed Article Critical of Darwinism by NAS Member, Evolution by Absence of Selection

recent molecular data supports the theory of mutation-driven evolution rather than neo-Darwinism.

Masotoshi Nei
Member National Academy of Sciences
Selectionism and Neutralism

Not only is the notion of Darwinism challenged by ID proponents and creationists, but it is also challenged by non-Darwinian theories of evolution. The competing schools of thought are the Mutationists and the Neutralists. Dawkins describes some of the history of the Mutationists versus the Darwinists:

It is hard to comprehend now but, in the early years of this [20th] century when the phenomenon of mutation was first named, it was not regarded as a necessary part of Darwinian theory but an alternative theory of evolution!

Richard Dawkins
Blindwatchmaker

Darwinism so dominates evolutionary thinking that most presume evolution must proceed under the influence of selection. Not so. In fact the absence of selection is also a mechanism of evolution! In the words of yet another member of the National Academy of Sciences:

many genomic features could not have emerged without a near-complete disengagement of the power of natural selection

Michael Lynch
The Origins of Genome Architecture, intro


Lynch and others have pointed out that Natural Selection may actually prevent evolution, not facilitate it. Lynch is not alone, some years ago, another researcher predicted the problems with selectionist theories of evolution:

a relative lack of natural selection may be the prerequisite for major evolutionary advance

Mae Wan Ho
Beyond neo-Darwinism

So bad is the situation, that Lynch felt compelled to take a subtle swipe at ultra-Darwinists (like Dawkins and Dennett), and did so using the strongest possible insult, likening them to ID proponents:

the uncritical acceptance of natural selection as an explanatory force for all aspects of biodiversity (without any direct evidence) is not much different than invoking an intelligent designer

Michael Lynch
The Origins of Genome Architecture, p 368

The problems Lynch and Mae Wan Ho describe are possibly related to the fact that selection can impede the evolution of function because selection can select against non-functioning pre-cursors to future organs and systems. In the words of Gould, “What good is half a jaw or half a wing?” And Walter Brown described it better: “A leg evolving into a wing would be a bad leg long before it was a good wing”.

[For a formal description of the problem, see Fitness Peaks in a Fitness Landscape. In a fitness peak, natural selection actually selects against potentially beneficial pre-cursors of functioning systems. Fitness peaks make the problem of irreducibly complexity worse for Darwinism but better for ID.]

But fitness peaks are only the beginning of problems for natural selection. Some of the real problems for Darwinism are posed by the mathematics of evolution, specifically the discipline of Population Biology. The problem is that Natural Selection has limited ability to manage very large genomes with only finite population resources. [To get a flavor of some of the issues (and there are many), see the youtube cartoon linked here: Nachman's Paradox Defeats Darwinism and Dawkins Weasel. ]

The start of forceful mathematical arguments against Darwinism was first put forward (unwittingly) by neo-Darwinist JBS Haldane in his celebrated 1957 paper, The Cost of Natural Selection. Haldane unwittingly provided ammunition to the non-Darwinians by showing that Natural Selection comes at high cost. The birth rates and death toll would be so high in order to effect change, that selection could not be the primary mechanism of evolution.

His paper was followed by one of the land mark papers by King and Jukes Non Darwinian Evolution where they argued the majority of evolution in proteins was not Darwinian. Almost simultaneously, one of James Crow’s students, Motoo Kimura published papers on his Neutral theory of Molecular Evolution which referenced Haldane’s work. All of these non-Darwinians gave token credit to Darwinism, but over time the uneasy truce between the Darwinists on one side and the Mutationists and Neutralists on the other was bound to break down.

How has Dawkins responded to the growing list of non-Darwinian rebels, he wrote in Blindwatchmaker:

“Molecular geneticists are like pernickety printers”.

And these “pernickety printers” continue to publish refutation after refutation of Darwinian evolution. One recent paper is by Pagels [See: Accidental Origins Where Species Come From]. Another such paper is by National Academy member Masotoshi Nei, and that paper is the focus of this thread.

I highlight passages from Nei paper below for those really interested. What I wrote above was to help introduce Nei’s paper. But for those who choose to forgo Nei’s torturous details, I close with this thought: Darwinism is being challenged by the issue of Irreducible Complexity, No Free Lunch, Genetic Entropy, fitness peaks, the Mutationist and Neutralist schools of evolution, etc. How long after suffering repeated falsifications, can Darwin’s ideas be propped up by pure dogma before it finally collapses?

HIGHLIGHTS OF NEI’S PAPER FOR INTERESTED READERS:

[The paper can be found here: Selectionism and Neutralism, Molecular Biology and Evolution 2005 22(12):2318-2342]

Before highlighting segments of the paper let me briefly summarize my take of Nei’s paper. Nei argues a lot of functional changes, as long as they aren’t fatal, just sort of pop up independent of Natural Selection’s guiding hand. He seems to argue that the appearance of design is just an artifact of our imagination, thus design needs no explanation since it isn’t there in the first place. No need of even a blind watchmaker, since the watch is merely a post-dictive illusion like seeing faces in the clouds.

Though ID proponents might dismiss Nei’s paper on the grounds that it doesn’t address the problem of design, the importance of the paper are its mathematical arguments against the ability of selection to manage very large genomes.

So in addition to NAS member Phil Skell we now have NAS member Masotoshi Nei who is quite willing to challenge Darwinian Evolution. Nei reported in the Journal of Molecular Biology an Evolution:

Charles Darwin proposed that evolution occurs primarily by natural selection, but this view has been controversial from the beginning. Two of the major opposing views have been mutationism and neutralism.

The rest of the paper is breathtaking but torturous read, not for the faint of heart. The paper is like Nei’s 40-year diary, detailing his fight against natural selection.

Nei even references the work of one of Allen MacNeill’s colleagues at Cornell, Will Provine:

In his book On the Origin of Species, Charles Darwin (1859) proposed that all organisms on earth evolved from a single proto-organism by descent with modification. He also proposed that the primary force of evolution is natural selection. Most biologists accepted the first proposition almost immediately, but the second proposal was controversial and was criticized by such prominent biologists as Thomas Huxley, Moritz Wagner, and William Bateson. These authors proposed various alternative mechanisms of evolution such as transmutation theory, Lamarckism, geographic isolation, and nonadaptive evolution (see Provine 1986, chap. 7). Because of these criticisms, Darwin later changed his view of the mechanism of evolution to some extent (Origin of Species 1872, chap. 7). He was a pluralistic man and accepted a weak form of Lamarkism and nonadaptive evolution (see Provine 1986). Nevertheless, he maintained the view that the natural selection operating on spontaneous variation is the primary factor of evolution. His main interest was in the evolutionary change of morphological or physiological characters and speciation.

Another critic of evolution by natural selection was the post-Mendelian geneticist Thomas Morgan. He rejected Lamarkism and any creative power of natural selection and argued that the most important factor of evolution is the occurrence of advantageous mutations and that natural selection is merely a sieve to save advantageous mutations and eliminate deleterious mutations (Morgan 1925, 1932). For this reason, his view is often called mutationism. However, this view should not be confused with the saltation theory of Bateson (1894) or the macromutation theory of De Vries (1901–1903), in which natural selection plays little role. In Morgan’s time the genetic basis of mutation was well established, and his theory of evolution was appealing to many geneticists. The only problem was that most mutations experimentally obtained were deleterious, and this observation hampered the general acceptance of his theory. He also proposed that some part of morphological evolution is caused by neutral mutation. In his 1932 book The Scientific Basis of Evolution, he stated “If the new mutant is neither more advantageous than the old character, nor less so, it may or may not replace the old character, depending partly on chance; but if the same mutation recurs again and again, it will most probably replace the original character” (p. 132).

In his book On the Origin of Species, Charles Darwin (1859) proposed that all organisms on earth evolved from a single proto-organism by descent with modification. He also proposed that the primary force of evolution is natural selection. Most biologists accepted the first proposition almost immediately, but the second proposal was controversial and was criticized by such prominent biologists as Thomas Huxley, Moritz Wagner, and William Bateson. These authors proposed various alternative mechanisms of evolution such as transmutation theory, Lamarckism, geographic isolation, and nonadaptive evolution (see Provine 1986, chap. 7). Because of these criticisms, Darwin later changed his view of the mechanism of evolution to some extent (Origin of Species 1872, chap. 7). He was a pluralistic man and accepted a weak form of Lamarkism and nonadaptive evolution (see Provine 1986). Nevertheless, he maintained the view that the natural selection operating on spontaneous variation is the primary factor of evolution. His main interest was in the evolutionary change of morphological or physiological characters and speciation.

Another critic of evolution by natural selection was the post-Mendelian geneticist Thomas Morgan. He rejected Lamarkism and any creative power of natural selection and argued that the most important factor of evolution is the occurrence of advantageous mutations and that natural selection is merely a sieve to save advantageous mutations and eliminate deleterious mutations (Morgan 1925, 1932). For this reason, his view is often called mutationism. However, this view should not be confused with the saltation theory of Bateson (1894) or the macromutation theory of De Vries (1901–1903), in which natural selection plays little role. In Morgan’s time the genetic basis of mutation was well established, and his theory of evolution was appealing to many geneticists. The only problem was that most mutations experimentally obtained were deleterious, and this observation hampered the general acceptance of his theory. He also proposed that some part of morphological evolution is caused by neutral mutation. In his 1932 book The Scientific Basis of Evolution, he stated “If the new mutant is neither more advantageous than the old character, nor less so, it may or may not replace the old character, depending partly on chance; but if the same mutation recurs again and again, it will most probably replace the original character” (p. 132).

However, Morgan’s mutation-selection theory or mutationism gradually became unpopular as the neo-Darwinism advocated by Fisher (1930), Wright (1931), Haldane (1932), Dobzhansky (1937, 1951), and others gained support from many investigators in the 1940s. In neo-Darwinism, natural selection is assumed to play a much more important role than mutation, sometimes creating new characters in the presence of genetic recombination. Although there are several reasons for this change (see Nei 1987, chap. 14), two are particularly important. First, most geneticists at that time believed that the amount of genetic variability contained in natural populations is so large that any genetic change can occur by natural selection without waiting for new mutations. Second, mathematical geneticists showed that the gene frequency change by mutation is much smaller than the change by natural selection. Neo-Darwinism reached its pinnacle in the 1950s and 1960s, and at this time almost every morphological or physiological character was thought to have evolved by natural selection (Dobzhansky 1951; Mayr 1963).

This situation again started to change as molecular data on evolution accumulated in the 1960s. Studying the GC content of the genomes of various organisms, early molecular evolutionists such as Sueoka (1962) and Freese (1962) indicated the possibility that the basic process of evolution at the nucleotide level is determined by mutation. Comparative study of amino acid sequences of hemoglobins, cytochrome c, and fibrinopeptides from various organisms also suggested that most amino acid substitutions in a protein do not change the protein function appreciably and are therefore selectively neutral or nearly neutral, as mentioned below. However, this interpretation was immediately challenged by eminent neo-Darwinians such as Simpson (1964) and Mayr (1965), and this initiated a heated controversy over selectionism versus neutralism.

An even more intense controversy on this subject was generated when protein electrophoresis revealed that the extent of genetic variation within populations is much higher than previously thought. At that time, most evolutionists believed that the high degree of genetic variation can be maintained only by some form of balancing selection (Mayr 1963; Ford 1964). However, a number of authors argued that this variation can also be explained by neutral mutations. From the beginning of the 1980s, the study of molecular evolution was conducted mainly at the DNA level, but the controversy is still continuing. This long-standing controversy over selectionism versus neutralism indicates that understanding of the mechanism of evolution is fundamental in biology and that the resolution of the problem is extremely complicated. However, some of the controversies were caused by misconceptions of the problems, misinterpretations of empirical observations, faulty statistical analysis, and others.

Because I have been involved in this issue for the last 40 years and have gained some insights, I would like to discuss this controversy with historical perspectives. Obviously, the discussion presented will be based on my experience and knowledge, and therefore it may be biased. In my view, however, we can now reach some consensus and examine what has been solved and what should be done in the future. Needless to say, I shall not be able to cover every subject matter in this short review, and I would like to discuss only fundamental issues.

and

Cost of Natural Selection
At this juncture, Kimura (1968a) and King and Jukes (1969) formally proposed the neutral theory of molecular evolution. Kimura first computed the average number of nucleotide substitutions per mammalian genome (4 x 109 nt) per year from data on amino acid substitutions in hemoglobins and a few other proteins and obtained about one substitution every 2 years. (Actually he used 3.3 x 109 nt as the mammalian genome size after elimination of silent nucleotide sites.) He then noted that this rate is enormously high compared with the estimate of Haldane (1957) of the upper limit of the rate of gene substitution by natural selection that is possible in mammalian organisms (one substitution every 300 generations or every 1,200 years if the average generation time is 4 years in mammals). Haldane’s estimate was based on the cost of natural selection that is tolerable by the average fertility of mammalian organisms. If we accept Haldane’s estimate, such a high rate of nucleotide substitution (one substitution every 2 years) cannot occur by natural selection alone, but if we assume that most substitutions are neutral or nearly neutral and are fixed by random genetic drift, any number of substitutions is possible as long as the substitution rate is lower than the mutation rate. For this reason, Kimura concluded that most nucleotide substitutions must be neutral or nearly neutral.

and

King and Jukes’ View

King and Jukes (1969) took a different route to reach the idea of neutral mutations. They examined extensive amounts of molecular data on protein evolution and polymorphism and proposed that a large portion of amino acid substitutions in proteins occurs by random fixation of neutral or nearly neutral mutations and that mutation is the primary force of evolution and the main role of natural selection is to eliminate mutations that are harmful to the gene function. This idea was similar to that of Morgan (1925, 1932) but was against the then popular neo-Darwinian view in which the high rate of evolution is achieved only by natural selection (Simpson 1964; Mayr 1965). According to King and Jukes, proteins requiring rigid functional and structural constraint (e.g., histone and cytochrome c) are expected to be subject to stronger purifying selection than proteins requiring weak functional constraints (e.g., fibrinopeptides), and therefore the rate of amino acid substitution would be lower in the former than in the latter. Extending the results obtained by Zuckerhandl and Pauling (1965) and Margoliash (1963), they also emphasized that the functionally important parts of proteins (e.g., the active center of cytochrome c) have lower substitution rates than the less important parts. Later, Dickerson (1971) confirmed this finding by using an even larger data set. They also noted that cytochrome c from different mammalian species is fully interchangeable when tested in vitro with intact mitochondrial cytochrome oxidase (Jacobs and Sanadi 1960). For many molecular biologists, these data were more convincing in supporting neutral theory than Kimura’s computation of the cost of natural selection.

and

Evolution of New Protein Function
Kimura (1983) proposed that molecular evolution occurs by random fixation of neutral or nearly neutral mutations, but he believed that the evolution of morphological or physiological characters occurs following the classical neo-Darwinian principle. However, we should note that all morphological characters are ultimately controlled by DNA, and therefore morphological evolution must be explained by molecular evolution of genes. In other words, evolution is not dichotomous as Kimura assumed, and we should be able to find the molecular basis of phenotypic evolution.

and finally the swipe against neo-Darwinism in favor of new theory:

This view of evolution is based on a large amount of molecular data, and in this sense it is different from Morgan’s mutationism, which was largely speculative. For this reason I have called it neomutationism (Nei 1983, 1984) or the neoclassical theory of evolution (Nei 1987, chap. 14). Whatever it is called, however, recent molecular data supports the theory of mutation-driven evolution rather than neo-Darwinism.

Further NOTES:
Pictured in the following link are some morphological features which Larry Moran and Richard Lewontin use to discuss features which might not necessarily be the product of selection: Visible Mutations and Evolution.

I mentioned Kimura was one of Crow’s students. Another of Crows students was Lynn Margulis and that perennial prodigal Son of ID, John A. Davison.

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33 Responses to Peer-Reviewed Article Critical of Darwinism by NAS Member, Evolution by Absence of Selection

  1. So now we have an elite member of the NAS expressing doubts about Darwinism.

    Nei even references some of John Davison’s favorite names like Bateson.

    To borrow a phrase from John, “I love it so!”

  2. Nei advocates the Mutationist school of thought, he highlights the problem with mutationism as it relates to Morgan’s hypothesis:

    The only problem was that most mutations experimentally obtained were deleterious, and this observation hampered the general acceptance of his [Morgan's] theory.

    Masotoshi Nei

    The problem of deleterious mutations has not disappeared. We recognize the problem to be even worse now. So Nei’s alternative to Darwinism is fatally flawed.

    Nei finds fatal flaws in Darwinism, but his position is also flawed. I suppose we take some of the bad with the good in Nei’s work.

    So the competing camps within evolution find fatal flaws in each other’s school of thought. Perhaps that means there is yet an alternative which is the correct one, but one which they all refuse to consider. :-)

  3. Allen MacNeill posed the very good challenge to ID proponents as to how to decide if a mutation (or change) was due to intelligence versus being random.

    The issue challenging Morgan and Nei is one of deleterious mutations. If it can be shown that a sufficient number of deleterious mutations (deleterious in the functional sense, not deleterious in the sense of immediate reproductive fitness) cannot be weeded out by selection, then it implies that the majority of changes in the genome were mysteriously fortuitous.

    This would suggest the mutations, could not have been random, since most random changes are neutral with respect to function or even deleterious.

    Such a line of reasoning doesn’t formally prove ID, but it elimates one of ID’s competitors, namely, “random mutation” as a mechanism. Thus it strengthens the indirect, circumstantial case for design.

    That is why, investigations into Sanford’s genetic entropy are a very relevant line of scientific inquiry.

    One of Sanford’s colleagues, Walter ReMine has taken a lot of flak regarding “Haldane’s Dilemma”. What is significant in Nei’s paper is that Haldane’s dilemma is presented in a favorable light, thus giving some vindication to Walter.

  4. Hello Scordova,

    Seeing that you (and many of us here in UD) are so impressed with John sanford’s idea of Genetic Entropy, I was wondering why you are not discussing this paper(link below)by Michael Lynch in UD. I was pleasantly surprise to read this paper (hopefully Sanford as well…. )

    http://www.pnas.org/content/10.....l.pdf+html

    http://www.pnas.org/content/107/3/961.full

  5. T. lise:

    I wasn’t aware of these papers. THANKS!!!!!!!!!!!!!!

    From the free abstract:

    Contributed by Michael Lynch, December 3, 2009 (sent for review September 13, 2009)

    Abstract
    Although mutation provides the fuel for phenotypic evolution, it also imposes a substantial burden on fitness through the production of predominantly deleterious alleles, a matter of concern from a human-health perspective. Here, recently established databases on de novo mutations for monogenic disorders are used to estimate the rate and molecular spectrum of spontaneously arising mutations and to derive a number of inferences with respect to eukaryotic genome evolution. Although the human per-generation mutation rate is exceptionally high, on a per-cell division basis, the human germline mutation rate is lower than that recorded for any other species. Comparison with data from other species demonstrates a universal mutational bias toward A/T composition, and leads to the hypothesis that genome-wide nucleotide composition generally evolves to the point at which the power of selection in favor of G/C is approximately balanced by the power of random genetic drift, such that variation in equilibrium genome-wide nucleotide composition is largely defined by variation in mutation biases. Quantification of the hazards associated with introns reveals that mutations at key splice-site residues are a major source of human mortality. Finally, a consideration of the long-term consequences of current human behavior for deleterious-mutation accumulation leads to the conclusion that a substantial reduction in human fitness can be expected over the next few centuries in industrialized societies unless novel means of genetic intervention are developed.

    WHOA!!!!

  6. T. ilse,

    As you can see it took me about a year to get around to reporting Nei’s paper.

    I’ll try to be faster in reporting on Lynch’s latest as soon as I can free my schedule.

    Please feel free to offer any highlights of Lynch’s paper here in this thread. The issues seem relevant to Nei’s paper, and even if it is a tangent, please speak freely as this is very interesting.

    Thank you, thank you, thank you!!!

    Sal

  7. @ Scordova 6,

    “Please feel free to offer any highlights of Lynch’s paper here in this thread..”

    Maybe I’ll wait for your post but just a note here: I couldn’t help but shock all the way as I read the last section ‘Long-Term Consequences of Germline Mutations.’ Lynch also (like Sanford) seems to hint that Eugenics won’t be able to help it…

    And felt really funny about his starting line (Abstract). It says “Although mutation provides the fuel for phenotypic evolution,…”

    Why he felt the need to say that????? Ever wondered!!??

    Glad that I happened to bring this to your notice. I thought you knew it.

  8. As for accumulation of mutation, he (Lynch) said:

    “once a particular chromosomal region has acquired a mutation load in all chromosomes, even if distributed over different loci in different chromosomes, a full reassertion of the power of natural selection would be incapable of returning the population to a state better than that represented by the leastloaded chromosomal segment unless the region experienced sufficient recombination to reestablish less-loaded chromosomal
    segments. This issue is nontrivial in that the amount of recombination
    per physical distance in human chromosomes is exceptionally
    low, averaging approximately 10?5 crossover events per kb perb meiosis, which is approximately 30% lower than the rate of origin of base-substitutional mutations alone in a 1-kb region

    As for the interference of Eugenics he said:

    “Muller was well aware of the enormous social barriers to solving the mutation-accumulation problem, but he held out hope that “a rationally directed guidance of reproduction” would eventually
    stabilize the situation. Unfortunately, it has become increasingly clear that most of the mutation load is associated with mutations with very small effects distributed at unpredictable locations over the entire genome, rendering the prospects for long-term management of the human gene pool by genetic counseling highly unlikely for all but perhaps a few hundred key loci underlying
    debilitating monogenic genetic disorders”

    The whole paper is even more revealing!!!!!!!!!!

  9. “with his scathing allegation that science presents the only reliable means by which to understand nature and the world around us”

    A few comments:
    1. Science IMO only covers the portion of reality that is open to scientific investigation not art, beauty, music and on and on.
    2. In some sense Science is not terribly reliable. After all Newtonian mechanics gave way to Einsteinian mechanics which in turn is already known to be in conflict with Quantum mechanics but there is no unified theory yet. Science is the best we have in its limited area of interest. Somebody named Popper said all scientific theories are open to being falsified by reality and then modified when a better theory is found. IMO Biological science is harder than Physical Science. The Human sciences are harder than biology…

    So given those caveats why does ID want to be science, please explain.

  10. gingoro,

    I think you posted to the wrong thread. This thread is about Nei.

    Good question though. Perhaps it can be persued in Robert Deyes thread.

    Sal

  11. Mr Lise,

    And felt really funny about his starting line (Abstract). It says “Although mutation provides the fuel for phenotypic evolution,…”

    Matches quite well with the last line of Nei’s abstract –
    It appears that mutation (including gene duplication and other DNA changes) is the driving force of evolution at both the genic and the phenotypic levels.

  12. scordova,

    As you can see it took me about a year to get around to reporting Nei’s paper.

    Is it 2006? Nei’s paper was published in 2005. Not sure if you blogged here about Nei previously.

  13. Yup wrong thread. Will re-post in the proper thread.

  14. Is it 2006? Nei’s paper was published in 2005. Not sure if you blogged here about Nei previously.

    I learned about Nei’s paper in 2009, so it’s taken a year since then to report on it, that’s what I meant.

    The paper was so obscure in ID circles, even Walter ReMine was unware of it. So I reporting on it now to raise attention to it.

    The data are not really that new, what Nei is reporting is known, but not widely accepted (by people like Dawkins).

  15. scordova,

    I’m not at all clear why you push papers like this. Nei’s position, that random mutation is responsible for most of the diversity around us, is even less comformable to Christian theology than selectionist positions. Its like anyone who is against the Big D is fine by you.

    It was the same thing with the Pagels paper and James Shapiro of UC. You’re happy that accidents of geology and the genome are getting the credit for life’s diversity?

    But anyway, thanks for showing the whole “academia is a closed shop” line is just cant. Nei has been hammering away at these points for 40 years.

  16. Here is a link to another paper by Nei.

    The title, interesting enough, is “The New Mutation Theory of Phenotypic Evolution.”

    In his “Discussion” section, he writes:

    Historically, the word mutationism
    was used to refer to William Bateson’s
    saltationism or similar ideas, in which
    natural selection plays little role. Later
    Morgan (109) presented a more reasonable
    form of mutationism taking into
    account the role of natural selection.
    His view was abstract and based on a
    few lines of speculative arguments.
    However, recent molecular studies of
    phenotypic evolution support the basic
    ideas of his view and have extended it to
    a more comprehensive view presented in
    this article.

    Sal writes above regarding Morgan’s theory:

    Another critic of evolution by natural selection was the post-Mendelian geneticist Thomas Morgan. He rejected Lamarkism and any creative power of natural selection and argued that the most important factor of evolution is the occurrence of advantageous mutations and that natural selection is merely a sieve to save advantageous mutations and eliminate deleterious mutations (Morgan 1925, 1932).

    Let’s note that Dawkin’s, in The Blind Watchmaker, presents NS as a “sieve-like” process, and then tries to argue that it is much more than that, an argument which, in the end, falls flat when he makes the statement (I paraphrase) “If, however, one could take a series of small steps, each with a positive reward, and in the right direction, one could easily go from a butterfly to a fox in the minimum number of steps . . .” But, of course, how is this reward ‘rewarded’? What is the mechanism?
    How can a mechanism be invoked that moves NS beyond its “sieve-like” function without telling us how it works? To invoke a mechanism that you cannot explain as the explanation of another mechanism simply puts one in the position of arguing in a circle. Where have I heard that criticism before?

    And, further, what does he mean by “right direction”? This amounts, really, to teleology.

    It is for this reason that I have for a long time now begun to view NS as no more than a sieve process with almost trivial consequences vis-a-vis progressive evolution. Nei seems to support Morgan; and Morgan seems to support my position. (jerry, are you reading this?)

    Over the last year, I’ve taken a longer look at population genetics and have come to the conclusion that it is almost not worth studying, so limited is its power to explain molecular evolution.

    My take on things is that “something has to give.” A “revolution” is in the making.

  17. This is an interesting paper, but I agree with Nakashima. scordova’s post reminds me of when anti-evolutionists would quote Gould and Lewontin because they critiqued the adaptationist paradigm. The same happened with Margulis.

    If it’s against the prevailing view, it must friendly to ID!

    People who know the field noticed this paper when it was published (it’s been cited 106 times). Not in the field, scordova noticed it late and associated it (inappropriately) with the same “critique of Darwinism” as ID. That’s ridiculous. First — let’s be honest — ID has had no measurable effect on the practice of science. Second, this is a paper about the material mechanisms of evolution. Intelligent design and/or intervention are nowhere to be seen.

  18. Another difference between this paper and ID: this paper reviews the literature and proposes the viability of neomutuationism. This can be tested and further investigated. ID, on the other hand, knows the answer in advance: design. Does anybody doubt that will remain the repeated answer no matter what the evidence?

    ID is like the joke my kid told me:

    Q: Why did Chuck Norris answer all the questions on his math test the same way?
    A: Because for Chuck Norris, violence is the answer to every question.”

  19. composer did you really mean this?

    “Another difference between this paper and ID: this paper reviews the literature and proposes the viability of neomutuationism. This can be tested and further investigated. ID, on the other hand,Does anybody doubt that will remain the repeated answer no matter what the evidence?”

    And do you suppose ID does not review all the evidence? Moreover Do you have any evidence whatsoever that undirected mutations can generate functional information over 140 Functional Bits (Fits)?

    Why must you insist that ID is close-minded to only one answer when it is the atheistic evolutionists themselves who refuse any answer other than neo-Darwinism. You don’t believe me? Just watch this paper though extremely fair in its criticism of natural selection to create information will be quickly forgotten, and neo-Darwinism will still be trumpted as the end all be all that is as sure as gravity.

    Which reminds me have they found the graviton yet (LOL)?

  20. The paper states:

    “Kimura (1983) proposed that molecular evolution occurs by random fixation of neutral or nearly neutral mutations, but he believed that the evolution of morphological or physiological characters occurs following the classical neo-Darwinian principle. However, we should note that all morphological characters are ultimately controlled by DNA, and therefore morphological evolution must be explained by molecular evolution of genes.”

    So his whole theory is built on the falsified premise of Genetic Reductionism. Does anybody want to break the news to him that DNA does not determine Body Plan Morphogenesis?

    This inability for the DNA code to account for body plans is also clearly shown by extensive mutation studies to the DNA of different organisms which show “exceedingly rare” major morphological effects from mutations to the DNA code.

    Stephen Meyer – Functional Proteins And Information For Body Plans – video
    http://www.metacafe.com/watch/4050681

    The Origin of Biological Information and the Higher Taxonomic Categories – Stephen Meyer”Neo-Darwinism seeks to explain the origin of new information, form, and structure as a result of selection acting on randomly arising variation at a very low level within the biological hierarchy, mainly, within the genetic text. Yet the major morphological innovations depend on a specificity of arrangement at a much higher level of the organizational hierarchy, a level that DNA alone does not determine. Yet if DNA is not wholly responsible for body plan morphogenesis, then DNA sequences can mutate indefinitely, without regard to realistic probabilistic limits, and still not produce a new body plan. Thus, the mechanism of natural selection acting on random mutations in DNA cannot in principle generate novel body plans, including those that first arose in the Cambrian explosion.”

    Hopeful monsters,’ transposons, and the Metazoan radiation:
    Excerpt: Viable mutations with major morphological or physiological effects are exceedingly rare and usually infertile; the chance of two identical rare mutant individuals arising in sufficient propinquity to produce offspring seems too small to consider as a significant evolutionary event. These problems of viable “hopeful monsters” render these explanations untenable.
    Paleobiologists Douglas Erwin and James Valentine

    “Yet by the late 1980s it was becoming obvious to most genetic researchers, including myself, since my own main research interest in the ‘80s and ‘90s was human genetics, that the heroic effort to find the information specifying life’s order in the genes had failed. There was no longer the slightest justification for believing that there exists anything in the genome remotely resembling a program capable of specifying in detail all the complex order of the phenotype (Body Plan).” Michael John Denton page 172 of Uncommon Dissent

    …Advantageous anatomical mutations are never observed. The four-winged fruit fly is a case in point: The second set of wings lacks flight muscles, so the useless appendages interfere with flying and mating, and the mutant fly cannot survive long outside the laboratory. Similar mutations in other genes also produce various anatomical deformations, but they are harmful, too. In 1963, Harvard evolutionary biologist Ernst Mayr wrote that the resulting mutants “are such evident freaks that these monsters can be designated only as ‘hopeless.’ They are so utterly unbalanced that they would not have the slightest chance of escaping elimination through natural selection.” – Jonathan Wells
    http://www.evolutionnews.org/2.....footnote19

    Darwin’s Theory – Fruit Flies and Morphology – video
    http://www.youtube.com/watch?v=hZJTIwRY0bs

    “There is now considerable evidence that genes alone do not control development. For example when an egg’s genes (DNA) are removed and replaced with genes (DNA) from another type of animal, development follows the pattern of the original egg until the embryo dies from lack of the right proteins. (The rare exceptions to this rule involve animals that could normally mate to produce hybrids.) The Jurassic Park approach of putting dinosaur DNA into ostrich eggs to produce a Tyrannosaurus rex makes exciting fiction but ignores scientific fact.”
    The Design of Life – William Dembski, Jonathan Wells Pg. 50

    DNA: The Alphabet of Life – David Klinghoffer
    Excerpt: But all this is trivial compared to the largely unheralded insight gained from the Human Genome Project, completed in 2003. The insight is disturbing. It is that while DNA codes for the cell’s building blocks, the information needed to build the rest of the creature is seemingly, in large measure, absent. ,,,The physically encoded information to form that mouse, as opposed to that fly, isn’t there. Instead, “It is as if the ‘idea’ of the fly (or any other organism) must somehow permeate the genome that gives rise to it.”

    The Coding Found In DNA Surpasses Man’s Ability To Code – Stephen Meyer – video
    http://www.metacafe.com/watch/4050638

    How DNA Compares To Human Language – Perry Marshall – video
    http://www.metacafe.com/watch/4298072

  21. Nakashima [15]:

    I’m not at all clear why you push papers like this. Nei’s position, that random mutation is responsible for most of the diversity around us, is even less comformable to Christian theology than selectionist positions. Its like anyone who is against the Big D is fine by you.

    Nei’s position is not necessarily that “random” mutations are the source of diversity. His position is that evolution is “change” driven, not NS driven. What biology can demonstrate are genomic differences; it presumes these differences are due to “random” mutations. Yet, how do we know that this is so? Where’s the proof? It’s not there.

    ID is all about showing that there are NO viable random mechanisms that overcome the improbabilities involved in the demonstrated “changes”.

    This is a ‘black-box’, as in “Darwin’s Black Box”. ID has two points to make:
    (1) that neo-Darwinism explains very little, and (2) “design” is a logical conclusion to the question as to how biological forms came into existence and “changed” over time.

    Let’s look at the miracles in the New Testament: a man was crippled; then he walked. We know the before and after; we don’t know exactly “how” this change came about. In biology all we have, more or less, is the before and after. No one is able to “see” exactly how this change came about.

    (I won’t be available until Monday. Happy Easter to all!)

  22. Mr BA^77,

    Moreover Do you have any evidence whatsoever that undirected mutations can generate functional information over 140 Functional Bits (Fits)?

    Does whole genome duplication count? :)

  23. Mr BA^77,

    Moreover Do you have any evidence whatsoever that undirected mutations can generate functional information over 140 Functional Bits (Fits)?

    Does whole genome duplication count?

    ——————

    Well geez Nak tell me did me copying and pasting your entire post increase the novel functional information of your post by 140 Fits?

  24. It really is silly Nak you know this stuff as well as any of the ID posters here, and you certainly ain’t know dummy as demonstrated by your resourceful and imaginative ways in which you try to find any chink in ID whatsoever, All of which fall apart,, So please Nak do tell why do you continue with your big charade that all is fine in Darwinianland? Did uncle Darwin promise you anything? No? Why the games then?

  25. Mr BA^77,

    This inability for the DNA code to account for body plans is also clearly shown by extensive mutation studies to the DNA of different organisms which show “exceedingly rare” major morphological effects from mutations to the DNA code.

    You should read the recent blog entry about comparison of Hox genes in the snake and lizard by PZ Meyers. (Not on his blog, Google “How to make a snake” to find it.)

  26. Nak,
    boring.

  27. Mr BA^77,

    Did uncle Darwin promise you anything?

    As you know, all the atheist boys and girls write letters to Santa Charles just before Darwinmas (Feb 12) asking for gifts. The legend goes that Santa Charles arrives at midnight on Darwinmas, riding a beagle pulled through the sky by eight finches, all slightly different.

    Now if the boy or girl was good that year (but not in an absolute or objective moral sense of the word), Santa Charles would look at the phylogenetic tree they had decorated and leave a present under the branches, down near LUCA. But if the child had been bad that year (in a strictly relative and socially or culturally determined sense), then they got a piece of metamorphosed Permian vegetation instead.

    My letter was always the same:
    Dear Santa Charles,
    How are you? I hear it is hot in the Galapagos, where you spend all year making presents for children with the help of some very dexterous pandas and an outsourcer in Hong Kong.
    A randomized telephone survey of my grandparents concluded that I was good this year, with an error band of plus or minus 3%. So I thought I would share with you some gift suggestions.”

    I always asked for the same two things, peace on earth, and a pet shark with a laser on its forehead. I never got either one. But I never got the metamorphosed Permian vegetation, so I think it was just the margin of error that was my problem.

  28. scordova,

    I’m not at all clear why you push papers like this

    It shows Darwian evolution is false.

    But the issue is not why I do things here at UD, the issue in this thread is whether Nei’s claims are correct, especially with respect to Darwinian evolution.

    Do you have any thing to say about whether Nei is correct or not?

    Sal

  29. composer:

    ID, on the other hand, knows the answer in advance: design. Does anybody doubt that will remain the repeated answer no matter what the evidence?

    No that is not correct, ID for certain features can be falsified or cast into doubt.

    Darwinian evolution had the chance to falsify ID, but it appears to have failed if Nei is correct in his critique that there are insufficient population resources to make possible Darwinian evolution.

    If it’s against the prevailing view, it must friendly to ID!

    If it is against Darwinism it is indirectly friendly to ID.

    But the topic of this thread is not specifically ID, it is about Nei’s paper.

    Does the paper convince you neo-Darwinism is wrong?

  30. composer wrote:

    People who know the field noticed this paper when it was published (it’s been cited 106 times).

    Well apparently Dawkins and Dennett and possibly Coyne and the NCSE haven’t gotten the memo. They still spew Darwinism as the majority answer to life’s mystery.

    So in that sense, if Nei is correct that neo-Darwinism is wrong, the crew of UD is way ahead of Dawkins and Dennett and the NCSE.

  31. scordova,

    Yes, I think mutation and selection are different pressures that come to the fore at different times. In large stable populations there is enough variation present that selection can track small changes in a local optimum pretty well. At other times, when a population shrinks dramatically, mutational pressures come to the fore and rapid changes (speciation) can happen.

    Neither a rigid selectionist or neo-mutationist stance is going to be correct all the time.

    However, it must be said that both stand for common descent, and the unity of life beginning from a common ancestor. Both stand for changes over time occuring by material means. Both account for evolution without appealing to intervention by externalities.

    You are typically and sadly overstating the case when you write

    So the competing camps within evolution find fatal flaws in each other’s school of thought.

    In Nei’s paper, he is forced to admit that the neutralism of Kimura and the seeming difficulties of Haldane’s cost of selection actually had to be significantly modified or abandoned. Mathematical results for an infinite population don’t hold up for finite populations. Nei ends up on a plaintive note, say that it wasn’t important whether Kimura was correct, just that he started the field.

    If we consider both the cost of natural selection and the mutation load, Kimura’s computation may not be so outrageous. Furthermore, what is important is the fact that Kimura initiated the study of population dynamics of neutral mutations and that he later became the strongest defender of the neutral theory and provided much evidence for it.

    In summary, this paper, and many like it that you cite, does not show Darwinian evolution is false. On the contrary, it assumes Darwinian evolution is true, and presents a very nuanced explanation of why the dynamic between variation and selection (the two parts of the iterative system of evolution identified by Darwin) is tipped in favor of variation when all the interesting things are happening.

    But why take my word for it? Dr Nei’s e-mail address is at the top of the paper. Just write him a note that says “I think your paper shows that Darwinian evolution is false. Do I understand you correctly?”

  32. BTW, since this paper is long and a bit dense for non-specialists, Larry Moran has a nice essay on adaptationism and mutationism that is easier to read.

  33. Nakashima-san:

    Neither a rigid selectionist or neo-mutationist stance is going to be correct all the time.

    That is partially correct. The better way to phrase it:

    Neither a rigid selectionist or neo-mutationist stance is going to be correct MOST of the time since they’re both generally wrong about the evolution of biological complexity.

    Why should I write Dr. Nei, he said it pretty plainly:

    recent molecular data supports the theory of mutation-driven evolution rather than neo-Darwinism.

    Therefore neo-Darwinism is false.

    On top of that if Pagels is right, Darwin is even further falsified.

    In summary, this paper, and many like it that you cite, does not show Darwinian evolution is false. On the contrary, it assumes Darwinian evolution is true,

    No, that mischaracterizes the paper. It does not assume Darwinism is true, the paper opens by saying Darwinism is controvesial and then gives evidence why Natural Selection is not the primary mechanism of evolution.

    I also opened up the thread by pointing out that various others think the power of selection would actually inhibit evolution!

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