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.