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Scientific Inaccuracies, False Accusations: Concluding My Response to Joseph Felsenstein

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Writing here yesterday I addressed some scientific inaccuracies in a post by University of Washington geneticist Joe Felsenstein at Panda's Thumb ("In Terror of Chipmunks: A Response to Joseph Felsenstein"). There are additional problems beyond those I have already noted. Before going on, however, I feel it is important to correct some accusations made against me.

Felsenstein asserts:

We can conclude that Dr. Lönnig is not familiar with theoretical population genetics. He is a retired plant breeder at the Max Planck Institute for Plant Breeding Research, who specialized in mutation effects in such plants as the "husk tomato" Physalis pubescens.

Just as an illustration: Imagine someone speaking of Charles Darwin as a pigeon breeder who strayed into the topic of the origin of species and evolution. Could anyone accept such a comment as an adequate assessment of Darwin's work?

Allow me, then, to introduce myself to Dr. Felsenstein. I am a transposon and mutation geneticist working with Pisum (for my PhD, see "Heterosis in Pisum sativum" (December 1979), for which I had checked also Falconer and Felsenstein), and then especially with Antirrhinum and Misopates and eventually also with Physalis (altogether in field trials alone with more than 2.1 million plants, not including thousands of greenhouse and climate chamber plants). You can find a list of my publications here. I also study plants and animals in the wild wherever I go. (Most recently, that was to Isla Contoy and elsewhere in Mexico.) I've published books on carnivorous plants, giraffes, and the origin of dogs. Almost all my biological studies, going back fifty years now -- from mutagenesis and natural selection to embryogenesis and the geographical distribution of plants and animals -- are made in view of and in connection with the topic of the origin of species and higher systematic categories.

Felsenstein continues:

I can understand why he might not have studied population genetics thoroughly.

I have carefully studied Haldane's dilemma, and some other aspects of population genetics. But, of course, I'm not a theoretical population geneticist but a mutation geneticist and naturalist studying the ongoing real processes in nature. On a small excursion last month, having examined several species of water plants (especially of the family of Scrophulariaceae), I was reminded again that in biology, nothing -- really nothing -- can wholly substitute for real contact with nature as part of our universe. As Haldane mused, nature "is not only queerer than we suppose, but also queerer than we can suppose." With due respect for Felsenstein's work, can theoretical population genetics really ever fully model the biological processes in the wild, of the "endless forms most beautiful," as Darwin said? To perhaps exaggerate the principle: No dry swimming exercise (helpful as it may be in certain cases) will ever substitute for the real thing, namely training in the pool, ocean, or river. Or, in the words of evolutionary biologist Lynn Margulis, member of the U.S. National Academy of Sciences, stating (1997, p. 279):

[T]he Academy guards, using neo-Darwinism as an inquisitory tool, superimpose a gigantic super-structure of mechanism and hierarchy that protects the throbbing biosphere from being directly sensed by these new scientists -- people most in need of sensing it. The dispensers of the funds for scientific research and education and other opportunity makers, herd the best minds and bodies into sterile laboratories and white-walled university cloisters to be catechized with dogmatic nonsense to such an extent that many doctoral graduates in the biological sciences cannot distinguish a nucleic acid solution from a cell suspension, a sedimentary from an igneous rock, a kelp from a cyanobacterium, or rye from ergot.

See also Margulis as quoted in the supplement below. But, of course, comprehensive research needs all three best in cooperation, the lab, the "cloister," and, last but not least, the field -- this essential, decisive, and most important but nowadays often forgotten direct contact with nature herself.

Felsenstein goes on:

But why then is he holding forth on the topic? This is easily explained. He is also a creationist, associated with the German creationist organization Wort und Wissen.

False, and embarrassingly so. I have never been associated with the German creationist organization Wort und Wissen for the simple reason that I do not subscribe to their agenda (the entire universe created some 6000 years ago and other regards). Nor have I ever been a member of ISCID or of Discovery Institute, as commenters on Felsenstein's post suggested. (If you doubt it, see my curriculum vitae.)

Felsenstein proceeds:

He formerly posted creationist material on his homepage at his Max Planck Institute. In a controversial move, the Institute forbade him to do this.

These posts consisted essentially of the discussion of biological facts not convincingly explained by Darwinism, not of "creationist material." Partial closure was solely due to pressure by neo-Darwinian activists from outside the Institute over the course of three years, first on a national scale and later internationally (see the details in my book about "Die Affäre Max Planck," die es nie gegeben hat). In this, there was no discussion of the contents of my homepage, which consisted in part of peer-reviewed and/or peer-edited papers.

Felsenstein continues:

If Dr. Lönnig wants to understand these matters more, I recommend to him that he visit a gambling casino -- in spite of the wild uncertainty of individual gambles, he might be surprised at how often he would lose his pocket money playing games that are mostly random, but slightly biased in favor of the house.

The proprietors of gambling casinos, slot machines, and lotteries have very intelligently calculated (that is, designed) this overall necessarily negative outcome for the players. (That's exactly why I'm a long-standing critic of such games of chance.) To adopt Felsenstein's metaphor, macroevolution would have long ago lost its money, as it were, if the process did not consist of much more than (and had to rely exclusively on) something like a gambling casino.

Returning to the question of population genetics, there have been some criticisms worth quoting, as for example, that by Samir Okasha (2006, substantive revision 2012):

It is clear that population genetics models rely on assumptions known to be false, and are subject to the realism / tractability trade-off. The simplest population-genetic models assume random mating, non-overlapping generations, infinite population size, perfect Mendelian segregation, frequency-independent genotype fitnesses, and the absence of stochastic effects; it is very unlikely (and in the case of the infinite population assumption, impossible) that any of these assumptions hold true of any actual biological population. More realistic models, that relax one of more of the above assumptions, have been constructed, but they are invariably much harder to analyze. It is an interesting historical question whether these 'standard' population-genetic assumptions were originally made because they simplified the mathematics, or because they were believed to be a reasonable approximation to reality, or both. This question is taken up by Morrison (2004) in relation to Fisher's early population-genetic work.

Just before, Okasha writes:

In a recent book, Sean Carroll, a leading evo-devo researcher, argues that population genetics no longer deserves pride-of-place on the evolutionary biology curriculum. He writes: "millions of biology students have been taught the view (from population genetics) that 'evolution is change in gene frequencies' ... This view forces the explanation toward mathematics and abstract descriptions of genes, and away from butterflies and zebras, or Australopithecines and Neanderthals" (2005 p. 294). A similar argument has been made by Massimo Pigliucci (2008). Carroll argues that instead of defining evolution as "change in gene frequencies," we should define it as "change in development," in recognition of the fact that most morphological evolution is brought about through mutations that affect organismic development. Carroll may be right that evo-devo makes for a more accessible introduction to evolutionary biology than population genetics, and that an exclusive focus on gene frequency dynamics is not the best way to understand all evolutionary phenomena; but population genetics arguably remains indispensable to a full understanding of the evolutionary process.

Now, to what extent has theoretical population genetics been successful in understanding the evolutionary process?

Compare, in his book on Theoretical Evolutionary Genetics, Professor Felsenstein's assertion that "population geneticists model all kinds of cases" with his ensuing statement on a comprehensive theory of evolution (2015, p. 49, emphasis added):

A comprehensive theory of evolution, one which does not yet exist, would integrate ecological processes (which determine the range of environments and the fitnesses of phenotypes), developmental processes (which determine the effect of genotype on phenotype), and population genetics (which tells us the changes in genetic composition of a population when the fitnesses of the genotypes are known). Lacking the other elements of this future theory, we concentrate here on the population genetics.

Regarding the present state of the art of population genetics for molecular sequences, Felsenstein states (p. 473):

Sampling methods (both IS and MCMC) are currently the state of the art in statistical inference from population samples of molecular sequences. The hope is that a "black box" can be constructed which will accommodate many of the possible complications of evolutionary models (multiple loci, diploid genotypes, recombination, population size changes, migration, even simple kinds of natural selection). The user will specify what evolutionary scenarios to allow and what kinds of data have been supplied. The user will need to understand the evolutionary models employed, but may be relatively insulated from having to master the details of the sampling. The program will then run the sampler and provide a likelihood surface, or a Bayesian posterior distribution, for the genetic or population parameters. We are not there yet, though many of the pieces have been tested. The great unknown is how much sampling will be necessary in complicated models.

If I had to write my encyclopedia article anew, I would probably also add some critical paragraphs on the presuppositions and limits of population genetics.

Now let's assume, for the sake of argument, that natural selection really comes "close to omnipotence," and that "both the beauty and the brilliance of natural selection are reflected in its omnipotence to explain the myriad observations of life," or that "natural selection is daily and hourly scrutinising, throughout the world, every variation, even the slightest; rejecting that which is bad, preserving and adding up all that is good." (All of this is, of course, nonsense as we've seen in my recent articles at Evolution News; see here and here.) In the absence of intelligent design and by selected mutations alone, would that solve the problem of the origin of the necessarily enormously complex information that is an integral part of all life forms?

Concerning mutations, Felsenstein points out correctly (2015, p. 133):

In a sense, it is a destructive force, making random changes in the genetic material. In any highly adapted organism such changes are overwhelmingly likely to be detrimental. The usual analogies we make in such cases involve making random adjustments in a finely constructed watch, or making random alterations of a carefully-written poem. While one will occasionally improve the timing of the watch or the effectiveness of the poem by random changes, with much greater probability one will make things worse.

Most probably I am not the only one who doubts that "random adjustments in a finely constructed watch...will occasionally improve the timing of the watch." Nevertheless, Felsenstein later asserts that "mutation holds a special place among these [migration and genetic drift], for without it the whole process of evolution would grind to a halt" (p. 134).

Although Felsenstein's models and calculations may to a certain degree be relevant for variation in natural populations, he never considers whether mutations really ever provide the raw materials for the creation of entirely new functional DNA sequences. Such sequences are required for constituting new genes and new gene reaction chains involved in the formation of novel synorganized anatomical structures and/or physiological functions for both the animal and plant kingdoms. That is, they are vital for the origin of all life forms on earth.

He simply assumes that this will be the case, and he builds his evolutionary worldview on exactly this delusion. For more information on mutations, see here for "Mutations: The Law of Recurrent Variation" (short version) or here for the long version. For additional papers I've written, see here. See also the calculations of Douglas Axe refereed to by Meyer, as well Axe's new book, Undeniable. Or in the words of Michael J. Behe:

A fundamental facet of rationality is our ability to discern the existence of other minds. In our world we perceive other minds through their physical effects. A theory which arbitrarily rules out mind as an explanation for certain physical effects has abandoned a facet of reason. Abandoning a facet of reason leads ultimately to irrationality. Life reeks of Design.

That is well said. For my part, Joe Felsenstein's criticisms aside, for many scientific reasons discussed elsewhere (see Lönnig from 1971 to the present ), I am entirely convinced that life displays ingenious design -- unparalleled, exceptional, unsurpassed, consummate, unique, and undeniable design.

Postscript:

See additionally Margulis on the state of biology especially in the USA (1997, p. 265) -- which appears to be very similar to the present state of affairs (emphasis added):

More and more, like the monasteries of the Middle Ages, today's universities and professional societies guard their knowledge. Collusively, the university biology curriculum, the textbook publishers, the National Science Foundation review committees, the Graduate Record examiners, and the various microbiological, evolutionary, and zoological societies map out domains of the known and knowable; they distinguish required from forbidden knowledge, subtly punishing the trespassers with rejection and oblivion; they award the faithful liturgists by granting degrees and dispersing funds and fellowships. Universities and academies, well within the boundaries of given disciplines (biology in my case), determine who is permitted to know and just what it is that he or she may know. Biology, botany, zoology, biochemistry, and microbiology departments within U.S. universities determine access to knowledge about life, dispensing it at high prices in peculiar parcels called credit hours.

(Margulis, L. and D. Sagan (1997): Slanted Truths: Essays on Gaia, Symbiosis, and Evolution. Springer-Verlag, Berlin. (See also here.))

And perhaps a question to Joe Felsenstein: How do you explain, for example, the origin of the Utricularia trap mechanism by mutations and natural selection? See here, here, and here.

Photo: Starling murmuration near Tønder, Denmark, by Tommy Hansen [Public domain], via Wikimedia Commons.