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A. L. Hughes’s New Non-Darwinian Mechanism of Adaption Was Discovered and Published in Detail by an ID Geneticist 25 Years Ago

Wolf-Ekkehard Lönnig

Editor’s Note: ENV is pleased to welcome the comments of Lönnig, Senior Scientist, Department of Molecular Plant Genetics, Max Planck Institute for Plant Breeding Research (retired).
Although not affiliated with Discovery Institute or the Center for Science and Culture, I was kindly invited to comment on Austin L. Hughes’s 2011 paper in Heredity, “Evolution of adaptive phenotypic traits without positive Darwinian selection.” P. J. Levi has aptly given the gist of the article here as follows:

Hughes now proposes a model he refers to as the plasticity-relaxation-mutation (PRM) model. PRM suggests that adaptive phenotypes arise as follows: (1) there exists a phenotypically plastic trait (i.e., one that changes with the environment, such as sweating in the summer heat); (2) the environment becomes constant, such that the trait assumes only one of its states for a lengthened period of time; and (3) during that time, deleterious mutations accumulate in the unused state of the trait, such that its genetic basis is subsequently lost.

As a geneticist, I have been “preaching” exactly this non-Darwinian kind of evolution and speciation since 1986, backed up by many genetic facts and arguments (see the list of references below).
Well, to a certain extent Hughes’s unawareness may be understandable. For the free flow of scientific theories and discoveries, the language barrier often poses a basic problem. Whatever has not been published in English but only in such “long-forgotten languages” as German, French or Spanish has a good chance of simply being ignored or overlooked (even if it is available on the Internet).
Nevertheless, one wouldn’t argue that Mendel did not discover the basic laws of heredity because they were first published in German (and only 36 years later in English by Bateson), not to mention the theories and discoveries of German Nobel Laureates like Einstein, Planck, Heisenberg and many others.
So what did I discover? In our peer-reviewed paper on “Biodiversity and Dollo’s law: to what extent can the phenotypic differences between Antirrhinum majus and Misopates orontium be bridged by mutagenesis?” (Bioremediation, Biodiversity and Bioavailability 1, 1-30 (2007)), I summed up Stubbe’s rule, which he had formulated after some 40 years of intense mutation research especially with Antirrhinum majus (snapdragon) as follows:

All alterations due to different environmental factors (modifications) have also been detected as mutants, but not all phenotypes due to mutations can be replicated by environmentally elicited modifications.

In agreement with my own work on more than two million plants at the University of Bonn and the Max-Planck-Institute for Plant Breeding Research, almost all mutations in plants are recessive and Stubbe himself had described some 500 such mutants. In genetic terms, what does recessivity mean? James D. Watson wrote in 1976 (p. 190; similarly 1987, p. 222; more details and quotations in Lönnig 1986, pp. 122 ff., 334 ff., 362-372, see also the version of 1993):

Most mutant genes are recessive with respect to wild-type genes. […] The recessive phenotype often results from the failure of mutant genes to produce any functional protein (enzyme).”

See also Fincham in his textbook Genetics (1983, p. 350), and many other authors documented by Lönnig 1986. Goldschmidt (1935, 1961) came to the same results on modifications and mutant phenotypes as did Stubbe especially in connection with his studies on phenocopies in Drosophila.
Here is a translation, with some help by Professor Granville Sewell, of my 1986 text, relevant to the question of non-Darwinian speciation referred to above (from Lönnig 1986, p. 473; when I say “all possible” please don’t take that too literally):

The original species had a greater genetic potential to adapt to all possible environments. In the course of time this broad capacity for adaptation has been steadily reduced in the respective habitats by the accumulation of slightly deleterious alleles (as well as total losses of genetic functions redundant for a habitat), with the exception, of course, of that part which was necessary for coping with a species’ particular environment….By mutative reduction of the genetic potential, modifications became “heritable”. — As strange as it may at first sound, however, this has nothing to do with the inheritance of acquired characteristics. For the characteristics were not acquired evolutionarily, but existed from the very beginning due to the greater adaptability. In many species only the genetic functions necessary for coping with the corresponding environment have been preserved from this adaptability potential. The “remainder” has been lost by mutations (accumulation of slightly disadvantageous alleles) — in the formation of secondary species.

These points are elaborated in the 539 pages of the 1986 book and in later editions in 624 pages with reference to adaptation, evolution and species formation due to losses of gene functions without positive Darwinian selection (in all editions with many biological examples, also in several peer-reviewed papers in such journals as Gene, Annual Review of Genetics and Advances in Botanical Research: see Kunze et al. 1997, Lönnig et al. 2007, Lönnig 2010, Lönnig and Saedler 1997, 2002). Michael Behe too has exhaustively treated the subject on the molecular level in microorganisms, while to a certain extent also reviewing examples of positive selection (Behe 2010).
Please compare the quotation/translation given above with the following sentences from Hughes’s Abstract (2011, p. 1):

Recent evidence suggests the frequent occurrence of a simple non-Darwinian (but non-Lamarckian) model for the evolution of adaptive phenotypic traits, here entitled the plasticity-relaxation-mutation (PRM) mechanism. This mechanism involves ancestral phenotypic plasticity followed by specialization in one alternative environment and thus the permanent expression of one alternative phenotype. Once this specialization occurs, purifying selection on the molecular basis of other phenotypes is relaxed. Finally, mutations that permanently eliminate the pathways leading to alternative phenotypes can be fixed by genetic drift.

I also argued (and thus agree with Hughes) that what he calls the PRM mechanism is widespread and that there is

evidence that phenotypic plasticity has preceded adaptation in a number of taxa and [that there is] evidence that adaptive traits have resulted from loss of alternative developmental pathways. The PRM mechanism can easily explain cases of explosive adaptive radiation, as well as recently reported cases of apparent adaptive evolution over ecological time.

For example, I explained the relatively recent radiation of the cichlids by virtually the same PRM mechanism as Hughes did on p. 6 of his 2011 paper, but with more detail and of course without using the same term “PRM” (Lönnig and Saedler 2002, Lönnig 2003; see also Lönnig 2002 for typolysis on the Galapagos Islands). I have also discussed examples of “closely related taxa, some of which show phenotypic plasticity with respect to a given trait, whereas others show apparent fixation of just one of the alternative phenotypes” (Hughes, p. 5).
Thus, non-Darwinian adaptation and evolution by the loss of gene functions seem to have been discovered and published by at least three different biologists, working independently of each other: Hughes (2011), Behe (2010), and Lönnig (1986, 1993, 2003, 2011 and in the peer-reviewed papers referred to above).
Although Hughes is correct in stating that “Relatively few authors have suggested that adaptive phenotypes might arise in the absence of positive Darwinian selection” (p. 2), I would like to point out that more biologists have done so than he was aware when he wrote that.
Finally, I would add that Richard Dawkins recently wrote the following about positive Darwinian selection and adaptation:

I have written many times that natural selection is NOT the only mechanism of evolution. I have said it is the only known mechanism of ADAPTIVE evolution. And I’ll say that again. Natural selection is the only known mechanism of adaptive evolution, meaning the evolution of complex adaptations carrying the illusion of design. If you have another candidate not involving selection, let’s hear it.

If Dawkins checked the points on adaptation without positive Darwinian selection mentioned above, he would probably object that natural selection nevertheless first evolved the originally greater genetic adaptability potential. However, this is at least a scientifically open question as shown by, to take a few recent examples, Axe (2010a, 2010b), Gauger et al. 2010, Gauger and Axe (2011).
Also, there are good scientific reasons to argue by concrete examples that the primary adaptability potential points to the reality of teleology and intelligent design (Lönnig 1986/1993, 2003, 2010). For, among other things, “Short-term benefit has always been the only thing that counts in evolution; long-term benefit has never counted” (Richard Dawkins in a discussion with Jaron Lanier 2008). The initially more extensive/comprehensive genetic adaptability potentials of species and genera clearly surpass short-term benefits. More research is needed to establish a series of biologically and molecularly detailed examples for this long-term benefit model of specified complexity and ingenious design.
References Cited
Axe DD (2010a) The limits of complex adaptation: An analysis based on a simple model of structured bacterial populations. BIO-Complexity 1, Issue 4, 1-10. http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2010.4
Axe DD (2010b) The case against a Darwinian origin of protein folds. BIO-Complexity 1, Issue 1, 1-12. http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2010.1/BIO-C.2010.1
Behe MJ (2010) Experimental evolution, loss-of-function mutations, and “the first rule of adaptive evolution.” The Quarterly Review of Biology 85:419-445.
Dawkins R (2011) http://whyevolutionistrue.wordpress.com/2011/11/24/rip-lynn-margulis-ctd/
Dawkins R and J Lanier (2008) http://richarddawkins.net/articles/2581?page=1
Gauger A and DD Axe (2011) The evolutionary accessibility of new enzyme functions: A case study from the biotin pathway. BIO-Complexity 2, Issue1, 1-17. http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2011.1/BIO-C.2011.1
Gauger AK, Ebnet S, Fahey PF and R Seelke (2010) Reductive evolution can presevent populations from taking simple adaptive paths to high fitness. BIO-Complexity 1, Issue 2, 1-9. http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2010.2/BIO-C.2010.2
Hughes AL (2011) Evolution of adaptive phenotypic traits without positive Darwinian selection. Heredity, advance online publication. doi:10.1038/hdy.2011.97
Kunze R, Saedler H and W-E Lönnig (1997) Plant transposable elements. Advances in Botanical Research 27, 331-470.
Levi PJ (2011) No positive selection, no Darwin: A new non-Darwinian mechanism for the origin of adaptive phenotypes: https://evolutionnews.org/2011/11/no_positive_selection_no_darwi052941.html
Lönnig W-E (1986) Artbegriff und Ursprung der Arten (Species Concepts and the Origin of Species; 540 pp, second revised printing also in 1986). Im Selbsverlag, Köln. As for my work in Bonn and Cologne, see also http://www.weloennig.de/CurriculumVitae.pdf
Lönnig W-E (1987, 1988 and 1993) Second (1987) and third edition (two impressions), the latter with the new title Artbegriff, Evolution und Schöpfung, (622 pp. the translated text again on p. 473 with additional material on pp. 586/587). Naturwissenschaftlicher Verlag Köln. ISBN 3-9801772-0-3. Internet edition 2002: http://www.weloennig.de/Artbegriff.html Chapter VII: http://www.weloennig.de/AesVII.html. See also the book review in Theoretical and Applied Genetics 79, 431 (1990): http://www.weloennig.de/AesBook.html (in English).
Lönnig W-E (2002) Galapagos als Evolutionsmodell: http://www.weloennig.de/NeoB.Ana2.html
Lönnig W-E (2003) Mutationen: Das Gesetz der recurrenten Variation: http://www.weloennig.de/Gesetz_Rekurrente_Variation.html#anhang
Lönnig, W-E (2010) Mutagenesis in Physalis pubescens L. ssp. floridana: Some further research on Dollo’s law and the law of recurrent variation. Floriculture and Ornamental Biotechnology 4 (Special Issue): 1-21. http://www.globalsciencebooks.info/JournalsSup/images/Sample/FOB_4(SI1)1-21o.pdf
Lönnig W-E (2011) Die Evolution der karnivoren Pflanzen (pp. 30 and 169): http://www.weloennig.de/Utricularia2011Buch.pdf
Lönnig W-E and H Saedler (1997) Plant transposons: contributors to evolution? Gene 205, 245-253.
Lönnig W-E und H Saedler (2002) Chromosome rearrangements and transposable elements. Annual Reviews of Genetics 36: 389-410.
Lönnig W-E, Stüber K, Saedler H. and J H Kim (2007) Biodiversity and Dollo’s law: to what extent can the phenotypic differences between Antirrhinum majus and Misopates orontium be bridged by mutagenesis? Bioremediation, Biodiversity and Bioavailability 1: 1-30. http://www.weloennig.de/Dollo-1a.pdf
Stubbe H (1966) Genetik und Zytologie von Antirrhinum L. sect. Antirrhinum. VEB Gustav Fischer Verlag Jena. (Hans Stubbe was professor and director of the Institute of Genetics of the University Halle-Wittenberg; see http://de.wikipedia.org/wiki/Hans_Stubbe.)