Polyploidy: Genetic fundamentalism is still looking for a job?

Here's a brief reference to the original paper associated with this thread: https://uncommondescent.com/evolution/a-third-way-of-evolution/#comment-619568 As one can see, they fail to answer the fundamental question "Where's the beef?" :)Dionisio

October 21, 2016

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News:

Paper. (paywall) – Adam M. Session et al., Genome evolution in the allotetraploid frog Xenopus laevis. Nature, 2016; 538 (7625): 336 DOI: 10.1038/nature19840

This seems like an interesting paper. Thank you for posting a reference to it here. Please, help me understand this. Why did you write (paywall)? Your link took me to an open paper. Here's the link to the PDF version of the paper: http://www.nature.com/nature/journal/v538/n7625/pdf/nature19840.pdf Perhaps I'm barking up the wrong tree? :) Thank you. [Emphasis added]Dionisio

October 21, 2016

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John Sanford, a leading expert in plant genetics, examines Polyploidy (Gene/Chromosome Duplication) fallacies in Appendix 4 of his book "Genetic Entropy and the mystery of the Genome".

"What about polyploidy plants? It has been claimed that since some plants are polyploidy (having double the normal chromosome numbers), this proves that duplication must be beneficial and must increase information. Polyploidy was my special area of study during my Ph.D. thesis. Interestingly, it makes a great deal of difference how a polyploid arises. If somatic (body) cells are treated with the chemical called colchicine, cell division is disrupted , resulting in chromosome doubling - but no new information arises. The plants that result are almost always very stunted, morphologically distorted, and generally sterile. The reason for this should be obvious - the plants must waste twice as much energy to make twice as much DNA, but with no new genetic information! The nucleus is also roughly twice as large, disrupting proper cell shape and cell size. In fact, the plants actually have less information than before, because a great deal of the information which controls gene regulation depends on gene dosage (copy number). Loss of regulatory control is loss of information. This is really the same reason why an extra chromosome causes Down's Syndrome. Thousands of genes become improperly improperly regulated, because of extra genic copies. If somatic polyploidization is consistently deleterious, why are there any polyploidy plants at all - such as potatoes? The reason is that polyploidy can arise by a different process - which is called sexual polyploidization.This happens when a unreduced sperm unites with a unreduced egg. In this special case, all of the information within the two parents is combined into the offspring, and there can be a net gain of information within that single individual. But there is no more total information within the population. the information within the two parents was simply pooled. In such a case we are seeing pooling of information, but not any new information.",,, "in some special cases, the extra level of gene backup within a polyploidy can outweigh the problems of disrupted gene regulation and reduced fertility - and so can result in a type of "net gain". But such a "net gain" is more accurately described as a net reduction in the rate of degeneration." John Sanford - Genetic Entropy & The Mystery of the Genome - pages 191-192 - Dr. John Sanford has been a Cornell University Professor for more that 25 years (being semi-retired since 1998). He received his Ph. D. from the University of Wisconsin in the area of plant breeding and plant genetics.,,, His most significant scientific contributions involved three inventions - the biolistic ("gene gun") process, pathogen-derived resistance, and genetic immunization. Double Your Pleasure: What Exactly Can You Get from Polyploidy? - October 10, 2014 Excerpt: "Stebbins viewed polyploid species as genetically depauperate with limited evolutionary potential. A new polyploidy species was envisioned as forming via a single polyploidization event and would therefore exhibit a high degree of genetic uniformity across individuals. Following this model of formation, an allopolyploid would exhibit no homologous, or segregating, variation, only homeologous (nonsegregating) variation. Furthermore, if a mutation were to arise in the polyploid, its effect would be masked by either the presence of a homeologous locus (in an allotetraploid) or multiple alleles (in an autopolyploid). Although not impossible, the fixation of a new mutation is much slower in a polyploid than in its diploid parents. Stebbins (1971 , p. 127) correctly noted that "...the large amount of gene duplication dilutes the effects of new mutations... polyploids have great difficulty evolving truly new adaptive gene complexes" and that "...chromosome doubling will most often have a retarding effect on evolutionary change via mutation, genetic recombination, and selection." Furthermore, this buffering effect of multiple genomes may extend to the origins of morphological variation in a polyploid (Stebbins, 1950 , 1971 [pp. 147-148]): "Very often, even in complexes on which the basis of phytogeographical evidence must be regarded as hundreds of thousands or even millions of years old, the range of morphological variability encompassed by all of the tetraploids is less than the total range of that found among the diploids...",,, http://www.evolutionnews.org/2014/10/double_your_ple090311.html Eel Migration Comes to Light – Oct. 10, 2016 Excerpt: Imagine a half-ton tuna laid out on a dock next to a seahorse, a minnow, and a moray eel. That's just a snapshot of the astonishing diversity found in the group of fishes called teleosts, or ray-finned fish, which today have 30,000 species -- more than all living mammals, birds, reptiles, and amphibians combined. For more than a decade, many researchers have assumed that teleosts' dizzying array of body types evolved because their immediate ancestor somehow duplicated its entire genome, leaving whole sets of genes free to take on other functions. Now, an examination of the fish fossil record challenges that view. Despite duplicating their genome about 160 million years ago, teleost fish hewed to a few conventional body types for their first 150 million years. Meanwhile, the holostean fishes, a related group with genomes that never underwent a doubling, evolved a stunning diversity of body plans. The work "demonstrates beautifully how necessary it is to look at the fossil record when testing hypotheses about ... large scale evolutionary changes," says Robert Sansom, a paleontologist at the University of Manchester in the United Kingdom. http://www.evolutionnews.org/2016/10/eel_migration_c103197.html Evolution by Gene Duplication Falsified - December 2010 Excerpt: The various postduplication mechanisms entailing random mutations and recombinations considered were observed to tweak, tinker, copy, cut, divide, and shuffle existing genetic information around, but fell short of generating genuinely distinct and entirely novel functionality. Contrary to Darwin’s view of the plasticity of biological features, successive modification and selection in genes does indeed appear to have real and inherent limits: it can serve to alter the sequence, size, and function of a gene to an extent, but this almost always amounts to a variation on the same theme—as with RNASE1B in colobine monkeys. The conservation of all-important motifs within gene families, such as the homeobox or the MADS-box motif, attests to the fact that gene duplication results in the copying and preservation of biological information, and not its transformation as something original. http://www.creationsafaris.com/crev201101.htm#20110103a Douglas Axe and Ann Gauger Argue that Design Best Explains New Biological Information - Casey Luskin August 26, 2013 Excerpt: Axe and Gauger observe that “The most widely accepted explanation for the origin of new enzymes is gene duplication and recruitment.” However, they cite experimental work showing that a duplicate gene is much more likely to be silenced (because of the costly resources expended in transcribing and translating it) than it is to acquire a new function. http://www.evolutionnews.org/2013/08/douglas_axe_and075601.html

bornagain77

October 20, 2016

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