Genomics: Hox Paradox described

_{Denyse O'Leary

February 21, 2011

Genomics}

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A friend put me onto a “neat” summation of the “Hox paradox” in Bioscience last year:

“Taken together, these findings presented researchers with a paradox. On one hand, the basic machinery underlying early development, such as the Hox genes, is widely conserved among divergent phyla. But at the same time, these genes also underlie the development of distinct morphologies between more closely related species. The resolution of this “Hox paradox” is that the general role of many genes in patterning the embryo has been preserved, but the precise pattern of their expression or their influence on later events of development have both changed. These modifications are possible only through changes in regulatory interactions, whether mediated through changes in protein or nucleic acid sequences.”

The Evolution of Gene Regulatory Interactions
David A. Garfield and Gregory A. Wray
BioScience
Vol. 60, No. 1 (January 2010), pp. 15-23
Published by: University of California Press on behalf of the American Institute of Biological Sciences Article DOI: 10.1525/bio.2010.60.1.6

My friend finds the proposed solution underwhelming. Thoughts?

Comments

For my as a programmer Hox-genes look very like polymorphism in object oriented programming. The same method call can call very different parts of code, depending on witch kind of object it is called. But the semantic meaning remains the same. Hox genes for producing light sensoring organs remain the same, even if the construcrion of that organ (the implementation) is very different. Surely the hox genes for don't contain the information, how that organ is constructed and works. It's 'simply' a switched, wich initiats the development of the eye. The informartion, how the eye is constructed is stored somewher else. Ohterwise the same gene couldn't result in so differently contructed eyes.Kajdron_{February 21, 2011
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Darwin's Theory - Fruit Flies and Morphology - video http://www.youtube.com/watch?v=hZJTIwRY0bs Deep Genomics: In the Case of DNA, the Package Can Be as Important as Its Contents, New Work With Fruit Flies Reveals - January 2011 http://www.sciencedaily.com/releases/2011/01/110113102158.htm Experimental Evolution in Fruit Flies (35 years of trying to force fruit flies to evolve in the laboratory fails, spectacularly) - October 2010 Excerpt: "Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.,,, "This research really upends the dominant paradigm about how species evolve," said ecology and evolutionary biology professor Anthony Long, the primary investigator. http://www.arn.org/blogs/index.php/literature/2010/10/07/experimental_evolution_in_fruit_fliesbornagain77_{February 21, 2011
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Many times evolutionists will mention evo-devo (Evolutionary Developmental Biology) to try to support the Darwinian claim that minor changes/mutations to DNA can drive major morphological novelty, yet, in this following comment, from a 2005 Nature review article, evolutionary geneticist Jerry Coyne expressed strong skepticism at the proposed mechanism of 'gene switches' for evo-devo: "The evidence for the adaptive divergence of gene switches is still thin. The best case involves the loss of protective armor and spines in sticklebacks, both due to changes in regulatory elements. But these elements represent the loss of traits, rather than the origin of evolutionary novelties...We now know that Hox genes and other transcription factors have many roles besides inducing body pattern, and their overall function in development - let alone in evolution - remains murky." http://www.evolutionnews.org/2010/06/scott_f_gilbert_developmental035931.html Here is a more thorough critique of evo-devo: Nature's "Gems": Microevolution Meets Microevolution - Casey Luskin - August 2010 http://www.evolutionnews.org/2010/08/nature_gems_microevolution_mee037171.html#more Here are many more lines of evidence arguing against any DNA mechanisms for body plan development, Evo-Devo included: Response to John Wise - October 2010 Excerpt: But there are solid empirical grounds for arguing that changes in DNA alone cannot produce new organs or body plans. A technique called "saturation mutagenesis"1,2 has been used to produce every possible developmental mutation in fruit flies (Drosophila melanogaster),3,4,5 roundworms (Caenorhabditis elegans),6,7 and zebrafish (Danio rerio),8,9,10 and the same technique is now being applied to mice (Mus musculus).11,12 None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans--because none of the observed developmental mutations benefit the organism. http://www.evolutionnews.org/2010/10/response_to_john_wise038811.html Cortical Inheritance: The Crushing Critique Against Genetic Reductionism - Arthur Jones - video http://www.metacafe.com/watch/4187488 The Case Against Molecular Reductionism - Rupert Sheldrake and Bruce Lipton - video http://www.metacafe.com/watch/4899469 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' beneficial morphological changes from mutations to the DNA code. 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." http://eyedesignbook.com/ch6/eyech6-append-d.html Stephen Meyer - Functional Proteins And Information For Body Plans - video http://www.metacafe.com/watch/4050681 Getting Over the Code Delusion (Epigenetics) - Talbot - November 2010 - Excellent Article for explaining exactly why epigentics falsifies the neo-Darwinian paradigm of genetic reductionism: http://www.thenewatlantis.com/publications/getting-over-the-code-delusion 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 This lack of beneficial morphological novelty also includes the highly touted four-winged fruit fly mutations: ...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/2008/08/inherit_the_spin_the_ncse_answ.html#footnote19bornagain77_{February 21, 2011
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