Classical naturalist tale about genes

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Ok News, so what exactly is a gene?

Around the time mark 4:40 in this video, titled "The integration of evolutionary biology with physiological science", Professor Denis Noble provides an interesting answer to the above quoted question: https://www.youtube.com/watch?v=A_q_bOWc8i0 Dionisio

A reasonable person would assume that genes aren’t nearly what they are made out to be. So the solution is

Ok News, so what exactly is a gene? And whats the solution?? .... and for that matter what was the problem? REW

OT:

If you’ve ever wondered how a diving beetle swims through the water or manages to rest just on the surface, the answer is in part because its foot is infinitely more complicated than your own. As seen above, this microscopic image of a male Acilius sulcatus (diving beetle) by photographer Igor Siwanowicz reveals the extraordinary complexity of this aquatic insect’s tiny appendage. This is just one of many examples of Siwanowicz’s work http://www.thisiscolossal.com/2016/10/insect-microscopy-igor-siwanowicz/ "One of my favorite images was this one from Igor Siwanowicz," notes Hanson. "That special gear-like structure planthoppers use to balance their jumping force. It looks like something an engineer would put together if you asked them to build you a jumping bug,,," Gears interlock in the hind legs of a planthopper nymph. Confocal 250x. Image: Dr. Igor Siwanowicz/Nikon Small Worlds http://images.earthtouchnews.com/media/1946933/nikon-siwanowicz_2016-10-22.jpg THE WORLD'S BEST MICROSCOPE PHOTOS ZOOM IN ON NATURE'S TINY WONDERS - OCTOBER 25 2016 http://www.earthtouchnews.com/in-the-field/film-and-photo/the-worlds-best-microscope-photos-zoom-in-on-natures-tiny-wonders

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So much wrong with the article to pick from, so little time to correct it all: So, to focus on just this one particular 'not even wrong' statement from the article: "The genes provide instructions on how and when to assemble the proteins that you’re made of and that carry out all the functions of life within your body." Actually, contrary to what the author may believe, it is the developmental Gene Regulatory Networks (dGRNs) that 'provide instructions on how and when to assemble the proteins' from the gene sequences. The gene sequences are basically passively sitting at the bottom level of multiple layers of very complex interweaving regulatory networks that are actually determining how and when the genetic sequences are being used. (Talbott 2015).

Genes and Organisms: Improvising the Dance of Life Stephen L. Talbott http://natureinstitute.org/txt/st/org/comm/ar/2015/genes_29.htm

Moreover, as Meyer pointed out in Darwin's Doubt, dGRNs are not compatible with the gradualist assumptions of Darwinian evolution:

Membrane Patterns Carry Ontogenetic Information That Is Specified Independently of DNA - Jonathan Wells - 2014 Excerpt: Embryo development (ontogeny) depends on developmental gene regulatory networks (dGRNs), but dGRNs depend on pre-existing spatial anisotropies that are defined by early embryonic axes, and those axes are established long before the embryo’s dGRNs are put in place.,,, DNA sequences do not specify the final functional forms of most membrane components. Still less does DNA specify the spatial arrangements of those components. Yet their spatial arrangements carry essential ontogenetic information. The fact that membrane patterns carry ontogenetic information that is not specified by DNA poses a problem for any theory of evolution (such as Neo-Darwinism) that attributes the origin of evolutionary novelties to changes in a genetic program—-whether at the level of DNA sequences or dGRNs. http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2014.2 A Listener's Guide to the Meyer-Marshall Debate: Focus on the Origin of Information Question - Casey Luskin - December 4, 2013 Excerpt: "There is always an observable consequence if a dGRN (developmental gene regulatory network) subcircuit is interrupted. Since these consequences are always catastrophically bad, flexibility is minimal, and since the subcircuits are all interconnected, the whole network partakes of the quality that there is only one way for things to work. And indeed the embryos of each species develop in only one way." - Eric Davidson - developmental biologist http://www.evolutionnews.org/2013/12/a_listeners_gui079811.html Stephen Meyer - Responding to Critics: Marshall, Part 2 (developmental Gene Regulatory Networks) - video https://www.youtube.com/watch?v=Cg8Mhn2EKvQ

Thus, where Darwinists most need plasticity in the genome to be viable as a theory, (i.e. developmental Gene Regulatory Networks), is the place where mutations are found to be almost 'always catastrophically bad'. Yet, it is exactly in this area of the genome (i.e. regulatory networks) where substantial differences are found between even the supposedly closely related species of chimps and humans.

Humans, Chimpanzees and Monkeys Share DNA but Not Gene Regulatory Mechanisms - (Nov. 6, 2012) Excerpt: Dr. Gilad reported that up to 40% of the differences in the expression or activity patterns of genes between humans, chimpanzees and rhesus monkeys can be explained by regulatory mechanisms that determine whether and how a gene's recipe for a protein is transcribed to the RNA molecule that carries the recipe instructions to the sites in cells where proteins are manufactured.,,, Dr. Gilad also determined that the epigenetics process known as histone modification also differs in the three species. The presence of histone marks during gene transcription indicates that the process is being prevented or modified. "These data allowed us to identify both conserved and species-specific enhancer and repressor regulatory elements, as well as characterize similarities and differences across species in transcription factor binding to these regulatory elements," Dr. Gilad said. http://www.sciencedaily.com/releases/2012/11/121106201124.htm Evolution by Splicing – Comparing gene transcripts from different species reveals surprising splicing diversity. – Ruth Williams – December 20, 2012 Excerpt: A major question in vertebrate evolutionary biology is “how do physical and behavioral differences arise if we have a very similar set of genes to that of the mouse, chicken, or frog?”,,, A commonly discussed mechanism was variable levels of gene expression, but both Blencowe and Chris Burge,,, found that gene expression is relatively conserved among species. On the other hand, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,” said Blencowe.,,, http://www.the-scientist.com/?articles.view%2FarticleNo%2F33782%2Ftitle%2FEvolution-by-Splicing%2F "Where (chimps and humans) really differ, and they differ by orders of magnitude, is in the genomic architecture outside the protein coding regions. They are vastly, vastly, different.,, The structural, the organization, the regulatory sequences, the hierarchy for how things are organized and used are vastly different between a chimpanzee and a human being in their genomes." Raymond Bohlin

Finding inflexible dGRNs and yet vastly different dGRNs is the exact opposite finding of what Darwinian evolution would have predicted should have been found. If Darwinian evolution were a normal falsifiable science, (instead of being basically a unfalsifiable religion for atheists), this finding would certainly have counted as one more nail in its scientific coffin. Of related note: King and Wilson, who started the whole 99% genetic similarity myth off in the 1970s, themselves argued that the regulatory regions must be very different between humans and chimps:

In “Science,” 1975, M-C King and A.C. Wilson were the first to publish a paper estimating the degree of similarity between the human and the chimpanzee genome. This documented the degree of genetic similarity between the two (approx. 99% amino acid similarity) ! The study, using a limited data set, found that we were far more similar than was thought possible at the time. Hence, we must be one with apes mustn't we? But…in the second section of their paper King and Wilson honestly describe the deficiencies of such reasoning: “The molecular similarity between chimpanzees and humans is extraordinary because they differ far more than sibling species in anatomy and way of life. Although humans and chimpanzees are rather similar in the structure of the thorax and arms, they differ substantially not only in brain size but also in the anatomy of the pelvis, foot, and jaws, as well as in relative lengths of limbs and digits (38). Humans and chimpanzees also differ significantly in many other anatomical respects, to the extent that nearly every bone in the body of a chimpanzee is readily distinguishable in shape or size from its human counterpart (38). Associated with these anatomical differences there are, of course, major differences in posture (see cover picture), mode of locomotion, methods of procuring food, and means of communication. Because of these major differences in anatomy and way of life, biologists place the two species not just in separate genera but in separate families (39). So it appears that molecular and organismal methods of evaluating the chimpanzee human difference yield quite different conclusions (40).” King and Wilson went on to suggest that the morphological and behavioral differences between humans and apes,, must be due to variations in their genomic regulatory systems. David Berlinski - The Devil's Delusion - Page 162&163 Evolution at Two Levels in Humans and Chimpanzees Mary-Claire King; A. C. Wilson - 1975 A Closer Look At Human/Chimp Similarities and Differences – video https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1134643976548534/?type=2&theater

of related note:

Comparing the human and chimpanzee genomes: Searching for needles in a haystack – Ajit Varki1 and Tasha K. Altheide – 2005 Excerpt: we have many characteristics that are uniquely human. Table 1 lists some of the definite and possible phenotypic traits that appear to differentiate us from chimpanzees and other “great apes”2. For the most part, we do not know which genetic features interact with the environment to generate these differences between the “phenomes”3 of our two species. The chimpanzee has also long been seen as a model for human diseases because of its close evolutionary relationship. This is indeed the case for a few disorders. Nevertheless, it is a striking paradox that chimpanzees are in fact not good models for many major human diseases/conditions (see Table 2) (Varki 2000; Olson and Varki 2003). http://genome.cshlp.org/content/15/12/1746.full.pdf+html Table 1. Some phenotypic traits of humans for comparison with those of great apes http://genome.cshlp.org/content/15/12/1746/T1.expansion.html

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