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More on “Epigenetics making Darwin’s followers uncomfortable”

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Recently, we noted an article in AAAS’s Science, according to which epigenetics is making biologists who “balk at suggestions that something other than changes in DNA sequences,” uncomfortable. In other words, it makes Darwin’s followers uncomfortable. Who else would either doubt it or care much? Remember, their natural selection mechanism that is supposed to do almost everything depends on the gene as the simple unit on which the miracle of natural selection works. Pennisi’s article is paywalled, as it happens, but here is the gist:

For 50 years, changes in an organism’s DNA sequence have been considered the sole currency of evolution. Epigenetic mechanisms—methylation and other chemical modi? cations that do not alter the sequence of DNA bases—can also influence a trait, by suppressing or promoting a gene’s activity. But those changes were thought to be too ephemeral to affect evolution. Although a few researchers have shown that epigenetic modifications can persist through several generations, critics would point out that these studies couldn’t rule out undiscovered genetic variation might really be in play. “The burden of proof is on the epigeneticist,” [Oliver] Bossdorf says.

Now, quantitative geneticist Frank Johannes of the University of Groningen in the Netherlands has tried to provide it…

Pennisi notes in closing that “And, [Christina] Richards adds, ‘people are really stubborn about accepting that that’s possible.’” Which is pretty much what was advertised and it certainly accords with our experience here.

Wonder why the article was paywalled.

This is probably the same article: . . . . . Evolution Heresy? Epigenetics Underlies Heritable Plant Traits Elizabeth Pennisi For some evolutionary biologists, just hearing the term epigenetics raises hackles. They balk at suggestions that something other than changes in DNA sequences, such as the chemical addition of methyl groups to DNA or other so-called epigenetic modifications, has a role in evolution. Yet a provocative study presented at an evolutionary biology meeting last month found that heritable changes in plant flowering time and other traits were the result of epigenetics alone, unaided by any sequence changes. Upright BiPed
Atlan and Koppel wrote in 1990 that advances in artificial intelligence showed that cellular operations are not controlled by a linear sequence of instructions in DNA but by a “distributed multilayer network”.
I find this amazing! It's as if DNA sequences, together with folding and epigenetic markers has been purposely *encrypted*. As an analogy (which no doubt can be improved), imagine taking a long, thin strip of paper and winding it in a spiral around a dowel of a specific diameter. Then write a message on the paper along the dowel, each letter being the width of the strip, line by line along the dowel. Then you wrap the same strip to spiral around a dowel of a different diameter, and based on additional marks on the paper, you encode a different message. Yes, it's more compact, but why go to the trouble? Querius
Moreover, neo-Darwinists simply have no evidence that 'random' mutations to DNA can produce novelty in the basic structure of a body plan:
Response to John Wise - October 2010 Excerpt: 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 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_flies http://eebweb.arizona.edu/nachman/Suggested%20Papers/Lab%20papers%20fall%202010/Burke_et_al_2010.pdf Darwin or Design? - Paul Nelson at Saddleback Church - Nov. 2012 - ontogenetic depth (excellent update) - video Text from one of the Saddleback slides: 1. Animal body plans are built in each generation by a stepwise process, from the fertilized egg to the many cells of the adult. The earliest stages in this process determine what follows. 2. Thus, to change -- that is, to evolve -- any body plan, mutations expressed early in development must occur, be viable, and be stably transmitted to offspring. 3. But such early-acting mutations of global effect are those least likely to be tolerated by the embryo. Losses of structures are the only exception to this otherwise universal generalization about animal development and evolution. Many species will tolerate phenotypic losses if their local (environmental) circumstances are favorable. Hence island or cave fauna often lose (for instance) wings or eyes. http://www.saddleback.com/mc/m/7ece8/
Thus, despite the arrogant, self-assured, nature of many neo-Darwinists, and the schoolyard bully tactics they use to try to intimidate anyone who questions their beloved atheistic/materialistic Darwinian view of reality, the fact of the matter is that have no evidence to support their reductionist claim and much compelling evidence that is directly opposed to their naive reductionist claim. Verse and Music:
Psalm 139:16 Your eyes saw my unformed substance; in your book were written, every one of them, the days that were formed for me, when as yet there was none of them. K-LOVE - Steven Curtis Chapman "Love Take Me Over" LIVE http://www.youtube.com/watch?v=Qn5mi5G9RQY
as to this comment:
They balk at suggestions that something other than changes in DNA sequences, such as the chemical addition of methyl groups to DNA or other so-called epigenetic modifications, has a role in evolution.
Other than the fact that 'non-random' epigenetics shows that,,
“The genome is an ‘organ of the cell’, not its dictator” - Denis Nobel – President of the International Union of Physiological Sciences http://musicoflife.co.uk/
Thus undermining the genetic reductionism, the 'central dogma', model of neo-Darwinism, (i.e. DNA makes RNA makes Protein), their are many other lines of evidence that have undermined that reductionist view of life. For instance, the ENCODE consortium released studies last September strongly suggesting a ‘redefinition of the concept of a gene',,
Landscape of transcription in human cells – Sept. 6, 2012 Excerpt: Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene. http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html
And as if ‘redefining the concept of a gene’ and the finding of trans-generational environmental epigenetics were not enough to overthrow the gene-centric view of reality that neo-Darwinists have, it is also now found that ‘mental states’, i.e. thoughts and feelings, can have pronounced effects on the way ‘genes’ are expressed:
Genie In Your Genes – video http://www.genieinyourgenes.com/ggtrailer.html Anxiety May Shorten Your Cell Life – July 12, 2012 Excerpt: These studies had the advantage of large data sets involving thousands of participants. If the correlations remain robust in similar studies, it would indicate that mental states and lifestyle choices can produce epigenetic effects on our genes. http://crev.info/2012/07/anxiety-may-shorten-your-cell-life/
If anyone doesn't think that is troublesome for molecular reductionism I have some swamp land,,, As well there are many lines of evidence that strongly suggest that Body Plan information does not reside in the DNA alone, and that DNA, in so far that it does effect Body Plan morphogenesis, (i.e. effect plasticity of body form), resides at a very low level of the information hierarchy of organisms,, For instance,,
Extreme Genome Repair - 2009 Excerpt: If its naming had followed, rather than preceded, molecular analyses of its DNA, the extremophile bacterium Deinococcus radiodurans might have been called Lazarus. After shattering of its 3.2 Mb genome into 20–30 kb pieces by desiccation or a high dose of ionizing radiation, D. radiodurans miraculously reassembles its genome such that only 3 hr later fully reconstituted nonrearranged chromosomes are present, and the cells carry on, alive as normal.,,, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3319128/
What Do Organisms Mean? Stephen L. Talbott - Winter 2011 Excerpt: Harvard biologist Richard Lewontin once described how you can excise the developing limb bud from an amphibian embryo, shake the cells loose from each other, allow them to reaggregate into a random lump, and then replace the lump in the embryo. A normal leg develops. Somehow the form of the limb as a whole is the ruling factor, redefining the parts according to the larger pattern. Lewontin went on to remark: "Unlike a machine whose totality is created by the juxtaposition of bits and pieces with different functions and properties, the bits and pieces of a developing organism seem to come into existence as a consequence of their spatial position at critical moments in the embryo’s development. Such an object is less like a machine than it is like a language whose elements... take unique meaning from their context.[3]",,, http://www.thenewatlantis.com/publications/what-do-organisms-mean
An Electric Face: A Rendering Worth a Thousand Falsifications - September 2011 Excerpt: The video suggests that bioelectric signals presage the morphological development of the face. It also, in an instant, gives a peak at the phenomenal processes at work in biology. As the lead researcher said, “It’s a jaw dropper.” https://www.youtube.com/watch?v=wi1Qn306IUU http://darwins-god.blogspot.com/2011/09/electric-face-rendering-worth-thousand.html
Not Junk After All—Conclusion - August 29, 2013 Excerpt: Many scientists have pointed out that the relationship between the genome and the organism — the genotype-phenotype mapping — cannot be reduced to a genetic program encoded in DNA sequences. Atlan and Koppel wrote in 1990 that advances in artificial intelligence showed that cellular operations are not controlled by a linear sequence of instructions in DNA but by a “distributed multilayer network” [150]. According to Denton and his co-workers, protein folding appears to involve formal causes that transcend material mechanisms [151], and according to Sternberg this is even more evident at higher levels of the genotype-phenotype mapping [152]. https://uncommondesc.wpengine.com/junk-dna/open-mike-cornell-obi-conference-chapter-11-not-junk-after-all-conclusion/

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