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Epigenetics could be the new “buzzword scienceyness”?

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But Darwinism, the ultimate in scienceyness, gets a pass? Legal enforcement?

From The Guardian:

Lots of real scientific terms – such as “neuro” or “nano” – get borrowed for a spot of buzzword scienceyness. Epigenetics is a real and important part of biology, but due to predictable quackery, it is threatening to become the new quantum.

All of your cells contain all of your 22,000 genes, but not all of them need to be active all the time. They need to be turned on or off, in the right tissue, at the right moment, and so we have incredible networks of control systems in our genomes – circuits, programmes, hierarchies. Epigenetics literally means “in addition to genetics” and is one such system – modifications to DNA without altering the gene sequence itself. Think of DNA as an orchestral score, the notes on the page unchanging. But the annotations on the manuscript will dictate how the music sounds, with crescendo and lento and adagio. The conductor and orchestra play their annotated manuscript, and each performance is unique, even when the original scores are identical.

Many individual genes are modulated, or tagged, like this too, and many corresponding traits are dependent on this system. We’ve known about this for decades. Rat mothers lick their pups, and those that are licked less have measurably higher stress levels, which correlates with less epigenetic tagging on genes associated with stress. What’s more, it’s reversible. So, the environment influences genetics. More.

Rutherford goes on to front Darwinism. But he has already said all we need to know in that case.

Too bad if Adam Rutherford has to do that to stay in print; worse if he believes it.

Hat tip: Stephanie West Allen at Brains on Purpose
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Comments
wd400
OK, so why do you think genetic control of epigenetics is “illogical” and “contradictory”.
You need to explain how 'genetic control' causes "changes in gene activity and expression without alteration in DNA sequence".
Epigenetics is defined as heritable changes in gene activity and expression that occur without alteration in DNA sequence [1, 2]. It is known these non-genetic alternations are tightly regulated by two major epigenetic modifications: chemical modifications to the cytosine residues of DNA (DNA methylation) and histone proteins associated with DNA (histone modifications) [1, 3]. Functionally, the patterns of epigenetic modifications can serve as epigenetic markers to represent gene activity and expression as well as chromatin state [3-6]. http://www.sabiosciences.com/pathway8_Epigenetic.php
You need to explain how "cells carrying identical DNA differentiate into different cell types, and how they maintain differentiated cellular states". Epigenetic changes in gene expression are not encoded in the DNA sequence itself. The epigenetic state is what regulates those aspects of cellular development and activation. If this was "controlled by DNA" (somehow, without observed changes in sequences), then there'd be no need to cite an epigenetic state. It would just be "ordinary genetics". But the modifications in gene expression are caused by factors external to the genome and are not caused by DNA.Silver Asiatic
July 20, 2015
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Tomorrow Eric Metaxas will have Stephen Meyer on his program to discuss the new book "Debating Darwin's Doubt". Listen online or find your station here: http://www.metaxastalk.com/ This is Zach Johnson's Official Twitter Page. Zach and his team will post news, photos, and more. God bless! Practice Hard, Play Hard, Pray Hard = PH3 https://twitter.com/zachjohnsonpga It appears the new Open champion, Zach Johnson, is a man of great faithbornagain77
July 20, 2015
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wd400 claims: "epigentic states are under the control of genetic elements." That claim is false.
“Live memory” of the cell, the other hereditary memory of living systems - 2005 Excerpt: To understand this notion of “live memory”, its role and interactions with DNA must be resituated; indeed, operational information belongs as much to the cell body and to its cytoplasmic regulatory protein components and other endogenous or exogenous ligands as it does to the DNA database. We will see in Section 2, using examples from recent experiments in biology, the principal roles of “live memory” in relation to the four aspects of cellular identity, memory of form, hereditary transmission and also working memory. http://www.ncbi.nlm.nih.gov/pubmed/15888340 Origin of life: A problem in the origin of information - April 2014 Excerpt: A hallmark of life is the way information flows between different levels of organization. In non-living systems, information flows from the bottom up–the properties of the individual parts determine the fate of the system. But with living systems, that flow goes both ways. Not only genes dictate the nature of proteins which in turn affect the functioning of cells, tissues and organisms, but the behavior of proteins, cells, and organisms also control gene expression. This is what Walker calls “top-down control” or “top-down causation.” And to Walker, this transition–from information seeping upward only to information flowing both up and down–is the key to understanding life’s origins. Put differently, the blueprint for building an organism isn’t stored in its DNA only, but it’s distributed in the state of the entire system. Dr. Sara Walker https://uncommondescent.com/intelligent-design/origin-of-life-a-problem-in-the-origin-of-information/ The Gene Myth, Part II - August 2010 Excerpt: “It was long believed that a protein molecule’s three-dimensional shape, on which its function depends, is uniquely determined by its amino acid sequence. But we now know that this is not always true – the rate at which a protein is synthesized, which depends on factors internal and external to the cell, affects the order in which its different portions fold. So even with the same sequence a given protein can have different shapes and functions. Furthermore, many proteins have no intrinsic shape, (intrinsically disoredered proteins), taking on different roles in different molecular contexts. So even though genes specify protein sequences they have only a tenuous (very weak or slight) influence over their functions. ,,,,So, to reiterate, the genes do not uniquely determine what is in the cell, but what is in the cell determines how the genes get used. Only if the pie were to rise up, take hold of the recipe book and rewrite the instructions for its own production, would this popular analogy for the role of genes be pertinent. Stuart A. Newman, Ph.D. – Professor of Cell Biology and Anatomy http://darwins-god.blogspot.com/2010/08/gene-myth-part-ii.html Metamorphic Proteins - 2008 Summary: Proteins that can adopt more than one native folded conformation may be more common than previously thought. http://www.sciencemag.org/content/320/5884/1725.summary Biology's Quiet Revolution - Jonathan Wells - September 8, 2014 Excerpt: In 1996, biologists discovered a protein that does not fold into a unique shape but can assume different shapes when it interacts with other molecules. Since then, many such proteins have been found; they are called "intrinsically disordered proteins," or IDPs. IDPs are surprisingly common, and their disordered regions play important functional roles.,,, So it is not true that biologists know all the basic features of living cells and are merely filling in the details. Nor is it true that Darwinian evolution is a settled scientific "fact," as its defenders claim. Huge unanswered questions remain, and they will only be answered by going beyond the discredited myth that "DNA makes RNA makes protein makes us." http://www.evolutionnews.org/2014/09/biologys_quiet_089651.html podcast - Dr. Jonathan Wells: Biology’s Quiet Revolution - September 17, 2014 "We are talking about 1/3 of the proteins in our body, (could be Intrinsically Disordered Proteins)" - Jonathan Wells http://www.discovery.org/multimedia/audio/idtf/2014/09/dr-jonathan-wells-biologys-quiet-revolution/ On this episode of ID the Future, Dr. Jonathan Wells discusses a popular claim, which he describes as “DNA makes RNA makes protein makes us”—or, every organism contains a program for itself in its DNA. Though this view fits neatly with the perspective of Darwinian evolution, it has been shown to be incorrect at every step. Listen in as Dr. Wells explains. Podcast - Jonathan Wells: Is There Biological Information Outside of the DNA?, pt. 4 - conclusion "Membrane Patterns Carry Ontogenetic Information That Is Specified Independently of DNA." http://intelligentdesign.podomatic.com/entry/2014-06-16T15_41_30-07_00
bornagain77
July 20, 2015
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OK, so why do you think genetic control of epigenetics is "illogical" and "contradictory". When a transcription factor binds to its binding site that's genes (both the site and the genetic sequencing defining the TF) establishing a new pattern of gene expression. Same goes for histones and DNA methylation. For the most part, epigentic states are under the control of genetic elements.wd400
July 20, 2015
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http://www.nature.com/ng/journal/v33/n3s/full/ng1089.html The term 'epigenetics', which literally means 'outside conventional genetics', is now used to describe the study of stable alterations in gene expression potential that arise during development and cell proliferation.Silver Asiatic
July 20, 2015
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What do you think "epigenetics" means?wd400
July 20, 2015
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SA: But with epigenetic changes, a new level is added, making it a ridiculously complex scenario. Non-genetic factors cause genes to express themselves differently. WD: In what sense is this new? The influence of environment on phenotypes has been obvious for a long time. It should be no suprise that evolutionary biologists invented quantative genetics o account for the influences of genes and environment on traits… in the 1920s. Similarly, understanding control of gene expression has been core to molecular biology more or less since that field existed.
The fact that it's not new only makes this worse for your side. Notice, you talk about "understanding gene expression". But you said nothing about the evolutionary origin of this mechanism. If you're just learning how the process works, it's clear that you can say nothing significant about how it evolved from some precursors.
If you mean that gene expression differences might be important for explaining the differences between humans and chimps then congratulations: you’ve caught up to where mainstream evolution biology was 30 years ago.
As above, if mainstream biology only knows that epigenetics might explain morphological differences, you've said absolutely nothing about the evolutionary origin of epigenetic changes (and made it clear that modern evolution doesn't know what it is).
Well, most epigenetics changes are in turn the result of genetic changes.
I'd like to see a reference for that. Again, we're looking for the origin of these changes. You're saying that epigenetics, a known a factor in the regulation of gene expression, evolved through genetic changes.
I can’t see how the second sentence follows from the first, even if it was true.
If similar gene sequences cause different morphological changes due to epigenetic factors, then epigenetic responses are driving the changes - and therefore is not traceable through DNA divergence.
Again, you do realize epigenetic states are mostly controlled by plain old genetics, right?
If someone else can explain what you're trying to say here, I would really appreciate it, because as I read it it's illogical and contradictory. And when we're done with the attempt to explain merely how it works, you can go back to explain how it evolved. That's what's missing.Silver Asiatic
July 20, 2015
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BA -- I guess that was wd400's explanation for the origin of epigenetic relationships. As stated, evolutionary theory has nothing to offer on this -- and wd400's response made that quite clear.Silver Asiatic
July 20, 2015
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"epigenetic states are mostly controlled by plain old genetics" Isn't that backwards, WD400? And how can plain old genetics "control"? Control means purposeful and guided.ppolish
July 20, 2015
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Well sorting all the gross mistakes out of wd400's comment should take you a while SA! :)bornagain77
July 20, 2015
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You are doing a fine job of demonstrating how epigenetics is becoming a buzzword -- something for various science-adjacent fields to attempt to attach their normal patter to...
Current evolutionary theory is gene-centric. Morphological changes are attributed to alteration in DNA through random errors in transcription which are fixed through selection or genetic drift and then inherited.
Most mutations are from replication, not transcription. But close enough.
But with epigenetic changes, a new level is added, making it a ridiculously complex scenario. Non-genetic factors cause genes to express themselves differently.
In what sense is this new? The influence of environment on phenotypes has been obvious for a long time. It should be no suprise that evolutionary biologists invented quantative genetics o account for the influences of genes and environment on traits... in the 1920s. Similarly, understanding control of gene expression has been core to molecular biology more or less since that field existed.
Morphological changes cannot be attributed merely to DNA change.
Correct. But this is Evolution 101 (changes in heritable traits and all that)
Claiming the morphological differences from chimp to human are explained in a 99% similarity in genotype says nothing about epigenetic factors.
I'm not sure exactly what you are saying here (one of the problems caused by the diluted meaning of 'epigenetic). If you mean that gene expression differences might be important for explaining the differences between humans and chimps then congratulations: you've caught up to where mainstream evolution biology was 30 years ago. If you mean the differences between human and chimp are mostly due to environmentally induced changes in gene expression then I look forward to the experiment!
If morphological differences are epigenetic, then genetic divergence is irrelevant to morphology. This alone proves evolutionary theory wrong.
Well, most epigenetics changes are in turn the result of genetic changes. I can't see how the second sentence follows from the first, even if it was true.
But far beyond this, modern evolution says nothing at all about the origin of this epigenetic relationship. It’s not merely a sequential progression of DNA alterations to be explained, but multi-level coding changes which are responsive to the environment and inherited.
Again, you do realize epigenetic states are mostly controlled by plain old genetics, right?wd400
July 20, 2015
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Perhaps you should let Lizzie know that she is arguing for intelligent design evolution.Virgil Cain
July 20, 2015
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I find it curious that Darwinists insist that as Stephanie Keep over at NCSE says: " ... This idea, that evolution is somehow a self-directed march toward complex perfection, is a fundamental misunderstanding. It’s not only wrong, it’s dangerous, because it has potential to feed into a common creationist argument that scientists believe in evolution because they don’t believe in God. ... " Reference: http://ayearningforpublius.wordpress.com/2015/06/15/there-is-no-try-in-evolution/ And yet as this OP indicates: " ... All of your cells contain all of your 22,000 genes, but not all of them need to be active all the time. They need to be turned on or off, in the right tissue, at the right moment, and so we have incredible networks of control systems in our genomes – circuits, programmes, hierarchies. Epigenetics literally means “in addition to genetics” and is one such system – modifications to DNA without altering the gene sequence itself. Think of DNA as an orchestral score, the notes on the page unchanging. But the annotations on the manuscript will dictate how the music sounds, with crescendo and lento and adagio. The conductor and orchestra play their annotated manuscript, and each performance is unique, even when the original scores are identical. ... " And migratory animals, seemingly at or approaching their evolutionary ideal, migrate to very specific places year after year - generation after generation. This seems to show that there is "somehow a self-directed march toward complex perfection."ayearningforpublius
July 20, 2015
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Well Virgil, anyone who is willing to argue that an intelligently designed program can produce ICness can't be all bad.Mung
July 20, 2015
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Mung- Lizzie ignored your link to Sanford's paper. Are you as unsurprised as I am?Virgil Cain
July 20, 2015
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I think I'm about to go epi on you Virgil!Mung
July 20, 2015
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FYI- The Type III Secretory System is also irreducibly complex. Just sayin'...Virgil Cain
July 20, 2015
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Thanks, BA. Now it's wd400's turn.Silver Asiatic
July 20, 2015
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OT: Why the Type III Secretory System Can't Be a Precursor to the Bacteria Flagellum Casey Luskin July 20, 2015 http://www.evolutionnews.org/2015/07/why_the_type_ii097821.htmlbornagain77
July 20, 2015
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Well said Silver Asiatic!bornagain77
July 20, 2015
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wd400
What about epigenetics proves “Darwin was wrong” (or actually, that modern evolutionary biology is wrong, since that field is happy to admit Darwin was wrong about plenty).
Current evolutionary theory is gene-centric. Morphological changes are attributed to alteration in DNA through random errors in transcription which are fixed through selection or genetic drift and then inherited. Evolutionary explanations attempt to offer some kind of sequence of steps in DNA modification to explain the massive diversity evident in the earth's biosphere. As it stands, that claim is absurdly improbable and indefensible as we see every day from evolutionary defenders here on UD. But with epigenetic changes, a new level is added, making it a ridiculously complex scenario. Non-genetic factors cause genes to express themselves differently. Morphological changes cannot be attributed merely to DNA change. Claiming the morphological differences from chimp to human are explained in a 99% similarity in genotype says nothing about epigenetic factors. If morphological differences are epigenetic, then genetic divergence is irrelevant to morphology. This alone proves evolutionary theory wrong. But far beyond this, modern evolution says nothing at all about the origin of this epigenetic relationship. It's not merely a sequential progression of DNA alterations to be explained, but multi-level coding changes which are responsive to the environment and inherited.
If the genome consists of multiple levels of coding, if code can be silenced and reactivated, and if the genome can reprogram itself by cues from the environment, then Darwin's 1859 hypothesis, even after its 1930s update, "neo-Darwinism," looks simplistic and antiquated. Clearly, the environment has no ability to cause adaptive effects, let along program or reprogram anything. Instead, the adaptability of the genome appears more like a design feature: a mechanism for the genome to remain robust through environmental perturbations. http://www.evolutionnews.org/2014/03/ghost_of_lamarc083371.html
Again, evolutionary theory has nothing to explain this. As Stephen Meyer puts it:
"Even in a best-case scenario—one that ignores the immense improbability of generating new genes by mutation and selection—mutations in DNA sequence would merely produce new genetic information. But building a new body plan requires more than just genetic information. It requires both genetic and epigenetic information—information by definition that is not stored in DNA and thus cannot be generated by mutations to the DNA. It follows that the mechanism of natural selection acting on random mutations in DNA cannot by itself generate novel body plans, such as those that first arose in the Cambrian explosion." -- Darwin's Doubt
Silver Asiatic
July 20, 2015
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wd400 asks:
"What about epigenetics proves “Darwin was wrong” (or actually, that modern evolutionary biology is wrong, since that field is happy to admit Darwin was wrong about plenty)."
Note that wd400 did not put a question mark in his supposed question of neo-Darwinism. This omission is telling because neo-Darwinists, such as wd400, never actually question neo-Darwinism to find out what is 'wrong' with neo-Darwinism. In other words, they never actually seek to falsify their theory. Instead neo-Darwinists become a sort of 'story telling' apologist who seeks to cover up embarrassing experimental shortcomings for neo-Darwinism. Indeed, there is no strict falsification criteria to be found anywhere within neo-Darwinism that would allow one to test against it to potentially 'scientifically' falsify neo-Darwinism.
“On the other hand, I disagree that Darwin’s theory is as `solid as any explanation in science.; Disagree? I regard the claim as preposterous. Quantum electrodynamics is accurate to thirteen or so decimal places; so, too, general relativity. A leaf trembling in the wrong way would suffice to shatter either theory. What can Darwinian theory offer in comparison?” - Berlinski, D., “A Scientific Scandal?: David Berlinski & Critics,” Commentary, July 8, 2003
And in so far as neo-Darwinism lacks a strict falsification criteria that one can test against to potentially falsify the theory, it is not even considered a proper 'science' in the first place but is more realistically considered to be a pseudo-science:
"In so far as a scientific statement speaks about reality, it must be falsifiable; and in so far as it is not falsifiable, it does not speak about reality." Karl Popper - The Two Fundamental Problems of the Theory of Knowledge (2014 edition), Routledge It’s (Much) Easier to Falsify Intelligent Design than Darwinian Evolution – Michael Behe, PhD https://www.youtube.com/watch?v=_T1v_VLueGk
In fact, it is interesting to note what J.B.S. Haldane, one of the founders of the modern synthesis, said.
J.B.S. Haldane worked out the mathematics of allele frequency change at a single gene locus under a broad range of conditions. http://en.wikipedia.org/wiki/Population_genetics#History
When asked what would falsify Darwinism, J. B. S. Haldane, one of the founders of population genetics, did not refer to any laboratory test to perform to test against his mathematical models, but instead stated that a ‘rabbit fossil in pre-Cambrian rocks would do quite nicely’.
Five Questions Evolutionists Would Rather Dodge 5. Testability What evidence would convince you that evolution is false? If no such evidence exists, or indeed could exist, how can evolution be a testable scientific theory?,,, The evolutionist J. B. S. Haldane, when asked what would convince him that evolution was false, replied that finding a rabbit fossil in pre-Cambrian rocks would do quite nicely. Such a fossil would, by standard geological dating, be out of sequence by several hundreds of millions of years. Certainly such a finding, if rigorously confirmed, would overturn the current understanding of the history of life. But it would not overturn evolution. Haldane’s rabbit is easily enough explained as an evolutionary convergence, in which essentially the same structure or life form evolves twice. In place of a common underlying intelligent design, evolutionists invoke evolutionary convergence whenever confronted with similar biological structures that cannot reasonably be traced back to a common evolutionary ancestor. So long as some unknown or unexplored evolutionary pathway might have led to the formation of some biological structure or organism, evolutionists prefer it over alternative explanations such as intelligent design. And since the unknown and unexplored allow for an infinity of loopholes, the committed evolutionist regards Darwinian and other materialist explanations of life’s origin and subsequent development as always trumping alternative explanations, regardless of the evidence. - By William A. Dembski http://www.brianauten.com/Apologetics/Five_Questions_Ev.pdf
That Haldane would appeal to a pre-Cambrian rabbit, instead of a laboratory test to test his mathematical models against is simply ludicrous! Moreover, even a Darwinist admitted that a ‘pre-Cambrian rabbit’ would not falsify Darwinism:
"In 2009, Steve Meyer and I spoke at the Sam Noble Museum of Natural History at the University of Oklahoma. The day before, the museum’s curator of invertebrate paleontology, Dr. Stephen Westrop, made a pre-emptive strike by giving his own talk about why the Cambrian explosion poses no challenge to Darwinian theory. He concluded by taking exception to J.B.S. Haldane’s claim that finding a fossil rabbit in the pre-Cambrian would prove Darwin’s theory wrong. If such a fossil were found, Westrop said, paleontologists would simply revise their reconstruction of the history of life. During the Q&A, one student asked him whether any fossil find could falsify Darwin’s theory, and Professor Westrop said “No,” since Darwin’s theory is really about natural selection, which operates on a much shorter time scale than the fossil record." https://uncommondescent.com/darwinism/actually-said-one-darwin-follower-a-rabbit-in-the-cambrian-would-be-no-problem/
As to epigenetic information itself, Dr. Meyer puts the enormous challenge for neo-Darwinism that epigentics presents as such:
"These different sources of epigenetic information in embryonic cells pose an enormous challenge to the sufficiency of the neo-Darwinian mechanism. According to neo-Darwinism, new information, form, and structure arise from natural selection acting on random mutations arising at a very low level within the biological hierarchy—within the genetic text. Yet both body-plan formation during embryological development and major morphological innovation during the history of life depend upon a specificity of arrangement at a much higher level of the organizational hierarchy, a level that DNA alone does not determine. If DNA isn’t wholly responsible for the way an embryo develops—for body-plan morphogenesis—then DNA sequences can mutate indefinitely and still not produce a new body plan, regardless of the amount of time and the number of mutational trials available to the evolutionary process. Genetic mutations are simply the wrong tool for the job at hand." Stephen Meyer - Darwin's Doubt (p. 281)
Of related note as to what is 'wrong' with the modern synthesis:
Podcast - Richard Sternberg PhD - On Human Origins: Is Our Genome Full of Junk DNA? Part 5 (emphasis on ENCODE findings and the loss of the term 'gene' as a accurate description in biology and also how that loss undermines the modern synthesis of neo-Darwinism) http://www.discovery.org/multimedia/audio/2014/11/on-human-origins-is-our-genome-full-of-junk-dna-pt-5/
also see James Shapiro and Denis Noblebornagain77
July 20, 2015
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Yes Wd400, both evolutionary biology and creationists know that Darwin was wrong about this and that. And those. These. Common ground right there. Why can't we just get along? Because it's a battle, that's why.ppolish
July 19, 2015
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What about epigenetics proves "Darwin was wrong" (or actually, that modern evolutionary biology is wrong, since that field is happy to admit Darwin was wrong about plenty).wd400
July 19, 2015
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You're looking at two points and only answering one: 1. Creationists cite epigenetics to assert that Darwin was wrong 2. and that epigenetics may show Lamarckian evolution #1 remains true even if the process isn't Lamarkian and even if the sequence isn't changed. Natural selection doesn't "act" on anything. Certain DNA changes can be preserved or lost, but evolution has to explain the origin and influence of epigenetic changes along with changes to DNA sequences. Neo-Darwinism (in its most contemporary form) is wrong to claim that natural selection acting on DNA sequence modifications alone is a sufficient explanation.Silver Asiatic
July 19, 2015
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I guess the "fronting Darwinism" bit is this passage:
. Creationists cite epigenetics to assert that Darwin was wrong, and that epigenetics may show Lamarckian evolution – that is, acquired during life. It doesn’t, as the changes do not alter the DNA sequence on which natural selection acts
Can anyone tell me why this isn't correct? It's not the whole of the reason that modern epigenetics isn't much like Lamarkian evolution, but it seems accurate enough to me.wd400
July 19, 2015
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