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Epi-epi-genetics

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Lamarckian giraffesWhen I first encountered epigenetic research, some 10 years ago, (where epigenetics is the modification of the genome by environmental factors) I remember the thrill of seeing Darwinism being disproven, well, the Neo-Darwinist Theory (NDT) synthesis anyway. Darwin himself had this archaic idea of “gemmules” carrying traits from the body to the gametes, but Mendel blew all that nonsense out of the water. Not until 50 years after Darwin’s death did his theory get resurrected with the discrete gene as the bearer of the all-important genetic blueprint. This led to the central dogma of NDT, that genes are the DNA blueprints for the cell, producing the RNA transcriptions that get converted into the proteins that make up a cell, a dogma where all the information flows in one direction. We were told that genes are impervious to their environment, being only mixed-and-matched during sex, though in an exact Mendelian fashion manipulated only through natural selection, which really should have been called selective extermination. This automation of inheritance into depersonalized gene sequences gave rise to a host of 20th century efforts to harness the power of the gene machine: eugenics, sterilization, Social Darwinism, genocide, sperm banks, and even war.

In this elevation of natural selection as the only motor that drove evolution, there had to be a corresponding battle against every other motor of change, such as Lamarckian environmental inheritance. Thus every biology textbook trashed Lamarck, despite the great similarity between his views and Darwin’s. He was worse than wrong, he was an apostate heretic.

Now pause a moment, and ask why natural selection had to be so exclusivist. Why couldn’t there be multiple ways to improve a species, why should every other method be invalid?

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Comments
he [Mike Gene] might move toward a more mathematically responsible theory, rather than pandering to the PZ crowd
Dr. Sheldon, I would not characterize Mike's work as pandering to PZ Myer's crowd. Further, basing views on amazon reviews of Mike's book versus what is actually said in Mike's book is only fair. At least you were forthright in stating you were basing your opinion on the amazon review, but perhaps it would only be fair to read the book before throwing around accusations of pandering to PZ Myer's crowd. I have provided a favorable review of some of Mike's work here at UD, and "pandering to PZ Myer's crowd" is certainly not a characteristic of anything I've read from Mike. regardsscordova
November 15, 2010
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It is interesting to see how Darwinists always stretch their theory to unbelievable proportions to gobble up any conflicting data and present them as new additives to Darwinism. It has become extremely elastic as someone noted earlier. I mean Who knows, maybe even if God shows himself to them they will say that the appearance of God was due to random variation & natural selection. There is either randomness or plan! If an event is planned it is not random, and if it was random then it's not planned. The NeoDarwinian notion of RM + NS has randomness in its basis (or at least it lacks a plan) and that is why it is favored by materialists. On the other hand, epigenetics is anything but random, therefore it is more relevant to plan & design. In any case, epigenetics is still a young field and is expanding as we speak with more & more observations. And if this is the primary method of adaption to the environment then it can only be a proof of an overall plan & design that pre-programmed the required genetic information and the environment simply happened to switch them on. Notice that the NeoDarwinian model requires the "creation" of this new adaptive information via random mutation. So in short, Darwinian adaptation is based on random variation that is independent of the environment. But epigenetical adaptation is dependent on the environment and is thus antithetical to NeoDarwinism. So I cannot see a marriage between the two.Shogun
November 8, 2010
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#21 But neither the giraffe babies nor the next generation of bacteria would have had a change in their genome unless somehow the stress purposefully caused that change. Why "purposefully"? All Lamarck is claiming that sometimes acquired characteristics are somehow passed on. It certainly wasn't the bacterium's plan to pass it on. It wasn’t random. Everyone agrees it isn’t a case of RM+NS, but of epigenetics. I don't think the epigenetics is the only proposed mechanism for Lamarckian inheritance - but that is not important. No this is not random mutation. It is change caused by the presence of acquired characteristics. That doesn't make it designed or planned or intended or purposeful or teleological change. So this effect was lying latent in the epigenetic machinery of the organism. Don't understand. In what sense latent? Does it matter really if it was the “will” of the bacterium or the “will” of bacterium designer that connected the stress and the gene change? In one case, the organism “plans” and in the other case, an intelligent agent outside the organism “plans”, but in both cases Lamarckian changes are a result of a plan. You have to put "plan" in quotes because you know bacteria don't actually plan anything and certainly not the characteristics of their offspring. Even humans can't do that to any significant degree. In fact Larmarckian inheritance it isn't like a plan at all. All that happens is the creature A acquires characteristic X and as a result the chances of its offspring having that characteristic increase.markf
November 5, 2010
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Markf, I think I'm beginning to understand your confusion. You think that just because giraffes strain for the leaves in the tops of the trees, doesn't mean they "plan" on passing to their babies long-neck genes, so the appearance of a "long-necked" gene in the next generation is not planned? (Okay, for a real example I could have used lactose stress on bacteria whose lactase gene was knocked out.) But neither the giraffe babies nor the next generation of bacteria would have had a change in their genome unless somehow the stress purposefully caused that change. It wasn't random. Everyone agrees it isn't a case of RM+NS, but of epigenetics. So this effect was lying latent in the epigenetic machinery of the organism. Does it matter really if it was the "will" of the bacterium or the "will" of bacterium designer that connected the stress and the gene change? In one case, the organism "plans" and in the other case, an intelligent agent outside the organism "plans", but in both cases Lamarckian changes are a result of a plan. Or are you saying that epigenetic machinery is itself a random mechanism that involves accidental correlations between stress and genome changes that reduce that stress? Can you explain to me how the environmental stressor and the genome change can be correlated without there being purpose, without teleology?Robert Sheldon
November 5, 2010
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#19 "In my dictionary, there is no difference between animal brains choosing certain epigenetic traits to express in the next generation and “planning”. Oh come on. I know of no theory which supposes that animals choose what traits to express in the next generation. It is certainly not what Lamarck proposed. All he said was that acquired characteristics may be inherited.markf
November 5, 2010
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NormO, You just made my point. If the bird's DNA isn't altered, but just the methylation, then there was no evolution. On the other hand, if methylation (or equivalent histone modification, imprinting etc) can achieve the effect of beak changes, then evolution to DNA is prevented from happening. second opinion, ToE = "theory of evolution" or "theory of everything"? Assuming the first definition, the motivation for Darwin is clear from his notebooks, his sojourn to Edinburgh at age 16, etc. He wanted to promote a metaphysical position. As for modern attempts, they are all over the map, and while a Coyne or a PZ Myers might be easy to bin, a Collins or a Penrose is a lot more slippery. Markf, You are somehow making a distinction with "teleology" that I don't understand. In my dictionary, there is no difference between animal brains choosing certain epigenetic traits to express in the next generation and "planning". Perhaps you mean that humans can anticipate the future and animals can't. But if humans have epigenetic abilities (as we know they do) then for starters, humans must evolve without NS. But if consciousness is some material property, then even this distinction disappears, and animals can plan too. So what is your distinction based on?Robert Sheldon
November 5, 2010
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Markf, I’m afraid you are disagreeing with Darwin if you say that Lamarck is not teleological. You are also disagreeing with standard college textbooks in biology. In fact, you are disagreeing with 90% of the “Darwin for dummies” websites on the Internet. You are welcome to try and renovate Lamarck, I think he’s had a bum rap for 150 years myself. Anyone with 4 first names never gets quoted nowadays I didn't express myself clearly. I know that Lamarck is discredited by Darwin and others - so the possibility that in some cases he may have been right is an interesting scientific development. But Larmarckism does not require or imply design or indeed any kind of intention or plan behind the evolution. It is a non-design alternative to natural selection (one of many). I challenge you to produce a single reference written by qualified biologist which claims that Lamarkism is teleological in the sense of being planned.markf
November 4, 2010
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Okay, maybe I should be more specific. What is in your opinion the scientific motivation behind the ToE?second opinion
November 4, 2010
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Robert Sheldon: So what NDT and nearly the whole literature have done, is find epigenetic effects and deem them evolution. Which is what Galapagos finch beaks or breeding pigeons, or lactose tolerance will tell you about. How are those examples of epigenetics? The finch beaks in particular was a carefully documented case of natural selection in action. When the environment became drier and seed coats became thicker and harder to open, the birds with thicker beaks differentially survived and reproduced. In no way was the environment actually modifying the bird's DNA.NormO
November 4, 2010
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Let me work backwards. Markf, NormO & gpuccio--certainly some epigenetics is methylation, but there's a lot of other mechanisms, some of which directly read back into the DNA. Retroviruses, for example, jumping genes, things we've known about for years. As a physicist, I'm looking at the time it takes for all these epigenetic effects to work. Methylation can occur in minutes and can persist for generations. Some of the other mechanisms, such as imprinting last only one generation. The point is that the environment has many different timescales, and for successful adaptation to occur, there has to be a feedback for each timescale. Homeostasis is seconds to minutes. Epigenetics is years to centuries. And DNA effects are millennia or longer. The lesson I learn from this comparison, is that there are 3 roughly distinct timescales of adaption, one for survival of the individual, one for survival of the tribe, and one for survival of the species. Darwin or NDT want everything shoehorned into the last, and then call it speciation. This is completely inverted. The error correction, the feedback timescale, the entire organism is designed to make DNA never change. This was Behe's point in "Edge". It just ain't gonna happen. So what NDT and nearly the whole literature have done, is find epigenetic effects and deem them evolution. Which is what Galapagos finch beaks or breeding pigeons, or lactose tolerance will tell you about. And this confusion of adaption or epigenetics with evolution and DNA has made it really hard to carry on a coherent conversation in the field. Second Opinion. You asked me a recursive question--do I believe myself. Were I to answer, "No, I always lie." would you be the slightest bit enlightened? This is the topic of my ThM thesis, and at some point I can send you 300 pages on the significance of recursive speech. But the short answer is, yes, I try hard to be truthful, for the truth is always greater than I. Markf, I'm afraid you are disagreeing with Darwin if you say that Lamarck is not teleological. You are also disagreeing with standard college textbooks in biology. In fact, you are disagreeing with 90% of the "Darwin for dummies" websites on the Internet. You are welcome to try and renovate Lamarck, I think he's had a bum rap for 150 years myself. Anyone with 4 first names never gets quoted nowadays. DATCG, I have not read Mike Gene's Design Matrix, but I did read a review over at Amazon.com. I would have to say that qualitatively we have a lot in common. Quantitatively though, he doesn't really understand the probabilities involved. In other words, he's a biologist. A physicist would say there's no argument when the probabilities are 10^123 power and greater. I have paper in peer review right now looking at the Origin-of-Life problem. In it I develop a non-local front-loading holographic solution to OOL, which is no more mathematically palatable than Mike Genes, but at least does indicate the limitations of the current paradigm (OOL on Earth some 3 billion years ago). I would hope that after Mike reads my paper, he might move toward a more mathematically responsible theory, rather than pandering to the PZ crowd. nullasalus You are right, NDT has become infinitely elastic. One day, perhaps soon, they will embrace ID as simply the obvious outcome of RM+NS. Which is to say, NDT has long ago stopped being a theory, and has become an ideology much like global warming/climate change/disruption. My biology prof colleagues tell me that the little kowtow toward evolution in the conclusion of every biology paper is a meaningless Shinto stunt that has zero relevance to the paper. Sort of like the statement on every New Scientist presser that this discovery "will help us cure cancer". The danger, of course, is that we stop doing science and don't realize it.Robert Sheldon
November 4, 2010
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Mark: In general, I can agree with you: epigenetics is not an answer to the problem of the origin of biological information. You know my position: only design is. But there are two important aspects which make epigenetics interesting. The first is that it could be part of adaptational mechanisms where a genetically controlled (designed) algorithm can incorporate information from the outer world to "tweak" existing functions, even at the genetic level. That is very different from the traditional darwinian concept of RV + NS. It implies intelligent interpretation of inputs, and intelligent management of the results. Obviously, in purely adaptive mechanisms, the "intelligence" would be only passive: implemented by the designer in the adaptive algorithm. But the incorporation of outer information would be a true bonus. Again, antibody maturation is a good example of that: a very intelligent adaptive mechanism which utilizes external information (a specific antigen) to modify the genetic information coding the antibody in order to gain affinity. The important point here is that the DNA in the B cells is effectively modified through a process of RV and Intelligent Selection, even if the result is not heritable (it remains confined to the specific B cell clone). So, it is possible in principle for the organism to modify its DNA. But that can never happen in a ateleological way: it requires specific intelligent algorithms already embedded in the organism. And Jerry Coyne is right, for once: the models of DNA methylation and similar, although interesting, are not really a fundamental revolution in our understanding of biological control. The second point which I find interesting in the concept of epigenetics is that not all the fundamental information is necessarily in DNA, but that some important part could pass through the cytoplasm. That is interesting, because one of the problems with explaining the development of multicellular beings from the zygote is that the genome is the same in the zygote as in any single final cell in the multicellular being (with few exceptions). And yet each cell expresses a specific transcriptome, both as a cell type and as a particular functional state at any moment. I maintain that that is a true and fascinating mystery, and that we have at present no real explanation. Evo devo tries to deal with that (which is a good thing), but I am not sure that its reductionist approach will be able to go far. Let's see. Anyway, one of the findings of evo devo, if I am not wrong, is that in drosophila some fundamental spacial distribution of transcription factors in the zygote cytoplasm is important to start a correct development. And that is an epigenetic principle. I believe that plasmids in bacteria and probably the transposone system may be linked to epigenetic rearrangement of genetic information.gpuccio
November 4, 2010
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I don't mean to be offensive but I am sincerely interested. And although this is a question I could have asked earlier at different posts I will ask it here: Do you really believe what you are writing? I mean since you have a PhD in physics did you check on the scientific details in your post?second opinion
November 4, 2010
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Jerry Coyne has a new post up about epigentics here. Here's a quote from the post:
Epigenetic inheritance, like methylated bits of DNA, histone modifications, and the like, constitute temporary “inheritance” that may transcend one or two generations but don’t have the permanance to effect evolutionary change. (Methylated DNA, for instance, is demethylated and reset in every generation.) Further, much epigenetic change, like methylation of DNA, is really coded for in the DNA, so what we have is simply a normal alteration of the phenotype (in this case the “phenotype” is DNA) by garden variety nucleotide mutations in the DNA. There’s nothing new here—certainly no new paradigm.
NormO
November 4, 2010
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markf:
The key point here is the Lamarckism is not teleological.
How do you know? What is your strongest evidence that natural selection or Lamarlism can construct a functional multi-part system? What's that? You don't have any evidence for that? OK thanks...Joseph
November 4, 2010
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The key point here is the Lamarckism is not teleological. It requires no design. It may well supersede natural selection in some respects (I believe they are very limited). So we have another non-teleological explanation for evolution. Natural selection does not have to be all or nothing. It can explain some aspects of evolution but not others. In fact that is pretty well established.markf
November 3, 2010
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Robert, after reading your article again. Would you consider your idea of epi-epigentics similar at all to Mike Gene's Design Matrix? Just curious. And thanks for reminding me of Susan Mazur's articles on post-evolutionary proceedings at Altenburg. I was unaware of her published expose' :) I enjoyed her articles so much back then. What a refreshing delight it was to see Neo-Darwinism exposed for all the failures and the bold questioning put forward in public. It is exactly the type of honest reporting we need today on scientific issues. nice article.DATCG
November 3, 2010
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markf, how bout banging drums? yeah... lets go back to banging drums... but wait, that is still intelligent communication w/ causality. Outcomes shared between sender and receiver that create other reactions. It is a simple relationship between two thinking minds, but nevertheless, a process of choice and thought. boom, boom, there is a storm coming bada boom boom, ok, we will prepare for rain boom bada bing bada boom, the storm is large, a tsunami of information bada bing, badaaaa boom! Understood. We will upgrade our Boom Boom drums to Smart Boom Boom drums to capture this information and spread the information to others. IOW, for complex interactions to take place, you need more complex designs. The days of blind evolution and failed gradualist theory are over.DATCG
November 3, 2010
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markf, how in the world is more regulation and interaction a disaster for Design? More complex interactions scream design. Or would you rather go back to Pony Express today?DATCG
November 3, 2010
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Robert, offtopic, maybe you or someone can review for possible future discussion? Celluar Printing... Printed in Elohym's Image? Cellular printing allows image building of specific cell type assignments to specific locations for the creation of living organs. I've been watching this area of research closely, including Model Print technology. Evoution is a bottom up accident. ID is a top down design technology. I hope someone at UD may cover latest advancements in Image Design and creation technology like this. This initiates questions and discussion about ID vs Darinism on current trends in bio-technology and image processing for future intelligent creation. And I think it covers areas relative to Designer questions as well. Thanks.DATCG
November 3, 2010
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I'm conflicted here, in part because I think Darwinism/Neo-Darwinism as is understood nowadays is tremendously elastic. I suspect that if ever it became a popular belief that IC structures just plain showed up inexplicably throughout evolutionary history with no precursors, quite a number of people would shrug, file it under 'variation' and consider the whole thing compatible with neo-Darwinism. The standard, as near as I can tell, is 'If natural selection ever happens for any reason in any magnitude, Darwin was completely right on everything that mattered and he's a genius.'nullasalus
November 3, 2010
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OK I am not getting this. Natural selection is a result of three processes- (chance) variation, heredity and differential reproduction. Whatever survives gets fed into the next round of inputs- that is (supposed to be) the feedback. It is that feedback that (allegedly) leads to cumulative selection. It's like a magical ratchet. And I am not sure that Darwin argued against Lamark or Darwinism excludes Lamarkism. That said epi-genetics seems to be a quick way to get populations to adapt to their environment- Dr Spetner's "built-in responses to environmental cues" perhaps.Joseph
November 3, 2010
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Mark, The shoe is on the other foot. In order for NS to work, nothing else is allowed to work faster. But directed searches are far more efficient and far faster than NS. Therefore NS never does any work. Let me say it another way. If I wanted to know which of my children could genetically find candy better, then I would not allow "warmer" and "colder" kibbutzing. This would poison the test, and prevent NS from functioning. The slightest amount, the most trivial amount of teleology, poisons Darwinism to its core. Because the most infinitesimal of feedback into the gene pool will totally swamp the NS signal. Darwinism in its present, anti-teleological incarnation, must reject all, any, and trivial feedback, it must reject all, any, and trivial teleology, or it is just another version of Lamarck. Your admission of limited Lamarck, is acknowledgement of defeat. It is Darwin who is all-or-nothing, for Lamarck can handle any amount of random mutations without losing his way, but Darwin cannot tolerate the smallest smidgen of feedback.Robert Sheldon
November 3, 2010
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Markf- Can you see no way in which a Lamarckian theory is incredibly supportice of design? It seems obvious to me.Phaedros
November 3, 2010
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It is extraordinary how epigenetics and Lamarckism - disasters for the design inference - are so often brought out in support of ID. There was a theory about how evolution happened based on Mendel. Because it was a proper theory with details of the mechanism scientists were able to do experiments and make observations. They discovered the theory was insufficient and modified their theory in various ways. One of the modifications was the (limited) role of Lamarck and epigenetics. Seems fair enough - that is what scientists do. Compare to ID - the only observations claimed in its support are observations about the supposed failure of RM+NS (see Behe). From which the argument goes: 1) RM+NS cannot explain it. 2) Therefore - no plausible natural explanation exists. 3) Therefore CSI. 4) Therefore design. Along come several alternative non-teleological explanations each with a role (how many others are there we haven't come across yet?) - argument falls apart at stage (2).markf
November 3, 2010
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