Epigenetics, revisited; new exciting studies (Introduction)

by David Turell @, Monday, September 26, 2011, 14:42 (4786 days ago)

It appears that transposons helped mammalian evolution jump from marsupial pouches to placentas:-
http://www.physorg.com/news/2011-09-invasion-genomic-parasites-triggered-modern.html

Epigenetics, revisited; new exciting studies

by David Turell @, Tuesday, September 27, 2011, 01:25 (4785 days ago) @ David Turell

Another verson of the same finding: develolping a placental way of pregnancy:-http://www.sciencedaily.com/releases/2011/09/110925185434.htm

Epigenetics, revisited; new exciting studies

by dhw, Tuesday, September 27, 2011, 14:44 (4785 days ago) @ David Turell

David has once more (actually twice!) drawn our attention to important discoveries:-DAVID: It appears that transposons helped mammalian evolution jump from marsupial pouches to placentas:-http://www.physorg.com/news/2011-09-invasion-genomic-parasites-triggered-modern.html-One quote in particular leaps from the page:-In the last two decades there have been dramatic changes in our understanding of how evolution works," said Gunter Wagner, the Alison Richard Professor of Ecology and Evolutionary Biology (EEB) and senior author of the paper. "We used to believe that changes only took place through small mutations in our DNA that accumulated over time. But in this case we found a huge cut-and-paste operation that altered wide areas of the genome to create large-scale morphological change."-Darwin wrote: "If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down."-Modern research is rapidly uncovering more and more cases that undermine the argument for gradualism, but I still can't understand why Darwin considered it to be so fundamental. As we keep saying, he had no way of knowing what we know now (e.g. about DNA, genetics and epigenetics), but the theory as a whole ... all forms of life descending from earlier forms, with changes taking place and surviving through a process of natural selection ... stands just as firmly as it ever did. The main controversy is not about whether evolution happened, but about how, why, and over what period the changes took place.

Epigenetics, revisited; new exciting studies

by David Turell @, Tuesday, September 27, 2011, 15:28 (4785 days ago) @ dhw


> Darwin wrote: "If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down."-This is not really an argument for gradualism. The argument here is irreducable compexity, a totally different philosophic beast. If you never have read Darwin's Black Box, it is a must to understand the true controversy. Can evolution make a liver? The liver digests, detoxifies (alters chemicals like antibiotics) perhaps more than the kidneys do, makes products like cholesterol, among other activities, and theis all coordinates with other organs doing their things. Gradualism relates solely to species change, and that gradualism is out the window!!
> 
> Modern research is rapidly uncovering more and more cases that undermine the argument for gradualism, but I still can't understand why Darwin considered it to be so fundamental.-I fully understand it!-> The main controversy is not about whether evolution happened, but about how, why, and over what period the changes took place.-No! The true controversy is can chance make the complexities of living organisms? It comes down to who (?) or (what chance process(?) made the liver and had it work with the other organs?

Epigenetics, revisited; new exciting studies

by dhw, Wednesday, September 28, 2011, 17:33 (4783 days ago) @ David Turell

Dhw: Darwin wrote: "If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down."-DAVID: This is not really an argument for gradualism. The argument here is irreducable complexity, a totally different philosophic beast. If you never have read Darwin's Black Box, it is a must to understand the true controversy. Can evolution make a liver? The liver digests, detoxifies (alters chemicals like antibiotics) perhaps more than the kidneys do, makes products like cholesterol, among other activities, and this all coordinates with other organs doing their things. Gradualism relates solely to species change, and that gradualism is out the window!!-Darwin is talking here specifically of complex organs ("Organs of extreme perfection and complication" in Difficulties on Theory), and in particular he deals with the eye. The articles you've drawn our attention to cover similarly complex mechanisms, e.g. what you call "the jump from marsupial pouches to placentas". Darwin even uses similar vocabulary to yours: "[Nature] can never take a leap, but must advance by short and slow steps." You're right, of course, that the ultimate controversy is chance v. design, but a crucial element of this discussion is whether complexity has arisen through tiny, gradual increments (Darwin) or major transformations over a short period. The atheist case is greatly strengthened by gradualism: the smaller the change, the less unlikely it will seem (Dawkins calls it "a continuous and shallow slope up Mount Improbable" ... The God Delusion, p. 124), but I'm suggesting that modern research is undermining that case: the shorter and steeper the route to complexity, the less likely it will seem that chance can produce it. -Since you yourself believe that evolution happened, the answer to your question "can evolution make a liver?" has to be yes! Your argument, however, if I've understood it correctly, is that something so complex cannot have assembled itself by chance, i.e. evolution is either programmed or (my designer alternative) guided by intervention.-Dhw: The main controversy is not about whether evolution happened, but about how, why, and over what period the changes took place.-DAVID: No! The true controversy is can chance make the complexities of living organisms? It comes down to who (?) or (what chance process(?) made the liver and had it work with the other organs?-Agreed, but the two controversies are interlinked. Going back to the quote at the head of this post, the demise of gradualism in the development of organs (and of species) would reduce the likelihood of chance processes, but that doesn't mean that all forms of life did not descend from preceding forms, that changes and innovations did not take place in existing organs and organisms, or that the filter of natural selection did not decide which changes did or didn't survive! I'm arguing simultaneously against chance but for evolution, and since Darwin was NOT trying to put the case for atheism, I still don't understand why he made his theory "absolutely" dependent on gradualism. You say you "fully understand it", so I'd be truly grateful if you would explain it to me!

Epigenetics, revisited; new exciting studies

by David Turell @, Wednesday, September 28, 2011, 23:11 (4783 days ago) @ dhw

I still don't understand why he made his theory "absolutely" dependent on gradualism. You say you "fully understand it", so I'd be truly grateful if you would explain it to me!-I think the difference between you and I and our interpretation of Darwin is organ vs. organism. Both of us agree that evolution occurred. And we see epigenetic effects and punctuated equilibrium (pe) as a source for sudden jumps in phenotype of species. So the gradualism for species is in doubt.-Organs themselves are extremely complex in advanced animals like humans, other mammalians, and even less advanced species like gastropods. Even octopi and for a fact, even lobsters have livers!-Now imagine yourself as Darwin. He looked at breeders and how they changed phenotypes, slowly and gradually. He thought that was the only way it could happen. He did not expect the jumps of PE. And he certinly had no idea of how complex the liver is. Cells were globules of matter to him, not the monsterously complex things they are. So he assumed gradualism. but as I've stated before, the real issue is, how do you make a liver (?) and how do you get it coordinated with the other organs; for example, the kidney has some of the same function in clearing the bolood. The vagus nerve, fairly automatically runs the abdominal organs of digestion. -I don't think that goes slowly, liver construction, that is. It must appear in jumps to work at all. That is the issue of irreducible complexity I've raised. I think I understand Darwin, I don't think he could have have understood, with his lack of what we know now, the underlying problems of how evolution works.

Epigenetics, revisited; new exciting studies

by dhw, Thursday, September 29, 2011, 19:59 (4782 days ago) @ David Turell

Dhw: I still don't understand why he [Darwin] made his theory "absolutely" dependent on gradualism. You say you "fully understand it", so I'd be truly grateful if you would explain it to me!-DAVID: I think the difference between you and I and our interpretation of Darwin is organ vs. organism. Both of us agree that evolution occurred. And we see epigenetic effects and punctuated equilibrium (pe) as a source for sudden jumps in phenotype of species. So the gradualism for species is in doubt. [...]-[...] I don't think that goes slowly, liver construction, that is. It must appear in jumps to work at all. That is the issue of irreducible complexity I've raised. I think I understand Darwin, I don't think he could have understood, with his lack of what we know now, the underlying problems of how evolution works.-I don't see any difference between our interpretations of Darwin. You have used the liver as an example of a complex organ, and he used the eye, and what baffles me is his assertion that if these organs were not the product of "numerous, successive, slight modifications" his theory would "absolutely break down". You and I agree that modern research suggests these organs were not the product of slight modifications but, as you say, of "jumps" ... the very process which Darwin says will wreck his theory. But how does it wreck his theory? It only wrecks the single strand of gradualism, not the overall pattern of evolution (all forms of life descending from earlier forms, adaptations and mutations, natural selection), so why, why, oh why did he think gradualism was all-important?
 
(Maybe this is boring, but at present you and I seem to be the only folk left in the universe, so I'll keep badgering you!)

Epigenetics, revisited; new exciting studies

by David Turell @, Thursday, September 29, 2011, 22:42 (4782 days ago) @ dhw

so why, why, oh why did he think gradualism was all-important?
> 
> (Maybe this is boring, but at present you and I seem to be the only folk left in the universe, so I'll keep badgering you!)-I've already made the point. Go back. He studied breeders and their results are slow and gradual. that's your answer. He never could have known about big jumps.

Epigenetics, revisited; new exciting studies

by BBella @, Saturday, October 01, 2011, 08:26 (4781 days ago) @ dhw

(Maybe this is boring, but at present you and I seem to be the only folk left in the universe, so I'll keep badgering you!)-There are 3 left in the universe! I'm just plugging along with the conversations, waiting for you guys to catch up.

Epigenetics, revisited; new exciting studies

by David Turell @, Friday, November 18, 2011, 15:59 (4732 days ago) @ BBella

Another study in plant epigenetics and what it all means, which we still don't know:

http://the-scientist.com/2011/10/01/evolution-tout-de-suite/

Epigenetics, revisited; new exciting studies

by dhw, Saturday, November 19, 2011, 17:32 (4731 days ago) @ David Turell

DAVID: Another study in plant epigenetics and what it all means, which we still don't know:

http://the-scientist.com/2011/10/01/evolution-tout-de-suite/

You’ve said on several occasions that you think epigenetics may hold the key to the way in which evolution works. Crucially, every article you refer us to has to hold back from the all-important conclusion that permanently heritable new forms may arise in response to environmental changes. Obviously the research goes on, but this conclusion would vastly reduce the highly suspect role hitherto played by random mutations, would explain punctuated equilibrium, and would fit in with the examples of rapid evolution that researchers seem to be accumulating. It seems logical that unless organisms can adapt rapidly (not over hundreds of generations) to dramatic changes, they are likely to die, and it’s not beyond the bounds of belief that environmental pressures could result in organisms finding NEW ways to cope – hence innovation as well as adaptation. I’d be interested to know if you think this really is the pattern that’s emerging, or am I jumping the gun here?

Epigenetics, revisited; new exciting studies

by David Turell @, Saturday, November 19, 2011, 19:34 (4731 days ago) @ dhw

I’d be interested to know if you think this really is the pattern that’s emerging, or am I jumping the gun here?

Your comments are exactly the point of Shapiro's book, but lots of research is needed before the expectations are solidified

Epigenetics, revisited; new exciting studies

by dhw, Sunday, November 20, 2011, 19:26 (4730 days ago) @ David Turell

I asked David if he thought the latest research was leading to the point where we could say that epigenetics, as permanently hereditary adaptations and innovations brought about by changes in the environment, are the key mechanism for evolution.

DAVID: Your comments are exactly the point of Shapiro's book, but lots of research is needed before the expectations are solidified.

Thank you. An article in today’s Sunday Times has the headline Climate change ‘drove ascent of man’. Details of the research are to be discussed at a Royal Society conference this week. The researchers have identified “five crucial eras when big changes in climate seem to have accelerated humanity’s genetic and social evolution.” The earliest was about 2m years ago, when East African forests turned into savannah, which brought our early ancestors down from the trees and turned them into running, hunting Homo erectus. I shan’t repeat the rest of the details, as I’m sure there will be wider and deeper coverage later in the specialist journals. The reason I’ve brought it up here is the clear suggestion that epigenetic mechanisms were at work: change in climate/environment leads to adaptation and innovation – there must have been major anatomical adjustments to allow for the switch from tree-dweller to grassland runner – and these all prove to be hereditary in the long-term. Another step closer to Shapiro, then?

Epigenetics, revisited; new exciting studies

by David Turell @, Thursday, November 24, 2011, 22:48 (4726 days ago) @ dhw

The reason I’ve brought it up here is the clear suggestion that epigenetic mechanisms were at work: change in climate/environment leads to adaptation and innovation – there must have been major anatomical adjustments to allow for the switch from tree-dweller to grassland runner – and these all prove to be hereditary in the long-term. Another step closer to Shapiro, then?

Bats have speciated rapidly in the past 15 million years. It raises the question suggested here: do epigenetic mechanisms lead to punctuated equilibrium?


http://www.eurekalert.org/pub_releases/2011-11/uoma-sbs112311.php

Epigenetics?; brain DNA

by David Turell @, Friday, December 02, 2011, 15:21 (4718 days ago) @ David Turell

Complicated article:
http://www.pnas.org/content/early/2010/04/01/0911249107.full.pdf+html

Look at this conclusion!:


"The finding that neural adaptation has occurred mainly via noncoding
changes is particularly important in view of the remarkable
cognitive innovations in the human lineage. It is consistent with the
hypothesis advanced 35 years ago that the major phenotypic differences
between humans and chimpanzees reflect changes in gene
regulation rather than in protein structure (22). Noncoding sequences
flagged by the surveys analyzed here and associated with neural
development and function are excellent candidates for research into
the genetics and evolution of human cognition."

Epigenetics, revisited; new exciting studies

by David Turell @, Monday, December 05, 2011, 17:54 (4715 days ago) @ David Turell

In this study immunity is passed from parent to child (C elegans, the worm)

http://www.physorg.com/news/2011-12-traits-inherited-small-rnas.html

Epigenetics, revisited; new exciting studies

by David Turell @, Monday, January 09, 2012, 16:39 (4680 days ago) @ David Turell
edited by unknown, Monday, January 09, 2012, 16:46

Epigenetics, revisited; new exciting studies

by David Turell @, Monday, January 16, 2012, 21:46 (4673 days ago) @ David Turell

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