Epigenetics, revisited (Introduction)
by David Turell 
, Wednesday, June 29, 2011, 15:19 (4896 days ago)
Here is a newly discovered epigenetic mechanism, which is inheritable. Change in chromatin under stress:- http://www.sciencedaily.com/releases/2011/06/110623130146.htm
Epigenetics, revisited
by xeno6696 , Sonoran Desert, Saturday, July 02, 2011, 13:54 (4893 days ago) @ David Turell
Here is a newly discovered epigenetic mechanism, which is inheritable. Change in chromatin under stress: > > > http://www.sciencedaily.com/releases/2011/06/110623130146.htm-I wish this explained the mechanism more... -Specifically, they talk about genes packed in heterochromatin, and that these packaged genes are passed to offspring... but how? My understanding of the process of life begins with a sperm and an egg. Where are these gene packs if they're not in the chromosomes of these sex cells?
--
\"Why is it, Master, that ascetics fight with ascetics?\"
\"It is, brahmin, because of attachment to views, adherence to views, fixation on views, addiction to views, obsession with views, holding firmly to views that ascetics fight with ascetics.\"
Epigenetics, revisited
by David Turell , Saturday, August 06, 2011, 22:00 (4858 days ago) @ David Turell
Here is a discovery of grazed plants growing faster and larger by reduplicating their chromosomes:-http://www.sciencedaily.com/releases/2011/08/110801094715.htm
Epigenetics, revisited
DAVID (under "Early Embryology"): I'd love some Darwinist explain this phenomenon to me. How did evolution add this protective mechanism to embryoes that are in the 3 to 5 day range of development? How does natural selection operate in this situation? -http://www.sciencedaily.com/releases/2011/07/110705071546.htm-In the good old days when George used to fire his atheist arrows at me, he often objected to my using the word "mechanism", but it's very difficult to avoid, as we can see from this latest article. Atheists don't like it because it automatically smacks of design, but the more complex the operations, the more difficult it is to avoid thinking and talking in such terms.-A new book called The Epigenetic Revolution by Nessa Carey (a lecturer in genetics at Imperial College) was reviewed last week in The Guardian. The review is too long for me to quote, but here are some interesting snippets:-"The cell tells the DNA what to do just as much as the DNA instructs the cell: you can't have one without the other."-"Epigenetics is what happens when genes are actually in action: in the growth of the foetus, in responding to hormones and environmental stress, to learning, to maturation at puberty. In all of these processes genes are modified slightly and act differently from that point on. In short, epigenetics is where nature meets nurture."-"It is almost certain that memory ... a classic nurture problem: we learn something and it becomes biologically encoded ... involves epigenetics. Once made, epigenetic changes can be very long lasting, which is how our long-term memory is possible."-" [...] it claims that some epigenetic changes are so long-lasting they cover several generations. This flouts one of biology's most cherished dogmas ... taught to all students ... namely that changes acquired during life cannot be passed on ... the heresy of Lamarckism."-"She hasn't, though, solved the problem of how to make the mind-numbing complexity of some genomic interactions and the confusing nomenclatures of genes palatable to the general reader. On one page alone, we encounter H3K4, H3K27, DNMT3L, EZH2, LSD1 and DNMT3A&B."-It is indeed mind-numbing. And all this, bear in mind, is part of a mechanism that actually works. It's "the book of life; a huge encyclopaedia; a sacred chain of code 3 bn characters long". You really have to admire the faith of those who reject even the possibility of design.
Epigenetics, revisited
by David Turell , Saturday, August 27, 2011, 15:35 (4837 days ago) @ dhw
> A new book called The Epigenetic Revolution by Nessa Carey (a lecturer in genetics at Imperial College) was reviewed last week in The Guardian. -> It is indeed mind-numbing. And all this, bear in mind, is part of a mechanism that actually works. It's "the book of life; a huge encyclopaedia; a sacred chain of code 3 bn characters long". You really have to admire the faith of those who reject even the possibility of design.-The reviewer does not recognize Shapiro's book, Evolution, which is just as complicated and just as startling in its conclusions. Larry Moran in Sandwalk blog is already attacking Shapiro, by claiming Shapiro makes mistakes in articles that are peer reviewed. This is one of Moran's methods, denegrate the person. Moran is quite the adolescent. Paradigms are changing and the old guard is resisting. (Kuhn!)
Epigenetics, revisited
by David Turell , Thursday, September 01, 2011, 23:43 (4832 days ago) @ David Turell
More epigenetics in the way RNA controls much DNA expression. Scientists are unravellilng a secondary coding system involving only RNA:- http://www.nature.com/news/2010/100505/full/465016a.html
Epigenetics, revisited
by David Turell , Friday, September 09, 2011, 15:30 (4824 days ago) @ David Turell
Transposons are another epigenetic mechanism:-http://www.sciencedaily.com/releases/2011/09/110906161634.htm
Epigenetics, revisited; new exciting studies
by David Turell , Saturday, September 17, 2011, 02:24 (4817 days ago) @ David Turell
Here is a plant study with rapid evolution:-http://www.physorg.com/news/2011-09-genes-destiny-hidden-code-dna.html-Also transplanted lizards changing head size and developing cecal valves in 30 years!:-http://www.physorg.com/news127667797.html
Epigenetics, revisited
by David Turell , Monday, September 19, 2011, 15:06 (4814 days ago) @ David Turell
Scientists at Scripps have uncovered an epigenetic mechanism for rapid methylation, changing plant characteristics quickly:-http://www.sciencedaily.com/releases/2011/09/110916152401.htm-This fits nicely with James Shapiro's theories of a 'third' way
Epigenetics, revisited
David has drawn our attention to an important study of epigenetic mechanisms in plants:-http://www.sciencedaily.com/releases/2011/09/110916152401.htm-I'm not sure whether I should get wildly excited over this or not. Maybe I've misunderstood the implications, so perhaps you can help me. Here is the crux of the matter:-This meant that not only was the epigenome of the plants morphing rapidly despite the absence of any strong environmental pressure, but that these changes could have a powerful influence on the plants' form and function.-Ecker said the results of the study provide some of the first evidence that the epigenetic code can be rewritten quickly and to dramatic effect. "This means that genes are not destiny," he said. "If we are anything like these plants, our epigenome may also undergo relatively rapid spontaneous change that could have a powerful influence on our biological traits."-The study seems to suggest that mutations can take place in plants, and possibly in the animal kingdom as well, independently of environmental pressures. Previously, we've talked of epigenetic changes in terms of adaptation ... i.e. the species remains basically the same. But if the changes are spontaneous and can change both form and function, doesn't this fit in perfectly well with Darwin's concept of innovation caused by mutations (of course he didn't know about DNA or epigenetics)? It's true that if these changes can be relatively quick and dramatic, they would knock his gradualism on the head, but I have never understood why he regarded gradualism as so central to the theory anyway. Are the Scripps researchers on the way to solving the innovation problem?
Epigenetics, revisited
by David Turell , Monday, September 19, 2011, 18:22 (4814 days ago) @ dhw
David has drawn our attention to an important study of epigenetic mechanisms in plants: > > http://www.sciencedaily.com/releases/2011/09/110916152401.htm > The study seems to suggest that mutations can take place in plants, and possibly in the animal kingdom as well, independently of environmental pressures. Previously, we've talked of epigenetic changes in terms of adaptation ... i.e. the species remains basically the same. But if the changes are spontaneous and can change both form and function, doesn't this fit in perfectly well with Darwin's concept of innovation caused by mutations (of course he didn't know about DNA or epigenetics)? It's true that if these changes can be relatively quick and dramatic, they would knock his gradualism on the head, but I have never understood why he regarded gradualism as so central to the theory anyway. Are the Scripps researchers on the way to solving the innovation problem?-Previously we have considered Darwin's approach as passive: random chance mutations and then a choice thru natural selection. Here we see active mutation not necessarily as an adaptation to environmental pressures. Scripps has shown a little more of the unravelling of the mystery of the epigenetic mechanisms, and again raises my contention that evolution is pre-planned by the UI. If organisms can partially or completely plan their own futures, then evolution is not passive!
Epigenetics, revisited
Dhw: The study seems to suggest that mutations can take place in plants, and possibly in the animal kingdom as well, independently of environmental pressures. Previously, we've talked of epigenetic changes in terms of adaptation ... i.e. the species remains basically the same. But if the changes are spontaneous and can change both form and function, doesn't this fit in perfectly well with Darwin's concept of innovation caused by mutations (of course he didn't know about DNA or epigenetics)? It's true that if these changes can be relatively quick and dramatic, they would knock his gradualism on the head, but I have never understood why he regarded gradualism as so central to the theory anyway. Are the Scripps researchers on the way to solving the innovation problem?-DAVID: Previously we have considered Darwin's approach as passive: random chance mutations and then a choice thru natural selection. Here we see active mutation not necessarily as an adaptation to environmental pressures. Scripps has shown a little more of the unravelling of the mystery of the epigenetic mechanisms, and again raises my contention that evolution is pre-planned by the UI. If organisms can partially or completely plan their own futures, then evolution is not passive!-Thank you for your answer. It appears to confirm Darwin's contention that innovation comes about through random mutations, but not necessarily in the tiny incremental stages that were essential to his gradualism. Many of the scientific articles you have drawn our attention to seem to suggest that even the tiniest particles have some form of "intelligence" (for want of a better word) that can result in new combinations. In other words, modern research into genetics and epigenetics supports the theory of evolution by innovation, adaptation and natural selection. You take this as back-up for the idea that "evolution is pre-planned by the UI". I agree, as usual, that it requires inordinate faith to believe that a mechanism capable of such astonishing creativity could fashion itself out of nothing. Exactly the same objection, however, applies to a UI. As for evolution, once that initial mechanism was in place, it could simply have gone its own random way, followed a course laid down for it at the beginning by a designer, or developed randomly with interventions by a designer. Personally I don't see how the apparently higgledy-piggledy history of life, with all its comings and goings, can be squared with pre-planning, but we have been over that objection many times, and I have far too much respect for you to dismiss the idea! What is exciting for me here is the fact that this latest research really does appear to open the way to our understanding of the innovations without which evolution could not happen. I see this as a massive vindication of Darwinism, which ... let me repeat for the umpteenth time ... offers no explanation for the origin of the "epigenetic mechanisms", and in that respect argues neither for nor against design.
Epigenetics, revisited
by David Turell , Tuesday, September 20, 2011, 21:59 (4813 days ago) @ dhw
> I agree, as usual, that it requires inordinate faith to believe that a mechanism capable of such astonishing creativity could fashion itself out of nothing. Exactly the same objection, however, applies to a UI. -My philosophy accepts a First Cause. Something or someone started all of this. Did this come from nothing? How? In our experience, everything has a cause. To say that the universe is eternal is a cop-out. Why is anything eternal? Back to the same old question: why is there something rather than nothing?
Epigenetics, revisited
Dhw: I agree, as usual, that it requires inordinate faith to believe that a mechanism capable of such astonishing creativity could fashion itself out of nothing. Exactly the same objection, however, applies to a UI. DAVID: My philosophy accepts a First Cause. Something or someone started all of this. Did this come from nothing? How? In our experience, everything has a cause. To say that the universe is eternal is a cop-out. Why is anything eternal? Back to the same old question: why is there something rather than nothing?-You have presented an excellent argument for agnosticism. If it is a cop-out to say that the universe is eternal, it is no less a cop-out to say that there is an eternal universal intelligence. Perhaps, though, we should try to describe this "first cause" you believe in. In other posts you have talked of everything being "energy" in one form or another, so let's say the first cause is primal energy. Perhaps this would even be acceptable to all theists, atheists and agnostics alike. But the theist says that primal energy is conscious of itself, the atheist says it's unconscious. The theist says that life and our universe are deliberate creations by conscious primal energy; the atheist says that unconscious primal energy has come up with life and our universe by chance after an eternity and infinity of accidental combinations. The agnostic says hmmmerrrummmphhh. The theist and the atheist are copper-outers because both explanations leave a multitude of unanswerable questions. However, it might also be argued that the agnostic is also a copper-outer because he refuses to believe in any answer to unanswerable questions. A fair summary?
Epigenetics, revisited
by David Turell , Wednesday, September 21, 2011, 23:34 (4812 days ago) @ dhw
In other posts you have talked of everything being "energy" in one form or another, so let's say the first cause is primal energy. Perhaps this would even be acceptable to all theists, atheists and agnostics alike. But the theist says that primal energy is conscious of itself, the atheist says it's unconscious. The theist says that life and our universe are deliberate creations by conscious primal energy; the atheist says that unconscious primal energy has come up with life and our universe by chance after an eternity and infinity of accidental combinations. The agnostic says hmmmerrrummmphhh. The theist and the atheist are copper-outers because both explanations leave a multitude of unanswerable questions. However, it might also be argued that the agnostic is also a copper-outer because he refuses to believe in any answer to unanswerable questions. A fair summary?-Very fair. But. We are left with the same old ending to the discussion. 'Something' must be eternal, a first cause. Since energy is all that is, to quote bBella in paraphrase, we must start with a consideration of energy. We are excluding the idea that the initial 'first cause' energy came from nothing. Nothin is a complete void, nothingness. So energy is always eternal, either in the form of this universe or a multiverse. Or it is just pure energy in the form of teleologic energy, purposeful energy. Why should we image a pure energy with no directionality? If we do that, then we have to summon forth a Darwinian mechanism to make that energy evolve into a body of energy with directionality. What would cause that? Pure energy floating around should have no impetus to change. Therefore the energy has a direction and and a purpose. Otherwise we wouldn't be here discussion this. My motto is FIRST CAUSE FOREVER!
Epigenetics, revisited
by David Turell , Thursday, September 22, 2011, 01:28 (4812 days ago) @ David Turell
A study which shows that in a species of plant epigenetic change by methylation may not be lasting. Of course methylation is only one form of epigenetics, and natural selection has to have its input as a final determinant. Some folks are trumpeting the end of the excitement about epigenetics with this one limited study. Don't be fooled.-http://www.sciencedaily.com/releases/2011/09/110920132628.htm
Epigenetics, revisited
DAVID: We are left with the same old ending to the discussion. 'Something' must be eternal, a first cause. Since energy is all that is, to quote bBella in paraphrase, we must start with a consideration of energy. We are excluding the idea that the initial 'first cause' energy came from nothing. Nothin is a complete void, nothingness. So energy is always eternal, either in the form of this universe or a multiverse. Or it is just pure energy in the form of teleologic energy, purposeful energy. Why should we image a pure energy with no directionality? If we do that, then we have to summon forth a Darwinian mechanism to make that energy evolve into a body of energy with directionality. What would cause that? Pure energy floating around should have no impetus to change. Therefore the energy has a direction and and a purpose. Otherwise we wouldn't be here discussion this. My motto is FIRST CAUSE FOREVER!-I like the alternative you give here of eternal energy "either in the form of this universe or a multiverse", though in view of the big bang theory I would feel more comfortable if we said this universe or earlier universes. The reason why I like it is that it allows us to conceive of primal energy in terms of matter, whereas your "pure energy" suggests something intangible. In that context one might well ask why "pure energy" should evolve into matter, but matter and movement as our first cause already presents us with an infinity of possible combinations. This, I suppose, might be another way of distinguishing between viewpoints. You see primal energy as "pure" ... a non-material consciousness that proceeds to manipulate energy into matter. The atheist may see primal energy as unconscious matter in perpetual motion, with change as its very essence; eventually its infinity of combinations yields the initial mechanism that has given rise to life and evolution. "Pure" conscious energy would, I agree, entail a teleology, but primal energy as ever-changing, unconscious matter would not. To add one more possibility, however, primal energy as matter might also be conscious (BBella's favourite?). Your motto of FIRST CAUSE FOREVER will therefore apply regardless which of these scenarios you choose ... "pure" energy, unconscious matter, conscious matter. So round we go again...
Epigenetics, revisited
by David Turell , Thursday, September 22, 2011, 23:15 (4811 days ago) @ dhw
(dhw) Your motto of FIRST CAUSE FOREVER will therefore apply regardless which of these scenarios you choose ... "pure" energy, unconscious matter, conscious matter. So round we go again...-We are not going round and round. Since matter and energy are the same in two different forms, first cause is energy. And to get to 'now' that energy had to be teleological. To become teleological by chance (back to Darwin) is beyond my abililty to believe. Remember the zoo of particles is highly ordered and involves symmetry and supersymmetry to make this universe from the Big Bang. Orgcanization of that sort requires planning by an intellect that creates purpose.
First Cause
As we have moved way off the subject of epigenetics, I'm rather belatedly putting our discussion under a different title, in the hope that others might extend it from their own perspectives.-DAVID: We are not going round and round. Since matter and energy are the same in two different forms, first cause is energy. And to get to 'now' that energy had to be teleological. To become teleological by chance (back to Darwin) is beyond my abililty to believe. Remember the zoo of particles is highly ordered and involves symmetry and supersymmetry to make this universe from the Big Bang. Organization of that sort requires planning by an intellect that creates purpose.-Since I have no explanation as to how we got here, there is no way that I am going to reject this argument. If the universe is designed, then obviously there is a God. However, to state that we and our universe are the result of purposeful planning is not to make it so. An atheist would reject the claim that "to get to 'now' that energy had to be teleological". He/she would also reject the claim that evolution is teleological. And he/she would (I presume) argue that the First Cause is mindless energy producing an infinity and eternity of random combinations, one of which eventually leads to 'now'. I am as dissatisfied with this explanation as I am with your own, but I cannot reject it. We do not and cannot know whether our universe is the result of purpose or chance. Even though the zoo of particles is highly ordered, and I too find it impossible to believe that the wonders of Nature, including our own astonishing intelligence, are the product of chance, I find it just as impossible to accept the logic of there being an infinitely more astonishing intelligence than ours which was not designed. In other words, if "organization of that sort requires planning by an intellect that creates purpose", one can scarcely argue that an organizing intellect of that sort that creates purpose does not require planning. It would be like saying that a computer must have been designed by a human brain, but the human brain can't have been designed ... a combination of ideas which you and I cannot swallow (although an atheist can). I'm afraid the magic formula "First Cause" doesn't make it any the more logical. And so, stuck between two exitless labyrinths, I remain on my picket fence.
First Cause
by David Turell , Saturday, September 24, 2011, 06:58 (4810 days ago) @ dhw
I'm afraid the magic formula "First Cause" doesn't make it any the more logical. And so, stuck between two exitless labyrinths, I remain on my picket fence.-But it does.Do you believe everything has a cause? In your experience have you ever seen a phenomenon or experienced one without a cause? Be definition there must be an uncaused first cause. There must be something to start off the progression of causes to us. Pure Aristotle.
First Cause
Dhw: I'm afraid the magic formula "First Cause" doesn't make it any the more logical. And so, stuck between two exitless labyrinths, I remain on my picket fence.-DAVID: But it does. Do you believe everything has a cause? In your experience have you ever seen a phenomenon or experienced one without a cause? By definition there must be an uncaused first cause. There must be something to start off the progression of causes to us. Pure Aristotle.-Round and round...If everything has a cause, by definition of what must there be an uncaused first cause? But I'm not objecting to the concept. I think it was Thomas Aquinas who took over the "first cause" argument to prove the existence of his version of God, and the term has been stuck with this connotation ever since ... much as "intelligent design" has been contaminated by the Creationists. In both cases, more's the pity. I'm merely pointing out that for you the uncaused first cause is conscious energy (a UI), and for an atheist it's "mindless energy producing an infinity and eternity of random combinations, one of which eventually leads to 'now'" (my post of 23 Sept. at 19.04). (I wish an atheist would confirm or correct this, as I'm reluctant to be their spokesman.) In my view, both "first causes" are equally inexplicable, inconceivable and unbelievable. One of them must be right, which shows how pathetic my judgement is, but ... again in my view ... we shall never know which one.
First Cause
by David Turell , Sunday, September 25, 2011, 06:25 (4809 days ago) @ dhw
> DAVID: But it does. Do you believe everything has a cause? In your experience have you ever seen a phenomenon or experienced one without a cause? -> In my view, both "first causes" are equally inexplicable, inconceivable and unbelievable. One of them must be right, which shows how pathetic my judgement is, but ... again in my view ... we shall never know which one.-OK, 'one of the first causes must be right'. Thank you for accepting 'first cause'. You are not pathetic. Since you cannot seem to accept chance by your previous statements, by a preponderance of what you find acceptable, you come down on the side of a first cause with direction and purpose. Will you or I ever be positively sure? No, but no one ever can be. That is our fate. So on your picket fence, as you teeter back and forth, the majority of your tipsy movements will be a majority on my side of the fence.
Epigenetics, revisited
by David Turell , Tuesday, September 20, 2011, 14:57 (4813 days ago) @ dhw
Another example of rapid evolution in insects with a caste system, ants and honey bees:-http://www.physorg.com/news/2011-09-diversity-fast-evolving-genes-developmental-differences.html-The exact genetic mechanism is not described.
Epigenetics, revisited
by David Turell , Tuesday, September 20, 2011, 18:20 (4813 days ago) @ David Turell
In this study plant miRNA (micoRNA, 22 bases long) is found in mamallian blood!:- http://the-scientist.com/2011/09/20/plant-rnas-found-in-mammals/-This has to be put in epigenetics, by definition, but this makes the genetics of life even more complex.