Saturday, March 05, 2011

A Creationist Objects


I get lots of email from theists and creationists. They remind me that the controversies over religion and evolution are complicated. Here's a recent letter that illustrates the problem. It's from a creationist who struggles to incorporate his understanding of evolution into a worldview that just can't accommodate it. The results are .... interesting.

I really don't know to respond to this letter.1 Where does one begin when trying to correct such a profound misunderstanding of science?
I love your new definition of evolution as "a change in the frequency of alleles in a population over time." What happened to spontaneous and random mutations? Epigenetics blew that out of the water. I find it amusing every time I hear some evolutionists claim evolution is fact and the evidence is "overwhelming." Evolutionists have given up on fruitless attempts to prove the impossible and have implemented a new strategy of just claiming evolution has been proved by mountains of evidence.

Epigenetics proves adaptation and nothing else. It controls gene expression driven by environmental stress. It, nor any of the other theories of evolution provide for mechanisms to increase information in genomes. Hence evolutionists are confined to wild extrapolation of adaptation to prove macro evolution. Why hasn't it occurred in experiments? 50,000 generations of bacteria and still no macro evolution nor even proof of a simple DNA change much less added information in the genome. Guess why? You can't get there from here. Evolutionists look like idiots trying to make a plausible explanation why provisions for adaptation reside in what they call "Junk DNA" for millions of years before the organism is exposed to environmental changes that calls upon for them to survive.

The next time you consider calling someone an idiot you might consider there are some reading your posts that are not impressed by your insane unfounded conclusions. Allele frequencies are not going to hide the obvious shortcomings of evolution theory. Proving allele frequencies change proves epigenetics and adaptation and nothing else unless you are an idiot.

Don Berry

I have the sense of the common cow who knows how to eat the grass and spit out the cockle burrs.


1. I do not publish email messages without first obtaining permission from the author.

239 comments :

  1. Don, you are an idiot and I am not impressed by your insane unfounded conclusions.

    Just for fun, can you explain what adaptation may be?

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  2. It is a hopeless task to attempt to respond to the inanities of creationists if the purpose of such responses is to show them the error of their ways. Anyone who thinks otherwise should read the post about Hugh Ross, which has now migrated to the third page and which has elicited, at this point in time, some 128 comments. Most of them are comments by a Mr. Denny, obviously a fellow traveler of Mr. Don Berry, and the responses to the formers nonsense. As Richard Dawkins once said in an essay about the creationist Kurt Wise, there is no evidence, no matter how extensive or overwhelming that will convince creationists that their notions are seriously in error.

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  3. You have said:
    "It's from a creationist who struggles to incorporate his understanding of evolution into a worldview that just can't accommodate it."

    I would say that you have misrepresented what Mr Berry is attempting to do. It seems to me that he is showing that "evolution" thinking does not make sense. That it does not explain what we observe.

    I would suggest that there are two ways of thinking about "epigenetics" ("above genetics").One is that the environment draws out certain inherent possibilities.

    The other is that there is some pattern "above" the physical level that the material level conforms to through the process we call "development".

    This pre-existing "pattern" is "epigenetic" (ie. ABOVE THE GENETIC).

    Biology has proven that there is something "above". If that understanding is actually pondered, it leads in the direction of a level of reality that the material level conforms to.
    It is an insight that Plato and many others realized. Science is catching up, but still not accepting the ramifications of what they are observing.

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  4. The hell?!

    What's the supposed link between allele frequencies and epigenetics here?

    No proof of DNA change in Lenski's E. coli, really?

    Lost cause.

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  5. Aside from the invective the writer has little to say. Evolution is a 2 stage process - the variation stage provides raw material, which is new information actually and the selection stage weeds out that which doesn't work well. (I know there is neutral evolution, genetic drift if that is the right term, but certainly selection has a role here).

    I assume the "50000" generation remark must refer to Lenski's experiments at Michigan State. If that is the case, the writer has the facts exactly backwards; Lenski in 50000 generations has evidence of genetic variation, selection and the acquisition of the ability to metabolize citrate, I believe, from the growth medium.

    Actually, the evidence for evolution has been observed since at least ancient Greece and its philosophers. Life is interconnected, sharing many characteristics and yet varying. Now with biochemistry we can see far more detailed similarities from lifeform to lifeform (the HOX genes are among the examples I know of and think are particularly interesting). The evolving theory first formulated by Darwin to explain the fact that life is interconnected and changes over time, has two stages both of which have been observed experimentally repeatedly (Lenski's experiment and the understanding of DNA mutations, recombinations, exchanged, transpositions and so on).

    For those who want to see, the view is inspiring. But there are none so blind as those who will not see.

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  6. I would suggest providing a few simple to understand links that address his difficulties. Explain - VERY briefly - the connections between the links you provide. The rest is up to him. You could spend years arguing/discussing with people like this and waste precious amounts of time. Personally I would not waste my time. My family is full of people who think exactly like this and there is no changing their minds. Maybe he'll spit out some burrs.

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  7. Interesting. I've given up arguing about evolution. What's the point? Rarely will one side convince the other. I'm saving my oxygen - may need it some day.

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  8. That sounds suspiciously like noted evolution forum troll supersport....

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  9. ""a change in the frequency of alleles in a population over time." What happened to spontaneous and random mutations?"

    What? I thought that random mutations change frequency of alleles in populations (like many more things do...)?

    I can't read the rest. My brains try to save themselves by shutting down after this one.

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  10. Perhaps one might aspire to have more sense than a common cow.

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  11. @Don Berry I have the sense of the common cow who knows how to eat the grass and spit out the cockle burrs.

    But the end product is still shit.

    Don, education is the anodyne to ignorance.

    However the world does not owe you one, it's about time you stopped putting your ignorance on an altar and worshipping it as a god.

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  12. This is like shooting fish in the barrel. C'mon people, find something intellectually challenging to debate!

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  13. 'Not even wrong...'

    Aaargh, Eamon beat me to it *shakes fist*. But still, Don lost me halfway through the first paragraph already...

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  14. Faultfinder said,
    To begin, let me say I greatly enjoyed all the comments posted. The one thing that jumps out at me is the almost universal ignorance of epigenetics in this group. Here are my consolidated replies:

    Mr. Haubrich, with respect to genetics, adaptation is the ability of an organism to change itself genetically in order to survive in a stressful environment. That sir, is quite different than current evolution theory which states that genetic change is driven by random and spontaneous gene mutations.

    The definition of random precludes stress having any part in that process.

    Mr Knight got it right. Epigenetics is a new and burgeoning field of science that explains much of what plain genetics and evolution has never explained. Simply put, epigenetics is responsive to environmental stress and controls exact gene expression that renders the organism “fit” to survive in said stress.

    When reading evolutionists attempts to explain why there is existing “junk DNA” which has existed for eons that provides for genetic change to alleviate current stress in an environment when needed, I am reminded of a sign I once saw outside a blacksmith shop, “All kinds of fancy twisting and turning done here.”

    Mr. Ostman, the link between epigenetics and alleles is gene expression.

    Mr. Gary, Lenski’s E Coli did not experience DNA change nor natural selection. They only experienced gene expression change as a result of environmental stress. DNA seldom changes and when it does mostly due to copying errors it is usually corrected by existing mechanisms in the organism. When an error does slip through the process it is usually negative or neutral rather than beneficial. The change we see in Lenski’s experiments and other E Coli experiments is not, therefore, due to random and spontaneous gene mutations, but rather to epigenetics sensing environmental stress and expressing genes in a fashion that renders the organism the ability to survive said stress.

    Dear Gary, we are living in the 21st century not the 20th century. Science is changing. Epigenetics now provides a far more encompassing and factual explanation for variation than random and spontaneous gene mutations coupled with natural selection ever could.
    There is no one so blind as one who holds to outdated theories and refuses to embrace the future.

    Dear Linzel, I just spit out your cockle burr.

    Dear Tuomo, epigenetics changes allele frequencies in a population in response to stress in the environment. Random mutations never did.

    Dear oberski, Your ignorance of epigenetics indicates you need to educate yourself. Try Google.

    Mr. Moran, I think you need to educate your protégés and perhaps yourself as well. Epigenetics changes everything.

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  15. Well it is obvious that this guy thinks he does understand evolution and biology, but it is also obvious that he is recycling what he heard/read from some higher-order creationist quack. He also thinks that by reciting whatever he got (which is nothing) from that higher-oder crap source we would certainly understand what he is talking about. After all, we are "evolutionists" and we know not only what "epigenetics" is, but also that it has blown evolution out of the water showing that there can only be "adaptation."

    But poor lad, little does he know that his comment does not make sense. That his construct shows that he has no idea about epigenetics, nor about what alleles are, nor how these alleles come to be.

    I don't know if I should feel sorry. I imagine Don feeling magnanimous and like such an intellectual sending around such a number of multisyllabic words. That'll teach them!

    You are right Larry. Where to start is the question.

    --

    Hey! Those exam questions! They are excellent! By the way, there is a new book "Evolution the Extended Synthesis " published by MIT Press. They had the great idea of also re-editing "the modern synthesis." So, two questions: 1. Have you read the extended synthesis yet? 2. If so, what's your opinion?

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  16. The first words in the Bible are; God created the heavens and the earth.

    The next part is about re building because something happened to make the earth void.

    Dosen't say how long the first time took. If Christians would read the Bible for what it actually says, there wouldn't be all this argument.

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  17. I have a question, and I will admit I am not a scientist in any shape or form. If evolution was a fact instead of a theory, why isn't there life on Mars or the moon? Evolution according to what I understand doesn't care, it will adjust to environment as needed and evolve into life out of nothing, no matter what the conditions are.

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  18. faultfinder says,

    The one thing that jumps out at me is the almost universal ignorance of epigenetics in this group.

    Yes, there are some people who don't understand epigenetics. Don Berry is one of them and you have just demonstrated that you are another.

    Epigenetics is a new and burgeoning field of science that explains much of what plain genetics and evolution has never explained. Simply put, epigenetics is responsive to environmental stress and controls exact gene expression that renders the organism “fit” to survive in said stress.

    Epigenetics is one of those slippery words that means different things to different people. However, the broadest definition is the heritable control of gene expression by changes that are not directly encoded by the nucleotide sequences in DNA.

    This understanding of regulation of gene expression is something I learned in school in the 1960's. Some of this understanding comes from the work of outstanding scientists such as Jacob and Monod who worked on the lac operon.

    It is not new and it is fully explained by plain genetics and evolution, with a bit of biochemistry thrown in for good measure.

    Dear Gary, we are living in the 21st century not the 20th century. Science is changing. Epigenetics now provides a far more encompassing and factual explanation for variation than random and spontaneous gene mutations coupled with natural selection ever could.

    We've understood the essentials of gene expression for decades and most of us don't think there's any conflict between epigenetics and evolution. Furthermore, we don't think that epigenetics explains any mystery that a proper understanding of evolution couldn't explain.

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  19. Negative Entropy asks,

    1. Have you read the extended synthesis yet? 2. If so, what's your opinion?

    1. Yes.

    2. Mostly self-serving hyperbole with little substance as far as evolutionary theory is concerned.

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  20. Star asks,

    If evolution was a fact instead of a theory, why isn't there life on Mars or the moon? Evolution according to what I understand doesn't care, it will adjust to environment as needed and evolve into life out of nothing, no matter what the conditions are.

    You are mixing up "evolution" and the origin of life. As far as we know life arose only once under conditions that were very special. If those same conditions occurred on other planets then maybe life arose there as well. What we know for certain is that our one example of life couldn't have originated on the moon but life may have arisen on Mars.

    We are absolutely certain that evolution occurs, and has occurred, on this planet. That's why it is a fact.

    ReplyDelete
  21. Faultfinder said;
    Mr. Gary, Lenski’s E Coli did not experience DNA change nor natural selection. They only experienced gene expression change as a result of environmental stress.

    Umm... I think this paper contradicts you assertion.

    et al. & Linsky Nature 461, 1243-1247 (2009)
    http://www.nature.com/nature/journal/v461/n7268/full/nature08480.html

    One key sentences from the abstract "This same population later evolved an elevated mutation rate and accumulated hundreds of additional mutations dominated by a neutral signature."

    ReplyDelete
  22. Well, you explain what epigenetics is not, but it is far from what it is.

    The outstanding characteristic of epigenetics is it is responsive to environmental stress. You left that out. DNA changes do not come about as a response to stress. You left that out also. Inheritable? Definitely, but usually only as long as the stress remains. Remove the subject organisms from the environmental stress and the gene expression reverts to the wild type. You left that out also. Are epigenetic changes a result of copying errors? No. You left that out also. It seems to me that you left out enough to fill a book. Are you quite sure you are capable of chiding me about what you think I don’t know?

    In the 1960’s the DNA responsible for epigenetic gene expressions was still called “junk DNA.” Even Darwin alluded to environmental influenced variation. Does that mean he also knew about epigenetics?

    Epigenetics is in no way explained by plain genetics and evolution no matter what you throw in. Randomness was part and parcel of plain genetics and evolution before epigenetics appeared. Randomness is completely foreign to epigenetics.

    So “we” are wrong. Please state how a proper understanding of evolution explains environmental stress related gene expressions. Are you so slow you cannot see the difference between random gene mutations and environmental stress driven gene expressions?

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  23. I've recently heard a former creationist/anti-evolutionist say (can't remember where, for the life of me), that, in his experience, there wasn't any real rejection of evolution, but rather a failure to let go of the Bible. Once that happens, they allow themselves to finally see the logic of evolutionary theory. Not sure how one does that, though. Everyone holds on to a different cherished story/feeling that religion has given them.

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  24. ... and the "work horse" of epigenetic signaling? A plain old boring set of genes. Evolving under all of the classic pop-gen rules.

    Epigenetics is an interesting phenotype. Not a game changer.

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  25. faultfinder writes: Are you so slow you cannot see the difference between random gene mutations and environmental stress driven gene expressions?

    What Dr. Moran tried (rather gently, I thought) to tell you is the science of evolution has had an exacting, detailed, and evidence-based understanding of random mutations, the role of the environment, the role of epigenetics in gene expression, the differences between them, and the commonalities among them, for decades; and that this understanding is far deeper than the late-night-drunken-dormroom-bs-session level of what you are posting. What you don't understand about evolution, mutation, epigenetics and environmental stress would fill volumes - in fact, has filled volumes, which you ought to read before thinking yourself capable of engaging in reasoned discussion of these subjects.

    (I suppose people through history have always debated from ignorance, but am I alone in thinking there is a new pride unto arrogance in the tone of ignorant debaters these days?)

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  26. The other Jim said:

    "Epigenetics is an interesting phenotype. Not a game changer."

    Yeah, that's what they said about genetics.

    ReplyDelete
  27. thishollowearth said:

    "I've recently heard a former creationist/anti-evolutionist say (can't remember where, for the life of me), that, in his experience, there wasn't any real rejection of evolution, but rather a failure to let go of the Bible. Once that happens, they allow themselves to finally see the logic of evolutionary theory."

    I am a former atheist. Once I saw the absurdity of evolution theory I was forced to seek other theories that explained change. Having found none in science, I turned to the Bible. Makes sense to me.

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  28. There exists an extensive population genetics literature on the genetics and evolution of phenotypic plasticity, one of the other terms used for 'epigenetic' phenomena.

    As to adaptation is the ability of an organism to change itself genetically in order to survive in a stressful environment: (1)if methylation patterns are meant, it is not persistent over generations; (2) if anything else than methylation patterns are meant, I would like to hear of an example; (3) adaptation is not restricted to stressful environments.

    What makes 'epigenetics' such a marker for crank views?

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  29. Re Haleen

    What makes 'epigenetics' such a marker for crank views?

    Biologists shouldn't feel too bad. Quantum mechanics is an even bigger marker for cranks (Deepak Chopra anyone).

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  30. This is a fascinating discussion.
    I have a question.
    It has been said that:
    "... and the "work horse" of epigenetic signaling? A plain old boring set of genes. Evolving under all of the classic pop-gen rules."

    I have a question about this "plain old boring set of genes".
    Were they themselves subject to epigenetic signaling? Or to put the question differently: how did the "plain old boring set of genes" come to be?

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  31. I am a former atheist. Once I saw the absurdity of evolution theory I was forced to seek other theories that explained change. Having found none in science, I turned to the Bible. Makes sense to me.

    Alternative faultfinder:

    I am a former atheist. Once I saw the absurdity of automotive engineering theory I was forced to seek other theories that explained how cars work. Having found none in science, I turned to the Bible. Makes sense to me.

    Two equally (il)logical and (in)valid statements. The Bible has as much that is factual and pertinent to say about evolution theory as it does about automotive engineering. And I daresay you know less about evolution than you do about cars (as you continue to demonstrate here). Indeed, you cannot have seen the absurdity of evolutionary theory any more than you could claim to understand the absurdity of automotive engineering, not understanding either.

    Yet I'm positive you'd be far less likely to insult your mechanic - calling him "slow," for example - or substitute your judgment for his than you evidently are willing to do with conscientious scientists who've spent decades on research and writing that you quite clearly do not begin to understand.

    When I'm confronted with something in nature I don't understand, and there's someone who's willing and eager to make it accessible to me, I cannot wait to take advantage of the opportunity to learn. It just amazes me that so many people not only fail to take advantage of such wonderful opportunities, but volubly insult those who so generously offer them.

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  32. I have a very basic question concerning the following:

    http://en.wikipedia.org/wiki/Epigenetics
    "
    More typically, the term [epigenetic code]is used in reference to systematic efforts to measure specific, relevant forms of epigenetic information such as the histone code or DNA methylation patterns."

    My question is - what creates the
    histone code or DNA methylation patterns?

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  33. Larry,

    I like the way you oftentimes handle these creationist questions by rather than trying to educate them in basic biology and then refute the arguments that have already been made a million times and that also have been refuted a million times and whose refutations can also be found on the internet extremely easily, you put the claims into a broader perspective like you did here with the first post by faultfinder.

    This does not only stop the discussions from clogging up with the same boring old stuff but also helps to dispel these myths that creationists like to create, like that biologist are so extremely surprised by the complexity or that something was just recently discovered. I appreciate that.

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  34. jud said:

    "When I'm confronted with something in nature I don't understand, and there's someone who's willing and eager to make it accessible to me, I cannot wait to take advantage of the opportunity to learn. It just amazes me that so many people not only fail to take advantage of such wonderful opportunities, but volubly insult those who so generously offer them."

    I have learned a great deal from evolutionists on debate forums. All I have received here is insults from pompous self styled experts who know less than I. That includes you.

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  35. anonymous said:

    "My question is - what creates the
    histone code or DNA methylation patterns?"

    Science has yet to discover either. There is a great deal of research going on in this area at the present. Regardless of the misinformation on this blog, epigenetics is a very new science. Only in the last five years has it become obvious that something was driving genetic change other than random mutations and natural selection. That was obvious because the time required for randomness was far too great to account for change in E Coli populations. In fact it is mathematically impossible given the time frames involved.

    What mechanisms account for specific gene expression driven by stress are still a mystery. I am not referring to histone code or methylation, but the mechanisms that can select a preexisting gene and contol it. I have no doubt those mechanisms will be found however, and when that happens targeted gene expressions will revolutionize medicine.

    I might add that the existence of preexisting non coding genes in what was formally called "junk DNA" is a mystery as well. Is there a mechanism in DNA that can fortell what stress will occur and provide a fix for it?

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  36. anonymous said:

    "This does not only stop the discussions from clogging up with the same boring old stuff but also helps to dispel these myths that creationists like to create, like that biologist are so extremely surprised by the complexity or that something was just recently discovered. I appreciate that."

    Please post a reference to epigenetics being responsible for gene expression driven by environmental stress published more than 20 years ago. I believe that is the least time "decades" can account for. Anything else you have to say on the matter is just inane blather.

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  37. There is no evidence, no matter how extensive or overwhelming that will convince evolutionists that their notions are seriously in error.

    Dr. Lee Spetner in his book, "Not by Chance" totally destroyed several of Dawkin's arguments. He showed mathematically that random mutations and natural selection could never take over a population of anything.

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  38. heleen said:

    "As to adaptation is the ability of an organism to change itself genetically in order to survive in a stressful environment: (1)if methylation patterns are meant, it is not persistent over generations;"

    Several experiments have shown genetic changes driven by environmental stress have persisted for a few generations even when the subjects were removed from the stressful environment. There is one experiment with fruit flies, however, that documented the epigenetic changes to persist for more than 200 generations after the flies were removed from the stressful environment. The researchers concluded this was evidence that the changes were permanent.

    The people on this blog are way behind the curve. You guys need to get out and google epigenetics and stress. I have a google alert that informs me of epigenetic news. I get an alert almost every day.

    Maybe I should post some news from this "decades" old science.

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  39. Epigenetics news:

    Epizyme is developing a new class of targeted therapeutics for the treatment of genetically-defined cancer patients based on breakthroughs in the field of epigenetics, according to Jason Rhodes, EVP and CBO, Epizyme.
    http://bostonrealestate.citybizlist.com/7/2011/3/6/Epizyme-Inc.-Signs-New-Headquarters-Lease-In-Cambridge-Mass.aspx

    “Your mother always told you to eat your vegetables, and she was right,” says co-author Trygve Tollefsbol, Ph.D., D.O., a biology professor in the UAB College of Arts and Sciences. “But now we better understand why she was right — compounds in many of these foods suppress gene aberrations that over time cause fatal diseases.”
    Epigenetics is the study of the changes in human gene expressions with time, changes that can cause cancer and Alzheimer’s, among other diseases. In recent years, epigenetics research worldwide, including numerous studies conducted at UAB, have identified specific food compounds that inhibit negative epigenetic effects.
    http://www.healthcanal.com/cancers/15047-UAB-biologists-show-how-veggies-work-cancer-fighting-diet.html

    Q. You work in a field called epigenetics, which is the study of traits that are inherited based on non-DNA information?
    A. That’s right. As it turns out, we inherit a lot of information beyond DNA sequence. Within one generation, epigenetic information plays a role in a number of diseases such as cancer, but in the context of our work, epigenetics also provides a way to transfer information between generations — it provides a plausible way for parents to tell their kids stuff.
    http://www.boston.com/lifestyle/health/articles/2011/03/07/dr_oliver_j_rando_discusses_his_work_in_the_field_of_epigenetics/

    Please don't bore me with comments pooh poohing all this as something you bright lads already knew.

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  40. @FaultFinder

    I'm afraid you are being swept up into the self-hyping tide of epigenetics (leaving aside the "and using it to convince yourself of a god" part). Epigenetic marks are regulated by enzymes. Knock out the genes for those enzymes and epigenetic signals ceases to exist. They are merely the phenotype of these enzymes. They do have interesting roles in the cell, but in the end, the do not exist without the genes.

    Are there living things that lack epigenetic marks? Very likely, actually[1]. Are there living organisms that lack genes within DNA[2]? At the moment, genetics looks more fundamental. I doubt this will change.

    Your previous discussions in this thread are the reasons for people being dismissive of you as a crank. Early on, you asserted that Lenski's E.coli did not mutate. I provided the reference that showed you were incorrect. Yet you just continue ranting. It seems to us that there is a severe hole in you knowledge on the subject, so yes, it is hard to take you seriously.

    If you want to have a serious discussion, lets do it. Just leave out the misinformation and pompus attitude.

    [1] It seems some authors are reluctant to allow the term epigenetics to be used on any non-genetic modification in bacterial systems.
    [2] Apologies to the viroligists for not saying "or RNA" ;-)

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  41. @ Anonymous Monday, March 07, 2011 12:37:00 PM

    Were they themselves subject to epigenetic signaling? Or to put the question differently: how did the "plain old boring set of genes" come to be?

    If you are asking if the 1st epigenetic enzyme was under epigenetic control, of course not. New genes, though rare, occur more often than a lay person would imagine. And they can quickly become indispensable (http://www.sciencemag.org/content/330/6011/1682.full).

    Anonymous @
    Monday, March 07, 2011 3:53:00 PM

    My question is - what creates the histone code or DNA methylation patterns?

    If this is a serious question, please clarify. This all sounds a bit too much like the tired old "if there is a code, there must be a code maker" logical fallacy.

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  42. @ faultfinder

    The problem is that I don't see your point. I don't know what you want to demonstrate. Maybe it would help if you first state you hypothesis that you want to demonstrate in one short sentence like you would do in mathematics. E.g.: the sum of angles in a triangle is 180°.

    As an aside: The ultimate goal of the ToE is not to account for adaptation. It just turns out that considering the evidence the ToE accounts for most of the adaptation we see.

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  43. faultfinder writes:

    I have learned a great deal from evolutionists on debate forums.

    Such as? We've seen no evidence of it.

    All I have received here is insults from pompous self styled experts who know less than I. That includes you.

    - I don't style myself an expert. I'm someone who has a lot to learn and is willing and eager to do so.

    - Odd that someone who refers to a professor who's written one of the leading biochemistry texts as "slow" would complain about being insulted.

    - As for any insults coming from me, please do show me where I indulged in any offensive personal comments along the lines of your "slow" remark. What I have said repeatedly is that you are demonstrating by your comments that you do not understand evolution, which is a plain statement of fact.

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  44. The other Jim said:

    "They do have interesting roles in the cell, but in the end, the do not exist without the genes."

    Who said they did? My comments have been relegated to "gene expression." That's rather difficult to do without genes. This is a rather rudimentary effort to trivialize epigenetics which is the most exciting thing going on in genetics.

    "Early on, you asserted that Lenski's E.coli did not mutate."

    What I was attempting to say was the DNA of the bacteria did not change. Epigenetics does not change the underlying DNA of an organism only the expressions of the genes.

    I find it deceitful of researchers to refer to changes in E Coli in experiments as proof of evolution without mentioning the fact that the DNA of the E Coli did not change. This leaves the uninitiated to assume the changes came by the normal mechanisms of evolution which is random changes in the DNA usually through copying errors and natural selection. That did not happen in Lenski's experiment. If it did it would have been monumental. The fact is science has never proven this mechanism for evolution. Zero experiments show this to have happened. Guess why? Because it is mathematically impossible.

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  45. Anonymous said:

    “The problem is that I don't see your point. I don't know what you want to demonstrate. Maybe it would help if you first state you hypothesis that you want to demonstrate in one short sentence like you would do in mathematics. E.g.: the sum of angles in a triangle is 180°.”

    It isn’t that simple. I have two premises to prove.
    1. TOE of random and spontaneous gene mutations coupled with natural selection does not work. When I speak of gene mutations I mean changes in DNA not gene expression.
    2. Epigenetics far better accounts for what we see in experiments that demonstrate change in the subjects. When I speak of epigenetics I speak of it in the context of environmental stress driven gene expressions. That does not change the DNA nor is it random. It does not require natural selection. It does not deal with evolution per se, but only with adaptation.

    “As an aside: The ultimate goal of the ToE is not to account for adaptation. It just turns out that considering the evidence the ToE accounts for most of the adaptation we see.”

    I can not imagine a more incorrect assumption. TOE accounts for no adaptation. Epigenetics accounts for adaptation. TOE accounts for DNA changes only. Those are permanent unless changed by another random mutation of DNA. Most of all, if not all of epigenetic changes last only while the causing stress is present. Usually shortly after the stress is removed the gene expression modifications revert back to the wild type. I know of only one experiment concerning fruit flies where the gene expression modifications continued for 200 generations after the causing stress was removed.

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  46. Whether or not I am a creationist has nothing to do with the science of epigenetics or TOE. All comments of me being a creationists are therefore superflous to the arguments at hand and denote an attempt to denigrate only. It is a common debating principle that if you cannot refute the argument attack the one who makes it.

    Mr. Moran attempted to do just that by attacking Cornelius Hunter's credentials.

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  47. Jud said:

    faultfinder writes:

    I have learned a great deal from evolutionists on debate forums.

    Such as? We've seen no evidence of it.

    All I have received here is insults from pompous self styled experts who know less than I. That includes you.

    - I don't style myself an expert. I'm someone who has a lot to learn and is willing and eager to do so.

    - Odd that someone who refers to a professor who's written one of the leading biochemistry texts as "slow" would complain about being insulted.

    - As for any insults coming from me, please do show me where I indulged in any offensive personal comments along the lines of your "slow" remark. What I have said repeatedly is that you are demonstrating by your comments that you do not understand evolution, which is a plain statement of fact.

    Facts exist only in the eye of the beholder. You have posted virtually nothing with respect to epigenetics. I suspect your continuous resorting to personal attacks is an attempt to mask your lack of expertise. “Such as? We’ve seen no evidence of it.” is a case in point. If you cannot mount a lucid argument then I will ignore your facts and posts.

    ReplyDelete
  48. There is one experiment with fruit flies, however, that documented the epigenetic changes to persist for more than 200 generations after the flies were removed from the stressful environment.

    If you do not provide a reference, such an assertion is nil and void.

    ReplyDelete
  49. faultfinder writes & quotes,

    Epigenetics is the study of the changes in human gene expressions with time, changes that can cause cancer and Alzheimer’s, among other diseases. In recent years, epigenetics research worldwide, including numerous studies conducted at UAB, have identified specific food compounds that inhibit negative epigenetic effects.

    Q. You work in a field called epigenetics, which is the study of traits that are inherited based on non-DNA information?
    A. That’s right. As it turns out, we inherit a lot of information beyond DNA sequence. Within one generation, epigenetic information plays a role in a number of diseases such as cancer, but in the context of our work, epigenetics also provides a way to transfer information between generations — it provides a plausible way for parents to tell their kids stuff.


    faultfinder, I'm will to make an attempt to answer your question and help you learn some biology but first I have to understand where you are going wrong.

    Is this the definition of epigenetics you are using: "the study of traits that are inherited based on non-DNA information"?

    That's certainly the common definition. It will be trivially easy to show you that we've known about "traits that are inherited based on non-DNA information" for over four decades. We've known about methylation for over three decades. We've known about DNA rearrangements for over three decades. We've understood histone modifications for more than 25 years.

    Is there some new aspect of epigenetics that I don't know about because it's just been discovered?

    ReplyDelete
  50. @Faultfinder
    Sunday, March 06, 2011 4:09:00 PM
    environmental stress driven gene expressions?
    Monday, March 07, 2011 7:42:00 PM
    Please post a reference to epigenetics being responsible for gene expression driven by environmental stress published more than 20 years ago

    Title: REGULATION OF GENE-EXPRESSION IN ENDOTHELIAL-CELLS EXPOSED TO SHEAR-STRESS - IMPLICATIONS FOR THROMBOSIS, ATHEROSCLEROSIS, AND INTIMAL HYPERPLASIA
    Author(s): MCINTIRE LV, DIAMOND SL, SHAREFKIN JD, et al.
    Source: ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY Volume: 200 Pages: 173-BIOT Part: Part 1 Published: AUG 26 1990

    Title: DIVERSE FORMS OF STRESS LEAD TO NEW PATTERNS OF GENE-EXPRESSION THROUGH A COMMON AND ESSENTIAL METABOLIC PATHWAY
    Author(s): HAMMOND GL, LAI YK, MARKERT CL
    Source: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA-BIOLOGICAL SCIENCES Volume: 79 Issue: 11 Pages: 3485-3488 Published: 1982


    Good enough? Just the first and the last of the list brought up by a search.

    I recommend, from the originator of the term epigenetics:
    Title: EPIGENETICS AND EVOLUTION
    Author(s): WADDINGTON CH
    Source: SYMPOSIA OF THE SOCIETY FOR EXPERIMENTAL BIOLOGY Volume: 7 Pages: 186-199 Published: 1953

    ReplyDelete
  51. faultfinder says,

    It isn’t that simple. I have two premises to prove.
    1. TOE of random and spontaneous gene mutations coupled with natural selection does not work.


    There is so much evidence in support of natural selection that it boggles the mind to see you write something like that.

    If you mean to say that natural selection is not SUFFICIENT to explain all of evolution then that's correct. Most of us know that already. It's why there's so much discussion about random genetic drift. Have you heard of random genetic drift?

    When I speak of gene mutations I mean changes in DNA not gene expression.
    2. Epigenetics far better accounts for what we see in experiments that demonstrate change in the subjects. When I speak of epigenetics I speak of it in the context of environmental stress driven gene expressions.


    This is a different definition than the one you quoted above. Do you now insist that the only valid definition of epigenetics is one that includes environmental stress as a trigger?

    If so, what do you mean by environmental stress? How about a situation where a common food source, such as lactose, is unavailable? Is that stressful?

    ReplyDelete
  52. faultfinder says,

    If you cannot mount a lucid argument then I will ignore your facts and posts.

    That sounds like a good plan for me as well.

    Waiting for a lucid argument from faultfinder ....

    ....

    ....


    ReplyDelete
  53. @faultfinder
    Monday, March 07, 2011 7:58:00 PM...

    There is one experiment with fruit flies, however, that documented the epigenetic changes to persist for more than 200 generations after the flies were removed from the stressful environment. The researchers concluded this was evidence that the changes were permanent.

    http://www.sciencedaily.com/releases/2011/01/110124151713.htm
    “ .. the genome of flies exposed to long-term hypoxia are changed to permanently affect gene expression.”
    “ .. the scientists studied populations of Drosophila melanogaster generated through long-term laboratory selection over 200 generations. These flies are capable of tolerating severe, normally fatal hypoxia, and pass their hypoxia tolerance trait to subsequent generations -- the trait persisting even in the absence of hypoxic stress, which suggests a genetic rather than a physiological mechanism is at play in adaption.”

    Did Faultfinder refer to this? I got this from Google asking for
    fruit flies epigenetic changes persist 200 generations stressful environment

    ReplyDelete
  54. You have posted virtually nothing with respect to epigenetics.

    Your wish is my command.

    Book length, and written for the layperson: Endless Forms Most Beautiful by Sean B. Carroll. Whole chapters devoted to how the regulation of genetic expression (i.e., epigenetics) and mutations in the genetic code have worked together to drive evolutionary development over many hundreds of millions of years.

    And yes, environmental factors are in there too, along with a brief but very good explanation of the mathematics of population genetics. This should help you understand why evolution is not an absurdity, but a process for which aspects of its mechanics have been worked out with literally mathematical precision.

    Published in 2005 and winner of many awards as one of the top science books of the year.

    ReplyDelete
  55. @faultfinder "Early on, you asserted that Lenski's E.coli did not mutate."

    What I was attempting to say was the DNA of the bacteria did not change.


    I read the Lenski paper, "Genome evolution and adaptation in a long-term experiment with Escherichia coli" and in it it is stated:

    ... we sequenced the genomes of E. coli clones sampled at generations 2,000, 5,000, 10,000, 15,000, 20,000 and 40,000 ... and The 45 mutations in the 20K clone include 29 single-nucleotide polymorphisms (SNPs) and 16 deletions, insertions and other polymorphisms (DIPs).

    At generation 20K the bacteria already exhibit 45 mutations.

    In what sense did the DNA of the bacteria not change ?

    ReplyDelete
  56. faultfinder posted:
    "... researchers refer to changes in E Coli in experiments as proof of evolution without mentioning the fact that the DNA of the E Coli did not change. This leaves the uninitiated to assume the changes came by the normal mechanisms of evolution which is random changes in the DNA usually through copying errors and natural selection. That did not happen in Lenski's experiment."

    Is that correct?

    ReplyDelete
  57. If I had a penny for every mistake in every sentence in that email, I would be so rich that I would be easily able to fund the activities of the DIscovery Institute.

    ReplyDelete
  58. It seems to me that we could understand the changes that occur as follows:
    In the face of the environment the organism responds with an epigentic change. This continues to the following generations, while the environment persists.
    If the environment then changes back in a relatively short period of time the epigentic change disappears.
    However if the environment remains that new way for an extended time the DNA is itself changed.

    I must not be the first person to think of this.
    Is there literature on this idea that I am expressing?

    ReplyDelete
  59. If the environment then changes back in a relatively short period of time the epigentic change disappears. However if the environment remains that new way for an extended time the DNA is itself changed.

    I must not be the first person to think of this. Is there literature on this idea that I am expressing?

    Very likely in something Lysenko wrote, but then it wouldn't be scientific literature. :-)

    ReplyDelete
  60. @Anonymous Tuesday, March 08, 2011 1:25:00 PM

    It seems to me that we could understand the changes that occur as follows
    What changes are referred to? Epigenetics has too many meanings to be very useful as a term.

    In the face of the environment the organism responds with an epigenetic change. This continues to the following generations, while the environment persists.
    If the environment then changes back in a relatively short period of time the epigenetic change disappears.
    However if the environment remains that new way for an extended time the DNA is itself changed.

    How do you suppose that change in DNA to happen: due to selection on genetic variation in the epigenetic change mechanism? That would work. But just extended time and epigenetics would not work.
    I must not be the first person to think of this.
    Is there literature on this idea that I am expressing?

    There is, both in the clear headed and fuzzy thinking variety. That is why it is necessary to specify the particular system that is the example.

    Could all Anonymous put in a counter at the end of their posts? Is it one Anonymous here or several people?

    ReplyDelete
  61. Larry Moran said that evolution is a fact, but it is a "fact and theory".
    I am sure most of you know that many things science discovered were mentioned in the Bible long before. Some like to scoff that the Bible says the world is flat, it says that God hangs the world on nothing,and that there are other worlds. You may not agree, but I have always thought that science is the study of God. You are just slowly understanding what
    He did.

    ReplyDelete
  62. Larry Moran said:

    "Is this the definition of epigenetics you are using: "the study of traits that are inherited based on non-DNA information"?"

    This definition, I think, is a little too vague. Here is a definition from SciencDaily:

    Definition Of 'Epigenetics' Clarified
    ScienceDaily (Apr. 1, 2009) — Ali Shilatifard, Ph.D., Investigator, has joined with a team of colleagues to propose an operational definition of “Epigenetics” — a rapidly growing research field that investigates heritable alterations in gene expression caused by mechanisms other than changes in DNA sequence.

    Even this definition leaves out what I consider to be the most importan aspect of epigenetic changes which is they are environmentally driven. They are not random nor spontaneous.

    A wonderful example is the Tibetans who were forced to relocate to a higher altitude oxygen poor environment. They developed larger lungs which were then inherited.

    I think some of the misunderstanding on this blog is due my referencing DNA changes rather than DNA sequencing changes. Epigenetic changes do not affect DNA sequencing. It has been my understanding that random and spontaneous mutations that are the basis for TOE have to do with DNA sequencing changes. Is this true? Can a change in gene expression be referred to as a DNA change? (not DNA sequencing)

    I appreciate your willingness to help. I have been on a dilligent cramming regimen for some time now. I admit I have a great deal to learn.

    ReplyDelete
  63. Larry Moran said:

    "There is so much evidence in support of natural selection that it boggles the mind to see you write something like that."

    Natural selection is determined by reverse engineering. If an organism became larger it is hypothesized there was an abundance of food. If the organism became smaller, it is hypothesized there was a scarcity of food. Everyone has 20/20 hind sight.

    The same arguments could be applied to environmental stress induced changes sans selection.

    Moran: "If you mean to say that natural selection is not SUFFICIENT to explain all of evolution then that's correct. Most of us know that already. It's why there's so much discussion about random genetic drift. Have you heard of random genetic drift?"

    I have read a little on genetic drift but am in no way fluent to discuss it. With respect to micro evolution, I think epigenetics explains it far better than random gene mutations and natural selection.

    When I speak of gene mutations I mean changes in DNA not gene expression.
    2. Epigenetics far better accounts for what we see in experiments that demonstrate change in the subjects. When I speak of epigenetics I speak of it in the context of environmental stress driven gene expressions.

    Moran: "This is a different definition than the one you quoted above. Do you now insist that the only valid definition of epigenetics is one that includes environmental stress as a trigger?"

    Everything I have read concerning epigenetics has to do with environmental stress. Perhaps that is the most exciting aspect of epigenetics and hence obscures other mechanisms from being involved. Random mutations fail to account for rapid change in organisms as it takes huge amounts of time. (generations)

    Moran: "If so, what do you mean by environmental stress? How about a situation where a common food source, such as lactose, is unavailable? Is that stressful?"

    Definitely. Lenski's 50,000 generation E Coli experiment were the bacteria developed the ability to transport citrate across the cell membrane is a case in point. He speaks of the E Coli becoming more robust, larger, and plentiful but does not mention anything about increasing their food supply. Could it be that the lack of food was the stress that brought about this new found capability? It makes more sense than random and spontaneous gene mutations.

    ReplyDelete
  64. heleen said:

    "Did Faultfinder refer to this? I got this from Google asking for
    fruit flies epigenetic changes persist 200 generations stressful environment"

    http://www.sciencedaily.com/releases/2011/01/110124151713.htm

    This is the study to which I was referring. It is the only thing I have found indicating a permanent DNA change resulting from epigenetics.

    ReplyDelete
  65. @faultfinder As someone [hopefully] about to embark on studying 'hardcore' (non-genomic) epigenetics, I have the following thorough analysis I'm willing to type up for you:

    You are wrong. And utterly clueless.


    ---
    Seriously though, it's the people who overhype and abuse epigenetics who ruin it for the rest of us, pushing mainstream [often also adaptationist] evolutionary biologists to shove epigenetics under the carpet as unimportant. Or downright hate it, eg. Coyne. It does not invalidate evolutionary theory, but it does add some interesting new angles to it, and it's quite amazing how many basic principles from genetic evolution may carry over quite nicely to epigenetics. The medium may be different, but evolutionary principles often remain the same. The faux 'revolutionaries' fuck it up for the saner among us. Fuck them for giving the field a bad name and making the funding situation even shittier.

    ReplyDelete
  66. I am hoping someone can respond to this:

    It seems to me that we could understand the changes that occur as follows:

    In the face of the environment the organism responds with an epigenetic change.
    While that environment persists this epigenetic change continues into the following generations.
    If the environment changes back within a relatively short period of time, the epigenetic change disappears.
    However if the environment remains for an extended time, the DNA is itself is changed.

    I must not be the first person to think of this.
    Is there literature on this idea that I am expressing?

    ReplyDelete
  67. anonymous said:

    "In the face of the environment the organism responds with an epigenetic change.
    While that environment persists this epigenetic change continues into the following generations.
    If the environment changes back within a relatively short period of time, the epigenetic change disappears.
    However if the environment remains for an extended time, the DNA is itself is changed."

    You got it all right except "if the environment remains for an extended time, the DNA is itself changed." The very definition of epigenetics states it governs change in gene expressions without changing the underlying DNA sequence.

    There is one instance were the epigenetic change persisted for 200 generations of fruit flies. Some interpret this to mean it became a permanent change. If it did become permanent it still did not change the underlying DNA sequence else the definition of epigenetics would have to be changed.

    ReplyDelete
  68. This article has been referred to:
    http://www.sciencedaily.com/releases/2011/01/110124151713.htm
    "We confirmed that change in the DNA, and not just a change in gene expression, results from long-term hypoxia exposure."

    It seems to be consistent with the idea that I have expressed.
    I do not know the mechanism but it seems others do not know it yet either.

    ReplyDelete
  69. Psi Wavefunction said:

    "Seriously though, it's the people who overhype and abuse epigenetics who ruin it for the rest of us, pushing mainstream [often also adaptationist] evolutionary biologists to shove epigenetics under the carpet as unimportant. Or downright hate it, eg. Coyne. It does not invalidate evolutionary theory, but it does add some interesting new angles to it, and it's quite amazing how many basic principles from genetic evolution may carry over quite nicely to epigenetics. The medium may be different, but evolutionary principles often remain the same. The faux 'revolutionaries' fuck it up for the saner among us. Fuck them for giving the field a bad name and making the funding situation even shittier."

    1. The importance of epigenetics cannot be overstated. It is the most exciting research in the field of genetics.
    2. If there are those who state epigenetics is unimportant they are idiots.
    3. Its importance in medicine cannot be overstated. Major investments are now being made to determine how the medical community can affect beneficial gene expressions.
    4. Epigenetics impacts TOE dramatically because it accounts for genetic change sans DNA sequence change. Say goodbye to randomness.

    My advice to you is get in, get out, or get out of the way. Epigenetics is the wave of the future.

    ReplyDelete
  70. heleen said above:
    "There is, both in the clear headed and fuzzy thinking variety."

    I am interested in all sources. Could you provide links of both the "clear headed" and "fuzzy" varieties please?
    I do not want to limit sources.
    Thanks.

    ReplyDelete
  71. Everything I have read concerning epigenetics has to do with environmental stress. Perhaps that is the most exciting aspect of epigenetics and hence obscures other mechanisms from being involved. Random mutations fail to account for rapid change in organisms as it takes huge amounts of time.

    I'm going to have to look at that fruit fly paper, because unless epigenetic changes can cross generations they by definition will have no effect on evolution.

    In other words, if you work out and become more muscular than others who work out due to some epigenetic factor, that's a change in you, but it's not a change in the species. If you experience some sort of change, such as a genetic mutation, that causes you to be more muscular and can be passed down through inheritance, there is a chance it will disseminate through and become fixed in the species. That's evolutionary change.

    A series of such changes that causes offspring after generations no longer to be able to interbreed with other offspring of their ancestors, thus producing a new species by the common definition for sexually reproducing life, would typically be considered "macro" evolution.

    Definitely. Lenski's 50,000 generation E Coli experiment were the bacteria developed the ability to transport citrate across the cell membrane is a case in point. He speaks of the E Coli becoming more robust, larger, and plentiful but does not mention anything about increasing their food supply. Could it be that the lack of food was the stress that brought about this new found capability? It makes more sense than random and spontaneous gene mutations.

    This is one point where you're at least apparently failing to catch the role of genetic mutation in evolution. It isn't exclusively environment or exclusively mutation. It is those "random and spontaneous gene mutations" working **with** environmental stress that produced the experimental result.

    This is classic Darwinian selection. The citrate metabolism mutation can occur in other E. coli, but confers no advantage because the regular food supply is present. When the regular food supply is removed, the mutation that allows feeding on citrate creates a significant advantage, so the bacteria descended from the one that had the mutation fare much better than those who don't have that particular mutation.

    If a particular bacterium had developed an ability to metabolize citrate, but that ability was somehow sited elsewhere than in the genes it passed to its descendants, then that's one happy bacterium, but it doesn't result in colonies of bacteria that can metabolize citrate, which is the result Lenski got.

    What you're thinking of - often referred to as "inheritance of acquired traits" or Lysenkoism, after the Soviet scientist who made that view enforced ideological orthodoxy under Stalin - may make some sort of intuitive sense, but it's been shown to be incorrect. So fight Stalinist orthodoxy, friend, and embrace modern evolutionary theory! ;-)

    ReplyDelete
  72. faultfinder says,

    Moran: "This is a different definition than the one you quoted above. Do you now insist that the only valid definition of epigenetics is one that includes environmental stress as a trigger?"

    Everything I have read concerning epigenetics has to do with environmental stress. Perhaps that is the most exciting aspect of epigenetics and hence obscures other mechanisms from being involved. Random mutations fail to account for rapid change in organisms as it takes huge amounts of time. (generations)


    Just because you are focused on environmental stress does not mean that you can co-opt the word "epigenetics" as a strawman for your anti-evolution position.

    I stand by my statement of fact. We've known about epigenetics for decades. It is not new. What you're trying to do is re-define the word in order to make it look more revolutionary. You're doing this because you have a hidden agenda.

    Moran: "If so, what do you mean by environmental stress? How about a situation where a common food source, such as lactose, is unavailable? Is that stressful?"

    Definitely. Lenski's 50,000 generation E Coli experiment were the bacteria developed the ability to transport citrate across the cell membrane is a case in point. He speaks of the E Coli becoming more robust, larger, and plentiful but does not mention anything about increasing their food supply. Could it be that the lack of food was the stress that brought about this new found capability? It makes more sense than random and spontaneous gene mutations.


    What Lenski was doing was to put the culture in a situation where adaptation would result in faster growth. The cultures did mutate to forms that grew faster. Lenski then identified some of those mutations and showed they were adaptive.

    In the case of citrate utilization, the example of evolution by fixation of mutations is extremely interesting. You can read about it at:

    Blount, Z.D., Borlandm, C.Z., and Lenski, R.E. (2008) Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proc. Natl. Acad. Sc. (USA) 105:7899-7906.

    Lenski's group is now identifying the mutations that gave rise to the Cit+ phenotype and you can anticipate a paper very soon. It will show that MUTATIONS are responsible—not epigenetics.

    ReplyDelete
  73. @faultfinder Tuesday, March 08, 2011 6:31:00 PM
    heleen said:

    "Did Faultfinder refer to this? I got this from Google asking for
    fruit flies epigenetic changes persist 200 generations stressful environment"

    http://www.sciencedaily.com/releases/2011/01/110124151713.htm

    This is the study to which I (Faultfinder) was referring. It is the only thing I have found indicating a permanent DNA change resulting from epigenetics.


    I hope Faultfinder noticed that the resistance to hypoxia was “generated through long-term laboratory selection over 200 generations” , but I’m afraid Faultfinder did not notice that. Faultfinder said:
    There is one experiment with fruit flies, however, that documented the epigenetic changes to persist for more than 200 generations after the flies were removed from the stressful environment.
    Faultfinder did not give a correct description of the experiment: the flies had 200 generation hypoxia. This is a standard type of selection experiment: genetic variation in a relevant DNA sequence and subsequent selection led to a sequence change in DNA leading to a change in gene expression. The genetic variation might have been present to start with (Drosophila has much genetic variation), or might have occurred during the 200 generations.

    Science Daily writes (italics added):
    "We set out to pinpoint the genomic regions responsible for the change in sequence, and prove that it was the DNA changes which led to gene expression and subsequent adaptation," said Haddad, who recently received a $10 million grant from the National Institute of Health's Heart, Lung and Blood Institute to study hypoxia tolerance. "We confirmed that change in the DNA, and not just a change in gene expression, results from long-term hypoxia exposure."

    Let us be clear: the change in DNA did not result from epigenetics. The change in gene expression resulted from present variation in DNA, and this change in DNA was adaptive under the 200 generation environmental conditions.

    Faultfinder simply misread Science Daily.

    ReplyDelete
  74. Faultfinder's Science Daily item does not even use the word 'epigenetics'.

    ReplyDelete
  75. I've now read the fruit fly article at Science Daily, as well as the following:

    A wonderful example is the Tibetans who were forced to relocate to a higher altitude oxygen poor environment. They developed larger lungs which were then inherited.

    ...and it now becomes evident where at least one of your misunderstandings lies. As I'd suspected, what you're thinking of as "epigenetics" is in fact Lysenkoism. There are very logical reasons why this concept doesn't work. I'll try to explain them. If I'm not clear, it's my own fault, not the fault of the science, which is very clear.

    Let's go back to the Lenski experiment. Millions or billions of bacteria, all under the same stress: Not enough of the regular food. There's lots of stuff (citrate) around that's available to be metabolized but the bacteria aren't able to consume it. Then as time goes on, more and more bacteria develop the ability to consume the citrate, though many are still unable to do so.

    Let's consider two possible mechanisms for what was observed in the experiment:

    1 - Epigenetic; all the bacteria have the genetic ability to metabolize citrate, and they can do so if the epigenetic system that regulates the expression of their genes kicks into gear.

    2 - Genetic; at first, none of the bacteria have the genetic ability to metabolize citrate. Over thousands of generations, mutations occur in a few of the millions or billions of bacteria that allow some limited citrate metabolism. Over more thousands of generations, additional mutations occur, until finally there is an accumulation of two or three mutations which together allow very good citrate metabolism. The bacterium that first had the accumulated mutations and its progeny are extraordinarily successful in the citrate-rich environment, soon outnumbering those without the mutations.

    If you read detailed reports of Lenski's experiments, #2 is exactly what happened. As for #1 - what the heck is the epigenetic system waiting for? If all the bacteria have the inborn ability to metabolize citrate and are all under the same environmental stress, why aren't they all doing it from the beginning?

    If you look at the report of the fruit fly experiment, it is in agreement with the genetic explanation, which - this is important - does *not* contradict a role for epigenetics. (You keep on conceiving of either/or situations - environment or genetics, epigenetics or genetics - when the actual answer is all of the above have their roles.)

    Quoting from the article: the scientists studied populations of Drosophila melanogaster generated through long-term laboratory selection over 200 generations. Long-term selection means more of the fruit flies that did best in the hypoxic environment survived to pass on their genes to future generations.

    Was that due to some trait the fruit flies acquired through an epigenetic reaction to stress, that somehow made its way into their DNA? Or was it, like Lenski's bacteria, the other way round - genetic mutations over the generations allowing the fruit flies with those mutations to survive and breed more successfully than others, so passing on the beneficial mutations until all the 200th generation had them? The lead researcher makes very clear which one it was: We set out to pinpoint the genomic regions responsible for the change in sequence, and prove that it was the DNA changes which led to gene expression and subsequent adaptation....

    So - first the beneficial genetic mutations (DNA changes), then the subsequent adaptation; not an epigenetic-driven adaptation that is then magically converted to genetic, heritable form.

    I'm guessing your reluctance to credit mutation is driven by erroneous understanding of how probability works. If you'd like, we can go there next.

    ReplyDelete
  76. Here is what I have been saying about a possible theory:

    In the face of the environment the organism responds with an epigenetic change.
    While that environment persists this epigenetic change continues into the following generations.
    If the environment changes back within a relatively short period of time, the epigenetic change disappears.
    However if the environment remains for an extended time, the DNA itself is changed.

    This is a new idea I am suggesting It could perhaps explain the results we observe in the various studies.
    Is there any study that absolutely could not be explained that way?

    By the way it is foolish to label any idea as magic at this point since mechanisms are not yet understood for a good deal of what is observed. So it is premature to begin closing down the doors on what is possible.

    ReplyDelete
  77. Here is something to think about.
    It is accepted that the epigenetic mechanism is "smart" enough to modify the expression of the genes based on such things as the environment.
    But it seems hard for people to think that the system could be "smart" enough to actually go the next step and modify the genome correspondingly, after a large number of generations.

    ReplyDelete
  78. Jud said:
    "In other words, if you work out and become more muscular than others who work out due to some epigenetic factor, that's a change in you, but it's not a change in the species. If you experience some sort of change, such as a genetic mutation, that causes you to be more muscular and can be passed down through inheritance, there is a chance it will disseminate through and become fixed in the species. That's evolutionary change."

    I think you got it right, but you are viewing epigenetics through a random and spontaneous DNA sequencing mutation coupled with natural selection prism.

    You need to think of a population rather than a species. A population seperated from others in the same species according to TOE can evolve and those of the same species in another location not evolve.

    Think of a population in the same environment. That environment provides some sort of stress on the population. Epigenetics causes certain existing genes to be regulated in a fashion that allows the population to survive. Its not about an individual in a population. If the entire population encounters the same stress the entire population will adapt by epigenetic changes. If some by chance do not adapt they will die.

    Epigenetic changes and random and spontaneous gene mutations both coupled with natural selection will in one sense lead to the same change in a population. How do we know which happened? By examining the DNA sequencing. If it has changed the population evolved by random and spontaneous gene mutations and will never revert back to their previous state. If the DNA sequencing has not changed the population adapted by epigenetic changes and the DNA sequencing remains the same. If the stress is removed in this case the population will most likely revert to its state prior to experiencing the stress.

    I submit that no population has ever changed by means of random and spontaneous gene mutations coupled with natural selection. I know of no experiment where this happened. We are usually left with conclusions that genes mutated. The question unanswered is did the DNA sequencing change?

    ReplyDelete
  79. While that environment persists this epigenetic change continues into the following generations. If the environment changes back within a relatively short period of time, the epigenetic change disappears.However if the environment remains for an extended time, the DNA itself is changed.

    This is a new idea I am suggesting

    It isn't. The suggestion of an epigenetic mechanism is newish, but the theory that non-genetic characteristics acquired during life can be passed to descendants dates back at least to 1928, when it was used to try to explain an agricultural technique that first came into widespread use in 1854. The theory was never scientifically accepted, in part because the claimed results weren't reproducible, i.e., the supposed evidence for it was a fraud.

    It could perhaps explain the results we observe in the various studies.
    Is there any study that absolutely could not be explained that way?


    No study can be explained that way. The theory does not work in practice. Back in the days of Lysenko the reasons why it didn't work weren't known. Now they are.

    By the way it is foolish to label any idea as magic at this point since mechanisms are not yet understood for a good deal of what is observed. So it is premature to begin closing down the doors on what is possible.

    If you are under the impression that no mechanisms are yet understood that would render your theory incorrect, you would be quite wrong. The mechanism that causes your theory to be wrong has been known for more than 50 years, and is so well-proved by this time that it is known as the Central Dogma of Molecular Biology.

    Look it up, read about it (Larry has posted some good articles on it himself), and you'll have an answer in no uncertain terms to the question of whether you've had some breakthrough idea.

    ReplyDelete
  80. Would Faultfinder be so good as to read what Jud and I said about your total misunderstanding of the Drosophila / hypoxia experiment? The article states in so many words epigenetics is not involved: 'a genetic rather than a physiological mechanism is at play in adaption' - epigenetics is a physiological mechanism.

    In other words, Faultfinder, you don't have the basic skill to read the paper and understand its conclusion.

    ReplyDelete
  81. @ Faultfinder Wednesday, March 09, 2011 8:22:00 PM

    The question unanswered is did the DNA sequencing change?
    You been given two examples of DNA change, for the two cases you brought up.

    ReplyDelete
  82. @Anonymous Wednesday, March 09, 2011 11:02:00 AM
    Could you provide links of both the "clear headed" and "fuzzy" varieties please?
    I do not want to limit sources.


    Fuzzy headed:
    First see what Jud Wednesday, March 09, 2011 12:56:00 PM had to say about Lysenkoism. You are proposing Lysenkoism.
    Then look up Eva Jablonka, Wikipedia will do. Idem 'Baldwin effect', at least mostly.

    More clear headed: look at phenotypic plasticity (Wikipedia). The book “Phenotypic Plasticity: Functional and Conceptual Approaches” perhaps, or “Phenotypic Plasticity: Beyond Nature and Nurture” but not the other books by Pigliucci.

    ReplyDelete
  83. @Anonymous Wednesday, March 09, 2011 3:17:00 PM
    It is accepted that the epigenetic mechanism is "smart" enough to modify the expression of the genes based on such things as the environment.
    But it seems hard for people to think that the system could be "smart" enough to actually go the next step and modify the genome correspondingly, after a large number of generations.
    .

    No, it is not hard to think that way: that is the way Lysenko thought. It is not that it is hard to think that way, but that it does not work that way.

    ReplyDelete
  84. annonymous said:

    "Here is something to think about.
    It is accepted that the epigenetic mechanism is "smart" enough to modify the expression of the genes based on such things as the environment.
    But it seems hard for people to think that the system could be "smart" enough to actually go the next step and modify the genome correspondingly, after a large number of generations."


    Actually I have just discovered proof that epigenetic changes have become permanent (DNA sequencing changes) in Fruit Fly experiment.

    http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000221

    I think this is the most exciting thing I have encountered since I began studying epigenetics.

    ReplyDelete
  85. We are usually left with conclusions that genes mutated. The question unanswered is did the DNA sequencing change?

    faultfinder, I don't know if you expressed exactly what you meant, and if I am reading you correctly, but if so, then I think you must misunderstand what genetic mutations are. Here's a medical dictionary definition:

    "Mutation: A permanent change, a structural alteration, in the DNA or RNA. In humans and many other organisms, mutations occur in DNA. However, in retroviruses like HIV, mutations occur in RNA which is the genetic material of retroviruses."

    So whenever you read a conclusion that genes mutated (in a living thing other than a retrovirus), that means by definition the DNA sequence changed.

    The two studies you've discussed in this thread - hypoxic fruit flies, E. coli with reduced food supply - both show exactly what you say you've never seen, random gene changes combined with natural selection.

    Quoting once again from the article in Science Daily you cited about the 200 generations of fruit flies living in a hypoxic environment, the lead researcher says: We confirmed that change in the DNA, and not just a change in gene expression, results from long-term hypoxia exposure. That's change in DNA (genetic mutation), not just gene expression (epigenetics).

    As for the Lenski E. coli study, here's a relevant quote from the paper Larry suggested you should read (and you should): "DNA sequencing also showed that Cit+ clones [E. coli that evolved to feed on citrate] have the same mutations in the pykF and nadR genes as do clones from earlier generations of the Ara-3 population, and each of these mutations distinguishes this population from all of the others (30). Therefore, the Cit+ variant arose within the LTEE and is not a contaminant."

    Regarding your speculation that epigenetics could account for what has been observed in Lenski's experiment, here's another quote from the paper: "No population evolved the capacity to exploit citrate for >30,000 generations, although each population tested billions of mutations. A citrate-using (Cit+) variant finally evolved in one population by 31,500 generations, causing an increase in population size and diversity."

    More than 30,000 generations until any of the E. coli could feed on citrate. As you said yourself, "If the entire population encounters the same stress the entire population will adapt by epigenetic changes." So what were these bacteria waiting 30,000 generations for? And even when citrate metabolism evolved, it was only in some, not all, of the population. By your own description of the characteristics of epigenetic changes, they couldn't have accounted for what was observed.

    ReplyDelete
  86. heleen said:

    "Would Faultfinder be so good as to read what Jud and I said about your total misunderstanding of the Drosophila / hypoxia experiment? The article states in so many words epigenetics is not involved: 'a genetic rather than a physiological mechanism is at play in adaption' - epigenetics is a physiological mechanism.

    In other words, Faultfinder, you don't have the basic skill to read the paper and understand its conclusion."

    What you have read and based your conclusion on is media hype. Please read the experiment data as it was published. You will find no references to genetic code modifications driving epigenetic changes as is in the hype.

    http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000221#s2

    It you are going to study science I suggest you do it scientifically.

    There is another experiment with fruit flies hypoxia which is far more extensive and detailed. It also shows no time based sequence between epigenetic and genetic code changes.

    http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000221

    What you are missing is the incredible fact that now we have both epigenetic and permanent genetic code changes in a species. The second thing that is huge is we now have permanent DNA sequencing changes that came about by environmental driven stress.

    I think the abandonment of random and spontaneous gene mutations is about to be removed from TOE.

    The second experiment shows that the genetic changes were found after the 32nd generation. Do you really think random and spontaneous gene mutations could take over a population in 32 generations? Do you know most of said mutations are negative? Do you know many of them are neutral? Do you know only a very few of them are beneficial? When they occur their is a proof reading mechanism that checks them for accuracy and changes them back to what they were pre-mutaion. Are you aware the math for mutations occurring from these kinds of changes dictates huge amounts of generations to take over a population? Time for these mechanisms to work has always been prohibitive. That's why evolutionists frequently speak of hundreds of millions of years.

    Epigenetics has been proven to be environmentally driven in most cases. That means it can begin its changes in a single generation. What do you think the odds are of a random and spontaneous gene mutation occurring before an epigenetic change? Think about it.

    As to Jud, he is in a sink hole of defending current TOE. I perceive him to be an intelligent and perceptive individual. Change comes hard. Many scientists have had difficulty in accepting changes to TOE. Opposition is what makes theories sound. If there was no resistance to theory change theories would run willy nilly everywhere. Negative feedback keeps progress on track.

    ReplyDelete
  87. heleen said:

    "In other words, Faultfinder, you don't have the basic skill to read the paper and understand its conclusion."

    An accurate assessment. I did, however, have the fact checking ability to look up the actual experiment.

    ReplyDelete
  88. heleen said:

    "No, it is not hard to think that way: that is the way Lysenko thought. It is not that it is hard to think that way, but that it does not work that way."

    I posted the discovery how the epigenetic modifications occur. Here it is again.

    http://www.sciencedaily.com/releases/2010/10/101018102239.htm

    Actually, because of epigenetics scientists are revisiting Lamarkian theory.

    ReplyDelete
  89. Jud said:

    "1 - Epigenetic; all the bacteria have the genetic ability to metabolize citrate, and they can do so if the epigenetic system that regulates the expression of their genes kicks into gear."

    You posted too much for a detailed debate so I have to break it up. You seem to presume (bad word) that all the subjects in an environment will respond exactly the same. Perhaps that is true if the stress is great enough. In this case the citrate was an additional not a necessary food supply. The subjects had grown larger with only the food supply provided. Conclusion, not much stress. Did the subjects compete for food? Probably. Did the smaller get less. Probably. Was the stress greater for the smaller? I would think so. Would the smaller be more likely to experience an epigenetic change. Seems logical to me. Would this explain why some, but not all of the subjects developed the ability to transport citrate across their membranes? Seems logical to me.

    I posted a link to a second fruit fly hypoxia experiment. In that experiment the researchers found changes after only 32 generations. Do you really think that is enough time for random and spontaneous gene mutations coupled with natural selection to work? If it is, let's proclaim it to the science world. It is a miracle!

    Could epigenetics account for changes in 32 generations? Epigenetics provides for changes in living subjects in one generation. Look at the graphs depicting change versus generations in E Coli experiments. Most of the change comes up front. I suspect Lenski's graph if he supplied one shows the same thing.

    I submit if the normal food supply for the subjects in the E Coli experiment you cite was reduced drastically more subjects would have had epigenetic changes far more quickly. We will never know, will we? You know why? Scientists perform experiments with a stated objective in mind. Proving the TOE is flawed is not one of them.

    ReplyDelete
  90. heleen writes:

    Fuzzy headed:
    First see what Jud Wednesday, March 09, 2011 12:56:00 PM had to say....


    Umm - thanks?

    ;-)

    ReplyDelete
  91. faultfinder writes:

    The second thing that is huge is we now have permanent DNA sequencing changes that came about by environmental driven stress.

    Welcome to your rediscovery of Charles Darwin's thought process in 1838 upon reading Thomas Malthus' Essay on the Principle of Population authored in 1798. You're right about one thing, though - Darwin's idea was and continues to be "huge."

    ReplyDelete
  92. Would the smaller be more likely to experience an epigenetic change. Seems logical to me. Would this explain why some, but not all of the subjects developed the ability to transport citrate across their membranes?

    Yep, now you can explain why those billions upon billions of E. coli didn't bother to develop those "epigenetic" changes for 30,000 generations. And why, after thousands of succeeding generations, now the majority of them suddenly have the ability to create these "epigenetic" changes. Were the first 30,000 generations "slackers" that just didn't want to change badly enough?

    The greater changes you noted toward the beginning of the experiment were in efficiency of glucose metabolism and had nothing to do with the mutations in the pykF and nadR genes - that is, the changes in DNA sequences - that finally allowed some E. coli to begin to metabolize citrate after 31,500 generations.

    ReplyDelete
  93. This seems interesting:
    http://en.wikipedia.org/wiki/Baldwin_effect
    "The "Baldwin effect" is better understood in evo-devo (evolutionary developmental biology) literature as a scenario in which a character or trait change occurring in an organism as a result of its interaction with its environment becomes gradually assimilated into its developmental genetic or epigenetic repertoire (Simpson, 1953; Newman, 2002)."

    ReplyDelete
  94. Another interesting reference:

    http://en.wikipedia.org/wiki/Eva_Jablonka
    "Secondly, at the epigenetic level involving variation in the “meaning” of given DNA strands, in which variations in DNA translation during developmental processes are subsequently transmitted during reproduction, which can then feed back into sequence modification of DNA itself."

    ReplyDelete
  95. @ faultfinder Thursday, March 10, 2011 7:14:00 AM

    http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000221

    Just like your earlier citing of this set of experiment, this is selection, and not epigenetics.

    ReplyDelete
  96. @ faultfinder Thursday, March 10, 2011 7:14:00 AM

    http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000221

    Just like your earlier citing of this set of experiment, this is selection, and not epigenetics. It is a nice study of genetic influences on gene regulation.

    Faultfinder seems to lack the ability to read a scientific paper.

    ReplyDelete
  97. @ Jud Thursday, March 10, 2011 9:53:00 AM
    heleen writes:

    Fuzzy headed:
    First see what Jud Wednesday, March 09, 2011 12:56:00 PM had to say....

    Umm - thanks?

    ;-)

    I’m sorry, Jud, I meant that Anonymous should take your comment to heart.

    ReplyDelete
  98. @Anonymous Thursday, March 10, 2011 10:49:00 AM

    http://en.wikipedia.org/wiki/Baldwin_effect
    "The "Baldwin effect" has little empirical or modelling support, even if evolutionary psychologists and people that are interested in evolution and learning occasionally enthuse over it. The ‘theorists’ referred to in the Wikipedia item are of the philosophizing kind, not the mathematical types. Note that the point is not whether phenotypic plasticity can evolve if genetic variation in phenotypic plasticity is present. The point with the Baldwin effect is that no initial genetic variation is present.

    ReplyDelete
  99. Could it be that an epigenetic change can be encoded in the DNA via the mechanisms of RNA editing and reverse transcription?

    ReplyDelete
  100. Interesting, yes. Having much to do with epigenetics, no.

    The article has mostly to do with speculation that learned behavior possibly creates selective pressure, which in turn provides environmental conditions to drive to fixation genetic variations that produce instinctive behaviors mirroring the former learned ones.

    ReplyDelete
  101. Re the Baldwin Effect article on Wikipedia:

    Interesting, yes. Having much to do with epigenetics, no.

    The article has mostly to do with speculation that learned behavior possibly creates selective pressure, which in turn provides environmental conditions to drive to fixation genetic variations that produce instinctive behaviors mirroring the former learned ones.

    ReplyDelete
  102. Jud said:

    "Welcome to your rediscovery of Charles Darwin's thought process in 1838 upon reading Thomas Malthus' Essay on the Principle of Population authored in 1798. You're right about one thing, though - Darwin's idea was and continues to be "huge.""

    Come on, guy. Neither had the sligtest inkling of DNA much less of environmental stress driven gene expression.

    Your over simplification is annoying.

    ReplyDelete
  103. Jud said:

    "Yep, now you can explain why those billions upon billions of E. coli didn't bother to develop those "epigenetic" changes for 30,000 generations. And why, after thousands of succeeding generations, now the majority of them suddenly have the ability to create these "epigenetic" changes. Were the first 30,000 generations "slackers" that just didn't want to change badly enough?"

    For the first 30,000 generations they had enough food. No stress, no new gene expressions. As the grew larger (that's what the experiment was about according to Moran) they needed more food. Did it ever occur to you that larger organisms consume more food?

    ReplyDelete
  104. Anonymous writes:

    Could it be that an epigenetic change can be encoded in the DNA via the mechanisms of RNA editing and reverse transcription?

    You referring to the theories of John Mattick, et al.? Here's a Q&A from an interview of Mattick:

    Did you ever believe that there was junk DNA?

    Mattick: Not really.

    OK, Anonymous, all you have left to do now is tell us why life is so much more complicated for onions than humans.

    Oh, and also why the "effect" (heritability of acquired traits) of this supposed "cause" hasn't been observed.

    ReplyDelete
  105. Jud said:

    "The greater changes you noted toward the beginning of the experiment were in efficiency of glucose metabolism and had nothing to do with the mutations in the pykF and nadR genes - that is, the changes in DNA sequences - that finally allowed some E. coli to begin to metabolize citrate after 31,500 generations."

    That wasn't my point, podnuh. The point was change is greater at the outset of an experiment because the stress is greater then. As the E Coli adapt the stress is lessened hence less change.

    This is precisely why epigenetics better explains these experiments than does random and spontaneous gene mutations. The randomness theory demands huge numbers of generations to work. In that case the graph should be inverted.

    I have already given a plausible explanation for the citrate metabolizing.

    ReplyDelete
  106. heleen said:

    "Just like your earlier citing of this set of experiment, this is selection, and not epigenetics."

    I know you think the sun rises and sets in your rear, but I need a little more evidence than your opinion.

    ReplyDelete
  107. heleen said:

    "Just like your earlier citing of this set of experiment, this is selection, and not epigenetics. It is a nice study of genetic influences on gene regulation.

    Faultfinder seems to lack the ability to read a scientific paper."

    To what "genetic influences" do you refer? It seems you have dreamed up a new theory.

    One of us lacks the ability to read a scientific paper but it is not me.

    ReplyDelete
  108. faultfinder writes:

    For the first 30,000 generations they had enough food. No stress, no new gene expressions. As the grew larger (that's what the experiment was about according to Moran) they needed more food. Did it ever occur to you that larger organisms consume more food?

    ...and faultfinder further writes:

    That wasn't my point, podnuh. The point was change is greater at the outset of an experiment because the stress is greater then. As the E Coli adapt the stress is lessened hence less change.

    This is precisely why epigenetics better explains these experiments than does random and spontaneous gene mutations.

    ...and faultfinder yet further writes (to heleen):

    I know you think the sun rises and sets in your rear, but I need a little more evidence than your opinion.
    * * *
    One of us lacks the ability to read a scientific paper but it is not me.

    Better give up now, heleen - faultfinder is surely the only one among us who knows how to draw two diametrically opposed sets of facts (there was no stress at the outset of the Lenski experiment; stress was greatest at the outset of the Lenski experiment) from a single paper.

    faultfinder: So we all better admit you're right or you'll draw your gun and shoot yourself in the other foot?

    Been fun, "podnuh." :-)

    ReplyDelete
  109. Jud said:

    "faultfinder writes:

    For the first 30,000 generations they had enough food. No stress, no new gene expressions. As the grew larger (that's what the experiment was about according to Moran) they needed more food. Did it ever occur to you that larger organisms consume more food?

    ...and faultfinder further writes:

    That wasn't my point, podnuh. The point was change is greater at the outset of an experiment because the stress is greater then. As the E Coli adapt the stress is lessened hence less change.

    This is precisely why epigenetics better explains these experiments than does random and spontaneous gene mutations.

    ...and faultfinder yet further writes (to heleen):

    I know you think the sun rises and sets in your rear, but I need a little more evidence than your opinion.
    * * *
    One of us lacks the ability to read a scientific paper but it is not me.

    Better give up now, heleen - faultfinder is surely the only one among us who knows how to draw two diametrically opposed sets of facts (there was no stress at the outset of the Lenski experiment; stress was greatest at the outset of the Lenski experiment) from a single paper.

    faultfinder: So we all better admit you're right or you'll draw your gun and shoot yourself in the other foot?

    Been fun, "podnuh." :-)"

    I was referring to two different experiments, podnuh. The quotes you posted came from two different posts. One experiment I have been reading about had to do with E Coli placed in an antibiotic laced environment. It was in that experiment that the greatest change took place at the outset of the experiment as was shown on a graph. I do not recall a graph showing rates of change versus time in Lenski's experiment.

    Oops, it looks like you just shot yourself in both feet.

    Here's a little gem for you:

    Lenski's experiment:

    "Bacteria in nature must survive multiple stresses and repeated shifts between feast and famine conditions. When Escherichia coli experiences nutritional deprivation, its growth rate decreases sharply and the cells become more spherical and resistant to various other environmental stresses (27). Many of the morphological and physiological changes that occur during entry into “stationary” phase are associated with the cell envelope, especially the cell wall."

    Whoa, baby. It looks like there was stress in Lenski's experiment. His bacteria became "more spherical" if I am not mistaken. It seems this new shape caused by stress was a precursor to citrate being taken across the cell wall. Hello, epigenetics.

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632098/?tool=pmcentrez

    I think maybe you might invest in steel toes shoes.

    ReplyDelete
  110. Fascinating news for epigenetics.

    http://www.genengnews.com/industry-updates/epizyme-enters-worldwide-strategic-partnership-with-eisai-for-cancer-therapeutics-targeting-ezh2/111467989/

    You guys better wake up and smell the coffee. Instead of acting like epigenetics is ancient history, maybe you should be researching what is going on in this "new" science.

    This site has several fascinating articles on fast breaking epigenetic news and discoveries. One thing is certain, those who make money from medical advances are investing multiplied millions in epigenetic research.

    ReplyDelete
  111. Hey faultfinder,

    Do you believe we share a common ancestor with all other species on earth?
    Do you believe that speciation happens?

    Just wondering.

    ReplyDelete
  112. faultfinder writes:

    I was referring to two different experiments, podnuh.

    Let's look back at those two comments. In the first, I said:

    Yep, now you can explain why those billions upon billions of E. coli didn't bother to develop those "epigenetic" changes for 30,000 generations.

    To which faultfinder replied:

    For the first 30,000 generations they had enough food. No stress, no new gene expressions.

    In the second, I said:

    The greater changes you noted toward the beginning of the experiment were in efficiency of glucose metabolism and had nothing to do with the mutations in the pykF and nadR genes - that is, the changes in DNA sequences - that finally allowed some E. coli to begin to metabolize citrate after 31,500 generations.

    To which faultfinder replied:

    That wasn't my point, podnuh. The point was change is greater at the outset of an experiment because the stress is greater then. As the E Coli adapt the stress is lessened hence less change.

    Oh, so in your second comment you were referring to that other, different experiment observing glucose and citrate metabolism in E. coli over 30,000+ generations.

    Yeah, right.

    I guess this is an appropriate time to call an end to my participation in this particular thread. Let me leave you, faultfinder, with the suggestion that next time you are reading your Bible, Exodus 20:16 is a fine passage.

    ReplyDelete
  113. @ faultfinder Thursday, March 10, 2011 4:44:00 PM

    heleen said:

    "Just like your earlier citing of this set of experiment, this is selection, and not epigenetics."

    I know you think the sun rises and sets in your rear, but I need a little more evidence than your opinion.


    The evidence is in both papers: this set of experiments is about selection, and differences in gene expression due to selection. If Faultfinder could read a scientific paper, he would see that. If he denies the evidence for selection is in the papers, Faultfinder provides evidence of his utter inability to read or understand scientific papers. Epigenetics as explanation is ruled out in so many words by the PI in the Science Daily write up.

    The problem with people like Faultfinder is a total lack of ability to understand what they read, coupled with a priory opinions that do not have any foundation in fact. Faultfinder is unable to see what the evidence in those experiments is. Moreover, he has no grasp of what constitutes evidence whatsoever. The last internet citation about cancer treatment has no relevance to evolution. So, why bring it up? Methylation patterns exist, that is not the subject of discussion.

    Another problem is that ignorant people like Faultfinder never understand the depth of their ignorance, but compensate for this by wild behaviour.

    ReplyDelete
  114. heleen said:

    "Epigenetics as explanation is ruled out in so many words by the PI in the Science Daily write up."

    The science daily write up was media hype. Please note the media link at the bottom. I posted a link to the actual experiment in which there is no reference to DNA sequencing occurring before epigenetic gene expressions. If you could read a scientific paper you would see that.

    heleen said:

    "The problem with people like Faultfinder is a total lack of ability to understand what they read, coupled with a priory opinions that do not have any foundation in fact. Faultfinder is unable to see what the evidence in those experiments is. Moreover, he has no grasp of what constitutes evidence whatsoever. The last internet citation about cancer treatment has no relevance to evolution. So, why bring it up? Methylation patterns exist, that is not the subject of discussion."

    The discussion is and has been about epigenetics. Methylation is a means of gene expression. How much more applicable can that be?

    As to understanding what I read, you indicate that it is based purely on the fact that I don't agree with your interpretation which is fallacious.

    Here is a brief synopsis of the experiment I referenced that Jud objected to:

    E Coli were placed in an antibiotic environment. Change occurred that allowed them to survive. The experiment lasted 20,000 generations. The researchers, blinded by their dogma, concluded evolution had occurred. That is, random and spontaneous gene mutations had happened and natural selection had shaped the population into antibiotic resistance.

    My interpretation was the antibiotic provided stress on the population and hence epigenetic genes expression had allowed the population to adapt and hence survive.

    Two interpretations based upon the same evidence. Which is correct? One has only to understand that random and spontaneous gene mutations coupled with natural selection takes huge amounts of generations (time). The graph supplied showing change versus time indicated by far the greatest change came at the outset of the experiment. So, epigenetics can account for that, but neo-darwinism cannot.

    In Lenski's 50,000 generation experiment it was shown that two preceding gene expressions came before the final change that enabled one population to metabolize citrate.

    I constantly state that mathematically neo-darwinian evolution is impossible. Can you even imagine what the odds are that three genetic changes working in concert happened randomly and spontaneously to enable citrate metabolism are? One in ... I can't think of a number big enough. It would not happen in 50,000 generations nor in 10^-1000 generations. The odds of it happening epigenetically, however, are very probable.

    There comes a point at which odds are so great that for all intents and purposes it becomes impossible. Neo-Darwinians have not figured that out yet.

    Ever since epigenetics has been discovered neo-darwinism has been on shakey ground. With each new discovery another supporting tenet is destroyed. It now is supported by dogmatic beliefs only.

    Lenski's experiment now can only be interpreted as a proof of the fallibility of neo-darwinism.

    ReplyDelete
  115. faultfinder, you have posted some very interesting and helpful material. It is a shame that jud and heleen have nothing to contribute except insults and distractions.

    ReplyDelete
  116. anonymous said:

    "faultfinder, you have posted some very interesting and helpful material. It is a shame that jud and heleen have nothing to contribute except insults and distractions."

    Thank you. I learned long ago that the chance of changing someone's position in a debate is very close to nil. Different people debate for different reasons. I debate evolution to learn from some very knowlegeable people and analytically test my theories.

    For Jud and heleen it is about winning at any cost. I ignore their insults and pick out things in their posts that enhance my understanding. Perhaps they will realize some day that insults and adhominems are usually an attempt to cover the weakness in one's arguments.

    ReplyDelete
  117. Scott asked:

    "Do you believe we share a common ancestor with all other species on earth?"

    Yes and the common ancestor is God.

    "Do you believe that speciation happens?"

    That depends on your definition of speciation. Evolutionists keep redefining it to water it down to the point it fits in TOE.

    I believe organisms change as a result of environmental stress and perhaps some other causes. If enough change can occur to render a much adapted organism to no longer be able to produce offspring when mating with a wild type, I am not sure. I know there are experiments that claim to show this, but I have questions about whether it has to do with the impossibility or is merely a result of preference. The only way to tell for sure is by artificial insemination. To my knowledge that has not been done.

    ReplyDelete
  118. Against stupidity ..
    the gods themselves ..
    contend in vain

    ReplyDelete
  119. Hello again faultfinder,

    So Your god was a single celled organism?

    Did your single celled god create Adam and Eve in its image.

    Or was you god look like an evolved primate that appeared to have a common ancestor with a chimpanzee.

    Also, do you refute the experiments done by Gregor Mendel, which were all performed under the same environmental stress conditions, yet the changes happened.

    Do you realize that we can breed all kinds of plants and animals in the same environment, yet change there phenotype dramatically.

    Also do you realize that you have accepted god as the most appropriate answer for how and why life exist. And that by doing so you will blind yourself to reality. At some point the evidence becomes so overwhelming that your arguments reduce themselves to absurdity.

    Your thoughts on evolution mirror that of Lamarkism, which is similar to Lysenkoism. That's the hypothesis that organisms can inherit acquired characteristics.

    This has been disproved over and over again. It doesn't work.

    ReplyDelete
  120. heleen said:

    "Against stupidity ..
    the gods themselves ..
    contend in vain "

    Well, at least you realize your plight.

    ReplyDelete
  121. faultfinder, as soon as I saw the original questions from scott, I knew his agenda and where his discussion would be going.

    ReplyDelete
  122. http://onlinelibrary.wiley.com/doi/10.1002/bies.080099/abstract;jsessionid=7FA03925C43710AB49C2134D02759A4D.d01t01

    "There is increasing evidence that dynamic changes to chromatin, chromosomes and nuclear architecture are regulated by RNA signalling. Although the precise molecular mechanisms are not well understood, they appear to involve the differential recruitment of a hierarchy of generic chromatin modifying complexes and DNA methyltransferases to specific loci by RNAs during differentiation and development. A significant fraction of the genome-wide transcription of non-protein coding RNAs may be involved in this process, comprising a previously hidden layer of intermediary genetic information that underpins developmental ontogeny and the differences between species, ecotypes and individuals. It is also evident that RNA editing is a primary means by which hardwired genetic information in animals can be altered by environmental signals, especially in the brain, indicating a dynamic RNA-mediated interplay between the transcriptome, the environment and the epigenome. Moreover, RNA-directed regulatory processes may also transfer epigenetic information not only within cells but also between cells and organ systems, as well as across generations."

    ReplyDelete
  123. anonymous said:

    "faultfinder, as soon as I saw the original questions from scott, I knew his agenda and where his discussion would be going."

    I did also. Its a game evolutionists play that makes them feel superior. Why should I deny him that?

    ReplyDelete
  124. scott said:

    "Also, do you refute the experiments done by Gregor Mendel, which were all performed under the same environmental stress conditions, yet the changes happened."

    I have no idea what you are trying to say here and I don't think you do either. If you are equating heridity experiments with gene mutations I see no hope of a debate.

    ReplyDelete
  125. scott said:

    "Also do you realize that you have accepted god as the most appropriate answer for how and why life exist. And that by doing so you will blind yourself to reality. At some point the evidence becomes so overwhelming that your arguments reduce themselves to absurdity."

    Do you realize that you have accepted theories that claim life sprang from non living elements. In so doing you demonstrate a faith in the impossible. At some point you will realize that and in so doing will understand all your arguments were absurd?

    ReplyDelete
  126. scott said:

    "Your thoughts on evolution mirror that of Lamarkism, which is similar to Lysenkoism. That's the hypothesis that organisms can inherit acquired characteristics.

    This has been disproved over and over again. It doesn't work."

    Actually many scientists are now revisiting Lamarcks theories. I thik a giraffes neck increasing in length so they could reach food is stretching a point. Personally, I think his theories are pretty far out, but at least he understood change can come about through environmental stress. That's more than I can say about some on this blog.

    ReplyDelete
  127. Here is another mind-boggling idea from the reference I posted earlier:

    http://onlinelibrary.wiley.com/doi/10.1002/bies.080099/full

    "However, these modifications must be purposefully directed to different positions in different loci in different cells, which implies that there must be another layer of information to guide this process."

    ReplyDelete
  128. anonymous said:

    "http://onlinelibrary.wiley.com/doi/10.1002/bies.080099/full

    "However, these modifications must be purposefully directed to different positions in different loci in different cells, which implies that there must be another layer of information to guide this process."

    Great link. It is no longer if the mechanisms of epigenetic gene expressions will be discovered, but when they will be discovered.

    Neo-Darwinism is on its last legs. The "mountains" of evidence supporting it are crumbling as we speak. I have always thought TOE made a lot of sense except the math didn't work. Too much chance.

    I worked as a troubleshooting specialist for a major airline for many years. There were times the evidence for faults added up to an inevitable conclusion but that conclusion was still wrong. There were times when tests pointed to the same conclusion but it was still wrong. This is the context into which I place TOE. Random and spontaneous mutations coupled with natural selection seemed unrefutable except for the math.

    Thanks for the reference. I am only surprised that further relevations in this scenario have not been forthcoming. Perhaps they have and I simply cannot find them. If I do, I will share them.

    ReplyDelete
  129. faultfinder said:

    "Random and spontaneous mutations coupled with natural selection seemed unrefutable except for the math."


    I guess if you think god created life about six thousand years ago, then I would agree, the math doesn't work. But knowing life on earth begun 3.8 billion years ago
    then evolved though random mutations, reshuffling genetic variations and non-random natural selection then the math isn't all that hard to conceive.

    Your argument is from your own personal incredulity regarding evolutionary time.

    ReplyDelete
  130. http://upload.wikimedia.org/wikipedia/en/thumb/d/dd/Extended_Central_Dogma_with_Enzymes.jpg/550px-Extended_Central_Dogma_with_Enzymes.jpg

    This reference is an overview that includes reverse transcription.
    I am suggesting that environmental factors modify the RNA (epigenetic change)and then this RNA, which has been changed, is reverse transcribed into the DNA.
    In other words, the mechanism of epigenetic changes going the next step, to change the DNA, via reverse transcription, is already known.

    ReplyDelete
  131. @faultfinder I worked as a troubleshooting specialist for a major airline for many years.

    I am seriously considering never flying again.

    ReplyDelete
  132. Scott said:

    "I guess if you think god created life about six thousand years ago, then I would agree, the math doesn't work."

    Do you often put words in another's mouth and then debate them? That's a classic strawman argument.

    and... "But knowing life on earth begun 3.8 billion years ago
    then evolved though random mutations, reshuffling genetic variations and non-random natural selection then the math isn't all that hard to conceive."

    You don't even know how to compute the odds so how can you make an affirmative statement?

    ReplyDelete
  133. oberski said:

    "I am seriously considering never flying again."

    Why steve, I didn't know you had wings.

    ReplyDelete
  134. I am suggesting that environmental factors modify the RNA (epigenetic change)and then this RNA, which has been changed, is reverse transcribed into the DNA.

    The theory sounds nice. The only problem is that there is absolutely no evidence that cDNA copies of the RNA sequence target and re-integrate into the DNA. There are also gene structure problems this mechanism would encounter (introns, etc).

    And this in not from a lack of looking. Molecular biologists work with RNA copies every day, and this has never been noted.

    This is the problem with this sort of out-of-lab hypothesizing. There are a series of thing that are observed every day in the lab. Our current models of molecular biology can predict and explain this. A hypothesis like the one you provided above sounds great, and picks out a few existing reactions and spins them into a story. But thing never happen that way in the lab.

    ReplyDelete

  135. You don't even know how to compute the odds so how can you make an affirmative statement?


    "The odds" have been computed. There is an entire discipline called population genetics that looks at, models, and tests these odds. Functional studies of specific genes that are then tested against evolutionary models are a rather powerful way to dissect (and so far, confirm) the process you are dismissing.

    One example that I left as a comment to another post...
    See;
    http://www.ncbi.nlm.nih.gov/pubmed/18768803?dopt=Abstract
    and http://www.ncbi.nlm.nih.gov/pubmed/18768804?dopt=Abstract

    ReplyDelete
  136. faultfinder, which god do you believe in?

    Is it the one from the old testament?

    Do you believe in original sin?

    Do you believe god gave his only child for our sins?

    I would really like to know the answers to these questions before we discuss this any further.

    If its not the god of the old testament, then please let me know which god it is that you think we share a common ancestor with. IT will help me understand where your coming from.

    ReplyDelete
  137. The other Jim said:

    ""The odds" have been computed. There is an entire discipline called population genetics that looks at, models, and tests these odds. Functional studies of specific genes that are then tested against evolutionary models are a rather powerful way to dissect (and so far, confirm) the process you are dismissing.

    One example that I left as a comment to another post...
    See;
    http://www.ncbi.nlm.nih.gov/pubmed/18768803?dopt=Abstract
    and http://www.ncbi.nlm.nih.gov/pubmed/18768804?dopt=Abstract"

    I followed both of your links and found nothing in either dealing with odds of a beneficial change coming about in an organism.

    The old theory of "one gene one trait" died.

    Its successor, "one gene one protein" suffered the same fate. (Nobel prize awarded for this mistake)

    Now we have the revelation that a single gene can produce 100 or more proteins. We have esitmates of the number of E Coli genes to be 3200. That means a mutation has the possibility to mutate the correct gene as 1 in 3200. Multiply that by the number of proteins that gene can produce, say 10 to be on the conservative side. That's 1 in 32000. Lensky admitted that it actually took three gene mutations for the E Coli to gain the ability to metabolize citrate. That's 1 in 3.2768 X 10^-13 if I counted my zeros correctly. In the real world you might want to factor in the probability of the single organism dies before reproducing. Then there is the size of the population to consider.

    I think you are living in a one gene one trait world. Even if that assumption were true the odds would still be incredibly small for a single gene mutation to produce a phenotype that would take over even a small population.

    There has been a study of how the Tibetans adapted to high altitude oxygen poor environment. Some 30 genes were involved. No data on how many proteins they code for. Would you like to calculate the odds of this happening spontaneously and by chance?

    ReplyDelete
  138. The other Jim said:

    "The theory sounds nice. The only problem is that there is absolutely no evidence that cDNA copies of the RNA sequence target and re-integrate into the DNA. There are also gene structure problems this mechanism would encounter (introns, etc).

    And this in not from a lack of looking. Molecular biologists work with RNA copies every day, and this has never been noted."

    To begin with I don't recall anonymous stating that cRNA was the mechanism responsible for his theory. Try "pRNA" as is shown in the following article.

    "In her most recent work, Grummt and her co-workers have shown for the first time that epigenetic regulation and regulation by noncoding RNAs interact. The scientists artificially introduced a noncoding RNA molecule called pRNA into cells. As a result, methyl labels are attached to a particular gene switch so that the genes behind it are not read. The trick is that pRNA exactly matches (is complementary to) the DNA sequence of this gene switch. The investigators found out that pRNA forms a kind of plait, or triple helix, with the two DNA strands in the area of this gene switch. Methyltransferases, in turn, are able to specifically dock to this 'plait' and are thus directed exactly to the place where a gene is to be blocked."
    http://www.sciencedaily.com/releases/2010/10/101018102239.htm

    Your egotism showed with the statement:

    "This is the problem with this sort of out-of-lab hypothesizing. There are a series of thing that are observed every day in the lab. Our current models of molecular biology can predict and explain this. A hypothesis like the one you provided above sounds great, and picks out a few existing reactions and spins them into a story. But thing never happen that way in the lab."

    Evolutionists never tire of denigrating another's knowledge. In doing so they frequently expose their own lack of knowledge as is shown here. Try getting down off your high horse and finding out what is going on in the scientific world. You might find your knowledge is dated.

    ReplyDelete
  139. scott said:

    "faultfinder, which god do you believe in?

    Is it the one from the old testament?

    Do you believe in original sin?

    Do you believe god gave his only child for our sins?

    I would really like to know the answers to these questions before we discuss this any further.

    If its not the god of the old testament, then please let me know which god it is that you think we share a common ancestor with. IT will help me understand where your coming from."

    I have not posted any serious comment concerning religion here. I do not discuss religion in scientific blogs. You are the only one attempting to bring religion into the discussion. I suggest you go to a religious blog.

    I know where you are coming from.

    ReplyDelete
  140. Hi The other Jim.
    You posted:
    "The only problem is that there is absolutely no evidence that cDNA copies of the RNA sequence target and re-integrate into the DNA."

    Is your point that they re-integrate but that the re-integration is not targeted?
    Or are you saying they are not even re-integrated?

    ReplyDelete
  141. faultfinder,

    I didn't bring religion into the discussion, you did. When I asked if you believed we all life shared a common ancestor your answer was, "Yes, and the common ancestor was God". It was at that point that religion was brought in.

    So, since this discussion is about evolution and you believe all life originated with god, I think the question of which god you believe in is relative.

    Why would you want to avoid discussing your position.

    If you "know where I'm coming from", yet you don't want to discuss it here, It leaves me to think you don't feel that confident that you could logically or rationally back up your position.

    Please answer my previous questions or at least acknowledge that you don't have a scientific explanation for your god hypothesis.

    ReplyDelete
  142. If the idea that I have been outlining is correct, we see a very elegant way Nature employs to adapt to the environment. First it does so by making epigenetic changes (without yet changing the DNA).
    Then after some number of generations, it goes the next step of changing the DNA.

    If this is correct it means that adaptation is based on a response to the environment. Adaptation is not based on the unlikely idea of random mutations.

    ReplyDelete
  143. @faultfinder Why steve, I didn't know you had wings.

    It was a simple, stress driven, epigenetic change.

    Happens all the time, you know.

    ReplyDelete
  144. scott said:

    "I didn't bring religion into the discussion, you did."

    Please don't distort my posts. I said, "I have not posted any SERIOUS comment concerning religion here." If you want to joke about religion or any other subject please do so and I will do the same, but intimating I tried to make religion a SERIOUS subject in this thread is just plain stupid. Didn't happen, and is not going to happen.

    If you want to make assinine statements about religion, be my guest. Debate yourself.

    ReplyDelete
  145. anonymous said:

    "If the idea that I have been outlining is correct, we see a very elegant way Nature employs to adapt to the environment. First it does so by making epigenetic changes (without yet changing the DNA).
    Then after some number of generations, it goes the next step of changing the DNA."


    What you state here is right on the mark. There is ample scientific evidence to back you up.

    Here are a couple of links you might find interesting:

    http://www.i-sis.org.uk/elephant.shtml

    http://www.spectator.org/archives/0104TAS/bethell0104.htm

    ReplyDelete
  146. faultfinder said:

    "I have not posted any SERIOUS comment concerning religion here."


    You haven't posted any SERIOUS comment concerning evolution either.

    ReplyDelete
  147. Oberski said:

    "It was a simple, stress driven, epigenetic change."

    Thanks for the feedback. It looks like I am getting my point across.

    ReplyDelete
  148. Scott said:

    "You haven't posted any SERIOUS comment concerning evolution either."

    That's because I think evolution is a bad joke.

    ReplyDelete
  149. @faultfinder Thanks for the feedback. It looks like I am getting my point across.

    Not the one you think you are.

    ReplyDelete
  150. I would like to take this idea another logical step.
    Here is what I have said so far:

    "If the idea that I have been outlining is correct, we see a very elegant way Nature employs to adapt to the environment. First it does so by making epigenetic changes (without yet changing the DNA).
    Then after some number of generations, it goes the next step of changing the DNA."

    AND we can see that reverse transcription of epigenetically-changed RNA may be the mechanism for changing the DNA.

    To take this one further step, let us consider what this means for evolution theory in general.
    What it means first is that adaptation can occur as a response to the environment. We can dispense with the idea of random mutations.

    Second we can begin to question whether random mutations are ever involved as the driver of change at the macroevolution level.

    ReplyDelete
  151. Anonymous said:
    "I would like to take this idea another logical step."

    How about reading a book on evolution, maybe The Greatest Show on Earth by Richard Dawkins, or Why Evolution is True by Jerry Coyne.

    Anonymous said:
    "If the idea that I have been outlining is correct,"

    Its not, so the rest of what you say is beside the point.

    Let me fix the last paragraph for you:

    Now That I've read about how evolution works, through random mutations and variation along with non-random natural selection, then I don't need to keep suggesting that epigentics is a new theory explaining macroevolution. That would be foolish of me knowing what I know now. I'm sure glad I read those books.

    Okay, I think that about fix's it for you.

    ReplyDelete
  152. Anonymous said:

    "Second we can begin to question whether random mutations are ever involved as the driver of change at the macroevolution level."

    And now you know why so many scientists are opposed to all the implications of epigenetics.

    With each new discovery in epigenetics the Neo-Darwinism TOE crumbles. It is no longer supported by evidence but by intransigence.

    ReplyDelete
  153. scott said:

    "Let me fix the last paragraph for you:

    Now That I've read about how evolution works, through random mutations and variation along with non-random natural selection, then I don't need to keep suggesting that epigentics is a new theory explaining macroevolution. That would be foolish of me knowing what I know now. I'm sure glad I read those books.

    Okay, I think that about fix's it for you."

    To begin, epigenesis does not explaing macroevolution. It explains adaptation. Nothing explains macroevolution.

    Let me rewrite your last paragraph:

    "Now That I've read a lot of inane explaination about how evolution is supposed to work, through random mutations and variation along with non-random natural selection, I am glad I know how epigentics explains what is really happening. Dawkins belongs in a loony bin and Coyle doesn't know come here from sic em. I'm sure glad I read those books as it has strengthened my understanding of how sadly mistaken scientists can be.

    ReplyDelete
  154. scott, I never said that epigenetics explains macroevolution. It does not.

    Do not put words in my mouth.

    ReplyDelete
  155. Anonymous said...

    "scott, I never said that epigenetics explains macroevolution. It does not.

    Do not put words in my mouth."

    Everything you've been saying would lead me to believe you think epigenetics is a better explanation for evolution instead of the current scientific theory/fact. Since we know macroevolution happens because of evolution, and you think epigenetics is a better explanation for evolution, then that only leaves me to believe that you think epigentics causes macroevolution. And if you don't think that, then what do you think causes macroevolution? Some kind of magical force or somthing?

    faultfinder said:

    "To begin, epigenesis does not explaing macroevolution. It explains adaptation. Nothing explains macroevolution."

    Wrong, the theory of evolution explains adaption. Which at first leads to microevolution. Those are changes within a species that lead to better survival. The more you adapt to a new or changing environment the less you are like your ancestors, as the changes pile up and accumulate you can become a new species given enough time. And time is something the theory of evolution has on its side. Thats macroevolution and theory of Evolution explains it perfectly.

    ReplyDelete
  156. My goodness, so this old thread is still going. We've now had time for faultfinder to give a 3rd contradictory explanation (though this time at last the right one) for Lenski's results:

    In Lenski's 50,000 generation experiment it was shown that two preceding gene expressions came before the final change that enabled one population to metabolize citrate.

    But that isn't the reason I thought the thread was worth returning to. Rather it's faultfinder's misunderstanding of probability math:

    Now we have the revelation that a single gene can produce 100 or more proteins. We have estimates of the number of E Coli genes to be 3200. That means a mutation has the possibility to mutate the correct gene as 1 in 3200. Multiply that by the number of proteins that gene can produce, say 10 to be on the conservative side. That's 1 in 32000. Lensky admitted that it actually took three gene mutations for the E Coli to gain the ability to metabolize citrate. That's 1 in 3.2768 X 10^-13 if I counted my zeros correctly.

    The error is contained in just three little words, "the correct gene." Evolution depends not on the "correct" mutation taking place, but on the effects of the mutations that constantly do take place (for humans, between 100 and 200 per generation on average). Three little words, but an enormous difference in probabilities.

    An easily understood example is the lottery. The odds of a $1 ticket winning the jackpot in the Powerball lottery in the U.S. are just slightly better than 200 million to one (see http://www.powerball.com/powerball/pb_prizes.asp). At the rate of one ticket/drawing per week, one wouldn't expect a "correct" winning ticket (yours, obviously:) more than once in 4 million years. But it's extremely unusual that someone doesn't win the Powerball within a 3 or 4 week period. So what makes the difference between a once-in-4 million years occurrence and something that happens once every week or few? That word "correct."

    Evolution isn't directed, so there is no "correct" outcome. New species can have any of a universe of genetic changes vs the ancestor species. Thus the evolution of myriad varied new species over long periods of time isn't improbable (like your winning the lottery would be), it's inevitable (like there being a lottery winner within a relatively short period of time).

    Getting back to the Lenski experiment, one of the fascinating things is his attempt to look for the "correct" mutation or series of mutations, the one(s) that would enable metabolism of a specific potential nutrient source. Just as you'd expect from probability math, getting the "correct" mutations is extremely unlikely. But if you looked at whether there were any mutations at all in these bacteria, there'd be a far different story.

    ReplyDelete
  157. Epigenetic change leading to DNA change is a better explanation of adaptation than the improbable idea of random mutations and natural selection.

    But epigenetic change leading to DNA change is not an explanation of macroevolution.

    But note that random mutation and natural selection is not an explanation of macroevolution either.

    ReplyDelete
  158. Anonymous writes:

    Epigenetic change leading to DNA change is a better explanation of adaptation....

    It's not a better explanation of anything if it seldom if ever occurs. If you think "random mutation" is rare, this sort of epigentic -> genetic change is much, much rarer to the extent it happens at all.

    From Wikipedia:

    The Weismann barrier is the principle that hereditary information moves only from genes to body cells, and never in reverse. In more precise terminology hereditary information moves only from germline cells to somatic cells (that is, soma to germline feedback is impossible).

    * * *

    In the late 20th century there have been criticisms of an impermeable Weismann barrier. These criticisms are all centered around the activities of an enzyme called reverse transcriptase.

    Evidence has begun to mount for horizontal gene transfer. Different species appear to be swapping genes through the activities of retroviruses. Retro-viruses are able to transfer genes between species because they reproduce by integrating their code into the genome of the host and they often move nearby code in the infected cell as well.

    * * *

    Other evidence against Weismann's barrier is found in the immune system. A controversial theory of Edward J. Steele's suggests that endogenous retroviruses carry new versions of V genes from soma cells in the immune system to the germ line cells.

    * * *

    Even if both of these possible exceptions turn out to be legitimate, the Weismann barrier just loses its absolute status. Without further examples, the penetration of the Weismann barrier is still very much an exception.

    Anonymous writes:

    ...the improbable idea of random mutations and natural selection....

    It's only improbable if you get the math wrong. If you have the math correct, it's not only not improbable, it's inevitable. See my previous response to faultfinder.

    But note that random mutation and natural selection is not an explanation of macroevolution either.

    The position you've taken makes no sense whatever if you think about it a little.

    I assume you're defining "microevolution" as change within a species and "macroevolution" as change from one species to a different one. Let's look at bacteria, which, like the majority of life on Earth, reproduce asexually. That means we can't use the "shorthand" definition for sexually reproducing species that one species can't interbreed with another. Let's look at what happens if, as sometimes occurs, what had been defined as one species is now classified as two. So the bacteria which were free to "micro-evolve" into each other as long as they were the same species have all now received some sort of email that tells them they can no longer do this because it would now be "macroevolution"?

    ReplyDelete
  159. Hi, The other Jim.
    You posted:
    "The only problem is that there is absolutely no evidence that cDNA copies of the RNA sequence target and re-integrate into the DNA."

    Is your point that they re-integrate but that the re-integration is not targeted?
    Or are you saying they are not even re-integrated?

    ReplyDelete
  160. The Weismann barrier has lost its absolute status.

    It is not an absolute barrier.
    Good to know. And consistent with what I have suggested.

    ReplyDelete
  161. What does this mean:

    http://en.wikipedia.org/wiki/Weismann_barrier

    "If the Weismann barrier is permeable, then genetic treatments of somatic cells may actually result in a heritable change to the genome, possibly resulting in the genetic engineering of the human species rather than just individuals."

    ReplyDelete
  162. anonymous writes:

    "The Weismann barrier has lost its absolute status."

    It is not an absolute barrier.
    Good to know. And consistent with what I have suggested.


    Your statement loses the context in the original article: Even if various controversial claims are true, all it means is that the Weismann barrier has lost its absolute status. However, such exceptions would be quite rare.

    Having very rare exceptions is not consistent with any suggestion that breaches of the Weismann barrier would be a better candidate to drive evolutionary change than the comparatively frequent 100-200 random genetic changes per human per generation.

    ReplyDelete
  163. anonymous asks what's meant by the following quote from Wikipedia:

    "If the Weismann barrier is permeable, then genetic treatments of somatic cells may actually result in a heritable change to the genome, possibly resulting in the genetic engineering of the human species rather than just individuals."

    My assumption is that it's contrasting current genetic therapies, which do not cause heritable changes and thus operate on an individual level, to the possibility, if the Weismann barrier can be overcome, of inducing heritable genetic changes and thus propagating those changes through the human species over generations.

    ReplyDelete
  164. Faultfinder and Anonymous stick to the same position: they are one person.

    ReplyDelete
  165. It is hard for some people here to grasp that two people could have similar ideas that are different than they have.

    ReplyDelete
  166. Thanks for the following Jud. What you say makes sense.

    "My assumption is that it's contrasting current genetic therapies, which do not cause heritable changes and thus operate on an individual level, to the possibility, if the Weismann barrier can be overcome, of inducing heritable genetic changes and thus propagating those changes through the human species over generations."

    And indeed, if what I have been proposing is correct (and I think it is) it would explain changes through any species, over generations.

    ReplyDelete
  167. Wikipedia
    Even if both of these possible exceptions turn out to be legitimate, the Weismann barrier just loses its absolute status. Without further examples, the penetration of the Weismann barrier is still very much an exception.
    Seems dismissing the Weismann barrier is premature - to the contrary, that dismissal is going to be another example of epigenetic nonsense put into the wastebin.

    ReplyDelete
  168. faultfnder said:
    "To begin, epigenesis does not explain macroevolution. "
    First correct statement by faultfinder.

    "It (epigenetics) explains adaptation."
    Epigenetics consists of a selected response to predictable environmental conditions, and is therefore part of the evolutionary adaptive repertoire. Epigenetics without any previous selection is not adaptive.

    "Nothing explains macroevolution"
    Here the creationist credentials come.....
    Waste of time to talk to.

    ReplyDelete
  169. http://en.wikipedia.org/wiki/Edward_J._Steele

    "Science philosopher Ross Honeywill highlighted Steele's work by proposing that in finding the mechanism for Lamarckian evolution Steele had simultaneously combined the best of Darwin and Lamarck. He proposed a modern, well-supported Lamarckian theory could be devised, consistent with well-documented parts of modern molecular genetics, able to be articulated with a surviving core of Darwinian natural selection: a kind of Meta-Lamarckism. "Steele identified RNA as the critical transcription vehicle because unlike DNA, it was the medium that was out there in contact with what was going on in the body. It was the obedient servant that knew the secret language, the secret handshake. What a breakthrough it was to discover from Lamarck via Steele that RNA could take vital changes back to the DNA for generational improvements. But imagine what it means if the RNA is capable of carrying its own information through generations; imagine the Meta-Lamarckian consequences and opportunities written all over these discoveries."[15]"

    ReplyDelete
  170. Anonymous writes:

    And indeed, if what I have been proposing is correct (and I think it is) it would explain changes through any species, over generations.

    Well, there are several problems with what you are proposing:

    - The particular Wikipedia quote you're referring to at the moment is talking about prospects of overcoming the Weismann barrier in the future, not whether the barrier has been crossed in the past.

    - There are mechanisms proposed for crossing of the barrier having taken place in the past. These are controversial - it hasn't been established that they've occurred.

    - Even if it is established that crossing of the barrier has taken place, the proposed mechanisms are not instances of a living thing's epigenetic regulatory changes propagating to its own DNA. Rather, the proposed epigenetic agent is a retrovirus, either (1) a currently viable retrovirus that changes the DNA of a germ cell, or (2) a retrovirus whose changes to DNA became incorporated into the germline long ago, i.e., an "endogenous retrovirus" (ERV). Such changes would be a subset of the normal genetic mutation rate, which those pushing epigenetics say cannot account for evolutionary change.

    That last point is worth additional comments.

    - First, note that so far speculation in the scientific community about ways to breach the Weismann barrier includes nothing along the lines of what I understand you to be proposing, that is, taking changes in a living thing's epigenetic regulatory mechanism and incorporating them in that same living thing's own germline DNA.

    - Second, even if the controversial mechanisms proposed in the Wikipedia article turn out to be correct, and even if, furthermore, transmission of changes from the epigenetic regulatory system to germline DNA turns out to be possible, it isn't relevant to evolution.

    Why not? Because the overall mutation rates for humans and other living things are measurable and have been the subjects of numerous experiments to determine those rates. No matter what the root cause of a particular mutation, it's part of that overall rate - the rate that people pushing epigenetics say is inadequate to support evolution. In other words, any genomic DNA mutations caused by epigenetics (even supposing a mechanism for that was found) don't add to the overall mutation rate, they're part of it.

    For example, the overall genetic mutation rate for humans amounts to somewhere between 100 - 200 per generation. If transmission of epigenetic change to the genome turns out to be possible, that overall number doesn't change, only the proportion of it which might be attributable to epigenetic versus other causes. Thus if the overall mutation rate is inadequate, epigenetics is part of the problem, not an alternative solution.

    Of course the overall mutation rate is mathematically adequate, as worked out by population geneticists almost a century ago and as illustrated in my previous response to faultfinder.

    ReplyDelete
  171. Jud, I appreciate that you respond in a decent way. May I suggest the following:

    Do not relate everything to the random changes that you see in the genome. I know you think of them as being very significant, but just put that idea to the side for the moment.

    The changes that I am suggesting are not part of the random mutations. They would be specific intended changes to incorporate the epigenetic info into the DNA. They are the drivers of adaptation. The random mutations are just noise that are not involved in adaptation.

    I know this line of thinking is hard for you because you think everything is related to random mutations.

    ReplyDelete
  172. http://lamarcksevolution.com/the-case-for-meta-lamarckism

    "Scientific focus is now shifting from DNA as the supposedly immutable architect of life’s blueprints, to RNA acting as a courier delivering myriad messages from everyday experiences back to an ever-changing genome in the DNA. RNA is constantly evaluating environmental conditions and not only carrying that information back to the DNA, but also making its own decisions about what cells were produced and the form organisms would take.

    Epigenetics—literally ‘above genetics’—has emerged as the new biology as Neo-Darwinian dogma falls from grace. Darwin’s natural selection is still considered to be the real thing, but the Neo-Darwinian obsession with random gene mutation as the determinant of evolutionary direction is increasingly seen for the fallacy it always was. It is as unreal as the Weismann Barrier. And today the world stands on the edge of a new scientific era."

    ReplyDelete
  173. Another interesting link:
    http://www.economist.com/node/9333471
    "IT IS beginning to dawn on biologists that they may have got it wrong. Not completely wrong, but wrong enough to be embarrassing. For half a century their subject had been built around the relation between two sorts of chemical. Proteins, in the form of enzymes, hormones and so on, made things happen. DNA, in the form of genes, contained the instructions for making proteins. Other molecules were involved, of course. Sugars and fats were abundant (too abundant, in some people). And various vitamins and minerals made an appearance, as well. Oh, and there was also a curious chemical called RNA, which looked a bit like DNA but wasn't. It obediently carried genetic information from DNA in the nucleus to the places in the cell where proteins are made, rounded up the amino-acid units out of which those proteins are constructed, and was found in the protein factories themselves.

    All that was worked out decades ago. Since then, RNA has been more or less neglected as a humble carrier of messages and fetcher of building materials. This account of the cell was so satisfying to biologists that few bothered to look beyond it. But they are looking now. For, suddenly, cells seem to be full of RNA doing who-knows-what."

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  174. Anonymous writes:

    Jud, I appreciate that you respond in a decent way.

    Thanks, same here.

    The changes that I am suggesting are not part of the random mutations. They would be specific intended changes to incorporate the epigenetic info into the DNA. They are the drivers of adaptation. The random mutations are just noise that are not involved in adaptation.

    As you note, in order to propagate across generations, changes must occur in DNA ("...changes to incorporate the epigenetic info in the DNA"). When experiments are done to compare DNA across generations, the experimental methodologies don't exclude changes from particular causes (e.g., epigenetic vs. cosmic rays) or look for directed vs. random changes. The machines don't know how to distinguish. They simply find every place where the "letters" of the DNA "code" have changed. The total number of changes found averages about 100-200 per generation for humans. So whether caused by changes in the epigenetic regulatory system or otherwise, and whether random or directed, 100-200 mutations is the sum total.

    Thus anyone who feels the number of mutations is insufficient to explain evolution is not helped by finding a different explanation for exactly the same total number of mutations.

    Regarding the distinct issue of whether the mutations are random or directed, there are reasons I would put my money on random if I were a betting man.

    First, if it is a directed process it is incredibly wasteful. The vast, vast majority of DNA changes from generation to generation have no significant impact whatever. (If this weren't so, and there were 100-200 significant changes per person per generation, humanity would soon die out [for an analogous idea, see "error catastrophe" in retroviruses] or become unrecognizable.)

    Second, why design by directed incremental changes through an evolutionary process? Such changes take a very long time to propagate through a species. Why would anything smart and powerful enough to direct all the changes that took the first of the homo genus to us over millions of years not just design the end product in the first place (whatever that is, since we're still mutating and evolving)? Instead of starting with something that looked like a dog with hooves and causing it to evolve over 55 million years into a large swimming creature with skeletal feet inside its body, why not just make a whale?

    There is also the problem of disease. Genetic diseases that cause millions of men, women and chidren to suffer and die are more indicative to me of random errors than intelligent planning, unless one attributes sheer malevolence to the planner. Immunity shows the same characteristics. Malaria parasites evolve immunity to drugs while the means of some small degree of human genetic resistance has caused millions to suffer with sickle cell trait. This certainly seems like a random mutation, usually negative, under strong positive selection by disease pressure, unless one wishes to attribute the lack of a more efficacious, less costly means of genetic resistance to incompetent or deliberately malevolent design.

    Finally, I must point out once again that this is a problem that doesn't need solving. The mutation rate we have and the causes of mutation we know about are perfectly adequate to explain, in mathematically unassailable terms, the evolutionary changes we see.

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  175. Jud you have said:
    "As you note, in order to propagate across generations, changes must occur in DNA ("...changes to incorporate the epigenetic info in the DNA"). When experiments are done to compare DNA across generations, the experimental methodologies don't exclude changes from particular causes (e.g., epigenetic vs. cosmic rays) or look for directed vs. random changes. The machines don't know how to distinguish. They simply find every place where the "letters" of the DNA "code" have changed. The total number of changes found averages about 100-200 per generation for humans. So whether caused by changes in the epigenetic regulatory system or otherwise, and whether random or directed, 100-200 mutations is the sum total."

    You are still missing the point that I am making.
    Adaptation does not occur from random mutations. Random mutations are noise.

    But instead of arguing this I am interested in your thoughts about a couple of questions.

    In your thinking what is the point of reverse transcription? Why does that process occur at all?

    and

    You mentioned "cosmic rays" as a possible cause.
    I do not know if you were kidding.
    Is there any argument that can be made for the evolution effect of cosmic rays?

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  176. Anonymous said:

    You mentioned "cosmic rays" as a possible cause. I do not know if you were kidding.
    Is there any argument that can be made for the evolution effect of cosmic rays?

    I know this was a question for Jud, but I thought I would try to tackle it if you don't mined.

    When radiation(cosmic rays) from the sun in the form of subatomic particles passes through our bodies, it sometimes hits a strand of DNA in our sex cells. This damages the DNA, as it "heals" or "repairs itself" the chemical structure will change (mutation).

    The mutations can be deleterious, neutral or beneficial, its completely random.

    An organism born with a "bad' mutation might not survive long enough to reproduce. Neutral mutations just kinda of go along for the ride and a lot will manage to get passed on without much evolutionary change. The rarer good mutations that benefit an organism and give it higher likelihood of survival to reproductive age will get passed on(selected naturally, because they were beneficial), hence Natural selection. Which isn't random, since it would only be logical for the good mutations to get passed on and the bad ones to not get passed on.

    This is widely thought to be one of the players in evolution by natural selection, along with a few others.

    In asexual organisms it is thought to be the dominant form of mutation and evolutionary change.

    I'm not a biologist, so my explanations are from a laymans point of view encompassing all the personal research I've done. I'm sure others here could explain in more precise detail. But I think I'm pretty much on the right track here.

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  177. Anonymous writes:

    You are still missing the point that I am making.
    Adaptation does not occur from random mutations. Random mutations are noise.


    Nope, not missing what you're saying at all. I'm simply saying, assuming for the sake of argument some mutations are directed rather than random, it doesn't make the total number of mutations greater. The numerous experiments that have been done don't distinguish among or exclude certain changes; they're all counted. So just giving an example with numbers: Assume an experimenter has counted 100 DNA changes between parent and child. If we could tell 20 changes were directed, that wouldn't make 120 changes, it would make 20 directed and 80 random.

    The reason I keep making that point is because of the folks who have got the probability math wrong and insist 100-200 mutations per generation isn't sufficient.

    In fact, you and I appear to be reasonably ad item regarding the math: You say most of the 100-200 changes are random noise, I say most of them have no significant impact, which amounts to pretty much the same thing. At the end of the day, we are both depending on some subset of that 100-200 mutation per generation total to account for the evolutionary changes we see.

    Where we differ, of course, is that you feel the mutations with evolutionary impact are directed, while I think the evidence is pretty tremendous they aren't (or if they are, the director has a lot to answer for on grounds of incompetence and malevolence). I've already gone into a few of the reasons for my conclusion in a previous comment, so they don't need to be repeated.

    You mentioned "cosmic rays" as a possible cause. I do not know if you were kidding. Is there any argument that can be made for the evolution effect of cosmic rays?

    Let me begin with a brief excerpt from a recent news story about radiation releases from the Japanese reactors:

    Kirby Kemper, a physicist at Florida State University, told MedPage Today and ABC News in an e-mail that the health risk attributable to low levels of radiation remains controversial.

    But, he noted by way of comparison, "people in Denver ... have about twice the background radiation level compared to people in Florida due to cosmic rays, but actually have a longer life span than people from Florida."

    Ionizing radiation, including cosmic rays, is a well-known mutagen. That's why the bib the dentist gives you when taking X-rays covers your reproductive organs.

    So we receive quite a bit more radiation in the form of cosmic rays than most people are aware of, and those cosmic rays can and do cause DNA mutations. I think such mutations are like all others - random, and may or may not have an evolutionary impact (likely not) - while I assume you would believe, since the mutations caused by cosmic rays are random, they would be "noise" and would by definition have no evolutionary impact.

    Fair characterization of your view?

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  178. Anonymous writes:

    In your thinking what is the point of reverse transcription? Why does that process occur at all?

    This is something like asking what the "point" is of nuclear fusion. It's a natural process that's also been harnessed for certain ends (currently by humans for bombs, though research on less terrible uses continues).

    Reverse transcription is used by viruses to replicate, creating awful diseases in humans and other animals (e.g., HIV/SIV causing AIDS in humans and simians, respectively).

    It is also used in eukaryotes by telomerase to add DNA sequence repeats to the ends of chromosomes, preventing loss of functional DNA when chromosomes are copied.

    It is also used by retrotransposons. From our old friend Wikipedia:

    Retrotransposons copy themselves to RNA and then back to DNA that may integrate back to the genome. The second step of forming DNA may be carried out by a reverse transcriptase which the retrotransposon encodes. Transposition and survival of retrotransposons within the host genome are possibly regulated both by retrotransposon- and host-encoded factors, to avoid deleterious effects on host and retrotransposon as well, in a relationship that has existed for many millions of years between retrotransposons and their plant hosts. The understanding of how retrotransposons and their hosts' genomes have co-evolved mechanisms to regulate transposition, insertion specificities, and mutational outcomes in order to optimize each other's survival is still in its infancy.

    However,

    Most retrotransposons are very old and through accumulated mutations, are no longer able to retrotranspose.

    Also note from the same Wikipedia article that retrotransposons make up a far greater proportion of plant than animal genomes.

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  179. Jud here is a question for you based on something the other Jim posted:
    "The only problem is that there is absolutely no evidence that cDNA copies of the RNA sequence target and re-integrate into the DNA."

    Is your point that they re-integrate but that the re-integration is not targeted?
    Or are you saying they are not even re-integrated?

    Jud, can you answer my question?

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  180. Jud you posted:

    "The reason I keep making that point is because of the folks who have got the probability math wrong and insist 100-200 mutations per generation isn't sufficient."

    The answer to this is the following:
    100-200 RANDOM mutations (changes) are not sufficient.
    100-200 DIRECTED changes are more than sufficient.

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  181. Jud, I had asked what was the purpose of reverse transcription. I am asking a fair question.
    For example, when we see repair mechanisms in the cell we say the purpose is to repair the cell.
    When we see "proof reading mechanisms we say the purpose is to ensure the fidelity of cell duplication.
    When we see the transcription and translation of DNA to RNA to protein we say that the purpose is to take the DNA instructions and produce the proteins for the functioning of the cell.

    You cannot avoid my question by saying that reverse transcription "just is".

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  182. Jud you posted:
    "people in Denver ... have about twice the background radiation level compared to people in Florida due to cosmic rays, but actually have a longer life span than people from Florida."

    So cosmic rays can have a beneficial effect.
    I wonder if genetic engineers have begun using controlled high energy charged particles (equivalent to "cosmic rays") for controlled genetic engineering.
    Is there anything in principle that rules this idea out?

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  183. Anonymous ask:

    So cosmic rays can have a beneficial effect.
    I wonder if genetic engineers have begun using controlled high energy charged particles (equivalent to "cosmic rays") for controlled genetic engineering.
    Is there anything in principle that rules this idea out?

    It has been used as a tool in artificial selection. Seeds are sometimes exposed to radiation then planted and grown in hopes of finding at least one plant with useful characteristics. That one plant is then selected and used for the next crop. It may be subjected to the same process in hopes of finding even more beneficial characteristics, and so on, and so on.

    I know this process has been used by cannabis cultivators trying to develop more powerful strains.

    I Think genetic engineering is a different process, using radiation like I've shown it to be used is just a rev'd up form of artificial selection.

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  184. Anonymous writes:

    Jud you posted:

    Fact A - "people in Denver ... have about twice the background radiation level compared to people in Florida due to cosmic rays, but actually have a longer life span than people from Florida."

    Proposition B - So cosmic rays can have a beneficial effect.

    [Elmer Fudd voice] Be vewwy, vewwy kehfuw:[/Elmer Fudd voice]

    Proposition B does not necessarily follow from Fact A.

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  185. Anonymous writes:

    For example, when we see repair mechanisms in the cell we say the purpose is to repair the cell....

    You cannot avoid my question by saying that reverse transcription "just is".

    Well, I responded to your question by saying the function of reverse transcription in retroviruses is to cause the host cell's DNA to replicate retrovirus. That seems pretty plain. And I said the function of telomerase is to protect genes during duplication. That seems pretty plain, too.

    But when Wikipedia says of retrotransposons in plant hosts -

    The understanding of how retrotransposons and their hosts' genomes have co-evolved mechanisms to regulate transposition, insertion specificities, and mutational outcomes in order to optimize each other's survival is still in its infancy.

    - then I don't want to hazard a guess as to what their function in human hosts is, if any.

    I don't consider that avoiding your question, I consider it due modesty. :-)

    Someone who has a much better basis for giving an opinion is Larry, and he has given it repeatedly in this blog. I haven't done the search myself, but perhaps Googling Sandwalk and "retrotransposons," "transposons," "LINEs" and "SINES" would be a good place to start.

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  186. Anonymous writes:

    The answer to this is the following:
    100-200 RANDOM mutations (changes) are not sufficient.
    100-200 DIRECTED changes are more than sufficient.


    The phrase "more than sufficient" regarding numbers of directed changes may be particularly apt, since with that many significant changes per generation we might be in "error catastrophe" equivalent territory.

    I'm guessing you aren't going to insist all the changes are directed, but would be willing to settle for some much lower number of impactful changes, the rest being "noise." As I mentioned previously, regarding numbers of significant changes (though not the question of directed vs. random) my impression is that we can probably come pretty close to agreement.

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  187. anonymous writes:

    Jud here is a question for you based on something the other Jim posted:

    "The only problem is that there is absolutely no evidence that cDNA copies of the RNA sequence target and re-integrate into the DNA."

    Is your point that they re-integrate but that the re-integration is not targeted?
    Or are you saying they are not even re-integrated?


    Jud, can you answer my question?

    The only instances in nature of integrating cDNA into the host genome I've been able to find in a brief search (which of course shouldn't be taken as authoritative, but as an attempt to provide whatever potentially responsive information I can) occur through the actions of the HIV and Herpes simplex viruses.

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  188. It will be very interesting when human genetic engineers begin to use
    high energy charged particles (equivalent to "cosmic rays") for controlled genetic engineering.

    It will then inspire some scientists to seriously analyze the rays from the sun and from the galaxy to see if there are patterns there and how cells could be responding to that information.

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  189. http://educate-yourself.org/be/lakhovskyindex.shtml

    "What Lakhovsky discovered was simply mind boggling: He postulated that all living cells (plants, people, bacteria, parasites, etc.) possess attributes which normally are associated with electronic circuits. These cellular attributes include resistance, capacitance, and inductance. These 3 electrical properties, when properly configured, will cause the recurrent generation or oscillation of high frequency sine waves when sustained by a small, steady supply of outside energy of the right frequency. This effect is known as resonance. It's easiest to compare it with a child swinging on a playground swing. As long as the parent pushes the swing a little at the right moment (the correct 'frequency'), the child will continue to swing high and continuously. In electronics, circuits which generate these recurrent sine waves can be called electromagnetic resonators, but more commonly they are referred to as oscillators. Lakhovsky tells us that not only do all living cells produce and radiate oscillations of very high frequencies, but they also receive and respond to oscillations imposed upon them from outside sources. This outside source of radiation or oscillations are due to cosmic rays which bombard the earth continuously. This stupendous realization, achieved during the golden years of radio, not only led to a new method of healing by the application of high frequency waves, but broadened appreciation for the newly emerging field of hidden science known as Radionics or Radiathesia."

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  190. We as humans understand the phenomena of radio. We know that radio waves can impart information.
    But we do not generalize that idea to the idea that other waves could impart information.
    We do not think that cosmic rays could be imparting information to the cell.
    This all stems back to the idea that humans think that we are the only level of intelligence. We think that there cannot be a level of intelligence operating at the level of the cell. We think that there cannot be a level of intelligence operating at the level of the sun.
    But all the evidence seems to show us (if our minds are open even a little bit) that there is intelligence at other levels.

    This is not a creationist idea. It is an idea based on levels of intelligence. Just as we recognize the level of human intelligence.

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  191. http://en.wikipedia.org/wiki/Directed_mutagenesis
    "Directed mutagenesis, also known as directed mutation, is a hypothesis proposing that organisms can respond to environmental stresses through directing mutations to certain genes or areas of the genome.
    The hypothesis was first proposed in 1988 by John Cairns, of Harvard University,[citation needed] who was studying Escherichia coli that lacked the ability to metabolize lactose. He grew these bacteria in media in which lactose was the only source of energy. In doing so, he found that the rate at which the bacteria evolved the ability to metabolize lactose was many orders of magnitude higher than would be expected if the mutations were truly random. This inspired him to propose that the mutations that had occurred had been directed at those genes involved in lactose utilization.[1][2]
    Later support for this hypothesis came from Susan Rosenberg, then at the University of Alberta, who found that an enzyme involved in DNA recombinational repair, recBCD, was necessary for the directed mutagenesis observed by Cairns and colleagues in 1989.
    The directed mutagenesis hypothesis was challenged in 2002, when John Roth and colleagues showed that the phenomenon was due to general hypermutability due to selected gene amplification, and was thus a "standard Darwinian process." Later research published in 2006 by Jeffrey D. Stumpf, Anthony R. Poteete, and Patricia L. Foster, however, concluded that amplification could not account for the adaptive mutation and that "mutants that appear during the first few days of lactose selection are true revertants that arise in a single step".

    This seems to be conclusive. Change is brought about by the organism itself and not though random changes.

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  192. Anonymous cites a Wikipedia article on "Directed mutagenesis" and writes:

    This seems to be conclusive. Change is brought about by the organism itself and not though random changes.

    The scientists who published the 2006 research cited in that Wikipedia article would be quite surprised by your statement. (Hint: When the citations in Wikipedia are to New Scientist magazine articles, you may - in fact, you should - go on to read the actual research papers.)

    First of all, they're not referring to it as "directed" anything now, they've switched to "adaptive mutation." (You might get an inkling of where this is going from the loss of the term "directed.")

    The 2006 article says that DNA amplification (sometimes misleadingly referred to as the "Darwinian" alternative) can't account for specific increased mutation activity observed in E. coli under a particular type of stress, and says instead that the following better fits the data:

    recombination-dependent mutation, which specifies that recombination occurring in nongrowing cells stimulates error-prone DNA synthesis

    Got that? "Error-prone," the exact opposite of "according to plan." As I've noted in comments on Sandwalk, other organisms displaying "error-prone" genetic duplication include retroviruses such as HIV. These retroviruses are often proposed to be living on the edge of "error catastrophe," where the errors in genetic duplication would mount up to such a degree that viability would suffer catastrophically and the population would collapse.

    So no, you haven't found some sort of revolutionary process outside evolutionary theory, you've just misunderstood an exciting research area (no great surprise when a Wikipedia article quotes New Scientist magazine).

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  193. Jud, I never said "according to plan".
    Where did you get that from?

    ReplyDelete
  194. Here is the article that Jud was referencing:

    http://www.ncbi.nlm.nih.gov/pubmed/17209030
    "When the Lac- strain of Escherichia coli, FC40, is incubated with lactose as its sole carbon and energy source, Lac+ revertants arise at a constant rate, a phenomenon known as adaptive mutation. Two alternative models for adaptive mutation have been proposed: (i) recombination-dependent mutation, which specifies that recombination occurring in nongrowing cells stimulates error-prone DNA synthesis, and (ii) amplification-dependent mutation, which specifies that amplification of the lac region and growth of the amplifying cells creates enough DNA replication to produce mutations at the normal rate. Here, we examined several of the predictions of the amplification-dependent mutation model and found that they are not fulfilled. First, inhibition of adaptive mutation by a gene that is toxic when overexpressed does not depend on the proximity of the gene to lac. Second, mutation at a second locus during selection for Lac+ revertants is also independent of the proximity of the locus to lac. Third, mutation at a second locus on the episome occurs even when the lac allele under selection is on the chromosome. Our results support the hypothesis that most Lac+ mutants that appear during lactose selection are true revertants that arise in a single step from Lac- cells, not from a population of growing or amplifying precursor cells."

    The authors show that alternative (ii) is not the explanation.
    This dos not mean that alternative (i) is correct.

    ReplyDelete
  195. http://en.wikipedia.org/wiki/Adaptive_mutation
    "Furthermore, when looking for additional mutations only in cells that have already reverted to Lac+, it would certainly be the case that other, unnecessary mutations would be less numerous - especially since most are deleterious. However, Barry Hall has provided evidence that the mutation rate in bacteria under environmental stress increases across the board, most likely indiscriminately. When testing for tryptophan revertants (trp− → trp+, i.e. cells that have regained the ability to make tryptophan), he found that occurrence of auxotrophic mutants increased as well. Tryptophan revertants, which had been exposed to the environmental stress of lacking the amino acid, saw a 1.8% rate of auxotrophy for any other amino acid. When testing for auxotrophy in cells in non-stressed colonies, he found a rate below 0.01%. From these data, Hall hypothesized that cells under stress enter a "hyper-mutable state," where cells increase their general rate of mutation, increasing the overall probability that they will acquire a mutation conferring a phenotype that aids their survival. Hall later determined that his mutants were the result of transposon activity, and concluded that his results were in fact about transposon biology, and not mutagenesis.

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  196. I think you are the same anonymous that I pointed this out to at another post. "Mutator" bacteria (those carrying a mutation in replication or DNA repair genes, that produce higher random mutation rates) have a competitive advantage in changing environments. This implies that random mutations are sufficient to produce the beneficial DNA changes. No purpose-driven re-writing of the genome required.

    Here is a paper that produces a simulation to model this phenomenon.


    Genetics, Vol. 164, 843-854, July 2003.

    Recent studies have found high frequencies of bacteria with increased genomic rates of mutation in both clinical and laboratory populations. These observations may seem surprising in light of earlier experimental and theoretical studies. Mutator genes (genes that elevate the genomic mutation rate) are likely to induce deleterious mutations and thus suffer an indirect selective disadvantage; at the same time, bacteria carrying them can increase in frequency only by generating beneficial mutations at other loci. When clones carrying mutator genes are rare, however, these beneficial mutations are far more likely to arise in members of the much larger nonmutator population. How then can mutators become prevalent? To address this question, we develop a model of the population dynamics of bacteria confronted with ever-changing environments. Using analytical and simulation procedures, we explore the process by which initially rare mutator alleles can rise in frequency. We demonstrate that subsequent to a shift in environmental conditions, there will be relatively long periods of time during which the mutator subpopulation can produce a beneficial mutation before the ancestral subpopulations are eliminated. If the beneficial mutation arises early enough, the overall frequency of mutators will climb to a point higher than when the process began. The probability of producing a subsequent beneficial mutation will then also increase. In this manner, mutators can increase in frequency over successive selective sweeps. We discuss the implications and predictions of these theoretical results in relation to antibiotic resistance and the evolution of mutation rates.

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  197. Anonymous writes:

    Jud, I never said "according to plan".

    Where did you get that from?

    Oh, from some fellow commenting under the 'nym "Anonymous" who wrote:

    This seems to be conclusive. Change is brought about by the organism itself and not through random changes.

    Non-random. That would mean in accordance with some sort of direction, pattern, or plan, would it not? How else would you tell it was not random than by comparison to a pattern?

    Instead, the research referenced by the Wikipedia article you quoted extensively says that in at least one stressful environment, E. Coli respond with a gene duplication process more subject to error, meaning less like the non-random pattern or template that is being duplicated.

    You then replied by saying that research wasn't necessarily correct, for which objection we have as evidence...well, umm, your opinion, I guess.

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  198. Jud, I can't tell whether you are just pretending to not get it, or whether you actually don't get it.
    But either way, I am coming to see that I am wasting my time responding to every misunderstanding you come up with.

    ReplyDelete