Monday, July 31, 2017

New Study: Transgenerational Epigenetics Can Have a Profound Impact

The Third Rail of Evolution

In the spring of 2006 I gave a talk on the campus of Cornell University and afterwards was joined by then Cornell professors Richard Harrison and Kern Reeve for a sort of panel discussion or debate about biological evidences and origins. I presented a dozen or so interesting and important evidences that I felt needed to be recognized in any discussion of origins. The evidences falsified key predictions of evolution and so needed to be acknowledged and reckoned with, one way or another. One of the items on my list was the so-called directed adaptation mechanisms which, broadly construed, can include everything from non random, directed, mutations to transgenerational epigenetic inheritance. But I was in for a big surprise when Harrison and Reeve gave their response.

Directed adaptation is reminiscent of Lamarckism. Rather than natural selection acting over long time periods on biological variation which is random with respect to need, directed adaptation mechanisms provide rapid biological change in response to environmental challenges. Like physiological responses, directed adaptation can help an organism adjust to shifts in the environment. But those adaptations can then be inherited by later generations. Stresses which your grandparents were subjected to may be playing out in your own cells.

In the twentieth century evolutionists had strongly rejected any such capability. Lamarckism was the third rail in evolutionary circles. And for good reason, for it would falsify evolutionary theory. But empirical evidence had long since pointed toward the unthinkable, and by the twenty first century the evidence was rapidly mounting.

While there was of course still much to learn in 2006 about directed adaptation (as there still is today for that matter), it could no longer be denied, and needed to be addressed. At least, that is what I thought.

I was shocked when Harrison and Reeve flatly denied the whole story. Rick waved it off as nothing more than some overblown and essentially discredited work done by Barry Hall and John Cairns, back in the 1970s and 80s (for example here).

But there was a body of work that had gone far beyond the work of Hall and Cairns. Incredulously I responded that entire books had been written on the subject. Rick was quick to respond that “entire books are written about all kinds of discredited things.”

True enough. It was me versus two professors on their home turf with a sympathetic audience, and there was no way that I was going to disabuse them of what they were convinced of.

Confirmation testing and theory-laden evidence are not merely philosophical notions. They are very real problems. I’m reminded of all this every time a new study adds yet more confirmation to the directed adaptation story, such as the recent paper out of Nicola Iovino’s lab on transgenerational epigenetic inheritance in house flies, which states:

Gametes carry parental genetic material to the next generation. Stress-induced epigenetic changes in the germ line can be inherited and can have a profound impact on offspring development.

The press release gives little indication of the controversy as it admits that these findings were once considered impossible:

It has long been thought that these epigenetic modifications never cross the border of generations. Scientists assumed that epigenetic memory accumulated throughout life is entirely cleared during the development of sperms and egg cells.

It is hard enough to see how organisms can respond intra-lifetime to environmental challenges, but how can it be inherited as well? For epigenetic changes that occur in somatic cells, that information must also enter into the germ line as well. Somehow it must be incorporated into the sperm and/or egg cells.

It is an enormous problem to explain how such capabilities evolved. Not only are a large number of mutations required to make this capability work, it would not be selected for until the particular environmental condition occurred. That means that, under evolution, it would be not preserved, even if it could somehow arise by chance.

56 comments:

  1. oh but it gets worse....Michael Skinner's labs have shown that epigenetics triggers mutations....talk about upending a theory.

    http://www.news-medical.net/news/20150803/Environmental-factors-promote-genetic-mutations-have-underappreciated-effect-on-disease-evolution.aspx

    ""The ability of environmental factors to promote epigenetic inheritance that subsequently promotes genetic mutations is a significant advance in our understanding of how the environment impacts disease and evolution," they write."

    "His recent study exposed gestating female rats to the fungicide vinclozolin. Sperm in the first generation of male offspring showed epimutations, or alterations in the methyl groups that stick to DNA and affect its activation.

    Third generation, or great-grand offspring, had increased genetic mutations, which the researchers saw in increased DNA structure changes known as copy-number variations. Multiple generations of control animals had no such variations.

    This, said Skinner, suggests that environment has a more important role in mutations, disease and evolution than previously appreciated, and appears to be one of the main drivers of intergenerational changes, not simply a passive component. In short, Skinner and his colleagues say, the environment and epigenetics can drive genetics.

    "There's not a type of genetic mutation known that's not potentially influenced by environmental epigenetic effects," Skinner said."

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    1. Thanks for that one Tommy. Skinner wrote a nice article which I discussed here:

      http://darwins-god.blogspot.com/2016/11/michael-skinner-on-epigenetics-stage.html

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  2. I don't see why you think that epigenetic traits cannot be impacted by natural selection in the same way that non-epigenetic traits are. In its simplest form, epigenetic is just two different phenotypic expressions of a gene as dictated by environmental factors.

    Most environmental stresses (e.g., temperature, draught, etc.) are cyclic in nature. If a gene has a mutation that allows an epigenetic expression different than than that of the "native" gene, and if the different expression has an increased fitness under the environmental trigger, then natural selection will act on it and increase the frequency of this mutated gene in the population. If the epigenetic expression has lower fitness under the environmental trigger, then it will be weeded out by natural selection.

    These can be reverend to as directed adaptations, but not in the sense of some intelligence directing them. They are still the result of random mutations (random with respect to fitness) and natural selection. With a healthy does of drift thrown in for good measure.

    Epigenetic expressions, and even inheritance of these expressions, is not a concern for what we understand that evolution is capable of. If you have examples of fixed epigenetic expressions that are not triggered by a cyclic environmental cue, then maybe the evolutionary theory (the one that Joe says doesn't exist but keeps fighting against) will have to be re-examined.

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    1. WS: Evolutionists resisted and rejected any such notion for good reason. Not only does the epigenetic mechanism require multiple mutations to construct in the first place (>>1) and so is beyond the reach of random mutations, but it wouldn't be selected for. Remember, "random with respect to fitness", so the mechanism isn't going to be constructed *in response* to an environmental challenge / need. Too much serendipity to claim it is luckily timed to coincide with the occasional need.

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    2. wee willie:
      (the one that Joe says doesn't exist but keeps fighting against)

      Totally clueless. I do not fight against any scientific theory of evolution for the simple reason a scientific theory of evolution does not exist. That said I do fight against evolutionism because it is unscientific claptrap. And wee willie's reposes always confirm that fact.

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  3. "Not only does the epigenetic mechanism require multiple mutations to construct in the first place (>>1) and so is beyond the reach of random mutations, but it wouldn't be selected for."

    This is unsupported assertion. There is no rule that says these mutations (if they are required) must be simultaneous, only that they are not so detrimental that they become removed.

    "Remember, "random with respect to fitness""

    Random with respect to fitness does not mean that the mutation doesn't increase fitness, or decrease fitness. If it increases fitness then it will be selected for. If it is neutral or weakly detrimental, it can still become fixed in the genome.

    "so the mechanism isn't going to be constructed *in response* to an environmental challenge / need."

    Who said that it was constructed in response to an environmental challenge/need?

    "Too much serendipity to claim it is luckily timed to coincide with the occasional need."

    Again, who said it is timed to coincide with anything. If it happens to have an epigenetic expression that is beneficial in a changed environment, it will be selected for and become available for future occasions when a similar environmental challenge is experienced.

    Remember, it can just as easily result in it being removed by selection, taking the normal expression of the gene along with it.

    Epigenetics cannot function without the underlying DNA. And if this DNA is functional, it can be acted on by selection.

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    1. There is no rule that says these mutations (if they are required) must be simultaneous, only that they are not so detrimental that they become removed.

      Agreed, I made no such claim. The problem is not that the mutations must occur simultaneously, it is that they have to occur, regardless of the time span. Anything requiring as little as half a dozen mutations is beyond the reach of evolution, let alone hundreds or thousands. The cell needs to be sensitive to environmental signals; proteins need to act on that and find the right place in the genome to attach epigenetic molecules, such as methane; proteins need to be able to carry and attach those molecules to the right place in the nucleotide or histone; once placed, those molecules need to have an effect on transcription; other proteins need to be able to remove or modify these molecules; other mechanisms need to transfer this information to the germ line cells. And so forth.

      All of this is beyond the reach of your random mutations. You are in denial of an obvious problem. Your view is not reckoning with the science.

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    2. Dirt worshipper writes:

      Again, who said it is timed to coincide with anything. If it happens to have an epigenetic expression that is beneficial in a changed environment, it will be selected for and become available for future occasions when a similar environmental challenge is experienced.

      This is pure superstition and pseudoscience that has already been falsified by the "curse of dimensionality." The combinatorial explosion kills the Darwinist credo. Dead.

      But dirt worshippers are condemned to worship dirt all the days of their lives. They deserve their stupidity.

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    3. CH: "Anything requiring as little as half a dozen mutations is beyond the reach of evolution, let alone hundreds or thousands."

      Can you provide a reference for this? Other than Behe who has already been debunked?

      If you are arguing the "combinatorial explosion" nonsense, you are using probabilities improperly.

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    4. If you are arguing the "combinatorial explosion" nonsense, you are using probabilities improperly.

      Says the gutless dirt worshipper.

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    5. Please Mapou. Adults are talking here.

      Delete
    6. Mapou: "You're a lying, gutless, dirt worshipping maggot."

      Well, that is the most mature, intelligent and inciteful response I have ever read. I concede defeat to a far superior intellect and mature individual. Your ID arguments are unassailable.

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    7. Go pack yams or something, maggot. Why would I argue with a stupid dirt worshipper? If I do present an argument, rest assured that you are not the intended recipient. Others may see it and find it useful.

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    8. wee willie:
      Epigenetics cannot function without the underlying DNA. And if this DNA is functional, it can be acted on by selection.

      Except evolutionism doesn't have an explanation for the existence of DNA-based organisms. I bet wee willie doesn't even know that natural selection is an eliminative process and there isn't any selection going on.

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    9. William,

      Louis: "You are not an adult. You're a lying, gutless, dirt worshipping maggot."

      Well, William, if that doesn't convince you of the errors of evolution nothing will. :)

      Delete
    10. Nic the spineless Christian: Well, William, if that doesn't convince you of the errors of evolution nothing will. :)

      Let me guess. You've spent years arguing with the jackass and you finally succeeded in convincing him by the sheer superiority of your arguments that he's a dishonest moron and that Darwinian evolution is pure unmitigated crap. Congratulations.

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    11. Nic, The fact that all wee willie can do is bluff, lie and misrepresent convinces everyone else that evolutionism has nothing.

      The only thing that will convince wee willie that evolutionism is wrong is a meeting with and a thorough demonstration from the Intelligent Designer. wee willie's ilk don't care about science.

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    12. Nic: "Well, William, if that doesn't convince you of the errors of evolution nothing will. :)"

      And don't forget : "Nic the spineless Christian....You've spent years arguing with the jackass and you finally succeeded in convincing him by the sheer superiority of your arguments that he's a dishonest moron and that Darwinian evolution is pure unmitigated crap."

      or: "The fact that all wee willie can do is bluff, lie and misrepresent convinces everyone else that evolutionism has nothing."

      With astute and thoughtful arguments like these, I am shocked that they have not convinced more people about the coherence of their arguments.

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    13. Hi Nic. I hope that you have fully recovered from your "skiing" accident.

      My wife and I took three short trips this year; Paris, Washington DC and St. John's. I highly recommend each of these, for different reasons.

      Delete
    14. LOL. A spineless dirt worshipper befriends a spineless Christian. Birds of a feather. You can take your arguments and pack them up you know where.

      ahahahahaha...AHAHAHAHA...ahahahaha...

      Delete
    15. William,

      "I hope that you have fully recovered from your "skiing" accident."

      It took a while, but I am pretty much back to where I was. Thanks for asking.

      We were to the East coast a few years ago and are planning to return in the next year or two. I am also wanting to do a trip through the American South West as well.

      I hope all is well with you and your family.

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  4. It is hard enough to see how organisms can respond intra-lifetime to environmental challenges, but how can it be inherited as well?

    In my opinion, intra-lifetime epigenetics is easily observable. Exercise, for example, modifies muscle genes to promote growth. Even something as common (and inexplicable by medicine) as the placebo effect is a form of epigenetics. There is a part of the brain that has a direct and profound effect on our genes. Identical twins raised in different environments look different. Educated individuals look markedly different than their non-educated siblings.

    As an aside (to those who have an ear to hear), my research into ancient occult texts, such as the Book of Revelation and parts of Genesis, supports this. The metaphor used in the texts to represent the genome is the "Tree of Life". That is to say, the genome is strictly organized hierarchically, like a tree.

    Just saying. Take it or leave it.

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  5. "Random with respect to fitness" is a canard. The actual claim is that mutations are random as in happenstance/ accidental occurrences.

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    1. Joe/ET/Virgil: ""Random with respect to fitness" is a canard. The actual claim is that mutations are random as in happenstance/ accidental occurrences."

      If misrepresenting what the scientists actually say makes your argument better, by all means go for it.

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    2. LoL! What I said Ernst Mayr said- read "What Evolution Is". The following also supports my claim:

      http://www.nature.com/scitable/topicpage/dna-replication-and-causes-of-mutation-409

      and from Larry Moran:

      http://bioinfo.med.utoronto.ca/Evolution_by_Accident/Evolution_by_Accident.html

      As I said, wee willie doesn't even understand the claims of his own position.

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    3. Joe/ET/Virgil, are you suggesting that the randomness that Moran and Mayr are talking about is not random with respect to fitness? Because it certainly is.

      Neither is saying that the spot on the DNA where a mutation may occur is random. Because it's not. Translocations do not occur randomly on the chromosome. Point mutations caused by UV do not occur at random points on the DNA strand. But when they do occur they are random with respect to fitness.

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    4. Shut up, wee willie. The claim ever since the modern synthesis is that mutations are random as in chance/ happenstance events. They are accidents, errors and/ or mistakes.

      "Random with respect to fitness" is a canard. Only people who don't understand the modern synthesis say such things.

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    5. Joe/ET/Virgil: ""Random with respect to fitness" is a canard. Only people who don't understand the modern synthesis say such things."

      Hmm. Have you read any evolution research since the late thirties? Most of us understand that the theory (the one that you say doesn't exist but have spent hundreds of hours arguing against) has changed since then. Darwin made mistakes. Wilson and Mayr made mistakes. Gould made mistakes. That's how science advances. I assume that you have heard about science. It is the discipline that ID avoids.

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    6. LoL! As I said above and you ignored:

      I do not fight against any scientific theory of evolution for the simple reason a scientific theory of evolution does not exist. That said I do fight against evolutionism because it is unscientific claptrap. And wee willie's reposes always confirm that fact.

      That said, again, I know evolutionism has evolved but the premise has always remained the same- mainly that it, evolution, proceeds via blind, mindless processes such as natural selection and drift. It is all based on the assumption that all genetic changes are accidents, as is unplanned, happenstance occurrences.

      None of that has changed. So clearly you are just a bluffing fool.

      https://whyevolutionistrue.wordpress.com/2011/02/21/natural-selection-and-evolution-material-blind-mindless-and-purposeless/

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    7. Joe/ET/Virgil: "That said, again, I know evolutionism has evolved...

      As has IDiocy.

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    8. No, your IDiocy has just degenerated.

      Delete
  6. Saying "mutations are random with respect to fitness"- fitness being an after-the-fact assessment- does NOT address whether or not the mutations are directed.

    Saying that random means happenstance/ chance occurrences, removes all doubt as to whether or not they are directed. That is why Mayr said what he did- that chance reigns supreme at the genetic variation level.

    So I must be as scientifically ignorant as Ernst Mayr

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  7. LoL! From the evo's own site (which BTW isn't written by any known evolutionary biologist):

    "As a general rule mutations should be considered to be accidents. They arise without being designed for a purpose, in the same sense that accidently breaking your coffee cup is not 'for' anything, it just happens."

    Whoopsie- exactly what I have been saying. So much for the ignorant claim that I am scientifically ignorant.

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  8. Joke: "LoL! From the evo's own site (which BTW isn't written by any known evolutionary biologist):"

    Professor at the Australian National University with over 80 publications in the last fifteen years. How many papers have you published?

    https://researchers.anu.edu.au/researchers/bromham-ld

    "Whoopsie- exactly what I have been saying. So much for the ignorant claim that I am scientifically ignorant."

    No, you have been saying that random with respect to fitness is a canard.

    "Saying "mutations are random with respect to fitness"- fitness being an after-the-fact assessment- does NOT address whether or not the mutations are directed."

    True. But it certainly begs the question, 'why would the designer direct a mutation that kills the individual?' Maybe there is a valid reason for this, but I can't figure out what the purpose of cystic fibrosis, Marfan syndrome, Huntington's, and a plethora of other diseases that are the result of a genetic mutation could be. Maybe the designer takes pleasure in watching people suffer. Or, just possibly, there is no direction and that these are just the result of mutations that are random with respect to fitness.

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    1. My ORIGINAL claim in this thread:

      The actual claim is that mutations are random as in happenstance/ accidental occurrences.

      It is so easy to refute wee willie...

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  9. clueless:
    Professor at the Australian National University with over 80 publications in the last fifteen years.

    So what? My point still stands.

    No, you have been saying that random with respect to fitness is a canard.

    You are clearly a loser and a moron. I ALSO said that mutations are considered to be accidents. And it is a canard. Mayr didn't use it. Dawkins didn't use it. Coyne didn't use it.

    But it certainly begs the question, 'why would the designer direct a mutation that kills the individual?'

    Strawman- no one said the designer directs mutations. And no one said all mutations are directed. You clearly have a very limited intellect, if it could be called an intellect...

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    1. Joke: "You are clearly a loser and a moron."

      I am always enthralled by the astuteness and impeccable logic of your arguments. I bow to your infinite wisdom. I am not worthy to even be in your shadow.

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    2. LoL! You ignore the arguments and focus on the minutiae

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  10. What we learned:

    Joke is wrong when he claims mutations aren't random with respect to fitness

    Joke is wrong when he claims mutations are purposely designed.

    What we already knew:

    Joke is a vile obnoxious excuse for a human as stupid as a sack of doorknobs. With apologies to the doorknobs.

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  11. is wrong when he claims mutations aren't random with respect to fitness

    Please link to the theory of evolution that makes the claim mutations are random with respect to fitness. Your source supports my claims with respect to mutations.

    is wrong when he claims mutations are purposely designed.

    I never made that claim.

    What we already knew- ghostrider is a crybaby loser and living proof humans mated with other species.

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  12. What is very telling is that neither ghostridingfool nor wee willie has linked to this alleged theory of evolution to support their claim about mutations being random with respect to fitness as opposed to being random as in accidental/ happenstance occurrences. Even ghostridingfool's source supports my claim:

    "As a general rule mutations should be considered to be accidents. They arise without being designed for a purpose, in the same sense that accidently breaking your coffee cup is not 'for' anything, it just happens."

    Just call it "it just happens" theory. How did the eye evolve? "it just happens and it happened many times"

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    1. Joke G: " to support their claim about mutations being random with respect to fitness as opposed to being random as in accidental/ happenstance occurrences."

      LOL! Good gravy Joke but you're a dumb one. It's not an either-or situation. Mutations are random (not designed) as to when and where on the genome they occur AND the effect they have on reproductive fitness is random.

      You've really been having a banner week in the stupidity mines. I laughed for hours at the moronic statement you made at UncommonlyDense:

      ET/Joke G : "Just because someone can imagine it doesn’t make it conceivable."

      That's right up there with your "ice isn't made of water" and "wavelength = frequency" industrial strength tard.

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    2. OK so that would be a "No" you cannot reference the alleged theory of evolution to support your claim. Figures.

      English 101- Saying mutations are random, as in unplanned/ accidents/ errors and/ or mistakes- covers everything. Adding the "with respect to fitness" is unnecessary. Darwin didn't use it. Mayr didn't use it.

      That said there isn't any way to test the claim that genetic accidents can accumulate in such a way as to give rise to protein machines like ATP synthase.

      BTW my claim was hail is made of ice and not water. Rain is made of water and not ice. Only drooling imbeciles would make an issue out of that and here you are.

      And no, timmy, just because you can imagine flying like Tinkerbelle doesn't mean it's conceivable.

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    3. "That's right up there with your "ice isn't made of water" and "wavelength = frequency""

      Surely nobody would be stupid enough to make claims like this. And, if someone did, surely they wouldn't be stupid enough to refuse to admit their error. To do both would require a really special kind of stupid. But I am sure that there is nobody commenting here who would do this.

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    4. It would probably be the same person so stupid he doesn't understand "conceivable" means "able to be imagined".

      There's no stupid like Joke G stupid. :)

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    5. Ernst Mayr did NOT say that mutations are random with respect to fitness. You are a liar. Your quote-mine doesn't help you.

      And conceivable, in CONTEXT, meant possible or plausible.

      It's as if you are proud to be an ignorant troll.

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    6. OK so still no link to this alleged theory of evolution to refute my claim. Gee I wonder why that is.

      That said there isn't any way to test the claim that genetic accidents can accumulate in such a way as to give rise to protein machines like ATP synthase. And that means your position is not scientific.

      But we all know that won't deter you two from continuing to spew your ignorance about science.

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    7. Joke: "Ernst Mayr did NOT say that mutations are random with respect to fitness. You are a liar. Your quote-mine doesn't help you."

      Do you even understand what "random with respect to fitness" means? If "there is no correlation between the production of new genotypes and the adaptational needs of an organism in a given environment", then it is random with respect to fitness.

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    8. LoL! Fitness is a measure of reproductive success. And there is a difference between adaptational needs and reproductive success.

      It is very telling that you chumps don't just link to the alleged theory of evolution to support your claims.

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  13. "All dirt worshippers (Darwinists) have these three things in common: cowardice, stupidity and dishonesty."

    Keep up those unassailable arguments against evolution. With insight like this, we are destined to be defeated. But only if you take over while the rest of us are busy rolling around on the floor laughing.

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  14. wee willie:
    Keep up those unassailable arguments against evolution.

    Who is assailing mere evolution? Why are you so willfully ignorant?

    Defeated? Your position was stillborn. And you prove that with your continued lies, bluffing and misrepresentations.

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  15. "And you prove that with your continued lies, bluffing and misrepresentations."

    "I ain't arguing with you, you spineless jackass. You're stupid or something."


    Intellectual gold. Evolution can't last much longer with ID supporters like these two.

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  16. Well, seeing that ID is NOT anti-evolution, wee willie's statement is proof of its willful ignorance.

    Amazing...

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  17. So how's everyone?

    ahahahaha...AHAHAHAHA...ahahahaha

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    Replies
    1. Why you ask?

      ahahahaha...AHAHAHAHA...ahahahaha

      Delete
    2. I didn't come to visit for a while, just saying hello

      ahahahaha...AHAHAHAHA...ahahahaha

      Delete