Saturday, January 07, 2017

What the heck is epigenetics?

"Epigenetics" is the (relatively) new buzzword. Old-fashioned genetics is boring so if you want to convince people (and grant agencies) you're on the frontlines of research you have to say you're working on epigenetics. Even better, you can tell them that you are on the verge of overthrowing Darwinism and bringing back Jean-Baptiste Lamarck.

But you need to be careful if you adopt this strategy. Don't let anyone pin you down by defining "epigenetics." It's best to leave it as ambiguous as possible so you can adopt the Humpty-Dumpty strategy.1 Sarah C.P. Williams made that mistake a few years ago and incurred the wrath of Mark Ptashne [Core Misconcept: Epigenetics].

Now Carrie Deans and Keith A. Maggert are giving it a try and they are far more successful (Deans and Maggert, 2015). I won't bore you with the history of the term "epigenetics" but, if you're interested, this paper gives a nice summary. The authors end up with two distinct definitions of "epigenetics" that they label the Waddington definition (after Conrad Waddington) and the Holliday definition (after Robin Holliday). The Waddington definition is essentially equivalent to saying that epigenetics is the regulation of gene expression. It's a common definition
[Jablonka's definition of epigenetics] but one that's not particularly useful. It means that calico cats are prime examples of epigenetics [Epigenetics and the Calico Cat], but so is regulation of the lac operon.

Deans and Maggert reject the old Waddington definition on the grounds that we now have a perfectly good substitute, "regulation of gene expression," and the mechanisms are well-understood.

The Holliday definition incorporates the idea of heritability that is not based on DNA sequence. A concise definition along these lines was proposed by Wu and Morris (2001),
[Epigenetics is] the study of changes in gene function that are mitotically and/or meiotically heritable and that do not entail a change in DNA sequence.
This doesn't seem to be any better than previous definitions so Deans and Maggert propose their own definition,
"... the study of phenomena and mechanisms that cause chromosome-bound, heritable, changes to gene expression that are not dependent on changes to DNA sequence."

We feel that this definition makes a strong distinction between gene regulation (Waddington's definition) and epigenetic inheritance (Holliday's definition), and also emphasizes that epigenetic phenomena must deal exclusively with chromosome-bound changes.
I think this is a useful definition. Nobody cares if dividing E. coi cells inherit molecules of lac repressor and continue to repress the lac operon. That's a trivial form of epigenetics that never posed a threat to our understanding of evolution.

The Dean and Maggert definition focuses attention on modification of DNA (e.g. methylation) and modification of histones (chromatin) that are passed from one cell to two daughter cells. That's where the action is in terms of the debate over the importance of epigenetics.

Methylation is trivial. Following semi-conservative DNA replication the new DNA strand will be hemi-methyalated because the old strand will still have a methyl group but the newly synhtesized strand will not. Hemi-methylated sites are the substrates for methylases so the site will be rapidly converted to a fully methylated site. This phenomenon was fully characterized almost 40 years ago [Restriction, Modification, and Epigenetics]. There's no mystery about the inheritance of DNA modifications and no threat to evolutionary theory.

Histone modifications are never inherited through sperm because the chromatin is restructured during spermatogenesis. Modifications that are present in the oocyte can be passed down to the egg cell because some of the histones remain bound to DNA and pass from cell to cell during mitosis/meiosis. The only difference between this and inheritance of lac repressors is that the histones remain bound to the DNA at specific sites while the repressor molecules are released during DNA replication and re-bind to the lac operator in the daughter cells [Repression of the lac Operon].

Some people think this overthrows modern evolutionary theory.


1. “When I use a word,” Humpty Dumpty said, in rather a scornful tone, “it means just what I choose it to mean—neither more nor less.” “The question is,” said Alice, “whether you can make words mean so many different things.” “The question is,” said Humpty Dumpty, “which is to be master—that’s all.” Lewis Carroll (Charles L. Dodgson) Through the Looking-Glass (1872)

Deans, C., and Maggert, K.A. (2015) What do you mean,“epigenetic”? Genetics, 199:887-896. [doi: 10.1534/genetics.114.173492]

86 comments :

  1. Nothing can overthrow the modern theory. It's an empty, unfalsifiable, non-scientific theory that only holds up in the minds of the faithful.

    So the problem is that if the vast majority of changes in nature, especially in regards to morphological changes, are related to epigenetic (aka regulation of gene expression) changes, and not genetics (aka random mutation) then there's a major problem with how genomes got built up. See, the construction of genomes over time is supposed to be correlated with the changes and/or buildup of populations, with the changes and/or buildup of bodies. Thus, when we look out into nature or in the fossil record and observe morphological changes, we are to likewise assume that changes in genomes were the cause. This is how and why science put molecular clocks on evolution. But if the majority of morphological adaptations in nature are decoupled from genomic changes, then suddenly we have a disconnect and suddenly we have no explanation for the buildup of genomes. See kids, the framers of the the theory of evolution constructed the theory the way they did for certain reasons. You can't just delete part of the equation, or start making major alterations to it without causing a major breakdown of the theory.

    Likewise you can't just start adding stuff willy-nilly to the theory without having major ramifications. You can't take a theory that says "only populations evolve," and then paste on top of it the notions that individuals can evolve as well, because the latter implicates lamarckism. You can't take a theory that says genomes got built up over time by small, mindless random (selected alterations) and add to it the notion that individuals can direct their own adaptive changes, because the latter upends naturalism and allows intelligence into the mix. You can't take a theory that says all adaptive populational changes happen by an external mechanism (selection) but then add to it the notion that individuals are dynamic and can adapt themselves by internal mechanisms....self-direction = intelligent design. All this stuff matters. If you people want to play like you have a purely mindless, purely mechanical, purely non-intelligent theory in play, then we on the other side are going to force your hand: if that's what you want, then all you get in regards to adaptive mechanism is RMNS.....the moment you go outside of that and start including adaptive internal mechanisms that spring into action upon a need, then you've suddenly abandoned your naturalism and joined the ranks of intelligent design. take your pick.

    What epigenetics, and all other internally-adaptive mechanisms do is not "overthrow" the sitting theory. Nothing can do that. Likewise nothing can "overthrow" that little green men live on Jupiter's moons. But what these other mechanisms do is provide an alternative to the modern theory. Something that can actually be tested, verified with actual repeatable science...which is something that the Modern Synthesis is foreign to.

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    1. So the problem is that if the vast majority of changes in nature, especially in regards to morphological changes, are related to epigenetic (aka regulation of gene expression) changes, and not genetics (aka random mutation) then there's a major problem with how genomes got built up.

      Yes, that would be a problem, if it were true. But, since it is not true, it would appear the only problem here is your ignorance.

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    2. Tommy Hall,

      "...the moment you go outside of that and start including adaptive internal mechanisms that spring into action upon a need….what these other mechanisms do is provide an alternative to the modern theory. …"

      One tenet of the modern synthesis says “Evolution is gradual: small genetic changes regulated by natural selection accumulate over long periods. Discontinuities amongst species (or other taxa) are explained as originating gradually through geographical separation and extinction.”

      Waddington recognized that this was inadequate back in 1942:

      ”Naturalists cannot fail to be continually and deeply impressed by the adaptation of an organism to its surroundings and of the parts of the organism to each other. These adaptive characters are inherited and some explanation of this must be provided. If we are deprived of the hypothesis of the inheritance of the effects of use and disuse, we seem thrown back on an exclusive reliance on the natural selection of merely chance mutations. It is doubtful, however, whether even the most statistically minded geneticists are entirely satisfied that nothing more is involved than the sorting out of random mutations by the natural selective filter.
      http://www.nature.com/nature/journal/v150/n3811/abs/150563a0.html

      Someone probably scolded him for his personal incredulity.

      Observed rapid adaptation has only highlighted the problem, and brought about (what should be embarrassing) proposals:

      ”Cryptic genetic variation (CGV) is invisible under normal conditions, but it can fuel evolution when circumstances change. In theory, CGV can represent a massive cache of adaptive potential or a pool of deleterious alleles that are in need of constant suppression.
      https://www.ncbi.nlm.nih.gov/pubmed/24614309/

      The idea of having deleterious genes waiting in the wings to impose blindness on cave fish on an as-needed basis may well be the case. And it does solve a problem. But as you note, it upends naturalism, and taxes the hell out of the notion that no intelligence is involved.

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    3. His reliance on "cutting edge" research from 1942 notwithstanding, would anyone be surprised to learn that txpiper, liar for Jesus that he is, wholly misrepresents Waddington's work?

      https://en.wikipedia.org/wiki/Canalisation_(genetics)

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    4. Tommy, if epigenetics is intelligent modification of genetics, you should be able to epigenetically modify problem genes, e.g. the genetic dominant that causes Huntington's disease. Can you? Can anyone? No?

      Epigenetics is very interesting, but it's not about intelligence modifying the path of evolution.

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    5. Tell us about butterfly wombs and vision beams, Tommy. And then tell us all about daphnia spines. and how the author of a paper on such things told you that you were wrong about his work, and you kept repeating the lies anyway. and then tell us all about your obsession with homosexual sex.

      Tommy = supersport = Guzman = worthless troll.

      Delete
  2. Epigenetic inheritance (using epigenetic in the Dean and Maggert sense) would be a major problem for contemporary evolutionary theory if this inheritance lasted for hundreds of thousands of generations before reverting.

    The existing evidence suggests that it does not even last tens of generations. A population could not have an epigenetic change fixed within it unless that change were stabilized by change in the DNA sequence.

    Anti-evolution folks love to invoke "epigenetics" as proving that evolutionary biologists don't know what they are talking about. But the anti-evolution types do not call attention to the short lifespan of epigenetic changes. It is they who do not know what they are talking about.

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    1. So now the question is: Who should we believe? Joe Felsenstein, or some internet creationist named "Tommy Hall"? Such a difficult decision.

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    2. I disagree with Joe here. It would not pose a major problem for contemporary evolutionary theory. In 1873 the question how probable it was for an aristocratic family name to become extinct was posed in Education magazine. Later in the same year an answer was proposed and the questioner and the person who replied jointly worked out the maths to more detail. The questioner was Darwins half-cousin Francis Galton, the reply came from Reverend Henry Willam Watson and their joint paper first described the Galton-Watson branching process. Now of course Galto-Watson processes turn up regularly in genetics and this is no surprise because if you try to formalize the concept of a gene without regard to substrate (like Williams did for instance) last names do meet the criteria. In the same vein, we can look at what happens if epigenetic inheritance is more stable and using Williams we find that there is a cut-off where it simply becomes genetics and it basically is an issue of how high the mutation rate (i.e. that of reversion in the sense above) is. I do not think population genetics requires genes to be DNA based as it is (in fact I would hold that it very useful to think of AA sequences as separate genes that are related to DNA sequences through linkage disequilibrium. And it is really useful to think of clade membership as genes, which makes phylogenetics a task of finding LD between our data and clade membership genes).

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    3. As I understand it, the problem here is with the modern synthesis of the mid 20th century. This was a fusion of Darwinism with Mendelism, and it effectively tied evolutionary theory to nucleic acids - via tenets such as:

      "All evolutionary phenomena can be explained in a way consistent with known genetic mechanisms".

      The modern synthesis was developed by people ignorant of cultural evolution and they failed to do very much to accommodate it. Once we get into the evolution of surnames, the modern synthesis of the 1940s is no longer applicable. Some researchers go back to Darwin to get hold of a version of evolutionary theory that is not busted in this way. Darwin at least understood that culture evolves.

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    4. Regarding instability, cultural mutations can last for hundreds of thousands of generations before reverting. Cultural evolution exhibits adaptations that mirror natural ones - cameras instead of eyes, knives instead of claws, blenders instead of teeth - clearly illustrating that cumulative adaptations in the cultural realm can be stable and aren't always swamped by cultural mutations. If stability is raised as an objection against "non-genetic" inheritance the simplest thing to do is to look to cultural evolution - since it can be pretty stable.

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    5. The epigenetics debate is complicated. Some changes, such as the methylation of restriction endonuclease sites, are perpetuated for millions and millions of years. Same goes for some heterochromatic regions of the genome such as most of chromosome 4 in Drosophila.

      The debate is centered on INDUCED changes in methylation and/or histone modifications. The argument is that these changes can be affected by the environment and then passed on to subsequent generations. That's how epigenetics is supposed to affect evolution.

      But those kinds of change are associated with the regulation of gene expression. That's why you can make the Lamarckian argument. (It's not clear whether they are cause or effect.) By definition, those kinds of change are reversible—that's how they arose in the first place.

      Joe is right about those epigenetic changes. They are not stable and make no contribution to evolution. The original sites were selected for regulation (reversible change).

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    6. I'm a little bit surprised by the enthusiasm with which temporary changes in gene expression are dismissed as making "no contribution to evolution". Individually-learned information is destroyed in every generation - and yet it can still contribute to evolution via the well-known mechanism of the Baldwin effect. It does this via making changes to the situation in which genes get selected.

      Also, if evolution is defined to be inherited changes in a population over time, then temporary changes surely still qualify. I never heard of a minimum number of generations being specified in the definition of the term "evolution". The number of generations changes persist for affects whether they are likely to contribute to cumulative adaptations - but that seems like a bit of a different question.

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    7. One of the main problems with "modern evolutionary theory"(whatever that means or stands for-I don't know anymore and whoever does needs to be reworded) is how epigenetics evolved.
      It seems that it could not have happened by any current Neo-Darwinian mechanisms; natural selection acting on random mutations.

      For epigenetics to evolve, in many cases, evolution processes would have to have at least some kind of foresight, which obviously wouldn't fly with the majority of the crowd here who would automatically dismiss it no matter what evidence is presented...

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    8. Don Quixote tries the old argument: "For epigenetics to evolve, in many cases, evolution processes would have to have at least some kind of foresight"

      Oh, creos say this about every conceivable thing. They can never back it up.

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    9. You obviously have (no doubt) experimental evidence to back up your shitty story...Let's see it...

      The truth is, we will never see it...never...ever...

      However, we are more than eager to replicate the processes, as per your specific instructions. What else do we need to do to make your shit believable?

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    10. Diogenes,

      "For epigenetics to evolve, in many cases, evolution processes would have to have at least some kind of foresight”

      Well, of course. That holds true for lots of things because the end results don’t appear to be accidental. The problem isn’t the questions, it is the answers. If a person is satisfied with evolutionary explanations for things like metamorphosis or mimicry, they might be committed to something, but it isn’t rational thought. You can try them on for yourself.

      https://en.wikipedia.org/wiki/Metamorphosis#Evolution
      https://en.wikipedia.org/wiki/Mimicry#Evolution

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    11. but it isn’t rational thought

      Says yet another creationist who maintains at one and the same time that organisms were "front-loaded" in order to pass that important genetic information on to...nothing. I.e., txpiper believes strongly both that there was front-loading and that there was no common ancestry but rather independent creation.

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    12. Txpiper, revised: "If a person is satisfied with magical explanations for things like metamorphosis or mimicry, they might be committed to something, but it isn’t rational thought."

      Fixed that for you. But your actual quote was just argument from incredulity. 'Gosh, there's no way a bug could evolve to look like a stick!'

      Yeah, and if we had video of a mantis evolving to be longer and thinner and browner, every one of you creationists would call it "microevolution" and "trivial" and "obvious." You call it "macroevolution" only up until the day we have a video of it.

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    13. tripper,

      The wikipedia entry on metamorphosis does not explain anything. But the mimicry one is actually very easy to understand. It makes a lot of sense. So what exactly would be the problem with the evolution of mimicry and what's your proposed alternative? Remember, your alternative must make at least as much sense as the evolutionary scenarios, and then some (has to be superior).

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    14. Diogenes,

      “if we had video of a mantis evolving to be longer and thinner and browner”

      But you don’t, because things like that only happen in the imaginations of people who believe that they do. However, if you find videos compelling, watch this one:

      https://www.youtube.com/watch?v=os6HD-sCRn8

      If you pause it at 1:04, you might notice that the rings on the tentacles are lined up to form stripes. That is some lucky evolutionary tinkering right there.

      ====

      photosynthesis,

      “The wikipedia entry on metamorphosis does not explain anything.”

      Well of course it doesn’t. If the subject was butterflies, how would anybody go about explaining how random replication errors could result in two completely different animal phenotypes in a single DNA profile?
      -
      “But the mimicry one is actually very easy to understand. It makes a lot of sense.”

      It is? It does? The only factual thing stated is that a completely implausible two-step model is widely accepted. It also says that:

      “This model is supported by empirical evidence that suggests that a few single point mutations cause large phenotypic effects, while numerous others produce smaller effects. Some regulatory elements collaborate to form a supergene for the development of butterfly color patterns. The model is supported by computational simulations of population genetics.”

      The writer is referring to this paper:
      https://pdfs.semanticscholar.org/f1a7/911b8637ac0d778915857917497356f3a5f5.pdf
      which is nothing more than assumptions and conjecture. Imagined simulations do not constitute empirical evidence, and couple of pinheads writing a paper full of speculation is not support.

      But that’s how it’s done.

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    15. txpiper,

      You did not answer. You deflected. Mimicry can evolve because predators, for example, would not see the life forms that look like something else. It can start just by some coloration, then better coloration, etc, and/or some shape, then better shape, etc. This makes a hell of a lot of sense. It's actually very easy to understand how that could happen in stages. So, again, according to you, what's wrong with that and what's your alternative?

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    16. photosynthesis,

      “Mimicry can evolve because predators, for example, would not see the life forms that look like something else.”

      Yeah, that would be a good reason for mimicry to evolve. But accidents don’t happen in response to need.
      -
      “It can start just by some coloration, then better coloration, etc, and/or some shape, then better shape, etc.”

      Same problem. It is unreasonable to attribute things like this:

      http://www.conservacionpatagonica.org/blog/wp-content/uploads/2012/11/50492701.jpg

      https://en.wikipedia.org/wiki/Eyespot_(mimicry)#/media/File:Mycalesis_patnia.jpg

      https://en.wikipedia.org/wiki/Eyespot_(mimicry)#/media/File:Gray_Hairstreak_(One_more_time...)_(6222138633).jpg

      https://en.wikipedia.org/wiki/Eyespot_(mimicry)#/media/File:Glaucidium_californicum_Verdi_Sierra_Pines_2.jpg

      https://en.wikipedia.org/wiki/Eyespot_(mimicry)#/media/File:Chaetodon_capistratus1.jpg

      to random processes. Things like that just don’t happen. Contrary to Orgel’s declaration, evolution is not smarter than you.

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    17. TX, Natural selection is not about adaptations evolving by accident. It's about an array of variations happening by mutations -- accidents -- and some of the variants surviving and reproducing better than others for very good reasons. Two steps. One random and one not.

      The evolution of mimics, of blind cave creatures, etc. don't look like an accident because it's not. Selection is involved. In other words, differential survival and reproduction are involved.

      Delete
    18. Ah yes BW, but that's not what Tx et al are attacking... they're attacking their windmill version of evolution (it's only random mutations/ chance), while thinking they're bravely attacking giants. Like Don Quixote in the stories.

      Tx unfortunately hasn't provided positive evidence in favor of ID yet, it's still "evolution can't do this, thus goddidit". A lot of people are eagerly awaiting this first ever positive shred of evidence.

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    19. Contrary to Orgel’s declaration, evolution is not smarter than you.

      OK then, make a chicken.

      Delete
    20. txpiper,

      As people explained above.

      Also:

      Failure 1. Your mere declaration that "it doesn't happen" does not make an evolutionary scenario irrational.

      Failure 2. You have no alternative explanations.

      I hope that helped you learn something.

      Delete
    21. and couple of pinheads writing a paper


      Use of a birth defect as an insult - once again we see how belief in God enables people to be morally upright.

      Delete
    22. Ed,

      “they're attacking their windmill version of evolution (it's only random mutations/ chance)”

      Actually, I think it is your version that is skimpy on substance. It is easy to hair-split over selection and drift, but if you really ever try to actually apply the theoretical mechanisms (and the formidable obstacles) to a real organism above bacteria, it is very discouraging. I’ve asked lots of people to pick an animal, or even an organ, and realistically appraise it in terms of mutations and natural selection. Nobody ever wants to dig into the details and show how the theory would actually produce anything because it is ridiculously complex, and just as unlikely. The pictures I linked to don’t even fetch a comment.

      If you ever have the time, this video illustrates the withering complexity that you guys trivialize away with one or two sentences.

      https://www.youtube.com/watch?annotation_id=annotation_128796&feature=iv&src_vid=bJ3yXJGIo4Y&v=8ncUVddkK3Q

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    23. If you ever have the time, this video illustrates the withering complexity that you guys trivialize away with one or two sentences.

      Yes, I noticed the extreme complexity right away - of the landscape they were boating past. Do you think geology is real and can create such complexity, or do you think those rocks needed a designer?

      Delete
    24. Tx, you wrote:
      "Nobody ever wants to dig into the details and show how the theory would actually produce anything because it is ridiculously complex"

      Yes it is, it's much more complex than your windmill version of evolution (mere random chance). Currently to the left of this post we can find Monod's quote:
      Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

      Tx continues:
      "and just as unlikely."

      Your claim, once again a variation of your "evolution can't do this, thus goddidit" claim.

      Tx, want to try to come up with evidence in favor of ID? You've ignored this question for quite some time now, does this mean you're very busy working in the lab on experiments to show proof in favor of ID?

      Delete
    25. You have to wonder what goes on in the brains of creationists (or whatever they have that passes for brains.) Evolution is the theory that provides an explanation for how complex biological structures and functions have arisen. So trying to refute it by pointing out the existence of complex biological structures or functions is pointless. It's like trying to refute the theory of gravity by dropping a rock onto the ground, and saying "Explain that!"

      Delete
    26. "Evolution is the theory that provides an explanation for how complex biological structures and functions have arisen."

      Okay, so here's a 26 second example.

      https://www.youtube.com/watch?v=YcpzubpIhtI

      Now, use the tenets of your theory, and explain how these complex biological structures and functions evolved. I'd like to understand what, if anything, goes on in your brain.

      Delete
    27. Ed,

      “Your claim, once again a variation of your "evolution can't do this, thus goddidit" claim.”

      You seem to think this is some kind of philosophical pinnacle. It isn’t. Evolution can be evaluated on its own merit, without reference to anything else, and you are ignoring a simple, glaring, fundamental, universal axiom. Accidents don’t result in intricacy. If they did, you’d have a smooth explanation for metamorphosis.

      Monod died of leukemia, which is the result of mutations.
      -
      “..evidence in favor of ID? You've ignored this question for quite some time now, does this mean you're very busy working in the lab on experiments to show proof in favor of ID?”

      I linked you to plenty of standing evidence. As to your question, I’ve ignored it because it is obtuse. Functional complexity is the evidence. Complex design demands a complex designer. According to your rationale, If you find a camera on the beach, you have to ask yourself if it is a natural formation. But you don’t because you’re not actually demented.

      Delete
    28. simple, glaring, fundamental, universal axiom. Accidents don’t result in intricacy

      Scientists did experiments to research one of the molecules responsible for one of the biggest changes in evolutionary history, the jump from single celled to multicellular organisms. Here's an excerpt from a report about it:

      "But how many mutations did it take to transform the molecule? That’s the most remarkable part of the new study. The scientists altered the gene for the ancestral enzyme with the earliest mutations that evolved in it. They found it took a single mutation to flip GK-PID from an enzyme [in single celled organisms] to a carabiner [responsible for helping cells multiply in order to grow tissue in multicellular organisms].

      'Genetically, it was much easier than we thought possible,' Dr. Thornton said. 'You don’t need some elaborate series of thousands of mutations in just the right order.'"

      Delete
    29. Pro tip, txpiper: When someone has just ridiculed you for doing something, doing the same thing again is not a meaningful response. HTH.

      Delete
    30. TX: "simple, glaring, fundamental, universal axiom. Accidents don’t result in intricacy"

      Again, evolution involves selection as well as mutation "accidents." It would be nice if you exhibited some understanding of the theory you're declaring impossible. This repetition of such a basic misunderstanding doesn't make you look right, it makes you look stupid. Now, I realize you might actually BE stupid, but your ability to type coherent sentences suggests maybe you're not. Try to grasp the importance of selection in the process of evolutionary change.

      Delete
    31. judmarc,

      “Scientists did experiments to research one of the molecules responsible for one of the biggest changes in evolutionary history, the jump from single celled to multicellular organisms."

      There are lots of statistical problems with accidental jumps like that.

      ”Genetically, it was much easier than we thought possible,' Dr. Thornton said. 'You don’t need some elaborate series of thousands of mutations in just the right order.”

      Actually yes, you do need those things. I think Dr. Thornton got a little too excited during the interview. The published paper was more subdued, and candid:

      ”Our analyses do not establish a complete history of the spindle orientation complex. Many key steps remain to be reconstructed, including how and when the interaction between GKPID and KHC- 73 evolved, the mechanisms by which Pins’ acquired its linker and GoLoco sequences, and the relationship of these components to other molecular complexes and pathways involved in animal spindle orientation.”
      elifesciences.org/content/5/e10147-download.pdf

      In other words, the altered enzyme would have no biological context. It would be meaningless information to adjacent cells. Just another meaningless replication error. No selective advantage at all.

      Delete
    32. Tx claims:
      "Evolution can be evaluated on its own merit, without reference to anything else,..."

      Yes, I agree, on daily basis in hunderds, perhaps even thousands of labs it's being tested.

      "and you are ignoring a simple, glaring, fundamental, universal axiom. Accidents don’t result in intricacy."

      Well done, attacking your own windmill version of evolution *again and again and again*. Unfortunately for you, what's being tested in the many labs all over the globe is the giant, evolutionary theory, not your windmill. This fact has been explained to you many, many times already, but for some reason the message doesn't seem to register. Why?

      "If they did, you’d have a smooth explanation for metamorphosis. "

      It's rather simple, the caterpillar as butterfly genes.
      Now can you explain with ID why we find in the wild, butterflies with many forms of gastro-intestical tracts when in fact butterflies can't shit? Some butterflies have an almost intact tract lacking only an anus, others a rudimental tract?

      Delete
    33. Just another meaningless replication error. No selective advantage at all.

      Just keep stickin' those fingers in your ears (and remember that you hear with bones adapted from fish gill arches). :-)

      Delete
    34. Oops a few typos:

      ...perhaps even thousands of labs it's being tested, validated and confirmed.

      It's rather simple, the caterpillar has butterfly genes.

      ...butterflies with many forms of non-functional gastro-intestical tracts when in fact butterflies can't shit?

      Delete
    35. Hey txpiper: You know how how I got from my bed to my bathroom after I woke up this morning? I levitated in the air, without touching the ground.

      What, you don't believe me? You think I walked instead? Fine, then. Tell me the exact time and location of every single step I took to get there.

      If you can't, then you must admit I am telling the truth, and I did levitate there. Agreed?

      Delete
    36. There were 500 first-person witnesses to lutesuite levitating to his bathroom. How do we know this? It says so right here in this post, and in addition to seeing it happen myself, I also personally interviewed each of the 500 direct eye-witnesses.

      Welcome to lutesuiteism.

      Delete
    37. bwilson295,

      “Again, evolution involves selection as well as mutation "accidents." It would be nice if you exhibited some understanding of the theory you're declaring impossible.”

      I do tend to ignore selection, because it is not a biological process. Less fit specimens just die, and and are deleted from the gene pool. Nothing is truly being selected. It would be more accurate to call it natural culling. The whole evolutionary show always depends on fortuitous DNA replication errors, and in truth, natural selection just removes abnormal organisms that are the result of those errors.

      Delete
    38. Tx:
      "I do tend to ignore selection, because it is not a biological process. Less fit specimens just die, and and are deleted from the gene pool. Nothing is truly being selected. "

      ...

      Delete
    39. Ed,

      “…what's being tested in the many labs all over the globe is the giant, evolutionary theory, not your windmill. This fact has been explained to you many, many times already, but for some reason the message doesn't seem to register. Why?”

      Because I recognize religious dogma when I see it. What lots of labs actually do is document the ugly results of mutations.
      -
      “It's rather simple, the caterpillar has butterfly genes.”

      Yes, but as lutesuite noted, “evolution is the theory that provides an explanation for how complex biological structures and functions have arisen”. Actually using the giant theory to explain how metamorphosis 'arose' is not simple at all. That's why you didn't attempt to do it.

      I often notice that in papers titled “The Evolution of whatever it is”, they do what you just did. They dwell on what is there, not how it got there.

      Delete
    40. Nothing is truly being selected. It would be more accurate to call it natural culling.


      Nothing is truly being "gravitated." It would be more accurate to call it natural falling.

      Delete
    41. txpiper,

      "Because I recognize religious dogma when I see it. What lots of labs actually do is document the ugly results of mutations."

      Hypocrite much? If you did recognize religious dogma, then you'd recognize your motivation to finding something you, particularly, have problem figuring how it could evolve, then claim that it could not possibly happen. Just on your say so. If you recognized religious dogma, at the very least, you'd be open to a natural explanation for those "problems" you perceive. but no, you will keep thinking of evolution as impossible, on your mere say so, and as long as you can see something and claim "not possible! accidents cannot do this!" Of course, you'll hold to the word accident. Thinking beyond that is forbidden by your religious dogma. Isn't it?

      "Actually using the giant theory to explain how metamorphosis 'arose' is not simple at all. That's why you didn't attempt to do it."

      While I have found very reasonable descriptions about how metamorphosis could have arisen, with organisms showing different levels of metamorphosis that are evidence that it can happen in stages, let's pretend there wasn't any studies about it yet. No data. No observations except for the most spectacular cases of metamorphosis. Why would a lack of detailed studies mean that evolution didn't happen, or that there should not be any natural explanations? Wouldn't the proper approach be to study what's right there, investigating for further data, examining more organisms searching for different levels of complexity in metamorphosis? For a reasonable person, the proper course of action is not merely declaring how impossible it must be, but to actually go and check what's going on. What evidence can be collected either way (for, against, natural selection acting, how it might act, what kinds of "steps" might be available). But mere declaration? From someone who doesn't even care to take a deep look into the natural world?

      So, mere declarations might be very convincing to you. You might deny that your motivation is religious dogma, but your lack of seriousness and your lack of reasoning tells otherwise. It tells me, plainly and unambiguously, that you're a hypocrite and a fool.

      Delete
    42. TX: "I do tend to ignore selection, because it is not a biological process. Less fit specimens just die, and and are deleted from the gene pool."

      Oh, TX. You truly, truly do not understand the theory you are criticizing.

      First, differential death rates and reproductive rates (summarized as "selection") are biological.

      Importantly, as only a portion of the genetic variation present in a population persists, the population changes. The different genotypes and phenotypes in these next generations change the context in which mutations are found to be successful or not. Thus, counter-intuitive though it may be, selection can actually have a creative effect on the population, turning it into something different than it was. Just as people do as we breed dogs or tomatoes, or other species.

      Delete
    43. Tx,

      do tell why should I try to explain anything how a caterpillar becomes a butterfly, when you won't accept the explanation anyway. With fundamentalist religious fervor you keep on attacking a windmill, like Don Quixote. It's "evolution can't do this, thus goddidit" *every* *single* *time*.

      Pity... Photosynthesis is right.

      Delete
    44. I do tend to ignore selection, because it is not a biological process. Less fit specimens just die, and and are deleted from the gene pool.

      Uh huh. And just how would you expect natural selection to operate if it were a biological process?

      Delete
    45. Say Tx - The American Cancer Society projects that 1170 children will die from cancer this year. If you chat with the Infinitely Merciful and Loving Designer of our genome, you wanna ask Him why He didn't do a better job?

      Delete
    46. photosynthesis,

      “Of course, you'll hold to the word accident. Thinking beyond that is forbidden by your religious dogma. Isn't it?”

      Is that word not accurate? What am I missing that you’ve discovered out there in the forbidden zone about mutations?

      ===

      bwilson295,

      “differential death rates and reproductive rates (summarized as "selection") are biological….Importantly, as only a portion of the genetic variation present in a population persists, the population changes…..”

      I understand the nuance. At the end of it, natural selection is a grossly over-hyped concept, amped up to agency status:

      “Natural selection is truly the ultimate inventor. A short list of some of its many "inventions" includes flight, celestial navigation, echolocation, insulation, infrared sensors, hypodermic needles, plus all sorts of useful biologically active chemicals such as antibiotics, analgesics, emetics, diuretics, laxatives, tranquilizers, contraceptives, hallucinogens, pain killers, and many, many more. Each of these has been fashioned by natural selection to meet the needs of particular organisms in specific environments.”
      http://www.biologyreference.com/Mo-Nu/Natural-Selection.html

      Muggeridge was right. We've educated ourselves into imbecility.

      ===

      judmarc,

      “The American Cancer Society projects that 1170 children will die from cancer this year. If you chat with the Infinitely Merciful and Loving Designer of our genome, you wanna ask Him why He didn't do a better job?”

      An extensive bulletin (1 Corinthians 15) was composed and published that addresses the issue of death. I don’t need to ask about it.

      Delete
    47. An extensive bulletin (1 Corinthians 15) was composed and published that addresses the issue of death. I don’t need to ask about it.

      Not to be cruel, though I'm sure it will sound that way to you, but the part of what Paul says that rings true to me is:

      "If there is no resurrection of the dead, then not even Christ has been raised. And if Christ has not been raised, our preaching is useless and so is your faith."

      Delete
    48. That doesn't sound cruel at all. It is a technical reality.

      Delete
    49. It is a technical reality.

      Then there is yet hope for you, my son. ;-)

      Delete
    50. tx - dopey unsupported folksy assertions might count as PROOF in your church, but in reality, they do not.

      Delete
  3. unfortunately for you, luitesuite, the evidence shows exactly that. Look at cichlids...look at finches...look at waterfleas...look at tadpoles, zebra fish, or any other well-studied organism in science and you will find that the vast majority of the morphological changes involve epigenetics, changes in gene expression, not mutation. Heres just one...I could give you hundreds....https://plus.google.com/+BeforeItsNewsAlto_News/posts/ZyZU57718mQ

    ReplyDelete
    Replies
    1. I must say, however, that I am heartened to see that creationists are beginning to accept that "microevolution" is still evolution.

      Delete
    2. @Tommy Hall
      The cause OF changes in gene expression between species is mutation, you dolt. Their genomes are not identical.

      It's like creationists are discovering the concept of gene regulation for the first time.

      Delete
    3. LS
      "unfortunately for you, luitesuite, the evidence shows exactly that. Look at cichlids...look at finches...look at waterfleas...look at tadpoles, zebra fish, or any other well-studied organism in science and you will find that the vast majority of the morphological changes involve epigenetics, changes in gene expression, not mutation."

      The above is not his argument ?

      Delete
    4. The above is not the argument you said it was. It is not synonymous with "gene expression drives morphology."

      Do you understand what John Harshman meant by "long-term heritable changes in gene expression are caused by mutations in the genome"? Do you agree with that, or are going to again pretend you understand biology better than he does?

      Delete
    5. LS
      "Do you understand what John Harshman meant by "long-term heritable changes in gene expression are caused by mutations in the genome"? Do you agree with that, or are going to again pretend you understand biology better than he does?"

      So you are suggesting this is absolute truth because John made the claim?

      Delete
    6. Bill Cole,

      The question was whether you understood that. Not whether you accepted it.

      Anyway, when people talk about gene expression, they don't mean "due to epigenetics." They just mean gene expression. If they meant "due to epigenetics," then they would explicitly say so. Otherwise it's assumed that everybody knows that gene expression and it's associated genetics are involved.

      Of course, you don't have to take my word for it. But you'll find that's the way it is once you start reading some articles. If you ever do.

      Delete
    7. Bill Cole ignores my question (of course) and instead disingenuously asks:

      So you are suggesting this is absolute truth because John made the claim?

      No.

      Let's pretend your creationist pal Tommy has half a clue what he is talking about, and evolutionary morphological change is due to "epigenetics" and not to mutations. That would mean a stickleback fish and an oak tree would have genomes that are indistinguishable from one another, or nearly so. And it would be possible to change a stickleback into an oak tree just by "epigenetically" changing gene expression, without any changes occurring in DNA sequences.

      Is it your understanding that the scientific evidence is compatible with Tommy's claim? Or is John Harshman's position a better representation of the truth?

      Delete
    8. LS
      "Let's pretend your creationist pal Tommy has half a clue what he is talking about, and evolutionary morphological change is due to "epigenetics" and not to mutations. That would mean a stickleback fish and an oak tree would have genomes that are indistinguishable from one another, or nearly so. And it would be possible to change a stickleback into an oak tree just by "epigenetically" changing gene expression, without any changes occurring in DNA sequences."

      What evidence do you have that all morphological change is due to mutations?

      Delete
    9. What evidence do you have that all morphological change is due to mutations?

      It isn't. Morphologically, I am several pounds heavier than I was prior to the Xmas holidays. That's not because of mutations, if I'm not mistaken.

      Is there some reason you persistently refuse to answer questions?

      Delete
    10. LS
      "Is there some reason you persistently refuse to answer questions?"

      At this point I don't have an answer to which argument is better. If I don't answer its because I don't have an opinion yet.

      Delete
    11. I'm not sure what further information you need. Evidence for long term heritable changes in morphology arising thru mutations abound. You are surely aware of this, since you have been discussing and investigating evolutionary theory, often with experts in the field, for years now. Evidence for long term heritable changes in morphology arising from "epigenetics" is non-existent. What else are you waiting for?

      It seems pretty clear to me that you know what the answer is. But it's not the answer you want, so you're just going to pretend the question remains unanswered.

      Delete
    12. LS
      "It seems pretty clear to me that you know what the answer is. But it's not the answer you want, so you're just going to pretend the question remains unanswered."

      Please support your claim. I have no pre conceived notion of this one. If you can support your claim with solid experimental evidence I will gladly agree with your position.

      Delete
    13. Well, fair enough. It's also possible you're just so plain stupid that you can't understand the evidence that has been laid out before you repeatedly on a silver platter. Take your pick, Bill.

      Delete
  4. LS
    "So now the question is: Who should we believe? Joe Felsenstein, or some internet creationist named "Tommy Hall"? Such a difficult decision."

    Why do you think Joe's argument about limited generational inheritance refutes Tommy's argument that gene expression drives morphology?

    ReplyDelete
    Replies
    1. To clarify: long-term heritable changes in gene expression are caused by mutations in the genome. What did you think?

      Delete
    2. @Bill Cole "Tommy's argument that gene expression drives morphology?".

      If that was Tommy's argument he would be stating basic Evo-devo theory. Of course gene expression is what gives drives morphology and so on. Who the hell says otherwise?

      Delete
  5. To reject Waddington's "epigenetics" terminologgy because the term "gene regulation" covers the topic (as Deans and Maggert apparently do) doesn't seem to make very much sense. Waddington's epigenetics referred to non-genetic aspects of development. There's more to development than gene regulation.

    ReplyDelete
  6. Try as I might I just can't understand how epigenetics challenges anything in evolutionary science other than the selfish gene/gene selectionist/adaptationist version, where DNA is a replicator rather than a cell. But, if that's the correct version, then there certainly is no need to hype epigenetics.

    ReplyDelete
    Replies
    1. S Johnson: "Try as I might I just can't understand how epigenetics challenges anything in evolutionary science"

      Look, suppose you want to call Newton a liar. Debunk the theory of gravity. You say, "According to that liar Newton, gravity is the only force in the universe, gravity does everything, and all objects always fall DOWNWARD!" Then you get some video of a magnet lifting a paper clip. Or a helium balloon rising. And you say, "See? Newton's a fraud: there is another force in the universe besides gravity. Checkmate, atheists!"

      Delete
  7. I realize that epigenetics is complex, but does it not boils down to how genes are expressed based on environmental cues? And if this is true, are not the two or more ways in which a gene can be expressed exposed to selection processes? If so, how is this not covered by evolutionary theory?

    Of course, it is possible that I don't know what I am talking about.

    ReplyDelete
  8. So miRNAs are no longer "epigenetic" ? I never understood why they were included anaway.

    ReplyDelete
  9. Histone modifications are never inherited through sperm because the chromatin is restructured during spermatogenesis.

    It is true that inheritance of histone modifications is mostly maternal, but there are some exceptions, for example in this study of disrupted histone methylation in mice and histone modifications involved in the establishment of heterochromatin in men.

    ReplyDelete
  10. One might just add that although the post has an image of Lamarck, his actual theories have nothing to do with epigenetics. He had a theory of inheritance of adaptive modifications that were produced by use-and-disuse (he also had a separate long-term complexifying force). Neither of these is reflected in epigenetics, which produces phenotypic modifications that are nor preferentially adaptive. Being exposed to a famine results in your grandchildren not becoming more able to resist famines, but instead more susceptible to heart disease. So no sign of Lamarck except that people like to call any inheritance of acquired characters "Lamarckian".

    ReplyDelete
  11. Mikkel Rumraket Rasmussen says,

    There were 500 first-person witnesses to lutesuite levitating to his bathroom. How do we know this? It says so right here in this post, and in addition to seeing it happen myself, I also personally interviewed each of the 500 direct eye-witnesses.

    That's ridiculous. No sane person would ever believe that people could fly.

    ReplyDelete
  12. Have you ALL adjusted to epigenetics yet? I know that Joe Felenstein still holds his fort while putting his reputation online that epigenetics has no influence on his beliefs...being evolution of within genes only...

    ReplyDelete
  13. |Larry, Does freedom of speech include misinformation? Especially Deliberate?

    ReplyDelete