Epigenetics News

Epigenetics: Cultural differences do affect DNA, researchers say

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methylated DNA molecule/Christoph Bock/CeMM

From ScienceDaily:

The study examined DNA methylation — an “annotation” of DNA that alters gene expression without changing the genomic sequence itself — in a group of diverse Latino children. Methylation is one type of “epigenetic mark” that previous research has shown can be either inherited or altered by life experience. The researchers identified several hundred differences in methylation associated with either Mexican or Puerto Rican ethnicity, but discovered that only three-quarters of the epigenetic difference between the two ethnic subgroups could be accounted for by differences in the children’s genetic ancestry. The rest of the epigenetic differences, the authors suggest, may reflect a biological stamp made by the different experiences, practices, and environmental exposures distinct to the two ethnic subgroups.

Researchers and clinicians have known for many years that different racial and ethnic populations get diseases at different rates, respond differently to medications, and show very different results on standard clinical tests: “For a whole range of medical tests, whether your physician is told that your lab result is normal or abnormal depends entirely on the race/ethnicity box that you tick on an intake form,” Zaitlen said.

The researchers turned to epigenetics to search for answers to these questions because these molecular annotations of the genetic code have a unique position between genetic ancestry and environmental influence. Unlike the rest of the genome, which is only inherited from an individual’s parents (with random mutations here and there), methylation and other epigenetic annotations can be modified based on experience. These modifications influence when and where particular genes are expressed and appear to have significant impacts on disease risk, suggesting explanations for how environmental factors such as maternal smoking during pregnancy can influence a child’s risk of later health problems. Paper. (public access) – Joshua M Galanter et al., Differential methylation between ethnic sub-groups reflects the effect of genetic ancestry and environmental exposures. eLife, 2017; 6 DOI: 10.7554/eLife.20532 More.

With luck, epigenetics can thread the defile between “scientific” racism and unquantifiable claims about “environment.” From an epigenetic perspective, whether a person will be affected by a given problem may depend not so much on the genes inherited but on where their switches have been set in recent generations. And switches can be reset, after all.

See also: Epigenetics: How many methylation patterns can be attributed to ethnic ancestry?

Epigenetics becomes, increasingly, a normal study area in science

and

Epigenetic change: Lamarck, wake up, you’re wanted in the conference room!

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58 Replies to “Epigenetics: Cultural differences do affect DNA, researchers say

  1. 1
    Dionisio says:

    Very interesting.

  2. 2
    bornagain77 says:

    Of semi-related note: Jonathan M has the Jonathan Wells video up:

    Design Beyond DNA: A Conversation with Dr. Jonathan Wells – video
    https://www.youtube.com/watch?v=ASAaANVBoiE

  3. 3
    Silver Asiatic says:

    I will reluctantly agree with wd400 … none of these papers ever say that such findings are a problem for evolution. Even though it really is! But we end up as the only ones drawing that conclusion.

  4. 4

    Forgive my ignorance, but I don’t really understand epigenetics. What is it in a nutshell and why is it a problem for evolution?

  5. 5
    daveS says:

    Silver Asiatic,

    I will reluctantly agree with wd400 … none of these papers ever say that such findings are a problem for evolution. Even though it really is! But we end up as the only ones drawing that conclusion.

    I don’t know anything about epigenetics, but could you explain how it is a problem for evolution? If I understand correctly, it concerns physical changes that can be inherited (for a few generations, at least). Does it contradict evolutionary theory?

  6. 6
    bornagain77 says:

    TWSYF:

    The Mysterious Epigenome. What lies beyond DNA – video
    http://www.youtube.com/watch?v=RpXs8uShFMo

    “The Mysterious Epigenome: What Lies Beyond DNA” – May 2012 – podcast
    http://intelligentdesign.podom.....7_28-07_00

    Chuan He: Evolution Created Epigenetics – Cornelius Hunter – PhD in Biophysics – May 3, 2015
    Excerpt: They never predicted it, then they denied it could be heritable, and then they denied it could cause lasting change. “It” in this case is epigenetics and in spite of being wrong, wrong and wrong again, and in spite of the fact that there is no scientific explanation for how epigenetics could have evolved, evolutionists nonetheless insist that it, in fact, must have evolved. Evolution loses every battle but claims to win the war.
    http://darwins-god.blogspot.co.....etics.html

    Michael Skinner on Epigenetics: Stage Three Alert – Cornelius Hunter – December 4, 2016
    Excerpt: What Skinner and the evolutionists don’t tell you is that in light of their theory, none of this makes sense. With epigenetics the biological variation evolution needs is not natural. It is not the mere consequence of biophysics — radiation, toxins, or other mishaps causing DNA mutations. Rather, it is a biological control system.
    It is not simple mistakes, but complex mechanisms. It is not random, but directed. It is not slow, but rapid. It is not a single mutation that is selected, but simultaneous changes across the population. This is not evolution.
    As Skinner inconveniently realizes, such epigenetics are found across a wide range of species. They are widely conserved and, for evolution, this is yet more bad news.
    http://www.evolutionnews.org/2.....03338.html

    The Science Contradicts The Theory – Cornelius Hunter – video – 42:00 minute mark
    https://youtu.be/HTIlHEn9hXs?t=2501

  7. 7
    Silver Asiatic says:

    daveS & TWSYF

    BA77’s links are very good, as always.

    It’s complicated because when we say “contradicts evolution” we have to mean strictly that it “contradicts the theory of evolution as claimed by mainstream science today”.

    What eventually happens is that term “evolution” will be used to cover the topic of epigenetic change also since organisms are seen to change. But that’s wrong because there is no theory that explains epigenetic change and nothing that explains its origin.

    wd400 for example, avoids this problem and just says something like “we’ve known about so-called [he doesn’t even like the term] ‘epigenetics’ for decades and it’s all fully a part of evolutionary theory.”

    But epigenetics is radically different from neo-Darwinian evolution. In epigenetic changes, the genome is responsive to environmental changes and DNA will adjust itself with built in markers that anticipate environmental stimulus.

    So, there’s a non-random relationship between the genetics of a population of organisms and the environment.

    Explaining the origin of this would require an explanation of the fitness benefit of a relationship that anticipates future changes – as well as the rapid modification of cell functions in response.

    In evolutionary theory, mutations occur randomly in individuals, and then by “selection” (the dying off of those that don’t have the beneficial mutation) the population gradually changes. There’s no response to the environment, although we mistakenly think it appears that there is. It’s really just an accidental mutation that enables an organism to survive better. The mutation doesn’t know or care about the environment – nor does the DNA itself.

    But with epigenetic changes, the organism is able to make genetic changes in response to the environment and it occurs within the population, not in an individual getting a random mutation and then waiting centuries for it to spread.

  8. 8

    Thank you SA and BA77. I will look at the links this evening.

  9. 9
    Silver Asiatic says:

    The article about Michael Skinner that BA77 posted is very good.

    As with the paper here in the OP, evolutionists will now talk about epigenetics as if there is no problem at all with evolutionary theory. It’s just called “epigenetic evolution”.

    Once you assume that evolutionary theory is true, there is never any need to prove the origin of anything found in biology. Even though such things like this contradict the theory.

    Some sort of mutational path has to be show for how an organism’s DNA can change when introduced to a new environment. In evolutionary theory, the organism should either die, or just get lucky with a mutation that enables survival for some. Eventually that should lead to a new species.

    Instead, the organism responds immediately and the changes occur in order to preserve itself, not to cause it to change into a new species.

  10. 10
    daveS says:

    Thanks, Silver Asiatic, I’ll take a closer look when I get a little free time.

  11. 11
    Silver Asiatic says:

    For some reason today I took a look at our competitor (they think they are) site The Skeptical Zone. From there I started reading VJ Torley’s comments on Early embryonic mutations, responding to Meyer & Axe’s top 5 problems with evolution.

    Within that, I noted Prof. Torley dismissing epigenetics as a problem stating “Professor Larry Moran has addressed it more than adequately in his recent post, What the Heck is Epigenetics?” and concluding “So much for epigenetics, then.”

    That struck my interest – certainly. So, off to Prof. Moran’s blog. And now my head still hurts – more from Prof. Torley than Moran. I’d expect some hand-waving from a committed evolutionist, but to cite that article as “so much for epigenetics?” He can’t be serious.

    No, you’re not supposed to just claim epigenetics as part of the theory – you have to explain the origin of this process. The Cornelius Hunter article is devastating in comparison.

    Moran, like wd400, doesn’t even want to admit that the term epigenetics has legitimacy. But then in the comments to the very same article that supposedly refutes the problem of epigenetics, Moran states:

    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.

    As above, he doesn’t understand the debate. It’s not a matter of how it affects evolution, which he admits he doesn’t understand anyway — but how that response mechanism arose through random mutations and selection over a long period of time. It’s the preservation of features for a future, unknown benefit – and evolution is not supposed to do that.

    Moran continues …

    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.

    That was good enough for Professor Torley to have no further concern?

  12. 12
    wd400 says:

    This illustrates a lot of what’s wrong with the way News and others report epigenetics.

    For the record. There is no reason to think any of these marks can be inherited over generations, the study itself shows most of the measured variation in methylation is the result of genetic variation (i.e. genetics is driving epigenetic states), there is no evidence that other marks are an adaptive response to the shared environment of the socially-constructed ethnicity (rather than passive consequence of shared exposure).

    No doubt some of the marks are in fact such a plastic response to an environmental cue. But it’s absolutely bizarre to imagine that regulation of gene expression and gene-environment interactions are not part of evoluioanry biology. Evolutionary biologists had to invent quantative genetics (in the 1920s!) to deal with these topics, and they’ve been a major focus ever since.

  13. 13
    wd400 says:

    I’ve said this before, but a good question for someone trying to make a lot out of an epigenetic result to ask is “how is this different than the lac operon?”

  14. 14
    wd400 says:

    SA,

    As above, he doesn’t understand the debate. It’s not a matter of how it affects evolution, which he admits he doesn’t understand anyway — but how that response mechanism arose through random mutations and selection over a long period of time.

    That might be your question, but I don’t think many anti-evolutionists are saying this. For the most part they conflate every epigenetic result with transgenerational epigenetics and say “Lamark was right, Darwin was wrong” and end about there.

    It’s the preservation of features for a future, unknown benefit – and evolution is not supposed to do that.

    Do have an example of this to cite? I don’t know now of any..

  15. 15
    Silver Asiatic says:

    wd400

    You stated:

    No doubt some of the marks are in fact such a plastic response to an environmental cue.

    The challenge is to explain how this genetic response mechanism arose, which is sensitive enough to respond to novel characteristics in the environment. Features in the organism, with no apparent, immediate fitness benefit, have to be preserved for the time when a new environmental trigger arises.

    An example:

    Mussels Evolve in an Evolutionary Heartbeat
    http://www.livescience.com/954.....tbeat.html

    “The mussel’s inducible response to H. sanguineus reflects natural selection favoring the recognition of this novel predator through rapid evolution of cue specificity or thresholds,” the researchers write in the Aug. 11 issue of the journal Science

    The mussels most likely evolved quickly because they are used to being prey to many species in these waters.

    “When Hemigrapsus came along the mussels’ wheels were well-greased to respond,” said co-author James Byers, associate professor of zoology at the university. “That’s our best guess.”

    As above, Prof. Byers uses the term “well-greased” meaning there is a function already in place, anticipating a future state which may or may not occur.

  16. 16
    wd400 says:

    The challenge is to explain how this genetic response mechanism arose, which is sensitive enough to respond to novel characteristics in the environment. Features in the organism, with no apparent, immediate fitness benefit, have to be preserved for the time when a new environmental trigger arises.

    Your example is not like this at all though? I’m not sure which bit of that study you are misunderstanding, so not sure how to correct you…

  17. 17
    Origenes says:

    For me this article by Stephen Talbott has been real eye-opener wrt DNA and epigenetics.

    Excerpt:

    If you arranged the DNA in a human cell linearly, it would extend for nearly two meters. How do you pack all that DNA into a cell nucleus just five or ten millionths of a meter in diameter? According to the usual comparison it’s as if you had to pack 24 miles (40 km) of extremely thin thread into a tennis ball. Moreover, this thread is divided into 46 pieces (individual chromosomes) averaging, in our tennis-ball analogy, over half a mile long. Can it be at all possible not only to pack the chromosomes into the nucleus, but also to keep them from becoming hopelessly entangled?

    … Histone proteins, several of which can bind together in the form of an extremely complex histone core particle, are the single most prominent constituent of this chromatin. Every cell contains numerous such core particles — there are some 30 million in a typical human cell — and the DNA double helix, after wrapping a couple of times around one of them, typically extends for a short stretch and then wraps around another one.
    … Histones can even be removed from a spool altogether, leaving it “incomplete.” And certain proteins can slide spools along the DNA, changing their position. As we have seen already, a shift of position by as little as two or three base pairs can make the difference between gene activation or repression, as can changes in the rotational orientation of the DNA on the face of the histone spool. … Further, not only the exact position of a nucleosome along the double helix, but also the precise rotation of the helix is important. “Rotation” refers to which part of the DNA faces toward a histone surface and which part faces outward.
    … The canonical nucleosome core particle is a complex of histone proteins, each of which has a flexible, filamentary “tail”. This tail can be modified through the addition of several different chemical groups — acetyl, methyl, phosphate, ubiquitin, and so on — at any of various locations along its length. A great variety of enzymes can apply and remove these chemical groups, and the groups themselves play a role in attracting a stunning array of gene regulatory proteins that restructure chromatin or otherwise help choreograph the drama of gene expression.
    … Nucleosomes will sometimes move — or be moved (the distinction between actor and acted upon is forever obscured in the living cell) — rhythmically back and forth along the DNA, shifting between alternative positions in order to enable multiple transcription passes over a gene. In stem cells a process some have called “histone modification pulsing” results in the continual application and removal of both gene-repressive and gene-activating modifications of nucleosomes. In this way a delicate balance is maintained around genes involved in development and cell differentiation. The genes are kept, so to speak, in a finely poised state of “suspended readiness”, so that when the decision to specialize is finally taken, the repressive modifications can be quickly lifted, leading to rapid gene expression

    It’s more than clear that something incredibly complex/mysterious is controlling gene expression

  18. 18
    Silver Asiatic says:

    Thanks to Origenes for the Stephen Talbott excerpt.

    The genes are kept, so to speak, in a finely poised state of “suspended readiness”, so that when the decision to specialize is finally taken, the repressive modifications can be quickly lifted, leading to rapid gene expression

    That’s what I said, wd400. The genes are “ready” for a future state.

    You said you don’t know of any examples of this.

    Perhaps you could ask Mr. Talbott for a better one than I gave you?

    I’ll add, this is not change by mutation and selection. Agreed?

  19. 19
    wd400 says:

    Again, I don’t think you are following what it being said. In that copy-paste the “future” state is part of the development of an organism, not an environment some descendant will face many generations hence…

  20. 20
    Origenes says:

    wd400: … genetics is driving epigenetic states …

    Simple question for wd400: what controls the differentiation of cell types, and how are they all coordinated so as to function as one organism?
    Do you seriously hold that differentiation of our cells is driven by DNA? Do you hold that DNA in ± 37 trillion cells have organism-wide control? If so, why is it that this makes sense to you? Frankly, I cannot even consider that possibility without making a grimace.

  21. 21
    wd400 says:

    Do you seriously hold that differentiation of our cells is driven by DNA

    Pretty much, yes.

    Do you hold that DNA in ± 37 trillion cells have organism-wide control?

    I don’t think any cell has “organism-wide control”. But the developmental program that let to creation of each cell is certainly in the DNA of every cell (with exceptions for mature red blood cells and a few somatic mutations etc)

  22. 22
    Origenes says:

    wd400:

    Origenes: Do you seriously hold that differentiation of our cells is driven by DNA?

    Pretty much, yes.

    The human body consists of ± 37 trillion cells that can differentiate in ± 200 different cell types. Do you agree that a coherent result is inconceivable without some higher level coordinative power? If not, why not?

    wd400: … the developmental program that let to creation of each cell is certainly in the DNA of every cell …

    How do you explain that 37 trillion separate programs function as one organism?

  23. 23
    Silver Asiatic says:

    wd400

    Again, I don’t think you are following what it being said. In that copy-paste the “future” state is part of the development of an organism, not an environment some descendant will face many generations hence…

    It’s a parallel idea.

    But back to the example given, where blue mussels adapted by thickening their shells when they encountered a new environment …

    Such rapid evolutionary response is a “nanosecond” compared with the thousands of years that it normally takes for a species to respond to a predator.

    What is your explanation for that? This was not a case where a beneficial mutation occurred in an individual and then spread through inheritance and selection for generations. This, instead, is called an example of epigenetic change.

  24. 24
    wd400 says:

    Origines,

    I’m not very interested in the 20 questions routine. Do you have an actual argument, or is it just your uninformed incredulity all the way down?

    If you are interested in how cells pull together to make an organism then I suggest you learn about the molecular basis of cancer. Cancer is, more or less, what happens when cells stop working together. This is very nearly universally the result of mutations in the DNA of the affected cells….

  25. 25
    Silver Asiatic says:

    I could attempt to structure an argument for wd400:

    1. Any number of organisms could either function as individual entities or as a unified whole.

    2. As with chemical bonds, the exactness of the presence of similar chemical properties (hydrogen, oxygen & heat = H2O) yields a higher probability of a bond, and a more variable, dissimilar properties yield a lower probability of a bond.

    3. The human body contains a large number of highly dissimilar elements (± 37 trillion cells that can differentiate in ± 200 different cell types).

    4. Therefore the likelihood of them bonding together into one unified entity is virtually zero.

    5. It follows then, that evolutionary theory, which claims it is highly likely that they will bond, fails.

  26. 26
    wd400 says:

    SA,

    Your new story with the mussels is different than the old one (that they were maintaining a response that will one day be adaptive but has no purpose at present). Nevertheless…

    Nothing in the mussel paper demonstrates an inherited epigenetic state. Mussels in all populations in the US harden their shells in response to native crabs, in the region exposed to the new crab species they do the same to this new crab too. That requires only a mutation to the protein that acts as receptor to the chemical cues given by the crabs. Such an allele might already have existed and low frequency or have been created by mutation after contact.

    We could now test that hypothesis with genomic sequencing. But there is certainly no evidence that this is an inherited epigenetic trait.

  27. 27
    wd400 says:

    SA @ 25,

    Is that at serious argument? This is “tornado in a junkyard” (one of the worst arguments going) taken to describe development instead of evolution? I really think this might be the least coherent argument against evolution I’ve ever heard.

  28. 28
    Origenes says:

    wd400: is it just your uninformed incredulity all the way down?

    “Functional coherence” wd400, it is in need of an explanation …
    Here is Douglas Axe:

    What enables inventions to perform so seamlessly is a property we’ll call functional coherence. It is nothing more than complete alignment of low-level functions in support of the top-level function.
    … Alphabetic written languages, for example, use letters as the basic building blocks at the bottom level. These letters are arranged according to the conventions of spelling to form words one level up. To reach the next higher level, words are chosen for the purpose of expressing a thought and arranged according to grammatical conventions of sentence structure in order for that thought to be intelligibly conveyed. … If the point is to convey one simple thought, a sentence should suffice. If it’s to carry readers through an extended thought process, many sentences will be needed, each carefully crafted to make its own point in a way that coheres with the preceding points and paves the way for subsequent points.
    … All we’re doing in this chapter is unpacking this intuition to show why our firm sense that certain things can’t happen by accident is absolutely correct. What we’re seeing is that the amount of functional coherence routinely produced by human insight truly can’t be produced by accident.
    … Whether we speak of impossible coincidences or impossible searches, the hard fact is exactly the same: high-level functional coherence can’t be found by any blind search because this would amount to an impossible coincidence. Only insight can hit a target like that, which is no coincidence. … Although we encountered this hard fact by looking at coherence at the low level of letter combinations, the situation only gets worse as we move up the hierarchy. … Like letters, words must be arranged coherently, which involves choosing good words and putting these words in good order. It isn’t as easy to calculate the likelihood of this happening blindly as it was for forming words from letters. Still, we can easily see that vocabulary is tightly constrained by the writing objective. … Here, then, are eleven seven-letter words chosen randomly from the 93,000-word dictionary that came with my computing software: luffing, dickens, numbers, inbound, roofers, incisor, overlap, Brownie, genomes, avenged, and tallier. In these words I submit there is no hint of a coherent theme.
    We need go no further. Blind searching fails at all levels. As people who write, we know that the need for insight grows as we move up the hierarchy, and that only makes the coincidence of blind coherence greater and greater. Any process that can’t substitute for competence in either spelling or vocabulary certainly can’t substitute for competence in grammar or composition. Our design intuition has this one exactly right. We need knowledge to write useful instructions, and no accidental process can replace that knowledge.
    [Douglas Axe, ‘Undeniable’, ch.9]

  29. 29
    wd400 says:

    So, no argument, no biology, just incredulity and copy-pasting? Guess we are done.

    I hope you research the cancer example a little though.

  30. 30
    Silver Asiatic says:

    wd400

    Nothing in the paper indicates when or how that new function arose in the species, through which mutation and for what fitness benefit at the time.

    Of course, you can come up with any number of speculative, ad hoc stories. If I had correctly anticipated that I wouldn’t have bothered to ask for your response. But I appreciate it anyway. You took the time and offered detailed reply, so I consider that a valuable contribution even though it does leave alternative scenarios open for speculation also.

    I’ll just repeat the theme of my first comment in this thread. Very often we read of the discovery of new functions or adaptations, but we only rarely see studies on how such things evolved.

  31. 31
    Silver Asiatic says:

    wd400 @ 27

    That argument has a number of distinctions.
    1. It’s totally unique and I’ve never seen anyone use that before – so it’s perhaps a first in world history or the history of science for that matter.
    2. It’s a very good argument which has never yet been refuted.
    3. You think it’s possibly the least coherent argument against evolution you have ever heard – which is, at least, a distinction.

  32. 32
    Origenes says:

    wd400: Is that at serious argument? This is “tornado in a junkyard” (one of the worst arguments going) taken to describe development instead of evolution?

    You don’t seem to know the reference of Hoyle’s excellent “tornado in a junkyard” comparison. It was about abiogenesis not evolution.

    wiki: He [Sir Fred Hoyle] would go on to compare the random emergence of even the simplest cell without panspermia to the likelihood that “a tornado sweeping through a junk-yard might assemble a Boeing 747 from the materials therein”.

    However, being a good sport, I would like to argue that Hoyle’s comparison is equally apt in the case of ‘evolution’. As I have argued before, natural selection only explains elimination, so, evolutionary theory is driven by blind luck alone. Pure chance is at the source of every innovation — from bacterium to man, like a tornado in a junkyard.

  33. 33
    wd400 says:

    I guess maybe read The Blind Watchmaker? For all of Dawkins’ recent ridiculousness, that book gives a pretty clear explanation of what you are missing (in short: that selection is non-random and cumulative, allowing lineages to “bank” adaptations from previous generations and build on them in subsequent ones. As a result the journey through the space all possible organisms is very different than a random walk).

    It’s also interesting that your quote is from De Vries at the turn of the 20th century. That was a mainstream position at the time (the so called “eclipse of Darwinsism”) and you can find people that went on to become important Darwinists (Morgan etc) saying the same thing at the time. Why do you think that view was replaced?

    (To save you a search: it was the (re-)discovery of “particulate” inheritance and the development of mathematical treatment of natural selection that could work on these genes by Fisher, Wright, Haldane et al).

  34. 34
    Origenes says:

    wd400,

    ‘Selection’ — read: elimination — has no part in the coming into existence of any innovation from bacterium to man.

    Some darwinists, and perhaps Dawkins is one of them, hold that the going out of existence of X, explains the existence of Y. However elimination (a.k.a. “natural selection”) explains only why some things are not, not why some things are.

    Given that natural selection is a process of elimination, existent organisms are the ones that got away. Instead of being created by ‘natural elimination’, exactly the opposite is true: they are “untouched” by ‘natural elimination’. Existent organisms are those organisms on which natural selection has precisely no bearing whatsoever. They are the undiluted products of chance.

  35. 35
    wd400 says:

    Given that natural selection is a process of elimination, existent organisms are the ones that got away. Instead of being created by ‘natural elimination’, exactly the opposite is true: they are “untouched” by ‘natural elimination’. Existent organisms are those organisms on which natural selection has precisely no bearing whatsoever. They are the undiluted products of chance.

    This is almost as dumb as SA’s argument. Extant organisms start where they are because of the results of thousands of generation of non-random survival of genetic variants (i.e. selection) and have a very small amount of random variation added. Even the “weasel” example from Dawkins books should demonstrate the importance of cumulative selection.

  36. 36
    Silver Asiatic says:

    wd400

    Even the “weasel” example from Dawkins books should demonstrate the importance of cumulative selection.

    The weasel program aims at a fixed, “fitness target”. But environmental variables in real life are random. Selection is banking mutations that are beneficial for a moment, but the target is changing due to the randomness of new mutations, new competition, changing food resources, changing climate. If it takes 10,000 years for a trait to become fixed in a population, it no longer has the same fitness benefit it did when it first appeared because of the randomization of many other factors during the same period of time.

    So, it’s random mutations, multiplied by random environmental variables. Fitness is the output of a random process. Selection is therefore the same kind of output.

  37. 37
    wd400 says:

    Yes, weasel is a toy example that demonstrates one aspect of the evolution that Origenes is failing to grasp. Not a perfect simulation of evolution.

    Fitness landscapes are random as in random variable, not random as in tornado in a junkyard.

  38. 38
    Origenes says:

    wd400: This is almost as dumb as SA’s argument.

    I quite like SA’s argument. What’s wrong with it?

    wd400: Extant organisms start where they are because of the results of thousands of generation of non-random survival of genetic variants (i.e. selection) …

    Not being eliminated is not ‘selection’. The force you are talking about is elimination, that is, what is being discussed here is a purely destructive force — not a creative force. The absence of destruction is not equal to ‘selection’.

    wd400: … and have a very small amount of random variation added.

    Added to what? Added to ‘not being eliminated’? So, add a little amount of random variation to a whole lot of ‘not being eliminated’ and the path from bacterium to man can be explained? I’m sorry but evolutionary theory is a hoax.

    wd400: Even the “weasel” example from Dawkins books should demonstrate the importance of cumulative selection.

    METHINKS*IT*IS*LIKE*A*WEASEL

  39. 39
    Origenes says:

    Douglas Axe on Dawkin’s weasel and ‘cumulative selection’.

    Dawkins designed his program to carry out two simple steps repeatedly. The first step was to produce lots of copies of the parent sequence, starting with the random one, with occasional random typos in them. In the second step, each copy was compared to the target sentence “METHINKS IT IS LIKE A WEASEL”, and the copy with the most correct letters, however few, was selected as the parent for making a new batch of copies, and so on. After about forty rounds of this, an exact match was found.
    Dawkins knew this wasn’t blind evolution, of course. His intended point was simply that cumulative selection, where improvements are allowed to build a little bit at a time, can accomplish what would never be accomplished if the whole finished thing had to appear at once. In his words, “If . . . there was a way in which the necessary conditions for cumulative selection could have been set up by the blind forces of nature, strange and wonderful might have been the consequences.” Granted. But then strange and wonderful assumptions often imply strange and wonderful consequences, don’t they?
    Once again, what’s envisioned here is an extensive network of natural stepping stones that happen to line up in ways that make selection take extraordinarily insightful paths. We’ve already exposed this ploy. Accidental stepping stones leading to these fantastically improbable destinations would themselves be fantastically improbable.

    … we instantly see that the following line of gibberish (presented by Dawkins as the first selected sequence) wouldn’t meet that need:

    WDLTMNLT DTJBSWIRZREZLMQCO P.

    Equally unintelligible sequences meet other needs, of course—long passwords or encrypted messages. What we can’t imagine, though, is an honest-to-goodness series of these unrelated needs just happening to line up in such a way that they connect Dawkins’s original random sequence to “METHINKS IT IS LIKE A WEASEL”. That definitely won’t happen by accident, which is why Dawkins had to line up the stepping stones himself. Somehow, though, he thinks the implausibly complex network of stepping stones that would be needed for life to evolve did line up by accident. And somehow he thinks his thoroughly unremarkable demonstration should convince us of that thoroughly unbelievable claim.
    We know better. Natural stepping stones may lead to strange and wonderful destinations in our imaginations, but the real world is different. Nothing becomes useful or wonderful until functional coherence is present in good measure, and whatever helpful things the natural world may supply in good measure, functional coherence isn’t among them.
    [Douglas Axe, ‘Undeniable’, ch. 11]

  40. 40
    wd400 says:

    There is lots of work on empirical fitness landscapes that Axe could talk about instead of speculating here. Why do you think he didn’t?

  41. 41
    Origenes says:

    I suppose you are aware of Axe’s paper ‘The Evolutionary Accessibility of New Enzymes Functions’?

  42. 42
    wd400 says:

    The enzyme crocoduck paper? Yeah, I’m aware of it.

  43. 43
    Silver Asiatic says:

    wd

    Fitness landscapes are random as in random variable, not random as in tornado in a junkyard.

    Fitness landscapes are modeled by random variables because because environmental factors are random. The environment is random as when tornadoes strike. Random mutations change the fitness environment, creating and removing niches, competition, food sources and parallel functional attributes that may contribute to survival or be a threat to it.

    To say that selection is non-random is false since the fitness benefit of whatever may be selected through inheritance, is entirely dependent on what conditions the randomness of the environment provides.

    A mutation that has a fitness benefit in one environment, may cause extinction of the species in another environment – for the very same species. The power of selection is entirely random since in the case of extinctions, selection has no power at all, even though certain mutations were beneficial at one time in some circumstances.

    Junkyards have some functional pieces scattered around. A tornado may bring some of those together to create some primitive functional unit of some kind (a chair and table as a dining room set). Random mutations, preserved and inherited due to reasons that are either benefits or threats, depending on the randomness of the environment, is very much like a tornado in a junkyard in that case.

  44. 44
    Silver Asiatic says:

    All Dawkins’ weasel had to do in order to mirror reality somewhat more, is to randomize the target phrase every few generations instead of using a fixed line from Shakespeare. Then, using the step by step approach (which still wrongly latches to the target, but we could give him that), see how long it takes to match the target. I’d bet it would never happen. As soon as the program latched to one version of the target, the environment would change the target (randomizing the target) so the program would be stuck with the wrong characters it latched to.
    That’s similar to the problem of where evolution gets stuck on peaks of function and the only way to move is to lose fitness and come down from the peaks.
    By latching to a target phrase which eventually has less fitness (because the target changed) would lead to extinction eventually since selection acts too slowly to change organisms to meet the demands of a randomizing environment.

  45. 45
    Origenes says:

    wd400 @42,

    In line with your theory, your link doesn’t do the job. I guess you meant to link to this non-argument by R.Hoppe, who implicitly assumes the existence of a common ancestor of the enzymes who can perform magic.

    Douglas Axe:

    … biologist Ann Gauger and I chose to work with two strikingly similar yet functionally distinct natural enzymes, which we’ll call enzyme A and enzyme B (Figure 6.3). Our aim was to determine whether it would be possible for enzyme A to evolve the function of enzyme B within a time frame of billions of years. If natural selection really coaxed sponges into becoming orcas in less time, inventing many new proteins along the way, we figured it should have ample power for this small transformation. But after carefully testing the mutations most likely to cause this functional change, we concluded it probably isn’t feasible by Darwinian evolution.2 Additional work supports this conclusion. Mariclair Reeves—like Ann Gauger, a biologist at Biologic Institute—painstakingly tested millions upon millions of random mutations, searching for any evolutionary possibility that we may have overlooked in our first study. She found none.
    [Douglas Axe, ‘Undeniable’, ch.6]

  46. 46
    Origenes says:

    What defines a ‘fitness landscape’? Fitness equals ‘not being eliminated’. Local peaks in the landscape mean ‘low elimination’, valleys mean ‘high elimination’.
    IOWs at the peaks organisms are produced by chance and next ‘not eliminated’, and in the valleys organisms are produced by chance and eliminated.
    ‘Natural selection elimination’ only explains why some organisms go out of existence (valleys), but does not explain why organisms come into existence.
    ‘Cumulative selection’ is a repetitive absence of elimination (valleys) wrt chance mutations. It is chance operating unhindered by elimination in a series of steps. IOWs the absence of ‘natural selection elimination’ is a good thing for innovative evolution.
    What transpires is that ‘natural elimination’ is not an asset but a problem for evolution. Perfectly viable organisms are eliminated on a whim. It’s a decrease of information, since it causes things to die.
    But somehow the evolutionary narrative has convinced some that elimination is helping things along. But how does it help evolution to have local peaks surrounded by deep valleys? It obviously does not help. However, producing valleys is all ‘natural elimination’ can do.

    There is a reason why evolutionists want mutations to be neutral—not being eliminated. They want junk-DNA to exist, in order to have chance unhindered by ‘selection elimination’.

  47. 47
    Silver Asiatic says:

    Origenes

    What transpires is that ‘natural elimination’ is not an asset but a problem for evolution. Perfectly viable organisms are eliminated on a whim. It’s a decrease of information, since it causes things to die.

    That is a fascinating and very innovative look at it. The fact that some were ‘selected’ means others were lost. However, selection will only create peaks which are vulnerable to random environmental changes. It would be better for evolution if there was no selection, since selection reduces variation.

    But somehow the evolutionary narrative has convinced some that elimination is helping things along. But how does it help evolution to have local peaks surrounded by deep valleys? It obviously does not help. However, producing valleys is all ‘natural elimination’ can do.

    Interesting again. The evolutionary narrative has deliberately made it appear as if some benefits are actively being selected. However, the only way beneficial mutations can spread in the population enough to actually create new features is if less-fit organisms are eliminated. But that makes the species less robust, more specified, less variable and with less opportunity for evolution.

    There is a reason why evolutionists want mutations to be neutral—not being eliminated. They want junk-DNA to exist, in order to have chance unhindered by ‘selection elimination’.

    Yes, exactly. They need all that extra material hanging around to provide chances for co-option and lucky reuse of non-functional mutations. That’s part of the evolutionary scam.

    The other part of the evolution-scam is the claim that evolution is non-random. It’s the strange world of evolutionary math.

    As wd explains, fitness is a random variable, but that means it’s not like a random output (???). That’s a good start on evolutionary-logic. In other words, don’t bother trying to take it seriously.

    But going farther, selection is supposedly non-random. However, the output that equals “what is selected” is the product of the multiplication of random variables. Again, magical evolutionary-mathematics here. Evolution does such things.

    x = random mutations. That’s a random variable because mutations are random (sorry, I’m just using logic here).
    y = environment. Random variable because environmental conditions (actually multiple conditions, let’s say 12) are random. So, we have 12y.
    z = survival instinct and reproduction. Non-random as long as organisms have not gone extinct. So call it the non-random constant 2.

    The evolutionary magical formula: x * 12y * 2 = Selection, a non random value. It’s magic. Just ask Richard Dawkins.

    We can plug in some numbers for x and y and the result will be non-random – because Dawkins said so. Evolution is destined to select features that have the most benefit, and create a consistent, linear, non-random improvement and refinement of features (fish, mammals, eyes, wings, human consciousness) over the course of centuries – while selection pressures driven by a dozen environmental variables change randomly, radically and continually over the same course of time.

  48. 48
    Origenes says:

    Silver Asiatic,

    I agree with most of what you say, but not this:

    Silver Asiatic: However, the only way beneficial mutations can spread in the population enough to actually create new features is if less-fit organisms are eliminated.

    How does elimination help? Let’s suppose that less-fit organisms are not being eliminated at all—no natural selection—, and life, driven by blind unhindered chance, veers off in all directions. Why does that stop the creation of new features? Quite the contrary, I would say.
    Or suppose that elimination happens on a much less scale, according to evolutionary theory it would result in much more variation. Less natural selection is more variation.
    IOWs natural selection removes features and does not create any. It hinders the creativity of evolution.
    An ice age only removes information, but does not create any. The organisms that survive already existed.

  49. 49
    Silver Asiatic says:

    Origenes,

    How does elimination help? Let’s suppose that less-fit organisms are not being eliminated at all—no natural selection—, and life, driven by blind unhindered chance, veers off in all directions. Why does that stop the creation of new features? Quite the contrary, I would say.

    Fascinating questions – yes, that could be right. There’s the assumption that since elimination enables a population to all share the same trait, then that’s good for evolution. But that’s only an after-the-fact story to explain why species don’t have all sorts of diverse features.

    Because if there was no elimination, a huge variety of beneficial features would appear within the same species.

    The fact that we don’t see this means that evolution has to come up with the story that all the less fit were eliminated. This assumes that competition for resources is so intense and dramatic, that it’s always a win-lose scenario. Either you get the resources or you go extinct.

    We see nothing like that with countless species on earth today who either compete or live harmoniously – they don’t put one or the other out of existence.

  50. 50
    Origenes says:

    This muddled thinking surrounding ‘natural selection’ … was it always like this?

    Charles Darwin: It is interesting to contemplate an entangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent on each other in so complex a manner, have all been produced by laws acting around us.

    So all life is produced by laws.

    These laws, taken in the largest sense, being Growth with Reproduction; Inheritance which is almost implied by reproduction; …

    And these laws presuppose life. Well, that’s some very smart thinking Charly …

    … Variability from the indirect and direct action of the external conditions of life, …

    Variability from the external conditions of life? As in, ‘natural selection leads to variability’? How can he say this? For me, it is clear as day that Darwin is dead wrong here: natural selection absolutely decreases variability.

    … and from use and disuse; a Ratio of Increase so high as to lead to a Struggle for Life, …

    BTW why is it that organisms struggle to survive? Do they fear death? Do animals and plants have a concept of death?

    … and as a consequence to Natural Selection, entailing Divergence of Character and the Extinction of less-improved forms.

    Here we go again; natural selection does not entail any divergence. Natural selection equals extinction of the unfit — improved or not.

    Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals, directly follows.

    What nonsense! War, famine and death are creative powers? Elimination has creative powers?

    There is grandeur in this view of life …

    Well, if you say so, problem is: it simply does not make any sense.

  51. 51
    Silver Asiatic says:

    Excellent analysis, Origenes. I have never looked at that before.

    It strikes me that Darwin remains the foundation of evolutionary theory today but how many evolutionists have actually looked at this text? I will guess that even the most passionate Darwinians haven’t really read Darwin.

    CD: … Variability from the indirect and direct action of the external conditions of life, …

    O: Variability from the external conditions of life? As in, ‘natural selection leads to variability’? How can he say this? For me, it is clear as day that Darwin is dead wrong here: natural selection absolutely decreases variability.

    As you say, this is very muddled thinking. First, the term “selection” was used to indicate a reduction in variation – just as you pointed out. Death is the ‘selector’ and whatever survives obviously is less variable than what the population had before death. Darwin was trying to have it both ways. Selection was going to magically choose a huge variety of organisms, but that’s dependent on mutations in a population – and the population becomes reduced by selection.

    Along with that, as I was trying to explain to wd400 – here Darwin admits that the environment is a random variable. According to him “the external conditions of life” produce variation. Funny how evolutionists forget to put that into their formulas when they claim that “evolution is non-random”.

    As Charlie says, the environment creates variabiilty. But that’s certainly a problem for selection because it has to wait around for beneficial mutations to appear. By the time those lucky mutations show up, their fitness benefit has changed because of the “external conditions of the environment”.

    Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals, directly follows.

    What nonsense! War, famine and death are creative powers? Elimination has creative powers?

    That is hilariously absurd. He says, from death “… higher animals directly follows”.

    Again, evolutionary math. Through subtraction by death, war and famine, more variation in life appears. 🙂 So, obviously, the more death we have, the more life. In fact, if we could maximize the quantity of death, and every living thing go extinct by the direct drivers of evolution, then there would be more variation (????).

    Poor Charlie. At times he sounds like a blithering idiot. But perhaps he had Alzheimers or something. His worshipers however, I have less sympathy for them. They don’t even want to look at what is blatantly obvious.

  52. 52
    Origenes says:

    Suppose, a world without natural selection — a world with unlimited space and resources. In this world, life, driven by chance mutations, veers off in all possible directions. All viable organisms capable of reproduction will live, prosper and evolve. Clearly, such a world would lead to a maximum variety of life forms, maximum exploration and innovation. It would be a world where chance rules supreme and every viable mutation becomes reality and is explored.

    Surely, there are concerns if such an ideal world can exist, e.g. some organisms eating each other, but, for the sake of argument, suppose that such a world, or something close to it, can exist.

    With this world in mind it’s easy to see, that every other world can only be less successful at finding innovations. Any elimination of viable organisms implies shutting down promising pathways.

    Darwin does not agree with me at all:

    Charles Darwin: Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals, directly follows.

    I much enjoyed Silver Asiatic commentary:

    That is hilariously absurd. He says, from death “… higher animals directly follows”.
    Again, evolutionary math. Through subtraction by death, war and famine, more variation in life appears. 🙂 So, obviously, the more death we have, the more life. In fact, if we could maximize the quantity of death, and every living thing go extinct by the direct drivers of evolution, then there would be more variation (????).

    What is Darwin talking about?

    In the Origin, Darwin argued that this process, natural selection acting on random variations, could alter the features of organisms just as intelligent selection by human breeders can. Nature itself could play the role of the breeder.
    Consider once more our flock of sheep. Imagine that instead of a human selecting the woolliest males and ewes to breed, a series of very cold winters ensures that all but the very woolliest sheep in a population die. Now again only very woolly sheep will remain to breed. If the cold winters continue over several generations, will the result not be the same as before? Won’t the population of sheep eventually become discernibly woollier?
    This was Darwin’s great insight. Nature—in the form of environmental changes or other factors—could have the same effect on a population of organisms as the intentional decisions of an intelligent agent. [S.Meyer, ‘Darwin’s Doubt’]

    A very cold winter shuts down the evolutionary pathway for all sheep except for the very woolliest sheep. And this shut-down is not the creation of wooly sheep; it is the elimination of the not so wooly sheep.
    The same result is achieved by human selecting only the woolliest males and ewes to breed. But again, this is not the creation of wooly sheep, it is the elimination of the not so wooly sheep.
    Without a very cold winter, or a breeder selecting, the very wooliest sheep would exist together with less wooly sheep.

    However, after a very cold winter, or breeder’s intervention, wooly ewes only breed with wooly males. So, selection does something: in this case, it increase the number of wooly sheep. This means that selection causes a more extensive exploration of the ‘wooly sheep evolutionary pathway’. Selection results in relatively more wooly sheep and therefore more exploration of mutations in the wooly sheep genome. That’s the only thing that can be said in favor of selection.
    IOWs selection intensifies the exploration of certain evolutionary pathways at the cost of abandoning the search along other pathways.

    Could it help? Well, sometimes selection could be right, it might just be the case that ‘the wooliest sheep pathway’ is the only fertile evolutionary pathway, so resources are well allocated. However, the opposite may just as well be true. It may even be the case that some of the not so wooly sheep were just a few mutations away from a breakthrough evolutionary discovery.
    As any investor will tell you, in general it’s best to diversify. Don’t invest all your money in one company. Never put all your eggs in one basket.

  53. 53
    Silver Asiatic says:

    Origenes

    It may even be the case that some of the not so wooly sheep were just a few mutations away from a breakthrough evolutionary discovery.

    True, because we have another factor in the evolutionary formula to consider, and that’s the reproductive rate of each. How many lambs each mother sheep has is again a random factor.
    Yes, the woolier sheep were more ready for the winter (but what about very hot summers that come a few decades later?) … but the less-wooly sheep may have more babies, for whatever reason.
    The population is mixed, woolly and less-woolly. They all survive. Some have more lambs than others. When the winter gets colder then what? The winter is so cold it kills off all the less woolly sheep? That would have to be a pretty cold winter – and an entire succession of them. If it was that cold, it would kill them all. But “no”, the evolutionists say, it was just cold enough to kill the less woolly, the more woolly survived! It would be nice if the climate worked like that – on a gentle gradual scale, so that enough sheep would survive.
    But wait! If it got just cold enough to kill not only the less woolly, but also the more woolly — we have evolution providing a lucky mutation that makes them even more woolly.
    Yes — that’s fine. The lucky mutation starts in an individual. Then, it is distributed through the population until only the more, more woolly sheep remain.
    But what about the cold winters? Did they just stop and wait until the beneficial mutation made the population woolly enough to survive? Because if it didn’t stop, all the sheep would be dead.

  54. 54
    wd400 says:

    I can’t decide is this is an elaborate troll, or you two are really so disconnected from reality that you think these posts represent a informed and substantive discussion about these topics.

    All I can say is that you should perhaps try and learn some evolutionary biology and the data and theory used to test ideas within that field. (It’s kind of amazing some one could write so much blather about a topic without once referring to a single result from the field!)

  55. 55
    Silver Asiatic says:

    wd400

    I am open to (and would appreciate) a reading-suggestion that explains how the multiplication of 3 random variables (mutation, environmental conditions, and reproductive success factors) lead to a non-random result.

    Additionally, any theoretical papers you can suggest that explain how a maximum value given to the parameter of selection by death leads to an increase of variability in the population.

    … or failing that, anything at all that touches on what we’ve been discussing would be greatly appreciated also.

  56. 56
    wd400 says:

    I already gave you one: The Blind Watchmaker would be a pretty good start.

    For the second point all you need to google is “diversifying selection” and “balancing selection” (within population) and understand speciation (the generation lineages with distinct evolutionary trajectories).

  57. 57
    Silver Asiatic says:

    wd400

    I already gave you one: The Blind Watchmaker would be a pretty good start.

    Yes, you did give that. You then pointed to the Weasel algorithm showing how evolution is non-random. Then you backed away from that calling it a “toy”. Yes, it’s a toy that does not show how the multiplication of random variables ends with a non-random result, so perhaps I’ll have to read the whole book to find that.

    For the second point all you need to google is “diversifying selection” and “balancing selection” (within population) and understand speciation (the generation lineages with distinct evolutionary trajectories).

    Ok, thank you. I have a feeling it is going to be more than merely ‘all I have to do’ to find the answer to that particular question, but I appreciate the suggestion and I will follow up on it.

  58. 58

    Basically epigenetics point to the DNA system as a whole functioning alike a world in it’s own right, same like human imagination is a world in it’s own right.

    This explains the functionally integrated complexity of organisms, how an organism develops to adulthood, and the autonomy of an organism (how it understands it’s environment).

    That the DNA system can change in a rational way epigenetically, shows that information is received from the external world, and then interpreted rationally in the DNA world of the organism.

    It means the DNA world can model the external world, can make representations of the external world. It can also make a representation of the adult form of the organism itself, which representation guides development of the organism to adulthood.

    This DNA world would also be the basis for the organism understanding things like food and predators. It means for instance an organism can have a representation of another organism in it’s DNA world, like a natural fear of snakes, or whatever.

    This is consistent with all the observations of organisms. But there is also direct evidence it is true.

    The mathematical ordering of the DNA system is exactly the same as the ordering of the universe. That is exactly what one would expect of a world in it’s own right operation, that it would have the same ordering as the universe itself!

    https://lh3.googleusercontent.com/-nAueZAjEzMU/U3N1B5CqkdI/AAAAAAAAAHk/rXLLwM9WD4g/w525-h420-p-rw/rewrite.png

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