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Darwin’s peppered myth: Turns out, peppered moths take care to protect themselves

A Darwin cult (the peppered myth) developed during the twentieth century around the peppered moths, with the recent “resounding triumph” that it turns out that pollution effects do favour dark coloured moths over light coloured ones in the same species, with no important changes.

Whoop whoop. That is all Darwinism can come up with, in real life, after all this time.

But so? Snowbelt effects explain why the Canadian Groundhog Day groundhog is white and the American one is brown. No evolution was ever harmed in the making of the diverting nonsense.

In “Peppered Moths Without Evolution” (July 31, 2012), Creation-Evolution Headlines comments , noting a recent, more detailed study,

Kettlewell and Majerus didn’t take into account the moths’ behavior. They treated moths as passive creatures that would alight on tree trunks at random. They placed the selective power in the environment, with lower contrast producing greater camouflage, leaving the high-contrast moths vulnerable to birds.

The South Korean researchers found, instead, that moth behavior plays a vital role in the camouflage. They “found out that moths are walking on the tree bark until they settle down for resting; the insects seem to actively search for a place and a body position that makes them practically invisible.” A video clip embedded in the article shows the moths doing this.

The article avoids superstitious homage to Darwin as well, apparently. That’s a start  in the right direction.

We always thought that the moth had more interest in protecting its hide than the researchers did, and guess what? But how do the moths know if, when they feel invisible, they really are invisible?

See also: US Darwinists (US ranked 14th) wail over South Korea (ranked 1st), supposedly “not able to compete”

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91 Responses to Darwin’s peppered myth: Turns out, peppered moths take care to protect themselves

  1. In the video (at PhysOrg), it looks like the moths are flapping their wings up and down so as to match the light intensity of their wings to that of the background, and orient their bodies until that happens.

  2. For a twist on this experiment that would really drive Darwinists bonkers, they could artificially darken or lighten some moths and see if their behavior adjusts accordingly. It would certainly raise some interesting issues if they did adjust their behavior, as well as throwing another monkey wrench into the Darwinian Icon of peppered moths

  3. Yet another example of why real biologists think creationists/IDists are kooks, and rightly so.

    Amongst the problems with this post and the young-earth creationist one that is referenced:

    1. You creationists screamed for 10 years about how the peppered moth example was a “peppered myth” because allegedly the evidence was against the bird predation/camouflage hypothesis first documented by Kettlewell. But it turned out Kettlewell was right, as was obvious throughout to anyone who carefully read Kettlewell’s research and the half dozen subsequent studies which confirmed Kettlewell’s basic conclusions. You don’t get to call something a myth when the evidence has confirmed it. Your position was the mythical one.

    2. The peppered moth isn’t “all Darwinism can come up with, in real life, after all this time”. That’s just silly taunting, even creationists know there are many other examples of natural selection in the wild, not to mention all of the other evidence for evolution, NS, etc. If there weren’t, you guys wouldn’t spend so much time talking about all of those other pieces of evidence.

    3. You quote Creation-Evolution Headlines saying “Kettlewell and Majerus didn’t take into account the moths’ behavior.” That’s just wrong. Both Kettlewell and Majerus, and other researchers, did work specifically on the resting behavior of peppered moths, and whether or not they sought out matching backgrounds or not. IIRC, Kettlewell thought they did, and proposed the “contrast/conflict” hypothesis as a behavioral explanation for how they might do it (by trying to minimize the contrast between a part of the body their eyes can see, and the surface beneath). However, the experimental tests of these ideas, including by Majerus IIRC, have not found much evidence for peppered moths specifically picking backgrounds matching their white or black body color. It looks like peppered moths, at least, just look for a shady spot on a tree. (And actually, this makes the bird predation/camouflage hypothesis even stronger, since if peppered moths picking matching backgrounds, this would weaken selection against white moths when soot darkened parts of the environment; the white moths would just behaviorally avoid darkened areas).

    4. The study being discussed is on moths in South Korea. These are not the same species as the peppered moth in England, even if the Korean moths are “peppered”. It looks like they’re not even the same genus. Some moths do indeed actively seek out matching backgrounds. This was known before the Korean study — e.g. Ted Sargent documented this in an American moth species in the 1990s IIRC.

    But it looks like, whatever those species do, the British peppered moth species doesn’t have this behavior. So the behavior of these other species is irrelevant to them. There are tens of thousands of moth species on the planet, you can’t just read something about a moth species in Korea and make wild, random claims about the implications for a species of moth on the other side of the planet in England which has been very well studied on its own.

    Short version: you and your YEC source made a complete incompetent hash of this story, if you had any sense of scientific propriety or care for truth you would issue a retraction, recommend that Creation-Evolution Headlines did the same, and write them off as anti-scientific yammerers who don’t care about research or accuracy if they don’t. This kind of thing is the *primary* reason creationists don’t get no respect from scientists. They don’t deserve it. They don’t earn it. In fact, what creationists earn is just pity and scorn, through confident-but-poorly-researched-and-inaccurate screeds like this one.

  4. Correct me if I’m wrong, but I could swear I saw this previously on this site. Is this a repeat or a replication?

  5. I’m with you Nick, it really is kind of kooky to try to prove anything conclusive about Darwinism with peppered moths. Perhaps we can get down to some real biology with winged insects?

    Bernard d’Abrera on Butterfly Mimicry and the Faith of the Evolutionist – October 5, 2011
    Excerpt: For it to happen in a single species once through chance, is mathematically highly improbable. But when it occurs so often, in so many species, and we are expected to apply mathematical probability yet again, then either mathematics is a useless tool, or we are being criminally blind.,,, Evolutionism (with its two eldest daughters, phylogenetics and cladistics) is the only systematic synthesis in the history of the universe that proposes an Effect without a Final Cause. It is a great fraud, and cannot be taken seriously because it outrageously attempts to defend the philosophically indefensible.
    http://www.evolutionnews.org/2.....51571.html

    Well that’s not good for your Darwinism Nick! Hey Nick I have another question for you, why do you still believe neo-Darwiniism to be true when, even if we had all the scientists and all the supercomputers in the world, you still cannot make even a single ‘simple’ insect wing from scratch?

  6. bornagain77,

    “For a twist on this experiment that would really drive Darwinists bonkers, they could artificially darken or lighten some moths and see if their behavior adjusts accordingly.”

    most insightful point. i myself would volunteer to assist in this excellent effort to advance science and intelligent design.

    sergio

  7. bornagain77,

    “you still cannot make even a single ‘simple’ insect wing from scratch?”

    impossible to humanly copy what God has already perfected, no?

    sergio

  8. Hey Nick, how can one tell natural selection from genetic drift, in the wild?

    And how can we test that either natural selection or genetic drift produced moths from non-moths? THAT is the myth Nick, that natural selction has anything to do with the arrival of moths.

    IOW what is the evidence that natural selection or genetic drift can do anything?

    Ya see Nick that is why the vast majority of people think that evolutionary biologists are kooks and liars- and rightly so.

  9. Ken Miller on the peppered moth:

    What we do know is that the rise and fall of dark-colored moths, a phenomenon known as “industrial melanism,” remains a striking and persuasive example of natural selection in action. What we have to be cautious about is attributing 100% of the work of natural selection in this case to the camouflage of the moths and their direct visibility to birds.

    That’s it? REALLY? If that is all natural selection can “do” then it is obvious that the theory of evolution is in deep poo….

  10. Hey Nick, how can one tell natural selection from genetic drift, in the wild?

    One could calculate the probabilistic resources needed to get the observed changes: the increase and subsequent decrease in melanism. Here’s a chance to throw some ID theory at a problem.

  11. Nick:

    You creationists screamed for 10 years about how the peppered moth example was a “peppered myth” because allegedly the evidence was against the bird predation/camouflage hypothesis first documented by Kettlewell. But it turned out Kettlewell was right, as was obvious throughout to anyone who carefully read Kettlewell’s research and the half dozen subsequent studies which confirmed Kettlewell’s basic conclusions.

    Judith Hooper, in her “Of Moths and Men”, raises substantial issues with Kettlewell’s study. She is neither a “creationist”, nor an ID adherent. So why go blaming IDists?

    And, there’s your mention of Ted Sargent. He is mentioned quite often in Hooper’s book. Here’s what he says about melanism:

    In this same way, I have suggested that melanic polymorphisms may actually be polyphenisms, with the gene (or genes) for melanism being expressed under some conditions, and not expressed under others. The fact that melanism acts like a Mendelian dominant is irrelevent to my suggestion. I would agree that the gene is a dominant one, and is inherited as such, under conditions where this gene is expressed. And, indeed, selection would act to increase or decrease the incidence of melanism under these conditions, since at least two phenotypes (“typical” and “melanic”) are being produced. But what I am also suggesting is that the gene in question (i.e., the dominant allele for melanism) may not be expressed under some conditions. This could give the impression that the “typical” form is due to a homozygous recessive genotype. But perhaps the moths in question possess the genetic potential to be either typical or melanic – and the dominant allele (for melanism) is not being expressed (just as the alleles for a “spring” form are not being expressed in the “fall” brood of species with seasonal forms). Thus, I am suggesting that gene (or allele) frequencies may not be changing in nature, at least to the extent suggested by the changing frequencies of the two forms that are seen in species exhibiting industrial melanism. Putting it another way, phenoypes may change without changes in the underlying genotypes. Or, at least there need not be a simple relationship between the two.

    Well, Nick, if Ted Sargent–an established scientist, not a Creationist, not an IDist–is correct, then “melanism” as an example of neo-Darwinian mechanisms looks like it might be completely wrongheaded.

    So, who’s guilty then of making “a complete incompetent hash of this story”, the IDists, or the evolutionists?

  12. When the changes were first noted the genetic basis was unknown, and one idea tried out was simply that the
    pollution on food plants caused the insects to become darker. However, the melanics are genetic (usually simple Mendelian dominants) and pollution has not been shown to change the color of adults, so the most likely selective agent is (visual) predation.

  13. 13

    Hey Nick, how can one tell natural selection from genetic drift, in the wild?

    This is easy, do you really not know this? We teach it to undergrads in genetics class.

  14. 14

    When the changes were first noted the genetic basis was unknown, and one idea tried out was simply that the
    pollution on food plants caused the insects to become darker. However, the melanics are genetic (usually simple Mendelian dominants) and pollution has not been shown to change the color of adults, so the most likely selective agent is (visual) predation.

    Yep.

  15. 15

    Wow, you IDists are so incredibly desperate to take down the peppered moth example, you will say almost anything, no matter if it contradicts even your own previous criticisms. Here’s the Discovery Institute Anony-News person:

    http://www.evolutionnews.org/2.....62781.html

    So, Kang et al. decided to go back to the original plan and let the moths do what they do naturally without investigators interfering. They let the moths choose the trees to land on, and they photographed what they did after they landed. It changed the picture entirely.

    Into the forest they went, releasing their captive moths (two native species), and watching them with Canon cameras in hand. They photographed the initial landing spot and orientation, then watched them come to a final resting spot and orientation — often some centimeters from where they initially landed. Calibrating their photographs carefully with controls, they brought these photographs into the lab, cropped them to remove extraneous cues, and showed them to human subjects as “experimental predators.”

    Using software that flashed the images on a screen, they asked the human predators to hunt for the moths in the photographs within a reasonable time limit. A major discovery followed. The moths were much harder to spot after they moved from their initial landing spot to the final resting spot. You can see this for yourself in some of the photographs they published. The moths moved around, some of them rotating, till they became almost invisible. You can also watch the moth behavior in movie clips from the Supporting Information page. Sure enough; those clever insects demonstrated an uncanny ability to blend perfectly into the bark by moving around. If you had photographed only their initial landing spot (or had glued them to the tree trunk), you wouldn’t know this.

    It’s astonishing (and deplorable) that during the 57 years that the peppered moth has been promoted as a stellar case of evolution in action, nobody performed this experiment until now: “… no direct test of adaptive role of this behavior has been conducted,” the team says on page 2, and again on page 5, “This is the first study that directly measures the detection of moths by visual predators before and after a moth performed the body positioning behavior.”

    Yet the behavior of the moth is key to the story. In the real world, as opposed to the staged peppered-moth photos we have all seen in textbooks, the moths would not have stood out like sore thumbs on the tree trunks. They would have wandered about for a place to blend in; most likely, they would not have landed in such conspicuous spots in the first place (Wells, p. 148). Letting the moths do what comes naturally is what the experimenters should have done. The old peppered moth experiments, consequently, have been invalidated (again).

    Over here in real life:

    1. Kettlewell and Majerus both *did do* bird predation experiments where the moths were allowed to find their own resting spots. The new study didn’t even do anything with bird predation.

    2. Wells himself, copying the critiques by Majerus and others of peppered moth work, claimed that it was a problem when (in some experiments) human vision was used to judge hiddenness, rather than bird vision. Some peppered moth work was also criticizied for artificiality, yet when the Korean study flashes images to humans on a dang computer screen, no such complaint is raised, even though this is far more artificial than anything done in the various classic peppered moth studies.

    When these sorts of points can be used against peppered moth work, it’s a huge crashing problem for peppered moth work! But when these Korean researchers ignored this and used human vision, oh that was just fine, and revolutionary work debunking the peppered moth example, somehow-or-other-we-wont-say. Get your dang story straight, guys.

    3. The DI post neglects to note that Kettlewell and Majerus did both explicitly study peppered moth resting and positioning behavior, and were well aware of its potential importance.

    4. It also failed to mention that the background-matching behavior observed in the Korea moths has been explicitly sought in the peppered moth, but the behavior isn’t really found in that species.

    Incompetence, thy name is creationism/ID.

  16. Starbuck, this is not a paper directly challenging natural selection per se in the shifts of light colored to dark colored moths. To be sure, Kang et al. do not deny that natural selection might be at work. This paper primarily points out how weak the experimental setup was in the first place. Moreover the paper reveals a highly sophisticated behavior in moths for searching out the best camouflage. Indeed I do not doubt that populations of moths have shifted in proportions to dark and light colors, but what I want to know is where did the moths get the genetic information for light and dark colors, and where did they get this highly sophisticated camouflaging behavior in the first place? Darwinists simply never address these important issues!

    ENV has weighed in:

    Journal of Evolutionary Biology Confirms Jonathan Wells (by Name) on Peppered Moth Myth – August 2012
    Excerpt: It’s astonishing (and deplorable) that during the 57 years that the peppered moth has been promoted as a stellar case of evolution in action, nobody performed this experiment until now: “… no direct test of adaptive role of this behavior has been conducted,” the team says on page 2, and again on page 5, “This is the first study that directly measures the detection of moths by visual predators before and after a moth performed the body positioning behavior.” ,,,
    Yet the behavior of the moth is key to the story. In the real world, as opposed to the staged peppered-moth photos we have all seen in textbooks, the moths would not have stood out like sore thumbs on the tree trunks. They would have wandered about for a place to blend in; most likely, they would not have landed in such conspicuous spots in the first place (Wells, p. 148). Letting the moths do what comes naturally is what the experimenters should have done. The old peppered moth experiments, consequently, have been invalidated (again).
    In summary, by using one of the iconic examples of evolution, we showed how a morphological adaptation cannot be fully understood without taking into account a full behavioural phenotype responsible in natural situations for increasing the adaptive function of the morphological trait.
    http://www.evolutionnews.org/2.....62781.html

  17. Nick states:

    Wow, you IDists are so incredibly desperate to take down the peppered moth example,

    I not desperate at all Nick. Indeed you scientifically inept Darwinists have taught me patience well. Please show me the exact experimental work that shows the origination of the light and dark colored gene(s), as well as the exact experimental work showing me exactly how this highly sophisticated camouflaging behavior arose?!?

  18. 18

    I not desperate at all Nick. Indeed you scientifically inept Darwinists have taught me patience well. Please show me the exact experimental work that shows the origination of the light and dark colored gene(s), as well as the exact experimental work showing me exactly how this highly sophisticated camouflaging behavior arose?!?

    Peppered moths don’t have highly sophisticated camouflaging behavior. They don’t look around for a matching spot. The junk you are reading on UD and the DI website is talking about a paper about moth species in Korea which are not the same species or even the same genus as the peppered moth. For some bizarre reason they are conflating these different species, even though it is easy to see that this is a huge, basic, mistake.

    As for the mutational change from light to dark in the peppered moth, we don’t quite know the exact mutational change yet, but it could well be just a point mutation. It’s not exactly hard for a mutation to push up the amount of melanin in an organism.


  19. Hey Nick, how can one tell natural selection from genetic drift, in the wild?

    This is easy, do you really not know this? We teach it to undergrads in genetics class.

    I don’t think it is possible, Nick. So it would be interesting to know exactly what is taught and exactly how it is verified- that natural selection, a result, didit.

    And what this new study demonstrates is that behavioural changes are the way to go as opposed to waiting for the right mutation to come along and change your color.

  20. http://www.evolutionnews.org/2.....62781.html

    Something for Nick to look at. All his arguments have aleady been considered, and in my view simply show him up.

  21. As typical Nick, instead of actual experimental evidence showing the origination of anything of significance by neo-Darwinian processes, as requested from you, I get excuses from you. Excuse making is NOT EMPIRICAL SCIENCE Nick!

    Nothing In Molecular Biology Is Gradual – Doug Axe PhD. – video
    http://www.metacafe.com/watch/5347797/

    “Charles Darwin said (paraphrase), ‘If anyone could find anything that could not be had through a number of slight, successive, modifications, my theory would absolutely break down.’ Well that condition has been met time and time again. Basically every gene, every protein fold. There is nothing of significance that we can show that can be had in a gradualist way. It’s a mirage. None of it happens that way. – Doug Axe PhD.

    Nick you can’t even demonstrate the fixation of a single beneficial mutation in a metazoan much less a gene/protein:

    Experimental Evolution in Fruit Flies (35 years of trying to force fruit flies to evolve in the laboratory fails, spectacularly) – October 2010
    Excerpt: “Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.,,, “This research really upends the dominant paradigm about how species evolve,” said ecology and evolutionary biology professor Anthony Long, the primary investigator.
    http://www.arn.org/blogs/index.....ruit_flies

    And Nick the fixation of advantageous mutations in bacteria are found to produce negative epistasis when combined:

    Mutations : when benefits level off – June 2011 – (Lenski’s e-coli after 50,000 generations)
    Excerpt: After having identified the first five beneficial mutations combined successively and spontaneously in the bacterial population, the scientists generated, from the ancestral bacterial strain, 32 mutant strains exhibiting all of the possible combinations of each of these five mutations. They then noted that the benefit linked to the simultaneous presence of five mutations was less than the sum of the individual benefits conferred by each mutation individually.
    http://www2.cnrs.fr/en/1867.htm?theme1=7

    You simply Nick, no matter how ‘desperate’ you are to deny it to the contrary, have no empirical evidence to support your ‘bottom up’ neo-Darwinian worldview!

    This ‘problem’ is even admitted in peer-review

    The Fate of Darwinism: Evolution After the Modern Synthesis – January 2012
    Excerpt: We trace the history of the Modern Evolutionary Synthesis, and of genetic Darwinism generally, with a view to showing why, even in its current versions, it can no longer serve as a general framework for evolutionary theory. The main reason is empirical. Genetical Darwinism cannot accommodate the role of development (and of genes in development) in many evolutionary processes.
    http://www.springerlink.com/co.....03g3t7002/

    Peer-Reviewed Paper Concludes that Darwinism “Has Pretty Much Reached the End of Its Rope” – Jonathan M. – February , 2012
    Excerpt: Contrary to the Darwin lobby’s oft-repeated assertion that there are absolutely no weaknesses in Darwinian theory, the paper offers the concession that the modern synthesis has never provided an account of “how major forms of life evolved” — an omission that is not unsubstantial, to put it mildly.
    http://www.evolutionnews.org/2.....55941.html

    further notes on the bankruptcy of Nick’s ‘bottom up’ neo-Darwinian worldview:

    More from Ann Gauger on why humans didn’t happen the way Darwin said – July 2012
    Excerpt: Each of these new features probably required multiple mutations. Getting a feature that requires six neutral mutations is the limit of what bacteria can produce. For primates (e.g., monkeys, apes and humans) the limit is much more severe. Because of much smaller effective population sizes (an estimated ten thousand for humans instead of a billion for bacteria) and longer generation times (fifteen to twenty years per generation for humans vs. a thousand generations per year for bacteria), it would take a very long time for even a single beneficial mutation to appear and become fixed in a human population.
    You don’t have to take my word for it. In 2007, Durrett and Schmidt estimated in the journal Genetics that for a single mutation to occur in a nucleotide-binding site and be fixed in a primate lineage would require a waiting time of six million years. The same authors later estimated it would take 216 million years for the binding site to acquire two mutations, if the first mutation was neutral in its effect.
    Facing Facts
    But six million years is the entire time allotted for the transition from our last common ancestor with chimps to us according to the standard evolutionary timescale. Two hundred and sixteen million years takes us back to the Triassic, when the very first mammals appeared. One or two mutations simply aren’t sufficient to produce the necessary changes— sixteen anatomical features—in the time available. At most, a new binding site might affect the regulation of one or two genes.
    http://www.uncommondescent.com.....rwin-said/

    Science & Human Origins: Interview With Dr. Douglas Axe (podcast on the strict limits found for changing proteins to other very similar proteins) – July 2012
    http://intelligentdesign.podom.....3_53-07_00

    Widespread ORFan Genes Challenge Common Descent – Paul Nelson – video with references
    http://www.vimeo.com/17135166

    Nick if you want to know where the massive amounts of complex functional information came from in life, indeed if you want to know where life itself came from, I will give you a huge hint:

    Verse and Music

    John 1:1-5
    In the beginning was the Word, and the Word was with God, and the Word was God. He was with God in the beginning. Through him all things were made; without him nothing was made that has been made. In him was life, and that life was the light of all mankind. The light shines in the darkness, and the darkness has not overcome it.

    Newsboys – God’s Not Dead
    http://www.godtube.com/watch/?v=FMF12FNU

  22. ” You don’t get to call something a myth when the evidence has confirmed it.” — Nick Matzke.

    You can of course, but you’ll rightly be called a blistering moron. And this is just how it should be. And just the same the you don’t get to call something a not-myth when the only evidence is mythology. Or, again, you can if you wish to be rightly called a blistering moron.

    “Wow, you IDists are so incredibly desperate to take down the peppered moth example, you will say almost anything, no matter if it contradicts even your own previous criticisms.”

    I thought this was known as ‘self-correcting’ rather than ‘desperation’. If there’s a difference between the two terms then I should sorely like to know what it is.

    “1. Kettlewell and Majerus both *did do* …”

    Truth in advertising is such a difficult thing. Kettlewell did not control for this appropriately and there were proper criticisms raised. However, Majerus did control for such things. And, if Wiki is to be considered faithful on the subject then indeed the peppered moth in question did prefer shaded areas. Which, really, isn’t terribly surprising at all.

    But if this is just a replication of the notion that moths prefer shady areas then there can hardly be an objection to it on that basis. And it’s hardly germane as to whether its the same or differing genus.

    Of course, the problem with experimental validation is never the experimental set up itself. It is always and only the conclusions that we draw from the experiment. And if the set up doesn’t permit us to draw the conclusions that we wish to draw then: Put a sock in it.

    I can’t fathom you disagreeing with any of these points, but if you do, then feel free to raise your objections.

    “2. Wells himself, copying the critiques by Majerus and others …”

    I agree. If one is to be speaking of bird vision in conclusion then one needs to include a tetrachromatic or pentachromatic model. Or show that the difference in cones are irrelevant for the given subject. Neither makes an issue for speaking of moth behaviour and camouflage with respect to the human visible spectra.

    “Peppered moths don’t have highly sophisticated camouflaging behavior.”

    That’s irrelevant. If they preferentially seek shaded areas then it is immaterial as to whether it is simple phototaxi behaviour or if it is predicated on the ability of moths to solve differntial equations with a slide rule.

    “As for the mutational change from light to dark in the peppered moth, we don’t quite know the exact mutational change yet, but it could well be just a point mutation.”

    Which is a fancy way to state “We don’t know. Full stop.”

    The problem here is that we are speaking only of the notion that predators can only predate what they can find and that predators are preferentially lazy. That predate first what’s easiest to go after. But that’s trivially observable without respect to any theory at all.

    And certainly if evolution were not consistent with such pedestrian notions then it would be a great charade. But of course, this is not the case. But what this doesn’t do is establish empirical evidence for evolution itself.

    It is, again, a problem of drawing conclusions that are supported by the experimental set up.

  23. I don’t think it is possible, Nick. So it would be interesting to know exactly what is taught and exactly how it is verified- that natural selection, a result, didit.

    Oh dear – there’s a whole book about it. There’s even papers specifically comparing drift and selection. How about pulling your head out of the sand and doing some research?

  24. Thou Shalt Not Put Evolutionary Theory to a Test – Douglas Axe – July 18, 2012
    Excerpt: “For example, McBride criticizes me for not mentioning genetic drift in my discussion of human origins, apparently without realizing that the result of Durrett and Schmidt rules drift out. Each and every specific genetic change needed to produce humans from apes would have to have conferred a significant selective advantage in order for humans to have appeared in the available time (i.e. the mutations cannot be ‘neutral’). Any aspect of the transition that requires two or more mutations to act in combination in order to increase fitness would take way too long (>100 million years).
    My challenge to McBride, and everyone else who believes the evolutionary story of human origins, is not to provide the list of mutations that did the trick, but rather a list of mutations that can do it. Otherwise they’re in the position of insisting that something is a scientific fact without having the faintest idea how it even could be.” Doug Axe PhD.
    http://www.evolutionnews.org/2.....62351.html

    Here is a Completely Different Way of Doing Science – Cornelius Hunter PhD. – April 2012
    Excerpt: But how then could evolution proceed if mutations were just neutral? The idea was that neutral mutations would accrue until finally an earthquake, comet, volcano or some such would cause a major environmental shift which suddenly could make use of all those neutral mutations. Suddenly, those old mutations went from goat-to-hero, providing just the designs that were needed to cope with the new environmental challenge. It was another example of the incredible serendipity that evolutionists call upon.
    Too good to be true? Not for evolutionists. The neutral theory became quite popular in the literature. The idea that mutations were not brimming with cool innovations but were mostly bad or at best neutral, for some, went from an anathema to orthodoxy. And the idea that those neutral mutations would later magically provide the needed innovations became another evolutionary just-so story, told with conviction as though it was a scientific finding.
    Another problem with the theory of neutral molecular evolution is that it made even more obvious the awkward question of where these genes came from in the first place.
    http://darwins-god.blogspot.co.....ay-of.html

    Majestic Ascent: Berlinski on Darwin on Trial – David Berlinski – November 2011
    Excerpt: The publication in 1983 of Motoo Kimura’s The Neutral Theory of Molecular Evolution consolidated ideas that Kimura had introduced in the late 1960s. On the molecular level, evolution is entirely stochastic, and if it proceeds at all, it proceeds by drift along a leaves-and-current model. Kimura’s theories left the emergence of complex biological structures an enigma, but they played an important role in the local economy of belief. They allowed biologists to affirm that they welcomed responsible criticism. “A critique of neo-Darwinism,” the Dutch biologist Gert Korthof boasted, “can be incorporated into neo-Darwinism if there is evidence and a good theory, which contributes to the progress of science.”
    By this standard, if the Archangel Gabriel were to accept personal responsibility for the Cambrian explosion, his views would be widely described as neo-Darwinian.
    http://www.evolutionnews.org/2.....53171.html

  25. A Gene- as I thought, post hoc and ad hoc speculations are nice but they do not amount to much scientifically.

    Ya see there is no way to predict what will be slected for at any point in time and there is no way to predict what variation will arise at any point in time, so all one can do is post hoc and ad hoc speculations.

    And none of that deals with the arrival of the organism in the forst place.

  26. Joe,

    Didn’t you want to know how you tell the difference between drift and selection in the wild? And didn’t you get told?

    What has any of that got to do with “speculation” or the predictions you’re going on about?

  27. wd400-

    The only way to tell the difference between genetic drift and natural selection in the wild is post hoc/ ad hoc speculation.

  28. 28

    Joe,

    “Ya see there is no way to predict what will be slected for at any point in time and there is no way to predict what variation will arise at any point in time, so all one can do is post hoc and ad hoc speculations.”

    I D most certainly against evolution, yes? I D acts to explain not needing “speculation”, yes? ["speculation" used in proper form, no? please correct if no]

    sergio

  29. You keep saying “speculation” – I don’t think you know what it means.

  30. The only way to tell the difference between genetic drift and natural selection in the wild is post hoc/ ad hoc speculation.

    Care to explain what you mean? Could you explain, precisely, the “post hoc/ ad hoc speculation” in this paper, for example?

    Or are you going to stick to your usual strategy of making general accusations, and avoiding backing them up?

  31. You might find this one interesting as well.

  32. F/N: Worth looking from ENV:

    Kang et al. do not deny that natural selection might be at work. They propose that morphological and behavioral adaptations might “co-evolve” to produce the moths’ highly effective camouflage. Some might criticize their methods on various grounds.

    Possible criticisms include: (1) “Human predators” are a poor substitute for the moths’ natural bird predators. The authors acknowledge this, but explain that both birds and humans rely on visual cues to first locate the moths; besides, previous investigators also used humans to test camouflage effectiveness. (2) UV light, to which some birds are sensitive, might affect the visibility of the moths on the trees. The authors took this into account, but from their measurements of the UV spectrum of tree trunks and moths, they believe it would be a minor factor, at most, for UV-sensing birds. (3) They only studied two Korean moth species, and not peppered moths. The authors realize this; they were not making a global generalization. They were just cautioning investigators to be aware that behavioral phenotypes must be considered in all future studies of adaptive camouflage; and, thereby, they invalidated all previous work that had ignored this factor . . .

    KF

  33. From A Gene’s link:

    The main result is that both drift and selection are significant factors affecting changes in the allele frequency of the medionigra gene.

    If one reads the paper they explain the difficulties in picking one gene. The other difficulty is the species you are going to study and the data you need. Then there is population size- the bigger the population the less effect natural selection will have- never mind changing environments shifting the selection pressures.

    Evolution cannot be plugged into any equation and have its history unfold. That is a fool’s errand.

  34. Starbuck- what about by design?

  35. Nick Matzke:

    Wow, you IDists are so incredibly desperate to take down the peppered moth example, you will say almost anything, no matter if it contradicts even your own previous criticisms.

    I think the real ‘desperation’ is on the part of the Darwinists. In fact, that is the whole undercurrent of Hooper’s book: that Ford, desperate to find evidence in nature for Darwinian mechanisms, pushed Kettlewell to come up with the ‘right’ statistical numbers for his experiment.

    Then there’s Ted Sargeant: his phenotypic induction hypothesis makes a lot of sense, has substantial evidence in its favor, and could even possibly, if not likely, apply to B. Betularia (that’s his opinion).

    It is Darwinists who want to insist that allelic frequencies changed in the B. Betularia population—something that is improbable on its surface. But, if they want to prove this to be the case, it is really quite simple to do: obviously the melanic form and dark form should have different allelic characters. So why not just sequence their genomes? What’s so hard about that?

    But, guess what, it hasn’t been done. Or, at least, it hadn’t been done when Majerus was writing this in 2004:

    So, what is needed to prove whether changes in
    frequencies of the peppered moth are indeed the result of differential bird predation?

    Two evidences for proof

    In my view, two pieces of evidence are critical (PP37). The first is that birds eliminate a greater proportion of one form than the other to an extent consistent with monitored
    changes in the frequencies of the forms. The second is that a connection should be made between the genotype and phenotype.

    The genotype – phenotype link

    Taking the second point first, it is an unfortunate omission that the multiple allelic gene that controls melanism in the peppered moth in Britain has not been identified and sequenced. The critical step of connecting genotype with phenotype has thus not been accomplished in this classical case of Darwinian evolution in action.

    However, this step has recently been accomplished in another case of adaptive melanism involving crypsis (Nachman et al., 2003) (PP38). The rock pocket mouse, Chaetodipus intermedius, varies in coat colour.

    I guess it’s still “unfortunate” that Darwinist haven’t bothered to check gene sequences and confirm changing alleles. Too bad. Maybe they’d find that the alleles are all there in each of the forms per Sargeant’s view. But, of course, that would ‘overturn’ an “icon of evolution”, and why take the risk. So, we’ll just push that down the road. (Who’s desperate here?)

    And then, to want to compare moths to mammals, and wing coloration to coat coloration? Isn’t this a bit of a stretch?

    So, here’s this real good scientist (we know this because he’s a Darwinist) who compares mammals to moths—and that’s OK. But we terrible “creationists” want to compare a moth in N. Korea to a moth in England. What’s the matter with us? What kind of scientific illiterates are we?

    Sorry for all the sarcasm, but I just can’t see what your ranting is all about. Industrial melanism, if conceded, is terribly inadequate to explain anything of importance in the progressive development of forms. The problem here is that it’s possible, almost likely, that it represents bad science. Why shouldn’t it be questioned? Or, IOW, why haven’t they sequenced B. Betularia yet?

    P.S.

    Just to cover myself, I did a Google search for sequencing. Here’s what I found:

    Industrial melanism in the peppered moth (Biston betularia) is an iconic case study of ecological genetics but the molecular identity of the gene determining the difference between the typical and melanic (carbonaria) morphs is entirely unknown. We applied the candidate gene approach to look for associations between genetic polymorphisms within sixteen a priori melanisation gene candidates and the carbonaria morph. The genes were isolated and sequence characterised in B. betularia using degenerate PCR and from whole-transcriptome sequence. The list of candidates contains all the genes previously implicated in melanisation pattern differences in other insects, including aaNAT, DOPA-decarboxylase, ebony, tan, tyrosine hydroxylase, yellow and yellow2 (yellow-fa). Co-segregation of candidate gene alleles and carbonaria morph was tested in 73 offspring of a carbonaria male-typical female backcross. Surprisingly, none of the sixteen candidate genes was in close linkage with the locus controlling the carbonaria-typical polymorphism. Our study demonstrates that the ‘carbonaria gene’ is not a structural variant of a canonical melanisation pathway gene, neither is it a cis-regulatory element of these enzyme-coding genes. The implication is either that we have failed to characterize an unknown enzyme-coding gene in the melanisation pathway, or more likely, that the ‘carbonaria gene’ is a higher level trans-acting factor which regulates the spatial expression of one or more of the melanisation candidates in this study to alter the pattern of melanin production.

    As to my comment about Majerus—this really good scientist—comparing mammals to insects, here’s a quote from the paper:

    In contrast to the success of the candidate gene approach applied to melanism in vertebrates, particularly through Mc1r [4], [5] but also tyrosinase-related protein 1 [41], Agouti [42], and K locus [43], the same strategy has been far less useful as a means to identifying polymorphisms controlling melanism in insects.

    Other than ruling out specific candidate genes, the present study does not bring us any closer to finding the ‘carbonaria gene’. Having effectively exhausted the a priori list of promising melanisation candidates, we are currently in the process of constructing a linkage map of B. betularia to identify the region that controls this famous polymorphism.

    Maybe it’s chemicals that control this putative ‘control region’, such as factory emissions, or tree bark chemicals themselves. This is the more likely explanation of “industrial melanization.” So, what, then, becomes of this “icon of evolution.”

    Read it and weep, Nick.

  36. Maybe it’s chemicals that control this putative ‘control region’, such as factory emissions, or tree bark chemicals themselves

    Nope, people tried that line in the 30s, turns out is a simple Mendelian trait, with carbonaria is dominant to the light-bodied form. Moreover, the gene has been mapped to a position homologous to silkworm chromosome 17:

    http://dx.doi.org/10.1126/science.1203043

    Note that study also found genomic evidence for recent rapid selection for the carbonaria allele – of the sort you’d expect if modern dark-bodied moths descend from one (or maybe a few) new mutants rather than from standing variation.

  37. Joe,

    The paper is an example (one of many…) of how to measure selection on an allele in the wild though, right? The thing you said you didn’t think would be possible?

  38. wd400-

    Just because someone can say they did it doesn’t mean it actually pertains to natural selection.

  39. wd400: From the abstract: “The rapid spread of a novel black form (known as carbonaria) of the peppered moth Biston betularia in 19th-century Britain is a textbook example of how an altered environment may produce morphological adaptation through genetic change.”

    From one of the authors: “‘We didn’t know if industrial melanism in the peppered moth is due to a single recent mutation or several, or if it came from outside Britain,’ explains Saccheri.”

    http://planetearth.nerc.ac.uk/.....spx?id=964

    Two points here: Again, to belabor the obvious, predators are lazy. And this can be verified by spending an afternoon watching any watering hole on the serengeti.

    And again, to belabor the obvious, this is not empirical evidence of where the mutation came from, or that the non-carbonaria morph has, will, or can be extinguished from the population. Yes, differing allele frequencies are one crucial component to things. But showing that allele frequencies can change is not the same showing from how and where they arise.

    Lastly, this distinguishes Evo from ID not a whit. Both make the statement that if *there already exist* given variants then the one that is most disadvantageous will be predated more.

  40. Joe,

    OK, so tell us where O’hara went wrong in that paper.

    Maus,

    This doesn’t seem to be related to the paper, which shows that the black moths likely descend form a single mutant. If you are squeezing your skepticism down to that mutation being somehow directed then you seem to be reaching beyond the testable?

  41. wd400: “This doesn’t seem to be related to the paper, which shows that the black moths likely descend form a single mutant.”

    How does one empirically demonstrate a ‘maybe’?

    ” If you are squeezing your skepticism down to that mutation being somehow directed then you seem to be reaching beyond the testable?”

    Allow me the cheek to quote myself from the post you’re responding to: “…this is not empirical evidence of where the mutation came from …” This applies to every theory at all. Or none if you prefer to go Hypothesis non fingo.

    But I am curious as to your standpoint. Do you believe that the inaccessible past is ‘testable’ in the absence of time machines?

  42. “How does one empirically demonstrate a ‘maybe’?”

    You calculate how likely that maybe is given the evidence that you see, obviously.

    Past events are testable, in the sense you calculate the probability of present-day items with or without those past events.

  43. wd400: “You calculate how likely that maybe is given the evidence that you see, obviously.”

    Sure, that’s statistics. You take a population and you study the present day frequency of the occurrence that you are interested in.

    “Past events are testable, in the sense you calculate the probability of present-day items with or without those past events.”

    Well, quite obviously we cannot count past events we do not have access to. But we can count the current ones. But in this case it would not then be a question of: ““‘We didn’t know if industrial melanism in the peppered moth is due to a single recent mutation or several, or if it came from outside Britain,’ explains Saccheri.”

    It would be the empirically derived statement that: “We have observed this mutation occur with x percent chance in y sized population over z time period.”

    But this has not been done.

  44. The whole peppered moth example of “evolution” is pretty amusing. If we carefully examine the storyline — indeed, if we even accept it hook-line-and-sinker as fact — what does it really show? That populations fluctuate around a norm without any meaningful evolutionary change occurring over time.

    As Philip Johnson has aptly noted, the peppered moth story has been trumpeted around the world to generations of unsuspecting students as a critical proof of Darwin’s theory. Yet nothing new emerged. The population essentially returned to a stable norm.

    Does it show natural selection making a difference? There can be some reasoned disagreement about this, but even if we grant it for sake of argument, it teaches us exactly zero about the larger evolutionary story. There is simply no rational reason to assume that the kinds of processes that led to a change in the ratio of light to dark moths had anything to do with bringing about moths in the first place.

    It is great fun, however, to see it still being upheld as one of the prime examples of “evolution” in action.

  45. Maus,

    Did you miss the tense of the statement you are quoting. “We didn’t…” now we do, because of statistics.

  46. Evolution cannot be plugged into any equation and have its history unfold. That is a fool’s errand.

    Err, but that’s what was done on the paper. I’ll second wd400′s question – what’s wrong with the paper? Please, give specific criticisms, not general denial or dismissal.

  47. wd400: “Did you miss the tense of the statement you are quoting. “We didn’t…” now we do, because of statistics.”

    Heh, I did miss that, my English teacher looks smug right now. But it simply emphasizes my point. Regardless, your answer is non responsive. If ‘now we do’ then what observations were we counting?

    A Gene: “Please, give specific criticisms, not general denial or dismissal.”

    For starters its a purely correlative issue, as all such genomic studies are; but it wishes to assign a causation. This is simply a Post Hoc Ergo Propter Hoc fallacy. If one states that this then confirms a prior statement then its Affirming the Consequent. Note, this is a formal fallacy.

    But as a larger problem, as I’ve been discussing with wd400, we can fudge these issues a bit by stating that ‘In 80% of the cases that we observed what caused x, y was the cause. Therefore, for any x there is an 80% change y was the cause’. However, we have not of course observed the carboneria mutation occur at all, let alone coincident with a demonstrable cause. So there is simply no ability to bean-count, collect up frequencies, and attempt this anyways.

    It is still either Post Hoc or Affirming the Consequent, but it is now mathematically illiterate as well. Which is not to state that the manner in which they isolated the locus was invalid or anything less than interesting. I assume good faith and accuracy in their work in such.

    The problem is that they’re preaching far in excess of what the empirical results allow.


  48. Evolution cannot be plugged into any equation and have its history unfold. That is a fool’s errand.

    Err, but that’s what was done on the paper.

    Errrrrr, that does not make it correct. And I gave specific criticisms.

  49. OK, so tell us where O’hara went wrong in that paper.

    For starters, attempting to do something that cannot be done.

  50. Evolution cannot be plugged into any equation and have its history unfold.

    Indeed math is not kind to Evolution in the least:

    Haldane’s Dilemma
    Haldane was the first to recognize there was a cost to selection which limited what it realistically could be expected to do. He did not fully realize that his thinking would create major problems for evolutionary theory. He calculated that in man it would take 6 million years to fix just 1,000 mutations (assuming 20 years per generation).,,, Man and chimp differ by at least 150 million nucleotides representing at least 40 million hypothetical mutations (Britten, 2002). So if man evolved from a chimp-like creature, then during that process there were at least 20 million mutations fixed within the human lineage (40 million divided by 2), yet natural selection could only have selected for 1,000 of those. All the rest would have had to been fixed by random drift – creating millions of nearly-neutral deleterious mutations. This would not just have made us inferior to our chimp-like ancestors – it surely would have killed us. Since Haldane’s dilemma there have been a number of efforts to sweep the problem under the rug, but the problem is still exactly the same. ReMine (1993, 2005) has extensively reviewed the problem, and has analyzed it using an entirely different mathematical formulation – but has obtained identical results.
    John Sanford PhD. – “Genetic Entropy and The Mystery of the Genome” – pg. 159-160

    Kimura’s Quandary
    Kimura realized that Haldane was correct,,, He developed his neutral theory in responce to this overwhelming evolutionary problem. Paradoxically, his theory led him to believe that most mutations are unselectable, and therefore,,, most ‘evolution’ must be independent of selection! Because he was totally committed to the primary axiom (neo-Darwinism), Kimura apparently never considered his cost arguments could most rationally be used to argue against the Axiom’s (neo-Darwinism’s) very validity.
    John Sanford PhD. – “Genetic Entropy and The Mystery of the Genome” – pg. 161 – 162

    In Barrow and Tippler’s book The Anthropic Cosmological Principle, they list ten steps necessary in the course of human evolution, each of which, is so improbable that if left to happen by chance alone, the sun would have ceased to be a main sequence star and would have incinerated the earth. They estimate that the odds of the evolution (by chance) of the human genome is somewhere between 4 to the negative 180th power, to the 110,000th power, and 4 to the negative 360th power, to the 110,000th power. Therefore, if evolution did occur, it literally would have been a miracle and evidence for the existence of God. William Lane Craig

    William Lane Craig – If Human Evolution Did Occur It Was A Miracle – video
    http://www.youtube.com/watch?v=GUxm8dXLRpA

    Darwin and the Mathematicians – David Berlinski
    “The formation within geological time of a human body by the laws of physics (or any other laws of similar nature), starting from a random distribution of elementary particles and the field, is as unlikely as the separation by chance of the atmosphere into its components.”
    Kurt Gödel, was a preeminent mathematician/logician who is considered one of the greatest to have ever lived. Of Note: Godel was a Christian Theist!
    http://www.evolutionnews.org/2.....cians.html

    “Darwin’s theory is easily the dumbest idea ever taken seriously by science.”
    Granville Sewell – Professor Of Mathematics – University Of Texas – El Paso

  51. >> OK, so tell us where O’hara went wrong in that paper.?

    > For starters, attempting to do something that cannot be done.

    Ha! The paper didn’t measure selection because Joe knows it’s not possible to measure selection. That’s beautiful.

  52. I like how Berlinski sums up the mathematical predicament that neo-Darwinism finds itself in:

    Majestic Ascent: Berlinski on Darwin on Trial – David Berlinski – November 2011
    Excerpt: The publication in 1983 of Motoo Kimura’s The Neutral Theory of Molecular Evolution consolidated ideas that Kimura had introduced in the late 1960s. On the molecular level, evolution is entirely stochastic, and if it proceeds at all, it proceeds by drift along a leaves-and-current model. Kimura’s theories left the emergence of complex biological structures an enigma, but they played an important role in the local economy of belief. They allowed biologists to affirm that they welcomed responsible criticism. “A critique of neo-Darwinism,” the Dutch biologist Gert Korthof boasted, “can be incorporated into neo-Darwinism if there is evidence and a good theory, which contributes to the progress of science.”
    By this standard, if the Archangel Gabriel were to accept personal responsibility for the Cambrian explosion, his views would be widely described as neo-Darwinian.
    http://www.evolutionnews.org/2.....53171.html

  53. Maus,

    Read the paper, it explains how you can use pattern of heterozygosity around an allele to infer a “selective sweep” in which an allele enters the population an becomes common more quickly than recombination can break it up from surrounding sequences.

  54. Hmm randomness assumed instead of proven?,,

    Revisiting the Central Dogma in the 21st Century – James A. Shapiro – 2009
    Excerpt (Page 12): Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations (106) or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules.(107–110) Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112).
    http://shapiro.bsd.uchicago.ed.....0Dogma.pdf

  55. wd400:

    Nope, people tried that line in the 30s, turns out is a simple Mendelian trait, with carbonaria is dominant to the light-bodied form. Moreover, the gene has been mapped to a position homologous to silkworm chromosome 17:

    If you took the time to read the paper I linked to, you’d see that there’s no question that the gene is ‘dominant’ in the Mendelian sense, i.e., in terms of inheritance. But the question is: what’s triggering the expression. So we’re talking about epigenetics. And that, clearly, can, and does, involve environmental factors.

  56. OK, so tell us where O’hara went wrong in that paper.?

    For starters, attempting to do something that cannot be done.

    Ha! The paper didn’t measure selection because Joe knows it’s not possible to measure selection. That’s beautiful

    LoL! Nice non-sequitur. You asked where the paper went wrong, not whether or not they measured, or said they did, selection.

    But now that you mention it, saying you are doing something is not the same as actually doing it. No one can verify it. They can only nod or mumble. I would rather stand up and state the obvious.

  57. wd400: “Read the paper, it explains how you can use pattern …”

    This is strictly incorrect. It can indicate recent fitness differences, but it cannot tell you when and were it came from. But this is again non responsive to the basic topic at hand. Again, count what?

  58. Joe @ 48 –

    Errrrrr, that does not make it correct. And I gave specific criticisms.

    Where? Comment 33? That raises a couple or irrelevant points (choosing the gene & species, well that was done by E.B. Ford), and the comment about selection being less effective when the population size is larger is just wrong: it’s the other way around (which is one of the points of the paper): the smaller the population size, the stronger the effect of drift.

    Try again?

  59. OT: New video uploads:

    Multidimensional Genome – Dr. Robert Carter – video (Notes in video description)
    http://www.metacafe.com/w/8905048

    What Is The Genome? It’s Not Junk! – Dr. Robert Carter – video – (Notes in video description)
    http://www.metacafe.com/w/8905583

  60. Maus,

    No, you just don’t understand the paper.

    Joe,

    Let’s try again: tell us why O’Hara failed to measure selection in a natural population.

  61. PaV,

    You’re going to have to explain to me how a trait can be Mendelian dominant in breeding experiments and “epigenetically” controlled.

    Well, actually, I wouldn’t bother. Even if the was some weird epigenetic thing going on, the evidence for strong selection on a newly arising mutant would still stand.

  62. wd400: “No, you just don’t understand the paper.”

    Then since you do we know you are perfectly capable of explaining it. You may begin by answering the continued question: What was counted?

  63. I am addressing only Nick’s first post and the first few responces. As a proponent of ID I read Nick’s post with interest and thought he made a few good points. In reading the responces I thought maybe I was on the Richard Dawkins site. His specific points went unanswered as only antidarwinian arguments were made. This long non sequiter approach was continued with a piling on effect. If consensus is of limited value among scientists, it has no value on web site for advocates. When you fall while water sking, let go of the rope. Admit his good points and move on. As for Nick’s name calling, please don’t emulate it. Never get in your opponents way when they are self destructing.

  64. Hi Carlg,

    I think you will find most of Nicks points are in some ways answered here.

    http://www.evolutionnews.org/2.....62781.html

    I think it may be why he hasn’t been back to this thread?

  65. CG: That first few responses thing is key, cf say 32 above (and there are others), which clips a key part of the just linked by PJ. Note for instance PaV at 11 and BA 77 at 16, which also points to and clips the ENV article. In short, the evidence is that NM was responded to fairly promptly and on the merits. KF

  66. Maybe it’s chemicals that control this putative ‘control region’, such as factory emissions, or tree bark chemicals themselves. This is the more likely explanation of “industrial melanization.” So, what, then, becomes of this “icon of evolution.”

    I don’t think you understood the use of the word ‘control’. They are talking about the genetic and developmental mechanism that underlies (‘controls’) the difference between the black (carbonaria) and peppered (typical) forms, which is ultimately determined by a difference in DNA base sequence (that we haven’t quite pinpointed yet). This difference is fixed within individuals irrespective of the environmental conditions the caterpillars grow up in. The
    relative survival of the dark and light forms is influenced by their visibility on different coloured resting surfaces, to bird predators.

    You should read a recent article, published in Biology Letters, dealing with the bird predation side of the story:

    http://rsbl.royalsocietypublis.....hort?rss=1

  67. Of related interest:

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

    Epigenetic changes don’t last – September 2011
    Excerpt: They found that epigenetic changes are many orders of magnitude more frequent than conventional DNA mutations, but also often short lived. They are therefore probably much less important for long-term evolution than previously thought.
    http://www.physorg.com/news/20.....-dont.html

  68. 68

    Ugh, this “discussion” thread just further illustrates the complete intellectual bankruptcy of the creo/ID side.

    1. There’s absolutely no evidence for environmental/epigenetic factors control whether a peppered moth is light or dark. This was suggested decades ago, looked for and not found. On the contrary, when scientists looked for Mendelian inheritance, the trait was found to be Mendelian. I.e., it’s genetic, like many other thousands of inherited traits in other species (e.g., flower color, eye color, hair color, etc.)

    Furthermore, recent studies in the last few years have narrowed down the region of the genome that controls melanism. As was mentioned, they also found classic genomic signatures of a selective sweep there (reduced diversity in that region). And this is exactly what you would expect if Majerus’s suggestion — that a point mutation swept through the population — is correct.

    You can’t just sit around and make half-baked comments suggesting that some already-refuted explanation is more plausible and expect to be taken seriously.

    And other creationists can’t just sit around and let junk like this get said by their side without correction. It completely discredits your claims to intellectual credibility.

    2. A similar attempt at distraction is the failure to admit that the DI/UD posts tried to use the Korean study to cast doubt on the British peppered moth studies, even though it is *already tested and known* that peppered moths don’t have the actively-search-for-matching-background behavior which was the major point of the Korean study. #1 and the points below have been raised just to avoid admitting the mistakes made by DI/UD.

    3. Another attempt at evasion/distraction is to pretend that the peppered moth study, by itself, is supposed to be some kind of universal proof of every piece of evolution. That’s just crazy. The peppered moth work does demonstrate several things: (1) NS is real; (2) it occurs in the wild, sometimes at rates that humans can observe over a few years; (3) selection can spread mutations from miniscule frequencies (the first dark moth was only observed in the 1800s IIRC) to very high frequencies (it was 99% in highly polluted regions); (4) the result of this process is a specific functional adaptation to the environment, i.e. camouflage, which “looks designed”.

    None of (1)-(4) should be controversial, even to IDists/creationists who usually say that they accept that at least natural selection at least exists, and it’s all just a product of demographics and differential survival rates over the course of a few decades. It’s not “mysterious”. But for some reason, probably just blind instinctive antievolutionism and hatred for evolution, you guys feel the need to dispute these.

    4. An even stranger claim some creationists/IDists have been making recently is something about how selection can’t fix mutations. In the peppered moth, we’ve observed melanism go from basically 0% frequency to 99% frequency in polluted regions. But you’re seriously going to try to make some kind of argument that getting from 99% to 100% is impossible? Why? Any change in allele frequency is just demographics. If you assert that fixation is impossible for some bizarre reason, you are asserting that it’s impossible for the 1% or 0.1% or whatever of a population to die off. Why, oh why, would this be impossible?

    5. Yet another bizarre claim is the idea that you can’t distinguish selection from drift. But it’s trivial to do so in a case like the peppered moth, where you have measurements of allele frequency for many years. Genetic drift is random. Allele frequencies randomly move up and down each generation. Natural selection is nonrandom. Allele frequencies move in whatever direction selection is pushing.

    When you graph these two options, they are totally different. In any large population, drift means the allele frequency exhibits brownian motion, i.e. “drifts” up and down, back and forth, etc. But selection means the allele frequency moves smoothly in one direction, in a smooth sigmoidal curve, until it hits fixation.

    In other words, for the love of God, look stuff up. Google is your friend. E.g.:

    http://www.nature.com/scitable.....w-15186648

    6. Lastly, yet one more bit of bizarre weirdness put forth in this thread is that the peppered moth example is irrelevant because the moths are going back to the light “peppered” form. But we know the cause of that — the cause is the Clean Air Act that England passed in the 1950s. Up until the 1950s, large parts of England were polluted by black soot “fallout” from the smokestacks of factories. Photos show soot coating buildings and trees. The peppered moth populations in polluted areas gradually turned melanic during this period. After the Clean Air Act, the environment became cleaner, and the lighter moths were favored again. Natural selection means that populations track the environment. If an environmental change is permanent, then the adaptive change will be also. But if it’s not, it’s not.

    When you make the “it’s irrelevant because the moths went back to light” argument, you are effectively saying “it’s irrelevant because the Brits passed the Clean Air Act, but if they had let the environment remain polluted, it would be relevant”. It’s a bizarre argument you are making. No well-informed scientist will ever take ID/creationism seriously when you make these sorts of arbitrary and confused claims, or leave them standing without rebuttal. The point of the peppered moth story is that natural selection changes allele frequencies in an adaptive direction. The fact that this happened both to make the species darker (in a polluted environment) and lighter (in a clean environment) makes the example stronger, not weaker.

    Short version: you’re not going to get any respect from the scientific community, nor deserve it, until you can eliminate your basic, crashingly basic, mistakes, and correct the mistakes from others on your side, and only criticize the science when you actually know what you are talking about and actually take the actual published data seriously.

  69. 69

    Oh yeah, I forgot to add:

    7. Bornagain77′s posts — what the heck? I mean, really, do you guys like having him/her on your side? That person specializes in thread derailment and in not engaging the actual topic under discussion. Are they just congenitally unable to focus on a topic and engage in actual discussion, rather than spamming with irrelevant, thrown-together links and quotes?

  70. NickMatzke_UD

    you state:

    Are they just congenitally unable to focus on a topic and engage in actual discussion, rather than spamming with irrelevant, thrown-together links and quotes

    Funny that when you make unsubstantiated claims that the cyclical variation within peppered moths is proof that all life arose by neo-Darwinian processes you do not consider this unmitigated hogwash, but when I pointed out that you can’t even establish the fixation of single random beneficial mutation in a fruit fly in 35 years of trying,,,

    http://www.uncommondescent.com.....ent-429167

    then you consider this ‘spam’? MMM Hmm, and exactly why is very speculative supporting evidence given such bias over direct empirical evidence in your ‘impartial’ view of science? Have you somehow been fiat right to dictate what evoidence we are allowed to consider and what evidence we are not allowed to consider. Sorry Nick, I’m not nearly as impressed with you hot air as you are!

  71. correction: Have you somehow been given fiat right to dictate evidence we are allowed to consider

  72. Funny also Nick that it still is commonly, and falsely, automatically assumed in the prevailing neo-Darwinian mindset that any mutations that generate any variations in any particular kind of species, such as the peppered moth variation, are completely random. Yet Shapiro, who is certainly not a IDists, has been creating quite a stir in recent years by pointing out that the vast majority of mutations that generate variations are NOT completely random as is required by within the modern synthesis of neo-Darwinism:

    Revisiting the Central Dogma in the 21st Century – James A. Shapiro – 2009
    Excerpt (Page 12): Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations (106) or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules.(107–110) Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112).
    http://shapiro.bsd.uchicago.ed.....0Dogma.pdf

    This, Nick, is not comforting in the least to your basic neo-Darwinian presuppositions that all life arose by purely random, unguided, processes! In fact when we test the central claim of neo-Darwinism, the claim that purely random variations can create novel beneficial features that can then be selected, we find, ‘surprisingly’, that neo-Darwinism’s central claim comes up woefully inadequate!

    Response to John Wise – October 2010
    Excerpt: But there are solid empirical grounds for arguing that changes in DNA alone cannot produce new organs or body plans. A technique called “saturation mutagenesis”1,2 has been used to produce every possible developmental mutation in fruit flies (Drosophila melanogaster),3,4,5 roundworms (Caenorhabditis elegans),6,7 and zebrafish (Danio rerio),8,9,10 and the same technique is now being applied to mice (Mus musculus).11,12 None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans–because none of the observed developmental mutations benefit the organism.
    http://www.evolutionnews.org/2.....38811.html

    Moreover, we now have solid evidence that your not even in the right ballpark with the reductive materialistic neo-Darwinian framework Nick!

    The Origin of Biological Information and the Higher Taxonomic Categories – Stephen Meyer
    “Neo-Darwinism seeks to explain the origin of new information, form, and structure as a result of selection acting on randomly arising variation at a very low level within the biological hierarchy, mainly, within the genetic text. Yet the major morphological innovations depend on a specificity of arrangement at a much higher level of the organizational hierarchy, a level that DNA alone does not determine. Yet if DNA is not wholly responsible for body plan morphogenesis, then DNA sequences can mutate indefinitely, without regard to realistic probabilistic limits, and still not produce a new body plan. Thus, the mechanism of natural selection acting on random mutations in DNA cannot in principle generate novel body plans, including those that first arose in the Cambrian explosion.”
    http://eyedesignbook.com/ch6/eyech6-append-d.html

    supplemental notes:

    The Fate of Darwinism: Evolution After the Modern Synthesis – David J. Depew and Bruce H. Weber – 2011
    Excerpt: We trace the history of the Modern Evolutionary Synthesis, and of genetic Darwinism generally, with a view to showing why, even in its current versions, it can no longer serve as a general framework for evolutionary theory. The main reason is empirical. Genetical Darwinism cannot accommodate the role of development (and of genes in development) in many evolutionary processes.,,,
    http://www.springerlink.com/co.....03g3t7002/

    The Rapid Origin of Domesticated Chicken – Cornelius Hunter – March 2012
    Excerpt: The research finds that epigenetic mechanisms may be the cause of the rapid origin of domesticated chickens brought about by breeding, and that these epigenetic changes are reliably and stably inherited, resulting in lasting change in a population.
    http://darwins-god.blogspot.co.....icken.html

  73. He worships a nasty God, too, Nick. Not good medicine.

  74. Of related interest, here are a few comments from the ‘non-Darwinian’ evolutionist, James A. Shapiro – PhD. Genetics

    Shapiro on Random Mutation:
    “What I ask others interested in evolution to give up is the notion of random accidental mutation.”
    http://www.huffingtonpost.com/.....11144.html
    -Comment section

    Shapiro on Natural Selection:
    “My argument remains that the innovative process in evolution is rapid natural genetic engineering rather than gradual selection of small changes over long periods of time. This argument does not deny a role for selection. I simply assert that it is unrealistic to ascribe a creative (virtually deus ex machina) role to natural selection.”
    http://www.huffingtonpost.com/.....94315.html

    Shapiro on Cell cognition:
    “Recent postings have provoked numerous questions about my application of the term “cognitive” to cell regulatory processes. I base this usage on the notion that cognitive actions are knowledge-based and involve decisions appropriate to acquired information. It is common today for molecular, cell and developmental biologists to speak of cells “knowing” and “choosing” what to do under various conditions. While most scientists using these terms would insist they are just handy metaphors, I argue here that we should take these instinctive words more literally. Cell cognition may well prove itself a fruitful scientific concept.”
    http://www.huffingtonpost.com/.....54889.html

    Of note: As with neo-Darwinists Shapiro admits he has no ‘real time’ empirical experiments for the origin of novel protein domains/genes by Darwinian processes (so as to be able to have the ‘protein domains’ to shuffle around in the first place) but must rely, as do neo-Darwinists, on the DNA/protein sequence similarity data to try to make his case that ‘natural genetic engineering’ occurred in the distant past so as to create the diversity we see in life on earth. Yet, just as with neo-Darwinists, Shapiro relying on sequence similarity Data to try to make his case for ‘natural genetic engineering’ has the very same ‘unscientific’ problem that neo-Darwinism has of assuming the conclusion beforehand to try to prove very question being asked. i.e. Can novel functional information be generated ‘bottom up’ by the material processes of neo-Darwinism?:

    Here is Shapiro admitting he must rely on sequence similarity data to try to make his case:

    How Natural Genetic Engineering Solves Problems in Protein Evolution – James Shapiro – May 2012
    Excerpt: When I pointed out the potential of domain shuffling by natural genetic engineering to Intelligent Design advocates who claimed protein evolution by natural mechanisms was impossible, they refused to recognize genomic data as irrefutable evidence and insisted on real-time experiments. I disagree with them strongly on the DNA sequence data.
    http://www.huffingtonpost.com/.....41180.html

    This elephant in the living room problem that Shapiro, and neo-Darwinists is exactly the question that needs to be asked! Doug Axe’s work on the rarity of proteins is focused exactly on the rarity of individual protein domains/folds themselves. Doug Axe addresses James Shapiro’s mistaken disagreement with Intelligent Design here:

    On Protein Origins, Getting to the Root of Our Disagreement with James Shapiro – Doug Axe – January 2012
    Excerpt: I know of many processes that people talk about as though they can do the job of inventing new proteins (and of many papers that have resulted from such talk), but when these ideas are pushed to the point of demonstration, they all seem to retreat into the realm of the theoretical.
    http://www.evolutionnews.org/2.....55471.html

    supplemental notes:

    Estimating the prevalence of protein sequences adopting functional enzyme folds: Doug Axe:
    Excerpt: The prevalence of low-level function in four such experiments indicates that roughly one in 10^64 signature-consistent sequences forms a working domain. Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences.
    http://www.ncbi.nlm.nih.gov/pubmed/15321723

    The Case Against a Darwinian Origin of Protein Folds – Douglas Axe – 2010
    Excerpt Pg. 11: “Based on analysis of the genomes of 447 bacterial species, the projected number of different domain structures per species averages 991. Comparing this to the number of pathways by which metabolic processes are carried out, which is around 263 for E. coli, provides a rough figure of three or four new domain folds being needed, on average, for every new metabolic pathway. In order to accomplish this successfully, an evolutionary search would need to be capable of locating sequences that amount to anything from one in 10^159 to one in 10^308 possibilities, something the neo-Darwinian model falls short of by a very wide margin.”
    http://bio-complexity.org/ojs/.....O-C.2010.1

    The Case Against a Darwinian Origin of Protein Folds – Douglas Axe, Jay Richards – audio
    http://intelligentdesign.podom.....9_03-07_00

    Seeing Past Darwin II: James A. Shapiro – James Barham – May 2012
    Excerpt: Much in our culture depends upon the public’s being made aware that Darwinian theory as standardly interpreted is intellectually bankrupt.(2) And little that I have encountered communicates this fact so well as the work of James A. Shapiro.
    http://www.thebestschools.org/.....a-shapiro/

  75. Axel you state:

    He worships a nasty God, too, Nick.

    actually Axel the new atheists are the ones who worship a ‘nasty’ god. The first part of this video shows what new atheists think of God:

    Ben Stein vs. Richard Dawkins Interview
    http://www.youtube.com/watch?v=GlZtEjtlirc

    Needless to say Dawkins view is NOT my view of God.

  76. Matzke:

    I.e., it’s genetic, like many other thousands of inherited traits in other species (e.g., flower color, eye color, hair color, etc.)

    Eye color: http://www.sciencedaily.com/re.....081315.htm

    “The two pictures show the eyes of two genetically identical flies. The difference in eye colour is determined by epigenetic factors.” — from the photo caption.

    Hair color: http://www.ncbi.nlm.nih.gov/pm.....MC2822875/

    “The degree of methylation within the 5? IAP long terminal repeat (LTR) varies dramatically among individual isogenic Avy/a mice, causing a wide variation in coat color ranging from yellow (unmethylated) to pseudoagouti (methylated) (Fig. 1B).” — text immediately preceeding Fig 1B.

    Flower color: http://www.ncbi.nlm.nih.gov/pubmed/15493332

    “The flower variegation patterns can be determined by the frequency and timing of the excision of these transposons, and their stable insertions produce plain color flowers without generating pigmented spots or sectors; furthermore, both genetic and epigenetic regulation appeared to play important roles in determining the frequency and timing of the excision of the transposons.”

    Of particular note with the last: Epigenetic factors plays a role in the transposons directly rather than the ‘pure, simple’ persisted methylation alteration.

    And while all of these notions are Mendelian in nature it is also the case that epigenetics plays a demonstrable role. The Eye and Hair color issues allow you to see that amount of variation of alebdo due epigenetics. Which is, really, the entire point here.

    It’s a safe presumption here that everything is some matter of genetics. But simply tipping your hat to the tautology does not demonstrate cause from correlation. And specifically, if we do not know the specific gene and mechanism at hand then we cannot rule out what sort of effects epigenetics may play. This is especially pertinent in the case I quoted about flower color.

    Strictly, you are speaking beyond what the evidence supports. Don’t do this, it is the sort of ‘intellectual bankruptcy’ that the YEC/ID side engages in, no?

    And this is exactly what you would expect if Majerus’s suggestion — that a point mutation swept through the population — is correct.

    ‘Expect if’ is a weasel word. It either is a valid demonstration or it is not. If you say it is then you have discarded Methodological Naturalism. There simply is no ‘point mutation’ specifically known and in evidence. It is a pure appeal to mythology and has no place in a discussion of the evidence.

    For bonus points: It is never the case that Reality is consistent with a theory. It is always the case that a Theory is consistent with, or refuted by, Reality. The distinction is crucial as the former allows soft-headed individuals to claim that ‘Reality shows x about a theory…’. This is never the case no matter how softly the notion is pedalled.

    You can’t just sit around and make half-baked comments suggesting that some already-refuted explanation is more plausible and expect to be taken seriously.

    See: The above issues on epigenetics.

    … even though it is *already tested and known* that peppered moths don’t have the actively-search-for-matching-background behavior which was the major point of the Korean study.

    And yet Majerus found that Moths preferred to stay in shaded areas. So if you’re stating that Majerus is incompetent and incapable of counting moths in light and shade, then I should sorely like to see a reference as to how he cocked it up and why.

    (1) NS is real; (2) it occurs in the wild, sometimes at rates that humans can observe over a few years; (3) selection can spread mutations from miniscule frequencies (the first dark moth was only observed in the 1800s IIRC) to very high frequencies (it was 99% in highly polluted regions); (4) the result of this process is a specific functional adaptation to the environment, i.e. camouflage, which “looks designed”.

    (1) It shows predation is real. But if NS is synonymous with predation then let us call it that. If it is not then you need to provide a definition for NS to use in this context. (2) Predation does occur in the wild. It’s called the food chain and is obvious. This does not follow from your first point until you can state what NS definitively is and is not. (3) No, it shows that predation can alter allele frequencies. I’m not entirely sure who disagrees with this notion. (4) Differential predation rates over pre-existing morphs does not show ‘specific functional adaptation’ unless you have some truly perverse idea about what a ’cause’ is and what an ‘effect’ is. This goes back to your statements in (1) again.

    I’ll stop here as it is already getting too long in the tooth. But if your statement is that the vocal and self-selected minority that argue for YEC/ID demonstrate that YEC/ID is ‘intellectually bankrupt’ on the basis of their fallacies and sophistries… Then you simply have no argument against me considering the same of not only YEC/ID but of Evo as well. If not based on the majority of argumentation witnessed by Evo proponents, then by your own inability to use any manner of rationality. Unless your argument is to state that ‘But it’s ok when my side does it.’

    But that doesn’t seem to improve things any.

  77. Maus,

    This is ridiculous. The trait acts as dominant in breeding experiments in which pollution or whatever environmental cue you want is taken out of the picture. Why dream up an epigenetic pattern for such a simple trait?

    Moreover, what difference would it make? If the dark-bodied allele is an epiallele that is inherited in such a strict Mendelian fashion, and has been subject to such strong selecton, then it makes no difference if it’s a point mutation or an methyl tag that brought the allele into existence.

  78. wd400-

    It is up to you and the author(s) to verify they measured natural selection- that is they measured the differential reproduction based on heritable random variation.

  79. And yes evos, TRAITS are genetic. Unfortunately, for you, “being a moth” is NOT a trait.

  80. Joe @78 – I don’t think they looked at differential reproduction, because the suspected mechanism was differential survival. Which Kettlewell did look at.

    BTW, I assume you’ve given up trying to explain what you think is wrong with the O’Hara paper.

  81. wd400:

    You’re going to have to explain to me how a trait can be Mendelian dominant in breeding experiments and “epigenetically” controlled.

    Well, actually, I wouldn’t bother. Even if the was some weird epigenetic thing going on, the evidence for strong selection on a newly arising mutant would still stand.

    There is no “carbonaria gene.” So state the authors. The gene pathway that leads to melanism is the same in the typicals and in the ‘carbonaria.’ What changes, apparently, is some kind of molecular ‘factor’. That’s why in the paper I cited they talk about a “control region.” The gene pathway segregates as normal, but it is this control factor that effects the inherited pathway.

    Now, the authors have a subsequent paper that has come out, and they seem to identify the SNP involved in this regulatory factor. Now, this might seem like straightforward “neo-Darwinian” evolution—trivial as it always is; however, can we just simply rule out some environmental factor leading, along its own pathway, to a “directed mutation”? I don’t think so.

    So, what we see is either completely non-neo-Darwinian in character, or, by default, it is a simple SNP, which, given a large population size can be arrived at fairly quickly. But, again, this is a trivial form of so-called “neo-Darwinian” evolution. There’s no new “gene” that has shown up (again, there’s no “carbonaria gene”); it’s a simply SNP—which fits right in with Behe’s conclusions about what so-called “neo-Darwinian” evolution can bring about. (obviously we’re talking about, at most, one, SINGLE, protein-to-protein bond here).

  82. 82

    And yet Majerus found that Moths preferred to stay in shaded areas.

    Which I’ve already said in this thread. The point is that peppered moths apparently don’t actively match backgrounds to their color, where dark moths rest on dark surfaces and light/peppered moths rest on light surfaces. Yet the DI/UD suggested that the peppered moth work was somehow impeached because some other random species from Korea have this behavior.

    Now, the authors have a subsequent paper that has come out, and they seem to identify the SNP involved in this regulatory factor. Now, this might seem like straightforward “neo-Darwinian” evolution—trivial as it always is; however, can we just simply rule out some environmental factor leading, along its own pathway, to a “directed mutation”? I don’t think so.

    They’ve identified the SNP? Where’s the paper, I haven’t seen it yet I think.

    PS: For all you mutation skeptics, SNP = single nucleotide polymorphism = point mutation.

  83. For all you mutation skeptics, SNP = single nucleotide polymorphism = point mutation.

    unfounded presupposition of ‘randomness’ again Nick???

    Already referenced Shapiro earlier, but to add that line of criticism,, Though SNP’s (random mutations) do get through to make some point mutations to DNA, the level of DNA repair that prevents them from happening is simply unfathomably complex:

    Quantum Dots Spotlight DNA-Repair Proteins in Motion – March 2010
    Excerpt: “How this system works is an important unanswered question in this field,” he said. “It has to be able to identify very small mistakes in a 3-dimensional morass of gene strands. It’s akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour.” Dr. Bennett Van Houten – of note: A bacterium has about 40 team members on its pothole crew. That allows its entire genome to be scanned for errors in 20 minutes, the typical doubling time.,, These smart machines can apparently also interact with other damage control teams if they cannot fix the problem on the spot.
    http://www.sciencedaily.com/re.....123522.htm

    A Look at the Quality Control System in the Protein Factory – JonathanM – March 2012
    Excerpt: The DNA damage response (DDR) system is like a cellular special ops force. The moment such damage is detected, an intricate network of communication and recruitment launches into action. If the cellular process for making proteins were a factory, this would be the most advanced quality-control system ever designed.
    http://www.evolutionnews.org/2.....57791.html

    Repair mechanisms in DNA include:

    A proofreading system that catches almost all errors
    A mismatch repair system to back up the proofreading system
    Photoreactivation (light repair)
    Removal of methyl or ethyl groups by O6 – methylguanine methyltransferase
    Base excision repair
    Nucleotide excision repair
    Double-strand DNA break repair
    Recombination repair
    Error-prone bypass
    http://www.newgeology.us/presentation32.html

    Although evolution depends on ‘mutations/errors’ to DNA to make evolution plausible, there are multiple layers of error correction in the cell to protect against any “random changes” to DNA from happening in the first place:

    The Evolutionary Dynamics of Digital and Nucleotide Codes: A Mutation Protection Perspective – February 2011
    Excerpt: “Unbounded random change of nucleotide codes through the accumulation of irreparable, advantageous, code-expanding, inheritable mutations at the level of individual nucleotides, as proposed by evolutionary theory, requires the mutation protection at the level of the individual nucleotides and at the higher levels of the code to be switched off or at least to dysfunction. Dysfunctioning mutation protection, however, is the origin of cancer and hereditary diseases, which reduce the capacity to live and to reproduce. Our mutation protection perspective of the evolutionary dynamics of digital and nucleotide codes thus reveals the presence of a paradox in evolutionary theory between the necessity and the disadvantage of dysfunctioning mutation protection. This mutation protection paradox, which is closely related with the paradox between evolvability and mutational robustness, needs further investigation.”
    http://www.arn.org/blogs/index....._contradic

    Contradiction in evolutionary theory – video – (The contradiction between extensive DNA repair mechanisms and the necessity of ‘random mutations/errors’ for Darwinian evolution)
    http://www.youtube.com/watch?v=dzh6Ct5cg1o

    The Darwinism contradiction of repair systems
    Excerpt: The bottom line is that repair mechanisms are incompatible with Darwinism in principle. Since sophisticated repair mechanisms do exist in the cell after all, then the thing to discard in the dilemma to avoid the contradiction necessarily is the Darwinist dogma.
    http://www.uncommondescent.com.....r-systems/

    Nick perhaps you want random unguided mutations to be true, but the fact is that mutations that happen to DNA are, as Shapiro has pointed out so eloquently, for the vast majority of times regulated, directed, changes to DNA that are governed. i.e. non-random with respect to true randomness! It is simply unwarranted for you to claim that this example is truly random, much less do you seem realize how trivial this example of cyclical variation is to the burden of proof for explain where moth wings and highly integrated DNA repair mechanisms came in the first place!

    etc.. etc.. etc…

  84. There is no “carbonaria gene.” So state the authors. The gene pathway that leads to melanism is the same in the typicals and in the ‘carbonaria.’ What changes, apparently, is some kind of molecular ‘factor’.

    It sounds like it’s the regulation of the gene that’s changed (which makes a lot of sense). It could be that it’s still the same gene, if the mutation is in the regions that control expression. Or it could be at another locus, which interacts with the region that control expression. I think this could reasonably be called a gene too.

  85. Nick Matzke:

    Furthermore, recent studies in the last few years have narrowed down the region of the genome that controls melanism. As was mentioned, they also found classic genomic signatures of a selective sweep there (reduced diversity in that region). And this is exactly what you would expect if Majerus’s suggestion — that a point mutation swept through the population — is correct.

    It was correct of you to point out that the genes for melanism didn’t change in the carbonaria morph. As the authors wrote: there is no ‘carbonaria gene.’ Was this what Darwinists expected? No. Why do I say that? Because they wrote that “surprisingly” none of the candidate genes turned out to be linked to the gene pathway associated with melanism.

    Yes, there appears to be a SNP. But, does this fit Majerus’ model? Not really—and for the same reason given above.

    Now, it could be argued that this confirms neo-Darwinian premises. But are we sure?

    Ted Sargeant’s reasons for invoking “induction” regarding B. betuleria is because the change occurred too rapidly. (He notes 47 years for the ‘carbonaria’ to develop, which, he writes, corresponds to a selection factor of .50, which is quite high as selection factors go.)

    At the time Sargeant questioned the “classical” theory regarding B. betularia, one of the denouncements of his theory was that it was Lamarkian. But we now know that this is a detectable phenomena in plants, and IIRC, even in animals, via RNA-mediated epigenetic mechanisms. And we also now know that not all mutations are random. IOW, are we dealing here with a case of a “directed mutation”?

    You can’t just sit around and make half-baked comments suggesting that some already-refuted explanation is more plausible and expect to be taken seriously.

    The questions raised above are scientific questions, not religious ones.

    Your question deserves to be turned around. The real question should be: why should science take Darwinism seriously.

    The mathematics make no sense at all.

    Behe’s work, first his computer simulation and then his “Edge of Evolution” make this quite clear. If you want to convince ID folks about evolution, either show us all the “intermediate forms” that Darwin expected to find in the fossil record, or show us some mathematical way of explaining how new genetic information comes about. Or, better yet, both.

    The genetic evidence so far for the ‘carbonaria’ is of a controlling region SNP. And the authors suggest that it is but one, single mutation. How did all of the other information in the mutated sequence come about? How is this type of change in any way impressive? Why should we go from the occurence of SNPs in bringing about very simple adaptive change, to wholesale changes in body-types? On what basis is such an extrapolation to be carried out? Because otherwise we have to invoke intelligent agency? Is it materialism then that requires this extrapolation? Is that science? Why should logical people be required to ‘believe’ this stuff?

    Let’s point out that Darwinists insisted that “junk-DNA” had no function and was a confirmation of their theory. ID said that didn’t make much sense. Who turned out to be right?

    ID said that if an intelligent agent is involved in the operation of the genome, then “front-loading” is a distinct possibility, as well as being more likely—i.e., a non-gene-centric position. And now we know that sea squirts have genes that are used for limb formation, a fact that buttresses the notion of “front-loading” and which points to regulatory pathways as determinative, rather than simply genes. (

    Darwinism is running out of time. Nothing about it makes much sense. When will all the ad hoc explanations finally stop? Hopefully soon.

  86. PaV,

    You really do talk a load of rubbish sometimes.

    No one has ever claimed that that the peppered moths explained “wholesale changes in body-types” – just that they form a nice example of adaptation in a changing environment.

    Creationist’s apoplexy about the peppered moths, and the bizzare things you’ll say to avoid the simple interpretation of the results, on the hand, seems to suggest they form some sort of problem for you guys?

  87. When evolutionary biologists use the null hypothesis to try to explain ancestor-descendant variations in genes, they look to examples such as the peppered moth for answers as to why neutral evolution fails. What would normally take neutral evolution 30 million years selection can do in two. Does this work for all cases? No, but it’s a good starting point and when it works we learn a lot.

  88. wd400:

    Who’s talking a load of rubbish here?

    The peppered moth is THE ICON of evolution. And evolution is supposed to tell us how bacteria became humans.

    And now you’re saying this: the peppered moth is “just …. a nice example of adaptation in a changing environment.”

    I’ve been saying for years that if Darwin entitled his book The Origin of Adaptations, that I’d probably not find too much wrong with it.

    Who are you kidding with this line of defense? You can’t have your cake,and eat it too.

    The reason I question the “classic” tale told of B. betularia is, first, because I suspect that neo-Darwinism can do even less than what it appears to be able to do. That’s just a personal suspicion based on a whole host of considerations. Hence, it borders on intuition.

    And, second, related to the first, I think that the amount of true “randomness” in mutations is far less than we think.

    And, third, because it seems that the gene frequencies of the alleles—whatever that means, if anything (whole genome analysis will eventually tell us just what it means; but, in the case at point, there WASN’T a “carbonaria gene”, an allele, but, rather, a modification factor, so how can we even talk about “changing gene/allele frequencies”?)—are changing so quickly, back and forth, traditional pop. gen. formulas don’t favor such an explanation. This is why Ted Sargeant had reservations. And, this is exactly why Haldane published his paper that later came to be known as Haldane’s Dilemma. (But, of course, there’s never a dilemma that a good “ad hoc”, Darwinian “just-so” story can’t remedy.)

    But, wd400, you’re right: all this is is a simple case of “adaptation.” New body-types aren’t going to emerge via these mechanism even if we had billion, trillion years available.

  89. Starbuck:

    What would normally take neutral evolution 30 million years selection can do in two. Does this work for all cases? No, but it’s a good starting point and when it works we learn a lot.

    I see you’re ready to throw neutral drift under the bus. But, of course, neutral theory developed because of the concept of “genetic load” owing to the fact that directional selection, such as you assume to be taking place here with B. betularia, requires lots of individuals to die. The “surprising” (Why do we hear biologists use that word over and over again? Is it because they have everything wrong?) level of protein polymorphisms led Kimura to propose the NT.

    So, as usual, you’re a Darwinist who will concede the inadequacies of one theory, only because he’s convinced of the power of another one. But, unfortunately, neither one is powerful enough—in a mathematical way—of explaining viable genetic pathways leading from sea squirts to humans, (let alone from cats to dogs) nor a combination of both.

    We’re incredibly huge orders of magnitude away from any sensible mathematical solution.

  90. See, this is the rubbish I’m talking about.

    Apart from all the noise, do you mind explaining why you think a “modification factor” that segregates in a simple Mendelian fashion isn’t an allele?

    Or what the near-fixation of one allele has to do with Haldane’s paper, which is about the cost fixation of multiple alleles (and based on shakey assumptions, which Haldane makes explicit if you actually read the paper).

    Seems a lot like the classic Gish Gallop to me…

  91. I am not throwing nt under the bus, just that it is the the null hypothesis , and sometimes the null hypothesis is correct , but when it isn’t we look to other explanations, like selection. We test , we poke, we prod. There’s no atheistic conspiracy we just want to understand.

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