Monday, August 06, 2012

Intelligent Design Creationists Attempt to (re)Define Junk DNA

Paul McBride is causing quite a stir among the creationists. His review of Science & Human Origins was so devastating that they couldn't ignore it.

Jonathan McLatchie (Jonathan M) is the latest creationist to attempt a defense of the home team. He concentrates on defending the Intelligent Design Creationist position on junk DNA [A Response to Paul McBride on Junk DNA].

On this topic (junk DNA), the IDiots make a lot of errors. One of them is to deliberately conflate "junk DNA" and "noncoding DNA" so that when they come up with evidence for function in noncoding DNA they can tout this as evidence against junk DNA. This error is so pervasive in the IDiot literature that Paul McBride even predicted that Casey Luskin would make this mistake in the book.

Here's how Jonathan McLatchie responds ..
In his review, McBride notes that he had predicted that Luskin would "conflate non-coding DNA and junk DNA, and that Luskin would exploit this erroneous conflation by pointing to known functions of non-coding DNA as evidence against junk DNA."

Of course, no one today (including the likes of Larry Moran, PZ Myers and T. Ryan Gregory) denies that at least some non-protein-coding DNA serves important functions. The term "junk DNA" was first coined in 1972 in a paper by Susumu Ohno. Although Ohno believed that the vast majority of the DNA that didn't code for proteins was "the remains of nature's experiments which failed," Ohno suggested that "these silent DNA base sequences may now be serving the useful but negative function of spacing [genes]."

McBride writes,
I'd like just once to see all these references where all these researchers are saying that if DNA does not code for a protein then it is junk.
As stated above, no credible scientist claims that all non-coding DNA is "junk."
Good for you, Jonathan McLatchie. You seem to be one of the few Intelligent Design Creationists who pay attention to the science. But now you need to go one step farther. You need to acknowledge that your colleagues are dead wrong. Casey Luskin, a lawyer, gets it wrong quite often but what about Jonathan Wells who wrote a whole book on the subject?

Here's an excerpt from an interview with Denyse O'Leary [Jonathan Wells on his book, The Myth of Junk DNA – yes, it is a Darwinist myth and he nails it as such].
Denyse O'Leary: So, for those who dropped science after Grade Ten, what is junk/non-coding DNA?

Jonathan Wells: “Non-coding” in this context means “non-protein-coding.” An important function of our DNA is to specific the sequences of subunits (amino acids) in the proteins that (along with other types of molecules) make up our bodies. When molecular biologists discovered in the 1970s that about 98% of our DNA does not code for proteins, some biologists called non-protein-coding DNA “junk.”
Oops! Jonathan Wells says that some biologists referred to all noncoding DNA as junk but McLatchie admits that this is not true.

Those two need to have a talk. It's what honest people do.


61 comments :

  1. Larry is being somewhat pedantic here. The vast majority of non-protein-coding DNA in his opinion is indeed "junk". Wells has never ever claimed that the scientists of the 1970s believed every single nucleotide of ncDNA to be junk (presumably they knew about promoters).

    There is indeed "junk" in the genome - not due to failed experimentation in evolution or vestigial genes - but to general degeneration of the kind that Sanford goes on about. It exists even within the bits that Larry regards as essential, such as the UTR.

    But all the available evidence shows that the likes of introns, intergenic regions and transposons do play a subtle but important role. Larry, however, prefers to ignore this research in order to continue assuming the role of "Professor Junk DNA". How sad.

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    1. @Atheistoclast:

      You lying little weasel! What do you think Jonathan Wells' book was about? What do you think YOU YOURSELF just got done saying-- that scientists believed non-coding DNA = Junk DNA! You lying little weasel, you said that many times! Now you think you can rewrite the history, take back what you wrote? Do you think we'll forget what you wrote?

      What do you think Casey Luskin wrote many times? And defended when I personally challenged him?Non-coding DNA = junk DNA! Now you'll rewrite history and make your pathetic lies disappear?

      Consider what you say now:

      Atheistoclast: "Wells has never ever claimed that the scientists of the 1970s believed every single nucleotide of ncDNA to be junk"

      You lying scum! What do you think Wells says above?

      Wells: "some biologists called non-protein-coding DNA “junk.”"

      Here is Atheistoclast lying about what scientists said about non-coding DNA, less than a week ago, on this very blog:

      Atheistoclast: "The search for more and more functional ncDNA, previously regarded as being junk, is now a major part of finding cures for genetic diseases." [http://sandwalk.blogspot.com/2012/07/darwinists-dont-believe-in-junk-dna.html]

      Now lying weasel Atheistoclast is trying to walk that back!

      Here's more from lying Jonathan Wells:

      Wells: "Yet by 1970 biologists already knew that much of our DNA does not encode proteins. Although some suggested that non-protein-coding DNA might help to regulate the production of proteins from DNA templates, the dominant view was that non-protein-coding regions had no function." [Wells, "Myth of Junk DNA", chapter 2]

      This quote of Wells was cited by lying creationist Jonathan M, against me, when I said that Wells had claimed scientists thought non-coding DNA = Junk. Now this is the same Jonathan M who now claims that ID proponents never said molecular biologists said non-coding DNA = junk!

      In fact Jonathan M's citation proved that I was right, but ENV closed all comments so that I could not expose lying Jonathan M and Jonathan Wells. See my comments here at ENV, where I kick Luskin's lying ass:

      [Luskin at ENV says scientists said Non-coding DNA = Junk.]

      Also note what a lying weasel Wells is! He wrote "some suggested that non-protein-coding DNA might help to regulate the production of proteins", which is a lie. Jacques Monod and co-workers proved it experimentally, they didn't suggest it, and they won the Nobel Prize for it in 1965, and all molecular biologists knew it had been proven and had to know it in order to employ it in their lab research every single day of their lives. Not "some suggested" as lying creationist Wells says.

      Wells: "Yet science depends on evidence and the tide of the evidence is clearly running against them... Anyone with a computer and an Internet connection can go to PubMed – a freely accessible database of scientific articles maintained by the U.S. National Institutes of Health – and find hundreds of additional articles about the functions of non-protein-coding DNA. ...Like Dawkins, Shermer and Kitcher, they [Coyne and Avise] have forfeited any claim they might have had to be speaking for science. [Wells, "The Myth of Junk DNA", pp. 97-98]

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    2. Here is what Luskin wrote, addressing me, to defend his scurrilous lie that scientists believed non-coding DNA was junk DNA:

      Luskin vs. Diogenes: "Contra your [Diogenes'] claims, many of these scientists essentially equated noncoding DNA with junk. As Jonathan Wells documents...

      [Luskin then lists many quote mines from Wells' book, in which Luskin and Wells insert ellipses and remove phrases and clauses to deceive non-scientist readers]

      Luskin vs. Diogenes: Many additional examples could be given. It's very convenient for some scientists to argue, in 2012, that the genome isn't full of useless junk. Good for them--they know to jump off a sinking ship when they see one. But that doesn't change the fact that for decades, evolutionary scientists presumed that non-coding DNA was largely junk. Your [Diogenes'] comment is attempting to rewrite history...

      But I [Casey Luskin] am claiming that for years, Darwinian scientists claimed that non-coding DNA was largely junk, and that we’ve discovered massive amounts of function for non-coding DNA, and that the trendline is strongly in favor of function...

      If you post the entire quote of a quote you only partly quoted, it shows that many biologists equated non-coding DNA with "junk" DNA....


      [quote mining a News and Views article by journalist at Nature]

      So there you have it. According to Nature, non-coding DNA “used to be called ‘junk’ DNA”, but we now know that many of these noncoding elements have regulatory functions…”" [Luskin at ENV]

      (Luskin above was citing Erika Check Hayden, a journalist in a News & Views article in Nature (March 2010), not a molecular biologist. She did not say that non-coding DNA used to be called junk DNA; that was Luskin's invention.)

      Luskin: there are literally hundreds [of papers] out there finding vast levels of functionality for non-coding DNA. [Luskin at ENV]

      Luskin: "In fact, the junk-DNA mindset, which was born and bred from the Darwinian paradigm, even stifled research... The journal Science reported that the junk DNA mindset "repelled mainstream researchers from studying non-coding DNA." [Luskin at ENV]

      (Here Luskin was misrepresenting Wojciech Makalowski (2003), another "Perspective" type article, which said no such thing.)

      Luskin: "In 2003, Scientific American reported that one type of non-coding DNA called introns 'were immediately assumed to be evolutionary junk.'"... [Luskin at ENV]

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    3. Here is more proof that creationists said that scientists said that non-coding DNA = junk. Now they are trying to re-write history.

      Here is creationist Russell W. Carlson, positively reviewing Wells' book:

      Russell W. Carlson: "In The Myth of Junk DNA Jonathan Wells tells the intriguing story of `junk' DNA-the idea that non-protein coding DNA, which accounts for the majority of the DNA in the genome, is non-functional and without purpose...In recent years, however, numerous researchers... have discovered many functions for non-protein coding DNA, which are thoroughly reviewed by Wells in this book. Unfortunately, in their effort to keep the `junk' label attached to non-protein coding DNA so that it remains in the box of Darwinian evolution, a number of prominent Darwinists continue to insist...that it is largely left-over waste from the evolutionary process. ...Wells's book not only informs its readers of very recent research results, but also encourages them to think objectively and clearly about a key discovery in biology...It is a great read."

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    4. Well now i feel like i should have been harsher with him as well...

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    5. Here is a video of Jonathan Wells, live, caught lying about how molecular biologists believed that non-coding DNA was junk.

      Watch Wells lie about what scientists said:

      [At 4:46] “In the 1960’s and 1970’s, however, molecular biologists discovered that most human DNA does not code for proteins. Since the Central Dogma is that "DNA makes RNA makes protein makes us," non-protein-coding DNA appeared to many biologists to be "junk."

      (This is false about non-coding DNA and it is also false about defining the Central Dogma of molecular biology, as Larry pointed out already.)

      [At 11:45] "In fact, about 98% of our genome is not protein coding, and this is what gave rise to the notion of junk DNA... this does not mean that that DNA [non-coding] is junk."

      Slide: “Evidence that non-protein-coding DNA is functional (most common slide in talk, appearing many times)

      [At 22:35] Slide: “Conclusion: There are still parts of non-protein-coding DNA for which no function is known. Yet new functions are constantly being discovered, so any argument for Darwinian evolution that rests on “junk DNA” (as Francis Collins’ does) must constantly retreat in the face of new evidence.

      Now lying creationist Jonathan M wants to re-write history and pretend that was never said.

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  2. So, atheistoclast, why do onions have so much more haploid DNA than we do? And why do different species of onions have much more haploid DNA than other species of onions? Is most of that DNA really functional when a plant has 10 or 50 times more DNA than a human?

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    1. I suspect it is doing something. Plants, in general, have a lot more retrotransoposons in their DNA. Several papers have revealed their contributions to plant evolution. I suggest this review paper as an excellent starting point:

      http://forest.mtu.edu/faculty/joshi/publish/pdf/amar.pdf

      Leaving aside haploids, polyploidy in plants does have real adaptive benefits and these are well known. I suggest this review as another useful introduction:

      http://www.ces.ncsu.edu/fletcher/mcilab/publications/ranney-2006.pdf

      The proliferation and acquisition of extra DNA does seem to contribute to the robustness and versatiity of the organism.

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    2. So, an onion has more "robustness and versatiity" than a human?

      In your case that's likely true.

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    3. Plants have to be more robust and versatile than metazoans. Any plant scientist will tell you as much.

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    4. But then that means gene duplication (or chromosome duplication) is beneficial. Yet ID proponents say that if you xerox a page, it does not increase information.

      So by the ID definition of "information", does gene duplication or chromosome duplication increase information or not?

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  3. McLatchie has learned well how to spin his rhetoric. Look at this sentence:
    "Of course, no one today (including the likes of Larry Moran, PZ Myers and T. Ryan Gregory) denies that at least some non-protein-coding DNA serves important functions"
    Hes implying that scientists "denied" evidence for non-coding DNA until the evidence became so overwhelming that they had to 'admit' it, with the deeper implication being that non-coding DNA is somehow a problem for evolution. I dont know if Beadum and Tattle discussed non-coding DNA but I know Jacob and Monod did in the 50s and 60s
    I wish both sides would just bypass all this nonsense and get to the real issue: transposable elements and repetitive DNA. Do these have any 'function' that is even remotely consistent with an intelligent designer

    RodW

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    1. Jonathan M is not spinning, he is outright lying. He has totally rewritten the history of Intelligent Design and that pathological liar, Jonathan Wells.

      Jonathan M writes: Notwithstanding what Paul McBride says, ID proponents are well aware of this literature and do not, as he claims, conflate "junk DNA" and "non-coding-DNA."

      This is an outright lie. That is exactly what Jonathan M, Jonathan Wells, Casey Luskin, Atheistoclast, Russell Carlson, and many other creationists wrote: they accused scientists of equating junk DNA and non-coding DNA.

      I demonstrate this in quotes from them above. Now lying creationists are trying to re-write history and re-write their own books and articles.

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    2. Diogenes, I think you should just calm down!

      Let's get 2 things straight. According to Larry:

      1. All "junk" DNA is non-coding DNA.

      2. The vast majority of non-coding DNA is "junk".


      Hence, Larry does appear to equate junk DNA with ncDNA except for things liker regulatory sequences, known to exist in the 1970s, and a lot of long ncRNA genes that were not. So, for all practical intents and purposes, Wells is right.

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    3. You and other creationists are lying sacks of crap, and we caught you lying. Molecular biologists certainly think

      (A) All non-functional DNA is a subset of non-coding DNA

      But lying creationists say that molecular biologists said

      (B) All non-coding DNA is a subset of non-functional DNA

      These are not the same, dumbass. You and your creationist authorities (Jonathan Wells, Casey Luskin, Jonathan M etc.) are lying sacks of crap and we caught you lying.

      Atheistoclast: Larry does appear to equate junk DNA with ncDNA except for...

      Except for many kinds of functional, important things, every single one of which were discovered by evolutionist scientists and not one of which were discovered by lying creationist weasels.

      Except of things that molecular biologists employ every day of their lives, like regulatory sequences, known in the 1960's. (Also RNA genes, telomeres, and many other things including STUFF THAT EVOLUTIONISTS, NOT CREATIONIST WON NOBEL PRIZES FOR DISCOVERING.)

      But when creationists say that "cutting edge" science has found function in junk DNA, what do they point to, mostly? Mostly, ERV's or pseudogenes in which ~a dozen bp got co-opted as regulatory elements.

      If molecular biologists always said that regulatory elements have function, which they did say, then when your creationist authorities cite any of them as evidence against the junk DNA hypothesis, you are lying sacks of shit.

      This is what it's like arguing with lying weasel creationists.

      Scientist: All bats are mammals.

      Creationist: Darwinists think all mammals are bats! Which proves how stupid they are. Cutting-edge science has proven that cats and buffaloes are mammals, but are not bats! Darwinism is a science stopper and prevented important research into the non-bat status of cats, buffaloes, and other mammals. Because of the atheist Darwinist "all mammals are bats" theory, medical discoveries were not discovered. Diseases were not cured. Countless lives were lost. They killed children!

      Scientist: I never said that. I said all bats are mammals.

      Creationist: Hear that? He said it again!

      Scientist: Said what?

      Creationist: He just said all mammals are bats!

      Scientist: No, I...

      Creationist: Darwinists killed babies! Creationists should control the universities and science labs, because Darwinists are so stupid, they thought all mammals are bats!

      Again, to repeat:

      Casey Luskin was lying, he is a lying sack of shit and he doubles down on his lies. We caught him.

      Jonathan Wells was lying, he is a lying sack of shit and he doubles down on his lies. We caught him.

      Jonathan M was lying, he is a lying sack of shit and he doubles down on his lies. We caught him.

      The scientific community will never forgive these lying creationist ID sacks of shit--Luskin, Wells, Maclatchie-- or their scurrilous lies. ID will never replace evolution because all ID proponents are lying, scurrilous sacks of shit and they suck at science, and they lie about it.

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    4. What the heck has bats got to do with this subject!? Like it or not, the vast regions of the genome that were previously regarded as being "junk" are now being found to be functional in one way or another. It doesn't matter one iota whether the scientists engaged in this research are creationists or evolutionists.

      These findings don't prove ID, nor do they in any way disprove Darwinism, but they do undermine the case made by folks like Larry that evolution is an accidental, haphazard and wasteful process.

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    5. @Atheistoclast:

      It doesn't matter one iota whether the scientists engaged in this research are creationists or evolutionists.

      Bull. That's not what your lying creationist authorities says. Let's compare this to what you and your ID authorities wrote quite recently:

      Casey Luskin: "In fact, the junk-DNA mindset, which was born and bred from the Darwinian paradigm, even stifled research... The journal Science reported that the junk DNA mindset "repelled mainstream researchers from studying non-coding DNA." [Luskin at ENV]

      Evolution News and Views: "A favorite criticism of ID is that it is a science stopper. The opposite is true... Evolutionary theory, in fact, has been worse than a science stopper: its predictions have been flat out wrong. ... Recently Darwinians made the same kind of mistake with their myth of "junk DNA" (see David Klinghoffer's take on that persistent myth).

      ...Intelligent design, in contrast, offers a host of promising questions for research. One wonders how much further along science would be today if ID scientists had the power to direct research about "vestigial organs" and "junk DNA" instead of letting the Darwin power structure tell everyone, "there's nothing to see here." One wonders, further, how much pain and suffering might have been avoided.”
      [Evolution News & Views, July 20, 2012.]

      Jonathan Wells: “Coyne and Avise are professors of genetics at major universities, so they cannot claim ignorance of the genomic evidence without thereby admitting negligence or incompetence... Like Dawkins, Shermer and Kitcher, they have forfeited any claim they might have had to be speaking for science. [Jonathan Wells, The Myth of Junk DNA, pp. 97-98]

      Atheistoclast: “Science is not easy. It is hard stuff. Those who put their hands up in the air and give up trying to find difficult answers to vexing problems, and who make unwarranted assertions, have no place within science. [Atheistoclast just last week]

      Let's be clear that ID creationists lied about what scientists said because they wanted to make scientists look stupid, so that they could get power over scientific research, power over labs and universities, without doing any work themselves. They lied about junk DNA to get power, as Wells' and the ENV quotes make quite clear. This is a power grab, pure and simple.

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    6. These "vast regions" of functionality total to a few percent of the eukaryote genome.

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  4. Come on. Transposons make copies of themselves and throw them haphazardly into other strings of DNA. They're almost half of our genome and they don't really do much to carry their own weight.

    Just the other day you were arguing that the cost of making a lot more DNA multiplied so many billion fold (number of cells in a body) must "add up" and matter for natural selection. You thought the cost was important, no matter how small. Now you think that the miniscule benefits from carrying around these huge burdens of DNA that just copy themselves matter while the cost of the DNA bases do not?

    I tried to be convincing in the other thread but it seems I convinced you WAY too hard.

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    1. If one has enough energy to play Xbox after a day of work then one has enough extra energy to sustain junk DNA with little worry...

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    2. Individuals wasting energy don't so immediately display any relevant decreases in their reproductive fitness.

      But yeah, it's a comparison between all other individuals competing for the same resources. Nucleotides are abundant enough that we don't even think about the cost of making them, instead simply looking at the time cost of stringing them together, and even then only in organisms that spend a significant portion of their cell cycle doing so.

      I'm just shocked at how quickly atheistoclast has switched gears to say that these enormous stretches of DNA make up for their size via minuscule effects that only begin to manifest after many generations of carrying around the increased (and ever increasing) load or otherwise wasteful base pairs.

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    3. I'm just shocked at how quickly atheistoclast has switched gears to say that these enormous stretches of DNA make up for their size via minuscule effects that only begin to manifest after many generations of carrying around the increased (and ever increasing) load

      More doublethink than gear-crunching, I think. "The fact that many retrotransposons are inactivated shows that I am right and Larry is wrong" (on the matter of the metabolic load of excess DNA). And yet these same nuisances are really a nifty design solution to the need to shake up the genome every now and again. They're junk, and need turning off, and they're not-junk, and should be celebrated.

      Perversely, both points are kind-of valid (if you throw out the unnecessary layer of design). Of course there is a load to overproducing DNA, all else being equal, but only if you have significantly more than the rest of the population. If you all keep closer in step then it can accumulate.

      And transposons do occasionally donate functional sequence - but in this, they are simply acting as mutagens. A proportion of mutations are beneficial, likewise a proportion of transpositional insertions. But this is no more a design feature than a polymerase misread or a cosmic ray zap.

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    4. Of course there is a load to overproducing DNA, all else being equal, but only if [...]

      ... and not forgetting the disadvantage that the deleterious mutational load of rampant transposition brings.

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  5. "And transposons do occasionally donate functional sequence - but in this, they are simply acting as mutagens. A proportion of mutations are beneficial, likewise a proportion of transpositional insertions. But this is no more a design feature than a polymerase misread or a cosmic ray zap."

    It could be a design feature, as follows:

    When a copy of a transposon remains with the genes it has affected, then it is selected with them. A transposon that does a particularly "good" mutation will increase its numbers because of that. And if "that thing that it does" is more likely to generate mutations that will be selected, then it will tend to win more when it puts copies in other locations too.

    If you get cosmic ray zap and it happens to have some beneficial effect, there is no obvious way to increase the chance that the next cosmic ray zap will also have a beneficial effect. But to the extent that there are patterns in beneficial mutations that transposons can provide, transposons may be selected to provide those patterns more othan other patterns.

    To me that would be a useful design feature.

    If it works.

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    1. Except that mutations are not due to cosmic ray zaps. The are overwhelmingly due to error in DNA replication.

      Could then replication errors be a design feature? People have tried to find adaptive grounds behind the mutation rate in replication, but the "neutral lower bound" hypothesis seems quite strong. So it does not look designed, either.

      http://www.indiana.edu/~lynchlab/PDF/Lynch183.pdf

      -The Other Jim

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    2. Except that mutations are not due to cosmic ray zaps.

      What, never?

      The are overwhelmingly due to error in DNA replication.

      Maybe so, but the other causes are not negligible. Particularly multi-base rearrangements, which may well be of greater evolutionary significance, and would seem to derive from other causes (mostly errors in meiosis - or good old transposition).

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    3. The problem with that thinking is that these don't have any tendency to cause any particular mutation. They simply copy themselves into DNA, sometimes into coding regions or regulators. Statistically the cause us a small amount of harm and grant a much smaller benefit, but the genetic mechanisms mix and sort those mutations like anything else- there's nothing special about any particular bit of parasitic DNA, it just comes along for the ride.

      -as for the cosmic ray I think that comes from a rather simplified way of looking at the energy barriers of basic chemistry. If you want to be accurate ditch the idea but otherwise just use it as a kind of shorthand when you're dealing with short attention spans.

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    4. This can sort of sometimes happen. Bacterial Transposons, for example, are generally pairs of Insertion Sequences (IS) (simpler Transposable Elements (TE)) that "carry" a useful gene with them, typically an antibiotic resistance gene. I don't think it is accurate to say that the flanking IS are "mutating" the antibiotic gene - the mutations were the original IS insertions without said gene, and then subsequent transpositions with said gene. Sometimes, as with antibiotic resistance, the association is so successful that the individual flanking IS degrade until the composite TE can only transpose as a unit. The original "selfish" IS generally still out-number the composite TEs, though, and most of their insertions are disadvantageous.

      My PhD thesis examined whether occasional beneficial mutations can maintain TEs in clonal populations of bacteria despite being usually disadvantageous. They can in certain circumstances but this is a long, long way from looking like anything resembling a good design feature. It is just yet another example of gene-centric evolution - a TE is not trying to be good or bad but will spread if it can increase it's frequency, essentially by reproducing quicker than selection removes it. It can do this by reproducing faster (though horizontal transfer) or by getting boosts through beneficial affects (which drag through other TE copies through hitch-hiking).

      Some TEs are quite discriminating about where they will insert but this is not spatial proximity, as you propose, but rather determined by sequence. It is not hard to speculate how such insertion hotspots could eventually evolve into simple recombination-based genetic control systems akin to VD(J) recombination. This would need to be a recurring need, however, and would still be under pressure to reduce spurious bad mutations.

      In other words, TEs can be functional, yes, but they do not look anything like an intelligently designed feature, and they do not have spatially connected effects like you suggest. There is no evidence to suggest that the mutations they create are anything but random with respect to the outcome. In other words, they increase the number and type of mutations but this is not inherently a good thing.

      Of course, if a TE-derived mutation does benefit a host, that host will spread with the consequence that the TEs within it also spread. This is a long, long way, however, from suggesting that the TE is a useful design feature because it created that particular mutation. Those who claim otherwise commit a standard Creationist/ID fallacy that if one example of a class can be shown to be useful, all members of that class must have a function. Evolution is notoriously opportunistic and if you were to apply this level of extrapolation across all of biology, you would quickly be contradicting yourself left, right and centre.

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    5. Shoku: The problem with that thinking is that these don't have any tendency to cause any particular mutation.

      As that follows on from my post, I'd just like to point out that I wasn't arguing they did - just to be clear!

      as for the cosmic ray I think that comes from a rather simplified way of looking at the energy barriers of basic chemistry. If you want to be accurate ditch the idea but otherwise just use it as a kind of shorthand when you're dealing with short attention spans.

      Which is how I was thinking when I - guilty! - introduced the term into the thread. The-generality-of-shit-that-happens which, occasionally, has benefit, to compare-and-contrast with the common ID-fuelled idea that transposons are kept around as some kind of 'useful mutagen'.

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    6. @ Allan Miller - yes I was only discussing substitutions. But they are ~25x more common than all other types.

      http://www.ncbi.nlm.nih.gov/pubmed/12497628

      -The other Jim

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    7. Thanks Jim - interesting.

      "deletions are approximately three times more common than insertions" ... the opposite of what I've been arguing! Of course, it must depend in part on how 'function-rich' the genome in question is - and whether any transposons are especially active at a given moment. I guess this report is just a snapshot of one species at a particular moment in its evolutionary history. But interesting.

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    8. At home now, without the paper (or net access).

      I also think size matter a lot here. If I recall, these are smaller ones discussed in the paper (but I am prepared to eat some crow tomorrow...). Huge deletions are probably rare, but likely to be nasty if the occur near anything useful.

      -The Other Jim

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    9. Allan Miller: You don't get to take shortcuts when talking about science because we're really pedantic :b

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  6. The Other Jim, it is possible to select for high mutation rates in bacteria. Four rounds of selection for rare mutants will do it. I can explain how it works, bu it would take a bunch of words so I won't unless somebody asks.

    Genes that create variant mutation rates exist. They can be selected. If in practice selection is for low rates, then that's just what s selected in those particular environments.

    Suppose that one source of mutation produces favorable mutations far more often than another source. Wouldn't the one that works, tend to survive along with the favorable mutants it creates? No, not in obligately sexual organisms. Not unless it mostly creates local mutations, close to its own site.

    Say you have a gene involved in DNA replication that mutates to give a higher mutation rate. It creates a favorable mutation on some random chromosome. How long does it get the selective benefit of that mutation? 50% for one generation, 75% for oe or two generations, etc. Say it creates an unfavorable mutation. It suffers more than its share of the effects because unfavorable mutations have less effect with time, not more. So it's completely reasonable that DNA replication genes would be selected to reduce mutations as much as possible, subject to other constraints like replication that's too slow.

    But a mutation that has local effects? It will be selected along with the mutations it creates. Do you know of something that can have local mutagenic effects, that can create local mutagenic effects at new sites, that is more likely to be copied to new sites if it increases its numbers at an old site?

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    1. The primary local effect of a transposon would be to bugger up nearby sequence. It may have struck lucky where it is, but luck is not heritable. It would be better getting as far away from itself as it possibly could!

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    2. @ J Thomas

      I am aware that mutation rates can vary, and that some like to point at this and scream "design". But you will read thorough bashing's of Shapiro's positions on this blog and others.

      - read the Lynch paper, then get back to me. This sort of hypothesizing falls apart when you apply the population genetics.

      -The Other Jim

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    3. The Other Jim, thank you for that link. I think I followed most of it, but it's likely to take me weeks to get the full implications. I'd like to respond before that but I might miss some important points. Maybe tomorrow....

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    4. @ J Thomas

      Reading Lynch's stuff has the same effect on me. ;-)

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  7. According to the christian bible (and most IDiots are christians), "God" created "Adam" (the alleged first human) from dust, and "Eve" (the alleged second human) from one of "Adam's" ribs.

    Maybe atheistoclast or one of the other IDiots would like to show where in the bible it says that "God" designed or tinkers with mutations, DNA, transposons, chromosomes, proteins, meiosis, genes, insertions, nucleotides, cells, and the other things or processes that SCIENCE (not religion) discovers, labels, and studies?

    Am I the only one who thinks it's hilariously desperate of the IDiots to argue about all that scientific stuff when they believe that their supernatural "God" magically poofed the first two humans into existence from dust and a rib?

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    1. "(and most IDiots are christians)"
      Not a safe assumption. We run into them more around here but in regions with differing dominant religions the local fundamentalists pull out an almost identical stance (nice and easy to shoot down,) that just has all the scripture references swapped out for whatever other holy writ.

      Not sure if they realize they are stealing material from each other quite so blatantly but it fits perfectly with their character.

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    2. Why do you keep associating me with Biblical literalists?

      But I do like the story of the creation of Adam and Eve because the Lord takes a rib from Adam in order to make Eve. He doesn't just poof Eve into being, but rather opportunistically uses bottom-up engineering to make her.

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    3. Am I the only one who thinks it's hilariously desperate of the IDiots to argue about all that scientific stuff when they believe that their supernatural "God" magically poofed the first two humans into existence from dust and a rib?

      Nope. It keeps us all entertained.

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    4. Atheistoclast:
      You get associated with them for using a lot of their rhetoric. ID has been quite thoroughly exposed as a relabeling of Christian Science (swap out every instance of the word creator with designer and created with designed, and the first textbook for ID is identical to previously rejected creationist propaganda.)

      There is still another way for us to interpret the situation, but I'm afraid it is rude even by comparison. You might just be stupid and really like the sound of the rhetoric instead of understanding even the most basic strategy behind it.

      I prefer to give you the benefit of the doubt and go with the (relatively) favorable option. You've got a god agenda to push and you do it the same way as a majority of people, instead of being severely impaired compared to them. Should I (/we) stop making this assumption and go with the worse interpretation of you?

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    5. I agree about the bottom up engineering of Eve, but there is a persistent rumour that this particular story is an explanation why humans have no baculum, while dogs and sheep have - sort of amusing sexual story for sheperds.

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  8. atheistoclast, you continue to play games and pretend that you're not a science denying creationist IDiot. It's obvious that the only reason you study the theory of evolution (but still don't understand it) is to try to find things wrong with it. jonathan wells must be proud of you.

    Hey atheistoclast, did I say that only "Biblical literalists" are IDiot creationists or that all IDiot creationists are "Biblical literalists" or that only "Biblical literalists" are trying to destroy science and replace it with their dominionist agenda?

    It is WELL known that so-called "Biblical literalists" have many disagreements about their interpretations of what is said in the bible, and of course there are multiple versions and translations of the bible. Tossing in the word "literalists" is just another one of your diversionary games, in a lame attempt to make it look as though you're not as extreme as "literalists" and therefor are not motivated by the same religious dogma.

    Even if you don't take every word in the bible literally, that wouldn't make you any less of an IDiot creationist. Since you push "Intelligent Design" it's obvious that you believe in a supernatural designer-creator-god.

    You've been asked to provide your specific alternative to naturalistic evolutionary processes but you dodge the requests, and it must be because you know that revealing your beliefs would show that you are just another typical god zombie. Like the other IDiots you constantly argue against natural evolutionary theory and processes but you don't present any positive evidence for a testable, verifiable 'design' alternative. And, like the other IDiots, you think that if you can find some tiny thing wrong with naturalistic evolutionary theory your religious beliefs should and will automatically be established as a fact.

    You IDiots never do anything positive. Everything you do is destructive. You don't add to scientific research or knowledge, you just try to tear it down. If you were really interested in advancing scientific research and knowledge you'd be working WITH science and using productive methods to find the answers to any unanswered questions and to promote and teach productive methods and the answers that have been found.

    If all the money and effort that is spent by religious zealots to fight against science were instead spent ON science, more discoveries would already have been made.

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    1. atheistoclast, you continue to play games and pretend that you're not a science denying creationist IDiot.

      Actually there's a fairly reasonable chance that he isn't any of the above and that he's conducting an extremely elaborate and enormously successful troll.

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    2. I do believe that I have been created and intelligently designed during my growth from a fertilized egg into a beautiful baby. But is that really what ID is all about?

      No. ID, like Darwinism, focuses on genetic information and its origination/evolution. They seem to both agree that DNA is omnipotent. I dispute this completely. I believe that genes did not create me - they just supplied the tools and parts, and that some other agency actually put me together. Hence, I am a "vitalist" rather than a "creationist". As such, I look forward to the collapse of the gene-centric paradigm of developmental biology, along with "evo-devo" as a whole, with every sinew of my body. I have wagered a bet with PZ Myers on this over at the PT.

      But I do think that the genome has itself been "designed" even if natural evolutionary processes, like retrotransposition and viral insertions, have since shaped it.

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    3. Richard Lewontin says things a lot like this and gets accused of being a commie. It always seems to get back to that level of abuse when it's skepticism of the supremacy of DNA.

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    4. Man, I'd feel really embarrassed to deny the function of DNA at this point. Yeah, you need a cell with some minimum of stuff in it in order to read the DNA but that minimum of stuff is universal to the point that effects arising from the cell independent of DNA are far too small to account for basically any of the form of life.

      It's almost like arguing that soon the thinking folk will agree that the circuits in a toy helicopter don't pick up signals from the remote and orchestrate movements but rather that all of these effects arise from ghosts inside of the battery.

      There is a good question to ask at this point though- do you think that you can get to this agency doing all the fine tuning to arrange you, from the ground up? That you can start from "I don't know or have any idea what does this" and then by looking at the processes you can piece together a rigorous proof that it is agency rather than the emergent properties of chemistry?

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  9. I believe that genes did not create me - they just supplied the tools and parts, and that some other agency actually put me together.

    I can kind of see that. It's like, when construction workers build a big structure, they depend on blueprints etc to tell them what to build. But the blueprints don't build it, they just say what to build.

    The DNA could be kind of like a library, and cells depend on all sorts of things to tell them what to look up. The library doesn't tell you which book to read, you have to figure that out some other way. Though you might choose to find a book that suggests a reading program, and you might then choose to read the books on its list in the order it suggests.

    I'm not sure that line of thought leads anywhere useful. But I do think it's a valid way to look at the situation.

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  10. What I can't get over is how half of this discussion is ultimately predicated on the presumption that discrediting any aspect of a naturalistic claim opens the floodgates entirely to asserting that therefore, nailing a guy to some pieces of wood a couple thousand years ago is the answer to life, the universe, and everything.

    It's absolutely hilarious when you step back and look at it from its widest perspective.

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  11. barefoot hiker, I can't get over how questioning any aspect of current dogma in biology leads you guys to flying off the handle that someone doing that has to be a biblical fundamentalist. When atheists like Lewontin and Gould do it someone like Dennett is ready to ascribe a search for "skyhooks" to them instead of addressing the substance of their points.

    Dogmatic thinking isn't limited to the religious. It's quite common among atheists as well.

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    1. There's this easy way to recognize what kind of motivations are behind the criticism of scientific dogma.
      This little form "(dogma) has the shortcomings of (x,y,z) and these cannot be accounted for by small tweaks to the model."

      The short way to recognize people posing skyhooks (short of when they actually state that they are certain agency is behind it as atheistoclast has,) is when they do not bother to give any elaboration on what those shortcomings are.

      A person could conceivably listen to such an argument and then just have those details go entirely over their heads but in those cases there would be a fairly clear trail back to the source where it was laid out in full.

      No, here we essentially see "I'm criticizing dogma x." Why? "Because I know it is wrong. Soon everyone will feel foolish when they realize this as well."

      However, these people do attempt to point out a shortcoming here and there. In that case then it becomes somewhat more difficult to distinguish what is going on. Provided that you've got a college degree on the material it is trivial to recognize if a particular speaker ever understood the basics of cell biology. More specifically is a "shortcoming" happens to be a topic that was specifically presented to you as an undergraduate but the person in front of you is trying to say that it has implications almost exactly opposite to those you learned-
      Well they might be right about the conclusions, a lot of these matters get quite complicated, but at the very least you know that modern theories have no problem accommodating that information so these fall outside of that important format I provided. You can at this point try to tease out exactly how they decided that these implications must follow, but again, there's this extremely harsh inability to express the ideas without invoking divine agents.

      Anybody genuinely versed in the dogma they are opposing ought to be able to just describe what it doesn't and logically can't explain in completely materialistic terms, yet what we see is this intense eagerness to fill any gap they can make with what they believe.


      Now, I understand that arguing against dogma is frustrating. The system is very resistant to changing these ideas, but it should be. If you've got valid criticism then you need to remain composed and slowly build up more and more support for it until people can see that there's really something to it. Trying to change the system from outside of it is kind of doomed to failure when research takes the kind of money that we spend on it today.

      But that really kind of gets at the metric we're actually dancing around here: what's the test to see if the dogma is false? What study could you do to show that it doesn't stand up? This would establish actual faults, which is a crucial step before you replace the dogma with something else. Provided that you actually get past that step then you need to come up with tests that show how your proposed replacement handles the established shortcomings of the old model.

      It is this lack of any interest in doing that, that clues us in to the lack of honesty in these challenges to the dogma. It demonstrates clearly that they prefer the methods of con artists, never knew what they were talking about, and have no interest in the honest pursuit of knowledge.

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  12. ttc, you're kidding, right?

    Just how naive do you think the non-IDiot people here are? Do you really think that atheistoclast and other religious zealots aren't easily recognizable as religious zealots who argue against science and evolution solely because of their religious beliefs? Do you really think that atheistoclast and the other IDiot creationists are interested in discussing biology/evolution/science from a strictly scientific point of view in order to have a better understanding, and do you really think that IDiot creationists "question" scientists and/or science supporters, and scientific theories/hypotheses/inferences (what you call "dogma"), in a legitimate, respectful, knowledgeable, scientific way? Do you really think that IDiot creationists are just trying to help science figure things out and expand knowledge?

    And isn't it revealing of your mindset that you used the word "dogma" when referring to biology? If you want to see "dogma" look at your fairy tale religious beliefs.

    Oh, and where did barefoot hiker say anything about a "biblical fundamentalist"? Lots and lots of people who would not call themselves biblical fundamentalists believe that a guy now called jesus was nailed to some pieces of wood a couple of thousand year ago and/or that discrediting any aspect of a naturalistic claim opens the floodgates entirely to asserting that the alleged crucifixion is the answer (or at least a lot of the answer) to life, the universe, and everything.

    And "flying off the handle"? You call that "flying off the handle"? Well, it's clear that you're easily offended by anyone who makes less than complimentary comments about your imaginary sky friend jesus.

    You obviously also have a problem with "atheists" working in biology. Do you think that the field of biology would be better off if religious beliefs were included in it? If so, whose religious beliefs exactly? harold camping's beliefs? pat robertson's? sarah palin's? mitt romney's? mahmoud ahmadinejad's? ken ham's? casey luskin's? david klinghoffer's? barry arrington's? dense oleary's? gordon e mullings'? pope benedict's? tenzin gyatso's? michelle bachman's? rick santorum's? william dembski's? phillip johnson's? atheistoclast's? michael behe's? Yours? Someone else's?

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  13. Actually we do use the term dogma in biology. It's a bit tongue in cheek but just look up the central dogma of molecular biology.
    Now that particular dogma is shown false as soon as you know much about how viruses work and a number of other specialized cases but it still works as a general rule for how cells in general behave without such interruptions.

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    1. Sigh...

      http://sandwalk.blogspot.de/2007/01/central-dogma-of-molecular-biology.html

      http://sandwalk.blogspot.de/2011/05/central-dogma-strawman.html

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    2. I made some effort to explain exactly that detail except for the bit where you really have to get at the definitions with tweezers, which seems like the appropriate level of detail for an audience that has never heard the term dogma used in science...
      I'll try and make sure I convey the full details of blog posts in these much smaller (and often times rushed) comments in the future.

      Now lets turn the criticism your way. How much lazier can you get than a single word to indicate that you're looking down on someone that was attempting to be helpful and some links to articles about a petty gripe you've got over the usage of a term? You can apparently find reason to complain that someone dares to post here without having read every single blog entry but you can't bother to write up a little description about what your complaint is? Try and actually give people the short version and then let the links give support to your claim. "That's not exactly the central dogma" would have been plenty here but you couldn't take the time so you decided to eat up mine instead? You went out of your way to correct me but gave me no reason to actually discover what my mistake was except my neurotic concern (not a safe assumption, though perhaps somewhat moreso than the base line if you've read many of my posts,) over why you would feel this was important?
      Try a little harder.

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    3. I will, once you can explain how viruses violate the Central Dogma of Molecular Biology. Silence means that you didn't read the links, and have the dogma incorrect.

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    4. Shoku writes,

      Now that particular dogma is shown false as soon as you know much about how viruses work and a number of other specialized cases but it still works as a general rule for how cells in general behave without such interruptions.

      This statement strongly suggests that you don't understand the Central Dogma of Molecular Biology. That's why someone supplied you with a link to my posts on the subject.

      The Central Dogma of Molecular Biology states that one information flows into protein it can't flow back to nucleic acids. It's difficult to see how an understanding of viruses affects that rule. I started studying the molecular biology of viruses back in 1968 and I haven't seen anything that contradicts the Central Dogma.

      Feel free to post your data.

      Shoku also said ...

      You went out of your way to correct me but gave me no reason to actually discover what my mistake was ...

      I thought that providing a link to the correct definition of the Central Dogma was a rather polite way to let you discover your mistakes.

      Now we have to resort to less polite ways.

      Put up or shut up.

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    5. I read the links. The way I wrote that was wrong. Only RNA ever "goes back" into DNA and my textbooks and professors simply copied this long running mistake. My criticism is that anonymous couldn't bother to write an abstract of the idea. That anonymous could be bothered to present even a single sentence to explain the point that was being made. Were I busy this week I wouldn't have even followed the links because of that and I'd never have known that I was educated incorrectly.

      These a huge difference in the politeness of "you've got a bit of a misconception there. Please follow these links" and "snort, haha, yet another unwashed peasant has made a humiliating mistake! link, link." I exaggerate but short the amusement the latter isn't so far from how that reads. I thought I made it perfectly clear that I already think this wasn't a polite way to do that, and I explained precisely the minimum requirements to not just give an impression of politeness but push back the veil of ambiguity that masks the actual intention behind something like a sigh.

      But this really has nothing to do with the topic. I'm probably being too sensitive for reasons completely unrelated to any of this.


      I was sarcastic and snarky sure, but I really can't see how you'd think I was arguing that proteins get translated into DNA in any of that. Nonetheless, I will strive to be clearer in my writing, and try to avoid repeatedly giving impressions like that.

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    6. Apologies - it was a general sigh, as this discussion occurs so often (even in the primary literature) that is almost needs to go in an FAQ. It was not meant to single you out.

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