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New book: Junk DNA junked … in favour of what?

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Jonathan Wells’ book, The Myth of Junk DNA (Discovery, 2011), is now being advertised at Amazon:

According to the modern version of Darwin’s theory, DNA contains a program for embryo development that is passed down from generation to generation; the program is implemented by proteins encoded by the DNA, and accidental DNA mutations introduce changes in those proteins that natural selection then shapes into new species, organs and body plans. When scientists discovered forty years ago that about 98% of our DNA does not encode proteins, the non-protein-coding portion was labeled “junk” and attributed to molecular accidents that have accumulated in the course of evolution.

Recent books by Richard Dawkins, Francis Collins and others have used this “junk DNA” as evidence for Darwinian evolution and evidence against intelligent design (since an intelligent designer would presumably not have filled our genome with so much garbage). But recent genome evidence shows that much of our non-protein-coding DNA performs essential biological functions.

The Myth of Junk DNA is written for a general audience by biologist Jonathan Wells, author of Icons of Evolution. Citing some of the abundant evidence from recent genome projects, the book shows that “junk DNA” is not science, but myth.

Junk DNA was one of those ideas that just had to be true. Genome mapper and NIH head Francis Collins saw it as a slam dunk for his beloved Darwinism in his first book, The Language of God, (“Darwin’s theory predicts … That is exactly what is observed”) but seems to have changed his tune in his second, The Language of Life.

I’ll be interviewing Wells on the book next week, but in the meantime, two questions occur to me: To what extent did Darwinism cause the myth to be retained longer than it otherwise would be? Given that Darwinists must now be in search of another guiding myth, any idea out there which one it will be?

Now, one prediction:

Darwinists who used to point to all the alleged junk in DNA, as Collins did, will resort – seeing anything they don’t like – to saying God wouldn’t have done it that way” implying that, unlike the rest of us, they are on familiar terms with God, and cold take over the desk themselves on his lunch break, with no interruption in service.

I thought Disney covered that one off in The Sorcerer’s Apprentice.

Comments
Larry Moran: "To me it sounds like you are questioning our intelligence. Do you have another way of putting it that doesn’t make us look stupid?" No. I do not question your intelligence or that of the other prominent ID critics (although I'm not so sure about some of the commenters I have read in this and other blogs). Notice that in my post I (carefully and deliberately) said that your implication that ID proponents were stupid makes you LOOK stupid, not that you ARE stupid. My beef is with you and other ID critics attempting to win points in the debate by denigrating the intelligence of your opponents, when beyond any question people like Behe and Dembski and the others I mentioned above are anything but stupid. It goes beyond an intelligent discussion of the issues into personal attack and insult, and these men have done nothing to deserve such treatment. That's why I say it does you no credit, and in fact damages your credibility.Bruce David
March 21, 2011
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Larry, I've been batting around another problem that perhaps you can help me with. You see Larry the problem starts like this, Quantum Entanglement falsifies local realism (reductive materialism),,, The Failure Of Local Realism - Materialism - Alain Aspect - video http://www.metacafe.com/w/4744145 Physicists close two loopholes while violating local realism - November 2010 Excerpt: The latest test in quantum mechanics provides even stronger support than before for the view that nature violates local realism and is thus in contradiction with a classical worldview. http://www.physorg.com/news/2010-11-physicists-loopholes-violating-local-realism.html Quantum Measurements: Common Sense Is Not Enough, Physicists Show - July 2009 Excerpt: scientists have now proven comprehensively in an experiment for the first time that the experimentally observed phenomena cannot be described by non-contextual models with hidden variables. http://www.sciencedaily.com/releases/2009/07/090722142824.htm ,, Moreover Larry, Quantum Entanglement/Information, is found to be instantaneous and universal in its actions; Wheeler's Classic Delayed Choice Experiment Excerpt: So it seems that time has nothing to do with effects of quantum mechanics. And, indeed, the original thought experiment was not based on any analysis of how particles evolve and behave over time – it was based on the mathematics. http://www.bottomlayer.com/bottom/basic_delayed_choice.htm Light and Quantum Entanglement Reflect Some Characteristics Of God - video http://www.metacafe.com/watch/4102182 ,,, And yet Larry, this 'spooky' Quantum Entanglement/Information effect, which falsified the 'local realism' of particles, and blatantly defies constraints of time of space, is now found in molecular biology,,, Quantum Information/Entanglement In DNA & Protein Folding - short video http://www.metacafe.com/watch/5936605/ Further evidence that quantum entanglement/information is found throughout entire protein structures: https://uncommondescent.com/intelligent-design/rescue-proteins-leave-evolutionists-in-the-ditch/#comment-373214 ,,, Thus my problem is as such Larry, the effect of quantum entanglement/information needs to be explained by a cause that is itself not constrained by time and space yet neo-Darwinism purports to explain all the wonder and diversity we see in life on earth by Random Variations/Mutations of particles.,, Thus Larry, how can a quantum effect in biology be explained by a material cause when the quantum effect falsified material particles as its causation in the first place? Appealing to the probability of various configurations of material particles simply will not help since a cause must be supplied beyond material particles! Do you see the problem Larry?bornagain77
March 21, 2011
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nullasalus asks,
Of course, that’d just lead me to ask again: If someone thinks your interpretation of the evolutionary data is wrong, Larry, are they calling you stupid?
In many cases there is genuine scientific controversy about some evolutionary interpretation. Since the science can't settle the issue right now, both sides have valid positions and neither side is stupid. (Although one side or the other might propose some stupid arguments to support their case.) In cases where there is no genuine scientific controversy, the anti-science proponents are usually either stupid or ignorant. Sometimes both. People who claim that the Earth is only 6000 years old (Young Earth Creationists) are good examples. Another example would be people who claim that the existence of junk DNA has been scientifically disproven. We've just seen a third example in one of the earlier comments: namely, people who claim that the sequences of the human and chimp genomes pose a problem for evolution. Larry Moran
March 21, 2011
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I’ve never thought of it that way. I suppose “atheists,” “agnostics,” and “Deists” would just about cover all the possibilities. Why do you ask? I don't know about Collin, but I'd ask because Jerry Coyne suggests otherwise. To him, to accept evolution as teleological means you reject evolutionary biology as scientists understand it. Are you saying the evolutionary biology, insofar as it is a science, is silent on the question of guidance or teleology? Because if so, it looks like your view is in dispute.nullasalus
March 21, 2011
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bornagain77 asks,
So basically Larry, do you see the problem here????
Nope. I'm well aware of all the papers you quoted and I don't see how any of them calls into question the idea that most of our genome is junk. They've all been discussed and debated among the experts. It will be fun to see how Jonathan Wells handles all the objections to those papers. I sure he's going to give the counter-arguments the full attention they deserve. Right? (Not holding my breath.)
you got far too much variation to account for, with precious little resources for evolution to experiment with.
I don't have any idea what you're talking about. Do you?
So again Larry, how much of the DNA do you say is functional?
I say that about 10% of our genome contains essential DNA that could not be removed without affecting the survivability of individuals. It's a much higher percentage in fruit flies and yeast and in bacteria it's about 90%. Larry Moran
March 21, 2011
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Larry Moran, Here are the facts. I didn't ask about junk DNA. You suggested that to view someone as wrong on a topic within their field, despite their having the right credentials and "spending their whole lives" studying said field, amounted to an accusation of stupidity. Again, here's what you said: I’m curious about something. There are quite a few scientists with the same credentials who fully accept evolution as the best explanation. They reject your criticisms of evolution. Some of them—I am one—have spend a lifetime studying evolution. You must honestly believe that we have failed to see the obvious flaws in evolution in spite of the fact we have credentials and many years of experience studying evolution. To me it sounds like you are questioning our intelligence. Do you have another way of putting it that doesn’t make us look stupid? I pointed out that if disagreeing with someone about a topic of evolution despite having "credentials and many years of experience studying evolution" amounted to a charge of stupidity, then you must think a fair share - maybe the lion's share - of evolutionary biologists are stupid, and that they in turn must think you're stupid. You insist now that 'neither side is stupid'. Alright, then apparently mere disagreement isn't a charge of stupidity after all. Or maybe you just aren't following your own reasoning. It would be very misleading to imply that the case against junk DNA has been proven to the satisfaction of informed evolutionary biologists and molecular biologists. That’s simply untrue. All of the data is in dispute and neither side is even close to surrender. So... what? There's two sides to this conflict, both sides think they're right and the other side is wrong, but all of the data is in dispute and no one is satisfied with the case one way or the other? Are you really telling me that if I ask any given person on either side of this dispute, that their response will be "This is what I think is the case. But all of the data is in dispute"? Not, "This is what I think is the case: The data says this, and the other guys are wrong."? Or respond to 'But Larry Moran disagrees' with "Larry is mistaken and isn't interpreting the data properly"? I'm pretty sure that sometimes scientists disagree, and that one interpretation one side says is in dispute, another side says "Talk of dispute is a load. This is the right interpretation, the other guys are wrong." Of course, that'd just lead me to ask again: If someone thinks your interpretation of the evolutionary data is wrong, Larry, are they calling you stupid? Are you calling them stupid if you say their interpretation is wrong?nullasalus
March 21, 2011
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bornagain77 asks,
Larry Moran, would you care to hazard a guess on what percentage of DNA is functional?
It depends on the genome. In the case of humans, I'm certain that more than half of our genome is junk [Genomes & Junk DNA]. As for the rest, in my opinion only about 10% has a function. That means that 90% is junk.
To put this mildly Larry, this huge +80% difference between chimps and humans is more than a slight problem for evolutionary materialists, ...
I guess we must be really stupid if we don't see a problem, right? Have you considered the possibility that your facts, and your understanding of evolution, might be wrong and that's why you see imaginary problems? Larry Moran
March 21, 2011
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Collin asks,
What term would you prefer that we use to refer to those who believe in non-teleological evolution?
I've never thought of it that way. I suppose "atheists," "agnostics," and "Deists" would just about cover all the possibilities. Why do you ask? Larry Moran
March 21, 2011
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nullasalus asks about junk DNA,
So, Larry, putting aside your estimations about what percentage of whom believed what… How do you prefer we frame this? Is it that you think the majority of evolutionary biologists are stupid? Or that a great many evolutionary biologists think you’re stupid?
Here are the facts. Something like 99.9% of evolutionary biologists agree that genomes contain junk DNA. Pseudogenes are the best example. A somewhat smaller percentage (99%) understand that degenerative virus genomes and transposons are another form of junk pseudogenes. Thus, the existence of junk DNA is not in dispute. It's a fact. The scientific debate is over how much of the genome is junk. It's also a fact that 99.9% of the experts know that noncoding DNA has lots of functions. Most of these functions have been known for 40-50 years. You're on safe grounds as long as you don't state or imply that the consensus view was that all noncoding DNA is junk. That would be a lie. The proper framework for the discussion is to point out that the experts in the field are debating whether there's a lot of junk DNA in our genome or just a small amount. Some of the issues have been decided but there's still lots of room for differing opinions. It would be very misleading to imply that the case against junk DNA has been proven to the satisfaction of informed evolutionary biologists and molecular biologists. That's simply untrue. All of the data is in dispute and neither side is even close to surrender. I'm looking forward to Wells' new book. It will provide plenty to blog about 'cause I just know he's going to distort the evidence and frame the discussion in terms of a diatribe against evolution. With respect to the genuine scientific controversy, neither side is stupid at the present time. The only stupid people are those who deny that there's a genuine scientific controversy. Larry Moran
March 21, 2011
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,,,as well Larry, not only are novel proteins rare but existing proteins are themselves found to be severely be intolerant to any variation,,, Stability effects of mutations and protein evolvability. October 2009 Excerpt: The accepted paradigm that proteins can tolerate nearly any amino acid substitution has been replaced by the view that the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major constraint on protein evolvability,, http://www.ncbi.nlm.nih.gov/pubmed/19765975 Severe Limits to Darwinian Evolution: - Michael Behe - Oct. 2009 Excerpt: The immediate, obvious implication is that the 2009 results render problematic even pretty small changes in structure/function for all proteins — not just the ones he worked on.,,,Thanks to Thornton’s impressive work, we can now see that the limits to Darwinian evolution are more severe than even I had supposed. http://www.evolutionnews.org/2009/10/severe_limits_to_darwinian_evo.html#more Proteins with cruise control provide new perspective: "A mathematical analysis of the experiments showed that the proteins themselves acted to correct any imbalance imposed on them through artificial mutations and restored the chain to working order." http://www.princeton.edu/main/news/archive/S22/60/95O56/ As well Larry Moran, finding severe polyfunctionality in the genome and protein interactions, strongly indicates there are no 'Junk proteins' for evolution to even experiment with in the first place; Astonishing DNA complexity demolishes neo-Darwinism - Alex Williams Excerpt: Not only has the ENCODE project elevated UTRs out of the ‘junk’ category, but it now appears that they are far more active than the translated regions (the genes), as measured by the number of DNA bases appearing in RNA transcripts. Genic regions are transcribed on average in five different overlapping and interleaved ways, while UTRs are transcribed on average in seven different overlapping and interleaved ways. Since there are about 33 times as many bases in UTRs than in genic regions, that makes the ‘junk’ about 50 times more active than the genes. http://creation.com/images/pdfs/tj/j21_3/j21_3_111-117.pdf Scientists Map All Mammalian Gene Interactions – August 2010 Excerpt: Mammals, including humans, have roughly 20,000 different genes.,,, They found a network of more than 7 million interactions encompassing essentially every one of the genes in the mammalian genome. http://www.sciencedaily.com/releases/2010/08/100809142044.htm Poly-Functional Complexity equals Poly-Constrained Complexity http://docs.google.com/Doc?docid=0AYmaSrBPNEmGZGM4ejY3d3pfMjdoZmd2emZncQ DNA - Evolution Vs. Polyfuctionality - video http://www.metacafe.com/watch/4614519 ,,,, So basically Larry, do you see the problem here???? you got far too much variation to account for, with precious little resources for evolution to experiment with. So again Larry, how much of the DNA do you say is functional?bornagain77
March 21, 2011
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Larry Moran, would you care to hazard a guess on what percentage of DNA is functional? Asking Darrel Falk to Pick a Number, Any Number Excerpt: So I have a question for him: Exactly what fraction of the transcribed 88.5% of our DNA are you willing to say "plays no role" or can be harmful? All I am asking for is a prediction, such as "90% of these DNA letters is superfluous" ("or 79.5% of the RNAs are nonsensical"). Since he also said "almost certainly" in the above statement, he must have a figure in mind. So I say pick a number, any number...But to be a good sport, I'll show my prediction: All of the expressed 88.5% of our DNA has diverse roles in our development. http://www.evolutionnews.org/2010/03/asking_darrel_falk_to_pick_a_n032871.html#more So what do you say the number is Larry Moran? A ball park figure will be fine. The reason I ask Larry is that the numbers just aren't working for neo-Darwinism. First even neglecting the fact that population genetics shows that it would take far too long to fix even a single coordinated beneficial mutation in the hominid lineage,,, Waiting Longer for Two Mutations, Part 5 - Michael Behe Excerpt: the appearance of a particular (beneficial) double mutation in humans would have an expected time of appearance of 216 million years, http://behe.uncommondescent.com/2009/03/waiting-longer-for-two-mutations-part-5/ ,,, is that scientists have uncovered entire genes that are completely unique to Humans,,, Human Gene Count Tumbles Again - 2008 Excerpt: Applying this technique to nearly 22,000 genes in the Ensembl gene catalog, the analysis revealed 1,177 “orphan” DNA sequences. ,,, After careful genomic comparisons, the orphan genes were found to be true to their name — they were absent from both primate genomes. http://www.sciencedaily.com/releases/2008/01/080113161406.htm ,,,And Larry, contrary to the preceding study of them dismissing the 1,177 ORFan genes as 'junk', simply because they are unique, ORFan genes are actually found to be functional. A survey of orphan enzyme activities Abstract: We demonstrate that for ~80% of sampled orphans, the absence of sequence data is bona fide. Our analyses further substantiate the notion that many of these (orfan) enzyme activities play biologically important roles. http://www.biomedcentral.com/1471-2105/8/244 ,,,As well Larry, completely contrary to evolutionary thought, these 'new' ORFan genes are recently found to be just as essential as 'old' genes for maintaining life,,, Age doesn't matter: New genes are as essential as ancient ones - December 2010 Excerpt: "A new gene is as essential as any other gene; the importance of a gene is independent of its age," said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. "New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked." http://www.sciencedaily.com/releases/2010/12/101216142523.htm ,,,But Larry the overwhelming problems is that finding JUST ONE completely unique gene is to be considered so rare as to defy comprehension,,, Could Chance Arrange the Code for (Just) One Gene? "our minds cannot grasp such an extremely small probability as that involved in the accidental arranging of even one gene (10^-236)." http://www.creationsafaris.com/epoi_c10.htm ,,,On top of that 'problem' Larry, +80% of proteins are found to be different between man and chimps: Chimps are not like humans - May 2004 Excerpt: the International Chimpanzee Chromosome 22 Consortium reports that 83% of chimpanzee chromosome 22 proteins are different from their human counterparts,,, The results reported this week showed that "83% of the genes have changed between the human and the chimpanzee—only 17% are identical—so that means that the impression that comes from the 1.2% [sequence] difference is [misleading]. In the case of protein structures, it has a big effect," Sakaki said. http://cmbi.bjmu.edu.cn/news/0405/119.htm Eighty percent of proteins are different between humans and chimpanzees; Gene; Volume 346, 14 February 2005: http://www.ncbi.nlm.nih.gov/pubmed/15716009 ,,,To put this mildly Larry, this huge +80% difference between chimps and humans is more than a slight problem for evolutionary materialists, for even neo-Darwinists themselves admit that finding unique functional proteins is exceeding rare,,, How Proteins Evolved - Cornelius Hunter - December 2010 Excerpt: Comparing ATP binding with the incredible feats of hemoglobin, for example, is like comparing a tricycle with a jet airplane. And even the one in 10^12 shot, though it pales in comparison to the odds of constructing a more useful protein machine, is no small barrier. If that is what is required to even achieve simple ATP binding, then evolution would need to be incessantly running unsuccessful trials. The machinery to construct, use and benefit from a potential protein product would have to be in place, while failure after failure results. Evolution would make Thomas Edison appear lazy, running millions of trials after millions of trials before finding even the tiniest of function. http://darwins-god.blogspot.com/2010/12/how-proteins-evolved.htmlbornagain77
March 21, 2011
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scordova says,
The quotation can be found on page 45. A full text can be found online at: http://www.arvindguptatoys.com.....owkins.pdf The page numbers of the PDF browser don’t necessarily align with the page numbers of the orignal books. On my PDF browser page 45 of Dawkins book is page 68 of my browser. The original page numbers can be seen in the PDF, and that should help you find the quote. It is the end of chapter three. Regarding the tandem repeats the quote was from Skeptic, “How Evolution Increases Information in the Genome”. It was not from his selfish gene book.
Thanks. I didn't have a problem with the first quotation because Dawkins is ascribing a function to this "apparently surplus DNA." He thinks that much of the extra DNA is selfish DNA. In fact, he repeats this claim in the article you quote below.
There are many nonfunctional pseudogenes (see below) and lots of repetitive nonsense, useful for forensic detectives but not translated into protein in the living cells. The crested newt has a bigger “hard disc” than we have, but since the great bulk of both our hard discs is unused, we needn’t feel insulted. Related species of newt have much smaller genomes. Why the Creator should have played fast and loose with the genome sizes of newts in such a capricious way is a problem that creationists might like to ponder. From an evolutionary point of view the explanation is simple (see The Selfish Gene pp 44?–?45 and p 275 in the Second Edition).
I did have a problem with the second part of your quotation since it was quite inconsistent with anything Dawkins would have said in 1976. You cleared that up by admitting that you made a mistake. The second quotation is from an article written 23 years later at a time when Dawkins has come to accept the existence of non-functional pseudogenes and degenerate transposons. I'm sorry you screwed up the original attribution but I appreciate the fact you admitted your mistake. Larry Moran
March 21, 2011
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Molch at 9: "So, how much of the 98% of our DNA that does not code for proteins has been found to perform essential biological functions? Any educated (and by that I mean: evidence-based) guesses in Wells’ book how many % might actually perform essential biological functions and what types of functions those are?" Molch, it's very difficult to form an educated guess about a large unknown, but I will ask Wells for an opinion when I interview him. Thanks for the suggestion. I can offer one suggestion of my own, which is: Look at the history of the 200 "vestigial" organs of the human body, almost all of which turned out to have a function, albeit a redundant one. Note: Confusion is created by two different meanings of the word "redundant": 1. The administrative meaning - For example, two different bureaucracies requiring functionally identical permits for the same project. Not only is it unnecessary, it is a huge source of avoidable error, conflict, and waste. 2. The systems meaning: A system works better if a number of components can participate in the same job as one of their functions. For example, all hospital medical staff know the Heimlich manoeuvre, to save choking victims. Here, redundancy pays. The benefit is that any medical personnel who spot the case can act. I suppose the human body often works this way, and seldom the first way. So if asked to predict the fate of junk DNA, I would be inclined to say that it will prove useful far more likely than not, simply because that is the way the body works in general, but some study may be required to discover the exact function of specific codes.O'Leary
March 21, 2011
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Dr. Moran, What term would you prefer that we use to refer to those who believe in non-teleological evolution? CollinCollin
March 21, 2011
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Dawkins in 1999: creationist might spend some earnest time speculating on why the Creator would bother to litter genome with untranslated pseudogenes
Err, Richard, in 2010 we have some answers as to what the Creator had in mind as hinited in Wiki:
some pseudogenes play a role in regulating protein-coding transcripts.[25][26] In June 2010, Nature published an article showing the mRNA levels of tumour suppressor PTEN and oncogenic KRAS is affected by their pseudogenes PTENP1 and KRAS1P. This discovery demonstrated an miRNA decoy function for pseudogenes and identified their transcripts as biologically active units in tumor biology; thus attributing a novel biological role to expressed pseudogenes, as they can regulate coding gene expression,
scordova
March 21, 2011
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Dr. Moran asked: P.S. Your Dawkins quotation from The Selfish Gene doesn’t seem right to me since it conflicts with statements he made later. Can you please supply a page number?
Dr. Moran, The quotation can be found on page 45. A full text can be found online at: http://www.arvindguptatoys.com/arvindgupta/selfishgene-dowkins.pdf The page numbers of the PDF browser don't necessarily align with the page numbers of the orignal books. On my PDF browser page 45 of Dawkins book is page 68 of my browser. The original page numbers can be seen in the PDF, and that should help you find the quote. It is the end of chapter three. Regarding the tandem repeats the quote was from Skeptic, "How Evolution Increases Information in the Genome". It was not from his selfish gene book. Available here: How Evolution Increases Information in the Genome
creationist might spend some earnest time speculating on why the Creator would bother to litter genome with untranslated pseudogenes and junk tandem repeats.
Back to the question:
P.S. Your Dawkins quotation from The Selfish Gene doesn’t seem right to me since it conflicts with statements he made later.
I suppose he'll have to admit he changed his mind or pretend he never said what is now in the historical record of his own writings. Regarding Tandem Repeats:
The fact that tandem repeats occur frequently throughout the genomes of many different species and are often highly conserved between species suggests that they serve important functions (Tompa, 2003; Buschiazzo and Gemmel, 2006). Evidence that tandem repeats can affect brain function and behavior has recently been reviewed (Fondon et al., 2008). However, tandem repeats can also affect other biological processes in a wide range of organisms, from yeast to humans, and may play important roles in evolution Genome Tandem Repeat Polymorphisms
Looks like Richard will have some backpedaling to do. :-)scordova
March 20, 2011
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I’m curious about something. There are quite a few scientists with the same credentials who fully accept evolution as the best explanation. They reject your criticisms of evolution. Some of them—I am one—have spend a lifetime studying evolution. You must honestly believe that we have failed to see the obvious flaws in evolution in spite of the fact we have credentials and many years of experience studying evolution. To me it sounds like you are questioning our intelligence. Do you have another way of putting it that doesn’t make us look stupid? Geez, Larry. By that standard anytime anyone disagrees with anyone about a topic involving their own profession, someone's being called stupid. And if disagreement suffices for an accusation of stupidity, then being shown to be wrong would have to be a demonstration of one's stupidity, eh? So with that in mind... As for junk DNA, a great many evolutionary biologists are skeptical about the existence of junk DNA. I think they’re wrong but that’s not the point. So, Larry, putting aside your estimations about what percentage of whom believed what... How do you prefer we frame this? Is it that you think the majority of evolutionary biologists are stupid? Or that a great many evolutionary biologists think you're stupid? (Of course, the alternative is that no, simply disagreeing with a professional about a subject in his field doesn't add up to a charge of stupidity. But if you believe it does, well...)nullasalus
March 20, 2011
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... I would stop referring to him as an Intelligent Design Creationist and an IDiot.
The hypocrite takes a bow. - - - - - - - "Sincerity makes the very least person to be of more value than the most talented hypocrite." - C SpurgeonUpright BiPed
March 20, 2011
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Some more numbers: total size of the RNA polymerase II “transcriptome” – 1.3*10^9 bp (from the preceding comment, assuming that these are released from moderation in the order in which I posted them) total size of the “stable” transcriptome (that which is not thrown away) – 10^8 bp percentage of all polII-transcribed RNA that is thrown away – 92% Again, readers who have looked through Wells’ book might tell us just how much of this 92% Wells proves to have function. (This is a tough one, since the RNA actually is not present in the cell, expect transiently). Please be as specific and quantitative as possible.Arthur Hunt
March 20, 2011
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Some (very round) numbers to keep in mind when discussing this subject: # of protein-coding genes in the human genome – 30,000 Average size of a protein – 1000 amino acids Average protein-coding capacity of a typical gene – 3000 nucleotides 1. Total number of protein-coding nucleotides – 10^8 nucleotides Total number of introns – 200,000 Average intron length – 6000 bp Total intronic content – 1.2*10^9 bp “functional” intronic sequences (these include splicing signals and intronic enhancer and suppressor elements) – 600 bp per intron (a very generous overestimate, since most introns probably have a fraction of this extent of functional sequence) 2. total “functional” intronic sequence content – 1.2*10^8 bp promoter elements per gene – 100 (this is probably a huge overestimate, but I have decided to round up to the nearest order of magnitude) size of a typical promoter element – 100 bp (another huge overestimate, made to give every benefit of the doubt to supporters of Wells et al.; in particular, it assumes that every human gene includes promoter elements derived from repetitive DNA, that could conceivably be as large as 100 bp) 3. total content of functional DNA in promoters – 3*10^8 bp upper range of estimates of non-coding RNAs (outside of stable RNAs) – 10,000 size of non-coding RNAs (another huge overestimate) – 10,000 nts 4. total content of non-coding RNAs – 10^8 bp total of “functional” DNA – sum of #’s 1-4 = 6.2 *10^8 bp fraction of the human genome that is functional (assume a haploid genome of 3*10^9 bp) – 20% So, even when we grant Wells et al. their each and every wish when it comes to functionality of non-protein-coding DNA, we can only account for 20% of the human genome. (Readers should note that this is a wild over-estimate, but it serves as a baseline for discussion.) So, for readers here who have looked through Well’s book – what specific and tangible data do Wells point to (or describe – maybe he has been doing some actual experiments) that support the standard ID assertion that there is no such thing as junk DNA? Not vague reference to experiments not done, not hopeful or wishful thinking, but solid experimental results that allow us to state that the remaining 80% of the human genome has some specifiable (and specific) function.Arthur Hunt
March 20, 2011
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Bruce David says,
Michael Behe, Jonathan Wells, Stephen Meyer, William Dembski, Douglas Axe, Phillip Johnson, Michael Denton, and J.C. Sanford, to name a few, are far from stupid, and they have the credentials to prove it. All have Ph.D.’s from major universities. Most have published papers in peer reviewed journals. One clerked for a Supreme Court Justice. Most have taught at the University level, many in top institutions, etc., etc. To imply that these men are stupid does you no credit.
I'm curious about something. There are quite a few scientists with the same credentials who fully accept evolution as the best explanation. They reject your criticisms of evolution. Some of them—I am one—have spend a lifetime studying evolution. You must honestly believe that we have failed to see the obvious flaws in evolution in spite of the fact we have credentials and many years of experience studying evolution. To me it sounds like you are questioning our intelligence. Do you have another way of putting it that doesn't make us look stupid? Larry Moran
March 20, 2011
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scordova says,
That’s revisionist history. Darwinists lined up on both sides of the issue, only lately pretending the majority rejected the notion of junk DNA.
So, we agree that evolutionary biologists lined up on both sides of the issue, right? Therefore, it would be completely wrong to say or imply that junk DNA was a myth that all Darwinists fell for, right? I hope you will correct all of your fellow travelers who make the mistake of assuming that all evolutionary biologists believed in junk DNA. Indeed, I expect that the new book will be full of statements from evolutionary biologists that dispute the notion of junk DNA. This is a genuine scientific controversy and it has been for 40 years. I believe that the majority of "Darwinists" did reject the notion of junk DNA but perhaps that's because I'm using a different definition of "Darwinist"? P.S. Your Dawkins quotation from The Selfish Gene doesn't seem right to me since it conflicts with statements he made later. Can you please supply a page number? Larry Moran
March 20, 2011
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Jonathan M asks,
Since you are so keen to see us stop (in your opinion) ‘mis-using’ the term “Darwinism”, would you care to stop using the terms “creationist” and “IDiot” to refer to ID proponents?
If Intelligent Design Creationists would stop referring to everyone as Darwinists then it wouldn't be right to call them IDiots. Some years ago I made a deal with Bill Dembski. If he would stop using the incorrect term "Darwinist" and stop misrepresenting evolution then I would stop referring to him as an Intelligent Design Creationist and an IDiot. It was too much for him to give up. His part of the bargain only lasted a few months. As for junk DNA, a great many evolutionary biologists are skeptical about the existence of junk DNA. I think they're wrong but that's not the point. The point is that it is completely incorrect to imply that all "Darwinists" believed in the "myth" of junk DNA. What I don't understand is whether Denyse and her friends are deliberately misrepresenting evolutionary biology or whether they are just uniformed. Larry Moran
March 20, 2011
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So, how much of the 98% of our DNA that does not code for proteins has been found to perform essential biological functions? Any educated (and by that I mean: evidence-based) guesses in Wells' book how many % might actually perform essential biological functions and what types of functions those are?molch
March 20, 2011
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QuiteID, Thank you, I stand corrected.Bruce David
March 20, 2011
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Bruce David, excellent point. A minor correction, though: Phillip Johnson does not have a Ph.D. He has a law degree.QuiteID
March 20, 2011
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Larry Moran, I'm sorry, but I have to weigh in on this one also. My biggest gripe with the opponents of ID is their habit of trashing the intelligence of the proponents of ID. You may disagree with them, but to call them IDiots and thus imply that they are stupid only makes YOU look stupid. Michael Behe, Jonathan Wells, Stephen Meyer, William Dembski, Douglas Axe, Phillip Johnson, Michael Denton, and J.C. Sanford, to name a few, are far from stupid, and they have the credentials to prove it. All have Ph.D.'s from major universities. Most have published papers in peer reviewed journals. One clerked for a Supreme Court Justice. Most have taught at the University level, many in top institutions, etc., etc. To imply that these men are stupid does you no credit. And by the way, your inability to distinguish between proponents of ID and creationists, when that distinction has been made crystal clear by ID proponents any number of times doesn't attest to any notable intelligence on your part, either. It is my opinion that the reason you and others fighting tooth and nail against ID resort to this tactic is that you are genuinely afraid that in an unbiased competition you will be unable to prevail in the court of public opinion. I can sympathize. I don't think you will be able to, either. Even so, resorting to the shabby tactic of belittling the intelligence of your opponents is not going to help you in the long run, and only serves to destroy your credibility.Bruce David
March 20, 2011
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Larry Moran -- Since you are so keen to see us stop (in your opinion) 'mis-using' the term "Darwinism", would you care to stop using the terms "creationist" and "IDiot" to refer to ID proponents? JJonathan M
March 20, 2011
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Adaptationism (Darwinism) is NOT consistent with junk DNA. That’s why Darwinists usually reject junk DNA. .... Those Darwinists are the ones who OPPOSE the concept of junk DNA. Dawkins is a good example.
That's revisionist history. Darwinists lined up on both sides of the issue, only lately pretending the majority rejected the notion of junk DNA.
Biologists are racking their brains trying to think what useful task this apparently surplus DNA is doing. But from the point of view of the selfish genes themselves, there is no paradox. The true “purpose” of DNA is to survive, no more and no less. The simplest way to explain the surplus DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA. .... “creationists...might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA.” Richard Dawkins Selfish Gene
You don't seem to well adapted for internet debate. That claim that Dawkins opposed the concept of junk is a howler.
I am not a Darwinist. Larry Moran
The goldmine quote of the day!scordova
March 20, 2011
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Excellent point upright! and Moran just to inform you, if you will even listen to an 'IDiot' (your words not mine), Junk DNA is used by all neo-Darwinists, no matter what their particular stripes, wherever and whenever it will suit their purpose, especially when they try to establish the case for common ancestry! Francis Collins, Darwin of the Gaps, and the Fallacy Of Junk DNA - video http://www.evolutionnews.org/2010/11/francis_collins_is_one_of040361.htmlbornagain77
March 20, 2011
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