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Sternberg Plasters Matheson

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“I think this will come to be a classic story of orthodoxy derailing objective analysis of the facts, in this case for a quarter of a century…The failure to recognize the full implications of this-particularly the possibility that the intervening noncoding sequences may be transmitting parallel information in the form of RNA molecules-may well go down as one of the biggest mistakes in the history of molecular biology.”

—John Mattick, Molecular biologist, University of Queensland, quoted in Scientific American

Steve Matheson, a teacher and Darwinist promoter at a religious school, repeats the biggest mistake in molecular biology. In contrast, Richard Sternberg, an evolutionary biologist at the Biologic Institute, defends objective analysis of the facts. See Sternberg’s defense of the facts against Matheson’s Darwinist ideology in the essay: Mathesons Intron Fairytale.

Comments
What I find surprising is that Matheson had already clarified what he meant by "Junk-DNA" not having a function in a previous blog post, which he specifically referenced in his criticism of Meyer's statement. This appears to be another example of the sort of misrepresentation he was referring to. You can find a follow up, in which Matheson addresses both his earlier post and Sternberg's reply here.veilsofmaya
June 14, 2010
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Of note to "Junk DNA"; Astonishing DNA complexity demolishes neo-Darwinism - Alex Williams 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.pdfbornagain77
June 14, 2010
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Art, Feel free to state what you think or link to what you may have already written. By the way, thanks for visiting. Salscordova
June 14, 2010
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Sal, Sternberg and Wells have made their positions clear. I was asking what you thought. More generally, should I believe that the current generation of ID proponents is going to be making the same (quite mistaken) claim? gpuccio, You say:
It’s not important to know if all introns cooperate in alternative splicing, or not. According to available data, it is perfectly reasonable to assume that many, probably most, of them do.
What data are you speaking of? Please be specific, and explain the contradiction with data such as is found in Sultan et al. (Science 15 August 2008: 956-960):
We observed 95% of the splicing events expected in this data set, given the current sequencing depth (Table 1) (16). We identified 4096 previously unknown splice junctions in 3106 genes, mostly called by single reads and unique to one cell type (Table 1). Many of these junctions were associated with actively transcribed genes exhibiting more exons than average, pointing to rare splicing events. Approximately 6% of all splice-junction reads identified AS events (6416 junctions in 3916 genes HEK and 5195 junctions in 3262 genes in B cells) (table S9).
In case the terminology is not clear, these authors are stating that their data shows that 6% of all splice junctions are from AS events. This is very, very different from Sternberg's and Wells number (100%). As far as the functional vs. non-functional business, there is one key fact that IDists ignore in all of this. I refer, of course, to the fact that intronic RNA is made and then thrown away. We don't call it "junk" because we don't know if it does anything, we call it so because it is discarded. (OK, OK, so maybe we should be calling it "garbage DNA" instead of "junk DNA".) As I learned on the 14th of May, and in many, many past discussions, the "garbage disposal" may be a central feature of the cell, required for all manner of molecular, physiological,and organismal function, but it is not on the IDists' radar screen.Arthur Hunt
June 14, 2010
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Arthur Hunt: I can certainly agree with the following claims made by me: a) It's not important to know if all introns cooperate in alternative splicing, or not. According to available data, it is perfectly reasonable to assume that many, probably most, of them do. b) It is, in the same way, perfectly reasonable to assume that introns take part also in other regulatory functions. Although many of them may at present not be known or clarified. c) What is absolutely not reasonable, instead, is to stick to a model according to which more than 30% of our genome (or more than 96%, if we add all other forms of non coding DNA) is non functional. Or to pretend that there are scientific reasons to think that way. Even if there were no clues to the function of non coding DNA (which, today, is certainly not true, because those clues are rapidly accumulating), two things remain certainly true: 1) Stating that 96% of our genome is non functional only because we don't understand its function is, at best, an argument from ignorance, and I would say a very big and bad one. Being understood by science is not certainly the only parameter to truth, otherwise science could not go on understanding new things. You certainly understand that science works by reasonable inferences, which try to explain whta is not yet known in detail: they are called theories, and they are the stuff of which science is made. 2) There is at least one heavy argument against the non functional model, and it is the fact that coding DNA is completely insufficient to explain what we observe in living beings: indeed, while it can explain the basic mass information for coding proteins, it explains very little of how all cellular processes are regulated and controlled in a differential way in all cell types and states, not to speak of all other complex higher level regulations. In that situation, the most reasonable assumption is that the remaining part of the genome can have an important part in all those processes we still don't understand. That's why all reasonable people have always believed that non coding DNA would be shown to be of regulatory importance, when unreasonable people with self-assured authority proclaimed that it was junk, probably only to support their own theories. Now, the crowd of "non-junk" people has certainly grown, well beyond the ID circle (maybe because facts continue to come in favour of that position?). But, as I said before, it's reassuring to find at least some people who remain consistent with their previous errors.gpuccio
June 14, 2010
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Art, I presume you can correspond with Rick or Jonathan and get their exact position. I'd prefer to do that than agree or disagree with your characterization of what they assert.scordova
June 13, 2010
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Are we all in agreement with Sternberg and Wells when they claim that every intron in every human gene whose RNAs are subject to alternative splicing are themselves alternatively spliced?Arthur Hunt
June 13, 2010
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bevets:
Todd Wood thinks Sternberg was unduly harsh. The vast majority of Dr. Sternberg's commenst was a careful and considered recitation of the state-of-the art in dispassionate terms, with no personal animosity. I could find only one part of Dr. Sternberg's response which might be considered "harsh":
"A job, obviously, that Matheson has not done—though whether through ignorance, sloth, or duplicity I cannot say.
And in this he was only quoting Matheson's original words made in reference to Dr. Meyer. So perhaps Todd Wood is unduly defensive.
SCheesman
June 13, 2010
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Todd Wood thinks Sternberg was unduly harsh.bevets
June 13, 2010
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One thing I don't understand: these people who still believe that junk DNA is junk, how do they explain the regulatory procedures which must exist, especially in multicellular organisms? I find it difficult to imagine how the information for the procedures can be coded in the genome, but at least I do believe in the functional importance of all the genome, and not only of 3.5% of it (speaking of humans). So, I can always think: "we don't know yet, but we are going to understand in time; all these introns, repetitive elements, and other mysterious sequences, must mean something. There is a lot to decode, a lot to discover". But our darwinist friends, what do they really think, when they are not busy bad mouthing ID? Are they really convinced that the procedures are not written anywhere? That there is no mass memory for them? That alternative splicing happens according to alternative lucky feedbacks? That the whole development of body plans from the zygote is effectively managed by the asymetrical epigenetic information in the ovum? That each specific transcriptome for each cell type and cell state is selected from the transcriptome space by mere mechanistic events, without any informational support? That the macroscopic and microscopic structure of human central nervous system are generated by some kind of fractal mechanism, without any informational support? And so on? Again, where are the procedures written? Non coding DNA is an important possibility, but if they don't believe even in that, what is left for them? Epigenetic? Confusion? Axioms?gpuccio
June 13, 2010
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Off topic CS Lewis radio address: "The lone surviving reel of audio with Lewis's voice on it. He deals with prayer and evolution (Evolution on the second installment). Recorded during WW ll these talks eventually became "Mere Christianity" C.S Lewis's surviving BBC radio address http://www.youtube.com/watch?v=JHxs3gdtV8A C.S Lewis's surviving BBC radio address: Part 2 http://www.youtube.com/watch?v=xYoU5_MQOU0 Evolution Vs. The Christian Experience - cartoon video http://www.metacafe.com/watch/4104600 CS Lewis song - Brooke Fraser http://www.youtube.com/watch?v=GHpuTGGRCbYbornagain77
June 13, 2010
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They predicted it while trumpeting it as a prime piece of evidence for evolution.Phaedros
June 13, 2010
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“It’s obvious that non coding DNA is important for regulation and for function. Whever said differently? Neo darwinism had always predicted that”. HAHA yea okPhaedros
June 13, 2010
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Well at least Matheson did display some honesty at one point in his exchange with Dr. Meyer, which is more than I can say for many evolutionists who disagree with Meyer, in when Dr. Matheson admitted ID had the superior case for establishing causality to the information we find embedded in life: here is the audio of the exchange: Stephen Meyer Has Even His Critics Agreeing: Intelligent Design Makes Sense http://www.idthefuture.com/2010/05/stephen_meyer_has_even_his_cri.html Though, I have to admit that that respect which Matheson had earned from me, for his honesty to Dr. Meyer, quickly evaporated by the less than forthright manner he handled Dr. Sternberg's rebuttal of his 95% Junk DNA position.bornagain77
June 13, 2010
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It's comforting to see that there are still good old darwinists whi stick to the belief that junk DNA is junk. Ah, that's what we expect from darwinists. Not the more recent "politically correct" attitude of the type: "It's obvious that non coding DNA is important for regulation and for function. Whever said differently? Neo darwinism had always predicted that". So, blessed aree the Morans, the Mathesons and the like of them. Good old people, loyal to the good old nonsense.gpuccio
June 13, 2010
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Sternberg observes:
On Friday, May 14, I watched as Steve Meyer faced his critics—two of them anyway, Art Hunt and Steve Matheson—at Biola University in Los Angeles. Matheson had previously claimed that Meyer misrepresented introns in his book, Signature in the Cell. (Introns are non-protein-coding sequences of DNA that occur within protein-coding regions.) In a blog post dated February 14, Matheson had accused Meyer of “some combination of ignorance, sloth, and duplicity” for stating in his book that although introns do not encode proteins they nevertheless “play many important functional roles in the cell.” Calling Meyer’s statement "ludicrous," Matheson wrote on his blog that biologists have identified functional roles for only "a handful" of the 190,000 or so introns in the human genome:
How many? Oh, probably a dozen, but let's be really generous. Let's say that a hundred introns in the human genome are known to have "important functional roles." Oh fine, let's make it a thousand. Well, guys, that leaves at least 189,000 introns without function.
Matheson added that "there are more layers of duplicity in the 'junk DNA' fairy tale than Meyer has included in his book," which (Matheson concluded) uses science to advance an agenda in which "rigorous scientific truth-telling is secondary." Naturally, I expected Matheson to bring up this devastating criticism at the Biola event on May 14. But he said nothing about Meyer’s "ludicrous" notions of intron functions that evening, and he was mum about all the other layers of duplicity that he claims to be privy to. This was probably wise, because Matheson is wrong about intron functionality.
scordova
June 13, 2010
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