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Ken Miller may face more embarrassing facts, Behe’s DBB vindicated

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[slight correction and update follows]

[update: I had previously taken a second hand quotation from Paul Nessleroade of Ken Miller here (2003 Wedge Update). Below I give a quote by Miller by a better source document here: Life’s Grand Design.

However, the more accurate quotation still demonstrates Miller made an embarrassing assessment about the architecture of DNA. I apologize to him for the inaccuracy, however, it was not a material inaccuracy as can be seen in the quotation from his website.

The greater burden is on Miller to retract his mistaken ideas from the public sphere. Further, he owes an apology to many in the ID movement for misrepresentations and errors of fact which he has promoted currently, over the years, and even under oath.]

the designer made serious errors, wasting millions of bases of DNA on a blueprint full of junk and scribbles.

Ken Miller, 1994

Empirical evidence 13 years later is putting some egg on Miller’s face [remember Ken Miller is the guy who made misrepresentations under oath in the Dover trial].

Encyclopedia Of DNA: New Findings Challenge Established Views On Human Genome

The new data indicate the genome contains very little unused sequences and, in fact, is a complex, interwoven network. In this network, genes are just one of many types of DNA sequences that have a functional impact. “Our perspective of transcription and genes may have to evolve,” the researchers state in their Nature paper, noting the network model of the genome “poses some interesting mechanistic questions” that have yet to be answered.

Other surprises in the ENCODE data have major implications for our understanding of the evolution of genomes, particularly mammalian genomes. Until recently, researchers had thought that most of the DNA sequences important for biological function would be in areas of the genome most subject to evolutionary constraint — that is, most likely to be conserved as species evolve. However, the ENCODE effort found about half of functional elements in the human genome do not appear to have been obviously constrained during evolution, at least when examined by current methods used by computational biologists.

According to ENCODE researchers, this lack of evolutionary constraint may indicate that many species’ genomes contain a pool of functional elements, including RNA transcripts, that provide no specific benefits in terms of survival or reproduction.

Behe 10 years ago, in Darwin’s Black Box (DBB) suggested junk DNA may not be junk after all. Behe has been vindicated by the facts, Miller refuted.

Finally, there is at least one other interesting fact in this article: “the ENCODE effort found about half of functional elements in the human genome do not appear to have been obviously constrained during evolution“. This means these designs NOT attributable to natural selection. Features in the genome have been shown not to be likely products of “slight successive modifications”. How I love science!

Comments
idnet.com.au, why do you think it is too early to know if the process I described is "correct"? Lots of work has been done on this mechanism in the past several years, and it seems to be very well-supported. DaveScot, I would encourage you to look at the specifics of the mouse experiment you described. I think you'll find that the "conservation" that is being trumpeted isn't all that conserved, and in fact has all the hallmarks of a region that is diverging by random drift. (Of course, that is apart from the genes that have subsequently been identified in the so-called gene deserts.) To help out, here is a link to the genome browser page. To look thru the respective genomes, use the appropriate pull-down menus. Choose the latest assembly. One of the mouse chr 3 gene deserts: chr3:146,629,000-149,000,000 The corresponding human genome position: chr1:82,073,954-84,900,793 Cut and paste exactly as given. There are lots of display options that appear after the picture. Explore and enjoy. As far as the paper whose abstract I posted, the general theme is something that most people tend to ignore. But it shouldn't be ignored. Turnover of proteins and RNA is a very important mechanism of regulation and , as I indicate here, central in the overall scheme of genomic "homeostasis".Art2
June 15, 2007
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Mung States: In another thread I raised the question of whether genetic entropy itself was not a major factor in the evolution of species. I don’t recall receiving a response, but here the claim is made explicitly. Evolution occurs because of genetic entropy, not in spite of it. Yet that is the opposite of what the “genetic entropy” originator argues in his book. To get a full grasp of how Genetic Entropy allows for limited beneficial adaptation away from a parent species, Let's look at the problems facing us with our food crops. For instance, man has artificially selected for higher yeilding corn for hundreds if not thousands of years. Now the corn yeild increase has leveled off. You could say we have "almost" reached a wall as far as yeild increase is concerned for the corn by artificial selection. Yet at the same time these corn crops are more susceptable to a single disease wiping out an entire crop since the variabilty of the corn is now severely limited... i.e. , the parent species of the sub-species has much more information for variability in its genome than the sub-species or pure breds do. This loss of information away from the parent species is an example of evolution at a cost to "Genetic Entropy". I hope I have made this clear for you Mung. If not, ask me and I will try to make it clearer for you.bornagain77
June 15, 2007
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Art2 You infer that the transcribed elements from areas of unknown function are accidentally transcribed and likely to be immediately chopped up for reuse. I think it is too early to know whether you are corrrect. Dave, The deletion of the non coding sequences in rats experiment found no problems. This does not mean that they tested for the function that the area coded for. Just say it is an area that ensures that rats don't eat a specific form of toxin. Would the lab rats who were not given an opportunity to eat the toxin demonstrate any difference from other lab rats who had that ability perserved? The same may go for specific immunogens. If the ability to fight rhodent malaria is conferred by that segment, and they didn't test the rats with malaria, how would they detect the problem? There are inumerable experiments that would need to be done to be able to truly conclude that one set of rats were equal to the other set. Ultimatly, releasing the cut down rat version into a competitive setting would be an important test.idnet.com.au
June 15, 2007
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Art re transcriptome and unused transcripts The proof of the pudding would be in deleting the DNA sequences that are suspected of having no use and seeing what effect if any it has on the organism. There may well be critical situations where the transcripts seen to be otherwise rapidly disposed of are instead used for some purpose and the transcript simply hasn't been observed in that situation. There sure are a growing number of anomalies that don't make sense in light of natural selection and non-coding DNA. I'm reminded of the experiment where 1000 non-coding highly conserved sequences between mice and men were knocked out of the mouse and there was no observed effect from it on the GM mice. If not selection then what acted to conserve those sequences for 100 million years? If selection conserved them why was there no observed effect on the mice when the conserved sequences were removed?DaveScot
June 15, 2007
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#10
The Science Daily article quotes the researchers with the first speculation on this: “According to ENCODE researchers, this lack of evolutionary constraint may indicate that many species’ genomes contain a pool of functional elements ...
I don't think that this is a speculation; they have simply stated a scientific hypotesis to try to explain datai within the current paradigm. But the result could be even more favourable for ID. After actual evidence of high % of useful DNA (first score) the researcher themselves are actually suggesting that DNA seems more and more FRONT LOADED (second score). Am I wrong?kairos
June 15, 2007
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[...] In yet another proof that it is good to maintain a degree of humility when drawing conclusions from the current body of scientific knowledge, it turns out that junk DNA isn’t junk after all.    [...]4Simpsons Blog Weekly roundup «
June 14, 2007
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Hi Sal, What is the impact of this on the whole "genetic entropy" argument? I ,eam, if genetic entropy isn't taking place in the "junk DNA," where is it taking place?
This is a further nail in the coffin for evolution for this only greatly strengthens the already unimpeached principle of Genetic Entropy of genomes. It is now virtually certain that genome wide inormation was introduced at the level of parent species with limited radiation of sub-species out from the parent species due to front loaded information that still obeys the principle of gentic entropy.
In another thread I raised the question of whether genetic entropy itself was not a major factor in the evolution of species. I don't recall receiving a response, but here the claim is made explicitly. Evolution occurs because of genetic entropy, not in spite of it. Yet that is the opposite of what the "genetic entropy" originator argues in his book.Mung
June 14, 2007
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Nothing like looking at the data: http://research.nhgri.nih.gov/ENCODEdb/Art2
June 14, 2007
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Behe's DBB conclusions about IC should be obvious to anyone who has dealt with even the most trivial real-world engineering problems. I'm reading The Edge of Evolution, and I must admit that I am somewhat mystified by the fact that such a book should need to be written. When the information-based nature of living systems was elucidated half a century ago, the entire Darwinian paradigm concerning biological innovation (i.e, stochastic processes filtered by natural selection) should have been discarded as obviously inadequate.GilDodgen
June 14, 2007
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I keyed in on this statement too. The ENCODE consortium’s major findings include the discovery that the majority of DNA in the human genome is transcribed into functional molecules, called RNA, and that these transcripts extensively overlap one another. Especially this part; these transcripts extensively overlap one another. This overlapping nature in conjunction with the poly-functional nature of the genome potentially raises the Complex Specified Information filter of Dembski up to the level whole genome. At least that is the impression I get from first glance of the evidence.bornagain77
June 14, 2007
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For what its worth, it would probably help if discussants here looked at the paper, and especially at the regions of the human genome that were selected for analysis. Also, the paper by Wyers et al. (2005) - Cryptic Pol II Transcripts Are Degraded by a Nuclear Quality Control Pathway Involving a New Poly(A) Polymerase, Cell121, 725-737 might cause some here to pause and re-think things. The abstract: ---------------------- Since detection of an RNA molecule is the major criterion to define transcriptional activity, the fraction of the genome that is expressed is generally considered to parallel the complexity of the transcriptome. We show here that several supposedly silent intergenic regions in the genome of S. cerevisiae are actually transcribed by RNA polymerase II, suggesting that the expressed fraction of the genome is higher than anticipated. Surprisingly, however, RNAs originating from these regions are rapidly degraded by the combined action of the exosome and a new poly(A) polymerase activity that is defined by the Trf4 protein and one of two RNA binding proteins, Air1p or Air2p. We show that such a polyadenylation-assisted degradation mechanism is also responsible for the degradation of several Pol I and Pol III transcripts. Our data strongly support the existence of a posttranscriptional quality control mechanism limiting inappropriate expression of genetic information. --------------------- I've been going on about the garbage disposal for some years. It's reports like this that make my ideas seem, well, almost sensible.Art2
June 14, 2007
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Looks like Nick Matzke and Larry Moran have egg on their face as well.
Larry Moran: Junk DNA is the DNA in your genome that has no function. Much of it accumulates mutations in a pattern that's consistent with random genetic drift implying strongly that the sequences in junk DNA are unimportant. In fact, the high frequency of sequence change (mutation plus fixation) is one of the most powerful bits of evidence for lack of function. ... Nick Matzke: Good post Larry.
Jehu
June 14, 2007
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From the article:
The ENCODE consortium's major findings include the discovery that the majority of DNA in the human genome is transcribed into functional molecules, called RNA, and that these transcripts extensively overlap one another. This broad pattern of transcription challenges the long-standing view that the human genome consists of a relatively small set of discrete genes, along with a vast amount of so-called junk DNA that is not biologically active.
Wow!Jehu
June 14, 2007
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It should be noted that they have now finally proven that most if not all of the DNA is not only functional but is also poly-functional, thus by logic it becomes much more severely constrained to any mutations to the DNA whatsoever(the chance of beneficial mutation to a poly-functional code is much much less than the chance of a beneficial mutation to a mono-funtional code). This is a further nail in the coffin for evolution for this only greatly strengthens the already unimpeached principle of Genetic Entropy of genomes. It is now virtually certain that genome wide inormation was introduced at the level of parent species with limited radiation of sub-species out from the parent species due to front loaded information that still obeys the principle of gentic entropy.bornagain77
June 14, 2007
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Predictions of non-functionality of "junk DNA" were made by Susumu Ohno (1972), Richard Dawkins (1976), Crick and Orgel (1980, Pagel and Johnstone (1992), and Ken Miller (1994), based on evolutionary presuppositions. By contrast, predictions of functionality of "junk DNA" were made based on teleological bases by Michael Denton (1986, 1998), Michael Behe (1996), John West (1998), William Dembski (1998), Richard Hirsch (2000), and Jonathan Wells (2004). These Intelligent Design predictions of are being confirmed. e.g., ENCODE's June 2007 results show substantial functionality across the genome in such "junk" DNA regions, including pseudogenes. These predictions are further detailed in: Junk DNA at Research Intelligent Design. http://www.researchintelligentdesign.org http://www.researchintelligentdesign.org/wiki/Junk_DNA Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. The ENCODE Project Consortium, Nature 447, 799—816 (14 June 2007) doi:10.1038/nature05874 http://www.nature.com/nature/journal/v447/n7146/pdf/nature05874.pdfDLH
June 14, 2007
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Unfortunately, as we have long observed, Darwinism is unfalsifiable. The editor of Nature and the researchers writing these papers obviously assumed these findings are easily accommodated into MET. Otherwise they would not have been published. Because of this, the new data will be blithely explained as usual with various "just so" stories. The Science Daily article quotes the researchers with the first speculation on this: "According to ENCODE researchers, this lack of evolutionary constraint may indicate that many species' genomes contain a pool of functional elements, including RNA transcripts, that provide no specific benefits in terms of survival or reproduction. As this pool turns over during evolutionary time, researchers speculate it may serve as a "warehouse" for natural selection by acting as a source of functional elements unique to each species and of elements that perform the similar functions among species despite having sequences that appear dissimilar." If this is a valid general hypothesis, how do the appropriate items from the "warehouse" just happen to be made available at the right time for natural selection? Even if all 2.7 billion base pairs or so are supposed to be available separately to express in every generation, there would still need to be a very elaborate filing and correlation mechanism that would also have to have evolved by RM & NS. “the ENCODE effort found about half of functional elements in the human genome do not appear to have been obviously constrained during evolution“ If they are described as not constrained, gene studies presumably showed a lot of (random?) changes in sequence in these regions between organisms belonging to different orders, classes, families, etc. having times of origination tens or hundreds of millions of years apart. If this large bulk of functional but nonconserved DNA had originated by natural selection we would see obvious build up of changes to "conserved" elements. This was not the case, so natural selection apparently wasn't involved. I wonder why Behe didn't refer to these research results in his new book. Unfortunately this large release of papers came out just after it was published.magnan
June 14, 2007
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Jeredl, "bFast, why would design detection fail if “junk DNA” were, indeed, junk?" This is Denton's contention, expressed clearly in "Nature's Destiny". I do not necessarily agree with him. However, there does seem to be something not very strategic about creating massive amounts of useless pseudoinformation. "Junk ain't junk" is certainly an ID prediction -- now a validated ID prediction. You and I might both contend that it is not a necessary prediction of ID, but Denton expressed it as exactly such. If you really want to understand his case in the matter, please feel free to read his case rather than my summary.bFast
June 14, 2007
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"The new data indicate the genome contains very little unused sequences and, in fact, is a complex, interwoven network." This is devastating to neo-Darwinism. Complex, interwoven network...like the neurons in our brains? That means DNA sequences are highly dependent to one another, and "evolution" certainly requires highly correlated, systemic or systematic, non-random changes taking place at various places at the same time. Irreducibly complex? But,
“the ENCODE effort found about half of functional elements in the human genome do not appear to have been obviously constrained during evolution“
I don't understand how the above finding leads to the following conclusion. Could you explain?
This means these designs NOT attributable to natural selection. Features in the genome have been shown not to be likely products of “slight successive modifications”.
MatthewTan
June 14, 2007
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We can add TalkOrigins and Richard Dawkins to the losers in this recent discovery. See: DNA researcher, Andras Pellionisz gives favorable review to a shredding of Dawkins and TalkOrigins
Richard Dawkins writes: And there’s lots more DNA that doesn’t even deserve the name pseudogene. It, too, is derived by duplication, but not duplication of functional genes. It consists of multiple copies of junk, “tandem repeats”, and other nonsense which may be useful for forensic detectives but which doesn’t seem to be used in the body itself.
scordova
June 14, 2007
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[update] I made a correction to my post, the quote I wished to highlight was:
the ENCODE effort found about half of functional elements in the human genome do not appear to have been obviously constrained during evolution
scordova
June 14, 2007
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bFast, why would design detection fail if "junk DNA" were, indeed, junk?jaredl
June 14, 2007
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The fact that Ken Miller is the author of the most popular high school text book and is working on a college level edition should make him suspect as a spokesperson. His income from his textbooks are probably over 200k a year and if he once told the truth about evolution, it would all disappear.jerry
June 14, 2007
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I point out why certain functional systems will be nearly if not completely invisible to natural selection. See: Airplane magnetos, contingency designs, and reasons ID will prevailscordova
June 14, 2007
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In Nature's Destiny, Michael Denton, Behe's mentor, was much stronger on this point. He held that ID would fall if junk DNA proved to be junk. This is surely the PRIMARY prediction of ID. Anybody who respects the predict and prove model of scientific theories must, in my opinion, give ID a seat at the table of science. Further, today Haldane's dilemma has become ten times the dilemma that it was prior to this finding. It is my opinion that at this point the ID community claim "scientific theory" status -- can the "hypothesis" bit.bFast
June 14, 2007
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By the way, Miller is author of a widely used high school biology textbook. Isn't that reassuring? (NOT)!scordova
June 14, 2007
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