Sunday, September 9, 2012

Darwinism and the consequences of junk DNA science


The remarkable ENCODE data published last week in Nature and several other biology journals is a final nail in the coffin of "junk DNA", a scientific myth that has been used by Darwinists to buttress their assertions that evolution is wholly the result of random genetic variation and natural selection.

Intelligent design scientists have predicted for decades that the genome is an elegantly organized system replete with purpose and that "junk DNA" is really functional DNA whose function remains to be understood.

It is important to understand that the ENCODE research published in Nature is not merely a vindication of the intelligent design prediction that most of the genome has function. Is is also a clear vindication of the insistence by intelligent design scientists that the design hypothesis is heuristic. The inference to design is essential to good science, because biological systems are intricately designed arrays of elements arranged for a purpose. If scientists begin with the inference to purposelessness, they will be misled. The denial of design in biology is bad science, with serious consequences.

The Nature authors point out the serious consequences of junk science:

“The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.” [emphasis added]

Two of the points that the Nature authors make are critical to understanding the catastrophe of "junk DNA":
 Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. 
 What the scientists are saying diplomatically is that the inference that these regulatory elements were "junk" has held back our insights into gene regulation. It is likely that if we had not assumed for 40 years that the genome was mostly junk we might now have a much better understanding of gene regulation.

Even more damning, they continue:
 The newly identified elements also show a statistical correspondence to sequence variants linked to human disease...
The assumption that most of the genome is Darwinian"junk" has seriously impaired medical research.

For decades Darwinists insisted that "junk DNA" was the expected consequence of 'random mutation and natural selection'. "Junk DNA" was presented as strong consensus evidence for Darwin's theory, and strong evidence against Intelligent Design.

How many scientists who were raised and suffocated under Darwinian bias failed to pursue focused research on "non-coding" DNA because of the assurance from the Darwinists that this DNA was junk, detritus accumulated over eons of evolution, and not an integral part of a meticulously designed system of cell regulation? How many scientists who did have the insight and courage to ask questions based on the inference to function and even purpose in the genome had their grants denied or their careers stymied? How many of those suppressed scientists were studying cancer, diabetes, and other diseases that will now be studied with the correct inference that the vast majority of the genome has elaborate function?

A major prediction of intelligent design science has been vindicated in what is likely the most important breakthrough in molecular genetics in 40 years, and the Darwinian prediction that most of the genome is junk is... junked.

Even now, in the wake of this massive evidence for the functionality of most of the DNA in the genome, Darwinist thugs like Larry Moran publish veiled threats against the careers of the scientists who published this groundbreaking data.

Moran wrote on his blog, on September 6, 2012, the day the data was published in Nature:

... I reserve my harshest criticism for the scientists, especially Ewan Birney who is the lead analysis coordinator for the project and who has taken on the role as spokesperson for the consortium. Unless other members of the consortium speak out, I'll assume they agree with Ewan Birney. They bear the same responsibility for what has happened.
Moran not-so-subtly threatens not only the lead author of the paper but all of the scientists in the consortium. They will "bear the same responsibility for what has happened".

What chance do you think these scientists' grant applications will stand if Moran is on the grant review panel? What chance do their tenure applications stand if Moran is on their tenure committee? Moran is a very influential senior scientist who is already on record advocating failing Christian undergraduates if they don't personally accept the Darwinist view of evolution, even if they pass all exams and classwork:

Of course, we all recognize the problem here. How do you distinguish between a good Christian who is lying for Jesus and one who has actually come to understand science? It seems really unfair to flunk the honest students who admit that they still reject science and pass the dishonest ones who hide their true beliefs...As we've seen time and time again on the blogs (and elsewhere), the Christian fundamentalists have erected very strong barriers against learning. It really doesn't matter how much they are exposed to rational thinking and basic scientific evidence. They still refuse to listen...This is one of the reasons why I would flunk them if they took biology and still rejected the core scientific principles. It's not good enough to just be able to mouth the "acceptable" version of the truth that the Professor wants. You actually have to open your mind to the possibility that science is correct and get an education. That's what university is all about. [emphasis mine]
Moran supported the denial of tenure to the superbly qualified astronomer Dr. Guillermo Gonzalez, simply because Gonzalez supported intelligent design:
I see nothing wrong here. I looks to me like this is grounds for tenure denial.
Moran has threatened other scientists and students who disagree with his Darwinist/atheist views as well.

In 2008, I noted:

Consider Dr. Moran's chilling comment about Kirk Durston, a Ph.D. candidate in biophysics at the University of Guelph. Mr. Durston has pointed out that intelligent design theory may be applied to an understanding of the enormous complexities of protein folding, which remains one of the deepest problems in molecular biology. Mr. Durston offered to visit and present his evidence at the University of Toronto. 
Dr. Moran replied:
I admire Kirk for his willingness to subject his scientific evidence for intelligent design to a group of experts on protein folding. It's very courageous of him since he's putting his scientific reputation on the line.
... Dr. Moran has even less tolerance for undergraduate students who express support for intelligent design. How would Dr. Moran deal with undergraduate students at the University of California at San Diego who do not believe in Darwinism? 
Dr. Moran:
Flunk the IDiots...40% of the freshman class [at UCSD] reject Darwinism... the university has become alarmed at the stupidity of its freshman class and has offered remedial instruction for those who believe in Intelligent Design Creationism...UCSD should not have required their uneducated students to attend remedial classes. Instead, they should never have admitted them in the first place...[T]he University should just flunk the lot of them and make room for smart students who have a chance of benefiting from a high quality education.
Do you think Moran and his fellow Darwinist thugs would bat an eye at expelling these scientists "who bear the... responsibility for what has happened."? 

But even threats from Darwinist thugs won't stop this science now. Even Moran's commentors on his blog have had enough of the thuggishness:


Crap... [You come] across as emotional, irrational and driven by adherence to dogma. You know you are right, so no need to read the 30 papers (yawn) or explore the interesting question of what does it mean for something to be "functional". You don't even quote the bit where he justifies why he settled on using the 80% figure as a summary. Just attack, attack, attack, like any good Creationist would. (Not suggesting that you are a Creationist, just that you are behaving like one.)
How any scientist can be faced with the publication of such an amazing resource as ENCODE, with all its data, all the questions it raises, all the interesting things to discuss (and not always agree about) and just focus on one or two sentences in the press releases that they don't like, boggles my mind. I know you are obsessed with neutrality and fighting Creationists but that is not all that science is about.
I am reminded why I stopped reading this blog for a while and think it is time for another break. If you give people a bit more benefit of the doubt and remember that they are (in the case of Ewan Birney anyway) highly intelligent, who knows, you might actually learn something - but that does not seem to be the goal of this blog. It is so much easier to criticise science than do it. And so much easier to twist someone's words into something you know how to attack than actually try to understand their data and what they might really be saying.
I would just ask you to consider all the damage that you are doing by your determination to drag the reputation of scientists - and science - through the mud but I know it is probably futile for frequenting this blog has made one thing very clear: Larry Moran is never wrong, has never made an error of judgement and already knows all the answers


One of Darwinists' fundamental arguments against intelligent design for the past 40 years is in flames, and it is clear that the Darwinian inference to randomness has seriously impeded both basic science and medical research. Even bluster and threats won't work any more.

Junk DNA is a Darwinian myth, and Darwinism is junk science.

38 comments:

  1. When I heard about this paper listening to NPR, I fully expected to see Egnor pounce.

    If you had been following developments in evolutionary developmental biology you wouldn’t have found any of this paper at all that surprising. The functioning of genetic switches that determine the development of bodies is dependant on their distance from the gene they switch. Certainly there are many sequences that do nothing by themselves but do contribute to the spacing and positioning of genetic switches. Because of this, it was already becoming apparent that all the genetic material contributes to the functioning of the genome.

    None of this changes the fact that biologists have found many copies of genes that are broken because the have accumulated mutations that render them non-functional. “Junk” certainly seemed like an apt term. Now we know that the presence of “Junk” does have an effect on the environment and functioning of the genome it also seems reasonable to refer to it as “noncoding DNA”.

    Like the genetic switches that have already been identified, there will undoubtedly be more interesting functionality found in the noncoding portions of the genome. The big clue is to look for sequences that are preserved. If sequences do nothing, then they will be allowed to accumulate mutations without being culled by selective pressure. There is also no doubt many sequences that do nothing beyond determining spacing of other elements will also be found as evidenced by their accumulation of non-deleterious mutations within populations.

    Evolution is safe. I.D. is still crap.

    -KW

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    1. @KW:

      You have utterly evaded the real issue, which is not the functionality of "junk DNA".

      The real issue is that Darwinists have used "junk DNA" for decades as evidence for their theory. ID scientists have disagreed, insisting that most DNA in the genome has function, albeit not yet discovered.

      The ID folks were right. Darwinists were wrong. Period.

      If most of the genome had been shown to be junk, Darwinists would be crowing.

      This is a disaster for Darwinists, and they know it.

      Delete
    2. Egnor: The real issue is that Darwinists have used "junk DNA" for decades as evidence for their theory. ID scientists have disagreed, insisting that most DNA in the genome has function, albeit not yet discovered.

      The ID folks were right. Darwinists were wrong. Period.


      The evolutionists were right. The ID folks were wrong.

      The ENCODE data showed that only about 9% of the genome is actually functional. If you include not-yet-tested transcription factors, Ewan Birney says it might go up to %20... real optimistic.

      About 76% is transcribed into RNA, much of that at very low levels, like one RNA molecule per cell. The 80% number included any transcription at any level as "functional", but that's not the function ID proponents allegedly predicted.

      IDers' religious beliefs require that things like transposons (which make up 45% of the genome) serve the human organism.

      In the 80% number, all transposons would be included as "functional" because they interact with other molecules in order to duplicate themselves.

      So if you want to call that "functional", OK, you must consider the possibility that humans have as their "function" and "purpose" the carrying around of large numbers of transposons.

      I suspect you will not consider that hypothesis because of your religion.

      As for real function, it's still 8% and that's after spending $200 million. So ID is disproven.

      Delete
  2. *sad sigh*

    This post just proves that you don't know a thing about either science or medicine. ;)

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  3. ENCODE by no means proves that most of the 3 billion base pairs in the human genome has a function. There's still likely to be a considerable percentage of DNA that's non-functional and for which the term junk DNA is a good term.

    The fact that the size of the genome varies so much over different species is a good indication that the genome isn't intelligently designed. The marbled lungfish for example has a genome of 130 billion base pairs. Certain ameba have even larger genomes.

    Even if ID proponents were suggesting that considerably more than the 5% of the genome we already were certain had a function (1.5% in the genes and 3.5% strongly conserved across species - and thus likely to be functional) it doesn't 'prove' ID which remains a non-theory; God did something somewhere somewhen for unknown reasons and by completely unknown mechanisms.

    This is just the way science progresses. Putting a place name such as 'junk DNA' on the parts of the genome for which there is no known function is quite reasonable. It hasn't delayed progress because it was necessary to develop methods of reading the genome to begin with, which was only achieved within the last 12 or so years.

    Research on the genome has been done by mainstream scientists, not ID proponents.

    And anyway, we know that a lot of the human genome is nonfunctional just based on the broken genes. 3% of the human genes are for olfactory receptors and about a half are broken, because humans rely more on vision than smell. Whales have the same suit of 1000 genes for olfactory receptors, and they're all broken.

    It's a prediction of evolutionary biology that genes that aren't necessary for survival, such as those for olfactory receptors in whales can accumulate mutations because natural selection doesn't punish them. ID makes no such prediction, unless you include Stephen Meyer's non-prediction in 'Signature in the Cell'; design is perfect, unless it isn't, in which case it's due to the Fall!

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    1. [ENCODE by no means proves that most of the 3 billion base pairs in the human genome has a function.]

      They showed that 80% of DNA (at least) has function. Read the paper.

      Darwinists were wrong in this, utterly. They used junk DNA as an argument for Darwinism, and now the ID guys are proven right.

      What's more is that Darwinism has held back research by decades.

      Delete
    2. Michael,

      No, it doesn't. The 80% figure is using the most liberal definition of 'function' to mean just being transcribed into RNA. Most of genes consists of introns, which when transcribed produce RNA much larger than the mRNA eventually translated. The excess RNA has to be spliced out to produce mRNA which are translated into protein. The introns could have a function, in allowing for alternate splicing and more than one protein product from the same gene. But it's unknown why the introns are so large, making up 95% of some large genes.

      Scientists before the results of the Human Genome Project were announced had a 'pool' going to predict the number of genes humans have. The winning prediction eventually turned out to be about twice the eventual answer of around 23,000. Genetics is still a science that will continue to produce surprises. It's just the nature of science.

      You haven't addressed the 'problem' of broken genes. Mutated genes which are no longer functional because they code for functions no longer needed or used. That's very much a prediction of evolutionary biology, not of ID.

      Delete
    3. @bach:

      You're tap dancing. Bottom line: Darwinists predicted that most of the genome is non-functional junk. ID's denied that.

      ID won. Darwinism lost.

      Darwinism, by perpetuating an inference that inhibited aggressive study of non-coding DNA, was an impediment to science. A major impediment, that has not least of all set back medical research.

      Did I hear you say "sorry"?

      Delete
    4. Michael,

      No it didn't. You don't have a clue. The genome of eukaryotic cells was originally assumed to be 'intelligently designed' in effect. Lean and mean with unnecessary DNA ruthlessly stripped out by natural selection, because having unnecessary DNA is a cost.

      The genome of eukaryotes was thought to be similar to that of prokaryotes, eubacteria and archaea, in fact, with no introns, little excess DNA between genes, few if any broken genes.

      It was a surprise that the genome was much larger with a lot of it without apparent function, and a lot of it is still without apparent function. Being transcribed into RNA isn't function. You still haven't addressed the 'problem' of broken genes. What's their function?

      ENCODE is still preliminary work. Being published doesn't mean that it's true, a line you follow with papers showing results you don't like. Peer review is only the first step. Science is often two steps forward, one step back. How do you think that medical research has been delayed by the concept of 'junk' DNA. It's only with the technology of DNA sequencing that we've been able to read the genome, something that was impossible back in the '70s. And we've still made progress. Such as knowing the genetics of Huntington disease with the number of repeats at the end of the Huntington gene determining age of onset and severity of disease. But we still don't know how the altered gene produces its effects.

      Even if much of the genome turns out to have a function, by no means certain, and you persist in ignoring broken genes, it doesn't mean that our general picture is wrong, and everything has to be abandoned.

      As an analogy, Newton had thought that the universe was infinite in size as an explanation as to why gravity hadn't caused the universe to collapse back onto its centre wrongly thinking that an infinite universe doesn't have a centre.

      Until the early 20th century, the universe was thought to consist of just the Milky Way Galaxy and nothing else. Newton, as far as we can tell, was right; the universe is infinite, but for the wrong reason. His being right on one point doesn't mean he was right in other points; he also thought that the orbits of the planets was inherently unstable and one of God's tasks was to give each planet a nudge from time to time. A task made unnecessary by Laplace's 1802 5 volume treatise on planetary mechanics.

      Working out what the genome does was done by non-ID proponents. Can you point to anything that ID proponents have done that has lead to any advance in knowledge?

      I don't need to say sorry, because I fascinated by how the world works, not by how I want the world to work. If my current understanding turns out to be wrong, and I learn a better understanding, then I'm happier.

      Delete
    5. bachfiend is correct in pointing out the liberal definition used by those involved with the ENCODE project. You really need to understand how they defined it because their idea of "functional" is nothing like the ID definition of "functional". But there is a bigger problem with their claim.

      In the operant training experiments I do we like to know how strong the association between a light stimulus signalling food availabilty and behavior to obtain that food is. If our rat sees a light come on and 80% of the time she presses the lever for food, that would mean there is a strong asociation, right? You would be tempted to say yes, but you could very well be wrong.

      It's not enough to compare the number of accurate responses to the total number of potential responses. We need to use a control rat that receives random presentations of light that have no association with food availibilty. We often find that such rats will still press the lever about 50% of the time after light presentation, even though the light serves no function.

      This is precisely the control the ENCODE groups needs to make their 80% claim. Throw a few random 10 kbp into the genome and see what percentage of that insert meets their definition of "functional". If it is truly random, then that would be the baseline against which they should compare.

      If you want more detail on this error, you should look at 'Crytogenomicon'.

      -L

      Delete
    6. @L:

      The ENCODE research is the work of over 400 scientists who are part of the National Human Genome research Institute, which is a part of the National Institutes of Health.

      No doubt they lack your skill in experimental design, never having done cheese-light experiments with rats.

      Please forward your concerns to them asap so they can issue a public correction.

      Delete
    7. mregnor,

      Is the lack of a baseline level of functionality for a random genome a legitimate criticism of the 80% interpretation, yes or no?

      -L

      Delete
    8. Michael,

      You still persist in being wrong. No matter the number of scientists involved and no matter how bright they may be, all results are provisional until verification, and even then it can be overturned later.

      That's just the nature of science.

      The CERN experiment, involving the brightest of particle physicists, the elite amongst scientists, with the most profound knowledge of computers and higher mathematics, 'demonstrated' faster-than-light neutrinos, a result which met with a lot of skepticism. But also, a lot of excitement, because it meant our understanding of physics was wrong and there was something new to be discovered.

      The experiment just turned out to be wrong, nothing more than a loose connection ...

      You still haven't answered the question; how did the concept of 'junk' DNA delay progress in impeding an aggressive attack on the nature of DNA. First reading the genome took years and a billion dollars and the work of many scientists. If junk DNA was accepted dogma, no one would bother doing such tedious, expensive and obviously futile work. But they did, disproving your thesis.

      We know DNA works, because obviously it does work. We don't know how, exactly, it does work, and that's a matter for continuing research. Or we can just stop and adopt your viewpoint and assume that God just gives a nudge to DNA now and then?

      I thought that you'd previously stated that you don't accept ID (whatever that is) preferring a model of 'hyelomrphic dualism + teleology (whatever that is).

      Delete
    9. @L:

      [Is the lack of a baseline level of functionality for a random genome a legitimate criticism of the 80% interpretation, yes or no?]

      For a "random" genome? Interesting concept.

      There are a million experiments that fall out of this work. This is a revolution in our understanding of the human genome. There are all sorts of things to be teased out of this.

      Why don't you use the "random genome" data that the Darwinists demanded for years before they made their junk DNA hypothesis?

      Oh-- that's right, Darwinists didn't care about such things until their ideology was threatened.

      Delete
    10. @bach:

      [how did the concept of 'junk' DNA delay progress in impeding an aggressive attack on the nature of DNA.]

      The answer is obvious. It discouraged scientists from studying it. It discouraged granting agencies from funding it.

      [I thought that you'd previously stated that you don't accept ID (whatever that is) preferring a model of 'hyelomrphic dualism + teleology (whatever that is).]

      I think that teleology is the stronger philosophical position. But the design inference in biology is a legitimate inference, and, as you can see with the junk DNA breakthrough, it is heuristic.

      The design inference is philosophically suboptimal, but it is leagues better than "shit happened and survivors survived".

      Delete
    11. mregnor said

      "Why don't you use the "random genome" data that the Darwinists demanded for years before they made their junk DNA hypothesis?"

      Scientists do. For gene insertion experiments the standard control has been to include a random genetic code of equal length to ascertain whether insertion of new code itself alters the functionality of the genome outside of the influence of the inserted gene. Gene insertion experiments have been going on for nearly 40 years now, so I am not suggesting anything new.

      " There are a million experiments that fall out of this work. This is a revolution in our understanding of the human genome. There are all sorts of things to be teased out of this. "

      I'm not talking about a follow on experiment. I'm talking about making sure their interpretation of the original data is accurate. First things first.

      " For a "random" genome? Interesting concept. "

      Yes it is. But you didn't answer the question, so I'll ask it again. Is the lack of a baseline level of functionality for a random genome a legitimate criticism of the 80% interpretation, yes or no?

      -L

      Delete
  4. Note to readers:

    This post was put up accidently, before I completed it. I'll leave it up, because people have already commented, but I will revise a few of the sections for coherence and readability.

    Sorry for the premature posting.

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    1. 'sall right, could happen to anyone. I mean, just look at KW and Bachfiend ... they put up "responses" without even reading your OP.

      Delete
  5. Dr. Larry Moran is invited to address a group of college students in preparation for university. He asks them if they know what a tragedy is?

    One student says a tragedy is when a man crossing the street gets hit by a car. Moran says no, that's not a tragedy, that's an accident.

    Another student says that if a bus full of people falls of a cliff and everybody dies, that's a tragedy. Again, Moran says no, it's a big loss but not a tragedy.

    A third student says a tragedy would be if a plane full of atheists were to be shot down by islamic fundamentalists. Now Moran agrees and asks the student why this would be a tragedy.

    "Because it's not an accident nor a big loss!" says the student who will now be certainly flunked!

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  6. "I presume you are referring to KW."

    Naaa, I was pretending to be the kinder, gentler version of KW. You know, in the manner that *any* expression of disagreement with Darwinism -- even such as pointing out that, and how, an assertion about biology (or about Darwinism) just made by a Darwinist is illogical -- is in itself sufficient proof that one is wholly ignorant about both biology and Darwinism, and that one is probably both stupid beyond words and a liar.

    Darwinists, Marxists, Freudians ... when it comes to reason and logic, there is nothing to recommend any of them above the others.

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    1. @Ilion:

      Good point. Sorry I was slow on the uptake.

      Delete
  7. This morning I came across the following interesting observations by Klaus Scherrer, of the Jaques Monod Institute in Paris, writing ca. 1988:

    We have found that eukaryotic DNA is systematically punctuated by AT-rich DNA segments which frame units of genome organisation of transcription and eventually genes and gene fragments (exons) in pre-mRNA. Integrating the known facts about these AT-rich elements in eukaryotic DNA...we are again faced by the old dilemma concerning eukaryotic DNA, that of "too much" (uneconomical!) and "of the wrong kind" (no reading frames), a dilemma exposed most concisely by the C-value paradox... So why does nature insist on piling up "unnecessary" DNA when scientists feel that the cell does not need it? It must be "junk" DNA...or worse, a kind of perversion of the "selfish" DNA! The attempt to overcome this intellectual deadlock must obviously consider the proposition that other possible functions may be ascribed to the surplus DNA; this is one of the main objectives of the Matrix Hypothesis developed here.

    If we begin by rejecting the
    a priori notion that all of this "junk" DNA is useless, and take more seriously what would otherwise be considered as spurious coincidence (and this choice is possibly rather a "philosophical" question or attitude) then a dual pattern of possible significance of this DNA seems to emerge. [Which Scherrer proceeds to describe.]

    (I've stripped out many of Scherrer's references, and some of his text; refer to the full text of the article for details. Citation follows at the bottom of this post.)

    A (hopefully) impartial reading of Scherrer leaves me with a few impressions:

    (1) Scherrer is familiar with the assertion that poorly-understood sections of DNA are "junk". (For brevity and clarity, I will label this assertion "JDA", short for "(the) junk-DNA assertion".) Scherrer recognizes (quite honestly) the epistemological status of JDA: it is an "a priori notion" -- no more.

    (2) He observes that a choice for or against JDA (as of the time of writing) "is possibly rather a 'philosophical' question or attitude". Presumably he means that absent compelling evidence one way or another, given the then-current state of scientific knowledge, an assumption accepting or rejecting JDA had to be chosen on other than scientific grounds.

    (3) "The attempt to overcome this intellectual deadlock must obviously consider the proposition that other possible functions may be ascribed to the surplus DNA...", writes Scherrer. "Deadlock" suggests obstruction -- an impediment to progress. Perhaps a fair paraphrase would be, "A stubborn insistence that 'surplus DNA' is 'junk' may well impede our progress towards a proper scientific understanding of DNA."

    (4) Why would Scherrer write the things he does, if JDA were not a significant, if not a prevailing, assumption in science ca. 1988? Which invites the question, Why presume in favor of junk, as opposed to something other than junk?

    Am I reading too much into Scherrer's comments?

    At any rate, one wonders why the scientific establishment seems to have a predisposition towards presumptions that are compatible with a materialistic view of the world. ("Junk" is hardly a neutral word.) That materialistic predisposition has much to do with religio-philosophical preference, and little to do with science. And the predisposition is not good for science.

    =====

    "A Unified Matrix Hypothesis of DNA-Directed Morphogenesis, Protodynamism and Growth Control"
    by Klaus Scherrer, Institut Jacques Monod, Paris
    Bioscience Reports, Vol. 9, No. 2, 1989
    (above quote is from page 159)

    Online in PDF form here.

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    1. Kent D:

      Excellent point. JDNA is an ideological viewpoint, more than a scientific viewpoint. It was just as reasonable to assume that the JDNA has a function yet undiscovered as it is to assume it is evolutionary detritus with no function.

      The assumption that it is junk is a consequence of materialism, and that assumption is plainly wrong.

      Materialism has set molecular genetics back decades.

      Delete
    2. What egnorance. Both Egnor and Kent D are willfully egnorant of the positive arguments for junk DNA, which are numerous and decades old, but no creationist will even admit they exist.

      Here are 10 positive arguments for junk DNA for the creationists to egnore:

      (1) Genetic load argument / each human gets about 50-150 more mutations than its parents; would be too many deleterious mutations if whole genome is functional --> extinction if no Junk

      (2) Large amounts of non-conserved regions (~95%) that evolve at rate of neutral drift

      (3) C-value paradox / onion test: huge variations in genome sizes between related species-- e.g. Drosophila vs. flies (flies have the same exons in the same order as drosophila but 10 times more non-coding spacer sequences between them), different species of onion, etc.

      (4) far, far larger genomes in many species / onion test again: marbled lungfish (130 Billion bp), Paris japonica, salamander, etc etc. (differences due mostly to transposons / parasitic elements)

      (5) far smaller genomes in some vertebrates: pufferfish, genome size 1/10 of human

      (6) wide variation across the eukaryotes in the proportion of non-coding to coding DNA, even within same genus or species

      (7) Megabase deletion mouse

      (8) Viability of large insertions of DNA at random places in the mouse genome (viable about ~25% of the time)

      (9) observation of insertion of DNA by viruses in present DNA

      (10) observation of duplicating transposons in present day

      That's 10 positive arguments for Junk DNA-- some of them decades old. Ryan Gregory has cited the original published literature, presenting proof that there was NEVER a historical era when the argument for Junk DNA was based only on "it doesn't have a function", or "evolutionary assumptions."

      Nevertheless, creationist continue to perpetuate this myth, which they cannot back up with evidence.

      Here's a transcript of Susumo Ohno at a meeting in 1973 introducing the concept of Junk DNA, which transcribes the scientists response. Not one of them assumes it's junk because we don't know its function or "evolutionary beliefs."

      Above I presented 10 positive arguments for Junk DNA, some decades old.

      I predict the creationists here will egnore every single one of them, and go on spouting that Junk DNA is based on "functions just unknown right now" or "evolutionary beliefs."

      Either way, the ENCODE data showed that only 9% of the genome is functional in terms of contributing to visible phenotype or viability of the cell, so ID is finished.

      Delete
    3. @Diogenes:

      You wrote:

      Both Egnor and Kent D are willfully egnorant of the positive arguments for junk DNA, which are numerous and decades old, but no creationist will even admit they exist.

      Either you are engaging in gross hyperbole, or you are simply unable to read. Michael himself referenced Sasumu Ohno near the top of his post. And although I did not mention Ohno explicitly, I am familiar with some of his work, and his place in the history of the "junk DNA" hypothesis. One can be familiar with an idea, and the proponents of that idea, without being persuaded by the idea. Why not engage on the issue, Diogenes, rather than engaging in ad hominem?

      A careful reading of my post will demonstrate that I said nothing directly against the idea junk DNA. What I questioned was a way of doing science. And my question was neither new nor original; Klaus Scherrer (and no doubt others) posed the question long before I did. Perhaps Scherrer is a closet creationist?

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    4. @Diogeness:

      Your "10 reasons (sounds like Letterman) to believe in junk DNA" makes my point, not yours.

      Despite a scientific consensus for the past five decades that most of the genome was junk, ID scientists have consistently asserted that most of the genome is functional.

      Now, more than 400 leading molecular geneticists associated with the National Human Genome Research Institute of the National Institutes of Health in 1600 data sets in 30 papers published in the leading scientific journals demonstrate that the ID hypothesis about junk DNA was the correct one, despite the "10" reasons to doubt it.

      My suggestion: don't make your bad science even worse by denying good science.

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    5. Egnor: the ID hypothesis about junk DNA was the correct one

      No, you egnored their data, and that is your problem. Please correct your statements. The ENCODE project showed that only 9% of the genome had function. Ewan Birney hypothesized that if they test many more transcription factors (another $200 million) they might get that up to 20% but that's it, in terms of sequence-dependent function.

      ID proponents all alleged that most DNA had to be functional. They always use vague, deniable language, but Jonathan M just said that it had to be most DNA, so that should be more than 50%. Right now it's 9%, so the ID hypothesis is disproven.

      The 80% of the genome touted by the muggle press was engaged in a molecular interaction with one of the tens of thousands of kinds of biomolecules. 76% of the DNA is transcribed and much of that at very low levels, maybe one RNA molecule per cell, so now there is a serious problem with Junk RNA-- another sign of bad design.

      If you put random DNA sequences in the genome, that would get transcribed and be "active" by ENCODE's definition. Certainly all transposon DNA is "active" by by ENCODE's definition.

      There is no evidence that this 76% that is transcribed is mostly sequence-dependent. 95% of the human genome is non-conserved and collects mutations at a nearly neutral rate. So we will still have proof of common descent-- there's still no other explanation for 98% similarity between human and chimp.

      If want to say "active" = "functional" as per the ENCODE press release, then ID is destroyed, because then random = "functional" by your new definition. That makes them "specified" according to Debmski's definition in "No Free Lunch" (functional = specified), and they're complex since they're long, so they have specified complexity, but they're random.

      Random = active, and by your new defintion, random = functional, and Dembski said functional = specified, so a long random sequence = specified complexity.

      If you catch a virus and it inserts it (retrotranscribed) DNA in your genome, that's "active" by the definition of ENCODE's press release. They call viral infections functional, if you want to, OK.

      Just about everything has specified complexity now, so if you want to redefine "functional" so everything is functional, as the ENCODE press release did-- great, ID is destroyed.

      Moreover, transposons are duplicated so that means specified complexity can be highly duplicative, all created by duplication.

      The marbled lungfish has 130 billion bp in its genome, so you say ID predicted all 130 billion bp are functional. Sure. They're all functional, all 130 billion bp. Suppose they are-- that means the marbled lungfish has 40 times as much "specified complexity" as the human.

      Every new human individual has 50-150 more mutations than its parent. Now you assert all 50-150 mutations are in functional, sequence dependent regions? OK, so many of those are deleterious mutations, added to each individual? If it's 5 new deleterious mutations per person, the human race should be extinct.

      And ID says all DNA is functional? Sure. So you can clip 1.5 million bp out of the gene deserts in mice, and they look just the same. So all DNA is functional? What did that 1.5 million bp clipped out of the mouse used to DO, anyway?

      According to your theory, that 1.5 million bp clipped out of the mouse had function. What was it?

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    6. @Kent:

      Either you are engaging in gross hyperbole, or you are simply unable to read. Michael himself referenced Sasumu Ohno near the top of his post.

      No he did NOT-- I see no such reference to Ohno. Search for Ohno. However, if there's some reference I missed, that makes it worse for Egnor. It means he understands Ohno's argument but he's lying about it. Ohno's was a positive argument for Junk DNA, based on the necessity of gene duplication, and for Ohno, Junk DNA meant pseudogenes only, a small fraction of non-coding DNA. But Egnor tells his readers scientists just used a negative argument: 'we assume it's non-functional only because we don't know its function.'

      Egnor and other ID creationists are lying to their readers when they tell people that scientists assumed there was non-functional DNA just because we didn't know it's function. I just listed 10 positive arguments for Junk DNA; some of those arguments go back decades; and not one of those arguments makes the assumption "because we don't know its function, it must be non-functional." Not one of those was an argument from ignorance.

      You cannot evade this by claiming you understand Ohno's argument. ID creationists say that scientists had only negative arguments, and that is a lie.

      Egnor wrote: The assumption that it is junk is a consequence of materialism, and that assumption is plainly wrong.

      He's lying. The existence of a half dozen to a dozen positive arguments for junk DNA refutes the ID creationist version of history in which scientists use only negative arguments based on ignorance.

      Kent: And although I did not mention Ohno explicitly, I am familiar with some of his work

      If you really understand it, then you must admit that scientists did NOT argue negatively, that if we don't know it's function right now, it must be junk. Admit it.

      Again: for Ohno, Junk DNA meant pseudogenes only, a small fraction of non-coding DNA. Non-coding DNA never equated to Junk DNA for any molecular biologist or geneticist ever-- that story was made up by ID creationists and the Muggle press.

      One can be familiar with an idea, and the proponents of that idea, without being persuaded by the idea.

      I don't care if you agree, but if you're just familiar with it, than you can't claim that scientists used only a negative argument, that we don't know it's function now so therefore it's non-functional.

      Klaus Scherrer (and no doubt others) posed the question long before I did. Perhaps Scherrer is a closet creationist?

      Of course not. Scherrer acknowledges the C-value paradox, and transposon DNA, which are POSITIVE arguments for Junk DNA. Creationists say that the arguments for Junk DNA were all NEGATIVE; thus, creationists pretend the C-value paradox doesn't exist.

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  8. Time for ID advocates to step up to the plate and explain why broken genes can accumulate mutations without consequence. They’ve been proclaiming that there is no junk DNA for so long you would think they have had ample opportunity to tackle this problem, but they haven’t.

    Perhaps the reason is they have no experts in the relevant fields. If you Google “intelligent design advocates” you will find that Wikipedia has a list that includes Dr. Egnor, Kirk Cameron, Rick Santorum, and jams Dobson. With a few exceptions like Egnor, the list reads like a who’s who of Christian pop culture and politics. There are no “experts” in the ID movement; only Christian cultural warriors.

    Perhaps that’s why all they really do is monitor the actual research by real scientists and glom-on to any piece of evidence they think supports their cause. Their only real expertise is in making bold pronouncements based on the work of others.

    -KW

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    1. @KW:

      You're right. There are very few ID scientists. Yet they got the junk DNA question right, and if they had been listened to, we would be decades further along in research on molecular genetics and on human diseases such as cancer, diabetes, etc.

      Darwinism has been a catastrophe for molecular genetics.

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    2. Michael,

      No, the ID scientists (an oxymoron if there ever was one) aren't right about junk DNA.

      Repeating the same lies doesn't make it true. It just makes you a bigger liar. The 80% figure comes from an extremely liberal definition of functional.

      The junk DNA hypothesis didn't delay molecular genetics. We read the genome when we had the technology to do so, and not before. It's still a robust hypothesis. The number of broken genes (and in humans, there's an enormous number) are inexplicable by the design hypothesis (unless you include the Fall as being the cause).

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    3. The NIH gave $200 million to the ENCODE project to go find functions in non-coding DNA.

      Explain to me again how Darwinism inhibited research into DNA?

      Perhaps Darwinists inhibited research into non-coding DNA by throwing $200 million at it?

      If so, Darwinists, please inhibit me too.

      Now it seems to me that creationist scientists are either many, or they are few.

      If scientists who believe in ID creationism are few, then the evidence for ID must not be persuasive.

      If ID creationist scientists are many, then creationists must be extraordinarily incompetent, because they have not discovered even one single base pair (out of ~3 billion in the genome) of non-coding DNA with a novel function.

      But let's quantify this.

      How much money did the Discovery Institute put into finding function in non-coding DNA? Let's compare. Are you ready to rumble?

      Now the ENCODE project cost $200 million, which was given to it by evolutionists who thought function could be found in non-coding DNA, under evolutionary assumptions. The money was given to evolutionists who then found functions in non-coding DNA, by using evolutionary assumptions.

      Now suppose you believe Egnor's claim that 80% of the human genome is "functional". That's 2.4 billion bp of "function" for $200 million evolutionist dollars, or 12 bp of "function" per evolutionist dollar.

      Contrast this with the creationists, using ID assumptions.

      The Discovery Institute put about $200,000+ (about 6% of their budget) into "research" at the Biologic Insititute, which did not research any non-coding DNA at all.

      If creationist assumptions were as efficient as evolutionist assumptions, with $200,000, at 12 bp per evolutionist dollar, the DI should have coughed up 2.4 million bp of function in non-coding regions.

      In fact, under creationist assumptions, they produced not one, not even one, bp of non-coding DNA with a novel function.

      Anti-Darwinism is a science stopper. Think of all the lives they could have saved-- the sick children with sad eyes they could have cured-- if their anti-Darwinist assumptions had not inhibited their research, thus killing small, adorable children.

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  9. If intelligent design needs an expert witness in court, I would bet that Dr. Egnor would be on the list of the 20 most qualified people to consider. That should tell you all you need to know about the validity of ID.

    -KW

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    1. If Dr. Egnor had been scheduled to testify at the 2005 Dover Trial, would he have testified, or would he have run away like Dr. Dr. Dembski?

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    2. @Paul: I believe that Egnor would not have been shceduled to testify because even ID proponents would have been embarrassed by his ignorance and stupidity.

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  10. I guess considering the average ID supporter believes “If we came from apes, why are there still apes?” is a valid argument, and that the Bible tells you all you really need to know, you really don’t have to set the bar very high. Just make sure you have a Dr. in front of someone’s name (it doesn’t matter what field), and mumble something about irreducible complexity and other sciecy sounding stuff. Rest easy knowing full well your supporters won’t really even make an attempt to follow the argument, they just want a couple of easy to remember catch phrases and a pat on the head. After all, you only need 50+1% and one more compliant Supreme Court Judge.

    -KW

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  11. Egnor hilariously twists around the plain meaning of scientific literature--

    Egnor: Two of the points that the Nature authors make are critical to understanding the catastrophe of "junk DNA":

    "Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation."

    What the scientists are saying...


    Here it comes. Wait for it now. The surgeon is going to tell us what the scientists are saying. I'm sure it will be insightful. Tell us, surgeon, what the scientists are saying.

    diplomatically is that the inference that these regulatory elements were "junk" has held back our insights into gene regulation.

    Oh, come on-- do you think we can't read g.d. English? Do you think we're total morons? Who do you expect to be fooled by this?

    And what do you mean "OUR insights into gene regulation"? Our? Us? What do you mean "We", kemosabe?

    You're a creationist-- there's no "we". Not one single base pair (out of 3 billion in the genome) of non-coding DNA had a novel function discovered by a creationist or ID proponent. Every nucleotide of non-coding DNA with a novel function was discovered by an evolutionist using evolutionary assumptions.

    Here's Ewan Birney, the co-ordinator of ENCODE, tells us just how much function there is in the human genome. From his blog:

    However, on the other end of the scale – using very strict, classical definitions of “functional” like bound motifs and DNaseI footprints; places where we are very confident that there is a specific DNA:protein contact, such as a transcription factor binding site to the actual bases – we see a cumulative occupation of 8% of the genome. With the exons (which most people would always classify as “functional” by intuition) that number goes up to 9%.

    So if it's really 9% functional, then the junk would be...let's see...100% minus 9%... math hard...

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