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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
StephenB says,
The term ID/ Creationist is used to OBFUSCATE. As anyone who cares knows, “Creationists” conduct a Forward analysis, that is, they assume a Biblical world view and seek to make the scientific evidence harmonize with that assumption.
Do you know who Phillip Johnson is? He's one of the founders of the intelligent design movement. Here's what he says in Darwin on Trial p. 113.
The essential point of creation has nothing to do with the timing or the mechanisms the Creator chose to employ, but with the element of design or purpose. In the broadest sense, a "creationist" is simply a person who believes that the world (and especially mankind) was designed, and exists for a purpose.
Are you a creationist in the sense that Johnson describes? Is Michael Behe? How about Bill Dembski?Larry Moran
March 21, 2011
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Joseph says,
Alternative gene splicing, overlapping genes-> evidence of planning.
We've understood alternative splicing and overlapping genes for thirty years. How come all evolutionary biologists haven't become believers in God? Is it because we're stupid? Or is it because we know more than you do?Larry Moran
March 21, 2011
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kuartus says (#42),
I believe that the whole “junk dna” concept is an argument from ingorance. Just because we dont know the function of some dna, doesnt mean there isnt any.
kuartus also says (#56),
Again, blah blah blah. You kept metioning things that are irrelevant and somehow got the idea that I think they are arguments from silence. Okay?
Okay. Goodbye.Larry Moran
March 21, 2011
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Bruce David says,
The word “evolutionist” carries with it the implicit assumption that the fact that life evolved implies a Darwinian or other naturalistic mechanism, which it does not.
Nonsense. When one describes someone as an evolutionist one clearly means that they accept evolution as the mechanism. That means natural selection, random genetic drift etc.etc. You can't just re-define words to suit your personal preferences.
And in fact, the fossil record supports ID as the “mechanism” better than any other that has been proposed.
There are several reasonably intelligent arguments for ID. That's not one of them.Larry Moran
March 21, 2011
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scordova says,
So you can quibble that the quote came from two writing by Dawkins, rather than one writing by Dawkins, but it doesn’t change the fact it was by Dawkins, and the fact it was in a later work makes it less excusable for him, and less excusable for you to assert he some how opposes the notion of junk DNA!
Let me try and explain this to you. Others have tried unsuccessfully but I still have hope that you can understand the concept of junk DNA. As I said earlier, no knowledgeable biologist would ever claim that junk DNA doesn't exist. They all accept the examples of pseudogenes. That includes Richard Dawkins and other Darwinists. The scientific debate is over the amount of junk DNA in our genome. Is most of it junk or only a small percentage? In general, adaptationists (Darwinists) are skeptical of claims that most of our genome is junk and other evolutionary biologists are more comfortable with the idea. Here's what Dawkins wrote in The Extended Phenoptype back in 1982.
This does not mean, however, that the so-called junk DNA is not subject to natural selection. Various "functions" for it have been proposed, where "function" means adaptive benefit to the organism. The "function" of extra DNA may "simply be to separate the genes" (Cohen, 1977). Even if a stretch of DNA is not itself transcribed, it can increase the frequency of crossovers between genes simply by occupying space between them, and this is a kind of phenotypic expression. Spacer DNA might, therefore, in some sense be favoured by natural selection because of its effects on crossover frequencies....
As far as I know, Dawkins still believes that a lot of what I call junk DNA has this kind of function. He does not believe that the majority of our genome is completely useless. At the same time, he understand that there are pseduogenes and degenerative transposons that represent real junk. He also talks about selfish DNA but that's not the same as junk. Does this help you understand where he's coming from? He oposes the concept of junk DNA where "concept" means huge amounts of junk in our genome. He and I have argued about this quite a few times. Why is it so important for you to show that Dawkins was a supporter of huge amounts of junk DNA? Will you turn into a pumpkin if you're wrong?Larry Moran
March 21, 2011
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Larry at 50: "how the genetic load argument is an argument from ignorance" Never said it was "the experiment where large segments of mouse DNA were deleted is an argument from ignorance" Didnt say it was an argument from ignorance.But that could be explained by genetic redundancy in the sense of making the system more robust. "Please explain how our understanding of Alu sequences is an argument from ignorance" Again, never even mentioned it. Are you impying alu sequences are functionless? Again, blah blah blah. You kept metioning things that are irrelevant and somehow got the idea that I think they are arguments from silence. Okay?kuartus
March 21, 2011
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Dr. Moran: "In some cases it’s used to describe those people who accept evolution as the best explanation of life even though they may not be experts. A better word would be 'evolutionists.'" My problem with the word "evolutionist" is that the evidence of the fossil record shows that life clearly evolved. The question between those who are ID proponents and the ones who are not is, "What was the mechanism?" The word "evolutionist" carries with it the implicit assumption that the fact that life evolved implies a Darwinian or other naturalistic mechanism, which it does not. And in fact, the fossil record supports ID as the "mechanism" better than any other that has been proposed.Bruce David
March 21, 2011
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Larry Moran:
Please explain how 50 years of discovery about the structure of genes and how they are regulated is an argument from ignorance.
It takes knowledge to regulate genes. That is what we are saying. The more that is being uncovered the better Intelligent Design looks. Alternative gene splicing, overlapping genes-> evidence of planning. Thanks, keep up the good work!Joseph
March 21, 2011
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Larry Moran:
In most cases the term “Darwinist” is used as a pejorative synonym for “evolutionary biologist.”
No. It is used to describe a specific type of evolutionary biologist- one who thinks chance and necessity explain life's diversity-> the blind watchmaker, if you will. What do you call people who accept the change in allele frquency within a population, accept change, but go along with the observable genetic evidence which points to limited variation and some phenotypic plasticity? Are we called realists? Also do yu agree with Richard Dawkins when he says we wouldbe looking at a totally different given a biology given a creator/ designer? Dawkins begins around 14:30Joseph
March 21, 2011
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--Larry Moran: "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." There is no moral or intellectual equivalence between these terms. "The term "Darwinism" is used to CLARIFY. As anyone who cares knows, Darwinists falsely accuse ID supporters of being "anti-evolution," when they know very well that it is the purposeless, unguided, and totally random variety of evolution that is being criticized. Thus, one can believe in “evolution” [emergence from a single cell or universal common descent] without believing in “Darwinism” [the claim that naturalistic forces alone could drive the process]. The term ID/ Creationist is used to OBFUSCATE. As anyone who cares knows, "Creationists" conduct a Forward analysis, that is, they assume a Biblical world view and seek to make the scientific evidence harmonize with that assumption. ID advocates, on the other hand, conduct a Reverse analysis, that is, they begin with scientific evidence and allow the evidence to speak for itself, even if that evidence happens to be consistent with a Biblical world view. Thus, ID proponents seek to clarify the meanings of words because they know that the evidence is on their side. Darwinists seek to conflate terms and sow confusion because they know that the evidence is not on their side.StephenB
March 21, 2011
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Dr. Moran, you said, "Don’t pretend that my side is the only side enjoying that kind of debate. It damages your credibility." I think, if you'll read the books, articles, and blogs by the proponents I mentioned in my first comment (Behe, Dembski, Wells, etc.), and if you watch their public interviews and debates, you will find that without exception, their arguments are based entirely on the scientific issues and that they do not stoop to "enjoying that kind of debate". In fact, in my opinion they are remarkably restrained, considering the ad hominem abuse that is heaped upon them by the likes of Coyne, Dawkins, and Myers (and apparently you as well). Of course, there will always be some supporters of any position who use less than stellar tactics to support it. However, to then use that as an excuse to attack others whose only guilt is by association is unjustified. And by the way, I think the scientific issues are fascinating in and of themselves, and an ongoing discussion that limited itself to them would not be boring at all.Bruce David
March 21, 2011
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kuartus says,
I believe that the whole “junk dna” concept is an argument from ingorance.
Please explain how the genetic load argument is an argument from ignorance. Please explain how the experiment where large segments of mouse DNA were deleted is an argument from ignorance. Please explain how the existence of pseudogenes is an argument from ignorance. Please explain how our understanding of Alu sequences is an argument from ignorance. Please explain how the C-Value Paradox and the Onion Test are arguments from ignorance. Please explain how genome sequences are arguments from ignorance. Please explain how 50 years of discovery about the structure of genes and how they are regulated is an argument from ignorance. Please explain how the frequency of fixation of mutations in junk DNA s an argument from ignorance. You don't know what you're talking about, do you? Biochemists and molecular biologists are NOT ignorant about these things.Larry Moran
March 21, 2011
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I'm curious in how intelligent design can predict that most or at least large portion of the “junk DNA” should be functional. Or in other words: Why would the designer not design “junk”? And related to what Joseph said: Does ID not say that mutations can't create any new functionalities but only alter or destroy information? Would one thus after these millions of years not expect the genome to be littered with deteriorated stuff?myname
March 21, 2011
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scordova, For the sake of clarity, how much of the human genome do you think is junk? Please don't say "zero" because that would indicate that you aren't interested in a serious scientific discussion.Larry Moran
March 21, 2011
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Collin asks,
I’m just looking for a term to replace Darwinist that would exclude creationists, ID-ists and would combine the term Darwinist and whatever it is that you are. In essence, the majority of biologists are what? Please don’t say “biologists” because some biologists are ID-ists or creationists.
In most cases the term "Darwinist" is used as a pejorative synonym for "evolutionary biologist." In some cases it's used to describe those people who accept evolution as the best explanation of life even though they may not be experts. A better word would be "evolutionists." The vast majority of practicing biologists (>99%) are evolutionists in this sense of the word. There are many people who believe in a Creator who also accept evolution. Ken Miller, Michael Denton, Francis Collins, and Michael Behe come to mind. These people are creationists AND evolutionists.Larry Moran
March 21, 2011
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Joseph: To follow up on your query, and to be a little provocative, let me ask this question: when Jesus healed the woman of her hemorrhaging, was it done through genetic alteration?PaV
March 21, 2011
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Christians- For the sake of clarity, wouldn't "the fall from Grace" explain the existence of non-coding, useless, junk DNA, excess baggage that may just explain why our lives are shorter than those depicted in Genesis? (Sanford's genetic entropy?) Thanks in advance. JoeJoseph
March 21, 2011
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Dr. Moran, For the sake of clairity, even though you've probably answered the question posed to Dr. Hunt, what is your view of junk DNA. Do you think most of the non-coding DNA is functionless for the organism that contains it? Thanks in advance. Salscordova
March 21, 2011
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Dr. Hunt, Just to be clear, what is your view of Junk DNA. Do you think most of non-coding DNA is functionless now? I'm actually unsure of what you've said. Thanks in advance. Salscordova
March 21, 2011
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I believe that the whole "junk dna" concept is an argument from ingorance. Just because we dont know the function of some dna, doesnt mean there isnt any.Similar to the whole vestigal organ argument.Its now seems there really arent any vestigal structures.And by the way the only reason vestigal structures were proposed was because the theory of evolution predicted it. It was a failed predicton. Same with junk dna. It wasnt because an observed portion of dna didnt exhibit obvious function, it was because the theory of evolution predicted it beforehand. http://creation.com/junk-dna-slow-death http://creation.com/images/pdfs/tj/j14_2/j14_2_18-30.pdfkuartus
March 21, 2011
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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.
Say what Dr. Moran? The attribution of those quotes is still to Richard Dawkins, the only mistake was one quote came from his Selfish Gene book and the other in his article years later where he said:
creationist might spend some earnest time speculating on why the Creator should bother to litter genome with untranslated pseudogenes and junk tandem repeats.
He is still making a mistaken claim and it is still at variance with your assertion Dawkins opposes the concept of Junk DNA. That's indpendent of whether my citation was intially to the selfish gene book when it should have been to a later work. The fact that is in a later work by Dawkins is actually worse for you and him, and my attribution to the earlier work would have given you and him the excuse that it was when Dawkins was more ignorant of reality. So you can quibble that the quote came from two writing by Dawkins, rather than one writing by Dawkins, but it doesn't change the fact it was by Dawkins, and the fact it was in a later work makes it less excusable for him, and less excusable for you to assert he some how opposes the notion of junk DNA! Your error is far more gigantic because you refuse to accept the implications what is evident in the record of Dawkins writings. The fact that I initially said both quotes came from his selfish gene book does not remove the fact Dawkins still made both those quotations, and that you keep asserting the same howler:
Darwinists are the ones who OPPOSE the concept of junk DNA. Dawkins is a good example
Hardly, he has been an advocate of the junk DNA hypothesis, and further he uses the junk claims against creationists:
creationist might spend some earnest time speculating on why the Creator would bother to litter genome with untranslated pseudogenes and junk tandem repeats. Dawkins
I respect the fact you're sticking up for your friend, but his error in two published works is still there, and worse, in light of his taunting of creationists, it seems science is putting points in their favor, not his. In any case the next round of debate, my citations will be cleaned up, but I suspect you'll still be asserting the same indefensible claims. Fine with me.scordova
March 21, 2011
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Larry, not to drag you away from your important work of determining when and where to belittle people with the word stupid, idiot, ignorant, and what not,, but could you help me with another problem since you don't seem to want to address the problem of quantum entanglement in molecular biology that can't be reduced to a particle basis. Larry it has to do with Junk DNA,,, Junk DNA" is found to have purpose in an astonishing way in this following paper: Shoddy Engineering or Intelligent Design? Case of the Mouse's Eye - April 2009 Excerpt: -- The (entire) nuclear genome is thus transformed into an optical device that is designed to assist in the capturing of photons. This chromatin-based convex (focusing) lens is so well constructed that it still works when lattices of rod cells are made to be disordered. Normal cell nuclei actually scatter light. -- So the next time someone tells you that it “strains credulity” to think that more than a few pieces of “junk DNA” could be functional in the cell - remind them of the rod cell nuclei of the humble mouse. http://www.evolutionnews.org/2009/04/shoddy_engineering_or_intellig.html#more Thus Larry, since you hold that a vast majority of the human DNA is junk,,,
I say that about 10% of our genome contains essential DNA that could not be removed without affecting the survivability of individuals.
,,, then how do you explain the fact that the entire nuclear genome of the mouse is transformed into a optical device??? If your conjecture for a large percentage of junk DNA was true should we not see discordance of some degree here??? Instead of tightly integrated functionality???bornagain77
March 21, 2011
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Dr. Moran, But not all people who believe in non-teleological evolution are non-believers. Some are full fledged theists. I'm just looking for a term to replace Darwinist that would exclude creationists, ID-ists and would combine the term Darwinist and whatever it is that you are. In essence, the majority of biologists are what? Please don't say "biologists" because some biologists are ID-ists or creationists.Collin
March 21, 2011
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One more thing: I'd like to coin a phrase, if I may. As Dr. Cornelius Hunter continues to point out, Darwin's argument is theological in character. The phrase I'd like to introduce is this: "The God of the Goofs". This is typical Darwinian argumentation. A God who is all-knowing and all-powerful certainly couldn't have done this, or that, or what have you. That is, God has "goofed up". And then, of course, we find out that there is indeed a function, an important function, to it all. It is this "God of the Goofs" that the Darwinists rail against. (Sorry, Larry, but Darwin is the person who claimed that natural forces alone can explain life's diversity and progression. The Neutral Theory is still a theory that invokes natural processes.) Finally, let us take note that the God of the Gaps is still there. Has science provided any credible intermediates? Can science document anything other than sudden emergence and sudden disappearance of species? As the power of microscopic techniques are enhanced, isn't there more and more difficulty explaining (whether via directed evolution or neutral drift) the complexity that is unearthed? So we have the 'God of the Goofs' disappearing while the 'God of the Gaps' just won't go away. I think I'm on the side of the trend-lines here.PaV
March 21, 2011
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Larry, Can you name even a single biological fact that ID theory contradicts? (fact= a documented, repeatable observation in biology)Upright BiPed
March 21, 2011
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Larry and Arthur: I welcome your comments on this PhysOrg article appearing today. Here's a quote:
For years, many biochemists were skeptical that lincRNA played any important role in a cell and considered the molecules just mere "noise," perhaps vestigial protein-coding genes that had mutated to become nonfunctional. Chang's group has been instrumental in proving that lincRNAs can play a critical regulatory role: determining what proteins a cell produces and, thereby, what identity it assumes.
New, critical functionality now ascribed to what was formerly, for the most part, considered "junk". When will this process end? Also, let's never forget that DNA is a physical object, and that physical constraints might require stretches of DNA that will not have function, but will only act as a kind of physical 'spacer'. Even this basic function is itself a function (whereas "junk DNA" is considered discarded and formerly functional DNA).PaV
March 21, 2011
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So when is the test going to hppen? The test that removes 90% of our genome and see if something can not only develop by survive and reproduce? Or is Larry blowing smoke? Larry Moran seems to think that essential means that which isn't essential is junk- nonsense. As someone who has worked with redundant systems there is a reason for the extra parts to be there. And Larry, Intelligent design Creationists only exist in the minds of the willfully ignorant- and here you are. Ypu want a no-holds barred fight, Larry? I'm your hucklebrry. ;)Joseph
March 21, 2011
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Thanks, Arthur (#13 & 14) - that gives a pretty good quantitative framework for my question in #9! Anybody else got anything quantitative and evidence-based to contribute?molch
March 21, 2011
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Larry: ID Creationists are stupid. Bruce: I'm not so certain about that. Larry: Your'e stupid too. Bruce: What I'm saying is that neither of you is stupid. Larry: That's boring.Upright BiPed
March 21, 2011
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Bruce David says,
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.
It would be really boring if the Intelligent Design Creationists started treating evolutionary biologist with respect and stopped insinuating that they are too stupid to understand their own discipline. It's a lot more fun to have a real no-holds-barred fight. Don't pretend that my side is the only side enjoying that kind of debate. It damages your credibility. Larry Moran
March 21, 2011
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