John Mattick and Jonathan Wells use the same arguments in defense of their position and they quote one another. Both of them misrepresent the history of the junk DNA debate and both of them use an incorrect version of the Central Dogma of Molecular Biology to make a case for the stupidity of scientists. Neither of them understand the basic biochemistry of DNA binding proteins leading them to misinterpret low level transcription as functional. Jonathan Wells and John Mattick ignore much of the scientific evidence in favor of junk DNA. They don't understand the significance of the so-called "C-Value Paradox" and they don't understand genetic load. Both of them claim that junk DNA is based on ignorance.
Both of them choose to emphasize selective examples of functional transposons and pseudgenes to make the case that most (or all) transposons and pseudogenes are functional. Neither one of them understands introns. Neither of them believes that lack of sequence conservation is an indication of non-functionality.
I could go on and on. The point it that we can't distinguish between the scientific arguments put forward by Jonathan Wells and those advocated by John Mattick. Yet one of them is considered to be a kook and the other was given a prestigious award by the Human Genome Organization.
What's the difference? In the case of Jonathan Wells, we know something about his motives. We know that he is an Intelligent Design Creationist and that he uses his arguments against junk DNA to support a creationist agenda. However, none of that appears in his book The Myth of Junk DNA. Shouldn't his arguments be judged on their merit and not on his motivation?
Theme
Genomes
& Junk DNAIn the case of John Mattick, we know nothing of his motives. I don't know if he is an atheist or a fundamentalist Christian. He could be a member of any religion or of none. (I have my suspicions). We are forced to judge his "science" on its merits and not on his motivations. When we do that we reach the same conclusion we reach with Jonathan Wells who we don't hesitate to label a "kook" or a "loon." Is this fair? Shouldn't Mattick also be a kook?
[Mattick has been] a true visionary in his field; he has demonstrated an extraordinary degree of perseverance and ingenuity in gradually proving his hypothesis over the course of 18 years.
Hugo Award Committee This is an important question since I'm about to start teaching my course on scientific misconceptions and the controversy over evolution and creationism. In preparation, I'm reading an anthology on the demarcation problem where a number of prominent philosophers discuss the difference between science and pseudoscience (Philosophy of Pseudoscience: Reconsidering the Demarcation Problem). Many of them think that Intelligent Design Creationism is not science so that means that Jonathan Wells is not doing science when he writes his book. Many of these philosophers point out that "bad" science is not the same as pseudoscience. Presumably, they would label Mattick's writing as bad science but not outside the bounds of science.
I don't get it. I think that Jonathan Wells and John Mattick are both doing bad science but I see no reason to distinguish between them by claiming that Wells is not doing science but Mattick is.
What do the rest of you think? Would it be okay to promote Mattick's views in a science course but not those of Jonathan Wells? If so, why?
Posts about John Mattick
The Junk DNA Controversy: John Mattick Defends Design
The Dark Matter Rises
How Not to Do Science
John Mattick on the Importance of Non-coding RNA
John Mattick Wins Chen Award for Distinguished Academic Achievement in Human Genetic and Genomic Research
International team cracks mammalian gene control code
Greg Laden Gets Suckered by John Mattick
How Much Junk in the Human Genome?
Genome Size, Complexity, and the C-Value Paradox
Posts about Jonathan Wells
Oh, one last thing: “paulmc” referred to an online review of my book by University of Toronto professor Larry Moran—a review that “paulmc” called both extensive and thorough. Well, saturation bombing is extensive and thorough, too. Although “paulmc” admitted to not having read more than the Preface to The Myth of Junk DNA, I have read Mr. Moran’s review, which is so driven by confused thinking and malicious misrepresentations of my work—not to mention personal insults—that addressing it would be like trying to reason with a lynch mob.
Jonathan Wells Some Questions for IDiots
American Loons: #409 Jonathan Wells and #411 John West
A Dishonest Intelligent Design Proponent?
We Called Out IDiot Jonathan Wells, and He Folded
Jonathan Wells Sends His Regrets
Watch Jonathan Wells Screw Up
Jonathan Wells Talks About Sequence Conservation
The Myth of Junk DNA by Jonathan Wells
- Jonathan, Moonies, and Junk DNA
- Junk & Jonathan: Part I—Getting the History Correct
- Junk & Jonathan: Part 2— What Did Biologists Really Say About Junk DNA?
- Junk & Jonathan: Part 3—The Preface
- Junk & Jonathan: Part 4—Chapter 1
- Junk & Jonathan: Part 5—Chapter 2
- Junk & Jonathan: Part 6—Chapter 3
- Junk & Jonathan: Part 7—Chapter 4
- Junk & Jonathan: Part 8—Chapter 5
- Junk & Jonathan: Part 9—Chapter 6
- Junk & Jonathan: Part 10—Chapter 7
- Junk & Jonathan: Part 11—Chapter 8
- Junk & Jonathan: Part 12—Chapter 9
- Junk & Jonathan: Part 13—Chapter 10
42 comments :
I just got my copy of Phil of PseduoSci too. One of the chapters compares pseudoscience to scientific fraud, as an attempt to distinguish between them and better mark the boundaries of pseudoscience. Perhaps one could look at Wells as a fraud, rather than a pseudoscientist.
There might be a difference between Mattick and Wells: Mattick, as far as I can tell, has actually done a fair amount of real science and published real papers, though not the ones you're talking about here. Wells, on the other hand, has never done any actual science, with the possible exception of his PhD research. Mattick, in other words, might be only a part-time kook, while Wells is full-time. A number of great scientists have adhered to a variety of crackpot ideas, yet they're great because of their other work.
I think the demarcation problem is fun mental exercise but ultimately futile. It seems to me there is no precise definition of science, therefore there can be no sharp boundary between science and pseudoscience. Things at the extremes, such as quantum mechanics or astrology are easy to label, but the whole point of having a discussion on this is to label the things in the fuzzy middle. So is Peter Deusberg's AIDs denialism science? I'm inclined to think that a persons motivation should matter in determining if they're doing science or pseudoscience despite the fact we can never really know anyone's motivation. The motivation behind science should be to figure out how the natural world works. To the extent that someones interpretation of results is biased by previous commitments to an ideology- religious, political even scientific - they're not doing science. I can immediately find problems with this: there's an admitted YEC who does legitimate work in geology where he publishes papers and gives talks that discuss formations that are millions of years old. And of course every legitimate scientist has prejudices. However flawed this idea is I think it should be part of any discussion on demarcation.
There's another thing I think should be considered which I haven't seen addressed before in discussions on this topic: The strength of science doesn't come from the rigor with which scientists perform individual experiments. It comes from the fact that everything scientists learn is placed into a huge web, a huge network of mutually consistent and mutually reinforcing understanding. Every new bit of knowledge must add to this network and must be explainable in terms of what's already known. When a paradigm shift comes along it must eventually lead to a more robust network.
I'm inclined to think that ID is not science and its because ID, along with other pseudosciences, doesn't operate this way. IDers seem to pick and choose what facts to focus on to support their case and ignore vast swaths of science that contradict it. They also refuse to explore the one topic that would be really fruitful, and engage with what is already known in that topic - the nature and behavior of designers.
RodW
I hate to make myself the object of ridicule but I think Mattick's views may not be entirely unreasonable.
Although I'm generally familiar with the topic, I read a paper in Cell a few weeks ago ( read part of a paper, and I forgot the ref) that suggested to me that its not unreasonable to think that much of this pervasive but exceedingly low level RNA transcription might be scaffolding and tethering for epigenetic regulation. If that is the case I would predict that most or all of these transcripts could be blocked with no ill effects. Its seems to me that such an RNA could be 10kb long but have very few nucleotides that performed any real function such as protein binding. Mattick could reasonably describe this as function while at the same time recognizing that 99.99% of the positions are flexible. This view of function would not collide with the c-value paradox or genetic load.
Of course, IDers would put their own spin on this and abuse the notion of function for their own ends, but Mattick shouldn't be blamed for this
NOT RodW!!
That's a proper distinction to make.
However, as much as I don't like postmodernist woo, there is a point to be acknowledged and it is that in real life, it is not generally possible to separate one's scientific work from one's prior ideological commitments. It is great if people can compartmentalize those things successfully, and everyone should be striving towards that, but it only really works 100% of the time when there is no relationship between what you're working on and what your other views are, and the examples of people who have failed to do so are so numerous that the null expectation should be that there is an ideological influence on one's science. Therefore it is good to know what people's non-scientific views are when thinking about the scientific arguments they're making.
Of course, in the case of religion, the above presupposes that there is a distinction between one's views on the existence of God and one's science. And I don't subscribe to that view because I think that the former is very much a scientific subject, and the two are therefore largely inseparable.
I don't think that the belief in pervasive function in the human genome can, on its own, be fairly labelled as pseudoscience, regardless of the motivation. This is mainly because the statement is testable, and therefore can be falsified by the methods of science. However, when the researcher starts inventing empty excuses to every possible falsification, to evade subjecting his or her ideas to rigorous testing, then here we turn from simply bad science to a distinctly pseudoscientific terrain.
The difference between Mattick's approach and Wells's pseudoscientific quibble in regards to this particular question is that Mattick does actually propose, somewhat vaguely at least, ways to test his propositions. And he does research to try to back up his claims (regardless of its quality). And as long as he proposes testable ideas that can definitely be falsified by the methods of science, I think his ideas are safely still within the boundaries of science.
His recent pronouncements about junk DNA in the HUGO paper have actually been falsified, according to his own criterion. In the previous thread, Diogenes and others have supplied numerous examples that, I believe, are devastating to his main thesis. I just hope that he will uphold his scientific integrity and admit that he either was wrong or his ideas have been miraculously misinterpreted by all those who read the paper.
By the way, Larry, why don't you expand and publish your response to his paper in a relevant science journal? Also, I wonder why the Philosophy of Pseudoscience book doesn't include Karl Popper's classic: Science as Falsification. You should add it maybe as an external reading to your course.
Also, I wonder why the Philosophy of Pseudoscience book doesn't include Karl Popper's classic: Science as Falsification. You should add it maybe as an external reading to your course.
There's plenty of discussion of Popper in the demarcation anthology. Most (all?) of the philosophers reject Popper's idea of falsification as a demarcation. I agree with them. Popper confused a lot of people in his time but we've moved on.
Jonathan Wells' ideas about junk DNA are all falsifiable as are most of the ideas that the Intelligent Design Creationists propose. Therefore Intelligent Design Creationism is science, right?
In my discussion above, I should have clarified that falsification isn't the only criterion, but still it's an important one. ID creationists don't (or barely do) produce original research, often intentionally misrepresent other people's views, don't actively participate in science conferences, and most of their ideas aren't testable. That's why it isn't science. I don't believe that their claim of pervasive functionality in the human genome, for instance, is a genuine prediction of ID. This is because it doesn't prohibit other possibilities, such as the adaptationist paradigm. Therefore, even if they could show somehow that the human genome is mostly functional, that still wouldn't count in favor of their theories.
Including Popper's article would be a good starting point in the discussion about the boundaries of science. Then you can proceed by showing its weak points and where it perhaps fails to successfully distinguish between genuine science and pseudoscience. Sometimes we learn better by seeing through the mistakes of other people (especially highly intelligent ones).
So your opinion would be that Theodosius Dobzhansky wasn't a great scientist?
Where did I say anything about who is a great scientist and who is not?
Saying that God exists may not be a scientific claim, but as soon as you start talking about supernatural agency in the world, these claims are fair game. If God acts in the world, how do you know? What is the mechanism by which God acts?
Georgi,
It follows from what you said, viz:
1. It's impossible to separate your scientific work from your ideological commitments unless there is no relationship.
2. With religion, there is a relationship, in fact no distinction.
3. The null hypothesis should be that one's religion affects one's science.
4. You don't say this explicitly, but I'm assuming the effect is negative.
5. Dobzhansky was religious, on which I assume we can agree.
6. Therefore, his religion affected his science negatively, which would I suppose detract from his greatness.
Now in fact I don't see any evidence for such a thing in Dobzhansky's case, or in a great many other cases. I believe that I'm disagreeing with premise #4. If you wish to disown premise #4, feel free. But I don't see a way, if you preserve it, to keep from dissing Dobzhansky, unless you take him as the rare exception, and I don't see any evidence for that. I also, by the way, know of at least two Nobelists who had really crazy ideas. Linus Pauling you probably know; Roger Sperry is less prominent.
Actually, that's not quite what I said.
I said that it is "not generally possible" to separate one's ideological commitments from one's science in the sense that it is very very difficult to do so, not that it's completely impossible. Therefore for any given person the expectation is that the two things are at least occasionally mixed up (unless the topics are completely unrelated - there are a lot fewer chemists involved in the debates about the existence of God than biologists and physicists, and for a reason; also, very little of chemistry is questioned on theological grounds), and it would be good to know what the prior ideological commitments are. If you can successfully keep those things apart, that's great. But it is reasonable to be suspicious until proven otherwise.
Note that when I say all of this, I am by no means falling in the trap of discounting everything anyone says as a scam - the logical consistency of arguments and the facts and data to back them up rule in the end. But there is a grey area of writings that are either mostly speculation, presenting new hypotheses, or are about subjects on which there is insufficient data to conclude much with certainty. There those things begin to matter, and it is not inconceivable that if a critical mass of people predisposed to a certain view by non-scientific factors is present, a field can be sent in the wrong direction for quite a while (eventually, the truth will prevail, of course). It's not like it hasn't happened in the past.
A lot of the literature on how much of the genome is functional belongs to one of those areas - we know quite a few things on the subject with reasonable certainty, however a lot of what has been written on it is largely speculation.
Since you asked the question directly, I will not chicken out and will reply to it directly. Yes, my personal opinion is that if you believe in God, you are less of a scientist than you would be if you did not. This has nothing to do with your contributions to the advancement of science - those stand on their own and they can still be enormous. However, believing things without evidence to back them up is such a fundamental violation of the way a scientist is supposed to think, and in this case, it is one of the biggest questions about the universe we live in that we're talking about, that I just can't hold any other position.
There is something I always think about when this subject comes up. Apparently, the NIH requires all grad programs to have courses on proper scientific conduct for students so that they do not later fake data, manipulate images, etc. . We had ours in our first year and we were shown real examples of misconduct. Some of them involved people so convinced that their scientific hypothesis was correct that they did not bother to do proper controls. We're not talking deliberate misconduct to deceive others, just honest belief and conviction that those controls did not matter so to save time and effort they can be omitted and faked.
I've never been able to quite see the difference between that and belief in God. It looks like exactly the same thing to me yet you get kicked out of science for one of them while you get highly praised for your ability to reconcile science and faith for the other.
I've also often wondered what would happen if I sent a grant proposal to NIH where the main argument that I should be given money to do research is what is written in a holy book or a revelation I had.
Like all demarcation problems, this one is one is not solvable and not even useful to solve. There was never a good answer as to what distinguishes science or porn from their non- counterparts. Yet this fact is of exactly zero importance in science (or porn, or whatever) existence and development. The only people seriously concerned with demarcation are people with too much time on their hands.
You appear to be claiming that Dobzhansky was less of a scientist than he could have been were he an atheist. I don't see any way to test that hypothesis. One might try to test the general case, with careful sampling. But there would be many problems with any such approach. All we are left with, apparently, are subjective impressions and anecdotes. I have examples of scientists who believed weird things but nevertheless made great contributions to science: Dobzhansky, Sperry, and Pauling so far. You haven't presented any examples so far, but certainly Jonathan Wells would count. Does it all come down to a matter of frequency and/or degree?
A colleague and I recently generated some 'random' DNA sequences (100 million nucs each) and ran them through some readily available software to search for transcription factor binding sites (soon to be submitted as a letter somewhere....). Oddly enough, more than 100 million were identified (via lots and lots of overlaps and both + and - strand coverage). If only 1% of them occur in an 'appropriate' order that might be found associated with 'real' genes, then even in randomly generated DNA sequences (and via analogy, mutationally-'created' DNA in real organisms) we should expect to find a million or more real sequences possessing 'biochemical activity.' Should that be interpreted as indicating that in even randomly generated sequences there is real "function"?
Larry:
Who gives a damn about Mattick or Wells' religion? Why should anyone care about your "suspicions"?
Evidence and correspondence between evidence and theory are what count. Mattick is a highly accomplished scientist, and he has vigorous critiques of your views, as you have of his.
Why not just engage the debate, without the insults and anti-Christian hate?
Put your scientific arguments out there, your opponents will put theirs out, and may the best argument win.
"Why not just engage the debate, without the insults and anti-Christian hate?"
I think that's exactly what Larry was advocating, which you might realize if you considered his argument without anti-atheist blinders on.
Would it be okay to promote Mattick's views in a science course but not those of Jonathan Wells?
Sure. For Mattick, the hypothesis that such-and-such an RNA possesses a function as a non-coding RNA follows from the fact that many such RNAs do possess such functions. It's a reasonable hypothesis, and one that has borne much fruit as far as the identification of new and interesting non-coding RNAs.
For Wells, functionality of so-called junk DNA is required by his religion, and has nothing to do with what he knows (which is pathetically little) about gene expression. Not much point in bringing this to a science class.
I've a question for Larry and commenters here - in your opinion, do RNA polymerases IV and V have functions?
I HAVE engaged the debate many times over the past few years. The question was whether there's a difference between the views of Mattick and Wells. I think they are both doing science. What do you think?
BTW, where has Mattick published a response to his critics? I must have missed it.
Motivations? Mattick's side job of giving seminars on cruise ships would be in trouble if his "post Darwinism" schtick goes bankrupt. ;-)
http://www.insightcruises.com/seminar_f/sa19_seminar.html
@Georgi Marinov
I've also often wondered what would happen if I sent a grant proposal to NIH where the main argument that I should be given money to do research is what is written in a holy book or a revelation I had.
Your chances would be a lot better if you sent that one to the John Templeton Foundation.
Don't forget to liberally lard it with variations on the them of compatibility between science and religion.
Wells' "science" is sufficiently shoddy to dismiss. The reason wells' science is so shoddy is because, in my opinion, of his religion. Instead of simply writing about science, he does the typical creationist hatchet jobs, quotes out of context, purposefully omits parts of quotes that would render his use of them irrelevant, etc. Centrioles are 'designed' because they sort of look like turbines? Really?
Mattick's just seems too hyper-focused and dismissive of anything that counters his pet ideas.
Wells' "science" is sufficiently shoddy to dismiss. The reason wells' science is so shoddy is because, in my opinion, of his religion. Instead of simply writing about science, he does the typical creationist hatchet jobs, quotes out of context, purposefully omits parts of quotes that would render his use of them irrelevant, etc. Centrioles are 'designed' because they sort of look like turbines? Really?
Mattick's just seems too hyper-focused and dismissive of anything that counters his pet ideas.
Harris:
You're going to find that larger and larger numbers of scientists are making many of the same scientific arguments that Wells makes. The several hundred molecular geneticists involved in the Nature Genetics papers on the myth of junk DNA and Mattick are examples, as well as Denis Noble.
(http://whyevolutionistrue.wordpress.com/2013/08/25/famous-physiologist-embarrasses-himself-by-claiming-that-the-modern-theory-of-evolution-is-in-tatters/)
Philosophers-- leading philosophers-- are turning on you as well. Nagel has made his disgust with Darwinian/materialist mythology clear in his book, and Jerry Fodor took natural selection apart with impressive and irrefutable skill.
Your materialist Darwinist paradigm is headed for the dust bin, along with Marxism and Freudianism, other late 19th century materialist myths.
What is most amusing is your reaction. You guys are nothing more than second rate minds pushing a third rate ideology. Materialists/atheists lack even minimal intellectual resources to understand the arguments demolishing their ideology, let along refute them.
From The Encyclopedia of American Loons - http://americanloons.blogspot.ca/2010/12/119-michael-egnor.html - Diagnosis: Blissfully ignorant, total moron and dependable fallacy generator.
Given the source I think reports of the death of the "materialist Darwinist paradigm" are greatly exaggerated.
I will grant your qualifications for detecting second rate minds and third rate ideologies.
It seems that Dr. Egnor has picked up the old creationist line about "an increasing number of scientists abandoning evolution". As Diogenes has documented, creationists have been preaching about the imminent death of evolutionary theory since the 1960s. But the reality is, as Diogenes put it: "The only place you will find 'a growing number' of creationists is in the cemetery." And that's as true as it gets.
The big issue from the ENCODE data dump has to do with the definition of "function". If "being transcribed" is your standard, well that's pretty low.
@Larry Moran
It's a touch harsh to compare these two (okay, very harsh).
Mattick might be three-shades-of-wrong but he has worked for decades in actively doing real science.
He also engages in debate - if you really think he avoids the debate, try this podcast (in which IMHO he can't be mistaken for a kook):
https://itunes.apple.com/gb/podcast/john-mattick-molecular-biologist/id322054392?i=113263226&mt=2
It's from December.
The interviewer does what he can with the very limited time available
(i.e. not sufficient).
Do you agree that there's very little difference between the arguments used by John Mattick and those usedby Jonathan Wells?
If Mattick's hypothesis is an example of good science then so is Wells' hypothesis. Right?
Most obvious difference is Wells' contempt for people of the contrary view to his, including the way he repeatedly misrepresents the history - as if he's the smart one who is attempting to end decades of error, waking up foolish biochemists driven by 'ideology' to want to find an abundance of junk DNA. Second, he is deceitful: he leads his readers to believe that he has good guesses as to what all the enigmatic parts of the genome might be doing; Mattick is more content to say it's a real mystery and time will tell. Third, I suppose it could be said that Mattick could reconsider (and certainly will, if the evidence plainly shows he is mistaken - I know, straight away your reply will be that the game is up already - he clearly thinks otherwise). Wells is like a broken record and will never, ever alter what he thinks (or, what he _claims_ to think! I understand very well the view that the guy is dishonest and he is quite capable of saying stuff he knows has previously been refuted, just to keep the audience he holds already and discourage them from listening to other voices).
Is that enough? Do either of them have any kind of answer to the onion test - I really don't think so but I have studied this very little - I'm not a working scientist. I would be interested to read something by Mattick that addresses this, if anyone has found some written material (or another podcast, or lecture)?
I thought the above podcast was very interesting indeed. I sense the guy is guile-less (I could be wrong). He strongly believes all of it. (Nor do I even sense he saying stuff to improve funding prospects, for cynical motives). He has real hopes for medical advances coming out of better understanding of non-coding DNA. It could be argued that a scientist if his persuasion is likely to stumble onto something neat, at least as likely as another group who thinks their time should be spent on a sub-set of the DNA where genes (in the traditional sense) are found.
I must add, finally, I'm more inclined towards your interpretation Larry. Makes better sense. In time, John Mattick is likely to be disappointed.
Mattick has less of a 'hypothesis' than Wells does, adopting the approach that much remains to be found out.
Wells is not a scientist at all and I am not convinced that he is doing 'science' at all. You will think I am mistaken - but that's my view.
(Enigmatic DNA: any chance the term will take off? Blame Birney).
One point I made which needs adding to: when high profile biochemists are convinced a lot of DNA is junk, and keep saying so, is not great for attracting funding to study it! When ENCODE - and scientists like Mattick - express a contrary view, this is both bad and also good at the same time. Yes they show lack of regard for the mainstream view (and the lines of evidence lying behind it) which is bad, and falsely suggest splits exist between scientists - also bad. Yet, by emphasising that more research is vital to bring out more function than is known at present (even if they are overselling the notion to an absurd degree), it will do no harm to the cause of those looking for funding, will it? More work will get supported than if ENCODE had endorsed a view that only 20% was functional, instead of the reverse.
1. ENCODE as a whole has not expressed a contrary view to the one that the most of the genome is junk
2. The statement that more work will be supported if the dominant view is that most of the genome is junk is false. Then the funding agencies can just say "Well, if it's junk there is no point studying it". If most of it is functional, then it's a different situation.
You seem to be under the impression that ENCODE has not only shown that most of the genome is functional but it has also found out what that function is. Neither is correct.
They've been at it a lot longer than the 1960's.
http://answersinscience.org/demise.html
@Georgi
You reversed my meaning. Proclaiming most DNA is squatting, doing very little (or nothing) - and that this is settled science - is fine up to a point. Majority view. It's honestly stated too. It is not a great selling-point if you then seek to do research on it and need to be funded, that's the question I asked. Birney and co. seem to have had their eyes open to this issue (was he less than honest in his interviews; but at the same time, was he just 'pragmatic'?). Politics.
For comparison here's a paper in which James Shapiro makes similarly confident assertions (his blog at HuffP has been dormant for almost five months but I guess he will restart it once this appears in print): http://shapiro.bsd.uchicago.edu/Shapiro.2013.How%20Life%20Changes%20Itself%20The%20Read-write%20(RW)%20Genome.Physics%20of%20Life%20Reviews.pdf
Has he gone any further in this paper than previously?
One JS quote: "As we are learning from the ENCODE project data, the vast majority of genomic DNA, including many so-called "non-coding" (nc) segments, participate in biologically specific molecular interactions [11]. Moreover, the term "gene" is a theoretical construct whose functional properties and physical structure have never been possible to define rigorously. It is telling that genome sequence annotators used to call protein-coding regions (chiefly in prokaryotic DNA) "genes," but now use the more neutral terms CDS, for "coding sequence".
This stuff can't be wished away. How _do_ you convince smart people like Mattick and Shapiro who must have heard all the junk-DNA arguments before?
""The only place you will find 'a growing number' of creationists is in the cemetery."
That's a good one. I'll be sure to quote it sometime, with appropriate credits.
"... the vast majority of genomic DNA, including many so-called "non-coding" (nc) segments, participate in biologically specific molecular interactions... "
No matter how you select "the vast majority of genomic DNA", it will necessarily include mostly non-coding sequences. Nobody denies that a lot of non-coding DNA is functional, but it doesn't add up to anything like a majority.
This stuff can't be wished away. How _do_ you convince smart people like Mattick and Shapiro who must have heard all the junk-DNA arguments before?
Is the purpose of science to convince everyone? There will always be dissenters, and there's nothing wrong with that. It's a healthy thing if mainstream views are constantly challenged. BTW, isn't the burden of the proof on those who claim that most of the genome is functional? If so, it's up to them to come up with something really convincing.
@Rkt
Proclaiming most DNA is squatting, doing very little (or nothing) - and that this is settled science - is fine up to a point. Majority view. It's honestly stated too. It is not a great selling-point if you then seek to do research on it and need to be funded, that's the question I asked.
I'm not a researcher, but I don't see why a funding committee would have any trouble with a statement that is simply accurate, along the lines of: "While there is considerable evidence that much, and probably most, of the human genome if functionless 'junk', there remains significant portions which may serve a function, even though that function is not yet understood. Our study will evaluate one such sequence, which we hypothesize may have the following function...."
That the concept of Junk DNA has stifled research of non-coding DNA is a common creationist claim, which has been comprehensively debunked by T. Ryan Gregory:
http://www.genomicron.evolverzone.com/2009/12/the-junk-dna-myth-or-lack-thereof-explained-one-more-time/
@Piotr
I share your perspective. It's too early for complete accord, and theories of how the genome got to where it is now are views to be debated, but all well-informed scientists see that we have junk DNA in some proportion - even Shapiro. I do think it funny, the two sides seeing each other as being not just wrong, but dead wrong. No quarter being given!
(Very wrong, however, are the ideologues who crave a genome that is completely functional ... for reasons unconnected to evidence or scientific analysis).
http://www.youtube.com/watch?v=ItYAjrVNpM8
Recently added - the lecture is also up on Soundcloud however the youtube location allows comments so this is the place to go for Larry (and others) to let Mattick know how you dispute what he says. The lecture itself was delivered 5 weeks ago.
Alternative:
https://soundcloud.com/#ansto-1/prof-john-mattick-most
As I have said previously I don't endorse these views, I just enjoy the cut and thrust. And the idea that progress could come from it.
My error - comments not allowed. Sorry.
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