8/12/2007

PLEASE JUNK THIS ARGUMENT

I'm warming up for my exchange with Vox Day by trading thoughts with some of his readership, and one of them repeated a trope that I hear a lot from people who profess to be interested in defending the integrity of science. They are concerned that 'evolutionary bias' may be preventing good science from being done: that is, that a current model for this or that phenomena, derived from evolutionary theory, is not going to be challenged even if false, etc.

That raises a number of points which we could debate another day: whether science is wedded to philosophical naturalism, as Philip Johnson has made a career of asserting, or the proper role of existing paradigms in guiding research programs, or whether astronomers have 'gravitational bias.' All interesting, but what I want to focus on is the 'junk DNA' version of this hypothesis. According to some, the suggestion that non-coding DNA was 'junk' was quickly embraced by scientists eager to deny design, and this bias harmed the practice of science.

Well. Larry Moran doesn't think much of this argument, and neither do I, but I actually had to research this for all of 15 minutes to place this it in context, and provide the facts needed for my reply, a truncated version of which follows:

" Introns were discovered by Sharp and Roberts's group at MIT in 1977, for which they were awarded the Nobel Prize (1993).

In 1978, Gilbert and others began interpreting this finding as implying that non-coding DNA is vestigial 'junk' with no function. The term 'junk DNA' is associated with two influential papers (Doolittle and Sapienza, Orgel and Crick) which appeared in Nature in 1980. The discussion of function in these papers was speculative, nuanced and there was a call for more research. These facts are often omitted by ID creationists eager to impute 'evolutionary bias.'

(T. Ryan Gregory is, if anything, even more alarmed at the way these ideas have been reported versus to how they were presented in the literature. He has some informative comments here, along with extensive quotes from the above papers demonstrating that they never ruled out functional explanations for non-coding DNA out of deference to evolution.)

That was less than 30 years ago. The necessary tools for testing these claims (PCR, DNA fingerprinting, etc.) did not exist at the time the Nature papers were published and they did not become widely available until the early 1990's.

Studies were published as early as 1992 that showed preferential sorting of 'junk DNA' within the genomes, and actual evidence of function for introns was published by 1994. By 2003, writing in Scientific American, W. Wayt Gibbs remarks, paraphrasing John Mattick, that the failure to recognize the importance of introns “may well go down as one of the biggest mistakes in the history of molecular biology.”

Yeah, well, it was a "mistake" that was corrected by the scientific community within less than two decades once the tools were developed to test the claim. Contrast that with the two millenia that Aristotelian essentialism hindered the emergence of population thinking in biology, or the long constraint that the church-endorsed Ptolemaic model held in astronomy.

I'm going to let Professor Moran have the last word, because he's so much more indignant than I am. Just remember, kids, that while individual scientists as a whole may be blinded to this or that piece of evidence (we're all human), the scientific community as a whole is always shining lights in dark holes, gradually bringing more and more of the natural world into sharper focus. Compared to the creationists, we are the one-eyed men, and that makes us kings.

22 comments:

Starwind said...

Hello Scott:

Permit me to offer a few cursory observations.

There are at least four "dogs in this hunt": ID-advocacy scientists, ID-laymen (like myself), Evolution-advocacy scientists (such as yourself), Evolution-laymen.

One can anticipate and reasonably dismiss a fair amount of irresponsible and uninformed 'cheer-leading' from the laymen on either side of this issue. However the bar is higher for the scientists, if they are to be worthy of that appellation. From scientists we expect cautious, methodical, conservative, fact-based research and little or no "guess-work" offered the guise of fact or findings.

To that end when, in 1978 and sometime thereafter, so-called non-coding DNA was dismissed as "junk-DNA" without in fact actually understanding the origin, purpose (if any), and operation of non-coding DNA, biologists and/or genetic scientists commited a serious intellectual disciplinary error. They "guessed" based on preconceived notions, and only after the necessary tools became available began the serious methodical investigation of non-coding DNA.

Arguably, other science disciplines are likewise guilty of similarly episodic remissions, but that is to be avoided, not propagated.

The point being, the understandable lack of tools is not an excuse or license for "scientists" to wildly speculate on something about which they self admittedly knew next to nothing:

Larry Moran: "The point is that we are extremely confident that a large amount of the mamalian genome really is junk. It's not just a definition based on ignorance. We've been working on the problem for over thirty years."

Larry Moran: "Furthermore, even when it comes to true junk DNA, properly defined, hundreds of papers have been published. Lots of us have been very interested in junk DNA—at least in part in order to find out whether it has a function. This work led to the indentification of hundreds of pseudogenes, the unimportance of most intron sequences, and the degeneracy of LINES and SINES. There's lots more."

i.e. there was a time when the definition "junk DNA" was based on ignorance.

While much has been learned and some of what was formerlly defined as "junk-DNA" has now been redefined as its utility is better understand, what remains (again for lack of tools and experimentation) is yet again "extremely confidently" declared to be junk-DNA.

Redundancy in various forms plays a large role in survivability. As complexity increases, redundancy increases more. "junk-DNA" (properly defined as Moran would say) may provide various kinds of redundancy necessary for survival. I can't say if this is true of DNA, but if not true it will be an exception.

Here's a "thought experiment" that ought to be pursued to the extent feasible: Remove all/most/some of the "junk-DNA" from some cloneable mammal, and see if you have a viable organism left. If you can't or don't, arguably the utility (or lack thereof) of "junk-DNA" still defies comprehension or the hypothesis defies testing.

Francis Collins is purported to have said: "a certain amount of hubris was required for anyone to call any part of the genome 'junk'"

Regardless of whether tools, logistics, or funding preclude confirmatory testing, and when additionals tests todate verify that what was formerly thought to have no utility turns out to have some utility, minimally scientific professionalism and discipline ought to suggest a more cautious stance, but if not bias then of ongoing hubris scientists like Moran seem to be guilty.

The Factician said...

starwind,

Here's a "thought experiment" that ought to be pursued to the extent feasible: Remove all/most/some of the "junk-DNA" from some cloneable mammal, and see if you have a viable organism left.

Several groups are doing just this with yeast and bacteria. It will be some time before the technology is cheap enough to do it with a larger organism (like a mouse) and I doubt it will ever be considered ethical to do that experiment in humans.

They "guessed" based on preconceived notions, and only after the necessary tools became available...

This is what scientists do. If we lack the tools to ask a question experimentally, we will often speculate about what the answer is. But we will present that as honest speculation, not as dogmatic fact.

Starwind said...

The Factician: If we lack the tools to ask a question experimentally, we will often speculate about what the answer is. But we will present that as honest speculation, not as dogmatic fact.

So, when Larry Moran says: "The point is that we are extremely confident that a large amount of the mamalian genome really is junk. It's not just a definition based on ignorance. We've been working on the problem for over thirty years."

Is he "honestly speculating" or is he "stating dogmatic facts", and on what conclusive evidence does his statement rest?

Jason F. said...

Scott,

I would also suggest another line of argument in your debate. It's one I've used often in my "discussions" with creationists and it seems to be one they have trouble addressing.

We're all familiar with the creationist argument that "Darwinism" is the dominant paradigm in biology because those who control the funding are part of the "Darwinian Orthodoxy". Government grants and such for research are all part of this conspiracy according to creationists.

The counter to this conspiracy theory is to point out that even in the private sector, evolutionary theory is the dominant paradigm.

Start off by describing how--contrary to government research--in the private sector the focus is overwhelmingly on making a profit. Private firms don't care one bit about allegiances to orthodoxies, adhering to conspiracies, or anything else. In private science, if a concept works and makes them money, they'll use it.

And guess what is the dominant paradigm in private sector biology? That's right, it's evolutionary theory. A good example is this paper:

http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pcbi.0010045&ct=1

It describes how when the concept of common ancestry via evolution is applied to genome databases for organisms as diverse as humans, worms, and flies, molecular function is determined to a 96% degree of accuracy (you have to do a little digging to see the list of organisms that are in the databases they use).

The point is clear: Evolutionary common descent works and provides useful, productive, and profitable results.

Don't think for a second that if intelligent design creationism were able to do the same, companies wouldn't drop evolution in a second. They simply go with what works and produces results.

But the fact is, no one is using intelligent design creationism in any biological research, and even in the private world where profits reign, evolutionary theory carries the day.

So how do creationists explain this if evolutionary theory is all wrong and creationism is all right?

plunge said...

Scott,

I think a really important point on this issue and others like it is how complicated a subject the issue of DNA coding really is. We're talking more than even just a few really rigorous college courses here, and writing about the history of scientific thinking about junkDNA, non-coding DNA, and other ideas, is something that even to describe to a layperson would take a good-sized, well researched book. Moran's discussion gives a decent sense of this, but even he is simplifying (and would say so) because there are just so many different things to discuss, so many oddities and different overlapping elements.

But look at what creationists like Day and others like him do: the self-appointed experts-in-everything. They sum up the issue in just a few sentences. First scientists believe that junkDNA has no function, and this proves evolution, and then it turns out that it does, and this proves evolution too.

That characterization is worse than bullshit. It's careless, thoughtless bullshit. What's worse is that anyone who actually sat down and read through the journals relevant to this subject would see how obviously bullshit it is. But someone like Day won't ever do that. He doesn't NEED to do that, because he has no need to learn anything about DNA, or even the history of science. All he needs are a scattering of quotes from random people and a sloppy understanding based on reading a few articles by breathless journalists who don't really understand what they are talking about either.

The best way I've found to deal with this dramatic disinterest in actual facts is basically to quiz the other guy on some very basic key points. I've found that most of the people that blather on about how Gould showed that there is no evidence of change in the fossil record can't even name the specific view he was attacking. How can you possibly know what the scope of relevance of Gould's claims were if you don't even know the NAME of the position he was criticizing, much less what it was, much less its relevance to evolutionary theory as a whole?

It's just utterly, utterly amazing, this stuff. It's one thing to be ignorant. It's quite another to have a few scattered bits of trivia, most of it misunderstood, and then to insist that you know better than the experts what this or that implies.

Vox also seems to be under the belief that scientists simply come up with a theory and then NEVER TEST IT. Again and again he talks about this or that being speculation without ever discussing the various checks and tests and additional evidence that are done and continue to be done in order to confirm one explanation over another. You really get the feeling that he just has no idea at all that any of this stuff exists, or that he just doesn't care.

plunge said...

starwind, by the way, your characterization is also bullshit.

The consensus in 1978 was NOT that non-coding DNA had no function, but that the burden of proof was on the claim that any particular sequence having a function: there wasn't any defacto reason to believe that just because it existed that it had a function, and there were and are lots of good reasons why we wouldn't expect everything there to have a function (reasons that you, by your comments, still appear to be ignorant of).

If you'd actually read the debates at this time, that would be clear. Instead... well, who knows where you get your ideas.

And in fact, your characterization especially looks like pure nonsense, because you'll find paper after paper even in the 80s of people discussing various possible functions for specific elements that are non-coding (though of course the ability to nail of of this down did not yet exist). Most of them not even particularly controversial or even notable. How is that possible when this supposed orthodoxy existed?

"Is he "honestly speculating" or is he "stating dogmatic facts", and on what conclusive evidence does his statement rest?"

Again, this is what I don't get. That you even ask this question suggests that you don't know the subject in question, and I guess more importantly, haven't tried to remedy your ignorance of it. Moran notes several different things, though he does by referring to concepts that, unless you had actually read something about the issue, you might be unfamiliar with. Clearly, you are unfamiliar with them since they didn't trigger any recognition or discussion and you seem to think he didn't mention anything. What I don't get is why that doesn't spur you to at least educated yourself a little on the subject before making grand pronouncements like that its all just speculation and so forth.

Likewise, you suggest that scientists should try confirming the idea by doing tests. And yet, you are again so ignorant of the subject that you don't seem to realize that this has already been done and IS done as a matter of course: done many times. In lots of ways. On lots of different species (for instance, mice).

I just don't get it. Really, I don't.

Starwind said...

plunge: First scientists believe that junkDNA has no function, and this proves evolution, and then it turns out that it does, and this proves evolution too.

That characterization is worse than bullshit.


I agree that characterization has problems, as well as being simplistic. Perhaps you should point that out to Moran? Larry Moran: The IDiots Don't Understand Junk DNA: "Here's a clue. Junk DNA is DNA that has no function. It is not non-coding DNA. Lots of non-coding DNA has a function (regulatory sequences, origins of replication, centromeres, telomeres, SARs, etc. etc). But, in mammals, most of it doesn't. Most of the human genome is junk."

Clearly, you are unfamiliar with them since they didn't trigger any recognition or discussion and you seem to think he didn't mention anything.:

Here's Larry Moran again: Noncoding DNA and Junk DNA: "I want to keep the term "junk DNA" to refer to all functionless DNA. That includes DNA for which we have direct and indirect evidence of no function (pseudogenes, most of intron DNA, corrupted transposons etc.) and it also includes the rest of the DNA for which no function has currently been discovered and we think it's junk because it's not conserved (among other reasons). Junk DNA is not noncoding DNA and anyone who claims otherwise just doesn't know what they're talking about."

Wikipedia: Transposon: "As an example about 48% of the human genome is composed of transposons and their defunct remnants."

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences:
"At least 16% of eutherian-specific conserved non-coding elements are clearly derived from transposons, implicating these elements as an important creative force in mammalian evolution." and "The most surprising discovery to emerge from comparative analyses of eutherian genomes is the finding that the majority of evolutionarily conserved sequence does not represent protein-coding genes, but rather are conserved non-coding elements (CNEs)7, 10. The opossum genome provides a well-positioned outgroup to study the origin and evolution of these elements."

First marsupial genome decoded: "Most surprisingly, many of the new DNA instructions are derived from the jumping genes, or “transposons”, which make up our so-called junk DNA. The percentage is at least 16% — and is likely much higher, as many transposon-derived sequences have mutated beyond the point of recognition."

So, 48% of the human genome is comprised of transposons, which transposons in eutherian genomes [not necessarily human] a surprsing 16% play "an important creative force in mammalian evolution", and arguably are not "junk DNA".

To what extent the study findings are directly applicable to human "junk DNA", aside from noting that humans are placental mammals (eutherians) seems not to have been specifically cited/studied. But the study findings clearly suggest that at least 16% of what Larry Moran says functionless "junk DNA" actually performs some function.

Moran's characterization is a self-serving tautology (again that definition is): "...for which no function has currently been discovered..." If a function has been discovered, then by Moran's definition it isn't "junk DNA", but as long as no function has been discovered, then by Moran's defintion those particular genome segements remain "junk DNA", and should a function for them be discovered, ostensibly they too will be redefined out of the "junk DNA" category.

So inspite of evidence demonstrating at least 16% of "junk DNA" (which includes transposon as defined by Moran), Moran employs a defintion for "junk DNA" which is automatically (by defintion) revised to comprise fewer and fewer constituents, all the while asserting with "extreme confidence" that "junk DNA" is junk, which will conveniently always be true even when the group has no member genes.

It's that "extreme confidence" in spite of the shifting evidence that I don't get.

And yet, you are again so ignorant of the subject that you don't seem to realize that this has already been done and IS done as a matter of course: done many times. In lots of ways. On lots of different species (for instance, mice).

So, no doubt you can cite those many tests wherein "junk DNA" has been removed from a mammal to see if a viable organism can be cloned? I'm especially interested to see the one with mice, as you purport it to have already been done.

Starwind said...

correcting an omission (in bold):

So inspite of evidence demonstrating at least 16% of "junk DNA" (which includes transposon as defined by Moran) plays "an important creative force in mammalian evolution", Moran employs a defintion for "junk DNA" ....

plunge said...

"Perhaps you should point that out to Moran?"

Not really, because he's using the concept differently than you folks are (as I characterized you using it), as he points out quite clearly in the very section that you quote! In fact, he's pretty clearly pointed out a glaring, first-principles confusion over what the term JunkDNA even means: sometimes it's simply treated as synonymous with non-coding DNA. Sometimes not. To be fair, the media, not just creationists, are all over the map on this usage as well. That's why Moran, for the purposes of clarity, says he wants to reserve the term for a specific usage. But of course, not everyone is going to conform to that usage, especially because JunkDNA is largely a buzzword, and one that, like "missing link" most scientists would rather see abandoned altogether for all the confusion it causes, but for some reason gets insisted on as trendy because it does great press.

Again, your confusion can be resolved when you realize, as I noted before, that the basic sensible treatment is "junk until proven functional" which is somewhat of the opposite of the burden of proof prior to the late 70s (up until then, everyone had suspected that DNA would be a very exacting straightforward program due to natural selection pruning out everything unnecessary, when in fact the way genomes change over time is far far more complicated than that).

And of course, your later discussion, yet again, simply decides that it will carry on in total ignorance of the reasons Moran cites for why there is so much confidence that not all of this stuff is functional. Aren't you even going to attempt to ask or learn what those might be?

Are you prepared to explain, for instance, why, say, very similar species have orders of magnitude differences in their genome sizes, or why the difference in size doesn't seem to correlate very well with any definition of expressed organism complexity?

"So, no doubt you can cite those many tests wherein "junk DNA" has been removed from a mammal to see if a viable organism can be cloned"

Sure. I'm not going to run a literature search this second, but any familiarity in this field would turn up countless experiments using knockout techniques (we don't use cloning specifically, because there's no real need to to study what we're after), or comparisons based on natural variations or sections that become "damaged" without us doing anything at all and can be examined by gene comparison (though it's not clear that it means anything to call "damaged" things that can vary randomly to no effect). A lot of them are copies of genes we are already familiar with in varying numbers of copies from individual to individual: sometimes to a ridiculous extent, sometimes degrading in different ways in different gene pools in ways that seem truly random as opposed to being preserved in a certain way by natural selection. Some are characteristic of viral insertions. Some we can measure whether or not they are "conserved" or not.

Again though, don't you think it would be a good idea to maybe, say, find out more about what alu is? I mean, you could write an entire book just on alu, and frankly, you'd probably need to read at least that book in order to get a sense of the complicated ways in which is it an isn't implicated in function in various parts of the primate genome.

Starwind said...

plunge:
To be fair, the media, not just creationists, are all over the map on this usage as well.

Actually, the media science writers took their lead from the wording of the study and press releases (see the links I cited). If you (or Moran) have an issue with the characterizations, take it up with the study authors.

That's why Moran, for the purposes of clarity, says he wants to reserve the term for a specific usage.

Yes, well as pointed out his "clarity" is at odds with the definitions and evidence reported in the studies I cited.

I'm not going to run a literature search this second,

No, of course you're not.

(we don't use cloning specifically, because there's no real need to to study what we're after),

No, of course you don't. You don't seem to be after proof that "junk DNA" can in fact be "junked" and retain a viable mammalian organism. That would require a precise defintion of "junk DNA" which you don't have, and a feasible means of proving viability, which you don't have.

But no doubt you remain "extremely confident" that what you don't have proves your case regardless, and anyone who doesn't take on faith your extreme confidence in what you don't have is confused and uninformed.

Jason F. said...

starwind bloats:

"No, of course you don't. You don't seem to be after proof that "junk DNA" can in fact be "junked" and retain a viable mammalian organism."

This is precisely why PZ Myers et al. advised against debating creationists.

Here, starwind asks a question about a citation where a mammal had alleged "junk" sections of its DNA removed and remained viable. Under most circumstances, any of us would be happy to oblige.

But with a creationist such as starwind, it's a pointless exercise. You see, starwind isn't asking out of genuine curiousity. If starwind really were interested in the answer, he would have looked himself in any of the number of searchable journal databases (and he would have found his answer).

So why didn't starwind do that?

Because creationists aren't interested in the answer! The only reason they ask such questions is in the hope they can "stump the evolutionist". And if a citation isn't given, they have something to crow about. But if a citation is given, they'll either baldly assert "it's all speculation", ignore it and move on to the next talking point, or simply disappear altogether.

I've done this I-don't-know-how-many-times, and not once have I ever seen a creationist respond with, "Huh. I wasn't aware of that. I guess I was wrong."

So Scott, this is what you have to look forward to. A lot of "Oh yeah? Show me this..." on one topic after another in a machine gun like manner. It's not about the answers you are able to give, it's about getting you to at least once say "I don't know".

Oh, and btw, large-scale deletion studies on lab mice have been done, and they confirmed the "junk DNA" notion. The mice were just fine.

http://www.stanford.edu/class/bio203/NobregaGeneDesertsNature.pdf

Jason F. said...

Hmmm....apparently the whole link didn't come through.

After the 203/ in the URL, the rest is...

NobregaGeneDesersNature.pdf

Jason F. said...

Ok, even more frustrating than I thought. Now it looks like that link doesn't work anymore. So here is the google scholar results for the title of the article, surely enough to point the genuinely interested in the right direction.

http://scholar.google.com/scholar?hl=en&lr=&cluster=9565083927860019930

Starwind said...

Thank you, Jason F.

That study may be found at: Megabase deletions of gene deserts result in viable mice wherein it concludes: "The deletions carried out in this study represent the largest reported viable homozygous deletions in mice and supports the existence of potentially “disposable DNA” in mammalian genomes. In assessing the impact of these deletions on the engineered mice, it is important to acknowledge that our ability to phenotype an organism will always miss some features no matter how detailed. It is possible, even likely, that the animals carrying the megabase-long genomic deletions do harbour abnormalities undetected in our assays, which might impact their fitness, in some other time scale or setting than the ones assayed in this study. Nonetheless, the lack of detectable phenotypes in these mice raises the possibility that the mammalian genome is not densely encoded and that significant reductions in genome size may be tolerated. Linked to this, the extensive degree of non-coding conservation in the deleted intervals brings into question the functionality, if any, of many of the large number of non-coding sequences shared among mammals."

So indeed in this case the "non-coding DNA" (unlike "junk DNA" as Moran prefers) seems discardable, given the caveats stated by the study authors.

It would be interesting to know to what extent the deleted non-coding sequences are derived from transposons and if as in the marsupial non-coding genome study (linked above) they are likewise implicated as a "creative force in mammalian evolution".

Scott Hatfield . . . said...

Wow. Greetings, gentlemen/women. What a spirited conversation. In general, I agree with Factician's brief about how scientists go about their business and, with plunge as to the tendency of creationists to engage in vacuous, misleading arguments.

However, I am willing to give Starwind a little slack because he rather graciously accepted my apology for misreading his views over at VD's place. Also, he does seem to be making an effort to show that he is digesting some relevant literature, which Jason F. has brought to our attention---thanks, Jason, I hadn't read that myself!

OK, so no low blows, let the best blogger win!

Anonymous said...

One thing you can try to do with VD is to steer the debate away from details (where you get bogged down in rather dense studies, and end up quibbling over details of wording) and go after the basic principles. Also, don't just defend, go on the attack... ask VD to explain his position, and provide evidence to support it. Don't be the one doing all the heavy lifting.

Creationists get their talking points fed to them, they don't actually understand what they are talking about. Asking them questions throws their game.

eg: Ask VD how forensic DNA analysis works. (the areas used are silent, that's how)

-Graculus

plunge said...

"Actually, the media science writers took their lead from the wording of the study and press releases (see the links I cited). If you (or Moran) have an issue with the characterizations, take it up with the study authors."

This is an incoherent response. The point I (and Moran) have made is that the term is used inconsistently, and yet creationists and media don't seem to realize this, so they treat every different usage as a debate or a fundamental disagreement. So, yes, Moran is taking it up with the study authors in a sense. But they don't have to listen to him. There is no central bureau of what buzzwords mean.

"Yes, well as pointed out his "clarity" is at odds with the definitions and evidence reported in the studies I cited."

Again, this is a nonsensical response. He's proposing to define the word in such a way to clear up the confusion caused by all those different and conflicting definitions! He's not denying that people define it differently.

If you read the history of the term, from Ohna on, you'll find that its meaning has changed very dramatically over time.
Here's a decent discussion of that history by the way:
http://genomicron.blogspot.com/2007/04/word-about-junk-dna.html

It's always a surprise to me that creationists don't make a big deal out of exactly the opposite in this case: that natural selection turns out not to be the all-powerful pruning force in the genome that everyone once expected. If anything was a scientific boner, that was!

"No, of course you're not."

So now that someone has pulled up an example, are you going to apologize to me for implying that I made it up, and for not doing a lit search for you the second you asked for it?

"No, of course you don't. You don't seem to be after proof that "junk DNA" can in fact be "junked" and retain a viable mammalian organism."

Actually, this IS an interesting issue, and I am interested in it. But cloning wouldn't really help that much in examining it, especially because clones are not necessarily functionally identical in any case, and actual clones are even worse, because our current technical means of creating them are pretty messy and can potentially cause a lot of noise and problems on their own. Knockouts and studies of natural mutational variations provide the sorts of things we need to look at just fine.

(And again, non-coding and junkDNA aren't synonymous IF you are understanding junkDNA to imply functionless: non-coding DNA is clearly not all functionless)

"That would require a precise defintion of "junk DNA" which you don't have, and a feasible means of proving viability, which you don't have."

Haven't I and Moran and others all been arguing that usage of JunkDNA is largely a buzzword that doesn't give one much of a real understanding of the complexity of DNA? Isn't that the point of Moran wanting it to be more strictly limited?

I don't know how much more feasible you want to be about measuring viability. When genes play a major role in the functioning of an organism, they should be relatively conserved over time throughout generations (rather than varying randomly), and all our experience with DNA leads us to expect that wholesale deleting large sections of them is going to have SOME sort of noticeable effect: certainly deleting entire chunks of many non-coding sites does so: often so dramatically that they never even develop properly as embryos.

"But no doubt you remain "extremely confident" that what you don't have proves your case regardless, and anyone who doesn't take on faith your extreme confidence in what you don't have is confused and uninformed."

Again, you are simply formulating arguments in the absence of any idea what scientists are talking about. I think you really do need to take a hard look at what that says about you.

The reasons Moran is confident have not been hidden from you. Which makes it even more amazing, really.

Starwind said...

plunge:
The point I (and Moran) have made is that the term ["junk DNA"] is used inconsistently, and yet creationists and media don't seem to realize this, so they treat every different usage as a debate or a fundamental disagreement.

Agreed its use is inconsistent and problematic, but Moran's tautological definition is no improvement (however self-consistent he may be).

Again, this is a nonsensical response. He's proposing to define the word in such a way to clear up the confusion caused by all those different and conflicting definitions!

As stated, his definition is tautological and perpetuates confusion. TR Gregory offered constructive criticism, to little avail.

Here's a decent discussion of that history by the way:

Yes, read it earlier.

So now that someone has pulled up an example, are you going to apologize to me for implying that I made it up, and for not doing a lit search for you the second you asked for it?

Yes, I do apologize, sincerely. I did in fact suspect you had made it up. I seldom accept unsupported statements at face value, especially on the internet, and certainly not in debate forums where ostensibly one of the goals/criteria is to support one's viewpoint with independent fact as opposed to naked assertion and opinion. But at least one such study had been done as you stated, though my thanks goes to Jason F. who made the effort (repeatedly) to provide the facts.

Haven't I and Moran and others all been arguing that usage of JunkDNA is largely a buzzword that doesn't give one much of a real understanding of the complexity of DNA? Isn't that the point of Moran wanting it to be more strictly limited?

But for a definition to be useful, not only should it be consistent it should also be correct and have precise, useful, meaning. Moran's doesn't.

I raised two issues in my original post:
1) That Moran's "extremely confident" assertions of "junk DNA" comprising a large amount of the mammilian genome seemed to me less like "honest speculation", and more like "dogmatic fact", to borrow The Factician's phrasing.
2) I suggested a (thought) experiment to test Moran's assertions.

As it turns out, I was mistaken in assuming such an experiment had not been done, as Jason F. corrected.

Though supportive of Moran's views, that experiment does not conclusively declare that a large amount of the mammilian genome can be discarded (i.e. "junked") as its author's cautioned in their conclusion. Their caution is further justified in two studies cited below which contradict Moran's views.


Moran's definition here: "I want to keep the term "junk DNA" to refer to all functionless DNA. That includes DNA for which we have direct and indirect evidence of no function (pseudogenes, most of intron DNA, corrupted transposons etc.) and it also includes the rest of the DNA for which no function has currently been discovered [that is the tautology] and we think it's junk because it's not conserved (among other reasons). Junk DNA is not noncoding DNA and anyone who claims otherwise just doesn't know what they're talking about." ... "I think most intron sequences are junk."

And yet, recent studies show conservation in human "gene deserts", including introns:

Ultraconserved Elements in the Human Genome: "Of the 481 ultraconserved elements, 111 overlap the mRNA of a known human protein-coding gene [including the untranslated regions (UTRs)], 256 show no evidence of transcription from any matching expressed sequence tag (EST) or mRNA from any species, and for the remaining 114 the evidence for transcription is inconclusive. We call these partly exonic (or exonic for short), nonexonic, and possibly exonic ultraconserved elements, respectively. A hundred nonexonic elements are located in introns of known genes and the rest are intergenic. The non-exonic elements, both intronic and intergenic, tend to congregate in clusters near transcription factors and developmental genes, whereas the exonic and possibly exonic elements are more randomly distributed along the chromosomes (Fig. 1). p2"

"Non-exonic ultraconserved elements are often found in “gene deserts” that extend more than a megabase. In particular, of the non-exonic elements, there are 140 that are more than 10 kilobases (kb) away from any known gene, and 88 that are more than 100 kb away. ... Non-exonic ultraconserved elements that lie in introns are also often associated with developmental genes. These include the neuroretina-specific enhancer in the fourth intron of PAX6 (uc.328), investigated in quail but shown to also be functionally conserved in mouse (22)." p3

"Although the minimal region of 100% conservation between human, mouse, and rat that was required to be included in the ultraconserved set was 200 bp, many elements were considerably longer. The longest elements (779, 770, and 731 bp) all lie in the last three introns in the 3 portion of POLA, the DNA polymerase alpha catalytic subunit (EC 2.7.7.7) on chromosome X, along with other shorter ultraconserved elements (Fig. 1)." p4

"The ultraconserved elements we found in introns seem to have been at one time rather fast-evolving as compared to the known coding exons in their genes." p5

"A more extensive analysis of paralogs, based on a recent global clustering of highly conserved noncoding human DNA (31), reveals several further highly conserved intronic and intergenic elements in functionally equivalent positions relative to paralogous genes. These were not classified as ultraconserved by our stringent criteria. ... If instead we demand at least a 100-bp exact match between humans and rodents, we get more than 5000 highly conserved elements. Tens of thousands more are found at lower cutoffs;" p5

Further, there is evidence that while some "gene deserts" are indeed deletable, others are rich in regulatory elements:

Evolution and functional classification of vertebrate gene deserts: "One of the unexplained architectural asymmetries observed in the human genome sequence is the uneven distribution of genes (Lander et al. 2001; Venter et al. 2001). Specifically, it has been estimated that ∼25% of the human genome consists of gene deserts, defined as long regions containing no protein-coding sequences and without obvious biological functions (Venter et al. 2001). Some of these gene deserts have been shown to contain regulatory sequences that act at large distances to control the expression of neighboring genes (Nobrega et al. 2003; Kimura-Yoshida et al. 2004; Uchikawa et al. 2004). By contrast, other large gene-sparse regions are potentially nonessential to genome function, since they can be deleted without significant phenotypic effect (Russell et al. 1982; Rinchik et al. 1990; Nobrega
2004). It is possible that these differences reflect the existence of distinct categories of gene deserts, such that some deserts harbor sequence elements with critically important and conserved biological roles whereas others do not." p2

"Stable gene deserts are thus prime candidates for regions with key distant gene REs in the human genome. The function of variable gene deserts is more ambiguous. They possibly represent recently evolved regions that have not yet been fixed; alternatively they may lack important function and represent genomic “junkyards.” This dichotomy potentially reconciles the apparent disparity in studies showing that while certain human gene deserts are rich in gene REs (Nobrega et al. 2003; Kimura-Yoshida et al. 2004; Uchikawa et al. 2004) some of these regions have no phenotypic impact when deleted from the mouse genome (Nobrega et al. 2004)." p8

The reasons Moran is confident have not been hidden from you.

Nor have they been correct.

Scott Hatfield . . . said...

Starwind:

I commend you for the obvious effort you are making to deal with the actual data and the scientific literature. You describe yourself as an 'ID-layman', but let me assure you that in my experience you have already displayed more humility and real scholarship than many who would no doubt identify themselves as 'ID-advocacy-scientists.'

I particularly admire your willingness to retract past statements or moves within an argument. This is a sign of confidence, and of the strength, rather than (as many YEC often hold) of the supposed weakness of science.

With the respect to the 'ultraconserved sequences', it's nice to see that you're au courant. Remember, though, that from my perspective 'ultraconserved' introns effectively means 'retained as the result of extraordinarily strong selection', especially as the introns are not directly expressed as protein!

Starwind said...

Scott Hatfield:

*blush*, thank you Scott.

I particularly admire your willingness to retract past statements or moves within an argument.

Well, there's just no future in being wrong and staying wrong.

This is a sign of confidence, and of the strength, rather than (as many YEC often hold) of the supposed weakness of science.

There's good and bad science on both sides of the aisle. Genuinely good science, like properly interpreted scripture, leads to a correct understanding that can only help.

from my perspective 'ultraconserved' introns effectively means 'retained as the result of extraordinarily strong selection', especially as the introns are not directly expressed as protein!

I'm uncertain as to your point here. Yes introns are spliced out of mRNAs and are not expressed, and they do have selection pressures to maintain their splicing signals and to avoid new splicing signals for incorrect locations.... beyond that ????

Scott Hatfield . . . said...

Starwind:

Sean Carroll has described these ultraconserved sequences as among the most impressive pieces of evidence for evolution:

http://seanbcarroll.com/books/The_Making_of_the_Fittest/excerpt/

Starwind said...

evidence for evolution ... The Making of the Fittest,

Ah, I understand.

I've not read Carroll's book(s) as I tend to avoid "popularizations" (they're oft loaded with too many presuppositions and apriori viewpoints which are very time consuming to filter through) and stick to the basic papers in any given discipline.

Were I to read it, I'd be looking for distinctions among "speciation", "macro-evolution", and abiogenesis, whatever hard science is presented in support of each, and then what extrapolations are requested or implied and the quality of any scientific support for those extrapolations.

I suspect Carroll comes from an apriori "common descent" viewpoint, which I would compare and contrast against my apriori "common designer" viewpoint.