“Junk DNA”

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A common comment by IDists concerns “junk DNA”: they will claim that it is only “evolutionists” who would have thought that so much of the genome was “junk,” but that an IDist would assume that what looked like junk was in fact there for a purpose. Therefore, as scientists start to learn about previously unknown functions for some of that “junk DNA,” some of the IDists are crowing “We told you so - if you just wouldn’t have been so dogmatically attached to your theory of blind, purposeless evolutionary processes, you wouldn’t have set research back by dismissing so much of the genome as “junk.” (I could go find quotes to this effect, but I will assume that those of you who keep up with the IDists know what I am talking about.)

Now in November of last year, Scientific American had an article, “The Unseen Genome: Gems Among the Junk,” in which writer W. Wayt Gibbs (not an IDist)summarized some of the new research on what has been considered the junk part of the genome, and in the process made some similar comments about how “dogmatism” has misled biologists into mislabeling and thus ignoring the “junk.”

However, in March of this year Scientific American published a letter by Harold Brown, a member of the philosophy department of Northern Illinois University, responding to this charge of dogmatism with some very pertinent points. I’d like to discuss what Brown had to say.

Here is the heart of what Brown wrote:

This narrow focus [on the “non-junk” part of the genome] by the research community led to detailed discoveries that have, in turn, challenged the the guiding dogma and done so in a relatively short time on the scale of human history.

Closely constrained communal research may be a more effective long-term means of pursuing knowledge than research in which resources are continually diverted to following up any apparent lead. The idea that tightly organized research leads (despite itself) to the recognition of anomalies that generate new approaches was one of the themes of Thomas S. Kuhn’s “The Structure of Scientific Revolutions.”

First let me make the obvious and important point that the discovery of these previously unknown functions has been made by mainstream biologists, not by IDists! It’s not very compelling for the IDist to say, effectively, “well, if we had been doing the research, we would have figured this out sooner,” when in fact they don’t do any research.

However, the more important point lies in Brown’s reference to Kuhn. One of Kuhn’s points is that true “paradigm shifting” only comes when one truly immerses oneself in the details of the current paradigm, for only then can one really understand the key issues upon which the paradign shift must occur. If one has but a shallow understanding of the current paradigm, it is easy to offer all sorts of possible paradigm shifts, but, being ungrounded in what is solidly known, such speculations are almost guaranteed to be wrong. That is, it’s really easy to come up with new ideas about how things might be if in fact you don’t know much (or choose to reject what is known for ideological reasons of one’s own) - bad ideas are a dime a dozen and are easy to come up with just sitting in the armchair, so to speak, but good ideas take hard-working immersion in the details.

The IDists are sitting in the armchairs, saying “I told you so” to the people out doing the hard work. So next time someone using this “junk DNA” argument in respect to ID, ask, “So who’s figuring out what part isn’t junk and what it in fact does?” Until the IDists get in there and do some of the research that will uncover the genuine anomalies in our current understanding, they have no cause to take any credit whatsoever for shifting the paradigm about “junk DNA.”

100 Comments

Jack Krebs wrote:

First let me make the obvious and important point that the discovery of these previously unknown functions has been made by mainstream biologists, not by IDists!!

Indeed. And not by evolutionary biologists either. Evolutionary biologists do no research into genome function. Rather, the work is done by molecular biologists and cell biologists who largely ignore the rantings of evolutionists, creationists or IDer’s. As I’ve said many times before, the notion of intelligent input is an interpretation of research data, not an area of research itself. It is disingenuous for anyone today to claim that the darwinian paradigm did not delay the understanding of these processes by declaring that non-coding DNA was “molecular garbage, left over from failed evolutionary experiments” and convincing large numbers of researchers that it was true.

BTW, you might be interested in looking here:

http://tinyurl.com/3vlmj

I’ve been arguing the case for the importance of “junk DNA” for at least 5 years and receieved nothing but scorn and ridicule from the PhD biologists on talk.origins like Dr. Moran, Dr. Myers, Dr. Taylor and Dr. Hershey. So far, no one has stepped foward and admitted that I was right.

Nice article, Jack.

But the problem with the IDist argument is worse than this. It assumes that 1) the mainstream position regards all sequences of unknown function to be “junk”, and 2) the sequences regarded as “junk” are of unknown origin. Neither is true.

Molecular biologists have long figured that there would be functional segments within the long stretches of noncoding regions, just that we didn’t yet know what those functions might be. So it’s no surprise that we find some. Afterall, the percentage of the genome that is functional can only increase as our knowledge increases, so it’s a no-brainer that we will continue to find functional sequences. For the IDists to claim that this is a sign of their success is intellectually lazy and betrays a misunderstanding of the state of the science.

Secondly, there are many sequences, such as endogenous retroviruses, pseudogenes, and tandem repeats, whose evolution is quite well known, so it’s not as if “junk DNA” has been ignored. It has in many cases been well studied precisely because it tells us a lot about evolution. Oftentimes, it’s not that these sequences don’t do anything, but what they do tends to facilitate their own replication, and doesn’t necessarily help the genome as a whole. (Which is why “junk” is usually placed in scare quotes.) If these sequences can evolve to help the genome as a whole (to become a mutualist, instead of a parasite, as it were) – or, if short duplicated segments can become functional – then so much the worse for IDology. IDists frequently claim that cooption doesn’t happen, or that new “information” can’t evolve. Finding functional DNA among the junk just goes to show that new functions can evolve through mundane mechanisms.

And finally, IDists, almost without exception, seem to vastly underestimate the scope of the problem. In the human genome, about 3% is coding, about 5% give or take is regulatory. (I forget what the latest numbers are.) Another 10-15% seems to be highly conserved with mouse and rat, so it too may be functional. But even if we’re generous, it would still remain that well over 50% of the genome is currently known as “junk”. What exactly are the IDists predicting here? That the whole thing is functional? If so, they need to own up to the fact that the evidence is stacked massively against them, and that small bits that are found to have a function – a fraction of a percent here and there – aren’t doing anything to save them.

On the other hand, maybe they have a more subtle understanding of what the genome is supposed to be like. If so, they haven’t bothered telling anyone. They haven’t provided any kind of framework through which to understand the genome, no hypotheses about what sorts of functions we should expect to find, much less any notion of how they originated. In other words, no science. It’s much easier to sit back and critique a strawman version of what the other side thinks rather than try to generate some kind of useful theory of your own. Which I take it is Jack’s point.

Charlie Wagner Wrote:

Evolutionary biologists do no research into genome function.

Charlie, you are an ignorant sod. Try doing a literature search and spend the five seconds it takes to disprove such a ridiculous statement.

I don’t know the history of this discussion, but here’s my take.

“Junk DNA” always struck me as an unfortunate coinage. To assume that what is known about the functionality of a particular stretch of DNA is all that will ever be known seems like Beheism, pure and simpleminded.

But I always assumed that what people meant by that term was DNA that was introduced into, or carried along in, genomes simply because that’s what DNA does. And like all DNA, it serves as raw material for evolution. Any particular stretch of DNA may or may not have become “dedicated” to a particular functionality, and some of these functionalities may be too subtle for us to detect or understand - at least yet.

So if that’s what Charlie was arguing, and others were arguing against, let me just say loud and clear:

********************************************************* **************CHARLIE WAS (IS) RIGHT!*************** ********************************************************* (imho)

Where this is at odds with standard “Darwinian” evolution, though, is too subtle a point for me to understand.

If, on the other hand, Charlie was arguing that association of any functionality with this unfortunately labled DNA provides evidence for intelligent design, I’d have to say, in the immortal words of Starkist Tuna, “Sorry Charlie”

Steve Reuland wrote:

Charlie, you are an ignorant sod. Try doing a literature search and spend the five seconds it takes to disprove such a ridiculous statement.

Cite one paper where an evolutionary biologist has published a paper on genome function and I’ll retract my statement. And try to dispence with the name calling. It doesn’t become you. Ball’s in your court…

Charlie: Cite one paper where an evolutionary biologist has published a paper on genome function and I’ll retract my statement

If I search PubMed for

evolutionary biology[ad] AND genome

I get 269 hits. Are you telling us not one of those qualifies?

A simple search for- evolutionary biology, genome function -will make your head swim. Why can’t we just have a copy/paste function here?

www.jgi.doe.gov/programs/comparative/ComparativeGenomics.html

www.geocities.com/Athens/Forum/8424/bio.html

www.biomedcentral.com/bmcevolbiol

www.rci.rutgers.edu/~ecolevol/fulldoc.html

www.bioinfo.rpi.edu/~zukerm/CIAR

www.beyondgenome.com/isb.asp

Here’s what Pubmed has to offer under evolutionary biology, genome function

Bob wrote:

A simple search for- evolutionary biology, genome function -will make your head swim.

Like I said, cite ONE paper by an evolutionary biologist describing research on genome function. That shouldn’t be too hard.

Take your pick, Charlie - there’s sure a lot to work with.

Russell wrote:

I get 269 hits. Are you telling us not one of those qualifies?

A few pointers: We’rer not searching “evolutionary biology”, we’re looking for paper related to genome function BY an evolutionary biologist. And don’t search genome function, put it in quotes, so it’s searched as a concept, not as individual words. I got 86 hits and only one was of interest and it’s a review paper:

Genome Res. 2003 Jun;13(6A):1029-41.

Genome function and nuclear architecture: from gene expression to nanoscience.

O’Brien TP, Bult CJ, Cremer C, Grunze M, Knowles BB, Langowski J, McNally J, Pederson T, Politz JC, Pombo A, Schmahl G, Spatz JP, van Driel R.

The Jackson Laboratory, Bar Harbor, Maine 04609, USA. [Enable javascript to see this email address.]

Biophysical, chemical, and nanoscience approaches to the study of nuclear structure and activity have been developing recently and hold considerable promise. A selection of fundamental problems in genome organization and function are reviewed and discussed in the context of these new perspectives and approaches. Advancing these concepts will require coordinated networks of physicists, chemists, and materials scientists collaborating with cell, developmental, and genome biologists.

I didn’t find any papers by evolutionary biologists. Perhaps you will have better luck

Bob wrote: Take your pick, Charlie - there’s sure a lot to work with. You know Bob, I’m old enough to remember Sen. McCarthy standing before the U.S. Senate committee shouting and waving a handful of papers. His words still ring in my ears: “I have here in my hand, evidence that there are over 300 communist sympathizers presently working in the Federal Government…”

Turns out, the pages were blank.

So, you pick ONE paper, and we’ll talk about it.

Charlie Wagner Wrote:

Cite one paper where an evolutionary biologist has published a paper on genome function and I’ll retract my statement.

I’m not sure what’s worse, the laziness, or the determination to drag the thread off-topic.

Anyway, a PubMed search of “genome evolution” turns up close to 12,000 hits. The articles are from people in a wide variety of departments, including genetics, molecular biology, biochemistry, cell biology, immunology, and yes, evolutionary biology. Many labs are interdisciplinary; in fact, evolution is firmly integrated with all biological research programs. And that, by the way, throughly disproves your other claim, which is that molecular biologists et al ignore evolutionary theory. Anyway, here are just a few examples. taken from the first page:

  • Chromosome Res. 2004;12(4):317-335. Evolution of Genome Organizations of Squirrels (Sciuridae) Revealed by Cross-Species Chromosome Painting.

    Li T, O’Brien PC, Biltueva L, Fu B, Wang J, Nie W, Ferguson-Smith MA, Graphodatsky AS, Yang F.

  • Proc Natl Acad Sci U S A. 2004 Jul 7 [Epub ahead of print]   Rapid recent growth and divergence of rice nuclear genomes.

    Ma J, Bennetzen JL.

  • Genome Biol. 2004;5(7):232. Epub 2004 Jun 21.   Cross-species comparison of genome-wide expression patterns.

    Zhou XJ, Gibson G.

There are 595 more pages. The first paper was published from a molecular evolution lab, and the other two were from genetics departments, which evolutionary biology programs are usually nested within.

Now, it didn’t exactly take much effort to do that search, which is the only reason I consented to do it. But really, couldn’t you have done it yourself? Don’t you think you should check on these things before making sweeping claims about them? I would hope that simple curiosity alone would be enough to encourage one to look through the literature.

And try to dispence with the name calling. It doesn’t become you.

I apologize. How about you try not to drive everyone nuts by making ludicrous claims? That way I won’t be tempted.

Charlie Wagner Wrote:

Evolutionary biologists do no research into genome function. Rather, the work is done by molecular biologists and cell biologists who largely ignore the rantings of evolutionists, creationists or IDer’s.

Doesn’t this statement depend upon rather artifical definitions? For example, how do you define ‘evolutionary biologist’? If it is someone who studies organisms, then it’s unlikely that they will also be a genomics expert. Does someone who studies genome evolution (and function), but doesn’t call themselves an evolutionary biologist count? There are many such people. And what does the phrase “research into genome function” mean? If the work of molecular biologists and/or cell biologists doesn’t count, what kind of research are you talking about? And what kind of genomes? Do bacteria count? How about yeast? C. elegans? Or only mammals? There have been lots of studies of bacterial genomic evolution.

Also, one has to keep in mind that we’ve only had whole genomes for less than 10 years, and it’s only in the last 5 or less that we’ve had enough to do large-scale comparative studies.

One of the difficulties is deciding who is an “evolutionary biologist.” That’s a bit like trying to decide who among chemists believes in the conservation of matter [and energy]. Biology is suffused with evolutionary thinking - so unless someone claims to be a non-evolutionary biologist, all biologists are evolutionary biologists in one sense or another.

The common thread through the arguments of IDC-ers, which Charlie parrots, is that if we don’t know exactly all the parameters of a phenomenon, then all explanations are possible, including IDC. That is true only to some philosophers - in real science, we assume that physical laws don’t change, nor do biological ones. Likewise, we take the simplest, most widely applicable principle to be true. The third principle is utility - an argument or possibility isn’t worth thinking about unless it leads somewhere (like new experiments or observations). Special creation (which is what IDC implies) has no place at the table. It violates all three principles.

Now if Charlie or someone else comes up with something that is simple (and not merely simply stated), is applicable across the observable universe and leads somewhere, they will be taken seriously. But until they do, the scienific (as opposed to political) claims aren’t even worth refuting.

Charlie:A few pointers: We’rer not searching “evolutionary biology”, we’re looking for paper related to genome function BY an evolutionary biologist

Thanks! You don’t by any chance offer a course or something where these tips are collected and organized so I can do my research more effectively?

Here’s a tip for you: if you put [ad] after ‘evolutionary biology’, you restrict the search to papers in which the authors are specifically, explicitly identified as being affiliated with a department or institution with the words ‘evolutionary biology’ in its title. I anticipated that you might treat us to some interesting redefinitions of terms, so I figured that any author that affiliates him/herself with a department called “evolutionary biology” would be a pretty good candidate for being an evolutionary biologist.

Mind you, I regard this as an extremely porous net. In my view, only a tiny fraction of “evolutionary biologists” are going to be explicitly associated with a department with that name.

Just out of curiosity, what did you think that ‘[ad]’ was doing there?

charlie wagner Wrote:

A few pointers:   We’rer not searching “evolutionary biology”, we’re looking for paper related to genome function BY an evolutionary biologist. And don’t search genome function, put it in quotes, so it’s searched as a concept, not as individual words.

Putting the words in quotes requires that the words (not the concept) appear one right after the other in the abstract. That’s a stupid way to do a search, unless you’re looking for a specific term.

I’m also seeing the infintely movable goal post criterion, as I should have expected. Since you want to limit this only to “evolutionary biologists”, please explain to us precisely what qualifies one as an evolutionary bioloigst, and exactly how you can determine such from a person’s name and affiliation.

You should really just go ahead and retract your statement and quit wasting everbody’s time. It’s so far off the mark that goal-post moving won’t save you.

Charlie I’m a application architech. I don’t write pappers on OS Kernal internals but that doesn’t mean I don’t believe in those functions.

Are you trying to make us believe that genetic biologists don’t believe in evolution? Please find me one that does real research that doesn’t believe in C.D.

Bio Engeneers are a prime example of a cross breed between genetic biologists and evolutionary biologist. I guess the guys and girls that create new plants who’s genes have been altered to include genes from bacillus thuringiensis to kill pests don’t care about evolution, according to you, because they are basically genetic biologists but wait! They also concern them selves with the problem of pests evolving to become resistant to the Bio Eng plants via another process you say can’t happen naturally, via random mutation and natural selection. I guess those alians of yours are watching and sending down space dust with tons of space viruses to alter the genome of the pests in an intelligent manner so they can feed on the Bio Eng plants agian.

Hmmm but wait we know that allowing a sufficiant population of the pests to survive, via plantings of non bio eng plants, can cause the resistant pests to not have enough of an impact on the entire population thus preventing evolution, because those of us that understand concepts of evolution know that evolution works on a population level not individual levels.

Anyway please list for us the names of scientist, genetic biologists, that don’t believe in evolution.

Charlie Wagner Wrote:

Evolutionary biologists do no research into genome function. Rather, the work is done by molecular biologists and cell biologists who largely ignore the rantings of evolutionists, creationists or IDer’s.

After searching for 30 seconds on the web I found Claude W. dePamphilis from Penn State who describes himself as a “plant evolutionary biologist” and does all kinds of work on plant genomes.

Here’s the intro to his site:

I am a plant evolutionary biologist with broad interests in processes and patterns of evolution at both the molecular and organismal levels. The main focus of our research is the study of parasitic plants – phylogeny, biology, and molecular evolution. Although most plants are autotrophic, several thousand species of angiosperms obtain water, minerals, and fixed carbon heterotrophically, using specially modified roots (haustoria) that extract these materials directly from a host plant. In addition to their intrinsic interest as organisms with complex adaptations for direct feeding upon other plants, some parasitic plants are highly destructive weeds of important crop plants, and thus of great economic significance. Furthermore, because some parasites have completely lost the ability to photosynthesize, these plants provide a powerful system for the investigation of the effects of drastically altered functional constraints on gene and genome evolution and function.

Syntax Error: not well-formed (invalid token) at line 3, column 1, byte 539 at /usr/local/lib/perl5/site_perl/5.16/mach/XML/Parser.pm line 187.

Ah heck, let’s pile on some more!

Charlie states,

Evolutionary biologists do no research into genome function.

I certainly think someone with the title “evolutionary geneticist” could be considered an evolutionary biologist who does research into genome function.

So a quick Google search turns up 780 hits for “evolutionary geneticist”. Now, unless Charlie wants to argue that none of these folks publish any research, I believe his assertion has been soundly refuted.

In one of Jason’s hits turns up this article, which even has a helpful diagram! (Acrobat reader required.)

Going back to the “junk” DNA story, I started grad school in Molecular Biology nearly 15 years ago now and even then no scientist that I recall was on the record saying that the repetitive nonsense coding sequences in the genome really was “junk” in the sense that it was entirely “genomic garbage” or a vast toilet on which DNA polymerases and recombinases squatted “just because.”

It was called “junk” DNA because most of it obviously didn’t encode anything and there was little or no information content. In other words, it LOOKED like junk. And “junk” is a short descriptive word that everyone just latched onto. But no one ever suggested that humans could delete every bit of it and survive. To the extent that some non-molecular biologists and non-scienstists were left with that impression, it’s an unfortunate side effect of using colorful nomenclature to describe something that is, like nearly everything else in molecular biology, extraordinarily complex.

I totally disagree with Brown’s reference to Kuhn’s overused “paradigm shift” claptrap. There was no “revolution” or “paradigm” shift with respect to “junk DNA”.

We’re again suffering from ANW’s “fallacy of misplaced concreteness”.

“We typically accept a high level of abstraction in what we believe and demand a high level of concreteness when we disbelieve”

Again this doesn’t imply that anyone’s wrong. It merely implies communication difficulties.

Since Charlie likes Bertrand Russell let me recommend rereading The Scientific Outlook. Russell discusses evolution in two places, Darwin early on, and then science and religion farther in. Russell sees no need for design, even though DNA hadn’t been discovered. The rule of thumb for complex organisms is that they look more alike at the DNA level than at the organismal level (the opposite of the situation for single celled organisms).

In a May 5, 2003 interview with Caltech president David Baltimore, James Watson, discover of DNA structure, was asked the following question:

Baltimore asked Watson about the 75% of non-coding DNA in the human genome that is repetitive, when other species have much less repetitive DNA: Do you think, he asked, that’s a proof that all of that excess DNA really is junk, sort of a parasitic DNA that only cares about itself?

“It’s more like 95 percent,” answered Watson. “As in the other species, it looks like there’s about 5 percent that’s conserved- 1 percent are amino-acid-specifying, and the other 4 percent are useful in regulating when, where, and to what extent individual genes function.” All human genetic variation resides in that 5 percent, he said.… “While many human attributes won’t have genetic causes, we shall probably be surprised by the extent that they do.”

IMHO, James Watson belongs to that class of Nobel laureates who received the prize not because they were brilliant scientists, but rather because they were clever enough to be in the right place at the right time with the right people (e.g., damn smart people like Francis Crick).

From the point of view of someone like Watson, the non-coding, non-regulatory DNA sequences in our genomes are, relatively speaking (relative to the regions encoding genes), fairly referred to as “junk.”

I do not believe that Watson ever contributed significantly to any experimental research relating specifically to determining any biological function (or lack therof) for so-called “junk” DNA.

For most of the modern molecular biological era, Watson’s contributions to science have been limited to the contributions expected of a political figurehead (and some contributions that weren’t expected).

For example:

Witnesses were flabbergasted when the 72-year-old discoverer of the double helix suggested there was a biochemical link between exposure to sunlight and sexual urges. “That’s why you have Latin lovers,” Watson said. “You’ve never heard of an English lover. Only an English patient.”

In a lecture hall jammed with more than 200 Berkeley students and faculty members, Watson showed a slide of sad-faced model Kate Moss to support his contention that thin people are unhappy and therefore more ambitious.

“Whenever you interview fat people, you feel bad, because you know you’re not going to hire them,” Watson said.

Regarding the above comments, Tom Cline (geneticist at UC) remarked, “[his lecture was] more embarrassing than having a creation scientist up there.”

See http://www.mindfully.org/GE/James-W[…]t-Sexist.htm for the rest of the juicy details.

Hello, I am rather new to this subject and stumbled across this site in research after reading a link reccommended to me. I think that you may find it interesting so please read this site, i will be back soon to see what you made of it, i hope you find it of interest. http://www.luisprada.com/Protected/[…]coveries.htm

btw, be nice to each other guys, this subject is tough enough without the tension, although i must admit it made interesting reading.

Michelle

After I read the sentence “human languages did not appear coincidentally but are a reflection of our inherent DNA,” I had a very very bad feeling. The article is 99.9% pure baloney.

Are you researching pseudoscience on the web? If so, it’s a good article for you.

Perhaps I’ll re-read it after I test my latest batch of LSD, but I don’t think my opinion will change.

Have a nice day.

I’m impressed, GWW. I couldn’t even bring myself to scroll down the page.

Glad to see some comments today. Here’s some responses:

Steve wrote,

It’s much easier to sit back and critique a strawman version of what the other side thinks rather than try to generate some kind of useful theory of your own.  Which I take it is Jack’s point.

Exactly

My thanks, also, to those of you who spent time answering Charlie.

I also appreciate Great White Wonder’s (GWW - are you the same guy who always posts as something Dylanesque?) bringing the thread back on topic (although it may quickly have wandered always again.)

But GWW said something that I need to respond to. He wrote,

I totally disagree with Brown’s reference to Kuhn’s overused “paradigm shift” claptrap.  There was no “revolution” or “paradigm” shift with respect to “junk DNA”.

Brown didn’t use the phrase “paradigm shift” - I did, and I didn’t mean to imply anything earth shattering. What Brown wrote was this,

The idea that tightly organized research leads (despite itself) to the recognition of anomalies that generate new approaches was one of the themes of Thomas S. Kuhn’s “The Structure of Scientific Revolutions.”

His point, which I think applies to learning at all levels and of all kinds, is that focusing closely and deeply on a subject at times is essential for really understanding its broader implications and connections. (Of course, you also have to have some knowledge of those broader connections - it is possible to over-focus and have an insufficient background, but that is the opposite problem of the one we are discussing.) But it is only by knowing a subject well that one is likely to be able to tell a true anomaly from an armchair strawman, and it is only by knowing a subject well that one is likely to be able to ask the questions that lead to knowledge that “breaks through” a logjam, so to speak, whether it be big or small.

So I want to make it clear that Brown wasn’t making the point that the work being done was “paradigm shifting” - he didn’t even use that phrase, and neither was I if that is meant to imply some large revolutionary upheaval in our understanding.

Charlie, I’d suggest that it was more a case of you making yourself look bad. You made a plainly worded statement, were called on it, and then issued a plainly worded challenge. I’m not usually a mind reader, don’t know about the rest of the folks here, so I try to go with what someone says, and there was nothing vague about what you said.

Les Lane wrote:

But where are the McDonalds on Pluto?

I don’t know about McDonald’s, but I’m pretty sure there are Wooly Mammoths on Pluto. I recall vividly my 3rd grade classroom. Around the room were paintings depicting what it might by like on other planets. Since I was “W” I always had the last seat in the last row, so I was right next to Pluto. I remember the Wooly Mammoths, covered with frozen icicles, shivering in the cold Plutonian darkness.

Russell wrote:

you’re sounding kind of paranoid.

That’s what happens to you after 5 years posting on talk.origins.

Getting back on the topic of the opening post, Charlie restates his thesis thusly:

in the period between 1975 and now, the majority of evolutionary biologists held the view that the noncoding DNA was molecular junk and contributed little research that attempted to elucidate any function in this portion of the genome. In the past few years, based on work done primarily by molecular biologists, it has become apparent to evolutionary biologists that they were wrong in underestimating the importance of the noncoding DNA and some of them have begun to do research in this area. The failure to recognize the full implications of this region of the genome, particularly the possibility that the intervening noncoding sequences may be transmitting parallel information in the form of RNA molecules, may well go down as one of the biggest mistakes in the history of biology.

[my emphasis]

This takes us back to the theme of Brown’s letter, where he wrote,

Closely constrained communal research may be a more effective long-term means of pursuing knowledge than research in which resources are continually diverted to following up any apparent lead. The idea that tightly organized research leads (despite itself) to the recognition of anomalies that generate new approaches was one of the themes of Thomas S. Kuhn’s “The Structure of Scientific Revolutions.

So I think that it is not at all reasonable to call this “failure to recognize, etc. … one of the biggest mistakes in the history of biology.” We have learned a tremendous amount about genes and all their related topics in the past 30 years, and I seriously that there were unused research talent and dollars during that time. As Brown says (more succinctly than I am about to), focusing on what is fertile new ground and is yielding results commensurate with the supply of research capital is a better us of scientist’s (and society’s) time than is spreading research efforts too thin.

One of the reasons for this, as Brown also says, goes beyond just economics: “tightly organized research,” by digging deeper, both sets the stage for and then uncovers the most pertinent questions to ask at the next stage of research. Without the deep knowledge built from the last 30 year’s research, we would be less likely to know how to make sense of the noncoding regions and less likely to know what questions to ask about their function.

So I don’t believe that it has been a big mistake (much less “one of the biggest mistakes in the history of biology) that this research into the noncoding regions has not been a focus of genomic research until recently.

I do agree that it was a mistake (in retrospect) to call these regions “junk” - this is similar to the problem I have every year trying to explain that imaginary numbers have been badly misnamed and are no more imaginary (or real) than any other number. On the other hand, physicists have named two of the quarks “charm and “strange” - think what problems they must have! :) So we do have to be careful what we call things.

Hmmm - it’s too bad we can’t edit post: I meant “I seriously doubt that there were unused research …”,

Earlier it took me about 30 seconds to find a discussion from 1998 where a grad student details the many functions known to so-called junk dna. In another 30 seconds, you can find papers dating back to 1993 positing various functions, and in-depth studies of the inter-species differences go back at least to 1980.

Russel Wrote:

RE: Dave S’s “rant” on junk DNA: Excellent analysis.

My whole problem with the term is the way it lends itself to DI-style distortion, relying exclusively on that last meaning from your word history:

Junk has gone on to mean useless waste as well.

Of course the original coiners of the term can hardly be faulted for not anticipating the philological fancy footwork of New Paleyists.

On a side note, the original meaning of this term is still in use in some parts. My father and his generation still call a piece of rope a junk and we also use it as a synonym for piece in general for casual conversation, as in having a junk of pie for instance.

It’s the concept that’s important, not how a word might possibly be misconstrued, whether accidentally or as a result of powerful biasing forces.

Charlie,

Can’t help but deconstruct and/or semantically writings that have no scientific merit whatsoever. I am still waiting for you to cite a scientific paper - not a pseudoscientific masterpiece - that talks of junk DNA in the same ways that you do. C’mon who is the “molecular biologist” who “criticises” “evolutionary biologists” for ignoring “junk DNA”?

Charlie,

Can’t help but deconstruct and/or semantically writings that have no scientific merit whatsoever. I am still waiting for you to cite a scientific paper - not a pseudoscientific masterpiece - that talks of junk DNA in the same ways that you do. C’mon who is the “molecular biologist” who “criticises” “evolutionary biologists” for ignoring “junk DNA”?

No TRUE Scotsman would make such an argument.

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This page contains a single entry by Jack Krebs published on July 14, 2004 8:07 AM.

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