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"Junk DNA"

Posted 14 July 2004 by Jack Krebs

↗ The current version of this post is on the live site: https://pandasthumb.org/archives/2004/07/junk-dna.html

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

charlie wagner · 14 July 2004

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.

Steve Reuland · 14 July 2004

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.

Steve Reuland · 14 July 2004

Evolutionary biologists do no research into genome function.

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

Russell · 14 July 2004

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"

charlie wagner · 14 July 2004

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...

Russell · 14 July 2004

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?

Bob Maurus · 14 July 2004

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

Bob Maurus · 14 July 2004

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

charlie wagner · 14 July 2004

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.

Bob Maurus · 14 July 2004

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

charlie wagner · 14 July 2004

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. tpo@jax.org 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

charlie wagner · 14 July 2004

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.

Steve Reuland · 14 July 2004

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

— Charlie Wagner
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.

    Mike S. · 14 July 2004

    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.

    — Charlie Wagner
    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.

    Frank Schmidt · 14 July 2004

    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.

    Russell · 14 July 2004

    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?

    Steve Reuland · 14 July 2004

    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.

    — charlie wagner
    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.

    Wayne Francis · 14 July 2004

    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.

    Dave S · 14 July 2004

    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.

    — Charlie Wagner
    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.

    shiva pennathur · 14 July 2004

    Ok. Charlie, if you have a problem accepting evolutionary theory you can try to learn more about it to dispel your doubts. Still not convinced, write a paper on it - it can be on any of the topics you have brought up on this forum (and had your argument on them refuted) - and get it published where we can find it. Can't write a paper - no problem - neither can I. Come up with a paper from PubMed (not some pseudoscientific archive from the CRS/ID trove) that says what you insist upon

    <>

    And then it can be discussed here.

    Jason · 14 July 2004

    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.

    Jim Anderson · 14 July 2004

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

    Great White Wonder · 14 July 2004

    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".

    Les Lane · 14 July 2004

    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).

    joel · 14 July 2004

    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."

    Great White Wonder · 14 July 2004

    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-Watson-Racist-Sexist.htm for the rest of the juicy details.

    michelle · 14 July 2004

    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/russian_dna_discoveries.htm

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

    Great White Wonder · 14 July 2004

    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.

    Ian Menzies · 14 July 2004

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

    Jack Krebs · 14 July 2004

    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.

    RBH · 14 July 2004

    In Michelle's link I got all the way to

    The human DNA is a biological Internet and superior in many aspects to the artificial one. The latest Russian scientific research directly or indirectly explains phenomena such as clairvoyance, intuition, spontaneous and remote acts of healing, self healing, affirmation techniques, unusual light/auras around people (namely spiritual masters), mind's influence on weather patterns and much more.

    Neat that it actually explains phenomena that don't occur. What more can one ask? RBH

    Great White Wonder · 14 July 2004

    Jack

    I catch your drift now. And I stand corrected re: my attributions to Brown. Thanks for the correction.

    I guess there is a mildly interesting topic lurking in the background which is the tendency of individual scientists (possibly as much as the media) to overstate the accordance of their peers' beliefs in order to make their "new" data/conclusions more "exciting" or "groundbreaking".

    My former P.I., for example, was an excellent scientist but a truly remarkable salesman, politician and public speaker. And honest, to boot.

    (side note re the pseudonym -- it's all in honor of our favorite creationist, Chaz Wagner; as to whether i've used other Zimmy-inspired pseudonyms, I plead the 5th ... ;)

    charlie wagner · 14 July 2004

    Steve Reuland wrote:

    or the determination to drag the thread off-topic.

    Ok, let's get back on topic. The original poster was talking about "junk DNA" and how scientists are learning about previously unknown functions for some of that DNA. The poster continued on to say "the discovery of these previously unknown functions has been made by mainstream biologists, not by IDists!". This was the statement I was responding to in my remarks, the previously unknown functions of some of the junk DNA. This was the context in which I used the expression "genome function" when I stated that "evolutionary biologists do no research into genome function". It looks a little different when it's placed in its proper context. So expanding my statement it becomes clear that what I said was "evolutionary biologists do no research into elucidating the previously unknown functions of the portion of the genome previously referred to as "junk DNA". Perhaps I was at fault for assuming that you understood the correct context and meaning of my statement. I looked at the three papers you offered and none of them says anything about the elucidation of previously unknown functions in "junk DNA". Therefore these examples are rejected and my statement stands as written. I did a more complete search of the literature and I have to tell you not to waste your time. There are no papers in the published literature in which an evolutionary biologist (not one who believes in evolution, but one whose primary focus is on evolution in his/her research) has done research into genome function.

    charlie wagner · 14 July 2004

    Russell wrote:

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

    I didn't have a clue. I guess I learned something new today. Thanks!

    charlie wagner · 14 July 2004

    GWW wrote:

    Perhaps I'll re-read it after I test my latest batch of LSD,

    You young folks still have to make the stuff? For old guys like me, the flashbacks are quite enough ;-)

    Jack Krebs · 14 July 2004

    to Charlie: So? How is your point on topic?

    My point is that mainstream scientists, not IDists, are the ones out there studying the genome and trying to figure it out. Furthermore, as Steve R. said above, you can't do that without an evolutionary background because one of the things you have to understand is past events that might account for what we find (endogenous retroviruses, pseudogenes, and tandem repeats, etc.) So molecular biologists and cell biologists have to use evolutionary concepts as part of their work. That's a pretty simple point.

    charlie wagner · 14 July 2004

    Steve Reuland wrote:

    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.

    That's easy. You cite the paper, and I'll call the guy on the phone and ask him/her: "are you an evolutionary biologist?"

    Nick · 14 July 2004

    Papers on genome function by an evolutionary biologist? Just this is a major research topic of one Thomas Cavalier-Smith. E.g.:

    Cavalier-Smith T. Nucleomorphs: enslaved algal nuclei. Curr Opin Microbiol. 2002 Dec;5(6):612-9. Nucleomorphs of cryptomonad and chlorarachnean algae are the relict, miniaturised nuclei of formerly independent red and green algae enslaved by separate eukaryote hosts over 500 million years ago. The complete 551 kb genome sequence of a cryptomonad nucleomorph confirms that cryptomonads are eukaryote-eukaryote chimeras and greatly illuminates the symbiogenetic event that created the kingdom Chromista and their alveolate protozoan sisters. Nucleomorph membranes may, like plasma membranes, be more enduring after secondary symbiogenesis than are their genomes. Partial sequences of chlorarachnean nucleomorphs indicate that genomic streamlining is limited by the mutational difficulty of removing useless introns. Nucleomorph miniaturisation emphasises that selection can dramatically reduce eukaryote genome size and eliminate most non-functional nuclear non-coding DNA. Given the differential scaling of nuclear and nucleomorph genomes with cell size, it follows that most non-coding nuclear DNA must have a bulk-sequence-independent function related to cell volume.

    See also related articles and the book that Cavalier-Smith edited, The Evolution of Genome Size. The Central Facts in this whole discussion are (1) the amount of DNA does not correlate with our traditional notions of organismal "complexity" -- there are "simpler" organisms (e.g. many plants) with much more DNA than us; (2) genome size does correlate with cell volume. Large cells have more DNA on average. Cavalier-Smith is a proponent of what I think is the most likely theory for the "function" of "junk" DNA, which is that it serves a skeletal function, perhaps as spacing for active genes (perhaps large-volume cells need more spacing in order to transcribe genes more quickly). On the other hand, perhaps large cells are simply more tolerant of extra DNA. Anyway, Charlie Wagner ought to retract his statement, because Cavalier-Smith is clearly an evolutionary biologist and clearly works on genome function. PS: See also the EvoWiki page on "junk" DNA.

    Russell · 14 July 2004

    OK. How about just about any paper from the lab of Margaret Kidwell. Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson,
    Phone: 520-621-1960

    Take this one, for instance:

    Vege and Mar: two novel hAT MITE families from Drosophila willistoni.

    Holyoake AJ, Kidwell MG.

    Russell · 14 July 2004

    (sorry... dropped the page ref:)

    Holyoake AJ, Kidwell MG
    Mol Biol Evol. 2003 Feb;20(2):163-7.

    charlie wagner · 14 July 2004

    Les Lane wrote:

    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.

    For some reason, I never read "The Scientific Outlook". I just ordered it and I'll put it on the top of my unread book pile, which now is over 3 feet high.

    Reed A. Cartwright · 14 July 2004

    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.

    — Steve in #5060
    I'd like to point out that this paper came from my department. Bennetzen is considered to be one of our evolutionary geneticists. Charlie is smacked down again.

    Russell · 14 July 2004

    Reed: Bennetzen is considered to be one of our evolutionary geneticists. Charlie is smacked down again.

    I think that's the same Jeff Bennetzen I trained in some virology scutwork when he was an undergraduate at UCSD.

    Hey Jeff: if you're reading this, "Hi!"

    steve · 14 July 2004

    Oxford University Press publishes a journal called "Molecular Biology and Evolution". Take a look at some of their abstracts if you're so insane you don't think molecular biologists study evolution.

    http://mbe.oupjournals.org/content/vol17/issue1/index.shtml

    Wayne Francis · 14 July 2004

    Charlie you are not being reasonable. Like I said before you try to get the ignorant to believe that genetic biologist don't really care about "evolution" via statements like

    Rather, the work is done by molecular biologists and cell biologists who largely ignore the rantings of evolutionists, creationists or IDer's.

    — Charlie
    Then you try to move the goal post by

    evolutionary biologists do no research into elucidating the previously unknown functions of the portion of the genome previously referred to as "junk DNA".

    — Charlie
    This is like saying Michael Schumaker doesn't race indy cars and that indy car drivers don't race F1 cars. Yet both races are very similar in many ways and they have alot of the same principals and Farrari actually deals across the 2.

    Perhaps I was at fault for assuming that you understood the correct context and meaning of my statement.

    — Charlie
    Perhaps you should not try to infer something that isn't true as with this

    work is done by molecular biologists and cell biologists who largely ignore the rantings of evolutionists

    — Charlie

    That's easy. You cite the paper, and I'll call the guy on the phone and ask him/her: "are you an evolutionary biologist?"

    — Charlie
    Where to start on this one. Well I'm sure many of them would say "No" I'm also sure, depending on how tolerant or used to crack pots, that call them up with stupid questions, they are many would have a following statement alongs the lines of "But I'm highly interested in the field and use many of the principals to do my work" and 99.9% of them would be thinking that if they didn't say it. Why don't you do something that is less vague and not as likely to be used out of context, like you question probably would be. Call up a few respected genetic biologist and ask each one of them "Do you believe in macro and micro evolution?" You show us just one that says "Nope" and don't try your conspiracy theory that they believe as you do but are to scared to admit it. I'm inventing a 3rd Acronym we need to start using. We have the YECers that believe in the biblical account but don't produce anything testible (the bible is not testible) or when they do its proven false and they ignore it. We have the mainstream IDers the believe in the divine "Intelligent Designer(s)" that created all species as they are and these species will never evolve but don't form any testible hypothises. We have CWers that believe in "Intelligent Designer(s)" of a non-divine origin that produce life here on earth because it is impossible to happen on its own but some how are included in the "natural laws" themselves but apparently excluded from those when it comes to their own origins All 3 of these groups seem to like to make wild statements that much of "mainstream science" is just off their rocker and involved in some huge conspiracy. Note I'm not bundling the IDers that don't distort the facts and accept that at this time evolution is the most plausible answer given the current data.

    Ian Menzies · 14 July 2004

    Paleyist

    steve · 14 July 2004

    Lunatic

    steve · 14 July 2004

    I think Creationist is best. It's honest, and everyone knows what a creationist is. Young Earth, Old Earth, ID, the details are slightly different but it's important to keep the fundamental nature in mind. I don't care if they don't believe in evolution because they think Peter Pan designed all multicellular animals on a Dell Inspiron, they're still essentially creationists. If distinguishing the types is so important, I vote for the terms YEC, OEC, IDC, because saying Young Earth Creationist is too much to type frequently, and it still preserves the understanding that these are types of creationist.

    Frank J · 15 July 2004

    I think Creationist is best. It's honest, and everyone knows what a creationist is. Young Earth, Old Earth, ID, the details are slightly different but it's important to keep the fundamental nature in mind.

    — Steve
    In terms of the origins models they promote (what they personally believe may be another story) the differences are anything but slight or "details." From the age of the earth (thousands to trillions or more years in non-biblical creationisms), to common descent, to the identity and abilities of the designer, these are fatal differences in any sense of the word. Unfortunately it's still a well-kept secret among the general public. Advocates of mainstream science have their differences, like the relative importance of selection and drift, but these are trivial compared the differences among creationists. And as you know, scientists are never shy about debating their differences in public, even if it risks being taken out of context by creationists. And as you also know creationists (including, and especially IDers) mostly hide their extreme differences for the sake of the big tent. Whatever we call them, and as you say, we should be explicit whether they are YEC, OEC, IDC, etc, the public must be made aware that what unites them is not any particular alternative model (they have nothing remotely resembling a theory), any particular religious motivation (some are agnostic, while many "evolutionists" are very religious) but a fierce need to misrepresent science. Their internal differences may be radical, but their tactics are amazingly similar.

    steve · 15 July 2004

    speaking of the cool topic of the microbiological study of evolution, here's a cool paper.

    Viral evolution: Influenza evolves
    Influenza epidemics, and the more widespread pandemics such as the Spanish flu of 1918, Asian flu of 1957 and Hong Kong flu of 1968 have made their mark on human history. Continued refinement of the mathematical modelling of the dynamics of influenza epidemics should make it possible to predict the spread of future pandemics, identify viral strains as potential vaccine candidates and anticipate the effect of vaccine use on viral evolution. Ferguson et al. use a model that combines epidemiological data with sequence-level evolution of the virus and find that short-lived strain-transcending immunity is essential to restrict viral diversity in the host population, and thus to explain key aspects of antigenic drift and shift dynamics.

    Ecological and immunological determinants of influenza evolution
    NEIL M. FERGUSON, ALISON P. GALVANI & ROBIN M. BUSH
    Nature 422, 428--433 (2003); doi:10.1038/nature01509
    | First Paragraph | Full Text (HTML / PDF) |

    charlie wagner · 15 July 2004

    Russell wrote:

    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"

    We are dealing with two separate issues here. Evolutionary biologists argued long and hard that the non-coding DNA was "molecular garbage, left over from millions of years of evolution". They were clearly wrong, and that issue is more or less settled. It's beginning to look to me like this "junk DNA" may turn out to actually be at least as important as the protein coding regions themselves. It may be that what makes a human different from a chimpanzee, or a mouse may not reside in the proteins themselves, but rather in the non-coding regions of the genome. The question of whether this functionality is the result of random, accidental processes or intelligent input is a separate issue. I believe that it was intelligently designed because highly organized, complex processes, structures and systems simply do not bootstrap themselves into existence from nothing. There is no evidence that this has ever happened before, or that it is even possible.

    Bob Maurus · 15 July 2004

    But Charlie, what evidence can you cite in support of "intelligent input"? And what evidence can you cite to support your statement that "highly organized, complex processes, structures and systems simply do not bootstrap themselves into existence from nothing"? I would suggest that in both cases the answer is "nothing."

    I would also suggest that, in the former, "There is no evidence that this has ever happened before, or that it is even possible", and in the latter you may be playing with red herrings and strawmen.

    G3 · 15 July 2004

    The question of whether this functionality is the result of random, accidental processes or intelligent input is a separate issue.

    — Charlie Wagner
    That is a good tactic, only bring up the Random Mutation part of the evolutionary algorithm when functionality is mentioned. When duplication and divergence is brought up, ignore Random Mutation and bring up how selection has nothing to work on, since you just have two identical copies. You are obviously an intelligent person Charlie, and seem to understand evolution well enough to hide the parts that go against your argument.

    Russell · 15 July 2004

    Charlie: Evolutionary biologists argued long and hard that the non-coding DNA was "molecular garbage, left over from millions of years of evolution". They were clearly wrong

    Aha! Sounds like we got them dead to rights! Now, let's nail down who were these biologists, where did they argue that, and we'll stick it to 'em!

    Charlie: this "junk DNA" may turn out to actually be at least as important as the protein coding regions themselves

    Well, that seems a bit of stretch. How did we get from "may have some functionality" to "at least as important"?

    Considering that the amount of "junk" DNA in vertebrates is wildly variable (compare Homo sapiens with Danio rerio, for example) but the coding sequences are not, I think I would challenge this assertion.

    Great White Wonder · 15 July 2004

    Charlie

    It may be that what makes a human different from a chimpanzee, or a mouse may not reside in the proteins themselves, but rather in the non-coding regions of the genome.

    Absurd. Even if this proposition was true, Charlie, so what? How do you explain the difference between E. coli and S. typhimurium? Or are bacteria the "exception" in your myopic view of life on earth?

    joel · 15 July 2004

    An article in May 23, 2003 issue of Science, "Not Junk After All", by Wojciech Makalowski states:

    "Most researchers have assumed that repetitive DNA elements do not have any function: They are simply useless, selfish DNA sequences that proliferate in our genome, making as many copies as possible. The late Sozumu Ohno coined the term "junk DNA" to describe these repetitive elements."

    "Although catchy, the term "junk DNA" for many years repelled mainstream researchers from studying noncoding DNA. Who, except a small number of genomic clochards, would like to dig through genomic garbage? However, in science as in normal life, there are some clochards who, at the risk of being ridiculed, explore unpopular territories. Because of them, the view of junk DNA, especially repetitive elements, began to change in the early 1990s. Now, more and more biologists regard repetitive elements as a genomic treasure."

    If what he is stating is true, it certainly wasn't due to to an
    intelligent design approach to the data.

    charlie wagner · 15 July 2004

    Russell wrote:

    Now, let's nail down who were these biologists, where did they argue that, and we'll stick it to 'em!

    Why? Who would waste their time doing that?

    Well, that seems a bit of stretch. How did we get from "may have some functionality" to "at least as important"?

    "In a region of DNA long considered a genetic wasteland, Harvard Medical School researchers have discovered a new class of gene. Most genes carry out their tasks by making a product-a protein or enzyme. This is true of those that provide the body's raw materials, the structural genes, and those that control other genes' activities, the regulatory genes. The new one, found in yeast, does not produce a protein. It performs its function, in this case to regulate a nearby gene, simply by being turned on." Read the entire article here: http://tinyurl.com/6a4qz

    Brad · 15 July 2004

    It may be that what makes a human different from a chimpanzee, or a mouse may not reside in the proteins themselves, but rather in the non-coding regions of the genome.

    This idea is actually not so absurd as GWW implied. It's also not all that new, though. An early, though nevertheless data-rich, articulation of this notion is the following paper: King, M and Wilson AC. 1975. Evolution at Two Levels in Humans and Chimpanzees. Science 188:107-116. The very first line under the title states "Their macromolecules are so alike that regulatory mutations may account for their biological differences." Regulatory regions are non-coding, so Charlie got that right. Of course, as others have stated, just because some non-coding regions have functions (as has been known for some time) doesn't mean that all non-coding regions have functions. In regards to regulatory regions, many biologists (Sean Carroll, Eric Davidson as two who have written textbooks on the subject) consider regulatory evolution to be the primary mechanism accounting for morphological diversification. Doesn't really help Charlie's point about evolutionary biologists and genomics research, though. Incidentally, the Genomes & Evolution 2004 conference was recently held at Penn State--I suspect that many of the researchers there would have considered themselves evolutionary biologists studying genomes... http://www.outreach.psu.edu/C&I/genomes/

    Great White Wonder · 15 July 2004

    This idea is actually not so absurd as GWW implied. It's also not all that new, though. An early, though nevertheless data-rich, articulation of this notion is the following paper:
    King, M and Wilson AC. 1975. Evolution at Two Levels in Humans and Chimpanzees. Science 188:107-116.

    The very first line under the title states "Their macromolecules are so alike that regulatory mutations may account for their biological differences." Regulatory regions are non-coding, so Charlie got that right.

    Heh. I actually rewrote my post at one point to offer a caveat about this "non-coding" argument. But then I read it closely and said screw it because Charlie included not just chimps and humans in his statement, but chimps, humans and MICE.

    So I stand by my evaluation: the statement is absurd.

    As a footnote, I'm also sure that Charlie was making this distinction between regulatory regions and the structural regions of genes. I think he might have been using "non-coding" as a synonym for "junk."

    charlie wagner · 15 July 2004

    Brad wrote:

    Doesn't really help Charlie's point about evolutionary biologists and genomics research, though.

    There is a God! ;-) Do you know how long I've waited to read this: The regulatory content of intergenic DNA shapes genome architecture Craig E Nelson* , Bradley M Hersh* and Sean B Carroll Genome Biology 2004, 5:R25 (quote from paper, not abstract) "Intergenic distance, and hence genome architecture, is highly nonrandom. Rather, it is shaped by regulatory information contained in noncoding DNA. Our findings suggest that in compact genomes, the species-specific loss of nonfunctional DNA reveals a landscape of regulatory information by leaving a profile of functional DNA in its wake." I have the greatest admiration for you folks, especially Dr. Carroll, whose work I follow with great interest. You guys know the truth. You have to know the truth. You're too smart NOT to.

    Russell · 15 July 2004

    Russell: Now, let's nail down who were these biologists, where did they argue that, and we'll stick it to 'em! Charlie: Why? Who would waste their time doing that? Well, my sense is that this whole thing is a red herring, that no serious biologist ever contended that all that "excess" DNA would forever remain unassociated with function, and that that notion was sort of a popular misunderstanding encouraged by the unfortunate label, "junk" DNA. But you seem to be saying that evolutionary biologists argued "long and hard" just exactly that. I think that would be scientifically indefensible, and I'd like to know: was this just idle chit-chat over a few beers, or did this actually make it into peer-reviewed literature? Thanks for the reference to Martens et al. That looks interesting. I don't think, though, that it goes very far in getting from "may have some functionality" to "at least as important as protein coding" - especially in light of that Danio rerio situation. Also, in light of all the documentation posted above of research on genome function by evolutionary biologists, did you retract that statement, as per

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

    charlie wagner · 15 July 2004

    Russell wrote:

    Also, in light of all the documentation posted above of research on genome function by evolutionary biologists, did you retract that statement, as per

    No. No such documentation has been presented. Evolutionary biologists mightily opposed the notion that the 95% of non-coding DNA had any function and engaged in no research to try to elucidate the function of this portion of the genome. I still have not seen one cite (despite all the huffing and puffing) in which an evolutionary biologist did research into the possible functions of what was referred to as "junk" DNA

    charlie wagner · 15 July 2004

    Brad wrote:

    This idea is actually not so absurd as GWW implied. It's also not all that new, though.

    Correct, it's been around since at least the 70's. I've been arguing this point for at least 10 years. But it makes one wonder why 30 years had to pass before it became accepted by mainstream science. Could it be that the power and influence of the darwinian paradigm was so deeply embedded in our consciousness that no one bothered to look into it?

    Russell · 15 July 2004

    Re: Charlie's excitement over the Carroll paper.

    I'm perplexed. Are you excited because you've learned something a new and unanticipated thing, or because you feel this somehow vindicates your dissent from mainstream biology?

    charlie wagner · 15 July 2004

    REVISED Brad wrote:

    This idea is actually not so absurd as GWW implied. It's also not all that new, though.

    Correct, it's been around since at least the 70's. I've been arguing this point for at least 10 years. But it makes one wonder why 30 years had to pass before it became accepted by mainstream science. Could it be that the power and influence of the darwinian paradigm was so deeply embedded in our consciousness that no one bothered to look into it? Did everyone think that these proteins, after being synthesized, just floated off and assembled themselves into complex, highly organized structures, processes and systems without any assistance? And what's worse, is this mindset still prevalent today and is it impeding new discoveries by trying to force new data into old, obsolete paradigms?

    charlie wagner · 15 July 2004

    Russell wrote:

    I'm perplexed. Are you excited because you've learned something a new and unanticipated thing, or because you feel this somehow vindicates your dissent from mainstream biology?

    I'm excited because it experimentally confirms what I've believed to be true for at least 10 years.

    Great White Wonder · 15 July 2004

    Good God, Charlie, control yourself.

    First you say you were spouting off for five years, now it's at least ten? (see post 5046)

    And you first posted that Carrol article months ago. Why are you getting all excited about it again???

    And finally, Charlie, could you clarify: do you understand the distinction between (1) non-coding DNA and (2) genes and (3) so-called "junk DNA"? And you understand that evolutionary biologists have understood and accepted the ESSENTIAL CRITICAL ROLE of regulatory regions (aka non-coding regions aka transcription-promoting sites and the like) in determining the phenotypes of organisms for as long as such regulatory regions have been known to exist?

    charlie wagner · 15 July 2004

    GWW wrote:

    And you first posted that Carrol article months ago. Why are you getting all excited about it again???

    Because in case you didn't notice, I was talking to the guy that wrote the paper.

    could you clarify: do you understand the distinction between (1) non-coding DNA and (2) genes and (3) so-called "junk DNA"? Those are just words, and they have no precise meaning or meanings that "evolve" as new data is discovered. I prefer to deal in concepts, which more accurately describe reality. And you understand that evolutionary biologists have understood and accepted the ESSENTIAL CRITICAL ROLE of regulatory regions (aka non-coding regions aka transcription-promoting sites and the like) in determining the phenotypes of organisms for as long as such regulatory regions have been known to exist?

    Of course. I was learning about the lac operon when you were still in diapers ;-) That's not at all what I'm talking about.

    charlie wagner · 15 July 2004

    REVISED GWW wrote:

    And you first posted that Carrol article months ago. Why are you getting all excited about it again???

    Because in case you didn't notice, I was talking to the guy that wrote the paper.

    could you clarify: do you understand the distinction between (1) non-coding DNA and (2) genes and (3) so-called "junk DNA"?

    Those are just words, and they have no precise meaning or meanings that "evolve" as new data is discovered. I prefer to deal in concepts, which more accurately describe reality.

    And you understand that evolutionary biologists have understood and accepted the ESSENTIAL CRITICAL ROLE of regulatory regions (aka non-coding regions aka transcription-promoting sites and the like) in determining the phenotypes of organisms for as long as such regulatory regions have been known to exist?

    Of course. I was learning about the lac operon when you were still in diapers ;-) That's not at all what I'm talking about.

    Great White Wonder · 15 July 2004

    Charlie:

    I prefer to deal in concepts, which more accurately describe reality.

    My head just exploded again. Damn it!

    Russell · 15 July 2004

    I'm excited because it experimentally confirms what I've believed to be true for at least 10 years.

    Which is....?

    Wayne Francis · 15 July 2004

    No such documentation has been presented. Evolutionary biologists mightily opposed the notion that the 95% of non-coding DNA had any function and engaged in no research to try to elucidate the function of this portion of the genome. I still have not seen one cite (despite all the huffing and puffing) in which an evolutionary biologist did research into the possible functions of what was referred to as "junk" DNA

    — Charlie
    Oh dear goal post moves agian First you say

    Evolutionary biologists do no research into genome function

    — Charlie
    then you say

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

    — Charlie
    To which many examples where cited then you say

    evolutionary biologists do no research into elucidating the previously unknown functions of the portion of the genome previously referred to as "junk DNA"

    — Charlie
    Show me one heart surgeon that writes papers on colon cancer. I'm sure that the gastro-instestinal specialists don't refute what the heart surgeon does. This said I'm sure one of the bright people in here will find a paper that fits your last goal post and you'll move it agian...how about something like

    evolutionary biologists do no research into elucidating the previously unknown functions of the portions of the genome referred to as "junk DNA" in the giant 3 toe sloth"

    — Future Charlie
    And by the way Charlie I really don't think anyone cares how old you are. Age has nothing to do with wisdom dispite the myths....it does have something to do with senility I should point out though. As far as name calling, referring to posters in here being so young that they where in diapers when you where learning about x doesn't really matter I believe. Agian you find me one genetic biologist that doesn't believe in evolution. Heck make it hard....use the bioligist that did this research. Lets see if they "ignore the rantings of evolutionists" or they themselves are evolutionists that specialise in genome research.

    Brad · 15 July 2004

    GWW wrote:

    But then I read it closely and said screw it because Charlie included not just chimps and humans in his statement, but chimps, humans and MICE.

    Frankly, at the protein-coding level, mice just aren't that far away. 80% of the protein-coding genes can be matched on a one-to-one correspondence between humans and mice, and less than 1% fail to match at all (the remaining 19% presumably are one-to-many and many-to-many matches). Again, what this suggests is that the interesting evolutionary changes are occurring at the regulatory level. I suspect you don't have any problem with that statement, so I'm just clearing up the notion that mice are incredibly distant from humans at the level of protein-coding genes. To really get some distance, you have to leave the mammals.

    The mouse and human genomes each seem to contain about 30,000 protein-coding genes. These refined estimates have been derived from both new evidence-based analyses that produce larger and more complete sets of gene predictions, and new de novo gene predictions that do not rely on previous evidence of transcription or homology. The proportion of mouse genes with a single identifiable orthologue in the human genome seems to be approximately 80%. The proportion of mouse genes without any homologue currently detectable in the human genome (and vice versa) seems to be less than 1%. Waterston et al., 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420:520-562.

    Another quote from that same paper also indicates that the authors are clearly proceeding with their genomic research from an evolutionary perspective, and are using that perspective to identify functional regions shared between the human and mouse genomes:

    Metaphorically, comparative genomics allows one to read evolution's laboratory notebook. In the roughly 75 million years since the divergence of the human and mouse lineages, the process of evolution has altered their genome sequences and caused them to diverge by nearly one substitution for every two nucleotides (see below) as well as by deletion and insertion. The divergence rate is low enough that one can still align orthologous sequences, but high enough so that one can recognize many functionally important elements by their greater degree of conservation. Studies of small genomic regions have demonstrated the power of such cross-species conservation to identify putative genes or regulatory elements. Genome-wide analysis of sequence conservation holds the prospect of systematically revealing such information for all genes. Genome-wide comparisons among organisms can also highlight key differences in the forces shaping their genomes, including differences in mutational and selective pressures.

    Regarding the Genome Biology paper, I'll be brief. Both flies and worms have a high rate of DNA deletion. It is this high deletion rate that sculpts the landscape of regulatory DNA in the genome. In genomes without a sufficiently high deletion rate, there is nothing that would prevent non-functional DNA from accumulating.

    Russell · 16 July 2004

    GWW: "But then I read it closely and said screw it because Charlie included not just chimps and humans in his statement, but chimps, humans and MICE."

    Brad: "Frankly, at the protein-coding level, mice just aren't that far away."

    My impression is close to Charlie's & Brad's here. But that's the "dogma" that I was taught 30 years ago!

    Russell · 16 July 2004

    Charlie: how is the paper you're so excited about not a perfect example of research on genome function by an evolutionary biologist?

    In what sense is Carroll not an "evolutionary biologist"?

    And aren't you a bit miffed they didn't even acknowledge you for helpful discussions?

    charlie wagner · 16 July 2004

    Brad wrote:

    It is this high deletion rate that sculpts the landscape of regulatory DNA in the genome. In genomes without a sufficiently high deletion rate, there is nothing that would prevent non-functional DNA from accumulating.

    and do you have any opinion about the cause of this high deletion rate? Do you suspect that these are random deletions or are they directed by the genome itself? Is it information that is scrolling into and out of the genome as processes and systems unfold?

    Dave S · 16 July 2004

    I don't know about the rest of you, but I've always found the term "junk DNA" to be appropriate. If you look up the word 'junk' for instance in the dictionary, you find:

    1. Discarded material, such as glass, rags, paper, or metal, some of which may be reused in some form. Word History: The word junk is an example of the change in meaning known as generalization, and very aptly too, since the amount of junk in the world seems to be generalizing and proliferating rapidly. The Middle English word jonk, ancestor of junk, originally had a very specific meaning restricted to nautical terminology. First recorded in 1353, the word meant "an old cable or rope." On a sailing ship it made little sense to throw away useful material since considerable time might pass before one could get new supplies. Old cable was used in a variety of ways, for example, to make fenders, that is, material hung over the side of the ship to protect it from scraping other ships or wharves. Junk came to refer to this old cable as well. The big leap in meaning taken by the word seems to have occurred when junk was applied to discarded but useful material in general. This extension may also have taken place in a nautical context, for the earliest, more generalized use of junk is found in the compound junk shop, referring to a store where old materials from ships were sold. Junk has gone on to mean useless waste as well.

    So while "junk" even in the colloquial sense can refer to something useless, it does not necessarily have to be useless. Pretty much everyone here has a junk drawer or an area where you have a pile of junk, perhaps the attic or garage or both. You don't save this stuff because it's worthless garbage, do you? The reason you save this 'junk' at all is precisely because it may have some use down the road that you can't envision at the moment. And it did have a use at some point but is no longer used for the original purpose, perhaps because it's broken, which is how it found itself in your junk pile in the first place. This is analogous to pseudogenes, which are similar to functional genes by have a mutation that makes them 'broken' but are still hanging around and may (or may not) eventually be found useful for some other purpose. Finding a use for a piece of "junk DNA" no more validates the claim that it's all really not junk, any more than does using that empty film container to hold thumbtacks mean the rest of the stuff in the drawer is no longer really junk. End rant.

    Russell · 16 July 2004

    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.

    steve · 16 July 2004

    Yes, the scientific community has assiduously denied 'junk dna' might have any function. Oh wait, that's total horseshit. It's common knowledge some of it has a variety of functions:

    --------------------------------------------------------------------------------

    Re: Redundant DNA
    Date: Wed Dec 9 12:35:01 1998
    Posted By: Joshua McElwee, Grad student, Molecular and Cellular Biology, University of Washington-Seattle
    Area of science: Genetics
    ID: 909779201.Ge
    --------------------------------------------------------------------------------
    Message:

    There are several thoughts on why cells still retain "junk" DNA. It is only been recently that groups have actually started to prove that much of this supposed useless DNA actually does indeed play important roles in gene regulation and chromosome structure.

    First, much of the "junk" DNA that doesn't code for protein is actually very important for gene structure and regulation. Promoters, regulatory regions, upstream and downstream untranslated regions, and introns, while not part of the coding region for proteins, are vitally important for the proper transcription, regulation, and translation of genes and proteins.

    Secondly, the idea of epigenetics is rapidly becoming accepted as useful methods to regulate genes. "junk" DNA is thought to play an important role in this regulatory process by the formation of heterochromatin. A great deal of the genome is present in the form of heterochromatin, which is normally an inactive form of DNA that doesn't allow transcription of genes within it to occur. DNA which doesn't encode proteins could still be very important for the formation of heterochromatin and the regulation of genes via epigenetic effects.

    Finally, this useless DNA also has been implicated in several structural roles within the nucleus. Repetitive sequences, like Alpha-sattelite DNA in humans, are thought to be vitally important for the formation of structures such as the centromere and telomeres within chromosomes. In addition, several other processes during mitosis and meiosis could involve non-coding DNA, such as chromosome compaction, X-inactivation, and sister chromatid pairing.

    If you're interested, here are some mini-reviews concerning these processes:

    Lewin, Benjamin, The Mystique of Epigenetics, Cell, Vol. 93, 301-303

    Wiens and Sorger, Centromeric Chromatin and Epigenetic Effects in
    Kinetochore Assembly, Cell, Vol 93, 313-316
    Actually, as i look at these, they're all apparently from one volume of Cell that was dedicated to epigenetics. So, check out Vol. 93 of Cell for more information.

    --------------------------------------------------------------------------------

    charlie wagner · 16 July 2004

    Russell wrote:

    Charlie: how is the paper you're so excited about not a perfect example of research on genome function by an evolutionary biologist?

    It is.

    In what sense is Carroll not an "evolutionary biologist"?

    Sean B. Carroll is an evolutionary biologist who does research on genome function. I could say more about this, but why bother. You're main goal seems to make me look bad, so have your moment. It's not all that important a point and it detracts attention from my main point, that evolutionary biologists refused by and large to accept the notion that the noncoding DNA had any function and held fast to the view that it was "molecular garbage, left over from millions of years of evolution." It isn't and they were wrong, so that's the important thing.

    And aren't you a bit miffed they didn't even acknowledge you for helpful discussions?

    No.

    Great White Sarcastic Wonder · 16 July 2004

    Brad, I can't let it slide. Nope. I stand by my opinion that the statement that what makes humans or chimps different from mice could be explained merely by differences in REGULATORY sequences is ABSURD. I chuckle heartily at the suggestion (made by Charlie "The Elder" Wagner). You wrote

    I'm just clearing up the notion that mice are incredibly distant from humans at the level of protein-coding genes.

    The strawman has been destroyed. Mission accomplished.

    Russell · 16 July 2004

    Thanks I appreciate that retraction. It's hard to know which claims are still out there being maintained and which have been abandoned, without some explicit acknowledgment of the fact. Now THIS is what I want to see documentation for.

    ...my main point, that evolutionary biologists refused by and large to accept the notion that the noncoding DNA had any function and held fast to the view that it was "molecular garbage, left over from millions of years of evolution

    I don't know if my mentors were way ahead of there time, or if your apparent perception of yourself as the Voice Crying in the Wilderness is delusional, but this was the "dogma" I was taught 30 years ago.

    Bob Maurus · 16 July 2004

    Charlie: "Sean B. Carroll is an evolutionary biologist who does research on genome function."

    Congratulations, Charlie! I'm impressed, even if the road to it was long and winding.

    Great White Wonder · 16 July 2004

    Russel wrote"

    I don't know if my mentors were way ahead of there time, or if your apparent perception of yourself as the Voice Crying in the Wilderness is delusional, but this was the "dogma" I was taught 30 years ago.

    You mean "wasn't the 'dogma'", right?

    charlie wagner · 16 July 2004

    Bob wrote:

    Congratulations, Charlie! I'm impressed, even if the road to it was long and winding.

    It's a common tactic to focus on one small insignificant point and make a big deal out of it to distract attention away from the main issue or to cast aspersion on the speaker. Anyone who put what I said into the context of the discussion wouldn't have had any problem with it. I'll replace it with a more specific statement: "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." Perhaps you like that better. Or would you prefer to deconstruct it and find semantic weaknesses that you can capitalize on?

    Les Lane · 16 July 2004

    I find "junk DNA" and biologists similar to "the surface of Pluto" and geologists. Geologists have studied Earth's surface extensively, but virtually ignored Pluto's surface. The reasons for ignoring junk DNA are similar to the reasons for ignoring Pluto.

    Charlie - careful not to take the metaphor too literally.

    Incidentally much junk DNA is relatively "modern".

    charlie wagner · 16 July 2004

    Les wrote:

    I find "junk DNA" and biologists similar to "the surface of Pluto" and geologists. Geologists have studied Earth's surface extensively, but virtually ignored Pluto's surface.

    http://tinyurl.com/3l34y ;-)

    Les Lane · 16 July 2004

    But where are the McDonalds on Pluto?

    Russell · 16 July 2004

    Russell: I don't know if my mentors were way ahead of there time, or if your apparent perception of yourself as the Voice Crying in the Wilderness is delusional, but this was the "dogma" I was taught 30 years ago. Charlie:You mean "wasn't the 'dogma'", right? Perhaps my use of the term is a little confusing. I use the term in "ironic" quotes because the anti-evo crowd often uses it dismissively to describe what all us sheep were spoon-fed in school and never had the courage or intellect to question. In fact, the way it was presented to me was that, given the similarity that was emerging in coding sequences, and the fact that the majority of the DNA was noncoding, it was very likely that much of the difference between Pan and Homo would turn out to reside in the regulatory sequences. That was 30 years ago in the Biochemistry program at UC Davis. I'm still waiting for you to show me where evolutionary biologists had it wrong all this time, even consistent with your New Revised Blanket Condemnation. With statements like

    You're main goal seems to make me look bad, so have your moment.

    and

    It's a common tactic to focus on one small insignificant point and make a big deal out of it to distract attention away from the main issue or to cast aspersion on the speaker

    and

    Or would you prefer to deconstruct it and find semantic weaknesses that you can capitalize on

    you're sounding kind of paranoid. You should know that, just as it is incumbent upon all us sheep to question the "dogma", it is incumbent upon us to challenge the Voices Crying in the Wilderness when they make assertions that can't be supported. It's not personal. In fact, I would say, far from "making you look bad", finally retracting that one howler makes you look less ridiculous. Too bad you felt the need to insist that it was an irrelevant detail that was only technically wrong because your persecutors maliciously misconstrued it.

    joel · 16 July 2004

    Previous "left overs" of evolution are now considered a
    mechanism for evolution.

    Why were the transposons considered useless DNA leftovers
    in the first place?

    http://www.eurekalert.org/pub_releases/2004-07/uadb-ngm071604.php

    A team of researchers from the Universitat Autònoma de Barcelona (UAB) has discovered that transposons, small DNA sequences that travel through the genomes, can silence the genes adjacent to them by inducing a molecule called antisense RNA. This is a new mechanism for evolution that has been unknown until now. The research has been recently published in the journal Proceedings of the National Academy of Sciences (PNAS).

    Transposons are repeated DNA sequences that move through the genomes. For a long time they have been considered as a useless part of genetic material, DNA left overs. However, it is more and more clear that transposons can cause favourable changes for the adaptation and survival of the organism.

    Bob Maurus · 16 July 2004

    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.

    charlie wagner · 16 July 2004

    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.

    charlie wagner · 16 July 2004

    Russell wrote:

    you're sounding kind of paranoid.

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

    Jack Krebs · 16 July 2004

    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.

    Jack Krebs · 16 July 2004

    Hmmm - it's too bad we can't edit post: I meant "I seriously doubt that there were unused research ...",

    steve · 16 July 2004

    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.

    Dave S. · 16 July 2004

    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.

    — Russel
    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.

    shiva pennathur · 16 July 2004

    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"?

    shiva pennathur · 16 July 2004

    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"?

    perianwyr · 19 July 2004

    No TRUE Scotsman would make such an argument.