Commentary on the so-called Creation/Evolution/Intelligent Design Debate and Right-Wing nuttery in general - and please ignore the typos (I make lots!)

Wednesday, July 25, 2007

Casey Luskin and the junk DNA conspiracy

Creationist lawyer and Discovery Institute propagandist Casey Luskin recently wrote yet another standard conspiracy theory hack-job, this time concerning 'Junk DNA.'
This time, he seems to have a compatriot - an actual researcher who claims to be experiencing suppression at the pro-evolution website The Panda's Thumb. This scientist, Dr. Andras J. Pellionisz, claims that The Panda's Thumb is refusing to print his stories about how "he has personally witnessed how the Darwinian consensus rejected suggestions that "junk" DNA had function" and that "suggestions that "junk"-DNA had function were ignored or rejected by most Darwinian scientists. " Pellionisz alludes to a supposed 'confrontation' of sorts between fellow 'junk DNA' denier Malcolm Simons and some unnamed pro-junk DNA 'darwinists':

How do you think his fellow-Darwinist scientists received his assertion (1987) that "Junk DNA" had a function?

"When I showed the professional geneticists the data, which indicated to me that the 95% non-coding region wasn't junk, and was ordered…The reaction was smiling disbelief at best - you're off your friggin' head and if you're any good at squash - stick to your day job [MJS]"

Note the date - 1987 - it is important.

If we are to believe Luskin and Pellionisz and Simons, 'darwinists' prevented any research from being done on junk DNA and are therefore somehow responsible for the people that have 'junk DNA'-related diseases.

Has the making of a good story. Has the making of spreading all sorts of angry feelings in the populace regarding those wicked 'darwinists' whose mind-schackling worldview prevented groundbreaking research from going forth in order to prop up their ideology.

The problem is - it is utter and total bullshit.

It seems that the whole story is one of self-promotion (primarily by Simons, but not too much less by Pellionisz) and a tendency to gloss over some basic facts. Simons, for example, has the following claim on his company's home page:

Dr Simons pioneered the concept that 'Junk' non-coding DNA could not be 'Junk' because the DNA sequence differences were ordered, and were conserved between humans of the same coding gene type. The ordered sequence patterns marked lengths of chromosomes, including adjacent and remote genes.

Simons pioneered that concept? Not likely... Got a patent onit, yes. Pioneered it? Not so sure.

An uneducated media is no help - in a story in the San Francisco Chronicle in 2002 (at least this is what is claimed at the 'junkDNA' site linked to above) the following statement can be found:

"In a provisional patent application filed July 31, Pellionisz claims to have unlocked a key to the hidden role junk DNA plays in growth -- and in life itself."

So, what does that imply? It implies that it was not until July, 2002, did anyone think 'junkDNA' did anything. That nobody thought there was a role for 'junk DNA' in 'growth and life' - and that it Andras Pellionisz and his radical bunch of compatriots that found it all out. Let's forget, for the moment, that Simons was trying to wear the mantle of 'genius of Junk DNA' for some time prior to that.
Again, this all makes for a wonderful story and plays very well into the hands of the anti-evolution crowd - the suppression of the maverick truth-seeking scientists by the darwinian orthodoxy, poor fellows just looking for the truth and the big, bad, evolutionist machine tells them NO!. But they soldier on in obscurity until they - and they alone - amass such evidence that cannot be ignored anymore, and the Establishment STILL will not give them their due!

But the media like controversey, and by doing such a smidgen of digging, I discovered that this sort of story - that everyone thought junk DNA was all just junk and that anyone daring to suggest it had a function was at best scoffed at - has been around a while. I found an interview with Francis Collins in 2003 in which he was asked about patents involving genes and the like. This exchange is most telling, any emphases mine:

What was known in your view about the non-coding genes, the so called junk DNA back in the early to mid 1980s, was it regarded by most geneticists as mere junk, as meaningless?

Collins: We've known for as long as we've had a decent grasp on human DNA by methods that came along, even before we could sequence it, that there was a lot of repetitive information in the human genome, perhaps half of it was consisting of the bland material that didn't seem to be very information laden. When sequencing came along, we got a much better fix on that and so certainly by 1980 it was quite clear that vast stretches of the human genome were not involved in coding for protein. Furthermore we knew that that could still be useful because information along a chromosome is in fact not independent of its neighbours and way back in 1978, W. Y. Kahn showed that you could measure a place in the non-coding DNA, look at its spelling, and predict whether there was a cycle mutation up stream of that, quite a number of thousands of base-pairs away indicating that while the non-coding DNA might seem not so interesting, it could still carry marker information that told you about what was next door that could be very interesting. And that was generalised by general advances made over the next two or three years by people like David
Botstein, published in distinguished journals and Alec Jeffries in the United Kingdom showed us in 1981 that in fact there was a lot of variation out there between individuals, maybe two or three places every thousand letters in the code where people would differ and that could be useful in terms of tracking what was happening, not necessarily of that particular spelling change but what was downstream or upstream from it that might have a medical consequence. So all of that information was well understood by the mid 1980s.

Did the discoveries made by Malcolm Simons which gave rise to the patents now held by Genetic Technologies, are they widely acknowledged, widely read, widely referred to in the genetic world today?

I don't believe most people were aware of Malcolm Simons' work until fairly recently because of the attention now focussed on this patent application and of course the patent was filed in 1990 and 13 years have really passed before much of anybody that I know was aware of the content of that particular patent which of course was disclosed as soon as the patent issued. So no I don't think scientifically there has been broad recognition of Dr Simons' contribution.

Does that mean that in your view his work was not especially significant, I mean we would have got by without it, would that be fair to say?

It's hard to judge the scientific contribution from reading a patent application, certainly when one looks at the claims of this patent, they are very broad and certainly when one considers the context of the work of many others over the preceding 20 years that breadth appears to many people somewhat surprising. To the extent that Dr Simons published his work in the scientific literature it did not attract a lot of attention which is the usual standard by which we evaluate the contribution to a particular body of scientific knowledge.

It is not like the reporter was convinced of the 'truth' of the spin that Simons and what I think can be called his worshippers has put on it, not at all. It is not like the reporter is asking leading questions, no sir. What it appears to boil down to is that Simons applied for and received a patent regarding 'junk DNA', and because nobody else had done such a thing, he is for some reason seen as a major player in the field and is receiving all manner of recognition that is not really warranted. He was certainly not the only one that thought junk DNA does something. And this can be proven by merely looking here, for just one example:

Cell. 1975

The general affinity of lac repressor for E. coli DNA: implications for gene regulation in procaryotes and eucaryotes.

By equilibrium competition experiments, the dissociation constant (K(RD)) of lac repressor for E. coli DNA carrying a deletion of the lac operon was measured at a variety of salt concentrations. These data are used in the consideration of several aspects of protein-DNA interaction: Quantitative estimates of specificity are made. Specificity changes only slightly with salt concentration. We calculate that in vivo, 98 percent or more of repressor is bound to DNA predominately at sites other than the lac operator. Inducers shift repressor from operator to nonoperator DNA, but do not free it from DNA. The general affinity of repressor for E. coli DNA is sufficient to support a model where repressor slides along DNA for significant distances. The effective dissociation constant of repressor for operator (K(eff)) is very sensitive to the total DNA concentration. We propose that "junk" DNA in eucaryotes functions to maintain total DNA at an optimum concentration. We consider the lac operon in the nucleus of a lymphocyte, point out that severe difficulties would be encountered, and suggest possible solutions.

Note the date. 1975. A full 12 years prior to Simons' supposed confrontation with genetics researchers who supposedly told him to 'stick to his day job' for suggesting that junk DNA did something as reported by Pellionisz. It is irrelevant as to whether or not the authors were correct in their proposal - the fact is they were considering functions for it in 1975, 3 years after Ohno coined the term 'junk DNA'. It should also be noted that Ohno did not appear to think 'junk DNA' did nothing, rather he was just attempting to describe how he thought it came to be, and he was referring to a particular type of noncoding DNA, not all of it. But don't tell Luskin and pals!

But let us do a quick search to see if Simons deserves the title 'genius of Junk.' A Pubmed search [for "Simons MJ"] reveals a rich publication history going back to the 1960s.
Now Ohno supposedly coined the term 'junk DNA' in 1972 (there is some scuttlebutt that someone else said it at a conference preceding Ohno's claims), and this was the date at which, supposedly, orthodox darwinism shut down research on noncoding DNA. Let's take a look at Simons' post-1972 publications and see which ones reveal his insights into 'junk DNA'...

The first paper I can identify which seems to have anything to do with DNA at all came out in 1984 - 9 years after the paper I cite above (there were earlier ones, but that was the first one with an available abstract), and judging from the abstract, it does not appear to be concerned with junk DNA. The first one I can find that appears to have any implication for functional noncoding DNA, again judging by the abtract, is this one published in 1989, 2 years after his supposed run-in with the orthodoxy-protecting geneticists who insited that junk DNA has no function (there was one other mentioning noncoding DNA, but it was in the context of describing a newly sequenced gene).

Can it still be that Simons is the genius of Junk? That he was the one that proposed/discovered that junk DNA controls things and regulates things and such?

If so, his discovery must have been cryptic, as it seems that Zuckerkandl scooped him, publication-wise, in 1981:

It is proposed that a general function of noncoding DNA and RNA sequences in higher organisms (intergenic and intervening sequences) is to provide multiple binding sites over long stretches of polynucleotide for certain types of regulatory proteins. Through the building up or abolishing of high-order structures, these proteins either sequester sites for the control of, e.g., transcription or make the sites available to local molecular signals. If this is to take place, the existence of a c-value paradox becomes a requirement. Multiple binding sites for a given protein may recur in the form of a sequence motif that is variable within certain limits. Noncoding sequences of the chicken ovalbumin gene furnish an appropriate example of a sequence motif, GAAAATT. Its improbably high frequency and significant periodicity are both absent from the coding sequences of the same gene and from the noncoding sequences of a differently controlled gene in the same organism, the preproinsulin gene. This distribution of a sequence motif is in keeping with the concepts outlined. Low specificity of sequences that bind protein is likely to be compatible with highly specific conformational changes.

Seems Zuckerkandl scooped all the IDcreationists who claim to have 'predicted' function in junk DNA as well...

So, anyway, back to Luskin and his disinformation campaign...

Pellionisz seems to have found a pal in the IDcreationist movement, as he has been cited by Salvador Cordova as an ally. No wonder he decided to confide in Luskin regarding his supposed 'suppression' at Panda's Thumb.

Of course, reality does not stop the ID creationists from, well, lying (or at least embellishing) about the history of junk DNA. In fact, on their slick disinformation site 'researchintelligentdesign' (which, by the way, contains no research), we see claims that it was ID creationists that "predicted" functions for junk DNA that were borne out by research done by... well, not any of them. This page indicates that ID 'theorists' were 'predicting' functions for junk DNA as far back as - get this - 1986! YEARS after there were already publications 'predicting' (and demonstrating) junk DNA functions by evolutionists! Boy, those IDers don't miss a trick! Making predictions in the present about things that had already come to pass - incredible!

Luskin and pals remind me of the castle guard in Monty Python and the Holy Grail, who, after watching Sir Lancelot run across an open field and kill the other guard then proceeds to run through the castle gate, which the guard was supposed to be, well, guarding, calls after him "Hey!"

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