Salvage prospect for 'junk' DNA #1

Salvage prospect for 'junk' DNA: The genome may possess far more complexity than was imagined, BBC, 26 April 2006, Paul Rincon ...

[Graphic: "What is junk DNA, and what is it worth?," Pennsylvania State University]

A mathematical analysis of the human genome suggests that so-called "junk DNA" might not be so useless after all. The term junk DNA refers to those portions of the genome which appear to have no specific purpose. But a team from IBM has identified patterns, or "motifs", that were found both in the junk areas of the genome and those which coded for proteins. The presence of the motifs in junk DNA suggests these portions of the genome may have an important functional role. The findings are reported in Proceedings of the National Academy of Sciences journal. But they will have to be verified by experimenters in the lab, the scientists behind the work point out. Dr Andrew McCallion, who was not an author on the new paper, commented: "Up until not so long ago, we were under the impression that the vast majority of information in the genome, if not all of it, was encoded in those stretches of DNA that encoded proteins. "We now understand there is much more complexity involved," . Lead author Isidore Rigoutsos and colleagues from IBM's Thomas J. Watson Research Center used a mathematical tool known as pattern discovery to tease out patterns in the genome. This technique is often used to mine useful information from very large repositories of data in the worlds of business and science. They sifted through the approximate total of six billion letters in the non-coding regions of the human genome and looked for repeating sequence fragments, or motifs. "One of the things that arises from this paper is that junk DNA may not be junk. But this needs to be verified," Dr Rigoutsos told the BBC News website. Dr Rigoutsos said his team's work suggested, "a connection between a vast area of the genome we didn't think was functional with the part of the genome we knew was functional". He explained that experimental work would be needed to establish this connection: "The average lab does not have the resources to prove or disprove this, so it will need a lot of effort by lots of people," he explained. The paper in PNAS suggests that the actual positioning of the motifs is associated with small RNA molecules that are involved with a process called post-transcriptional gene silencing (PTGS). "A human embryo starts out as a single fertilised cell and rapidly divides into a widely complex series of cells that become a human being," explained Dr McCallion. "Every cell in that human being contains the same complement of genes and what makes each cell different is the precise way that genes are turned on and turned off." PTGS turns genes off after the process of transcription has taken place. One way in which this occurs is through "RNA interference", which involves the introduction of double-stranded RNA molecules. These trigger the degradation of another type of RNA molecule known as messenger RNA (mRNA), "down-regulating" the gene. During transcription, this molecule encodes and carries information from genes to sites of protein synthesis. "These regions may indeed contain structure that we haven't seen before," said Dr Rigoutsos. "If indeed one of them corresponds to an active element that is involved in some kind of process, then the extent of cell process regulation that actually takes place is way beyond anything we have seen in the last decade." ... [As I have said before, I well remember in earlier days debating Darwinists who used to cite it as an argument against design that genomes contained so much "junk DNA." For example, the Darwinist philosopher David Hull, in his 1991 review in Nature of the first edition of Phil Johnson's Darwin on Trial, cited it as an argument against design that "95 per cent of the DNA that an organism contains has no function":

"What kind of God can one infer from the sort of phenomena epitomized by the species on Darwin's Galapagos Islands? The evolutionary process is rife with happenstance, contingency, incredible waste. death, pain and horror. Millions of sperm and ova are produced that never unite to form a zygote. Of the millions of zygotes that are produced, only a few ever reach maturity. On current estimates, 95 per cent of the DNA that an organism contains has no function." (Hull D.L., "The God of the Galapagos." Review of "Darwin on Trial," by Phillip E. Johnson, Regnery Gateway: Washington DC, 1991. Nature, Vol. 352, 8 August 1991, p.486).

In fact my strongly Darwinist genetics textbook as late as 2002 was still using the term "junk DNA":

"This repetitive DNA comprises at least three categories. One is `junk' DNA, DNA that is not useful to the organism, made up of untranscribed and parasitic sequences (selfish DNA). ... Much eukaryotic DNA is junk, apparently doing no harm. In some cases, 97% of the host genome is composed of junk DNA. Recent work seems to indicate that gross differences in DNA content between higher organisms may be due to the differing abilities of different species to rid themselves of this parasitic DNA. If it builds up without being removed, the DNA content of the species can soar. Thus, the wide differences in DNA content among higher eukaryotes mentioned at the beginning of this section have little to do with the complexity of the organism, but rather with the ability of the organism to remove junk DNA as it forms." (Tamarin, R.H., "Principles of Genetics," International Edition, [1996], McGraw-Hill: New York, Seventh Edition, 2002, pp.458-459)

But as Dembski pointed out in 1999 (indeed in a 1998 article in First Things which used virtually identical language), that while "on an evolutionary view we [would] expect a lot of useless DNA," on an ID view we would "expect DNA as much as possible to exhibit function":

"Design is not a science-stopper. Indeed design can foster inquiry where traditional evolutionary approaches obstruct it. Consider the term `junk DNA.' Implicit in this term is the view that because the genome of an organism has been cobbled together through a long, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA as much as possible to exhibit function. And indeed the most recent findings suggest that designating DNA as `junk' merely cloaks our current lack of knowledge about function. For instance, in a 1997 issue of the Journal of Theoretical Biology, John Bodnar and his colleagues describe how `non-coding DNA in eukaryotic genomes encodes a language which programs organismal growth and development.' [Bodnar, J.W., Killian, J., Nagle, M. & Ramchandani, S., "Deciphering the Language of the Genome," Journal of Theoretical Biology, 189, 1997, p.183] Design encourages scientists to look for function where evolution discourages it." (Dembski W.A., "Intelligent Design: The Bridge Between Science and Theology," InterVarsity Press: Downers Grove IL, 1999, p.150)

As the Discovery Institute's John West responded (presumably referring to Dembski's abovementioned article), "In 1998 an ID theorist, reckoning that an intelligent designer would not fill animals' genomes with DNA that had no use, predicted that much of the `junk' DNA will someday be found to have a function":

"By contrast, said Alan Leshner, chief executive of the American Association for the Advancement of Science, Intelligent Design offers nothing in the way of testable predictions. `Just because they call it a theory doesn't make it a scientific theory,' Leshner said. `The concept of an intelligent designer is not a scientifically testable assertion.' Asked to provide examples of non-obvious, testable predictions made by the theory of Intelligent Design, John West, an associate director of the Discovery Institute, a Seattle-based ID think tank, offered one: In 1998, he said, an ID theorist, reckoning that an intelligent designer would not fill animals' genomes with DNA that had no use, predicted that much of the `junk' DNA in animals' genomes -long seen as the detritus of evolutionary processes - will someday be found to have a function. (In fact, some `junk' DNA has indeed been found to be functional in recent years, though more than 90 percent of human DNA still appears to be the flotsam of biological history.) In any case, West said, it is up to Darwinists to prove ID wrong." (Weiss R. & Brown D., "New Analyses Bolster Central Tenets of Evolution Theory: Pa. Trial Will Ask Whether 'Alternatives' Can Pass as Science, Washington Post, September 26, 2005)

And note the anti-IDist authors responding that "more than 90 percent of human DNA still appears to be the flotsam of biological history"!

The fact that more and more of the genome previously thought to be "junk" is turning out to have, not just a function, but a highly sophisticated function, is more evidence for design and against Darwinism.

I had intended to add, for possible inclusion in my Quotes Book (which will now probably be a self-published eBook), brief quotes, with equally brief comments, in date order, from news articles I had on so-called "junk DNA." But there tuned out to be too many which would make this post too long. Especially as I want also to quote from Dawkins and Dennett, where Dawkins based part (perhaps a large part-since Dennett cites it as evidence) of his "selfish-gene" theory on `junk-DNA' (which he called "selfish-DNA"). So I will split this post into two parts and continue later with just the quotes and my comments in part #2]

Stephen E. Jones, BSc (Biol).
"Problems of Evolution"