IBM Discovery Could Shed New Light on Workings of the Human Genome

Posted 29 April 2006 by PvM

IBM researchers have shown how science explores new and innovative approaches to discover DNA patterns which are shared by areas of the human genome that were considered to have little or no influence on its function and areas which do have function. From the IBM Press Release

As reported today in the Proceedings of the National Academy of Sciences (PNAS), regions of the human genome that were assumed to largely contain evolutionary leftovers (called "junk DNA") may actually hold significant clues that can add to scientists' understanding of cellular processes. IBM researchers have discovered that these regions contain numerous, short DNA "motifs," or repeating sequence fragments, which also are present in the parts of the genome that give rise to proteins.

The work was also reported in PNAS in an Open Access Article Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes by isidore Rigoutsos, Tien Huynh, Kevin Miranda, Aristotelis Tsirigos, Alice McHardy, and Daniel Platt, PNAS | April 25, 2006 | vol. 103 | no. 17 | 6605-6610

Abstract Using an unsupervised pattern-discovery method, we processed the human intergenic and intronic regions and catalogued all variable-length patterns with identically conserved copies and multiplicities above what is expected by chance. Among the millions of discovered patterns, we found a subset of 127,998 patterns, termed pyknons, which have additional nonoverlapping instances in the untranslated and protein-coding regions of 30,675 transcripts from 20,059 human genes. The pyknons arrange combinatorially in the untranslated and coding regions of numerous human genes where they form mosaics. Consecutive instances of pyknons in these regions show a strong bias in their relative placement, favoring distances of {approx}22 nucleotides. We also found pyknons to be enriched in a statistically significant manner in genes involved in specific processes, e.g., cell communication, transcription, regulation of transcription, signaling, transport, etc. For {approx}1/3 of the pyknons, the intergenic/intronic instances of their reverse complement lie within 380,084 nonoverlapping regions, typically 60--80 nucleotides long, which are predicted to form double-stranded, energetically stable, hairpin-shaped RNA secondary structures; additionally, the pyknons subsume {approx}40% of the known microRNA sequences, thus suggesting a possible link with posttranscriptional gene silencing and RNA interference. Cross-genome comparisons reveal that many of the pyknons have instances in the 3' UTRs of genes from other vertebrates and invertebrates where they are overrepresented in similar biological processes, as in the human genome. These unexpected findings suggest potential unique functional connections between the coding and noncoding parts of the human genome.

Exciting new findings which show how real science explores 'junk DNA' The BBC reported on this research in an article titled Salvage prospect for 'junk' DNA

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," Dr McCallion, from the McKusick-Nathans Institute of Genetic Medicine at the Johns Hopkins University School of Medicine in Baltimore, US, told the BBC News website.

I am sure ID activists are going to conflate the newly found 'complexity' in the genome with their flawed Design Inference... But science has already blocked any such design inference by providing a plausible hypothesis

Gene silencing 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."

Many websites are reporting on these exciting new findings

If verified experimentally, the discovery suggests a potential connection between these coding and non-coding parts of the human genome that could have a profound impact on genomic research and provide important insights on the workings of cells.

IBM Discovery Could Shed New Light on Workings of the Human Genome at Physorg.com

31 Comments

steve s · 29 April 2006

Indeed, some IDiots are claiming to have predicted this.

PvM · 29 April 2006

Sigh... Don't these people realize that 'junk DNA' is not exactly what the name may suggest. If ID believes that they predicted this then how come that they have done NO research at all to verify their 'predictions'? In fact, ID provides no logical support for the claim that it predicted this. The reasons for ID to insist that "Junk DNA" has some function is because of their theological foundations not because of anything the theory of ID would predict. In fact, I argue that without a theological foundation, ID could not have made such a prediction, showing once again that ID is not about science but all about religion. Those more familiar with the history of this term would realize that

n molecular biology, "junk" DNA is a collective label for the portions of the DNA sequence of a chromosome or a genome for which no function has yet been identified. About 98.5% of the human genome has been designated as "junk", including most sequences within introns and most intergenic DNA. While much of this sequence is probably an evolutionary artefact that serves no present-day purpose, some may function in ways that are not currently understood. In fact, recent studies have suggested functions for certain portions of what has been called junk DNA. Moreover, the conservation of some "junk" DNA over many millions of years of evolution may imply an essential function. The "junk" label is therefore recognized as something of a misnomer, and many would prefer the more neutral term "noncoding DNA" (although it assumes so).

Wikipedia No wonder the IDEA club confused Junk DNA with actual 'junk', unfamiliar apparantly with the historical meaning of the term. So far it is science not ID which has been uncovering these gems in 'Junk DNA'. Until ID can explain why 'Junk DNA' should have a function after all, claims of predictions are ad hoc.

JSB · 29 April 2006

"There is a widespread belief among Darwinians that such apparently unnecessary DNA would have been eliminated long ago by natural selection if it did not have some, as of yet undiscovered, function."

- Ernst Mayr, What Evolution Is, p. 108, Box 5.5.

normdoering · 29 April 2006

JSB quoted:

"There is a widespread belief among Darwinians that such apparently unnecessary DNA would have been eliminated long ago by natural selection if it did not have some, as of yet undiscovered, function." - Ernst Mayr, What Evolution Is, p. 108, Box 5.5.

Hasn't Dembski speculated that the "as of yet undiscovered function" of junk DNA will be some kind of instruction manual or message from God? This doesn't mean anything one way or the other yet.

PvM · 29 April 2006

Hat tip to Joel

The May 23, 2003 issue of Science contained an article titled: "Not Junk After All" "So, the question is, "Why do we need so much DNA?" 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. Genomes are dynamic entities: New functional elements appear and old ones become extinct. It appears that transposable elements are not useless DNA. They interact with the surrounding genomic environment and increase the ability of the organism to evolve. They do this by serving as recombination hotspots, and providing a mechanism for genomic shuffling and a source of "ready-to-use" motifs for new transcriptional regulatory elements, polyadenylation signals, and protein-coding sequences. The last of these is especially exciting because it has a direct influence on protein evolution."

PvM · 29 April 2006

The 97% of the human genome that is repetitive sequence and does not contain exons. The term "junk DNA" was coined by molecular geneticist and Nobel laureate Sydney Brenner, to refer to the DNA that does not appear to do anything. When challenged by someone with the argument that God would not have created us with 97 per cent of redundant or useless DNA, Brenner is said to have retorted, "I said it was 'junk' DNA, not 'trash'. Everyone knows that you throw away trash. But junk we keep in the attic until there may be some need for it."

Source Seems that some other creationists saw junk DNA to be quite compatible with a God. So explain to me again, how does ID reach its 'prediction'? My prediction is that similar to the last time an IDer was challenged (Salvador), these questions will remain unaddressed by ID, showing once again the scientific vacuity of ID.

'Rev Dr' Lenny Flank · 29 April 2006

Indeed, some IDiots are claiming to have predicted this.

Wow, if ID is really this useful and predictive, one wonders then why the ID-ites have now dropped ID like a hot potato, switched to the "teach the controversy" BS, and heatedly deny that anything they are doing now is even remotely connected to ID "theory" . . . . . . . .

Reed A. Cartwright · 30 April 2006

Indeed, some IDiots are claiming to have predicted this.
— steve s

Since they do claim to be the experts on this, I would love to see the creationists (ID or YE) explain how Amoeba dubia has a genome rougly 200 times larger than ours. http://www.genomenewsnetwork.org/articles/02_01/Sizing_genomes.shtml

Bob O'H · 30 April 2006

So explain to me again, how does ID reach its 'prediction'?

I assume from the argument that The Designer wouldn't put in something that's useless, and which is just costly to make. Which, curiously enough, is almost the same argument that can be used by a Panglossian evolutionary biologist: if it's just costly, it'll be selected out. One thing I haven't dared to ask: does ID predict that all junk DNA has a function? Bob

Registered User · 30 April 2006

Bob doesn't dare to ask

One thing I haven't dared to ask: does ID predict that all junk DNA has a function?

ID predicts that every new discovery about biology supports ID.

In the golden age of Panda's Thumb, this strange character named Charlie Wagner was the living embodiment of this axiom. He'd pick pretty much any DNA sequencing paper related to evolution, quote the abstract, and write something like, "See, what did I tell you?"

Then we'd all scratch our heads (or asses) and wonder what the hell he was talking about.

Ah, memories.

djlactin · 30 April 2006

here "Registered User": a free trip down memory lane---

"Frontloading, Frontloading!"

feel assuaged?

Reed A. Cartwright · 30 April 2006

I assume from the argument that The Designer wouldn't put in something that's useless, and which is just costly to make.
— Bob O'H

But according to the party line, ID doesn't make any claims about ~~God, Almighty~~ the Designer, so it would be inconsistent for them to claim ~~God, Almighty~~ He/She/It would or wouldn't design something someway.

deadman_932 · 30 April 2006

Mr. van Meurs: I feel kind of happy that I might be able to contribute a couple of things here.

Susumu Ohno wrote a paper called "So Much 'Junk DNA' in our Genome" back in 1972 for In Evolution of Genetic Systems. H.H. Smith, ed. pp. 366- 70. New York: Gordon and Breach. Ohno concentrated on pseudogenes, but as the term caught on in the 1980's, it eventually became attached to introns sequences, regulatory stretches, transposons, blah, blah, blah. You guys know all that stuff.

I also found something serendipitously the other day, in an obscure little book called "The Encyclopedia of Ignorance." (1977) Ronald Duncan and Miranda Weston-Smith, eds. Pergamon Press, N.Y.

It was an article by Roy J. Britten on "the Sources of Variation in Evolution (pp.209-217, above) in which he speculates that non-coding DNA involved in the "C-Value Paradox" would likely (at least) be related to gene regulation. So much for ID's precedence in predicting function for "junk."

deadman_932 · 30 April 2006

Ah, hell, you already mentioned Ohno -- and Britten is emeritus at CalTech. I have an excuse: it's 3 AM here and I was up all night working on things. That's my story and I'm sticking to it. :|

Russell · 30 April 2006

Since they do claim to be the experts on this, I would love to see the creationists (ID or YE) explain how Amoeba dubia has a genome rougly 200 times larger than ours.

Last I checked, that estimate - from quite a while ago - was (you'll pardon the expression) rather dubious. The fact that the link you gave overstates the HIV genome size by 2X makes me suspect they haven't done a lot of fact-checking.

steve s · 30 April 2006

So ID theory leads to knowledge and understanding. What would Judge Jones say? Comment by tribune7 --- April 30, 2006 @ 7:08 am (http://www.uncommondescent.com/index.php/archives/1084#comment-32998)

Reed A. Cartwright · 30 April 2006

Last I checked, that estimate - from quite a while ago - was (you'll pardon the expression) rather dubious. The fact that the link you gave overstates the HIV genome size by 2X makes me suspect they haven't done a lot of fact-checking.
— Russell

The link is a few years old. I used it because it was a nicer format than the genomie size databases that say the same thing: amoebas are the champions of genome size.

Russell · 30 April 2006

...the genomie size databases that say the same thing: amoebas are the champions of genome size.

Three points: 1. Amoebas (amoebae?) do indeed seem to maintain prodigious amounts of DNA relative to other creatures. 2. I believe all those other databases are relying on the same old and shaky report on this particular datum. 3. The premier position accorded to Amoeba dubya was not honestly earned; it was awarded by a 5-4 vote of Supreme Amoebas, largely appointed by dubya's progenitor, Amoeba herberwalkeri.

David B. Benson · 30 April 2006

Russell, my 1947 desk dictionary allows either plural. It first lists -bae and then -bas, if that means anything.

PvM · 30 April 2006

So ID theory leads to knowledge and understanding. What would Judge Jones say?

Judge Jones:

ID proponents support their assertion that evolutionary theory cannot account for life's complexity by pointing to real gaps in scientific knowledge, which indisputably exist in all scientific theories, but also by misrepresenting wellestablished scientific propositions. (1:112, 1:122, 1:136-37 (Miller); 16:74-79, 17:45-46 (Padian)).

In the mean time, science, realizing that it was unlikely that all so called 'junk DNA' was without function, set out to study it and in the early 1990's exciting new data started to pour in. In the mean time, ID, repeating creationist arguments, argued that 'junk DNA' would have to have function. Since this argument cannot follow logically from the premise of ID, it has to come from side-knowledge, in this case the assumption of a Christian Designer On Uncommon Descent DaveScott comes to the rescue

This brings up a closely related dialog with someone here who was repeatedly asking Dembski to use design detection formula to discriminate between "junk DNA" that has no function and DNA that has no *known* function. I kept telling the guy it doesn't work that way. Before something is a candidate for design detection it must first have specificity. Junk DNA, by definition, has no known function. It is thus unspecified and not a candidate for making a design inference.
— DaveScott

Link In other words, ID activists' claims that ID 'predicted' function for Junk DNA does not follow from their own assumptions. Thanks Dave

PvM · 30 April 2006

Dembski:

But 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.

This expectation does not follow from ID unless one can make assumptions as to how the designer(s) would design. Since ID cannot be used to detect function, since function defines specification, ID has no reason to make such claims. After all, ID can involve front loading and thus evolutionary processes would explain the existence of Junk DNA. Only by limiting ID artificially to religious foundations, can ID make such claims.

Henry J · 30 April 2006

Re "Since they do claim to be the experts on this, I would love to see the creationists (ID or YE) explain how Amoeba dubia has a genome rougly 200 times larger than ours."

It was front-loaded, of course. What else? ;)

Henry

The Ridger · 30 April 2006

David, your dictionary is either saying (I don't know which dictionary you have) that "amoebae" is the older or the preferred plural. Merriam Webster 2002 lists "amoebas" as the preferred.

If we were speaking Latin, I'd say go with the Latin (New Latin, borrowed from Greek), but since we're speaking English, we might as well treat it like an English word.

Bob O'H · 30 April 2006

David, your dictionary is either saying (I don't know which dictionary you have) that "amoebae" is the older or the preferred plural. Merriam Webster 2002 lists "amoebas" as the preferred. If we were speaking Latin, I'd say go with the Latin (New Latin, borrowed from Greek), but since we're speaking English, we might as well treat it like an English word.

Ah, but British English, or American English? Amoebae is correct (or more correct) in British English. What you colonials wish to do to the language is your own affair. Bob

Corbs · 1 May 2006

I have not read the paper, but why does this study have more credibility than the ridiculous efforts to mine the bible for patterns that have apparently deep significance?

Dave S. · 2 May 2006

Looks like we need a new way to determine design. I know, let's see what Bill Dembski is saying today...

Georgia Tech's Center for Biologically Inspired Design (CBID) Here's how it works: we find some amazing system in the biological realm, determine how to reverse engineer it, and then design and build a parallel system to serve our needs. But of course, the original system evolved by blind trial-and-error tinkering (random variation and natural selection). To think that it was actually designed because we had to design its human counterpart is just plain stupid.

Hmmm...yes, that is stupid Bill. Unless you want to argue that since the snowflake shaped Christmas ornaments I just got around to removing had to be designed by humans, that real snowflakes therefore indicate actual design too. Maybe that argument only works in the biological realm. For some reason.

Corkscrew · 2 May 2006

I have not read the paper, but why does this study have more credibility than the ridiculous efforts to mine the bible for patterns that have apparently deep significance?

Because this actually makes testable predictions. And scientists are going to go out and get more information and squeeze even more testable predictions out of it.

The Constructivist · 3 May 2006

I know you all focus on evolution/ID debates, but I'm currently in a discussion over at Objectivist v. Constructivist on race v. racialization where some commenters from the blog Gene Expression are suggesting that social constructionists who deny new advances in population genetics, evolutionary biology, and other scientific fields that examine human genetic differences are the left equivalent of ID. Was wondering if you all have any opinions on this analogy....

Steviepinhead · 4 May 2006

This doesn't really belong in this thread, but at least it's a new discovery:

"Common ancestor of fish, land animals found
405-million-year-old fossilized fish gives insight into evolutionary fork"

http://www.msnbc.msn.com/id/12614851/

Since this find relates to an evolutionary "fork," near the base of the tetrapod and bony fish clades, one assumes the IDiots will now be able to blame scientists for "creating" three new gaps in the fossil record.

Perhaps it's those pesky gaps that are just irreducibly, um, vacant? vacuous? in any event, requiring a non-naturalistic explanation for their incredible fecundity and proliferation.

And maybe that will be the new forefront of ID "theorizing": Intelligent Designer Feverishly Busy, Inventing New Gaps to Surround Latest Fossil Finds!

Henry J · 4 May 2006

Yeah, to them that discovery might be a bit uh fishy. (punfully intended.)

Henry

Mike Flacklestein · 13 July 2006

I live at 68275 Commonwealth in Seattle. Been up here before?