Posted on 06/14/2007 7:49:46 AM PDT by TChris
An international research consortium today published a set of papers that promise to reshape our understanding of how the human genome functions. The findings challenge the traditional view of our genetic blueprint as a tidy collection of independent genes, pointing instead to a complex network in which genes, along with regulatory elements and other types of DNA sequences that do not code for proteins, interact in overlapping ways not yet fully understood.
In a group paper published in the June 14 issue of Nature and in 28 companion papers published in the June issue of Genome Research, the ENCyclopedia Of DNA Elements (ENCODE) consortium, which is organized by the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH), reported results of its exhaustive, four-year effort to build a parts list of all biologically functional elements in 1 percent of the human genome. Carried out by 35 groups from 80 organizations around the world, the research served as a pilot to test the feasibility of a full-scale initiative to produce a comprehensive catalog of all components of the human genome crucial for biological function.
“This impressive effort has uncovered many exciting surprises and blazed the way for future efforts to explore the functional landscape of the entire human genome,” said NHGRI Director Francis S. Collins, M.D., Ph.D. “Because of the hard work and keen insights of the ENCODE consortium, the scientific community will need to rethink some long-held views about what genes are and what they do, as well as how the genome’s functional elements have evolved. This could have significant implications for efforts to identify the DNA sequences involved in many human diseases.”
(Excerpt) Read more at scienceblog.com ...
Needs abstracted and bulleted. Should be nothing but surprises.
This part is pretty interesting:
The ENCODE consortium’s major findings include the discovery that the majority of DNA in the human genome is transcribed into functional molecules, called RNA, and that these transcripts extensively overlap one another. This broad pattern of transcription challenges the long-standing view that the human genome consists of a relatively small set of discrete genes, along with a vast amount of so-called junk DNA that is not biologically active.The new data indicate the genome contains very little unused sequences and, in fact, is a complex, interwoven network. In this network, genes are just one of many types of DNA sequences that have a functional impact. “Our perspective of transcription and genes may have to evolve,” the researchers state in their Nature paper, noting the network model of the genome “poses some interesting mechanistic questions” that have yet to be answered.
(Emphasis Added)
bump
Is this a gentler way of saying, "Hmm... We were wrong."?
“the genome contains very little unused sequences and, in fact, is a complex, interwoven network.”
“God don’t make junk”
One thing I know or have read about recently is that the neurotransmitters, some of them, are created on a demand basis by reference to the DNA or RNA itself, which unzips, forms the chemical and rezips, and does this several times a second. Busy stuff.
Not wrong. Simply low res. As the view becomes more detailed more is seen. So far they have barely made out that there is structure and don’t have much detail. It is at the Canals on Mars stage.
Thanks. Good analogy.
Sounds like...design
Yes. Odd, isn't it? :-)
...and a very intricate, complex design at that!
The Great Spaghetti Monster works in mysterious ways.
This may suggest a "genes as software" approach, with perhaps an "object-oriented" flavor, such that certain RNA sequences have a "class" aspect, used intensively as part of gene "functions".
Ah, but "junk DNA" was supposed to be Important Evidence for the evolution-by-random-mutation hypothesis. If Collins is correct, the so-called evidence will have to be discarded ... which presents a rather serious difficulty for the random mutation hypothesis.
So your flippancy, while predictable, is probably not very well-founded.
Flippancy? I thought ID didn’t posit any particular god as being the intelligence behind the design. Ergo, the great spaghetti monster is as likely as any other mythical creature to fit the bill.
Well, yes, flippancy, since the FSM is meant to be a joke.
And since it's not ID, but rather its "adversary" that's in trouble here, I'd think you'd be less willing to draw attention to yourself by invoking the FSM.
It's worth asking, though ... if you were to make an ID hypothesis (irrespective of agent), would this finding support it?
No, it doesn't. From an old post:
Evolutionary theory would in fact predict emerging functions for junk DNA. In all the junk DNA that accumulates through various mechanisms there is a lot of variation, and mutation occurs, and variation plus mutation is acted upon by natural selection to produce novel and unexpected functions.Sometimes segments of the genome including genes do get duplicated. If this happens and there is a lot of that gene product needed evolution will favor the eventual emergence of a whole series of genes for this product, like the genes for ribosomes. If only a bit of the gene product is needed, the duplicate is then free to mutate and natural selection can drive a divergence between the two genes so that you get two specialized gene products fulfilling the need that was met before by a single ancestor gene product. This is what we've seen with the hemoglobin family or HOX genes. Other times a mutation kills the duplicated gene, converting it into a pseudogene, which typically is not transcribed. Usually these are relics in the genome that are not active and are only valuable to science for their use in tracing genetic phylogenies. Occasionally you'll find a pseudogene that is transcribed into RNA, but not processed into a protein. Most of these transcribed pseudogenes don't "do" anything--the RNA is degraded. However, some of them are fortuitously able to interact with the parent gene and regulate its transcription in a variety of ways.
Another example of non-coding but non-junk DNA is the palindromic sequences on the Y chromosome accumulated during its evolution. The Y chromosome is incapable of recombining with the X chromosome except at the tip, a pseudoautosomal region. Non-recombining chromosomes have a tendency to deteriorate with time as mutations build up and deletions occur. This is known as Muller's ratchet. Part of the Y chromosome's sequence is a reverse copy of important regions. The Y chromosome so far has escaped the ratchet by essentially recombining with itself. There's no guarantee for its long-term survival, though--one species of mole vole has dispensed with the Y chromosome altogether!
A final example of how junk DNA may not be junk DNA is that the three-dimensional shape of the chromosome can be important in gene transcription. A certain length of DNA may be useful between two chromosome regions for optimal transcription of these genes. Perhaps the DNA copes all right with a shorter segment in between, but when a retrotransposon (perhaps the fossil of an ancient virus?) splices itself in between these two regions and gives the chromosome some extra flexibility that aids transcription and makes the organism even more effective.
I expect we will find in future more adapted functions for junk DNA, although much of it will not yet have acquired a function.
And here is an example of a gene constructed from noncoding DNA.
Read again:
The new data indicate the genome contains very little unused sequences and, in fact, is a complex, interwoven network. In this network, genes are just one of many types of DNA sequences that have a functional impact. “Our perspective of transcription and genes may have to evolve,” the researchers state in their Nature paper, noting the network model of the genome “poses some interesting mechanistic questions” that have yet to be answered.
If that assertion is correct, then there is not a whole lot of that "junk DNA" on which the "emerging functions" mechanism would work.
The whole point of Collins' statement is that supposedly "junk" DNA actually has a great deal of functionality. It suggests an apparent error on the part of those who assign "junk" status to sections of DNA for which they cannot assign a purpose.
Exactly as I said. Evolutionary theory would predict that where we have variation and where we have mutation, we will find emerging function. My post was prophetic—that was written probably more than a year ago.
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