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

IBM ^

[Tribune7]

Yorktown Heights, NY, April 25, 2006 – IBM today announced its researchers have discovered numerous DNA patterns shared by areas of the human genome that were thought to have little or no influence on its function and those areas that do.

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.

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.

“Our goal is to apply advanced computational techniques to analyze the workings of processes and systems, in this case the function of the human genome,” said Ajay Royyuru, head of the Computational Biology Center at IBM Research. “Using these tools, we’ve been able to shed new light on parts of the DNA that were traditionally thought of as not having a specific purpose. We believe the innovative application of technology can provide further understanding in the life sciences at large.”

The IBM team used a mathematical tool called pattern-discovery, often applied to mine useful information from very large repositories of data in both business and scientific applications, to sift through the approximately six billion letters in the non-coding regions of the human genome and look for repeating sequence fragments, or motifs.

Among the millions of discovered motifs, the team identified approximately 128,000 that also occur in the coding region of the genome and are significantly over-represented in genes involved in specific biological processes such as cell communication, regulation of transcription, transport and others. In fact, copies of one or more of these motifs can be found in over 90 percent of all known human gene sequences, as well as some genes of other animals where they associate with similar biological processes.

The report on this work “Short blocks from the non-coding 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 of IBM’s T. J. Watson Research Center, Yorktown Heights, NY appeared on April 24th in the early edition of the journal PNAS.

[Tribune7]

I

[Tribune7]

ping

[Tribune7]

Here you go tallhappy. An example of how evolutionary theory is expanding our knowledge of the genome < /sarcasm>

[Tribune7]

for your list

[facedown]

Yet another case of one man's junk being another man's treasure.

[ahayes]

I like PNAS--open access article found here.

[VOA]

Yet another case of one man's junk being another man's treasure.

You nicely summed it up.
This is sort of like the venerable term "secondary metabolism" that
natural product chemists used to apply to the making of a number of
compounds that seem to have little if any importance to the
central metabolism of the organism.

But...the longer they look, some important use appears, such as
importance of a "secondary product" as a scent for attracting mates.
Or producing a compound that is both an anti-bacterial AND a precursor
to an defense compound to ward off insects.

The more we look, the more we learn...how ignorant we are.

[ahayes]

Ping for possible interest.

[Jazzman1]

Gee, I wonder why arab or muslim controlled populations dont EVER come up with scientific breakthroughs like this? hmmm...

[bubman]

IBM searching for God?

[VOA]

Well, I do know of one professor that had an Arab/Muslim grad. student
(in biochemistry).
The project: develop rapid gas chromatography methods to check for
adulteration/contamination of food products with pork material.

Of course, the student decided to visit The Great Satan in order to learn
the technology...

Oh, a good book on your main point:
"The Victory of Reason"
by Rodney Stark
It discusses why real science didn't develop in the Islamic or
in the Greek cultures.

[Chode]

i've wondered if the "JunkDNA" isn't more or less a counter or clock.
when some other part reached a given stage, it could then go back to producing useful DNA again.

[PatrickHenry]

Archive

[Fitzcarraldo]

The supposed non-coding DNA could be a genetic booby-trap, set to go off if humans start tinkering with their own DNA.

[adorno]

Gee, I wonder why arab or muslim controlled populations dont EVER come up with scientific breakthroughs like this?

They were put here on earth to provide the 'counter' to everything the civilized world does.

Sort of like what the democrats role is in congress.

[Psycho_Bunny]

regions of the human genome that were assumed to largely contain evolutionary leftovers (called “junk DNA”)

If you don't understand something as a whole, why would you assume parts of it are junk?

[Chode]

wouldn't THAT be a bite in the azz... 8^)

[Fester Chugabrew]

Further details on organized matter performing specific functions. But we don't dare infer and teach intelligent design from such things. That's illegal and unsceintific dontcha know. (Separation of science and relgion and all that.)