Posted on 04/30/2006 5:57:12 AM PDT by 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, weve 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 IBMs T. J. Watson Research Center, Yorktown Heights, NY appeared on April 24th in the early edition of the journal PNAS.
As I see it, a 21st Century view of evolution has to include the following features:
? Major alterations in the content and distribution of repetitive DNA elements results in a reformatting of the genome to function in novel ways --without major alterations of protein coding sequences. These reformattings would be particularly important in adaptive radiations within taxonomic groups that use the same basic materials to make a wide variety of morphologically distinct species (e.g. birds and mammals).
? Large-scale genome-wide reorganizations occur rapidly (potentially within a single generation) following activation of natural genetic engineering systems in response to a major evolutionary challenge. The cellular regulation of natural genetic engineering automatically imposes a punctuated tempo on the process of evolutionary change.
? Targeting of natural genetic engineering processes by cellular control networks to particular regions of the genome enhances the probability of generating useful new multi-locus systems. (Exactly how far the computational capacity of cells can influence complex genome rearrangements needs to be investigated. This area also holds promise for powerful new biotechnologies.)
? Natural selection following genome reorganization eliminates the misfits whose new genetic structures are non-functional. In this sense, natural selection plays an essentially negative role, as postulated by many early thinkers about evolution (e.g. 53). Once organisms with functional new genomes appear, however, natural selection may play a positive role in fine-tuning novel genetic systems by the kind of micro-evolutionary processes currently studied in the laboratory.
Oh, but the mathematical tool to discover these patterns was designed "to mine useful information from very large repositories of data in both business and scientific applications."
IOW, something designed to find intelligently designed patterns found patterns in the genome.
Thanks for the ping!
"junk" DNA = "We haven't figured out it's purpose, but we're too smug to admit it" DNA
Just wait until it gets sorted enough for Edward O. Wilson's science on the genetic basis for behavior can be applied to humans.
Now I'm not saying there aren't Beagles out there that are excellent retrievers during duck season, it's just not that common.
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