"JunkDNA" (98.7% of DNA in human) is not "Junk" - requiring a generalization of the "Gene concept". On http://www.junkdna.com website news items are posted (some of them reproduced here from http://www.junkdna.com/new_citations.html ) - to be discussed. My "two cents" is FractoGene (see similar website and upcoming book), a geometrization that has received now experimental support for its first prediction.

Tuesday, May 31, 2005

The "Big One" is coming: Information Technology & JunkDNA

[See article at http://www.junkdna.com/new_citations.html]

NEW YORK, May 31 (GenomeWeb News)

Agilent Technologies and Rosetta Biosoftware are integrating the Rosetta Resolver and Agilent GeneSpring software packages for gene expression analysis.The integration is being facilitated by the Resolver Software Development Kit, the companies said. Further details were not disclosed.

Agilent is the exclusive distributor of the Rosetta's gene expression analysis software.

Monday, May 30, 2005

The Information Technology Challenge of JunkDNA

[see full article at http://www.junkdna.com/new_citations.html ]

By Sharon Kanon

IHC Abstract

Israeli company Rosetta Genomics has developed a way of discovering micro-RNAs (gene regulators). Until now, all DNA research has concerned itself with the two percent of the DNA that encodes proteins. Micro-RNAs (once called junk DNA) are the other 98% of DNA. They were considered to have no function...

The conventional approach to studying RNA was first to remove it from the cell. Rosetta, however, has developed a computer system that enables them to identify genes by analyzing the genomic formats. Only afterwards do they verify their existence in the biological laboratory. A second stage is to link segments of genes to diseases. Then an effort can be made to devise treatments for the diseases from these segments.

Rosetta Genomics has attracted wide interest in both the scientific and business communities.

Saturday, May 28, 2005

Prize for Junk?

(See full article at http://www.junkdna.com/new_citations.html)

Rosaleen Gibbons, a Ph.D. student in the Biochemistry and Molecular Biology Graduate Program received the Mary and Randolph Wedding Award for 2005
(May 27, 2005)

RIVERSIDE, Calif.

Gibbons received the prize, which carries a $2,000 cash ...She has carried out her research under the direction of Professor Achilles Dugaiczyk, a distinguished scientist researching the role of the Alu DNA in primate evolution. Alu DNA are short, interspersed elements, often referred to as “junk DNA” because they don’t code for any particular proteins...

“My paper found a 250-fold increase in the differences between human and chimpanzee DNA than had been previously thought,” Gibbons said. “Although 98 percent of DNA is identified with differences between humans and chimps, we looked at that remaining 2 percent.”
That 2 percent, and the differences, are likely involved with developmental processes in humans and chimpanzees, Gibbons said.

----

Thursday, May 26, 2005

Agilent / Affymetrix Duel on the Informatics Turf

Agilent to Acquire Informatics Company Scientific Software for Undisclosed Amount
By a GenomeWeb News reporter

NEW YORK, May 25 - Agilent Technologies plans to acquire informatics company Scientific Software for an undisclosed sum, the company said today.

The deal would give Agilent one of the largest installed bases of chromatographic data systems -- SSI has more than 120,000 installations - and a broad portfolio of laboratory informatics software in the life science and chemical industries.

The acquisition would enable Agilent to provide a "family" of software products that "addresses the complete life cycle of analytical information, from data acquisition to knowledge management and retention."

Agilent did not say when it expects the acquisition to close, but the spokesperson said it will likely take one month

Friday, May 20, 2005

Best investment in Genomics?

See full article at http://www.junkdna.com/new_citations.html

Israel's Rosetta Genomics - cracking the RNA code
By Sharon Kanon May 22, 2005

... Most genomic research has been concerned with proteins, and the genes that encode proteins and turn them into cells of a certain type. The DNA region that encodes these proteins, however, constitutes only 2% of DNA. Up until two years ago, the other 98% of the genome was considered to serve no function. It was even known as 'junk DNA'.
"For 40 years, research has focused on protein encoding DNA, because it was assumed that all the rest was just there, serving no purpose," said Bentwich. "We focused our attention on a field that was rather neglected. The basic idea was to look for a new group of genes that did not encode proteins. The amazing thing is that we found them."
Bentwich calls what followed "a scientific earthquake."

... Rosetta Genomics has found a way of using advanced computer technology to reveal the encoding genes through the microRNA genes. This is now one of the hottest topics in biology. Published research in the field shows that these genes are linked to, and affect, a variety of diseases, such as diabetes, cancer, anemia, and neurological disorders.

...Rosetta's other edge in the field is its computer system.
"Up until now, the conventional approach was biological, based on the removal of RNA from the cell. Our approach is innovative in that it identifies genes by computer, and only afterwards verifies their existence in a biological laboratory.

..."These treatments will be based on microRNA, which scientists until recently thought were junk genes. It is now clear to everyone that they are goldmines.

... It is utilizing scientific discoveries that have changed the previous paradigm. That's a revolution."

The Dogmatists' New Clothes

Creationism is an example of what Richard Dawkins calls a “virus of the mind,” ...
... Why have those resources been used to elevate pseudoscience? The Stanford community deserves an explanation.

An article by Paul Laddis, see at
http://www.junkdna.com/new_citations.html

Are Darwinists Chickens?

... If the evidence is so strongly in favor of evolution, and if intelligent design is so clearly wrong, what is the Darwinian establishment afraid of?

(article by Tristan Abbey, see in http://www.junkdna.com/new_citations.html )

Thursday, May 19, 2005

Gene researchers find variations by ancestry

DISCOVERY COULD HELP PREVENT, TREAT DISEASES AMONG GROUPS

an article By Lisa M. Krieger and Esther Landhuis

Under the skin, we're all the same. That's been the warm-and-fuzzy wisdom of modern genetics, based on the first efforts to sequence the human genome.But a closer look by Mountain View biotech company Perlegen Sciences has found small genetic differences that vary in prevalence among people of different ancestries ...

See at http://www.junkdna.com/new_citations.html

Wednesday, May 18, 2005

New Theory of Life's Digital Complexity

By Graeme O'Neill
...Understanding where the points of regulatory saturation and technological limitation occur will be necessary to break through present and future complexity barriers...

See at http://www.junkdna.com/new_citations.html

The 64-bit (64 billion dollars) question

(See articles at http://www.junkdna.com/new_citations.html )

Apple/Genentech (A/G) BLAST is an enhanced, platform-specific optimization of NCBI's standalone Basic Local Alignment Search Tool (BLAST) developed by Apple's Advanced Computation Group... BLASTn (which finds similarities between nucleotide sequences) for the PowerPC G4/G5 processors and Mac OS X [now running with Tiger...]

Monday, May 16, 2005

slashdot.org 300+ postings 1 day on FractoGene

When FractoGene first emerged publicly (21st of November, 2002), slashdot.org posted over 300 opinions in a single day, see a digest at:

http://fractogene.com/full_genome/investorstatements.html

That was before the sequencing of mouse DNA revealed (5th of December, 2002) that the "genes" in the mouse and homo sapiens are 99% homologous.

It was also before a peer-reviewed manuscript was submitted (27th of March, 2005) to show experimental evidence supporting the first prediction of FractoGene.

Major investment to biotechnology


By a GenomeWeb staff reporter
NEW YORK, Jan. 7 (GenomeWeb News) - Burrill & Company, a San Francisco-based life sciences merchant bank, is launching a $300-million to $500-million venture capital fund dedicated to biotechnology, personalized medicine, new diagnostics, and devices...

Burrill & Company currently has $500 million under management. BLSCF III is Burrill's third generation of venture funds.

(see full article at http://www.junkdna.com/new_citations.html )

Protein-based Nanotechnology - examples

See full article at http://www.usa-siliconvalley.com/new_citations.html

Date: 2005-01-19 Rockville, MD

Scientists have deciphered the genome sequence of a microbe that can be used to clean up pollution by chlorinated solvents a major category of groundwater contaminants that are often left as byproducts of dry cleaning or industrial production ...

... TIGR has now deciphered the genome sequences of numerous microbes that have potential for use in bioremediation.

* Geobacter sulfurreducens, which can help mop up uranium pollution and produce energy in the process.
* Desulfovibrio vulgaris, which can help remediate metallic pollutants such as uranium and chromium.
* Shewanella oneidensis, which can remove metals such as chromium and uranium from water.
* Pseudomonas putida, a soil bacterium that breaks down organic pollutants.
* Deinococcus radiodurans, a radiation-resistant bacterium that can be used to help bioremediate radionucleotides at radioactive waste sites.
* Caulobacter crescentus, which could be used for bioremediation in low-nutrient aquatic environments