Sep 2012
The Alien Genome
18/09/12 13:20 Filed in: GenomeWeb Daily Scan
Craig Venter, speaking at the Wired Health Conference in New York, said that his company Synthetic Genomics and the J. Craig Venter Institute plan to develop a machine capable of sequencing and beaming back DNA data from Mars to support a search for extra-terrestrial genomes. S. Pelech argues that this proposition may not be so audacious as there are many biochemical observations that support the concept that life on Earth may have originated from Mars. Read More...
Giant Viruses Are Ancient Living Organisms
14/09/12 13:17 Filed in: Laboratory Equipment
Gustavo Caetano-Anollés at the Univ. of Illinois Crop Sciences and Institute for Genomic Biology and his colleagues completed a study of giant viruses that supports the idea that viruses are ancient living organisms that may have arisen from a fourth branch of life, alongside bacteria, archaea and eukarya. The researchers conducted a census of all the protein folds occurring in more than 1,000 organisms representing bacteria, viruses, the microbes known as archaea and all other living things, and found that the genomes of some giant viruses exceeded the genetic endowments of the simplest bacteria. S. Pelech envisions that giant viruses evolved from invasive bacteria that eventually become mobile parasites that utilized the proteins encoded by their hosts to facilitate their own replication. Consequently, it is not necessary to invoke the existence of a fourth branch of life that predated or co-existed with the three known superkingdoms to explain their ubiquitous presence. Read More...
Deeper Impact
07/09/12 13:15 Filed in: GenomeWeb Daily Scan
Victor Henning and William Gunn in the Guardian's Higher Education Network blog questioned the usefulness of the impact factor as a measure of an academic publication's influence. They suggest newer tools for calculating the value of a publication including the "Total-Impact" aggregator, as well as Henning and Gunn's own company, Mendeley, which rely on growing openness and "interoperability" in scientific and academic publishing that reviews papers on rigour and technical merit, rather than perceived significance. S. Pelech points out that while the impact factor of a journal might reflect some general measure of quality and significance, this is does not necessarily equally apply to the degree of rigour of performance, peer-review and importance of individual scientific reports within the same journal. He proposes that the best indication of the impact of a scientific manuscript is how highly it becomes cited by others over time, and foresees an increase in self-publication of scientific work. Read More...
ENCODE Explosion
06/09/12 13:12 Filed in: GenomeWeb Daily Scan
The Encyclopedia of DNA Elements (ENCODE) project has generated more than 30 publications in a variety of journals from more than 440 researchers, and it has been suggested that as much as 80 percent of the human genome has a biochemical function, including at least four million gene switches that once were dismissed as 'junk DNA." However, others, including Michael Eisen, T. Ryan Gregory and Leonid Kruglyak at their blog sites and Tweeter feeds have challenged this estimate. S. Pelech presents his own arguments for why the bulk of the DNA in the human genome is dispensable and points out that such biological inefficiency is actually very common place. Read More...
Bits of Mystery DNA, Far From ‘Junk,’ Play Crucial Role
05/09/12 13:09 Filed in: New York Times
The ENCODE project undertaken by 440 scientists from 32 labs since 2003 claimed to uncover at least four million gene regulatory elements that were previously dismissed as “junk,” and proposed that at least 80% of the human genome sequence is functional. The group has suggested that this has enormous implications for human health, because many complex diseases such as multiple sclerosis, lupus, rheumatoid arthritis, Crohn’s disease, and celiac disease appear to be caused by tiny changes in hundreds of gene switches. S. Pelech points out that less than 3% of the human genome actually encodes proteins or RNA, and about 8% of the human genome features remnants of viral DNA that were integrated into the genomes of our ancestors over millions of years. He rebukes the notion of 80% of the human genome sequence as being functional and important based on comparative genomics studies with many other species that have revealed extreme ranges in the sizes of their genomes, whilst still having a relatively similar number of genes. Read More...
'Gene Machines'
03/09/12 13:06 Filed in: GenomeWeb Daily Scan
Tim Radford at the Guardian recently reviewed Richard Dawkins' The Selfish Gene 30 years after it publication, and noted how little was known about genes at the time. He wrote that, "(Dawkins) starts to work out how genes might survive to confer just enough advantage to allow their 'survival machines' to pass those genes on to a new generation," and that "Biological behavior arises to maximize a gene's chance of continuing on to the next generation." S. Pelech provides a series arguments to dispell the concept of "selfish genes" and the notion that natural selection works simply at the level of the gene and individual. He points out that if total biomass and persistence are the best measures for the most successful species on the planet, then eusociality plays as much if not a greater role than the individual. Read More...