Blog Comments

Kinetica Online is pleased to provide direct links to commentaries from our senior editor Dr. Steven Pelech has posted on other blogs sites. Most of these comments appear on the GenomeWeb Daily Scan website, which in turn highlight interesting blogs that have been posted at numerous sites in the blogosphere since the beginning of 2010. A wide variety of topical subjects are covered ranging from the latest scientific breakthroughs, research trends, politics and career advice. The original blogs and Dr. Pelech’s comments are summarized here under the title of the original blog. Should viewers wish to add to these discussions, they should add their comments at the original blog sites.

The views expressed by Dr. Pelech do not necessarily reflect those of the other management and staff at Kinexus Bioinformatics Corporation. However, we wish to encourage healthy debate that might spur improvements in how biomedical research is supported and conducted.

Not So Much 'R' and Not So Much 'D'

Duff Wilson at The New York Times Prescriptions blog suggested that outside business deals are keeping the pipelines of the major drug companies healthy, instead of internal research projects as many companies such as Pfizer are slashing spending on R&D. Fitch Ratings indicates that primarily acquisition and licensing deals may allow the major pharma companies to reproduce meeting last year's level of 21 new drugs approved in the United States and Europe. S. Pelech laments that at a time when we are learning so much about the mechanisms of human disease that our progress on actually treating them is steadily waning - large pharma had 25 of their new drugs approved in 2009, and 24 approved in 2008. According to Thomas Reuters for 2010, there was a 47% drop in phase I human trials, more than a 50% decline in phase II studies, and a doubling of the rate of early termination of phase III human trials. Read More...

Evolution in Action

Bob Holmes at the New Scientist described the work of Dr. William Ratcliff and his colleagues at the University of Minnesota in St. Paul to select unicellular brewer's yeast that clump into a "snowflake" form as a model to study the evolution of single-celled organisms to multicellularity. After several hundred generations of selection, the yeast snowflakes began to show reproductive properties with some cells undergoing cell death to provide weak points for other cells to break off, allowing the snowflake to create offspring while leaving the clump strong enough to survive. S. Pelech points out that yeast like Saccharomyces cerevisiae are well known to naturally form pseudohyphal filaments depending on the nutrient conditions in their environment, so the formation of cell aggregates is already an inherent property of these types of fungi. The fact that some cells in Dr. Ratcliff's "snowflakes" die, most likely from competition for food and toxic products produced by neighbouring cells, is hardly a measure of cooperation amongst cells for the survival of the colony. Read More...

Of the People, By the People

The Wellcome Trust, Howard Hughes Medical Institute, and the Max Planck Society announced that they'll be jointly launching a new, open-access scientific journal that will ensure fair, swift and transparent editorial decisions followed by rapid online publication. S. Pelech comments that it is commendable that these agencies that are funding biomedical research are taking a greater initiative to ensure that the fruit of their investments are going to reach a larger number of scientists with open-access publication. Read More...

Where No Genome Has Gone Before

The US Defense Advanced Research Projects Agency — DARPA — called for abstracts for papers or topics and suggestions for discussion for its 100 Year Starship Study Symposium to be held in Orlando, Fla., this fall which could lead to the award of a contract in the ballpark of $500,000. Craig Venter, according to Rebecca Boyle in Popular Science, proposed that "fragmented human genomes could be shipped toward the stars and reconstructed upon their arrival, spawning the first interstellar citizens and avoiding the problems of long-distance space survival." S. Pelech sheepishly comments that rather than sending fragmented human genomes, wouldn't it be simpler to send frozen human embryos that are nurtured with robotic systems? It might be a good idea to also include the embryos and seeds from a wide range of other organisms too, because it would be pretty dreary with only humans around. Read More...

Nancy Drew and the Mystery of the Whole Genome

Blogger Richard Knox at the NPR Shots blog offered the example of Alexis and Noah Beery — 14-year-old twins afflicted with a rare disease called dopa-responsive dystonia — to show how knowledge from whole genome sequencing can provide more precise diagnosis and suggest effective disease therapy. S. Pelech questions whether it was even necessary to perform genome-wide sequencing of these twins, their parents and grandparents if the treating clinicians had a better understanding of basic biochemistry and performed obvious tests of serotonin levels, as it is well known that many cases of dystonia that are DOPA-responsive can arise from sepiapterin reductase (SPR) deficiency. Read More...

Scores and Output

Jeremy Berg at the NIGMS Feedback Loop reported from the examination of 789 R01 grants that NIGMS funded during fiscal year 2006 that these linked to 6,554 publications from fiscal years 2007 through 2010, and have been cited over 79,295 times as of two months ago. With respect to the percentile score of these grants, this was said to correlate best with the number of overall citations and least with the number of highly cited publications. S. Pelech argues that this NIGMS peer-review study actually demonstrated a relatively poor correlation between peer review scores and various measures of scientific output, especially within the top 20 percentile of peer review scores. Read More...