GenomeWeb Daily Scan
The Sum of Your Experiences
09/09/13 15:42
David Dobbs at Pacific Standard magazine writes that your experiences can shape the expression patterns of your genes, and cited studies undertaken with kidnapped European honeybees that were raised with African bees and vice versa. The kidnapped bees exhibited the gene expression and behavior of their foster colony. Dobbs also described environment induce genetic changes in humans and other animals. S. Pelech argues that while altered gene expression clearly contributes to the phenotypic changes in behaviour, a variety of other interacting molecular and cellular intelligence systems play equally important roles. He also discusses the case of the domesticated pig that goes "hog wild."
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Surrounded by Viruses
05/09/13 16:32
Simon Anthony and his colleagues at Columbia University identified 58 viruses by genetic analyses in specimens sampled from the Indian Flying Fox, Pteropus giganteus, and based on this they extrapolated that there are at least 320,000 viruses waiting to be uncovered in other mammals. S. Pelech provides his own calculations for the number of mammalian viruses based also on the latest human virus data and comes up with a similar number. Read More...
Microbes of Cancer
28/06/13 16:29
Shin Yoshimoto from the Japanese Foundation for Cancer Research and colleagues reported that although mice fed a high-fat or a lean diet did not have differing rates of hepatocellular carcinoma, when mice on those diets were also exposed to a carcinogen, namely DMBA, mice on the high-fat developed liver cancer while those on the lean diet did not. The investigators implicated the gut microbiome has a hand in this effect as the fatty diet leads to changes in the levels of deoxycholic acid (DCA) present in the gut. S. Pelech wonders about the novelty of these findings as it has been known for more than 20 years that bile acids such as DCA and other derivatives produced by microbial action from cholic acid secreted by the liver into the gut are activators of protein kinase C (PKC) isoforms in intestinal epithelial and other types of cells. PKC isoforms are the best known targets for a diversity of tumour promoting compounds. Read More...
Return on Investment
12/06/13 16:28
A new report from United for Medical Research and Battelle claimed that while the US government invested about $14.5 billion between 1988 and 2012 in the Human Genome Project, it has reaped $59 billion in tax revenue and $965 billion in economic impact. The report further suggests that the investment has lead to 53,000 genomics-related jobs and $293 billion in personal income. S. Pelech notes the timing of the release of the report with the reduction of NIH research funding through the sequestration, and challenges some of the conclusions of the study. He notes that there has been essentially no growth in employment in any of the various genomics sectors in the last 5 years. Read More...
After the Test
14/05/13 16:26
Actress Angelina Jolie wrote in the New York Times that she decided to undergo a preventive double mastectomy after learning that she carries a mutation in her BRCA1 gene. Jolie's doctors estimated that she had an 87 percent risk of developing breast cancer and a 50 percent risk of ovarian cancer. S. Pelech questions whether it was really necessary for Angelina to undergo the radical surgery based simply on the presence of a mutation in her BRCA1 gene, and discusses how other tumour suppressor genes are much more frequently found in breast cancer patients. Read More...
The Microbes You Share
19/04/13 16:23
Rob Knight at the University of Colorado and his colleagues examined the fecal, oral, and skin microbiota of 60 families with and without children or dogs, and reported that cohabitating partners shared many microbes, especially Prevotella and Veillonella. People also had similar microbial communities as their dogs. S. Pelech points out that animal companions can also provide us the opportunity to become immunized against many pathogens, and describes how cat owners may have been more resistant to infection by the SARS coronavirus. Read More...
BRAIN Game
02/04/13 16:21
US President Barack Obama announced his $100 million initiative called the Brain Research Through Advancing Innovative Neurotechnologies or BRAIN Project. The project will involve a number of agencies, including the National Institutes of Health, National Science Foundation, and the Defense Advanced Research Projects Agency, and a so-called "dream team" of researchers led by Rockefeller University's Cori Bargmann and William Newsome from Stanford University will be developing a specific plan and goals for the project. S. Pelech acknowledges that a commitment to increase spending for neuroscience-based research is sorely needed, but it would appear from preliminary descriptions of the research program that very little of the new funding will actually be applied to the study of neurological diseases in humans. Read More...
Learnt Lessons
25/03/13 16:19
When the genome of HeLa cancer cell line was published, it turned out that Henrietta Lacks' family did not appear to give its consent to have the genome published. Jeri Lacks-Whye, Lacks' granddaughter in a New York Times op-ed complained that the HeLa genome sequence should not have been published without their consent as it might have compromised their family's privacy. As a consequence, the researchers who published the HeLa genome apologized to the family, edited their news release, and took the HeLa data down. S. Pelech questions the value of sequencing genomes without strong phenotypic data to correlate with genetic variants, and finds it hard to accept that the privacy of Lacks' family was actually compromised in a meaningful way. HeLa cells are amongst the best characterized of these established cancer cell lines, so it is a real shame that the HeLa cell genome sequence will not be broadly accessible to cancer researchers to improve our understanding of this most deadly disease. Read More...
Night of the Living Dead Pigeon
15/03/13 16:18
Ben Novak, is a 26-year-old genetics student who has put his graduate studies on hold to help bring the extinct passenger pigeon back from the dead by sequencing available fragments of the genome of the passenger pigeon from the slime left in museum specimens and comparing them to the genome of its cousin, the band-tailed pigeon. Working with evolutionary biologist Beth Shapiro at the University of California, Santa Cruz, Novak hopes to complete full sequences of the passenger and band-tailed pigeon genomes within a year. S. Pelech comments that even with the successful sequencing of the complete genome of the passenger pigeon, the site-directed mutagenesis of the genome of a living pigeon relative to convert it into a passenger pigeon is just too expensive and time-consuming to be worthwhile. Read More...
The Proteoform
06/03/13 16:16
Lloyd Smith, Neil Kelleher, and the Consortium for Top Down Proteomics in a correspondence to Nature Methods suggested the term "proteoform" to describe all the shapes that a protein can assume and to differentiate it from isoforms that arise from alternative splicing of the same gene. S. Pelech suggested that if the word "proteoform" was extended to include protein complexes, the meaning of term would be too diluted and it would be overly broad. Instead, he proposed adoption of another term "proteocomplex" to refer to the specific composition and stoichiometry of subunits in protein complexes. Read More...
Billion-Dollar Brain Map
18/02/13 16:10
The New York Times reported that the Obama Administration is set to announce a large-scale, decade-long project to map the activity of the human brain. Proponents such as George Church at Harvard University have argued that the Brain Activity Map could provide a much-needed financial boost for neuroscience in the order of $300 million a year. S. Pelech seriously questions the wisdom of diverting a significant amount of the limited resources available at this juncture for basic scientific research towards the specific goal of mapping brain activity patterns at the cellular level in high resolution. He notes a huge litany of issues ranging from technical, economic, and practical to profound ethical considerations associated with such a proposal. Read More...
A Good Return
14/02/13 16:08
In his recent State of the Union address, US President Barack Obama made mention of how for every dollar the US government invested to map the human genome, $140 was returned to the US economy. This was based on a 2011 report by the Battelle Technology Partnership Practice, which calculated the direct, indirect, and induced impacts of human genome sequencing on employment, personal income, output, and tax revenue. S. Pelech challenges the accuracy of these estimates and pointed out that private industry and non-HGP government- and charity-funded investigator-driven projects really made the major in-roads in the identification and characterization of most of the human genes that have been targeted by the pharmaceutical and biotech industry to date. He also takes issue with the claims of the actual direct economic and scientific benefits of the Human Genome Project. Read More...
Gross, but Appears to Work
17/01/13 16:05
In The New England Journal of Medicine, Amsterdam researchers reported that fecal transplantation worked 3- to 4-times better than vancomycin therapy to treat recurrent Clostridium difficile infections. The treatment is thought to work by altering the composition of the patients' gut microbiome and increasing its bacterial diversity. S. Pelech comments that the introduction of transplanted fecal material at the bottom end provides for restoration of the resident flora just as does the eating of probiotic yogurt at the front end. However, it would be better to develop drugs that are actually more highly selective for Clostridium and other pathogenic bacteria, and the growing availability of the genomes of these and other bacteria will surely aid such efforts. Read More...
A Case for the Ages
11/01/13 16:03
Brooke Greenberg is a 20 years old that appears to be the age of a toddler. While her doctors do not know the root of her apparent inability to age, Eric Schadt at Mount Sinai has been studying her genome to learn more about the aging process. S. Pelech provides some further details about this fascinating and tragic case. Read More...
The Repurpose
29/11/12 16:01
Fierce Biotech reported that The Broad Institute will be searching through Roche's catalogue of more than 300 failed compounds to find new possible uses for those drugs, and noted that similar drug repurposing efforts are underway at the US National Institutes of Health's National Center for Translational Science and at the UK's Medical Research Council. S. Pelech describes the excellent opportunities for repurposing the large arsenal of potent protein kinases inhibitors that has been amassing over the last decade, and mentions efforts at Kinexus Bioinformatics Corporation to identify off-targets for these kinase inhibitors. (This work resulted in the recent release of the DrugKiNET SigNET KnowledgeBase in Kinetica Online.) Read More...
Early Arrival
07/11/12 13:27
In Lancet Neurology, a team of researchers reported a high prevelance of mutations in the presenilin 1, or PSEN1, gene linked to Alzheimer's that were apparent in 20 of 44 young adults from Colombia at least 20 years before the onset of symptoms. Apart from differences in brain structure and function between the two groups, the researchers also detected increased cerebrospinal fluid levels of amyloid beta. S. Pelech notes that in many clinical studies with Alzheimer's patients, there is actually usually a DECREASE in the level of the pathogenic 42 kDa beta-amyloid (A-beta42) protein in their CSF relative to healthy controls and patients with Parkinson's disease and progressive supra nuclear palsy. He further describes research at Kinexus Bioinformatics Corporation using antibody microarrays that uncovered 36 proteins that displayed abnormal phosphorylation or expression in peripheral blood lymphocytes from Alzheimer's patients as compared to controls that were only mildly cognitively impaired or had other neurological disorders. Read More...
Mapping the Brain's 'Symphony'
06/11/12 13:25
Francis Collins at the NIH in his new blog discussed the Human Connectome Project, an NIH-funded effort to map all the neural connections in the human brain. He noted that whereas before only an isolated region of the brain might have been analyzed, recent advances in computer science, math, imaging, and data visualization can now allow researchers to study the human brain as an entire organ. S. Pelech is astonished that "the Human Connectome Project, has set out to map the brain’s neural connections in their ENTIRETY." He questions whether the project proponents truly appreciate the scale of such as proposal and whether the knowledge gained from such an undertaking is really worth the costs. Read More...
Science Philanthropy for the 99 Percent
12/10/12 13:23
Bitesize Bio highlighted a new website, called Flintwave, that combines social networking and crowdfunding to support specific projects. Scientists can use the site to share videos, posts, and presentations that "science enthusiasts" can follow and fund. It joins a host of other science crowdsourcing sites that have popped up recently, including Open Genius, the SciFund Challenge (hosted by RocketHub), IAMscientist, Microryza, and Petridish. Eva Amsen at the Occam's Typewriter Irregulars questions whether the model can be as fruitful for scientific research projects as it is for other disciplines as much higher levels of fundraising are required and a direct return on investment is much less likely. S. Pelech calculates that the research behind the average NIH-funded scientific paper with a 5.5 impact costs at least US$ 128,000 to fund, and figures that in view of this cost, the number of biomedical research projects that are likely to be funded by crowdsourcing online is probably much too small to be of real significance in the progress of scientific research as a whole. Read More...
The Alien Genome
18/09/12 13:20
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...
Deeper Impact
07/09/12 13:15
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
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...
'Gene Machines'
03/09/12 13:06
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...
The Biofueled Military
28/08/12 13:04
With its Great Green Fleet demonstration, the US Navy has shown that it can run on alternative fuels, including diesel from algae and chicken fat, although the costs can be as high as $424 a gallon for biofuels. Rep. Mike Conaway (R-Tex.) questioned the value of this biofuels program supported by the Department of Defense. S. Pelech points out that as long as major populations continue to rely on fossil fuels to supply their energy needs, the potential risks of environmental damage as well as the costs to consumers will only increase at an accelerating pace. Alternative sources of energy will continue to be less competitive if there is a lack of political will and action to innovate and develop these options by military and civilian branches of governments world-wide. Biotechnology has a lot of offer towards these ends if societies chose to exploit it much more aggressively for such purposes. Read More...
A Happy Sequencing Ending
27/08/12 13:02
Genome sequencing of the Beerys fraternal twins living near San Diego with neurological issues revealed that in addition to having dopa-responsive dystonia, the twins also had a serotonin deficiency. Based on the genetic data, the twins were effectively treated. S. Pelech notes that this is one of the rare examples of where whole genome-wide DNA sequencing is reported to have provided vital clues as to the underlying nature of a baffling illness that afflicted children. However, it is unclear that genome-wide DNA sequencing of these twins, their parents and grandparents was even necessary in this case if the treating clinicians had a better understanding of basic biochemistry. Read More...
Core Concept
24/08/12 13:00
Richard Wintle from the Hospital for Sick Children in Toronto described how core lab scientists allow for efficient and cost-effective research. S. Pelech concurs that the establishment of core facilities for undertaking specialized analyses that require expensive equipment, specialized reagents and high expertise can make a lot of financial sense, especially because this minimizes redundancies in resources for biomedical research. However, such core facilities are often under utilized, because there are still significant cost barriers to accessing their services for the vast majority of university and small biotech company scientists. Local research scientists could benefit from core facilities and adopt the new technologies to take their research to higher levels if the cost of accessing these core facilities was much cheaper for academic and industrial researchers from the same area from which the government funding was procured. Read More...
Strength in Numbers
08/08/12 12:57
University of Chicago in Illinois' Tim Wootton and Cathy Pfister suggest that sheer numbers are more important than genetic diversity for preserving species threatened with extinction based on their 12 years of breeding studies of the sea palm Postelsia. Genetic diversity did not influence the odds of a population's survival, whereas the size of the population was more critical. S. Pelech points out that preservation of habitat that is rich in biological diversity seems to be the best solution to ensure survival of most species facing extinction today due to their interdependence. He notes that there are many examples, including humans and whales, where genetic diversity appears to be less critical for avoiding extinction than population size. When one looks closely at the various genes encoded in diverse animal species, the number of genes and their nucleotide sequences are remarkably similar. It seems that phenotypic differences arise primarily from where and when the proteins encoded from these genes are produced. Read More...
Are You Sure?
31/07/12 12:55
Daniel MacArthur at Massachusetts General Hospital suggests that false positives are a given in genomic research, especially due to the large size of genomes and errors from high-throughput sequencing. Ann Buchanan at Penn State University also notes for these and a variety of other reasons there many sequence errors in genomics manuscripts and online databases and a higher rate of retractions. S. Pelech argues that the increased rate of retraction of scientific research results in publications in general actually reflects a wide variety of confounding factors beside greater error rates from higher throughput technologies. These include amongst others premature submission for publication due to financial and continuing employment requirements, poorer peer-review, and a proliferation of new journals eager to acquire manuscripts, which can result in outright plagiarism and even fraudulent data. Read More...
But What Does That Really Mean?
30/07/12 12:53
Adam Rutherford at Nature suggested that "the present gains and future benefits of synthetic biology are too great for it to be written off with fear-mongering maxims about "playing God." Gerhard Adam in his Blog questioned what it really means to "play God", and that if we now have the power to improve our ability to cure diseases, then we have a moral responsibility to do so. S. Pelech agrees and takes issue with the very concept of "Playing God" and wonders why if people believe in divine intervention they don't also believe that scientists are guided in their actions directly by "God." Read More...
Sperm Seq
30/07/12 12:51
Stephen Quake at Stanford University and his colleagues reported the first genetic comparison of 91 single sperm cells using a microfluidic chip and found that some of the cells had recombined in unexpected places. This recombination contributes to the genetic diversity between siblings, and this methodology might be used to diagnose male fertility, select eggs for in vitro fertilization, and identify mutated genes in individual cancer cells. S. Pelech points out that the ability to sequence genomes in single haploid cells provides the unique opportunity to examine the actual clustering of specific mutations on the very same protein and explore the possibilities of synergistic and antagonistic mutations. Read More...
Lab-Less Research
18/07/12 12:56
Monya Baker at Nature News described how public data repositories like the NCBI's Gene Expression Omnibus (GEO) have been a boon for researchers, who are using the information they store to study genetic associations to diseases without ever having to go near a microarray. S. Pelech pointed out that while this is wonderful resource for examination of the changes in gene expression within individual studies, it is difficult to compare the data across different studies. At Kinexus, we retrieved from the GEO database the human gene expression data from over 900 different studies with over 6000 biological specimens and systematically normalized the results to permit queries of mRNA levels for 23,000 genes in the open-access website TranscriptoNET (www.transcriptonet.ca). TranscriptoNET features comprehensive information on the mRNA expression levels in about 600 types of human organs, tissues, tumours and cancer cell lines. Read More...
Where Are You From?
06/06/12 13:03
Ewen Callaway at Nature News pointed out that whole-genome sequencing is already being used by companies for ancestry testing. S. Pelech notes that there are 7 billion people on the planet with ancestral roots that run deep in time, and ultimately these roots all trace back to a small family of Homo sapiens about 200,000 years ago that lived in Africa. While very human-like creatures such as Homo erectus (the ax maker) existed nearly 2 million years, it would appear that Homo sapiens were on the verge of extinction back around 200,000 years ago. Read More...
Global Scientific Principles
16/05/12 13:05
The Nature News blog reported the creation of the Global Research Council (GRC) by a group of research agencies leaders from nearly 50 countries. The GRC plans to discuss "shared goals, aspirations, and principles, and provide a vehicle to unify science across the globe." op, where research agencies agree on broad-brush issues but do little to resolve practical differences." S. Pelech questions whether further politicization and standardization of scientific research is so desirable. While a strong case can be made for international funding of a few large scale projects for the common good, he argues most research in academia and industry should be investigator-driven and collaborations should be dynamic and naturally arise from the science rather than the desires of politicians and bureaucrats to see further interactions with their favoured countries. He describes three trends related to the financing of scientific research endeavours that he finds particularly disturbing. Read More...
Not Worth It Anymore
10/05/12 16:09
Bloomberg reported that a survey conducted by the National Venture Capital Association found that about 40 percent of the 150 venture capital firms that responded decreased their life science investment in the last three years. Bloomberg also observed that biotech stocks are now tending to fall even after firms receive approval for their drugs. S. Pelech comments that it is not surprising that venture capitalists and other investors are very wary of investing in biotechnology companies based on the last decade of very poor returns from this sector. However, roughly half of the new drugs entering the market place today originate from the biotechnology industry and large pharma relies on a healthy biotech industry to meet its R&D needs, often by acquisition. These big fish will have a lot fewer small fish to sustain them the way things are going. Read More...
Let the Games Begin
09/05/12 18:33
Rebecca Boyle in Popular Science highlighted how the success of games like Foldit has shown researchers how useful it can be to put a problem in front of a wide group of gamers and science buffs to get help in solving it. S. Pelech argues that to tackle most problems in molecular biology and other life sciences, the recruitment of gamers is really impractical. Unless savants are engaged in these problems, the data are just too complex for meaningful explorations within video games on i-Pads. Read More...
Cloudy, With a Chance of (Data) Showers
09/05/12 13:08
Adina Mangubat, CEO of Spiral Genetics, wrote in Xconomy that the $1,000 genome won't do any good for science if researchers can't interpret it, and she points to a need to continue aggressive development of bioinformatics software that works in a cloud environment. S. Pelech comments that this is only part of the solution, and suggests that greater emphasis should be directed towards the collection and consolidation of large data sets from high throughput genomics, proteomics and metabolomics measurements of clinical specimens, and the development of predictive biochemistry algorithms that can efficiently interrogate this meta-data. Read More...
Oh, the Pressure
08/05/12 22:49
David Colquhoun from University College London wrote in the Guardian that the pressure to publish scientific papers has led to the ability to publish just about anything, whether the paper merits publication or not and this can reduce the quality of science. S. Pelech comments that in the scientific research endeavor, discovery is of limited value if it is not disseminated, but most research findings are of interest to a rather select group of aficionados. The best measure of impact is how highly cited the work becomes and this is evident only after a period of years. Read More...
In Defense of Risk
27/04/12 13:10
Blogger Proflike Substance questioned the adversity of federal agencies to funding risky research, since this can offer the biggest rewards. S. Pelech figures that all experimental research should have risk if it is truly original and not merely confirmatory. The decision to carry out a specific experiment or line of enquiry is dictated by the rewards verses the costs, which include time, money, and lost opportunity to pursue more productive directions. Granting agencies generally support low risk, hypothesis-driven research, because this is often believed to lead to better designed experiments that produce clearer answers to the questions posed, but S. Pelech challenges this view. Read More...
Pity the Poor Fraudster?
19/04/12 14:46
Brian Deer at the Guardian wondered whether the problem of more research fraud stems from increased misconduct or because other researchers are getting better at catching it? He somewhat sympathized with Peter Francis, who due to the stiff compeption for research support, applied for a grant using fabricated data, was caught by his university, and was investigated by the US Office of Research Integrity. While S. Pelech finds it hard to accept Dr. Francis as a victim of the present system, he comments that Dr. Francis' behaviour does reveal how easily it can be abused. He suggests that a better grant funding system that takes into account the realities of scientific research would be to fund established investigators primarily on the basis of their recent productivity and less so on their ideas. Read More...
Well, This Is Awkward
18/04/12 13:44
Mark Czarnecki at the Walrus magazine noted that while researchers have not yet nailed down their interpretations of the human genome, direct-to-consumer firms are hawking genetic tests and that offer to "detail your risks for a menu of diseases." Czarnecki stated that, "with whole-genome sequencing providing so much data that is so little understood, making the best ethical choice (of what to do) is more difficult than ever." S. Pelech cautions that the tendency of many to use the reductionist view that diseases primarily arise from defects in the genome will ultimately lead to a lot of wasted expense and unnecessary added worry. Disease arises from a complex interplay of genetic and environmental factors. Read More...
Going, Going, Gone?
16/04/12 14:37
Blogger Ken Weiss in the Mermaid's Tale blog wondered whether from interest in whole-genome sequencing is "fading." He thinks that money should be spent on looking at specific problem-causing genes. S. Pelech takes sickle cell anemia as an example of how the identification of disease-causing genes is only the first step in a long road towards successful diagnosis and treatment of illness. He points out that environmental factors clearly have a major influence on whether most common diseases will materialize, and these can exacerbate or compensate for genetic defects. Read More...
Questioning Science
11/04/12 12:23
ScienceInsider reported that a Tennessee anti-evolution bill has become law, although without the signature of the state's governor Bill Haslam. According to the Tennessean, the bill encourages students to question accepted scientific theories — listing as examples evolution, the chemical origins of life, global warming, and cloning — and it protects teachers from punishment if they teach creationism." S. Pelech wonders whether the Bill might in fact not be a bad thing. As long as the Bill truly provides for healthy debate, maybe it is a good idea that scientific thought is open to challenge, since this is a primary difference between the development of scientific knowledge and religious beliefs. Read More...
Learn a Lesson from the Past
03/04/12 12:31
Ed Yong at Nature News cautioned that while sequencing the human microbiome could lead to exciting and important discoveries for human health, researchers working with the microbiome should avoid overhyping their work so that it does not suffer the same backlash as the Human Genome Project. S. Pelech comments that defining what is meant by the human microbiome "sequence" is even more elusive than the relatively static human genome "sequence" even if this is only from one person out of 7 billion on this planet. He argues that what we really need to do is to identify the specific bacteria that are problematic and cause disease, and differentiate them from the vast majority that are benign or even essential to human health. Read More...
Mind the Gaps
02/04/12 12:26
Daniel MacArthur and his colleagues' in their recently published Science paper described a systematic survey of loss-of-function variants in human protein-coding genes using data from the 1,000 Genomes Project that revealed that genomes of healthy individuals each contain about 100 LoF [loss-of-function] variants, and approximately 20 of these genes are completely inactivated. S. Pelech comments that while the genomes of healthy people can harbour many defective tumour suppressor genes without any manifestation of cancer, it also likely that they might also have activated oncogenes, which alone are insufficient to induce full neoplastic transformation. He also points out a recent study with 53,666 identical twins in registries from the United States and Europe that showed they had similar risks for 24 different diseases as seen they were when compared to the general population. Read More...
'Like Insider Trading'
01/04/12 12:28
Bloggers Proflife Substance, Namnezia and Athene Donald explored the dilemma that arises when reviewing grant proposals or submitted scientific manuscripts can directly influence the research of the reviewer - the inside knowledge might serve as a trigger for independent thought through to being a source of outright theft of the author's ideas. S. Pelech comments that with the thousands of information bytes that we receive daily during readings, viewings, and discourses with others, it is hard to tell when original thoughts truly emerge as opposed to ideas that were forgotten and triggered for remembrance. Creativity in scientific thinking seems to stem from the ability to string diverse ideas together in novel ways that explain observations or reveal previously unappreciated relationships. Read More...
Poop Speaks
30/03/12 12:46
Bloomberg Businessweek reported that Eric Schadt at the Mount Sinai School of Medicine and Pacific Biosciences predicts a future in which special toilets collect stool samples that can then be sent off for sequencing to identify pathogens in spots like airports or emergency rooms to monitor public health concerns, like flu outbreaks. S. Pelech comments that it's kind of appropriate! Since most of the DNA sequence in genomes is crap, we may as well sequence DNA in crap. Read More...
Down with Dry Writing
28/03/12 12:30
Adam Ruben in Science Careers wondered why scientific articles are not written as more interesting and dynamic stories? He mentions that scientists are often taught to avoid writing in the first person, and that many journals prefer manuscripts be written in past tense. S. Pelech notes that scientific research manuscripts are written more often by committees than individuals so they will appear to be very impersonal despite the passion that underlies the work. He suggests that authors may as well make them as complete and interesting as possible, and emphasize personal perspectives that are being offered in the discussion and conclusions. Read More...
Cellular Computations
28/03/12 12:29
Pankaj Mehta at Boston University and David Schwab at Princeton University in a paper posted online at arXivSimilar that suggested like computing on chips, the biochemical networks behind cellular computations are also constrained by energetic considerations. S. Pelech disagrees and explains that life is actually remarkably inefficient at the molecular level. While bacteria in general have evolved to become more energy efficient, with multicellular animals and microbes, improvements in the ability to predate other organisms more than compensate for deficiencies in biochemistry. Read More...
Test the Waters
27/03/12 13:20
The Vancouver Sun reported that researchers at British Columbia's public health laboratories are developing a metagenomics-based test to detect contaminated water through the presence of pathogens' DNA. S. Pelech offers a number of reasons why he thinks that the GenomeBC- and GenomeCanada-funded project to create a metagenomics-based test for detection of bacterial contaminants in community drinking water seems rather ill-conceived. He further questions the decision of the Government of Canada to provide up to $40 million to GenomeCanada and up to $22.5 million to the Canadian Institutes for Health Research (CIHR) for new multi-million dollar proposals for projects that use genomics to advance personalized health care delivery. Read More...
Blurry Lines and the Cost Curve
27/03/12 01:54
The New York Times featured an article focusing on Complete Genomics' efforts to offer cheaper sequencing through the combination of biology, chemistry, and computing, and mentions the stiff competition in the field. S. Pelech mentions the results of a completed detailed meta-analysis of all of the reported mutations in over 3000 human genes that have been linked with cancer in one way or another that was performed at Kinexus Bioinformatics Corporation out of curiosity to see what might be expected from random sequencing of cancer genomes. These studies revealed that the vast majority of these cancer genes feature mutations that are apparently randomly distributed throughout their entire sequences, and in most cases less than 1% of their amino acids have been observed to be altered with any cancer. Moreover, for more than half of these cancer-associated genes, either none or only 1 or 2 mutations were reported. Read More...
Going Back to Go Forward
23/03/12 14:21
Helen Pearson in Nature News reported how University of Oregon, researcher Joe Thornton and his colleagues are analyzing proteins that are hundreds of millions of years old in an attempt to better understand how organisms evolved. Thornton tracked the genes for steroid hormone receptors from several living organisms back through their evolutionary trees to determine the most likely common ancestor, and then built the gene and inserted it into cells that could manufacture the ancient protein. S. Pelech comments that careful alignment of the amino acids in functional protein domains might reveal what the likely primary structures of these domains resembled when they first appeared in organisms on this planet. Comparison of such consensus sequences for each defined protein domain can further provide clues as to how they may have evolved from each other and ultimately how the hundreds of functional domains found within all of the known proteins may have emerged from a very small number. He notes that this approach has been successfully usedby Kinexus Bioinformatics Corporation to identify glutamine tRNA synthetase as the precursor of the typical protein kinases and the choline/ethanolamine kinases. Read More...
It's Not a Pet
22/03/12 14:10
Rebecca Boyle in Popular Science suggested that personalized mouse models might eventually be used for testing the effectiveness of drugs. The mice are implanted with tissue (e.g. tumours or blood cells) from the patient that can mimic their biology and then are used to pre-test drugs or treatments to see if they will potentially work in the patient. S. Pelech comments that immune compromised mice have also long been used for cultivation of human tumours from transplanted cancer cells, but the identification of the driver cancer mutations in the sequenced genome from the tumour of a patient is itself a very challenging task. Due to the acquisition of new mutations in growing tumours from defects in DNA repair proteins, the genetic profiles of descendant tumours in the mice could actually be quite diverse and respond differently to even the same drugs. Ultimately, an entire customized research program would be required to deliver personalized medicine as proposed by Ms. Boyle. Read More...
Prometheus Struck Down by the Gods…
21/03/12 13:49
Sabrina Richards in The Scientist reported that the US Supreme Court has overturned two methods patents on drug dose calibration held by biotech company Prometheus Laboratories. The Mayo Clinic claimed that the patents relied on natural phenomena, which are unpatentable, and the case went all the way to the US Supreme Court after the Federal District Court upheld the patents. S. Pelech comments that the US Supreme Court's ruling on the patentability of observations of natural phenomena like biomarkers seems pretty sensible for a myriad reasons, including the fact that their recognition come from acts of discovery as opposed to invention. Also with such an abundance of biomarkers, there could otherwise be a strong temptation to file a lot of ultimately useless patents that would really only benefit patent law firms. Read More...
Containing the Deluge
19/03/12 14:59
Blogger Derek Lowe in the Pipeline called for more standardization in how data is stored, integrated and retrieved. While proprietary software is often developed for such purposes, sometimes MS-Excel spreadsheets are adequate for simplier projects. S. Pelech comments that Kinexus Bioinformatics Corporation originally had custom algorithms produced from a local software company to manage the data that was being generated with their multi-immunoblotting analyses, but the company subsequently went out of business and it has not been possible to update or modify their proprietary software. Kinexus now uses off the shelf programming software to create web-based interfaces that permit users to access its data. Read More...
The Real-time In-depth-ome
16/03/12 14:35
Rebecca Boyle at Popular Science reported that Michael Snyder at Stanford University has been studying his own genome, transcriptome, proteome and metabolome in an effort to make as detailed a personal 'omics profile over two years, and now the results of this study have been published in Cell. S. Pelech questions that since Dr. Snyder's academic research is primarily funded with public grant funding, is it ethical to have these resources spent in such a manner that he will be the primary beneficiary? Read More...
Is the US Losing its Edge in Science?
16/03/12 14:15
Michael Price at ScienceInsider reported that the health-research organization Research!America has conducted a new poll that shows that about half of Americans think that another country will surpass the US in healthcare, science, and technology prowess by the year 2020. "Of the 1,005 likely voters polled, 47 percent said they thought the United States would lead the world in healthcare by 2020. … Only 42 percent said they thought the United States would retain its position as the world leader in science and technology by 2020, while 26 percent predicted China would assume that mantle, and 23 percent chose India." S. Pelech reflects that a lot of the present rhetoric going around about the decline of American dominance in science and technology reminds him about the hype in the late 50's and 60's about the West lagging behind the East (at that time the East meant the Soviet Union) with the space and nuclear arms race. The calls to action resulted a marked escalation of funding to advance scientific research in the West. Read More...
The Next Big Frontier?
16/03/12 13:43
Andrew Hessel from Singularity University in the Huffington Post's Science blog called for a second Human Genome Project in which a complete 3 billion basepair human genome is synthesized, correctly organized into 23 chromosomes, and packaged into a nucleus to become functional when microinjected into a cultured cell. S. Pelech offers a number of reasons why the concept of chemically synthesizing a complete human genome at this time is just plain silly. Read More...
US Universities Hold Strong
15/03/12 13:31
Times Higher Education released its compilation of the top universities by reputation for 2012, which was led by Harvard University, followed by Massachusetts Institute of Technology, the University of Cambridge in the UK, Stanford University, and the University of California, Berkeley. Among the top 50 universities ranked by reputation, 30 are in the US, 6 are in the UK, 3 each are in Australia and Canada, 2 each are in China and Japan, and one each are in Germany, Hong Kong, Singapore, and Switzerland. S. Pelech notes that this survey is based on the opinions of only 50 people in 15 countries around the world with 90% of the scoring based equally on the quality of teaching, research and publication citation - industry income as a measure of innovation only counted for 2.5%. Read More...
Extended Employment
14/03/12 18:33
Virginia Gewin in Nature suggested that "academics who delay retirement could create roadblocks for early-career researchers." Graeme Hugo at the University of Adelaide in Australia told Gewin that more than half of the academic workforce is over 50 years old, but while around 40 percent of that workforce may retire in the next decade, the vacated permanent posts are being divided into contractual, non-tenure-track jobs. S. Pelech comments that the current supply of academic scientists is probably optimal for the good of the general public at present and in the near future. He points out that more experienced active scientists should be better at undertaking and successfully completing more challenging research projects than junior investigators, and also be better educators with their more extensive knowledge-base. Read More...
Stop That!
14/03/12 17:52
Elizabeth Pennisi in ScienceInsider reported that a group of 111 watchdog and other organizations are calling for a moratorium on synthetic biology research until there is more oversight and governmental regulation. The group released a report that calls for more regulation with specific recommendations for "managing new biological techniques for building and remaking organisms for research and commercial uses." S. Pelech comments that humanity has been performing selective breeding of plants and animals for our purposes for over 10,000 years, and synthetic biology is just another advancement in our ability to modify other organisms or ourselves in an intelligent way. Recommendations related to ethics considerations that encompass religious concerns are likely to severely handicap adoption of synthetic biology research projects in the US. Read More...
Kitchen Biology
07/03/12 14:42
Blogger Veronique Greenwood at the 80beats blog offered a new program on PBS, NOVA's "Cracking Your Genetic Code," as a good example of why DIY (do-it-yourself) biohacking has taken hold. A PBS promotional video shows how simple it can be to extract DNA using common household products. Prompted by the video, S. Pelech recalls an encounter with a venture capitalist that had not actually taken any formal training in the life sciences, but who had control of the investment of over $100 million dollars of funding into biotechnology companies for more than 10 years and served on the board of directors of several of these firms. Read More...
Chinese Scientists Celebrate
06/03/12 14:07
Mara Hvistendahl in ScienceInsider reported that China's Premier Wen Jiabao announced his government has earmarked $5.14 billion for basic research in 2012, a 26 percent increase from 2011. Overall spending on science and technology in China will rise 12.4 percent to $36.23 billion. S. Pelech feels that it is actually wonderful to see places like China contribute more significantly to the growth of biomedical research, because ultimately we will all benefit in terms of improved diagnostics and therapeutics as well as new knowledge. He speculates that the rise of the Far East might actually further encourage North America and Europe to increase their own commitments to biomedical research. Read More...
The Cellular CPU
05/03/12 15:52
The Economist reported that researchers are hard at work trying to write code made of DNA and RNA to program a living cell in order to control it. Microsoft researcher Luca Cardelli told the magazine that "if you can program events at a molecular level in cells, you can cure or kill cells which are sick or in trouble and leave the other ones intact." S. Pelech finds it amusing to see a business magazine promoting to the general public hare-brain ideas from computer software programmers about how to genetically engineer cells by mucking with their DNA to create molecular logic circuits. It may be possible to design DNA-based computers that solve the most simple of problems within test tubes or in in silico simulations, but not for the applications contemplated in this Economist article. Read More...
The State of Sequencing
05/03/12 14:02
Art Wuster at Seqonomics wrote that the state of DNA sequencing capability in Japan is surprisingly low, espcially when compared to the Netherlands or in Spain, both of which spend only a fraction of what Japan does on research and development. S. Pelech comments that there is already a tsunami of DNA sequence data to go around today that could keep researchers busy for many years to come. He suspects that the Japanese are probably strategically inclined to be more translational and pragmatic in their research and exploit what is already been harvested. Read More...
'A Lie and a Sham'
02/03/12 18:54
Blogger DrugMonkey ranted that co-first authorship on scientific papers is "a lie and a sham and an embarrassment to our profession." S. Pelech notes that the assignment of authorship order in scientific manuscripts is almost always a political issue, especially for research projects that require multiple techniques, diverse expertise, and extensive collaboration. A large number of first and senior author publications will indicate that the researcher is truly talented and productive. A one hit wonder or a missed first authorship will ultimately mean relatively little to one's career. Read More...
A Bargain Made
24/02/12 00:15
Blogger Ananyo Bhattacharya at The Guardian 's Notes & Theories blog wrote that conventional thinking in science policy, which promotes a utilitarian view that research should be at the heart of sustainable economic growth and should serve the public interest, can result a dramatic undervaluation of basic research. S. Pelech comments that especially in the last 50 years, governments throughout the developed world have steadily built up their basic research capacities in the life sciences in universities, hospitals and government laboratories, but the translational gap between basic and applied research appears to have continued to widen. He explores the various reasons for this disconnect. Read More...
Dissecting DIY Letters of Rec
21/02/12 21:52
Blogger Damn Good Technician is irritated that research supervisors sometime instruct their trainees to help prepare their own letters of reference. S. Pelech points out that when he requests such a draft letter, it is because it often provides a useful self-assessment by the person for their own benefit, so they can appreciate the amount of time that it takes to produce a good letter, and to improve the prospects of including points that might have over looked that could benefit the individual. Read More...
Cuts at AstraZeneca
03/02/12 18:28
The Wall Street Journal reported that AstraZeneca announced that it will be eliminating 7,300 jobs by the end of 2014, which will bring the company's total jobs cuts during the past five years to about 30,000. S. Pelech comments that the AstraZeneca's announcement is symptomatic of recent trends with several other major pharmaceutical companies, and it is likely that many of these jobs will ultimately be re-directed to emerging opportunities in Asia. He questions the wisdom of AstraZeneca instead to forge virtual alliances with small biotech and university-based researchers to help fill its drug pipeline. Read More...
Hold the Arsenic
03/02/12 14:39
Rosemary Redfield at the University of British Columbia posted a paper on ArXiv that refutes NASA astrobiologist Wolfe-Simon's conclusions that described a bacterium that seemed to grow on arsenic and incorporate it into its DNA. S. Pelech provided a summary of many problematic aspects of the Wolfe-Simon NASA study in a previous commentary in GenomeWeb's The Daily Scan (url: http://www.genomeweb.com/blog/arsenic-yes-please). Read More...
The Other Side
30/01/12 14:41
Mike Taylor of the University of Bristol wrote in the Guardian that the Research Works Act, a bill currently being considered by the US Congress, has been roundly disparaged by the research community as an attempt by publishers to make more money by restricting the public's access to research. Graham Taylor, director of academic, educational, and professional publishing at the UK Publishers Association, responded in the Guardian that publishers aren't anti-science or anti-publication, but in reality have made research available to more readers for less money. S. Pelech notes that the steady growth in the number of new journals supports the contention that scientific publication can still be lucrative, especially if advertising opportunities exist, and that it is markedly cheaper and faster to disseminate scientific knowledge today than before with improved technologies and the Internet. Read More...
Turn 'Oops' into 'Oooh'
18/01/12 15:16
Ivan Oransky at Nature Retraction Watch notes that while positive publication bias is problematic phenomena, researchers should also recognize the value of having negative results in scientific publications. S. Pelech comments that negative results can arise from the testing of hypotheses that turn out to be incorrect and/or because there are problems with the methodologies used to test the hypotheses. If the methodologies are sound and properly executed, the resulting data remains invaluable, even if they do not support the original hypothesis. He notes that probably more than 90% of the scientific data that are generated by scientists are never published. Read More...
To the Committee
12/01/12 15:54
Michael Eisen at the University of California, Berkeley wrote in the New York Times about his concerns about the proposed Research Works Act, which could result in most Americans having to buy access to individual articles containing the results of federally funded research at a cost of $15 or $30 apiece. S. Pelech notes that the more restrictions that are placed on the publication of scientific research results, be they financial or prior acceptance by a couple of anonymous peers, the lower the value of that research endeavor with reduced dissemination of the findings. Open access journals have been a major step forward, but they don't have transparency in peer-review, the authors bear even higher publication costs and post-publication review is still problematic. Read More...
Now You See it, Now You Don't
12/01/12 15:21
Blogger Jonathan Eisen at The Tree of Life blog asked New York Congresswoman Carolyn Maloney and California Congressman Darrell Issa if they were serious about a new bill they've co-sponsored that would limit public access to NIH-funded research, and pointed out that both have received donations from the publisher Elsevier, which has come out against an open-access model of scientific publishing. S. Pelech speculates that if the Research Works Act goes forward in the US, and such attitudes are not embraced and adopted elsewhere, scientists in other countries as well as domestically in the US will become even less able to access the latest research findings from US labs. This could reduce the US influence in international biomedical research. Read More...
Nothing Is Sacred
22/12/11 13:16
Adam Marcus and Ivan Oransky at Nature, Retraction Watch wrote that the increase in retractions of scientific papers isn't necessarily a bad thing, and that journal editors and researchers should embrace the idea of post-publication peer review. They stated that "in the new system, a fleshed-out addendum, or correction, could suffice if the paper included some of the post-publication discussion." S. Pelech comments that with around a million scientific papers published annually, the overall numbers of flagged publications are still relatively miniscule. He agrees that needs to be the wide spread implementation of post-publication peer review that is directly linked to the original scientific work. Read More...
Investment in China
13/12/11 13:19
Hao Xin in ScienceInsider wrote that Merck plans to spend about $1.5 billion on R&D in China over the next five years, starting with a staff of 260 in a Beijing facility to be expanded to ultimately 600. S. Pelech comments that Merck's increased investment in research in China will most likely be accompanied by further reductions in R&D spending in Europe and North America. The Chinese government's policy of restricting the export of clinical material out of China has made it necessary for pharmaceutical companies to undertake the evaluations of their clinical trials within that country. Read More...
It Lives!
09/12/11 17:07
Jennifer Viegas in Discovery News predicts that within five years woolly mammoths may roam the Earth once again based on the work of researchers in Russia and Japan to try to clone the extinct species from a recently found mammoth thigh bone with well-preserved bone marrow. S. Pelech comments that this may not only be too technological challenging and too expensive to be economically justifiable in the face of the pending extinction of current endangered species, but with the global warming resulting in the rapid melting of glaciers and the thawing of frozen mammoths, time may be running out to retrieve high quality specimens from enough diverse mammoths to enable their successful cloning. Read More...
NHGRI's Early Independents
01/12/11 17:28
The National Human Genome Research Institute profiled four of its intramural postdoctoral fellows and three extramural researchers that it funds, all of whom recently received National Institutes of Health Pathway to Independence Awards. S. Pelech comments that it's interesting that two of the seven awardees of the NIH Pathway to Independence Awards are or were post-doctoral fellows with the Director of the NIH, Dr. Francis Collins. Read More...
In Your Food
30/11/11 17:14
Nanjing University researchers reported in Cell Research that plant microRNAs could be found in the sera and tissues of animals that eat those plants. They determined that MIR168a, which is found in rice, can bind to the human/mouse low-density lipoprotein receptor adapter protein mRNA and prevent its expression in liver, decreasing LDL removal from the bloodstream. S. Pelech is skeptical about the far reaching conclusions from this study and outlines some of his concerns. Read More...
Whole-Genome Liability
25/11/11 14:02
Bloggers Gary Marchant and Rachel Lindor from Future Tense suggested that as whole-genome sequencing becomes more common in the clinic, doctors may be facing the consequences of the technological shift, including the possibility of lawsuits if they do not recognize the significance of a variant or do not disclose medically relevant findings to patients' relatives. S. Pelech seriously doubts that with over 60 million SNP's and millions of positive and negative interactions between the proteins encoded by the ~23,000 genes in the human genome, physicians will be liable for not recognizing potential problems from genome-wide sequence data. The adoption of personalized medicine will probably mean that patients that rely on this technology will also have to accept more personal responsibility. Read More...
Lynn Margulis Dies
23/11/11 13:33
Lynn Margulis from University of Massachusetts has died. She originally developed the endosymbiotic theory for the origins of some cellular organelles, and was also known for her contributions to James Lovelock's Gaia hypothesis that the living and non-living components of the Earth together comprise a self-regulating system. S. Pelech comments further on the role of mitochondria in the origin of eukaryotic cells and their symbiotic/parasitic relationship. Read More...
The Originality of Humans
21/11/11 20:00
Blogger Iddo Friedberg at Byte Size Biology described efforts to identify there are de novo genes found only in humans that contribute the differences between us and our closest primate cousins, including the chimp, orangutan, and rhesus macaque. In a new paper published in PLoS Genetics, around 60 de novo human genes were identified that are expressed in 11 human tissues, and that the testes and the cerebral cortex of humans have the highest expression of these genes. S. Pelech argues that while there may be human genes that are not expressed in our primate cousins, this does not mean that they are "exclusively human" and could be present in our more distant ancestors. He also challenges the concept that the high expression of some of these genes may account for our "greater" intelligence. Read More...
Healthcare Costs Sap Biotech VC
17/11/11 15:12
Christopher Weaver at the Washington Post pointed out that "over the past two decades, venture capitalists helped make possible striking advances in health care, including robotic surgery, cancer vaccines, and genomics," but "the share of venture dollars flowing to seed and early-stage investments in biotechnology and medical devices has plummeted since 2007." S. Pelech comments that despite the poor returns in recent years for investors in the biotech industry, the health, food, security and other welfare problems confronting humanity are only becoming more critical over time as our population continues to explode in size. In view of this need, he remains optimistic about the prospects of the biotech industry and its workers in the long run. Read More...
The Synthetic Surge
08/11/11 13:44
Researchers at the University of Nottingham in the UK are leading an international team of synthetic biologists in a project that aims to try to create a "reprogrammable cell that can act as the in vivo cell equivalent to a computer's operating system. Clay Dillow in Popular Science wrote that amongst other things, "customized living cells could be tailored to clean up environmental disasters, scrub unwanted carbon from the air, pull pollutants from drinking water, attack pathogens inside the human body, (and) protect food sources from agricultural pests." S. Pelech comments that the use of such terminology such as the creation of "cellular software that would let researchers alter living cells without changing their hardware" and that this would produce a "reprogrammable cell that can act as the in vivo cell equivalent to a computer's operating system" reveals a lack of basic understanding cell biology and what is actually meant by "synthetic biology". Read More...
Where Science Meets Foreign Policy
03/11/11 13:50
John Holdren, director of the White House Office of Science and Technology Policy, has argued that by working with China, the US can encourage the country to change, while Frank Wolf (R-Va.) has suggested detachment would show that the US opposes a number of China's policies, and has drawn up a proposal for a ban on bilateral science talks with China. S. Pelech points out that government organizations in numerous countries have designated significant funding to support scientific research with specific partnering countries to induce collaborations, but this is usually at the expense of funding for other research programs that are less politically-motivated. Effective collaborations arise from the congruent interests of scientists throughout the world, and geography is not really a barrier except when politics intervenes. Read More...
Trim or 'Fatten' the Pyramid?
02/11/11 13:58
Blogger Jennifer Rohn at Mind the Gap summarized a recent round table discussion that highlighted significant structural problems and instabilities in the academic workforce, and differing opinions on how to deal with the issue, including restriction into entry, training graduates better for industry or encouraging early academic career retirement. S. Pelech concurs that there are too many scientists at present and we are training new investigators at a faster rate than ever before, which is exacerbating the problem. However, the solution is not to encourage early retirement of senior scientists, but rather to increase in private-public partnerships to foster the growth of jobs in the biotech/biopharma industry. Read More...
Solutions for the Peer Review Problem
31/10/11 14:02
Blogger Michael Eisen at It Is Not Junk blog noted that the current peer review system is plagued with problems, including domination by a few gate-keeper journals, overly lengthy, conservative and intrusive reviews, and failure to ensure that high-quality science gets published, but fraudulent or otherwise "flawed" science does not. He advocates that pre-review system in which an assigned editor, who would make a first assessment as to the suitability for publication, and if it passes the screen, it then gets sent to peer reviewers, who assess the technical validity of the paper and the intended audience. S. Pelech doubts that with over a million scientific publications appearing annually from thousands of scientific journals world-wide, that "a handful of journals are considered the "gatekeepers of success in science." He also finds the concept that a scientific paper should be pre-reviewed by a full-time journal editor disturbing as individuals in these positions often have much less actual research experience and are probably less informed about advancements in specialized fields. Read More...
Is This the End?
14/10/11 15:33
Blogger Alan Marnett at Benchfly stated that it's time to start thinking about the "impending death of scientific journals" and just what kind of "fast-paced, technologically savvy" system might suitably replace them. He suggested not to obliterate the scientific journal itself, but to change the way it is constructed and presented, using modern technologies and solicitation of feedback could come from a large online community. In a Benchfly poll, 31 percent of respondents indicated that they think journals will no longer be the primary mode for scientific publication in the next 10 years. S. Pelech reveals that Kinexus Bioinformatics Corporation plans to to launch Kinetica Online, as an open-access, meta-website dedicated to supporting cell signaling research. He also suggests that for laboratories in academic settings, it should become feasible for the universities to host open-access websites that allows for the dissemination of results from their faculties. Read More...
The Long and Short of It
04/10/11 13:12
Elizabeth Blackburn at the University of California, San Francisco started a company that will measure telomere shortness to predict risk for conditions such as cardiovascular disease, diabetes, Alzheimer's, certain cancers, and even for mortality. S. Pelech outlines the problems associated with interpretation of what a shortened telomer means and suggests that it would be naive to relate telomere length to one's current health status. It would make a lot more sense to focus on better immediate acute biomarkers of pathology such as stress protein levels and protein phosphorylation. Read More...
Animators Aid Science
20/09/11 12:42
Corie Lok at Nature reported that biomedical illustrators are increasingly working aside researchers in academia, industry, and elsewhere to create scientifically accurate and visually pleasing animations, illustrations, and Web sites. Data from a 2009 Association of Medical Illustrators survey, indicates that illustrators and animators employed full-time earn a median salary of US$52,000 at the start of their careers, $65,000 in mid-career and up to $150,000 as seasoned veterans, whereas those who work on a freelance basis earn on average $79,000 annually. S. Pelech comments that if a picture is worth a thousand words, a movie is probably worth a million words! Read More...
A Cap on Grant Applications — Does it Work?
14/09/11 19:48
Blogger DrugMonkey wrote that in March of 2009, the UK Engineering and Physical Sciences Research Council proposed and later instituted a new grant application system in which researchers are banned from applying for research funding for 12 months if they've had three or more proposals ranked in the bottom half of a funding prioritization list during the past two years, or have had less than 25 percent of the proposals funded in that time. The Nature News Blog reported that grant applications in the UK are down from about 5,000 a year in the 2005-2006 cycle to less than 3,000 in the 2010-2011 cycle, and success rates are actually up. S. Pelech comments that if fewer investigators submit grant applications, then of course success rates would appear higher, even though less grant proposals are actually funded. He concludes that agencies should just award more grants with slightly lower than average budgets, and leave it to the investigators to prudently use these funds as they see most fit. Read More...
Positive Results Can Be Negative
13/09/11 14:22
Daniele Fanelli at the University of Edinburgh examined more than 4,600 scientific papers published between 1990 and 2007, and found "a steady decline in studies in which the findings contradicted scientific hypotheses." During those 17 years, positive results increased from around 70 percent in 1990 to about 86 percent in 2007, and she speculates that the growing pressure to report only positive results may lead to a "decline" in scientific research around the world. S. Pelech observes that with the rapid progress made in the biological sciences with improved tools and techniques over the last few decades, it is not surprising that our knowledge about the world is becoming increasingly extensive. Nevertheless, it is striking that with around 23,000 proteins encoded by the human genome, it appears that over 95% of the biochemistry/molecular biology publications arise from less than 5% of these proteins. It would seem likely then that there is in fact a high degree of redundancy in scientific publications, which contributes to a very high rate of positive results. Read More...
Has Anyone Seen the Superglue?
12/09/11 16:39
Blogger Morgan Giddings at the Naturally Selected blog is concerned that with the emphasis at many universities these days on fast "translation," it seems that the whole endeavor has lost sight of the fact that all innovation and science takes time. She noted that there are several problems that make universities poorly equipped to reach the goal of fast translation — problems like bureaucracy, science by committee, and the "mixed mission" of a university that requires it to play a large array of roles. S. Pelech acknowledges that government organizations and the general public expect academic university-based researchers to improve the translation of their research into economically useful outcomes, but the current grant-funding system does not really facilitate innovative research, and government laboratories and universities often actively discourage their faculty from starting or working with commercial enterprises. Read More...
That's Called Thinking Ahead
01/09/11 15:41
Blogger Ed Yong at Not Exactly Rocket wrote that while antibiotic resistance is a problem for modern medicine, antibiotic resistance was developed by bacteria at least tens of thousands of years ago, long before antibiotics came about. Researchers from McMaster University found bacteria in 30,000-year-old frozen soil samples that feature a wide variety of antibiotic resistance genes against modern drugs such as tetracyclines and vancomycin. S. Pelech comments that in the battle for survival, all organisms have apparently developed mechanisms to detoxify compounds that are found in their environments. For example, our livers provide essential protection against diverse and even new compounds in the natural and processed foods that we take for granted in our diet. Read More...
Dreamless?
19/08/11 13:10
Blogger Paul Knoepfler wrote that he sometimes lets himself dream big as a scientist, but recognized that those dreams may not necessarily come true tomorrow. S. Pelech adds that "Big dreamers hardly sleep!" Read More...
Take That Back
12/08/11 16:16
Blogger Derek Lowe at the Pipeline described what appears to be seems to be a dramatic increase in the frequency of retracted papers based on data from Thomson Reuters, which reported that the number of papers published has risen 44 percent since 2001, while the retraction rate has risen 15-fold. A chart of PubMed retractions shows many of them are from top journals. S. Pelech comments that with over a million new scientific manuscripts published annually, the actual increase in retracted publications over the last decade is actually pretty inconsequential. Read More...
Take it Easy
04/08/11 01:07
John Horgan at the Scientific American Cross-check blog suggested that when researchers rush to publish their results, they can make mistakes and exaggerate the importance of their work, cut corners, and sometimes commit fraud. This is why some researchers are now championing what's being called the "slow science movement," which calls on researchers to be deliberate and cautious in what they choose to print. S. Pelech comments that slow science does not necessarily equate with better science, and exaggeration of the importance of research findings, cutting corners and committing fraud are not really linked to performing faster science, it just bad science at any speed. Read More...
Print to PDF
26/07/11 14:09
Bruce Caron at the New Media Research Institute observed that the number of posters presented at academic professional meetings (perhaps 250,000 per year) is astounding, and he and his colleagues at the institute have announced their intention to build a service, which they dubbed Skolr, that would "ingest meeting posters as PDF files" and make them easily searchable online. S. Pelech comments that while Skolr seems to be a worthwhile endeavor if it is open-access, it would be even better if it was also possible to download video clips of authors presenting their posters. Read More...
Why Compete? Collaborate!
22/07/11 17:38
Jeffrey Sheehan from the University of Pennsylvania in Business Insider described two talks related to collaboration and research productivity given by Jeremy Siegel and Craig Venter at the Wharton Global Alumni Forum held in San Francisco in June. Sheehan says these talks led him to realize that communication and cooperation are key "to enhance productivity and ... spread prosperity." S. Pelech comments that it seems like a no-brainer that collaboration is likely to be far more effective than competition, especially when there is a common goal where all participants benefit. He notes that the more funding that a research lab receives, the less likely that it will collaborate with other research groups, and that as a research team expands with higher funding, there is even more competition within the same group. Read More...
An App for Papers?
14/07/11 14:31
Blogger Joe Pickrell at Genomes Unzipped questioned why researchers publish their work in peer-reviewed journals, which among other things, is costly, time-consuming, and random. Pickrell proposes a system of immediate publication, connected to a social media network, in which readers could recommend papers and researchers could search for them based on the community's opinions or rankings. S. Pelech agrees with Joe Pickrell that the current journal system is fast becoming obsolete on many fronts, including mounting costs, publication speed, labour, environmental problems and the fact that few scientists actually search online for articles based on the reputations of scientific journals. In the end, it is the number of times that a particular scientific paper is quoted that counts and not the impact factor of the journal that it appears in. Read More...
Saving Lives
05/07/11 15:40
Matthew Herper in Forbes recounted how genome-wide sequencing has helped Sesha Lundell - whose son and nephews died in infancy of a rare disease that had also affected her brothers. Researchers were able to find the gene for the disease in 16 months, and this could potentially offer Ms. Lundell the opportunity to have children via in vitro fertilization, and select the embryos that don't have the gene. S. Pelech suggests that a better title for this blog should really have been "Eliminating Lives!" as undesirable embryos are killed off earlier. However, selection of embryos for implantation based on genetic information does provide for improved prospects to raise babies that have fewer in-born errors that culminate in malformations and disease. Read More...
Not So Much 'R' and Not So Much 'D'
28/06/11 15:43
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
28/06/11 14:34
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
27/06/11 16:52
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
17/06/11 13:22
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
16/06/11 14:50
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
06/06/11 14:08
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...
A Return to Decency
20/05/11 23:57
William Deresiewicz at The Nation wrote that because there are too many PhDs for the number of academic jobs available, they are "cheaper to hire and easier to fire, and save institutions money. Dr. Deresiewicz suggests that tenured professors need to speak out and spear-head initiatives to create better opportunities for new faculty with longer term prospects. S. Pelech comments that it is untenable that university or government lab positions could or should be available for the vast majority, and that industry has to be able to employ these highly trained and skilled individuals. Academic institutes and government agencies should be facilitating the ability of entrepreneurial professors to create companies rather than erecting barriers that stifle such activities, for example, on the basis of conflict of interest. Read More...
It's Everyone's Problem
20/05/11 14:35
Blogger Razib Khan at the Gene Expression blog claimed that bias is "rife in any science which utilizes statistics." The GiveWell blog has suggested researchers publish their questions, theories, and planned methods of data collection before their begin their work, so that if the results come out differently from what the researchers expected, then this cannot be hidden. S. Pelech argues that one of the major reasons why bias can have such a profound impact on the outcome of a scientific study is that there is so much emphasis on conducting hypothesis-driven research. In conducting system-wide, unbaised research to seek what is really going on inside of organisms and their cells, half the battle is to collect sufficient data and the other half is to look at the results with fresh eyes and let the data reveal to the observer what is happening. Read More...
Reports Tout Return on NIH's Investment
13/05/11 05:28
A new report from the advocacy group United for Medical Research, and authored by economist Everett Ehrilich predicts that "the gene sequencing business will grow by 20 percent a year and become a $1.7 billion industry by 2015. According to a separate report authored by the nonprofit Battelle Memorial Institute, the National Institutes of Health's $3.8 billion investment in the Human Genome Project, along with subsequent capital provided by the government and the private sector, generated a total return of roughly $49 billion in direct and indirect federal tax revenues over the last two decades or so. S. Pelech questions the validity of estimates of the economic benefits from the direct investment of the NIH in the Human Genome Project (HGP), especially since private industry and non-HGP government- and charity-funded investigator-driven projects made major in-roads in the identification and characterization of most of the human genes that have actually been targeted by the industry to date. Read More...
What Do Your Telomeres Say About You?
09/05/11 14:43
Nobel laureate Elizabeth Blackburn has launched a company called Telome Health to provide a commercial genetic test for less than $200 to measure telomere shortening, to give people insight on their aging process. It would entail taking a blood or saliva sample, and measuring the telomere length in white blood cells, to determine if people need to change their lifestyles, such as reducing stress and cessation of smoking. S. Pelech is dubious about using telomere length to assess one's current health status considering all of the variables including one's age, and suggests focusing on more accute and dynamic biomarkers such as stress protein levels and protein phosphorylation. Read More...
Will It Be Good or Bad for Science?
05/05/11 15:22
Karen Birchard at The Chronicle of Higher Education speculates that the victory for Prime Minister Stephen Harper and the Conservative Party in the recent election might lead to increased investment in research, but Blogger David Ng at The Intersection, suggests the opposite — that a Conservative majority "is a step back for science" in Canada. He argues that "the Harper government has consistently ignored whatever sound utility the scientific endeavor can provide, and by doing so, has put the future of Canadian science at risk." S. Pelech comments that overall government investment in science in Canada has not really differed that much between the Liberal and Conservative Parties when they have been in power in the past few decades. However, he argues that the diversion of precious research dollars to initiatives such as GenomeCanada has most likely contributed to the decline of the biotechnology industry in Canada and the plight that most Canadian biomedical scientists face today in getting support for their research. Read More...
'That Doesn't Sound So Terrible'
29/03/11 15:32
Blogger Roxanne Palmer at Slate's Brow Beat blog wrote that the late actress Elizabeth Taylor's most famed physical feature — her eyes, "arresting: large, liquid, and framed by a thick fringe of eyelashes" — may have resulted from a mutation at FOXC2 that resulted in two sets of eyelashes. One potential complication is that damage to the cornea can result if the extra eyelashes grow inward, and FOXC2 mutations are also associated with lymphedema-distichiasis syndrome, a hereditary disease that can cause disorders of the lymphatic system. S. Pelech raises the ethical question that if Elizabeth Taylor's parents had amniocentesis and genome-wide sequencing performed when she was just a tiny fetus and they learned that she had a genetic mutation that could cause immune and vision problems, would they have elected to have the pregnancy terminated? Read More...
Devils' Disease and Diversity
25/03/11 13:37
Pennsylvania State University's Stephan Schuster and his colleagues aim in a conservation effort called "Project Ark" to help save the endangered Tasmanian devil — whose population is dwindling due to the rapid spread of a species-specific infectious cancer, devil tumor facial disease — using a genomics-based approach to genotype up to 500 Tasmanian devils. S. Pelech comments that with about 40% of the world's estimated 10 million species of life facing extinction, one of the real bonuses of plummeting genome-wide sequencing costs is the possibility it offers to remediate some of the damage that humankind has wrought on this planet in the future. The advantage of a database with the full sequences of thousands of diverse genomes is that it can be easily copied on a wide-scale onto small storage devices for broad dissemination, even into space. Read More...
Eric Schadt's Network
24/03/11 14:55
Eric Schadt at Pacific Biosciences argued that the one-gene-at-a-time approach doesn't seem to be working, and greater emphasis should be placed on the examination of many genes and proteins and their interactions in networks. S. Pelech echos many of Eric Shadt's sentiments and takes the opportunity to outline three forms of intelligence: molecular intelligence that operates inside of living cells, cellular intelligence that permits the cells in an organism to communicate with each other and also monitor the external environment, and social intelligence that permits organisms within a group to function together. The same kind of organizing principles are at play at each of these levels despite the vast differences in their scale. Read More...
Who's Paying For This?
24/03/11 14:04
Blogger Avik Roy at The Apothecary blog stated that comparative effectiveness research is necessary so physicians, researchers, and patients, know how different drugs stack up against each other, and the NIH should help fund this activity. S. Pelech comments that one of the dilemmas confronting drug comparative effectiveness research, apart from who is going to pay for it, is its usefulness once personalized medicine really starts to take hold. As the pharmaceutical industry increasingly integrates biomarker evaluation as a critical component of clinical trials, it will become less important of how the "average" person will react to two competing medicinal drugs for the same disease indication. Rather, it will matter more how well the drug matches the biomarker profile of the person who needs medication. Read More...
Fine, Be That Way
21/03/11 14:04
Blogger Nathan Ley in the Guardian described the difficulty he and his acquaintances have recently experienced in getting accepted into a PhD training in graduate school due in part to cutbacks in science funding and the stiff competition for limited spots. S. Pelech notes that without any advertisement, last year he has received over 150 enquiries for a graduate student position in his academic lab, the vast majority arising from China, India and Iran. China's higher education institutes had over 31 million students, an increase of some 35% from 2005 levels, so it is not surprising that many of the best and brightest of students from China and other developing countries are looking to the West for graduate and post-graduate training, and probably subsequently permanent jobs. Read More...
Survival of the Fittest … Labs
18/03/11 00:35
Blogger Odyssey at Pondering Blather argued that Darwin's theory of evolution applies to research labs, and they are under selective pressure to become efficient, flexible and collaborative or go obsolete. S. Pelech comments that while there has been a tendency to apply Darwin's theory of evolution to a wider range of phenomena including the survival of businesses in the competitive market place, this is simplistic and does not sufficiently account for the importance of social intelligence and collaboration. He agrees with Odyssey that key factors for the success of a research laboratory are a broad range of knowledge and capabilities, careful monitoring of the environment, and effective working relationships. Read More...
High-Tech Biology
10/03/11 14:35
Paul Krugman of The New York Times wrote that many jobs for recent college grads are being rendered "obsolete" by advances in technology. Blogger Mike the Mad Biologist envisions that with increasing automation there will be less opportunities for researchers involved in data generation, but more need for those with informatics training on data data analysis. S. Pelech comments that Biology has been primarily a descriptive science and the sequencing of genomes and determination of the 3D structures of the proteins encoded by their genes has really just carried on this tradition. However, he envisions that we are at the brink of a major paradigm shift in which molecular and cellular biology are on the verge of becoming much more constructive and predictive, and this will spur on innovation and creativity that can truly transform health care and many diverse industries including those for food, clothing, shelter and energy production. Such a biorevolution will be achieved by a work force of scientists that will require a lot more training than what we actually typically offer today. Read More...
A Clinical Option
09/03/11 00:18
Based on the successful identification through genome-wide sequencing of a mutation associated with immune disorders on the X chromosome of six-year-old Nicholas Volker that could be behind his severe inflammatory bowel disease, it has been proposed by Howard Jacob, director the Human and Molecular Genetics Center at the Medical College of Wisconsin that similar genome sequencing should be a standard clinical option for children with rare, inherited diseases. S. Pelech comments that gene-wide-sequencing is impractical for the diagnoses of common diseases in the general population where most health care costs are borne. He also notes that in the case of Nicholas Volker's genome, it was not established that this mutation actually produces an immune disorder, nor was it clear that even with a causal link to the responsible gene that this knowledge could lead to an effective treatment. Read More...
Happy Is as Happy Does
07/03/11 15:56
Irvine, Calif.-based firm CareerBliss conducted 200,000 independent employee reviews from 70,000 jobs all over the US and concluded that biotechnology employees are happier with their jobs than workers in any other professions. Measures of workplace happiness included the worker's relationship with their boss and co-workers, work environment, job resources, compensation, growth opportunities, company culture, company reputation, daily tasks and job control over the work that they do on a daily basis. S. Pelech comments that if one is engaged in a decent paying job where you are intellectually stimulated by the tasks at hand, work with other highly intelligent people who are also employees, collaborators or customers, and are dedicated towards such laudable goals as to improve the health of the sick, it is hard to imagine a better vocation. Read More...
Animal Research Provokes Some 'Misgivings'
25/02/11 16:43
A recent Nature poll of 1,000 international biomedical researchers showed that while 90 percent of them say research on animals is "essential," 16 percent say they have "misgivings" about using animals, and 33 percent had "ethical concerns" about the role animals play in their research. However, only apparently, only 15% of the respondents claimed to have changed the direction or practice of their research by the actions of animal activists. S. Pelech comments that whenever possible one should find alternative approaches to minimize the use of experimental animals, but acknowledges that it is impossible to eliminate the use of animals in biomedical research. He notes that less than 0.25% of the land animals killed by humans are used for research purposes of any kind and suggests that it would be far more impactful for animal activists to tackle the food industry and the greater than 95% of the world population that are consumers of meat products. Read More...
Faster, Faster!
24/02/11 15:34
Blogger Matthew Yglesias at Think Progress wondered if computing power has improved at an "un-optimally rapid pace" that does not permit people sufficient time to develop better ideas for what to do with all this computing power. Blogger Mike the Mad Biologist thinks that instead of slowing down the pace of technological advancement, we need to speed it up to have enough computing power to handle all the data being generate, as the cost of DNA interpretation rather than DNA sequencing is becoming the bottleneck. S. Pelech suggests that the real problem arises when other supporting areas of science and technology become underfunded or relatively neglected relative to the more outwardly sexier endeavors that suck up the lion's share of funding, and this ultimately severely compromises realization of the true value of the public investment in science and engineering. Read More...
'CEOmics'
22/02/11 15:13
Blogger Daniel MacArthur in Wired's Genetic Future blog observed that senior biotech executives are making their genomes public in what could be a "pragmatic" move to help their businesses grow by trying to convince the medical establishment (and the public) that genome sequencing will provide health benefits that outweigh the potential privacy risks. S. Pelech comments that these executives are willing to have their genome sequences revealed to the broad research community, because it may promote their business, they really have nothing to loose, and there is a slight possibility to personally benefit with researchers focused on their individual genomes. He argues that if these executives and some prominent scientists are willing to disclose their full medical, life and family histories coupled with a willingness to subject themselves to a wide barrage of medical tests and publicly disclose the results, this might actually be useful in helping to make some sense of our genetic differences. Read More...
A Challenge for Scientists
21/02/11 14:13
John Beddington, the UK government's chief scientific advisor, in New Scientist suggested that true progress in science is attained through "criticism, skepticism and debate." He argues that "Great" researchers challenge the status quo, but only if they have the facts and evidence to back themselves up and also remain honest about the uncertainties associated with the work. S. Pelech agrees that scientific progress works best when it is pursued with a mix of healthy skepticism and open-mindedness. It is critical that those scientists that are highly informed on a controversial subject speak out to the general public through the popular media, even if it is revealing of our actual ignorance on that subject. If anything, it justifies the need for further research. Read More...
Blogger: Three Years is Plenty
11/02/11 23:15
Blogger Cath@VWXYNot argues that a 3-year PhD degree that dispenses with courses and results in few publications is not necessarily inferior to more demanding PhD programs. S. Pelech cautions that in the absence of previous Master's level training, this strategy is not recommended if one is contemplating a serious research career. Ultimately, the ability of a trainee to secure a permanent job in academia or industry will require clear demonstration of research ability through many original scientific publications in which the trainee has played a major role. Read More...
Glug, Glug, Glug …
11/02/11 14:16
Josh Fischman at The Chronicle of Higher Education observed that a recent series of 10 articles published in Science highlights the problem of "data deluge" and the difficulties in sharing such data due to the diversity of data formats and the lack of "a common language for tagging their data." S. Pelech comments that there remains of wealth of largely ignored genomics and proteomics data available in many open-access repositories on-line that is easily retrievable, and the real problem is the lack of expertise available within the scientific community to interpret this data. More researchers need to markedly expand their biomolecular vocabularies about proteins and their activities to generate actual knowledge from the raw data. Read More...
The Politics of Science
08/02/11 14:55
A recent Pew survey reported that more than half of scientists (~55%) consider themselves Democrats, compared to about a third (~35%) of the general public. Blogger Chris Mooney at The Intersection also wondered why about 52 percent of scientists call themselves liberals, whereas only 20 percent of the public does so. S. Pelech outlines several factors that predispose its practitioners of science to be more "liberal" in their outlooks. He also questions generalizations about the differences between "Republicans" and "Liberals" in the US with respect to their perceived value of science, especially since both types of administrations have strongly supported scientific research activities in the past. Read More...
The Rise and Fall of RNAi
08/02/11 14:17
Andrew Pollack in the New York Times concluded that pharmaceutical companies' interest in RNA interference is waning as other opportunities have higher priorities. The delivery of RNAi still remains a major challenge that is being addressed by a few academics and companies. S. Pelech notes that it took about two decades before the relatively simple process of how to produce monoclonal antibodies ultimately resulted in government-approved drugs for treatment of cancer and other diseases. The application of RNAi to mitigate the actions of specific micro-RNA might ultimately prove to be the best therapeutic use of RNA intereference. Read More...
Maybe You're Born With It?
27/01/11 21:46
Blogger The Meandering Scholar wondered whether grantsmanship is a task that can be mastered from training or is primarily a more ingrained skill set. Bloggers ChemicalBiLOLogy and BrooksPhD argued that grant-writing is a skill that can be improved upon and adapted to become competitive. S. Pelech wryly comments that it is highly unlikely that some of our ancient ancestors sitting on the plains in Africa were selected for survival and reproduction based on their ability to write research grants. Grant writing is just not an innate ability that one is born with. Read More...
Journal Impact Versus Paper Impact
26/01/11 02:08
Blogger Prodigal Academic suggested that when you are choosing where to submit a manuscript, it is important to consider the target audience of who is most likely to actually read it rather than just the overall impact factor of the scientific journal. S. Pelech comments that the speciality focus of a journal now has relatively little impact on whether members of the scientific community will notice a publication. Rather, most researchers find scientific papers through PubMed, Google and other search engines and those publications with open-access are likely to receive the widest dissemination. Read More...
Stupendous! Amazing! 'Astonishing!'
07/01/11 16:58
Blogger Zen Faulkes at NeuroDojo described as depressing a 2005 report on the state of US science (Rsing Above the Gathering Storm) and its recent followup, while Beryl Benderly in Science predicts that more American corporations will be increasingly out-sourcing their research work overseas leaving few prospects for PhD scientists in the US outside of academia. S. Pelech observes that nearly 60% of biomedical research in the U.S. is funded by industry, so this is a legitimate concern for American jobs. He advocates that one solution would be to provide a markedly increased number of fellowships awards available from government and charitable agencies for post-doctoral fellows to work in U.S. biotechnology and pharmaceutical companies. Read More...
We Remember Memorizing That
21/12/10 19:08
Lawrence David and Eric Alm at the Massachusetts Institute of Technology developed a new phylogenomic approach called AnGST — for analyzer of gene and species trees — that they used to study the evolutionary histories of nearly 4,000 gene families and observed that genes first appearing during this Archaean expansion (between 3.33 and 2.85 billion years ago) are commonly involved in electron-transport and respiratory pathways, which was probably spurred on by the increases in toxic oxygen in the atmosphere. S. Pelech comments that such strategies can be extended towards the more ambitious goal of deducing the origins of life by focusing on the functional domains found in the proteins encoded by genes, which can then be used to elucidation of a "molecular" tree of life. Read More...
What's the Point?
17/12/10 23:19
Blogger Hannah Waters wonder why science stories like the NASA arsenic bacterium sometimes get overhyped and "out of hand," and she concludes that researchers feel the need to be "purposeful" while doing their work as government grants with public money requires some ultimate benefit for the public. S. Pelech comments that the real value of basic research is well appreciated amongst those practitioners within the scientific community and it should be funded based solely on its own realistic merits. However, since the bulk of the grant funding for biochemistry and molecular biology research comes from government and charitable agencies that are mandated to improving human health, there is a clear obligation to work towards more practical outcomes with these particular funds. Read More...
Collins 'a Guy in a Hurry' for Translational Research
14/12/10 20:40
Francis Collins, the director of the NIH, is eager to establish the National Center for Advancing Translational Sciences, despite the extra budgetary considerations, so that the agency can plug certain therapeutic development holes left open by pharma, such as for rare and neglected diseases. S. Pelech cautions that this proposal will most likely further exacerbate an already very difficult funding situation for basic researchers in the U.S. based on past experience of Canadian academic researchers with the creation of the Canadian Institutes for Health Research. Read More...
How Come My Gel Bands Aren't that Discrete?
08/12/10 17:21
Bogger Jade Ed said the "same standards for good scientific practice" that research groups must adhere to when reporting results should also apply to life science vendors that are marketing products, only high-quality, accurate data should accompany the images in their ads. S. Pelech reports that when tested by Kinexus more than 80% of 3500 commercial antibodies from over 25 different vendors were determined to be either impotent (i.e. weak), non-specific ("dirty") or both. The wide dissemination of such poor reagents ultimately results in a lot of wasted time, money and effort, and is a great disservice to the scientific community. Read More...
Arsenic? Yes, Please!
04/12/10 15:26
NASA researchers reported that the bacterial strain GFAJ-1 of the Halomonadaceae family of Gammaproteobacteria, when grown for months in a lab mixture containing arsenic, could swap its phosphorous content out for the more poisonous element, and have proposed that arsenate may replace phosphate in DNA in early life and potentially alien life forms. S. Pelech provides a lengthy critique of these findings that challenges these assumptions and provides alternative explanations for the study's results. Read More...
Quantification Quandary
02/12/10 16:04
Blogger Michael Nielsen noted that it is "very, very difficult for even the best scientists to accurately assess the value of scientific discoveries," but as a practical matter we are forced to make such evaluations in hiring scientists and judging grant applications on committees. S. Pelech points out several of the difficulties associated with measurement of scientific impact, and argues that it is time to overhaul the grant funding system to support a larger percentage of the biomedical researchers with, if need be, small grants. Read More...
The Rise of Asia
24/11/10 18:39
The Economist reported that in 1990, North America, Europe, and Japan carried out more than 95 percent of the R&D done in the world, and by 2007 that number had dropped to 76 percent, while China's spending on R&D is skyrocketing and the number of scientists there is set to overtake both the US and the EU. S. Pelech comments that while much of the research in North America is actually performed by Asian researchers living abroad, and it is actually nice to see places like China and India contribute more to the growth of global biomedical research, because ultimately we will all benefit in terms of improved diagnostics and therapeutics as well as new knowledge. Read More...
Something You Don't See Every Day (Anymore)
23/11/10 15:43
Blogger Genomic Repairman described how charming it was to get a hard-copy reprint request in the mail. S. Pelech also recalls the pleasures of receiving posted reprint requests, but notes the advantages of the Internet for spreading new scientific knowledge, which include the extremely rapid exchange of electronic files in various formats including MS-Word, html and pdf documents for dissemination of scientific articles, blogs, private e-mails and more. Read More...
(Don't) Be Still My Beating Heart
22/11/10 18:56
Jonathan Seidman at Harvard Medical School made a case for the importance of studying rare genetic variants that cause cardiomyopathy, while there are several common variants, there are multiple rare variants that can significantly increase a patient's chances of suffering from the disease. S. Pelech comments that while the rates of heart disease and stroke in North America and Europe have temporarily declined, the future is much bleaker for the younger generation with more than a 5-fold in child obesity in the last 25 years. Although the study of genetic mutations in families with documented histories of diseases has proven to be very insightful and worthy of continuation, the identification of SNP variants in the general population that are linked to predisposed risks for these and other diseases of aging by random genome wide sequencing will be immensely more challenging. Read More...
The Human Collective
21/11/10 21:02
The virome in even the feces of identical twins humans vary widely from one another, and from their mothers, in contrast to findings that family members tend to have similar microbiomes. S. pelech points out that the unique resident flora of each person with some 10 trillion bacteria arises from a combination diverse factors, and it largely protects us from pathogenic strains and provide nutrients in a symbiotic relationship. Even within our individual cells, bacterial-like entities known as mitochondria are essential for our good health. Read More...
Are Leaders Born or Taught?
21/11/10 20:10
Blogger DrdrA at at Blue Lab Coats suggested that grad schools teach students how to hypothesize, design experiments, analyze the data, and write research papers, but not how to lead a group or become an effective PI that can build a strong research team and program. S. Pelech points out that there are also many other qualities, such as the ability to teach, fund raise, and budget, that are also ingredients to success, and while leadership ability might be partly genetic, it is further developed during a lifetime of observation and experience. Read More...
'How Not to Get a Postdoc'
21/11/10 18:12
At Isis the Scientist's blog, a new faculty principal investigator shared satirical "tips on how NOT to get a postdoc in academia. S. Pelech shares his observations with applications from hundreds of graduate students and post-doctoral fellows to his research laboratory over the last 24 years, and offers useful advice on finding and getting the right matches. Read More...
Graphs on Grants
21/11/10 17:43
Jeremy Berg, the director of National Institute of General Medical Sciences observed in his analysis of NIGMS R01 applications from January 2010 that "many of the awards made for applications with less favorable percentile scores go to early stage and new investigators." S. Pelech comments that while this is not surprising, it is disturbing that new grant applications from experienced investigators that have a track record of successful funding have about the same chance at getting funded as a new investigator with little experience and no track record as an independent scientist. Read More...
Genotype-Phenotype Correlations Confer 'Chaotic' Evolution
21/11/10 03:24
Keith Bennett at Queen's University Belfast examined the burgeoning "chaos theory of evolution," and argues that the connection between environmental change and evolutionary change is weak, which is not what might have been expected from Darwin's hypothesis, and that macroevolution may, over the longer-term, be driven largely by internally generated genetic change, not adaptation to a changing environment. S. Pelech comments that it would be unwise to under-estimate the impact of a rapidly changing environment on evolution, including the rapid disappearance of dinosaurs following an asteroid impact 65 million years ago or as a consequence of human activity today. Read More...
The Happy Medium
19/11/10 16:45
Jeremy Berg, the director of National Institute of General Medical Sciences, suggested that mid-sized labs do best from his analysis of NIH data to study correlations between grant size and scientific output. S. Pelech comments that Dr. Berg's data confirms what he and many others have suspected all along, i.e. too high amounts of funding for a laboratory group can provide diminishing returns and this has enormous implications for the funding of mega projects. Based on US NIGMS data from 2007 to mid-2010, the Division of Information Services in the NIH Office of Extramural Research determined that the median annual total direct cost was $220,000 in funding, the median number of grant-linked publications was six, and the median journal average impact factor was 5.5, which indicates that the typical costs of a scientific paper with a 5.5 impact factor is about $128,000. Read More...
Save Data to Gene
19/11/10 04:10
Georg Fritz at the University of Cologne and his colleagues say that a network of genes can act in a circuit as a "conditional memory" that stores or ignores information when told to do so, somewhat similar to a 'data latch' in an electronic circuit. S. Pelech comments that Dr. Fritz's work is entirely theoretical, no evidence is available for whether conditional memory circuits as proposed actually exist in real genetic networks, and that proteins would have to be equally important components in memory circuits. Read More...
Bias in the Peer-Review Buddy System?
19/11/10 03:00
Blogger Ewen Callaway in Nature's The Great Beyond critiqued a PLoS One paper in which researchers analyze whether open peer review systems discourage biases, such as those that often surface when authors request specific reviewers for their manuscripts (e.g. "on papers where there was disagreement among ... reviewers, those recommended by the author were more likely to provide favorable feedback and accept a paper than the editor-recommended reviewer."). S. Pelech notes that at the end of the day, it is really up the to general scientific community to accept or disregard the validity of the data and conclusions in a paper, and advocates that peer-review should not be completely anonymous. Read More...
Make Your Application Memorable
19/11/10 02:12
Blogger Odyssey at Pondering Blather offered advice on how applicants for faculty positions can distinguish themselves to improve their employment prospects, including thoroughly researching their prospective institution, crafting an intuitive, easy-to-follow CV and a comprehensive — yet concise — research plan and teaching statement, and having "the important stuff up front." S. Pelech comments that while this can help, applicants must also suitably prepare themselves well in advance for such an undertaking. If the applicant does not have the requisite training with clear evidence of research, teaching and management ability, then he or she should acquire such capabilities first. Read More...
What Work/Life Balance?
11/11/10 14:34
Justine Cassell, the incoming director of Carnegie Mellon University's Human Computer Interaction Institute, in a Q&A-style profile for the Anita Borg Institute for Women and Technology, explained how she deals with "with work/life balance" by trying to integrate her work and her life in a synergy model. S. Pelech observes that while there are some less desirable aspects of an academic researcher's job, such as grant application writing and committee service, research and teaching is generally an extremely pleasurable experience. Naturally then, it is not surprising that many scientists are engaged for long hours almost every day in activities related to their scientific passions. Read More...
Bigger Not Always Better
09/11/10 15:09
Blogger Massimo Boninsegni at Exponential Book said that when it comes to choosing a lab group with which to work, there is an approximate "optimal" lab size, "beyond which productivity ... no longer grows proportionally to the monetary investment, and even the effectiveness [of the lab] as a training and educational venue decreases. S. Pelech agrees and further points out that lab politics can be very problematic in "sink or swim" lab groups, when the principal investigator is just too busy to attend to the needs of each trainee. Read More...
The Business of Basic Research
09/11/10 14:47
Nicholas Wade at the New York Times characterized NIH's funding of basic research as a risky government venture that produces far fewer hits than misses, but blogger Michael White at Science 2.0 thinks that basic research proceeds more through a series of "incremental" advancements that ultimately lead to success. S. Pelech agrees with Dr. White and notes that grant panels favour "safe" research where there are solid hypotheses and a wealth of preliminary data from investigators with the consequence that most basic research is pedestrian and plodding, but steady in its progress. Read More...
Going 'Beyond the Genome'
14/10/10 14:08
The most accurate estimate of the number of human genes is 22,333 human genes, and about 2,000 are highly predictive and medically actionable according to presentations given at BioMed Central's Beyond the Genome conference. S. Pelech wonders why despite the complete sequencing of the human genome for nearly a decade, it is still unresolved exactly how many human genes actually exist. He notes that phosphosites have been identified by mass spectrometry in cell lysate proteins that have since been deleted from Uniprot, while about 4 to 5 percent of human proteins predicted by genome sequencing are still not yet tracked in this repository. Read More...
Move Aside, Genome … It’s the Interactome’s Time to Shine
11/10/10 20:37
The New Scientist proposed that after genome sequencing, it’s the interactome (detailed maps maps of interactions between proteins, RNA, and genes) and the phenome (sum total of all traits, from genes to behaviour, that make up a living thing) that will take genetics to the next level. S. Pelech comments that based on data from the 1000 Genomes Project around 60 million human single nucleotide polymorphisms (SNPs) are projected to exist, and it will likely take several decades before most of the critical SNP's are actually identified and related to phenotype. Moreover, based on current capabilities and efforts expended on the proteomics front, linking the genomics and proteomics data towards a rationale and predictable understanding of phenotype is a herculean effort that will probably take another hundred years. Read More...
Human Genome Times 50 in One Small Flower
08/10/10 15:26
The rare white flower from Japan, the Paris japonica, has been found to have the longest genome in the world that with about 150 billion base pairs is about 50 times longer than that of a human being, and blogger Elizabeth Pennisi at ScienceShot suggests that "plants with lots of DNA have more trouble tolerating pollution and extreme climatic extinctions — and they grow more slowly than plants with less DNA, because it takes so long to replicate their genome." Based on other evidence, S. Pelech disagrees and provides several examples of species where there is a poor link if any between the size of a genome and the rate of growth, life span or evolutionary selection for these organisms. Read More...
What to Do with All That Data?
07/10/10 18:41
Blogger Mike the Mad Biologist proposed that with genome sequencing getting faster and cheaper, the problem is evolving from how to sequence genomes to storing, processing and best make use of the information. S. Pelech agrees and notes that unless there is a well funded parallel program of biomedical research that can make sense of the genomics data from a proteomics perspective, the genome sequencing efforts will yield primarily correlative data that will offer limited risk assessment at best. Read More...
Hey Scientists! (Don't) Get a Life!
05/10/10 15:07
Scott Kern at Johns Hopkins' Sidney Kimmel Comprehensive Cancer Center has observed that researchers — particularly cancer researchers at his institution — have apparently lost their passion for their work, and that patients are suffering as a result. His criticisms has raised the ire of many other bloggers , who have challenged his view. S. Pelech notes that the absence of trainees and established scientists during weekends and evenings in institutions does not mean that they are not still working. With the the advent of personal computers and the Internet, it is not necessary to come to work to read the literature, plan experiments and analyze the results. Read More...
The Hard Decisions
29/09/10 02:54
Funding success rates are down, in part because of the economic downturn, and this has further increased competition for funding and placed more pressure on applicants and reviewers. S. Pelech comments that in his experience, while there has been a steady improvement in the quality of submitted grant applications over the last 25 years, there has also been a concurrent errosion in the quality of grant reviews. He also notes that the growing trend towards funding mega-projects has also resulted in less demonstrated productivity per research dollar invested. Read More...
A Look at Chemical Biology
23/09/10 14:09
Blogger Derek Lowe at Pipeline stated that the combination of organic chemistry and molecular biology with chemical biology is an interesting and productive research frontier, especially with the ability to modify existing enzymes for new purposes. S. Pelech further adds that nature could be significantly improved upon by intelligent design, and that new proteins could be designed that feature more than 20 amino acids with an expanded genetic code with less redundancy. Read More...
Evolution of a Fruit Fly, Evolution of a Human
22/09/10 18:19
Researchers at UC Irvine have published research results with fruit flies that confirm the so-called "soft sweep" theory of evolutionary that the exploitation of small differences in many different genes were responsible for the emergence of new traits, rather that a large mutation in single genes. "If complex traits, including susceptibility to disease, are influenced by tens or hundreds of genes, then treatments targeted to single genes won't be very effective". S. Pelech questions the applicability of studies with flies that can bred after 8.5 days with humans that must be about 12 years old before they are capable of reproduction, but notes that it is already well appreciated that many genes influence complex traits, and susceptibility to diseases does not arise from just a few genes. Read More...
Early-Warning DNA Sequencing System
21/09/10 15:12
Using DNA sequencing, researchers at Pacific Biosciences have started a project called the Disease Weather Map, which monitors viruses from locations like sewage stations, toilet handles, and people's mouths, in an effort to measure pathogen flux over time and track the emergence of new pathogen variants. S. Pelech comments that a cost-benefit analyses of doing this should quickly reveal its impracticality, and that it would be much cheaper to track where and when people are getting sick, and then rapidly identify the culprit. Read More...
George Williams Dies
16/09/10 18:30
Evolutionary biologist George Williams, who died at 83 years of age in 2010, was widely regarded by peers in his field as one of the most influential and incisive evolutionary theorists of the 20th century and advanced the argument that natural selection works at the level of the gene and individual. S. Pelech argues it would be a mistake to believe that natural selection works simply at the level of the gene and individual, but that eusociality plays as much if not a greater role than the individual. The concept of the gene as being the basic unit of natural selection arises from the bigotry of those that hold a strong genopocentric perspective. Read More...
The Money of Sequencing
16/09/10 17:41
Matthew Herper of Forbes noted that there has been an increasing number of cases in which people have been helped medically by knowing their genome and wonders how in the future how this will be monetized into a business. S. Pelech remarks that there have only been a few scattered reports where people have actually been helped medically by knowing their full genome, and points out that if genome sequencing is to become widely used for diagnostics, then it will have to be ultimately funded by government agencies that pay for health care or insurance companies. Read More...
Suggestions for Drug Approvals
14/09/10 14:41
Blogger Derek Lowe in the Pipeline ackowledged that a regulatory system for approving new drugs is certainly necessary, but wondered whether instead of a system that makes binary decisions, an adaptive system would be better that makes faster decisions based on the data, that are then modified accordingly when additional findings come out. S. Pelech cautions that it is possible that drugs used for treatment of chronic conditions might have much wider dispersion before it is realized that they can have very serious longer-term side-effects in a significant portion of users. He also emphasizes the need for clinical testing of drug combinations, which may become more difficult as the number of possibilities escalates with the appearance of promising new drugs and the number of available patients for a specific trial declines with the identification of more biomarkers to stratify them. Read More...
The Misunderstood Gene
09/09/10 13:03
University of Oxford neuropsychology professor Dorothy Bishop wanted to know where people get the idea that traits like intelligent could be determined by individual genes. S. Pelech points that intelligence is not really a single trait but the manifestation of a series of complex behaviours that arise from both multi-gene influences and the environment, and cautions that genetic profiling companies that advertise that they can identify inborn talents & personality traits from genome sequencing or SNP analyses are plainly deceiving the public. Read More...
It Was the Best of Times, It Was the Worst of Times...
08/09/10 19:49
Physician James Le Fanu has suggested that research institutions have never been so impressive and well funded, but their recent output has been rather disappointing when compared to the beginning of the 20th century, and this has generated a lot of negative feedback from the biomedical research community. S. Pelech accepts some and challenges many of Dr. Le Fanu criticisms about biomedical research progress, but points out that the US citizen commitment to finance biomedical research has actually been very modest in real numbers when income, taxation and inflation are factored in. Read More...
Craig Venter, "Hopeless Businessman"
06/09/10 17:03
In a New York Times article, Craig Venter is quoted saying that he has been "successful in his finding alternate ways to fund research," although one of his venture capitalist friends, Alan Walton has commented that "Craig is just a hopeless businessman." S. Pelech points out that Dr. Venter is amongst those rare visionaries that are really driving scientific advancement forward, with or without the help of government agencies and charitable organizations, but also aided by other individuals of financial means or know how that share their visions. Read More...
Tips for Successful Grants
01/09/10 19:15
Blogger Morgan at The Scientist's Naturally Selected blog offered some tips for writing successful grant applications. S. Pelech suggests that a strategy, that while humorous, seems to work quite well based on his experience in grant panels. Read More...
Do We Really Need Posters?
31/08/10 16:54
Blogger Ms.PhD at YoungFemaleScientist questioned whether giving and viewing poster presentations at scientific meetings todays are really worthwhile. S. Pelech argues that scientific meeting are usually called conferences, because they are venues for discussion, and scientific posters offers opportunity for discourse between new trainees and established scientists that should not be underestimated. Read More...
A Dispassionate Look at Gene Patenting
31/08/10 14:50
Duke Law School professor James Boyle argued that gene patents are necessary to spur biotech growth, and that opponents of gene patenting are arguing from a "moral" point of view, "protesting the hubris and in some eyes, heresy, of claiming to own the human genome." S. Pelech comments that it is rather late to get worked up about patenting genes, especially since the vast majority of gene sequence information has been generated at public expense. However, he also believes that the public funding of the human genome project may well have hurt the viability of many biotech companies and the industry, and this has delayed the translation of genomic information into practical applications. Read More...
The 'Arbimagical' Goal of the $1,000 Genome
30/08/10 16:08
Blogger Keith Robison at Omics! Omics! wants to know which gene sequencing platform, from contending companies like ABI, Complete Genomics, GNUBio, Illumina, InoTorret and Life Technologies, will win the race to the 30X, $1,000 genome. S. Pelech wonders how much it is really going to cost to have a person's genome sequenced and get the DNA sequence analyzed to yield personal information of practical value, and who is going to pay for it? Read More...
Six Degrees of Scientific Misconduct
30/08/10 15:03
Bloggers have debated over how Marc Hauser, a high-profile and prolific researcher that was caught allegedly fabricating data, should be punished, including whether he should be exiled from science or be able to be redeemed. S. Pelech comments that the falsification of data is seen as a very serious offense in the scientific community, because scientists formulate their research plans around what is currently known, and a great deal of time, energy and resources can be wasted. However, minor falsification of data is probably pretty wide spread and is inherent in "hypothesis-driven" research, but fortunately the self-correcting nature of scientific research will eventually get to the truth of the matter. Read More...
Making a Case for Lab Rotations
23/08/10 15:25
Blogger Comrade PhysioProf makes a case for the usefulness of lab rotations for graduate students as part of the selection process for their research supervisor and training. S. Pelech lists a few negatives for long lab rotations and describes how shorter lab rotations are used at the University of British Columbia in the Experimental Medicine Graduate Program. Read More...
The Genome of Sitting Bull
23/08/10 14:21
Science News reported that there are plans to sequence the genomes of Sitting Bull and some would like to similarly examine the genome sequences of other famous people in history. S. Pelech wonders about the merits and logic of sequencing the genomes of long dead celebrities at this time when our knowledge of the proteome is still so limited and funding is tight, and there are more pressing demands with dealing with a depressed global economy and major environmental problems. Read More...
Mysteries of the Human Brain
19/08/10 20:44
Ray Kurzweil in an interview in Gizmodo said that we are very close to reverse-engineering the human brain, perhaps within a decade, and that the design of the brain lies in the genome. S. Pelech argues that complexity of the brain and its formation cannot be explained from purely genetic data, but must also encompass many external factors including sensory inputs, changing effector output needs depending on the environment, energy and nutrient supply, blood flow, temperature, exposure to toxins, trauma, and psychological stress. Moreover, elucidation of the linkages between proteins and other gene products within neurons will be even more challenging. Read More...
A Good Biomarker Is Hard to Find
17/08/10 20:32
Blogger Monica Desai of the Guardian's science blog noted that despite the discovery of thousands of biomarkers, only a small percentage reach the clinic so expectations need to be tempered about the finding of a promising new biomarker. S. Pelech observes that if one considers that many common diseases such as cancer arise from particular combinations of defective proteins, then it becomes feasible to not only provide an accurate diagnosis based on monitoring of multiple biomarkers but also to develop effective strategies for therapeutic intervention. Read More...
Make Way
16/08/10 14:39
With the disappearance of mandatory retirement, a debate is growing as to whether younger scholars' careers are blocked by their older (and tenured) professors. S. Pelech observes that the tenure debate has been ranging long before mandatory retirement was abolished in many countries and that tenure permits university faculty to tackle riskier research that can lead to scientific breakthroughs. Read More...
Francis Collins' Funding Problem
13/08/10 15:27
Despite possible cutbacks in the NIH's 2012 budget, its Director Francis Collins plans to launch an award in 2011 that would make it possible for promising young investigators to skip the postdoc stage and give them five years of funding to open their own labs. S. Pelech questions whether allowing these recent graduate students to skip the postdoc stage and to providing them with 5 years of funding to open their own labs is really a faster way to waste money and doom a promising young investigator to early failure. Read More...
A Waste of Time?
11/08/10 15:31
Blogger Robert Langreth at Forbes' Treatments observed that pharmaceutical companies have been spending a lot of money on new cancer treatments, but the results have been less than stellar, perhaps because targeted cancer treatment can't work due to the active production of more mutations in tumour cell genomes than the treatments could possibly target. S. Pelech argues that the deployment of a panel of two or three specific drugs against oncoproteins that are simultaneously overactive in the same cancer should produce a nearly 100% kill rate and effectively cure the disease if these defective proteins can be succesfully identified in biopsied specimens from a patient's tumour. Read More...
Planning, Precision, and Profit Margins
11/08/10 15:01
Blogger Holly at From Bench to Business described four issues for any scientist-entrepreneur to consider before beginning their own bio-business: potential for failure, transition from science to business interests, development and application of a comprehensive business plan, and timelines to success. S. Pelech provides further reflections on the demands and obstacles confronting a scientist trying to start and build a biotech company. Read More...
Speculating on the Significance of the Sponge Genome
05/08/10 14:42
Blogger T. Ryan Gregory at Genomicron observed that the recent sequencing of the Amphimedon queenslandica sponge genome is being promoted in the popular media for its potential insights into life's origins, evolution and medical significance to cancer research. S. Pelech notes that the increasingly commonplace genome sequencing of diverse organisms is really just a continuation and refinement of the Victorian tradition of naming organisms, where the DNA sequence itself is its ultimate name, albeit rather long. Read More...
Taking the Conflict-of-Interest Heat
04/08/10 14:24
The University of Wisconsin-Madison investigated the working relationship between cancer treatment device producer TomoTherapy and one of its cancer researchers Minesh Mehta, who subsequently resigned, apparently for other reasons. S. Pelech wonders why there seems to be relatively little concern when faculty in engineering departments provide consulting to industry or clinical scientists see patients to derive extra income, but it seems to be a huge sacrilege for faculty members in life sciences departments to consult with biotech companies and large pharma for a fee. Read More...
The Sound of Genetics
31/07/10 14:51
The Wellcome Trust has funded a project to investigate the genetic determinants of musical ability, which has included the composition by Michael Zev and presentation by the New London Chamber Choir (NLCC) of a new choral work called 'Allele,' which is based on DNA sequence data from the 41 members of the NLCC. S. Pelech thinks that using DNA sequences is about as meaningful for composing a symphony or choral work as using stock market quotations, sport statistics or actuary data as inspirational sources, and wonders whether this is an appropriate choice for Wellcome Trust funding. Read More...
Too Much to Read
21/07/10 16:53
Blogger Pedro Beltrao at Public Rambling noted that 848,865 papers were added to PubMed in 2009, and he says that there needs to be improvements in how researchers are able to find the publications that are particular important to them. S. Pelech proposes that we need to completely re-think and re-engineer how we disseminate the data from scientific research so that it is more efficiently found and utilized in databases that are directly queryable. Read More...
Ain't Nothing Gonna Break My Stride
20/07/10 15:19
Nicholas Wade at the New York Times highlighted some studies that point to natural selection-driven, relatively recent genetic changes in human groups. S. Pelech points out that selective breeding in a relatively small number of generations can lead to profound changes in the appearance and physiology in animals, and eventually we will likely be genetically engineering human genomes to get rid of deleterious mutations and make further improvements, including adaptation to alien environments and cyborg acclimation. Read More...
New Blog on the Block
14/07/10 15:30
Genomes Unzipped is a new blog site that aims to provide independent and informed analysis of developments in the field of genetics, with a particular focus on implications for the budding industry of personal genomics. S. Pelech welcomes more critical analyses in this area, especially since only about 3% of the human genome actually encodes proteins and other recognizable RNA elements such as tRNA, rRNA and microRNA, and the rest is probably filler or "junk" DNA. He argues that the current euphoria and focus on genome sequencing in thousands of humans and hundreds of other species will lead to a major diversion of funding and research that will be insufficient to support the delivery of personalized medicine. Read More...
What to Do About Review
13/07/10 14:38
Blogger Glyn Moody at Open … argues that in the Internet age it may be unnecessary to have pre-publication peer-review of a scientific paper if scientists are able to provide a rating of its content post-publication, whereas blogger Deepak Singh feels that while there are problems with the existing peer-review system, it can be a source of advice that improves the quality of science. With diminishing quality of peer-review, in part due to reviewer fatigue, S. Pelech observes that the best science is no longer necessarily funded and much of the published science is incremental, redundant and flawed. Read More...
What About Hedgehog, Buttonhead, and Bride of Sevenless?
09/07/10 03:06
Blogger Norman Johnson at Watching the Detectives dissected "the art and science of naming genes" and suggests that while "standardization has its place," the colorful naming of fly genes allows for easier recall of the genes, which leads to better communication between scientists. S. Pelech suspects that it also serves politically to flag the these gene as yet other examples of fly genes that have counterparts in humans and other species. However, these genes are more often than not regulated quite distinctly and have different substrates and functions depending on the species. Read More...
The Evolution of Evolution
02/07/10 21:19
Dan Jones at the New Scientist wondered whether the capacity for evolutionary innovation is built into the fabric of life and if such "evolvability" is reflected in an organism's ability to adapt to its environment that can be passed down to subsequent generations. S. Pelech proposes that enhancements of one or more levels of "hierarchical intelligence" - molecular, cellular or social - may play a central role in the development of evolvability. Read More...
The Benefit of a Grant
21/06/10 15:12
The US NIH spends more than $21 billion a year on research grants, and the STAR METRICS program aims to determine the economic impact of this investment, although other studies indicate that it may take about 17 years for an investment in research to visibly pay off in some way. S. Pelech wonders why such an accountability has not been mandated sooner, and notes that in Canada, it seems that the economic returns for the funding of genomics mega projects has been extremely poor. Read More...
The Genome and the Economy
18/06/10 13:34
Mike Mandel at Mandel on Innovation and Growth has blogged that after a decade, the Human Genome Project has failed to deliver medically significant results, but he is optimistic that a significant economic impact will emerge over the next 5 to 10 years. S. Pelech argues that the true dividend from the sequencing of the human genome will not materialize until we can make sense of what all of the expressed proteins and functional RNA oligonucleotides are actually doing, but instead current efforts remain fixated on continuing to sequence the genomes of hundreds of different species and thousands of different people. Read More...
Small Prize, Big Question
18/06/10 13:08
Blogger Anthony Goldbloom at Kaggie has offered a modest $100 award to the person who gives the best short answer to the question: "What has bioinformatics ever done for us?" S. Pelech, who did not win the prize, responds: "No Bioinformatics = No gene sequencing analysis = No genetic engineering = No biotechnology industry = No commercial recombinant protein, peptide or oligonucleotide production = No molecular diagnostics + therapeutics = No personalized medicine. Read More...
GSA: 'Cardinal' Organisms to Human Biology
15/06/10 00:47
Gary Ruvkun at Harvard Medical School suggested renaming "model organisms" as "cardinal organisms" in view of their importance in basic research and in the clinic. S. Pelech argues that this suggestion is rather self-serving and markedly overstates the real value of the study of invertebrates for understanding human pathology and further perpetuates the mythology that genomics analyses of organisms such as yeast, flies and worms are providing continuing breakthroughs in clinical research. Read More...
Quality vs. Quantity
03/06/10 14:46
Bloggers Massimo and DrugMonkey have questioned whether it is reasonable to expect graduate student trainees to have multiple publications result from their thesis research. S. Pelech maintains that every effort should be expended for graduate students to publish original research in scientific journals, but they should still be able to receive a graduate degree if their thesis research in a competitive area has been scooped and no longer has sufficient novelty upon its completion to be published. Read More...
Why Craig Venter Isn't Actually God
28/05/10 12:50
Many bloggers have been critical of the hype that Craig Venter has generated with the successful transplantation of a synthetic genome into a bacteria. S. Pelech feels that this achievement from Dr. Venter and his team is monumental, even if it is incremental, and that Dr. Venter has been entirely frank and reasonable about the accomplishment and its implications in public interviews. Read More...
'Overstepping Your Authority' With Online Comments?
21/05/10 12:50
Blogger Prof-like Substance questioned whether publicly commenting on journal articles is worth the professional risk that it entails as there may be damaging repercussions of publicly criticizing another colleague's work. S. Pelech notes that with the variable quality in peer reviews for published scientific manuscripts, despite the associated personal risks, it does not serve the scientific community if researchers refrain from an active dialogue in search of the truth and fail to be critical of problematic research results. Read More...
The Changing Roles of 'The Sequencers'
17/05/10 12:49
Kelly Rae Chi at Nature noted that as the DNA sequencing process becomes more and more automated, the analysis of the data is becoming more challenging and requires increasing bioinformatics expertise. S. Pelech argues that while it is desirable to have in-house programmers to help analyze data, it is necessary to train more graduate students and post-doctoral fellows with a much deeper and broader understanding of biochemistry, systems and molecular biology than what is typically offered today. Read More...
HIV Makes Music
13/05/10 12:47
University of Georgia graduate student Alexandra Pajak has composed original music based on the DNA of HIV, which has been recorded with the Atlanta Symphony Orchestra. S. Pelech mentions that Kinexus Bioinformatics Corporation has converted the amino acid sequences of several signal transduction proteins into musical notes based on their hydrophobicity to produce a unique melody for each of these proteins that can be freely downloaded at http://www.kinexus.ca/scienceTechnology/gallery/music/music.html. Read More...
Letting Go of the Details
10/05/10 12:45
Bloggers Candid Engineer, DrugMonkey and Comrade PhysioProf have suggested that principal investigators should let their trainees have more free rein in the design, execution and interpretation of experiments, and that the PI's should really focus on getting funding, recruiting, training, and trouble-shooting after the fact. S. Pelech argues that a PI should definitely be very familiar with the underlying theory and limitations of technologies that are being used by the trainees under their supervision and take a strong and active lead in guiding the research of their more junior trainees to avoid waste and unnecessarily prolongation of M.Sc. and Ph.D. thesis projects. Read More...
Systems Biology Meets 'Real' Biology
07/05/10 03:59
Tim Hunt encouraged practicing systems biologists to spend plenty of time talking to real biologists as it's difficult to map interactions among systems "when you don't even know what the players are." S. Pelech comments that Dr. Hunt's major criticisms of systems biology really arise from the infancy of the field, and the enthusiasm of those in this area to make sense of the limited data that is currently available about proteins. Genomics research has provided the identification of the protein players and data about where and when they are produced. Proteomics reseach is revealing how these proteins are modified and their interactions with each other. Read More...
Because That Would Make Too Much Sense
05/05/10 12:41
Bloggers DrugMonkey and Thomas Mailund have wondered why authors are not able to have more control of where the figures appear in their published manuscripts. S. Pelech points out that the size and placement of the figures in the final journal print format can be tricky, and if authors embedded figures with the text in their submitted manuscripts, there is a high chance that the text of the figures may be too small to discern or the figures may be of too low resolution. Read More...
Oh, the Vanity
03/05/10 12:39
Apparently authors with connections to industry are more than twice as likely to pay open access fees to make their work free — a bias that some think could lead to preferential publishing and reading of pro-industry results. S. Pelech argues that even with the traditional journal subscription model, there has alway been an "author-pays' element to scientific publishing in most cases and academic authors are just as inclined to publish "favorable work" as industrial authors, because they are subjected to even more pressure to publish or perish that those in industry. Ultimately, a scientific manuscript stil has to pass independent, scrutiny from peer-review before it is published. Read More...
Study: Discoveries in Non-Human Species Could Directly Benefit Man
28/04/10 12:37
The uncovering by deep homology of human genes in diverse model organisms such as yeast, worms and plants has prompted some scientists to propose that useful insights into the aetiology of human diseases such as cancer could be learned from these species. S. Pelech challenges this notion and argues that outside of insights into the most basic mechanisms of cell division and death, regulatory pathways with these highly conserved genes in these model organisms actually control very different processes and extrapolations from research findings with them can be very misleading. Read More...
Free Personal Genome, with a Catch
27/04/10 12:35
Blogger Iddo Friedberg at Byte Size Biology asked if people are willing to have their genomes sequenced for free if it was also made available for public research use along with some personal information, such as age, height, sex and disese history? However, wiith so many SNPs in the human genome, and over-riding factors such as epigenomic, transcriptional, translational and post-translational regulation affected by external factors, S. Pelech wonders just how useful knowledge of the sequence of one's genome will actually be in the near future. Read More...
Paul Nurse on Funding
26/04/10 12:33
Paul Nurse proposed that the most elite scientists should receive more funding, because it is these individuals that are the most likely to make the big breakthroughs that will drive science forward. S. Pelech disagrees and argues that even with more limited funding, the greater the number of different scientists involved in the discovery process, especially with cross-disciplinary expertise, the better the prospects for scientific advancement. Read More...
Rocket Scientists, Brain Surgeons, and All That
15/04/10 12:31
Success in science is proposed by blogger Zen Faulkes at NeuroDojo to depend more on perseverence than genius. S. Pelech agrees and notes that high curiosity and a real passion for their work gives leading scientists an edge. Read More...
Arguing Over the Epigenome
31/03/10 11:47
The notion published in Nature editorial that epigenetics could explain much about how similar genetic codes are expressed uniquely in different cells, in different environmental conditions and at different times was challenged by Mark Ptashne, Oliver Hobert, and Eric Davidson who advocated that the diversity arises primarily from difference in primary gene sequence. S.Pelech agrees and laments that there is no equivalent of the International Human Epigenome Consortium to promote advancement in the study of protein phosphorylation and other types of covalent modification of proteins. Read More...
Creatures of the Deep Provide Insight into Diabetes
23/03/10 11:46
Maurice Elphick from Queen Mary's School of Biological and Chemical Sciences say NG peptides from marine animals such as sea urchins and acorn worms are made by a gene similar to the mutated vasopressin gene in humans that causes diabetes insipidus. S. Pelech argues that it is a long stretch to extrapolate from sea urchin research to developing strategies to counteract human diabetes. Read More...
The Human Genome Bubble
17/03/10 11:44
The Human Genome Project generated high expectations, which spurred the US government to invest in the effort, which some argue catalyzed long-term investments by the private sector. S. Pelech argues that industry actually led the way to whole genome sequencing, and that since then insufficient followup work on the proteins encoded by genes has handicapped the potential of the Human Genome Project to yield better diagnostic tools and therapeutics. Read More...
The Surprising Variability of Mitochondrial DNA
09/03/10 11:41
Different versions of the mitochondrial genome can be found in different organs from the same person, with single-letter DNA changes that occur in as few as one in 10,000 mitochondria. S. Pelech notes that this is not surprising and may arise from the presence of thousands of mitochondria in the fertilized egg that become portioned out during early reductive cell divisions that give rise ultimately to the distinct tissues and organs. Read More...
A Link Between Breast Cancer and Estrogen
03/03/10 11:40
A new study in Cancer Research from Loyola University Chicago Stritch School of Medicine researchers shed further light on how estrogen may fuel many breast cancers, which may be in part due to inhibition of the pro-apoptotic activity of the protein kinase MLK3. However, S. Pelech notes that the highly conserved MLK3 pathways acts upstream of JNK signalling, which can act in an anti-apoptotic manner to enhance tumour cell survivability. Read More...
'Grantwriter's Agony'
19/02/10 11:37
Blogger DrugMonkey described how triage of a grant application is typically determined by only three assigned reviewers. S. Pelech comments on the poor success rates of grants and the implications this has on fairness, productivity and innovation. Read More...
Not So Useful?
17/02/10 11:32
Tracking 101 SNPs linked to the incidence of cardiovascular disease in 19,313 Caucasian women for a median of 12.3 years failed to show any better discrimination than self reported family history. S. Pelech argues that environmental factors may play a much stronger role in the development of cardiovascular diseases, which may have more complex and diverse etiologies than generally appreciated. Read More...
Lazy Snobs and Conflict of Interest
29/01/10 16:05
John Tierney of the New York Times noted that having a corporate connection does not necessarily bias a researcher’s work, but many journals insist on declarations of corporate sponsorship from industry. S. Pelech argues that research biases exist just as much in publications arising from universities and research institutes as from industrial labs. Read More...