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...

Tags: Scientific Manuscripts

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...

Tags: Metagenomics, Water testing, GenomeCanada

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...

Tags: Genomics, Computing, Cancer gene mutation

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...

Tags: Protein Evolution

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...

Tags: Cancer, Transgenics, Personalized Medicine

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...

Tags: Biomarkers, Patents

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...

Tags: Data Storage

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...

Tags: Personalized Medicine, Michael Snyder

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...

Tags: Research Competition, China

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...

Tags: Megaprojects, Synthetic Biology

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...

Tags: University Rankings

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...

Tags: Jobs, Retirement

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...

Tags: Synthetic Biology

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...

Tags: DNA, Venture Capitalists

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...

Tags: China

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...

Tags: DNA Computers

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...

Tags: Gene Sequencing, Japan

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...

Tags: Authorship