The DNA Network |
| Mixed feelings about an “easier” colon test [The Navigator - Navigenics Blog] Posted: 23 Oct 2008 09:43 PM CDT Michael Nierenberg, M.D.
"Scans provide alternative to colonoscopies in spotting cancer," read one headline. "Virtual colonoscopies ready for prime time" said another. For anyone who could think of a thousand things they'd rather be doing than undergoing a traditional colonoscopy, it sounded like wonderful news. A federal study of CT colonography or "virtual colonoscopy" determined that the X-ray procedure was effective at detecting large cancers and precancerous growths in people with an average risk of colon cancer. No general anesthesia? No need to take a day off from work? No problem! Those were no doubt the thoughts of many patients who are skittish about traditional colonoscopies – and the bowel preparation that accompanies them. Some experts expressed hopes that this vote of confidence in an alternative screening method which is less invasive and cumbersome would encourage more people to be checked for colon cancer, the second leading cause of cancer deaths in the United States. Now, I am all for appropriate colon screening. But as a practicing physician for more than 30 years, I have strong feelings against this procedure, and here's why: |
| Science and Spore. [Genomicron] Posted: 23 Oct 2008 08:19 PM CDT Tomorrow's issue of Science features a new installment of "The Gonzo Scientist" by writer John Bohannon. This edition is all about Spore, the game that is based on "evolution" from primordial ooze to interstellar society [Flunking Spore]. I had heard about the game on blogs, but I had not really planned to play it until John asked a few of us to give our perspective on the science behind it. I can't say I didn't have fun with this, although it is a shame that the game bears little relation to actual evolution (see here for apparent claims otherwise). Here's the creature Niles Eldredge and I came up with, dubbed Punky Quilibra:  |
| Posted: 23 Oct 2008 07:15 PM CDT I was looking forward to the morning session at the Genome Canada International Conference. Too often as the Communications guy I find myself answering questions from people who see genomics and genetics as something unnatural or artifical. If nothing else I hoped the session called 'Green Genomics' would help me with those answers. For the most part it didn't give me that, but it certainly gave me lots to talk about when people come knocking and ask what genomics is all about. |
| Urban dictionary for science? [Bayblab] Posted: 23 Oct 2008 04:16 PM CDT Nature this week has a news feature concerning the erosion of the definitions of certain terms. It is a pet peeve of mine to hear epigenetic (it has to be heritable!) and de-differentiation (hint: if you're talking mammalian cell, you're probably wrong) misused. And I find stem cell is being used so loosely that it has sort of lost its meaning as we've discussed before. The article tackles (excerpts to follow): -paradigm shift: "Unless a Nobel prize is in the offing, it might be wise for scientists to adopt the caution of contemporary historians of science and think twice before using a phrase with a complex meaning and a whiff of self promotion." -epigenetic: "The NIH is careful to define the epigenetics it is paying for as including both heritable and non-heritable changes in gene activity, something that Ptashne describes as "a complete joke".) Bird says he remains in favour of a relaxed usage. "Epigenetics is a useful word if you don't know what's going on — if you do, you use something else," he says." -complexity "Even within the precise world of binary code and bit strings, there was computational complexity, which describes how much memory and processing is required to carry out a calculation; algorithmic complexity, which is related to how much a digital description of something can be compressed; and any number of combinations and variations. "So my bottom line is, add an adjective to 'complexity'," Crutchfield says." -race "Race was long used to imply a shared, distinct ancestry [...] But in other contexts researchers are abandoning the term in favour of other ways to group humans, by 'population,' genetic ancestry' or 'geographic ancestry'" -tipping point "The term was originally coined in 1958 by sociologist Morton Grodzins in the context of studies on the racial makeup of US neighbourhoods. He found that when the migration of African-Americans into traditionally white neighbourhoods had reached a certain level, whites began to move out." ""There is no convincing theoretical argument or model that at some point the planet as a whole will snap into a second state of system," says Timothy Lenton, an Earth scientist at the University of East Anglia, UK." -stem cell "Alleged 'stem cells' can fail to meet the definition on many counts. Stem cells should persist long term, yet many 'stem cells' exist only in the fetus. Multipotency — the ability to generate multiple cell types — is a criterion for a haematopoietic, or blood-forming, stem cell, but spermatagonial stem cells only produce sperm. Stem cells specific to tissue such as cartilage, the kidney and the cornea have been reported, with varying degrees of acceptance. The quest for a 'stemness signature', a collection of markers common to all stem cells, has been met with frustration." -significant "Most statisticians resign themselves to abuse of the term's strict definition. But more grievous trespasses abound. "Statistical significance is neither a necessary nor a sufficient condition for proving a scientific result," says Stephen Ziliak, an economist at Roosevelt University in Chicago, Illinois, and co-author of The Cult of Statistical Significance. P-values are often used to emphasize the certainty of data, but they are only a passive read-out of a statistical test and do not take into account how well an experiment was designed." -consciousness "Many definitions of consciousness include the ability to sort through the relentless onslaught of incoming data to create and respond to an internal model of the external world. And some believe that simply gathering data about neurons and behaviours will not be enough." |
| I'd love to go paperless [adaptivecomplexity's blog] Posted: 23 Oct 2008 03:41 PM CDT Spending all day reading from a computer monitor is a drag. By the end of the day reading from a monitor drives me crazy, which means that I end up printing out hard copies of way too many papers. Amazon's Kindle looks like an intriguing solution, but I think this reader is going to be much, much better. |
| George Church on Ira Flatow’s Science Friday 2pm ET [The Personal Genome] Posted: 23 Oct 2008 01:38 PM CDT George Church, founder of the Personal Genome Project, will be a guest on Science Friday with Ira Flatow, tomorrow at 2pm ET. Details on how to tune in to this October 24th broadcast. |
| Press Conference Video Footage featuring the PGP-10 [The Personal Genome] Posted: 23 Oct 2008 01:22 PM CDT After an all day meeting of talks and discussion, the PGP-10 participated in a press conference. NECN has some video footage from that event: Scot Yount. Researchers intend to build online DNA database. NECN, October 21, 2008. |
| Mr. Green Genes glows on video [Discovering Biology in a Digital World] Posted: 23 Oct 2008 11:47 AM CDT This video from WDSU shows Mr. Green Genes, the transgenic kitty, in the dark and in the light. There's also an interview with Dr. Betsy Dresser, who very briefly talks about the work at the Audubon Center for Research on Endangered Species. Other than clips of the cat, and Dr. Dresser, the video mostly shows people taking frozen samples out of liquid nitrogen, but there's an interesting bit towards the end where they show a pipette transferring material into the nucleus of an egg cell. Mr. Green Genes is certainly a cute cat.
Thanks go to David Ricks for sending links to the photos and video. Read the comments on this post... |
| Small genome sizes in pterosaurs, too. [Genomicron] Posted: 23 Oct 2008 10:45 AM CDT My colleagues Chris Organ and Andrew Shedlock, who provided evidence that theropod dinosaurs already had (somewhat) reduced genome sizes prior to the evolution of birds (Organ et al. 2007) have followed up their study by estimating the genome sizes of several species of pterosaurs. Pterosaurs were the first vertebrates to evolve powered flight, having taken to the air 70 million years before birds and 150 million years prior to bats. Interestingly (though perhaps not surprisingly at this point), they seem to have possessed reduced genome sizes, and these downsizings of DNA amount began before flight arose. On the other hand, it is clear that the estimates for non-avian dinosaurs are not as small as modern birds and that the estimated ancestral genome size for birds was larger than the genome seen in various groups. Patterns can be observed in terms of flight ability across living avian species. Notably, my student Chandler Andrews showed that genome size is correlated with wing loading (and indication of flight capacity) within perching birds, and we are currently writing up major projects on bird groups with different flight ability as well as a study of hummingbirds; Jill Smith, another student, also has a large bat study to write up. The story thus seems to be that genome reduction occurred in the dinosaur lineage of which birds are descendants before flight (so did feathers, bipedalism, and other characteristics), but were later further adjusted when flight arose (as were feathers, etc.). The same reductions before flight probably occurred in the pterosaur and bat ancestors. So it's not flight per se that matters, but a feature linked with flight. As Organ and Shedlock put it, "we hypothesize that a metabolic intensity required for flight, not flight itself, explains the correlated evolution between genome size and flight in amniotes." -- this seems very plausible given the growing amount of data on this topic. References Andrews, C.B., S.A. Mackenzie, and T.R. Gregory. Genome size and wing parameters in passerine birds. Proceedings of the Royal Society of London B, in press. Organ, C.L., A.M. Shedlock, A. Meade, M. Pagel, and S.V. Edwards. 2007. Origin of avian genome size and structure in non-avian dinosaurs. Nature 446: 180-184. Organ, C.L. and A.M. Shedlock. 2008. Palaeogenomics of pterosaurs and the evolution of small genome size in flying vertebrates. Biology Letters, in press. Zimmer, C. 2007. Jurassic genome. Science 315: 1358-1359. |
| DNA Testing on Unusual Samples: Paraffin Blocks Now Accepted [DNA Testing Blog] Posted: 23 Oct 2008 10:39 AM CDT DDC is pleased to announce that it is now accepting paraffin-embedded tissue samples as a source of DNA for paternity testing. This may be very useful in cases where the alleged father or child is deceased or missing, and a medical examiner, coroner, or hospital pathologist has previously collected tissue samples and preserved them in [...] |
| PGP volunteers note: it's hard to hide your APOE status [Genetic Future] Posted: 23 Oct 2008 10:22 AM CDT When James Watson's genome sequence was publicly released earlier this year, Watson famously kept only one region of his DNA a secret - the region encoding the APOE gene, which contains common variants that contribute substantially to the risk of late-onset Alzheimer's, and also affect predisposition to other diseases. A recent article in the European Journal of Human Genetics shows something that shouldn't have come as a surprise to anyone familiar with human genetics: simply removing the APOE gene was not enough to prevent someone from inferring whether or not Watson carries the riskier versions of this gene, because other markers around the gene can also indirectly convey this information through the magic of linkage disequilibrium. The authors kindly don't reveal Watson's APOE status, and in fact note that they warned Watson prior to publishing their paper so that he had time to take appropriate actions. He has since responded by removing an additional 2 million bases around the APOE gene from his public sequence. That action largely removes the possibility of inferring his risk genotype using linkage - in fact, the authors note with dry Australian understatement that the removal of 2 million bases is "likely excessive". Watson could have used linkage information from the HapMap project to delineate the smallest required region, but apparently decided that overkill was the best policy. It's worth noting that once we have complete genome sequences from sufficient individuals it will be straightforward to determine which DNA positions provide linkage-based information about a particular risk polymorphism (in a specific population, at least). That would allow the clean excision of only those bases that are absolutely required, thus having a smaller impact on research into the rest of the genome. (Of course, that relies on at least some people releasing their APOE sequence into the public domain, even if it turns out to carry the riskier version - I guess it's lucky for us we have anonymous genome sequencing projects like 1000 Genomes.) The whole episode must be raising questions in the mind of some of the Personal Genome Project volunteers as they consider the prospect of releasing their own genome sequences to the world (participant number 8 has already raised the prospect of redacting his APOE sequence, according to New Scientist, while Misha Angrist is reserving the right to hold back, well, anything). Are there genes they should be hiding? If so, how much sequence do they need to delete? Ultimately, how do projects like the PGP reconcile the desire for partial genome privacy with the need to get sequences out there in the public domain to further genomic research? Mind you, given the quality of the sequence data released so far, they probably don't need to worry too much for the moment...
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| PGP sequence data disappointing [Genetic Future] Posted: 23 Oct 2008 10:10 AM CDT
So far raw sequence data files have been posted on the PGP profile sites of only four of the ten volunteers: George Church, John Halamka, Esther Dyson and James Sherley. The files are apparently the result of targeted resequencing of a proportion (perhaps 20%) of the protein-coding regions of the genome (called exons). Although a relatively small proportion of the genome as a whole, exons are highly enriched for functionally important sequence, so this tiny slice of sequence could actually be quite informative about the genetic variants associated with diseases and physical variation. However, when I downloaded and examined the files my hopes weren't too high - participant Misha Angrist had already warned on his blog that the data release was not the world-changing event that the media circus might lead you to believe: I have to say, this whole extravaganza felt more like a walk-through or a dress rehearsal. Several of us did not get our sequence data yesterday and those who did got very rough, low-coverage data. After checking over the files I can confirm that Misha is certainly not wrong about the "rough, low-coverage" bit - the data released so far makes for pretty desultory reading. For instance, here's a snippet from Esther Dyson's file: Read the rest of this post... | Read the comments on this post... |
| Posted: 23 Oct 2008 10:00 AM CDT Two interesting events are happening, Monday night, Oct. 27th. At the UW: Josh Rosenau from the National Center for Science Education will be speaking at 6 pm about Creationist attacks on science education. (Josh is also a Science Blogger). In Ravenna, at Third Place Pub: Ted White from the Seattle Biomedical Research Institute will be talking at 7 pm about infectious disease. Read the rest of this post... | Read the comments on this post... |
| 2008 Presidential Candidates on the Issues of Biomedical Research and Healthcare [Highlight HEALTH] Posted: 23 Oct 2008 08:32 AM CDT A major determinant of America’s health and competitiveness in the world is progress in the life sciences. Over the past twenty years, the life sciences have had a tremendous impact on human health through the understanding of the molecular basis of disease and the development of new diagnostics, therapeutics and other medical products. Given the significance of biomedical research on healthcare, I felt it was important to highlight the 2008 presidential candidates’ positions. A number of online resources are discussed in this post and listed at the end of the article. With the election less than two weeks away, it is paramount that voters know where the presidential candidates’ stand on these essential issues.
Biomedical ResearchScience Debate 2008, an effort endorsed by leading scientific organizations, called for a public debate in which the U.S. presidential candidates were asked to share their views on the issues of the environment, health and medicine, and science and technology policy. Each candidate answered questions regarding their respective positions on matters of scientific innovation. Their responses to the top 14 science questions facing America, including positions on scientific integrity, genetics research and stem cells, are presented in an easy-to-read side-by-side comparison at Sciencedebate2008.com. The side-by-side comparison Science Debate 2008: 14 Answers Obama McCain is also free for download as a PDF [1]. What follows is brief synopsis of their answers. Scientific integrity Senators Barack Obama and John McCain agree that policy should be based on science. Both candidates criticize the current administration for denying facts and basing government decisions on ideological predispositions instead of scientific evidence. Obama promises to restore the role of the President’s Council on Science and Technology (PCAST) as advisor to the President. McCain pledges to have a science and technology advisor in the White House. Genetics research Both candidates recognize the ethical, legal and social issues associated with genetics research. Obama supports the Genetic Information Non-Discrimination Act (GINA) and introduced the Genomics and Personalized Medicine Act of 2007, which is aimed at ensuring the safety and accuracy of genetic testing. McCain speaks less of genomics or personalized medicine and more about ensuring the privacy of electronic heath records and the fostering of a “new Green Revolution” in agriculture to improve crop yields. Stem cells Obama and McCain both support federal funding for stem cell research. McCain also supports funding for other research, including amniotic fluid and adult stem cell research. Obama favors responsible oversight of embryonic stem cell research and an expanded federally supported stem cell research program. Research and development funding With respect to research and development funding, there is a sharp contrast between the two candidates. Obama looks to renew the government’s commitment to investing in biomedical research, which has suffered a major lapse over under the current administration, and pledges to double the basic research budgets of key science agencies such as the National Institutes of Health (NIH), the National Science Foundation (NSF), the Department of Energy’s Office of Science (DOE) and the National Institute of Standards and Technology (NIST) over the next 10 years. McCain plans to freeze all discretionary spending for one year, which would effect the research budgets of all the science agencies listed above, continuing the trend over the last five years of effectively reducing biomedical research funding. Research!America, the nation’s largest non-profit public education and advocacy alliance, is committed to making research to improve health a higher national priority. You can read more about the presidential candidates and medical and health research issues at the Research!America blog. Additional information on what Senators Obama and McCain have said regarding important science policy issues is also presented at Scientists and Engineers for America, a nonprofit, nonpartisan, educational organization. The side-by-side comparison documents quotes from each of the candidates with links to news and media websites.
HealthcareA principle difference between the two presidential candidates is their philosophical difference on healthcare. In the second presidential debate, Senators Barack Obama and John McCain were asked, “Is healthcare in America a privilege, a right or a responsibility?” [2]. Obama believes it is a right while McCain views it instead as a responsibility. The Obama plan emphasizes increased health insurance regulation while the McCain plan stresses deregulation. To reduce costs, the McCain plan also emphasizes deregulation of health benefits and tax reform. In contrast, the Obama plan will establish a national minimum standard of coverage and aspires to control healthcare costs through government interventions. This months edition of The New England Journal of Medicine includes perspectives from the two candidates on healthcare reform. The journal editors asked each of the candidates to describe their plans for reforming the U.S. healthcare system. A side-by-side perspective on Health Care Reform and the Presidential Candidates is free for download as a PDF [3]. Republished below are excerpts from the article. Barack Obama:
John McCain:
Similar estimates were made in another independent analysis, which found that the McCain plan would not enable many more Americans to obtain health insurance [5]. Indeed, the study found that “Over time, a refundable tax credit would not automatically adjust as health care costs increase — which is quite different from the current tax exclusion of employer premium payments. Thus, the effectiveness of the tax credit in inducing people to buy coverage would inevitably decline over time. Even if the tax credit were indexed to the Consumer Price Index (CPI), if the annual growth in premiums exceeded CPI-measured inflation by 6 percent — as was the case between 1999 and 2007 — the value of the credit would be eroded so much that in just five years, five million more people would be uninsured.” Further resources for comparing the candidates’ positions on healthcare can be found at 2008 Presidential Candidates: Health Care Issues Side-by-Side. In addition, 2008 Your Candidates. Your Health. educates voters on both presidential and congressional candidates. Rational voting decisions require informed citizens. Take the time to learn about the candidates’ positions on biomedical research and healthcare so that you can make an educated choice. Online ResourcesOnline resources highlighted in this article:
References
This article was published on Highlight HEALTH. Other Articles You May Like |
| The Secondary Genomic Market and Medical Interpretation at HelixGene [Think Gene] Posted: 23 Oct 2008 02:35 AM CDT Adriano Squecco of DNA-forums.org is collecting Y Chromosome information from DTC consumers and compiling an open community ancestry database: Y-DNA-FORUMS [excel spreadsheet] (my results are under “Yates” on the 23andMe v1 page) Interestingly, he is advertising his project on the 23andMe user boards, which is how I found Adriano and his project. Since users can download their 23andMe (or deCODEme) genomic test results as a text file, any 3rd-party service in a secondary genomic market can provide interpretation and collaboration services without ever handling biological samples over the internet. This is the future. The sequencing of the genome itself isn’t as interesting because we know what the end is: a cheap, accurate, complete genomic sequence. We may think of genomic testing today as an obscure luxury service, but the technology will bottom out and sequencing companies will consolidate, all offering the same undifferentiated sequence, all competing on price, economy of scale, and marketing. Instead, what is interesting, what offers an unlimited potential for differentiation, competition, and innovation —is the secondary genomic market, services which accept biological test results and produce research and interpretation. And while genomic testing is the obvious start for a secondary medical information market, why not any medical test? We already send away blood and cultures to a lab and get back data at medical facilities, why not cut out the middle and do it directly through the mail and the Web? Que Dr. Steven Murphy freaking out about involving doctors and irresponsibility… except, now we got smart. We’re going to beat the “hackers” at their own game, right Steve? Introducing HelixGeneIntroducing: HelixGene Foundation for Better Genomic Medicine. You email us your medical questions about genomics, our licensed medical genomic doctors email answers. This announcement is our soft-launch: we are accepting and answering emails and paid subscriptions, but we are still building the service and have not officially launched. Our genomic specialist physicians include: Steven A. R. Murphy, MD (also known as The Gene Sherpa) Adam J. Messenger, MD Matthew B. Lubin, MD Jennifer Ibrahim, MD Joy Samanich, MD Our general subscription is $14.95 per month (FREE first month alpha accounts) to post medical genomic questions to HelixGene’s public forum by email. Private emails are $145 each and will be answered by a HelixGene health professional in 48 to 72 hours. We DO discuss the medical validity and implications of all DTC genomic tests in a medical setting including: 23andMe, deCODEme, and Navigenics. For the press, we provide expert opinion services for journalists and sell expert review subscriptions for mass media publications including medical genomic information. To enforce accountability we feel is lacking in medical reporting in the mass media today, HelixGene publishes medical genomic report cards for publications. Pre-submitting your publications and consulting with our experts helps us help you accurately and honestly report medical genomic information to the general public. Ask our about media medical consulting plans including those for bloggers, independent journalists, and major publications. Email us for pricing. We also host a private, invitation-only genomic specialist forum which is free. If you are qualified, ask for an invitation to our expert forum. This is a forum for doctors and scientists to discuss academic issues, particularly to discuss the merits of new genomic services, academic issues, and troubling medical genomic reporting in the popular media. Email us for an invitation. Secondary Market DatabaseI’ve started a database for secondary genomic market services. Please leave a comment here to report new services or send Think Gene an email. |
| Journal Club: Focus on Next Gen Sequencing [FinchTalk] Posted: 22 Oct 2008 09:54 PM CDT Yesterday I received my issue of Nature Biotechnology. This month it features Next-Generation (Next Gen) Sequencing. One editorial, one profile, three news features, a commentary, two perspectives,... |
| Do you want a chance to inspire the scientists of tomorrow? [Discovering Biology in a Digital World] Posted: 22 Oct 2008 09:40 PM CDT Are you interested in global health? The Washington Global Health Alliance is looking for an education professional, with a life science or science education background (BS or higher) to help train faculty and students at the high school level. The complete announcement is below, the appointment would be at the Seattle Biomedical Research Institute in the BioQuest program. Read the rest of this post... | Read the comments on this post... |
| Is that a phantom in your pocket, or are you happy to see me? [Bayblab] Posted: 22 Oct 2008 09:40 PM CDT Phantom limb syndrome is a well documented and apparantly quite common phenomenon among amputees. It's the sensation that a missing limb is still there, and even responding to stimuli. But the upper and lower extremities (i.e. legs and arms) aren't the only body parts surgically removed. What happens, for example, when a man has his penis removed as part of a sex-change operation? Wonder no more: [R]eports on the phantom penis and its treatment are very rare. We experienced a patient who underwent sex reassignment surgery in whom the sensation of a phantom erectile penis persisted.The case study, publised in Acta Medica Okayama this past year, is freely available here (and complete with pictures) and describes the case of a 52-year old man who had male-to-female transgender surgery. Phantom erections are quite common after penis amputation either from sex reassignment or trauma (such as being assaulted by Lorena Bobbitt) but usually stop after a couple of weeks. This man's persisted for over 6 months before he returned to the operating room to have it fixed. The surgeons removed some of the underlying erectile tissue shortly after which the invisible hard-on disappeared. Neurotopia has a more detailed discussion of this case, and the underlying neurology of phantom limbs in general. |
| The Howard Stern of Genomics...... [The Gene Sherpa: Personalized Medicine and You] Posted: 22 Oct 2008 10:53 AM CDT The other day I was talking with Misha Angrist, who BTW is writing a book about this great adventure known as personalized medicine....... I had been telling him about how my views had been pissing... [[ This is a content summary only. Visit my website for full links, other content, and more! ]] |
| Posted: 22 Oct 2008 09:30 AM CDT I'm guessing that the title for this week's Genome Canada International Conference is both a play on the acuity of normal vision and a suggestion that the conference will be looking well into the future. Considering the pace of change that might be a pretty grand ambition for the conference but I'm here in Vancouver to attend the conference for a variety of reasons. First off we had a meeting of all the communicators from the various Genome Centres across the country. I'm part of a panel tonight at a Public Forum called "The Genetic Test Results Are In .... Now What?", and then of course there is the conference itself and its great line-up of speakers. |
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