The DNA Network |
| Eureka! Algorithms bring us science news [business|bytes|genes|molecules] Posted: 05 Jun 2008 07:54 PM CDT
The site looks great. The quality of stories seems to be good (only time will tell). Regardless, if only cause of the design and the algorithmic nature of the site, I am quite pumped and hope it turns out to be good over time. So how does it work. The Drupal post has the details, but the site itself has the concise version.
Would be cool if we could get programmatic access to this though. An API which we could use to build mashups with E! Science News as one of the components would be great. Technorati Tags: Science, News, Algorithms  |
| BioFuel in Your Car AND Food in Your Belly?? [Bayblab] Posted: 05 Jun 2008 07:50 PM CDT McGill plant biologist Donald Smith has a nice little article: "Not all biofuels take food off the table" in the Globe and Mail, ending with a call to action: "We can produce biofuels that won't exacerbate the global food crisis. We should be working as hard as we can right now to do just that." Good to know some Canadian research dollars are being used to think about what is becoming the single most important economic issue of our time. My guess is not nearly enough - although I confess I'm ignorant as to exactly how much we invest in agricultural and energy research. Maybe it should be one field....agro-energetics... |
| ELSI After Francis Collins: What Now? [PredictER Blog] Posted: 05 Jun 2008 05:49 PM CDT In an editorial published today, "This time it's personal" (Nature 453, 697 (2008) | doi:10.1038/453697a ), Nature adds to the many comments on Francis Collins's announcement that he will step down from his 15 year position as head of the US National Human Genome Research Institute (NHGRI). Like most comments on Collins's career at NHGRI, the editorial praises the leader for his ambition, political acumen, and emphasis on the ethical implications of genomic research. In addition to leading the Institute to the successful sequencing of the genome in 2003, Collins helped to initiated the International HapMap Project, ENCODE, and the 1,000 Genomes Project. He also lobbied for the passage of GINA (H.R. 493) and was a constant advocate for the inclusion of public outreach and ethics education in genomic research. Collins's emphasis on the ethical issues and the NHGRI's ELSI program laid the conceptual groundwork that informs much of the work we do here at PredictER. In fact, thanks to the support of The Richard M. Fairbanks Foundation, Inc, the Indiana University Center for Bioethics has been answering Collins's call to address the ethical implications of genetic and genomic research by focusing on both research ethics and medical ethics as the science is translated into current and future predictive health care. The editorial also mentions some of the challenges that the next director of NHGRI will face. These challenges include a shrinking budget and waning political support: Although Collins says he has no concrete plans … the future of NHGRI is more cloudy than his own. The funding situation of the NIH has been gloomy for years, with flat budgets stifling many potentially worthy projects. And with Collins gone, the NHGRI may become more of a target for politicians who feel it has run its course. Of course, the challenges also include existing and unanticipated ethical and legal issues. As the Nature editorial notes: "Genomics is now at a point where the science and technology are moving much faster than society's ability to assimilate and make sense of the information". One challenge that this editorial does not mention directly, but seems, nevertheless, to be implied by the shrinking public budget, is the fact that much predictive health research will be (and currently is) receiving commercial support. This should not be a surprise. If we want genomic research to result in better personalized medicine, we should expect that the life science industry will invest in the research. At the same time, however, there's no better moment than now to accelerate the investigation of the specific ethical issues of doing commercially supported genomic and predictive health research. For example, here are a few questions that jump to my mind: Must a research biobank disclose to donors in the informed consent policy that research results may result in commercial products? Must or should these biobanks share the income from tissue or data sales with donors? Should pharmacogenomic companies and other patent holders be expected to share financial rewards with research participants or even with the communities to which these participants belong? - J.O. |
| From the Mouths of Babes [The Gene Sherpa: Personalized Medicine and You] Posted: 05 Jun 2008 01:28 PM CDT To get ready for my talk with the Connecticut Geriatrics Society. I warmed up by taking 3 hours today and spending it with the Future of Genomic Medicine. Yes, that's right. Pubescent Teenagers!!!! I... [[ This is a content summary only. Visit my website for full links, other content, and more! ]] |
| Diverse set of Americans typed at 500K SNPs [Yann Klimentidis' Weblog] Posted: 05 Jun 2008 12:56 PM CDT 102 Americans (25 of each major ethnicity) were typed and they looked at genes where there were several SNPs that had large frequency differences. A spermatogenesis related gene showed up, like they do in several of the signature of positive selection studies. What's up with that?...no one really talks about it. They also find LYST, involved in immune function and skin color. They find no fixed differences for any SNP between any of the subpopulations (maybe because they're all somewhat admixed). There's also issues about how these SNPs were ascertained and the fact that less than one percent are in exons... I wish they had some more detailed information on the ethnicity of the typed individuals. Finally, the discussion has an interesting part on the under-appreciated role of purifying selection (or relaxation thereof) in genetic differences between groups and this paragraph, which I'm still trying to fully digest: Moreover, from the point of view of identifying the genetic basis of health differences between human subpopulations, it may not be particularly important whether drift or selection is responsible for a given difference. In either case, the relaxation of purifying selection on a given SNP site implies that the allelic differences at this site are not likely to be deleterious. This in turn implies that major health differences between human subpopulations are likely to involve not deleterious genes per se but rather deleterious gene-by-environment interactions.Genome-wide SNP typing reveals signatures of population history Austin L. Hughes, Robert Welch, Vinita Puri, Casey Matthews, Kashif Haque, Stephen J. Chanock and Meredith Yeager Genomics Available online 16 May 2008. Abstract: Single-nucleotide polymorphism (SNP) arrays have become a popular technology for disease-association studies, but they also have potential for studying the genetic differentiation of human populations. Application of the Affymetrix GeneChip Human Mapping 500K Array Set to a population of 102 individuals representing the major ethnic groups in the United States (African, Asian, European, and Hispanic) revealed patterns of gene diversity and genetic distance that reflected population history. We analyzed allelic frequencies at 388,654 autosomal SNP sites that showed some variation in our study population and 10% or fewer missing values. Despite the small size (23–31 individuals) of each subpopulation, there were no fixed differences at any site between any two subpopulations. As expected from the African origin of modern humans, greater gene diversity was seen in Africans than in either Asians or Europeans, and the genetic distance between the Asian and the European populations was significantly lower than that between either of these two populations and Africans. Principal components analysis applied to a correlation matrix among individuals was able to separate completely the major continental groups of humans (Africans, Asians, and Europeans), while Hispanics overlapped all three of these groups. Genes containing two or more markers with extraordinarily high genetic distance between subpopulations were identified as candidate genes for health differences between subpopulations. The results show that, even with modest sample sizes, genome-wide SNP genotyping technologies have great promise for capturing signatures of gene frequency difference between human subpopulations, with applications in areas as diverse as forensics and the study of ethnic health disparities. |
| Jay Parkinson and Hello Health [ScienceRoll] Posted: 05 Jun 2008 12:48 PM CDT First, you know well who Jay Parkinson is and why he is an example for all of us in the health 2.0 world. Second, I’ve already presented some services that provide online medical consultation. Of course, the simplest conclusion is Jay must launch a similar service. And here is Hello Health.
Let’s see what you have to do if you would like to see a doctor online:
You can choose video chat; IM; in-person visit or e-mail. Ok, despite all the dangers it can lead to, this is the future. I must state that medicine will never be an online service, but there will be more and more patients who want to have a GP who can be contacted online anytime it’s needed. And if you would like to hear more from Jay himself, here are some videos and interviews: Hello Health:
Jay on Health 2.0:
YourWiredMD.com: Jay Parkinson, MD
Further reading:
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| The FDA Takes the Science of Clinical Trials Down A Notch [adaptivecomplexity's column] Posted: 05 Jun 2008 12:21 PM CDT Let's say you're going to test a new ACE inhibitor drug for lowering high blood pressure. You would think that one of the obvious questions you want answered in this trial is whether the new medication is better than the existing drugs on the market. If the new drug isn't any better, then the only purpose it serves is to pad a drug company's profits, by giving that company a new exclusive drug to market. If your clinical trial doesn't compare the new drug to older drugs, if instead you just compare your new drug to a placebo, then you have no idea which one is better. Even worse, you put half the subjects in your blood pressure study at risk by using a placebo - if a good treatment already exists, it's unethical to deny patients that treatment and give them a placebo instead. |
| How’s this for probabilistic risk? [genomeboy.com] Posted: 05 Jun 2008 12:19 PM CDT “Vegas Solves Health Care Crisis!” |
| Google Health: Slideshow [ScienceRoll] Posted: 05 Jun 2008 11:52 AM CDT I introduced the new service of Google Health some weeks ago. Now Matthew Holt, the author of The Health Care Blog created a nice slideshow about it: (Via Kevin, MD) Further reading:         |
| Finishing in the Future [FinchTalk] Posted: 05 Jun 2008 10:14 AM CDT "The data sets are astronomical," "the data that needs to be attached to sequences is unbelievable," and "browsing [data] is incomprehensible." These are just three of the many quotes I heard about... |
| Exploring Life's Origins with Janet Iwasa [The Daily Transcript] Posted: 05 Jun 2008 07:50 AM CDT From Andre at biocurious: Janet Iwasa has had an unusual scientific career. After finishing her PhD with Dyche Mullins at UCSF she started a postdoc in Jack Szostak's lab at Harvard but not to do bench work or even simulations like her postdoc colleagues. Instead, Janet is a full time animator and graphic designer. Some of Janet's work can be viewed at her website, onemicron.com. Her latest work, a website called Exploring Life's Origins explores the early evolution of cellular life, including the RNA world hypothesis and the emergence of a protocell. Also check out this piece at Nature Networks on Janet's work. Read the comments on this post... |
| Molecular and Cell Biology Carnival: On Scienceroll! [ScienceRoll] Posted: 05 Jun 2008 03:39 AM CDT Steppen Wolf gave me the opportunity to host this week’s Molecular and Cell Biology Carnival on the 8th of June (this Sunday). Please send me your submissions via the official form or by e-mail (berci.mesko at gmail.com). The deadline is June, 7 at 12:00 PM. I’ve only hosted Grand rounds, Medicine 2.0 and Gene Genie so far, so it’s going to be fun to be involved in the molecular biology community.         |
| Estrogen applied to the human penis could stop the spread of HIV [trash] [Think Gene] Posted: 05 Jun 2008 03:29 AM CDT In a world first, a University of Melbourne study has shown that topical estrogen could help prevent HIV infection by blocking entry of the virus into the human penis. [editor's note] (Andrew): The only reason I’m not scrubbing this trash study off my website is to mock it. First, there is no clinical application. Rather than a CONDOM, which costs nothing, works immediately, is everywhere, works for everyone, has no side effects, and prevents every STD up to and including pregnancy itself by almost 100%, I’m supposed to sagely ponder rubbing female hormones on my penis to “toughen it up” by “15%” which might increase my resistance to HIV a week later? And this is suggested as viable solution for AIDS control in countries with pervasive cultural taboos about the penis? Total, absolute bullshit. Second, the sample size of this study is: TWO. Yes, two. Ok, eight if you include the foreskin donors. And the study only tested keratin coverage and presented some untested hypotheses regarding a couple tangential studies as conclusions regarding HIV prevention. But good news for readers, because I’m awarding a Think Gene coffee mug to the first reader who forwards me a spam email hawking topical oestrogen as an “all natural” penis cream to “u last longr.” The study to be published in PLoS ONE journal today reveals that application of estrogen to the human penis increased the thickness of the natural keratin layer on the skin, which could prevent HIV from infecting the male. The epithelium of the human penis is richly supplied with estrogen receptors suggesting it could respond to topical estrogen. Dr Andrew Pask from the Department of Zoology at the University of Melbourne analyzed the tissue samples from 12 foreskins and made the discovery. "This suggested that estrogen could induce a thickening of the keratin layer of the foreskin epidermis in the same way as it acts in the vagina," said Dr Pask. "Keratin on our skin acts a barrier to viral infection. We hope to be able to enhance this protection with the use of a naturally occurring, weak estrogen," said Professor Roger Short of the Faculty of Medicine, Dentistry and Health Sciences who lead the research. To confirm its effect, topical estrogen was applied to the human foreskin for a two week trial. This resulted in a rapid and substantial increase in keratin thickness. "We have found a new avenue to possibly prevent HIV infection of the penis." HIV is one of the greatest health crises the world has ever seen, and affects over 40 million people worldwide. Source: The University of Melbourne Kevin: HIV is on the rise around the world and a treatment such as this could have a great where condoms are not socially acceptable because of adverse societal influence. Estrogen on the penis would be fine, and while it’s not as good as condoms for preventing HIV (and anti-retrovirals at your local free HIV drug stand) this could really mean something around the world in terms of harm reduction |
| How to reduce your lab’s environmental impact [Bitesize Bio] Posted: 05 Jun 2008 02:49 AM CDT Maybe I’m wrong, but I tend to think that people are attracted to biological research because of an interest in nature and the noble desire to make the world a better place. Those ideals are often stripped away in the realities and demands of working life - it turns out that it’s not so easy for one person to save the world, and you have to be more interested in Nature than nature to be successful. But I’ve always found it a bit paradoxical that from those eco-aware origins, we end up working in labs that generate vast amounts of waste and consume a lot of power. Of course, much of this waste and consumption is unavoidable but there are a lot of ways that we can reduce the environmental impact of our labs by improving our practices. Here are 12 ways to start with: 1. Hold completed overnight PCR reactions at 10°C instead of 4°C. It won’t affect the product, but it will save a considerable amount of energy. 2. Replace falcon tubes with re-usable 50mL glass bottles in experiments that don’t require you to centrifuge the contents. 3. Close or switch off the fume hood. Fume hoods use vast amounts of power and the amount they consume is proportional to how far they are opened. 4. Buy reagents from on-site stores / freezer programs where possible. Does your BamHI really need to be chauffeur driven to you? On-site stores transports reagents in bulk, which saves fuel. 5. Find out if there are greener alternatives to the reagents you use. MIT’s “Green alternatives wizard” will help. 6. Buy service contracts for your equipment. That shiny new HPLC/spec/PCR machine looks great but 10 years down the road it’s going to be land-fill fodder if it’s not looked after. An annual service contract will prolong the life of your equipment, reducing waste, and keep your lab ticking over more reliably. 7. Recycle. We’ve told you about electroporation cuvettes and DNA columns - what else can you recycle in the lab? 8. Donate surplus equipment like computers to local schools, community groups or Freecycle. 9. Label lab equipment that can’t be turned off. That way people in the lab know they are free to turn off un-labelled equipment overnight or over the weekend. 10. Use non-mercury thermometers. Alcohol/glycol or digital thermometers are just as good. 11. Keep an up-to-date inventory of your lab’s chemicals to avoid duplicate orders. 12. Order only the amount that you need. How often have you bought a chemical only for most of it to languish on the shelf for years? What are your ideas for reducing waste in the lab? Tell us in the comments. |
| All these tools : How do people use them? [business|bytes|genes|molecules] Posted: 05 Jun 2008 01:01 AM CDT
It also points to the importance of access to underlying data, e.g. 23andme etc allowing customers to export their genotypes (and the panels), without which tools like SNPedia and Promethease would not be too useful. But looking at Prometheus, at Foldit, at folding@home, the molecular workbench or even the rather nice tools provided by 23andme got me thinking. May people get interested in computers at a young age, programming, hacking. Some people become makers in their teens. I wonder, that with open data and scientific apps that are easy to use and accessible by many, are there kids actually playing around with them? When they use folding@home as a screensaver, do people wonder about what’s going on under the hood? I suppose where I am going with this completely haphazard ramble is that there are tools now which allow us to ask some interesting scientific questions. The other day I talking about Brian Greene’s thoughts on science and the wonders of science. In keeping with that train of though, are today’s kids, or even adults for that matter, learning from the tools mentioned above, playing with them? Is anyone telling them what is happening? I am very very curious. Update: Changed the title. That’s what happens when you’re half asleep and hit publish Image via Wikipedia Technorati Tags: Education, Science, Molecular Modeling, Bioinformatics  |
| Synthetic Biology - the journal [My Biotech Life] Posted: 04 Jun 2008 11:59 PM CDT
The new journal will be published by Wiley & Sons and has a respectable editorial board headed by Adam P. Arkin (Berkeley). The board includes well known researchers in this emerging field of bioengineering like Pamela Silver (Harvard), Luis Serrano (EMBL Spain), Ron Weiss (Princeton), Christina Smolke (Caltech) and more. The new journal is described as follows:
The journal is now accepting research articles, perspectives, reviews and spec sheets. I find the idea of spec sheets in biology, just brilliant (ex: BBa_F2620 Data Sheet pdf). Post from: My Biotech Life |
| Evolution on Televison [Think Gene] Posted: 04 Jun 2008 11:00 PM CDT The top three evolution parodies on the top three parody television shows: South Park, Family Guy, and The Simpsons. South Park South Park, as usual, is “I’m so much smarter than all you idiots that I can flaunt my total disregard for all social norms… especially intellectualism.” They say “butt sex retard fish squirrel!” L0LZ!1 Yet, South Park is the only one of the three top shows that parodies not the surface debate itself as some cheap ploy for relevance, but how people actually behave and what people actually believe —not what they say. The gag is: The substance of Mr. Garrison’s opinions are always irrelevant. It’s his zealotry that’s the joke, and zealotry can be about anything. The scenario could be reversed to the same effect: an atheist zealot could be denouncing religion while begrudgingly subscribing to an institutionally-enforced liberal ideology of tolerance (*cough* academia *cough*). That zealotry would be as equally absurd. And —that’s exactly the plot of the full South Park two-episode plot arc. In fact, the ultimate gag is that Mr. Garrison and Richard Dawkins so strongly reflect each other’s narcissistic zealotry that when fused in some horrible bout of filthy monkey sex, the greater Garrison-Dawkins achieves world domination. Cartman must sabotage their relationship to save the world from a dystopic future of warring factions of religiously-atheist zealots. Richard Dawkins on “Go God Go:”
…and, that’s why I’m #1 on Google for “Richard Dawkins Idiot.” South Park, as usual, is the funniest, most relevant, and insightful. Family Guy Oh ha ha! The evolution-creationism debate is relevant! So it’s funny! Get it, religious people are stupid and Americans are stupid! Jesus was a pretty cool dude, though. I’d smoke a bowl with Jesus. Oh dude! Did you finish your comm 200 paper for tomorrow? Dude, it’s already like, 2am. Family Guy: non sequitur, every episode, nothing of lasting substance Simpsons No statement, just the animators amusing themselves by paying homage to an old film cliche in The Simpsons’ artistic style. By this season, the message is: we’ve become a cultural icon on the merits of our past work, but we’ve long since sold out, so just let us this one guilty pleasure before we’re reduced to grinding out this week’s episode, OK? For old-time’s sake. Simpsons: A small gasp of creativity from the genre-making giant too huge to die without a stinking, bloated corpse. |
| File under: Duh [genomeboy.com] Posted: 04 Jun 2008 08:55 PM CDT Although the price tag for genetic studies is dropping, clinicians’ expertise remains expensive, and that worries Brunner. "Certainly with the amount of money people are spending genotyping thousands of patients, they are finding that the quality of the phenotype data is crucial," Brunner says. That’s why, he says, a ‘phenome project’ is needed to investigate connections between phenotypes. The idea has been proposed before but stalled for lack of funding. |
| Your tax dollars at work [genomeboy.com] Posted: 04 Jun 2008 08:55 PM CDT
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