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| Final report on pharmacogenomics [ScienceRoll] Posted: 22 Jun 2008 04:13 PM CDT If we have evidence-based web 2.0, we need evidence-based pharmacogenomics as well. That is why I try to create a database of real clinical implications. The final report on pharmacogenomics released by US Advisory Committee is a must-read for medical professionals. Some excerpts:
Further reading:         |
| So you want to get a job in biology [adaptivecomplexity's column] Posted: 22 Jun 2008 03:25 PM CDT What does it take to get a job in science, and what role do universities play? There has been some discussion of these issues in the blogging community lately (here, here, and my thoughts are here). Being on the inside, it doesn't seem that complicated to me, but to someone considering a career in science, choosing a college, or just starting college, it can seem very confusing. On occasion I supervise undergraduate summer students, and from their questions, it's clear students aren't so sure about what job opportunities there are in science, and what educational pathways are involved in getting those jobs. |
| Blogging Back from Boston [Tomorrow's Table] Posted: 22 Jun 2008 03:15 PM CDT I spent the last two days at the Center for Cancer Systems Biology then at a meeting at Center Director Marc Vidal's beach house with his coPIs Joe Ecker, Pascal Braun and David Hill and their staff and scientific advisory board members (Rod Wing, Fritz Roth and Mike Snyder) to learn how to create REALLY LARGE datasets of interacting proteins. The Vidal lab makes these kinds of datasets for yeast and human and now, oh happy day, they are going to tackle rice. This kind of data can reveal candidate functions for many new genes. For example if protein x is known to be important for a defense response and it is found to interact with protein y then that implicates protein y in the same defense pathway. This kind of approach was used to create a human "diseasome" as described in a recent NYT Science times article that is being used to predict which proteins are involved in which disease. In rice, we can use this information to identify new forms of genes (alleles) that can help the rice plant resist disease or tolerate stress. You can see some examples of the rice interactome here. We watched slides and discussed the data in the cabin's living room. From my chair I could consider the view of the broad lawn and beyond, a tangle of flowering shrubs and small trees surrounding a steep bank that dropped down to the Gloucester Bay. During a break, we followed Marc down a footpath lined by rose bushes and granite boulders, to a diving platform near a rocky beach. The water below looked clean and inviting. My plan was to dive in and then swim to the spit of land across the bay and back. I quickly changed my mind after diving into the icey water. We took turns hauling each other out over the seaweed-coated rocks. We returned to the cabin for a short discussion and then moved on to barbequed organic chicken, homemade potato salad, cucumber green salad, roasted asparagus and corn on the cob. And wines. Lots of wine. And ice cream- 6 flavors of Haagen Daz and Ben and Jerrys- to choose from and then bread and cheese and then… Oh oh. I just realized my science blog is being overrun by descriptions of Marc and Roseanne's beach house and good cooking. Sorry about that. Back to business here. The previous day I visited Fred Ausubel's lab at the Dept of Molecular Biology, Harvard Medical School where I learned all kinds of neat and efficient ways to infect Arabidopsis with bacterial pathogens and insect pests. The reason for this is not simply to torture the tiny, gentle, leafy, green plants, but to figure out which varieties are resistant to pathogens. Scientists can then take that information to generate new crop varieties. I also gave a talk about our book "Tomorrow's Table". This was the second time that one of my university hosts asked me to talk about the book rather than my research. Either my research talks have gotten really boring or there is a lot of interest in organic farming, genetics and the future of food. A Whole Foods market is located right next door to the lecture hall, just a few steps away. I wished I had though to recruit some shoppers to my talk. Many of them are interested in these kinds of food things. I don't mean to imply that the medical students weren't interested, after all about 50 showed up, but I do wonder if they were more interested in my brief discussion of the enhanced risk of prostate cancer in farmworkers exposed to pesticides than to the discussion of Raoul's organic farm. If you are interested in what I had to say, check out Anna Kushnir' blog post here: Anna is a newly minted Harvard PhD and blogger for Nature Networks. Aside from Jonathan Eisen, whom everyone has met, this is the first time I have met a blogger. On this trip I had the pleasure to meet Rob Paarlberg for lunch. You should check out his excellent book called Starved for Science (with a forward by Norman Borlaug and Jimmy Carter). After lunch we stopped by the Harvard Coop bookstore to sign books at my publishers request. The salesclerk helping us was very nice enthusiastic and said he had 24 books in stock "Right up front". The three of us looked in front, and then on the side aisles and then in the back. I am still not sure if they ever found them. Ah the life of famous authors. |
| Hey Mom, Jimmy's cloning again! [Mary Meets Dolly] Posted: 22 Jun 2008 01:47 PM CDT As I read this blog entry at Discover, I heard my children screaming about a toy. "Mine." "No, its mine." "MINE!" "Mom, Sarah took my toy!" The new fight in cloning is about who owns the patent on cloning dogs:
Hah! If anyone thinks this isn't going to be the case if human therapeutic cloning hits the market, they are crazy. I can hear the press release now:
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| Evolution meeting -- blogs mention genome size presentation. [T Ryan Gregory's column] Posted: 22 Jun 2008 01:11 PM CDT I don't attend the big conferences in my field that often anymore. |
| What to expect when you’re expecting [genomeboy.com] Posted: 22 Jun 2008 09:42 AM CDT "This is just a neat human-interest story about a particular couple using the reproductive capabilities they have," said Mara Kiesling, director of the National Center for Transgender Equality in Washington. "There's really nothing remarkable" about the Beatie pregnancy, she said. |
| Of gruff genomes and meiotic drive [genomeboy.com] Posted: 22 Jun 2008 09:35 AM CDT The gruff DNA of the Yankees had been passed on to him, yet it did not travel well when he took over the Mets, who have no residual ethos. - George Vescey on fired Mets manager Willie Randolph |
| Creationism at home. [T Ryan Gregory's column] Posted: 22 Jun 2008 09:10 AM CDT I received this from my mother this morning. Looks like my home town is having a little event. I live a few hours away, so I won't be present. |
| Massive Moths! (Genomes, Not So Big) [T Ryan Gregory's column] Posted: 22 Jun 2008 08:35 AM CDT Like several other insect orders, the Lepidoptera is staggeringly diverse -- there are about 180,000 described species in the order and an untold number that remain unknown to biologists. (For comparison, there are about 5,000 mammal species). Most people know the Lepidoptera ("leps" to entomologists) as moths and butterflies. The incompleteness of their taxonomic descriptions reflects their sheer diversity rather than academic neglect -- leps have been collected and studied for centuries. As it turns out, the distinction between moths and butterflies probably is not phylogenetically meaningful, as the "butterflies" (which includes three superfamilies: true butterflies, skipper butterflies, and moth-butterflies), though probably monophyletic as a group, may represent a clade nested within the other moths. However, I won't complain if these terms survive as they are useful in non-phylogenetic contexts. |
| How Darwin won the evolution race [The Tree of Life] Posted: 22 Jun 2008 12:45 AM CDT There is a cool article in the Observer today on the "race" between Darwin and Wallace on publishing the theory of natural selection (How Darwin won the evolution race | Science | The Observer). When I read this I cannot help wonder what would have happened if this race had happened today. With publishing and the spread of ideas occurring at a much slower pace in the past, Darwin could afford a bit of time to polish up all the lines of thought and evidence presented in the Origin of Species. It is really his work on building up such evidence that helped convince people of the importance of natural selection. So - if this had happened today - Darwin and Wallace would certainly have been on Science Friday. Lots of bloggers would have written about it. But would Darwin have taken the time to polish up his loose ends or would he have just rushed out his short paper on natural selection and then gotten caught up in the hype and debate? Anyway, the article has some good bits both about the history and about the acceptance (or lack thereof) of evolution and natural selection today. My favorite lines is: Natural selection is simply too important for society to live without it, he (Steven Jones) argues. It is the grammar of the living world and provides biologists with the means to make sense of our planet's myriad plants and animals |
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