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Finding the mechanism through clever sleuthing.
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How do you isolate new cellulolytic genes from microbes in a cow rumen? Easy, poke a hole in the side of the cow (a fistula), throw in some bags of grass, pull out grass later and isolate bugs breaking down the grass. A great example of old-time microbiology and new-fangled metagenomic.
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Educators, hobbyists, entrepreneurs, investigators – which are you? [Meant to bookmark this long ago.]
links for 2011-02-04
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The world is spiky. And science is a northern endeavor.
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"A row has broken out in France over whether 15- and 16-year-olds should be allowed to create transgenic Escherichia coli bacteria in the classroom."
links for 2011-01-28
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Live imaging is the foochur.
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"There are several canards about scientists, but one is more pernicious simply because so many scientists themselves repeat it: scientists are not good communicators."
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“Our cognitive incapacity to perceive large-scale and long-term changes is a major obstacle to rational environmental policies,”
Finn wins prestigious award.
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"Berg too says he expects more routes to be uncovered. "The diversity of life is bigger than we know now," he says. The research may also offer evolutionary insight. In analysing the enzymes that propel the methylaspartate cycle, the authors found striking similarities to enzymes identified in ancient bacteria, an indication that H. marismortui grabbed the genes needed for the cycle by lateral gene transfer."
Cool in so many ways.
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"About 500,000–750,000 years before the extinction event, magma swelled up underground and hit a layer of coal."
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Incisive commentary on earlier Nature article on scientists, blogs, and tweets.
links for 2011-01-27
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"Tasty Labs wants to create a marketplace or forum in which people can state their needs and available talents."
Are scientists afraid of blogs and tweets?
Nature has a nice wee article (no subscription required to read this one, FTW!) on the state of what one might call “informal” peer review – the challenges and questions to published works that come from blogs and tweets and the like.
For those of us who have been talking about the changes needed in the whole infrastructure and culture of science discourse (particularly the lock publishers have on research papers), this Nature article holds no surprises. Indeed, it comes off making some scientists seem a bit whiny.
The article points to some recent events where scientists have been skewered online for papers or claims made. This reminds me of the early days of blogging when folks were trying hard to control the message and were freaking out when anyone said anything.
The paper does have some great examples and quotes though. For example, David Goldstein, from Duke’s Center for Human Genome Variation, is quoted saying, “if the work is solid, it hold up over time”. And the efforts by PLoS with comments on papers, how arXiv.org works, and ratings from F1000 are good to show to those who are probably reading the article to figure out how to survive the blogosphere.
My favorite comment by the author, though, is:
One solution may lie in new ways of capturing, organizing and measuring all these scattered inputs, so that they end up making a coherent contribution to science instead of just fading back into the blogosphere.
I’ve been harping on this for a while and still think there’s an opportunity to create a solution like this. I think there is a lot of good thinking, plenty of examples in other industries, and folks are doing parts of this solution, such as trying to think of other ways to change how we calculate the impact of a paper (à la Technorati or through real-time stats), author ID systems, or ways to turn the science paper into the social object. The article also mentions Jason Priem’s work on alternate paper metrics (alt-metrics).
It feels like 2004 all over again as another industry discovers the power of devolving the power back to the masses. And the Web was initially designed by scientists, for scientist – what’s there to fear?
UPDATE 28jan11: Related to this topic, Zachary Knight has an incisive commentary on how all this was protrayed.
Image from Mike Babcock
Human microbial ecology – cool study
I mentioned a few weeks back a review in Nature about a trio of scientists studying the contributions of gut microbial ecology in preemies that get necrotizing enterocolitis (NEC). Sneaky, sneaky, it turns out that a paper on this work was posted that the review didn't mention or link to. I subsequently found a great article out of the UC Berkeley media relations team that is an even better review of the work, with some excellent quotes from the investigators themselves.
Link: Scientists sequence gut microbes of premature infant
It's a fascinating story. The microbes in preemie feces were collected daily and either sequenced completely or identified by 16S rRNA sequences. The investigators were then able to visualize a time course of the abundance of different microbes (image to upper-right) and to start to understand the contributions of these microbes to pathology, particularly NEC.
It's cool to see the shifts in population as the gut microbes settle in. Interestingly (and not surprising), there were some microbes that are known to be pathogenic, but didn't really affect the preemie's health.
The thought, though, is that there might be some strain specificity within microbe species, or something related to the balance of all the other bacteria. This seems to correlate well with the findings from folks studying the contribution of gut microbes to immune system development.
If you're into developments in human microbial ecology (which I highly recommend new grad students study), I urge you to read this paper (here's the link from the article linked above) and the back story in the article linked above.
What do you think of this?
Image from the paper showing a time course of the gut microbial species
links for 2011-01-23
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"Scientists have for the first time sequenced and reconstructed the genomes of most of the microbes in the gut of a premature newborn and documented how the microbe populations changed over time."
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"Blogs and tweets are ripping papers apart within days of publication, leaving researchers unsure how to react."
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Nice examples. Cool analysis. Must read for visu-heads.
links for 2011-01-22
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from the makers of HEXBUGs
Doing stand-up at IgniteAmherst Feb 8th
Just a note that I'll be doing a 5-minute stand-up act at IngiteAmherst at the Eric Carle Museum of Picture Book Art (125 West Bay Road, Amherst, MA).
Link: IngiteAmherst: Making stuff
Our theme is "Making Stuff". Our valley is steeped in a rich history of making stuff, from the straw hat industry of Amherst to Holyoke and Springfield and Northampton. That tradition continues and we'll hear thought-provoking Ignites from folks Making Stuff in our valley.
There'll be folks talking about Fish, Games, Museums, and Biz. I'll be on hand to give a whirlwind tour of DIYBio (working title "The past, present, and future of making stuff through biology").
My plan (working on talk today) will be about all the ways we use biology to make stuff, starting with practical microbiology (of course), then making the leap to synthetic biology, and then spending some time showing examples of all the cool things happening among DIYbio folks. Of course, the emphasis will be on all the "making". And, I'm sure as I develop the outline, I'll start winnowing away the extra and find that one thing I am excited to focus on.
Let's see what actually turns out. The talks will be pecha kucha – 20 slides automatically flipping in 5 minutes – which I've never done before. Thankfully, I do NOT think 5 minutes is too short to share something that excites me.
Looking forward to a great evening!