OK, I am getting worried.
As I wrote a few weeks ago, there is a new movie coming out supposedly next year called "The Tree of Life" starring Brad Pitt, Sean Penn and others. Well, the movie sounds like it could be good. But though this may sound like a cool thing to those of you out there who study the Tree of Life in some way, we are at risk here.
There will soon be 100s of blogs, web pages, news stories, etc. writing about the Tree of Life movie. And uses of the Tree of Life by evolutionary biologists will lose their google rankings. The term "The Tree of Life" is at risk of a form of extinction.
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About Jonathan
I am an evolutionary biologist and a Professor at the University of California, Davis.
My research focuses on the origin of novelty (how
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Well, you know microbes must really be cool because Olivia Judson is blogging about them. You see, Olivia is also known as Dr. Tatiana. Judson's book "Dr. Tatiana's Sex Advice to All Creation" created and still creates a stir and helped make Olivia one of the go to people for discussions of the biology of sex and weird sex practices in the natural world. Now she has a blog (with what appear to be entries once a week) on the New York Times web site called "The Wild Side."
Normally, everything I write about here is at least indirectly connected to science in some way. However, today I am drifting into the world of music. The New York Times had an article a few days ago about Trent Reznor (Trent Reznor’s Frustration and Fury - Take It. It’s Free). Trent, the brains behind the band Nine Inch Nails (full disclosure - I am a fan of his music), has been railing against the constraints of the music industry for year.
And now he is going even further and in essence putting his music into the public domain as much as possible (see his web site NIN.com for more detail). For example
And now he is going even further and in essence putting his music into the public domain as much as possible (see his web site NIN.com for more detail). For example
Well, I have previously started an "Open Evolution" series here and now I am starting an "Open Metagenomics" series. I know, I have gotten grief from some out there (yes, you Rob Edwards - see comments here) about my support for somewhat non-open things in metagenomics, so I am going to try and make up for that as much as possible.
In the first installment, I am pointing people to a new paper on PLoS Genetics "Trends in Selenium Utilization in Marine Microbial World Revealed through the Analysis of the Global Ocean Sampling (GOS) Project" by Yan Zhang, Vadim N. Gladyshev (hat tip to Katie Pollard for pointing out this paper).
In the first installment, I am pointing people to a new paper on PLoS Genetics "Trends in Selenium Utilization in Marine Microbial World Revealed through the Analysis of the Global Ocean Sampling (GOS) Project" by Yan Zhang, Vadim N. Gladyshev (hat tip to Katie Pollard for pointing out this paper).
In this paper the authors study selenium utilization using data from the first part of the Venter Global Ocean Survey (GOS) which was metagneomic sequencing from multiple samples - mostly surface ocean water. The GOS data they use comes from the Rusch et al. paper in PLoS Biology (note for full disclosure ... I was a co-author on this paper.)
A fascinating story in the New York Times today on kin recognition in plants (see Plants Found to Show Preferences for Their Relatives ).
They report
They report
Sorry - just had to make up that little title because I had a funny conversaiton with someone where I was trying to say, concisely, that Ryan Gregory, who has a nice blog called Genomicron, had blogged about how Science Magazine had written an article where they referenced my blog about "Genomics by Press Release."
But I was tired and it did not come out so well when I said "A science blogger wrote about science blogging and how Science wrote about my blog".
But I was tired and it did not come out so well when I said "A science blogger wrote about science blogging and how Science wrote about my blog".
Now - I confess I was really impressed with how ASM handled this enormous meeting I was just at. If you are going to have a big meeting, ASM does a smashing job. And I can see how such big meetings can have their appeal - the diversity of work and activities relating to Microbiology are amazing. However, big meetings are still not my cup of tea.
So here is my top 10 list of "You know the conference you are at is too big when ..." and all are based on experiences from this meeting.
Well, I just gave my talk on phylogenomic and functional predictions and am going to try and catch up with blogging.
In my talk I discussed how an understanding of function and prediction of function requires an understanding of how functions have evolved. I am trying to get my talk slides posted here but, alas, I need to deal with some Copyright issues first (OK - here is a little slideshow of my talk ... no audio sorry)
Patricia Babbitt gave a talk after mine on another aspect of phylogenomics and functional predictions. She has done some really interesting studies (see her lab site here) of functional diversifications and the molecular level by integrating genomic, structural, biochemical and phylogenetic analyses. She showed some really nice tools for clustering and visualization protein families that, although not phylogenetic, seemed to be very useful for the onslaught of genome data. Unfortunately, most of her publications are not in OA journals so I cannot use any of the figures here and am not going to bother linking to the papers.
Nice blog today on mutualisms by Olivia Judson who writes the Wild Side blog/column for the New York Times (I seem to be writing a lot about writers for the NY Times these days ... not sure what is going on with that).
Well, today is the day. The day after the new NIH mandate on Open Access (also see here for more information) to publications has begun. I think this is a great great day for science. And for society and Congress should be commended for doing something that is good for the country and the world that may have upset some of their big donors (i.e., the publishing industry).
And I think we all owe a big round of thanks to those who worked towards this goal.
And I think we all owe a big round of thanks to those who worked towards this goal.
