Category: Misc.

Underselling Genomics Award #1: David Whitworth for "Genomes and Knowledge: A questionable relationship"

I do not normally write too much here about non Open Access publications but this one is so good I had to. Everyone with access to Trends in Microbiology should check out Julian Parkhill‘s rebuttal to an article written by David Whitworth in the same issue. Whitworth’s article is “Genomes and knowledge – a questionable relationship? ” and it is in my opinion, filled with some unsuppoerted and over the top statements. In essence, he is arguing that we should stop genome sequencing because there are a bunch of genomes out there already and after all, all that matters is work on model organisms so if you have enough genomes related to your model organism you should move on. Alas I do not have time to detail them here. But fortunately, Parkhill does a great job of responding in his article Time to remove the model organism blinkers. The end of his article reflects how I feel too:

In the end, when faced with the astonishing diversity of microorganisms, if all we manage to do is to describe a few random organisms in painstaking detail, then we will have failed to understand microbiology. To suggest we curtail the remit of microbial genomics is bad enough; to suggest it now, when we are on the brink of finally being able to truly study genomic diversity, is absurd.

So sure, sometimes we in genomics oversell the benefits of genome sequence data (and in fact, I give out a little award here for those people). But Whitworth is at the other end of the spectrum, wearing, as Parkhill states “blinkers” to the benefits of genome sequence data. As a reflection of how much I disagree with most of Whitworth’s implications, I am giving him my first “Underselling Genomics Award”.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Outdoor art at the Farmer’s Market







Love the outdoor art in the renovated Gardens in Central Park in Davis …



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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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DNA Dynasty "Company" – Stealing and Lying

Well, just adding my two cents to the pissed off blogosphere regarding a company in Singapore called DNA Dynasty.  Not only are they purveying complete crap in terms of genetics/genomics (e.g., they say they have a genetic test to determine the innate abilities of your children) but they have apparently stolen the logo of the DNA Network of which I am a member.  Lovely.  I figure, if we make enough blogging noise, then when people search for them with google they will at least also see some of our postings.  So here is mine.  See also

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Metagenomics 2008 Meeting Notes

I am going to post notes here for the Metagenomics 2008 meeting.

#1 – most everyone here seems really happy about the election
#2 – mooched a ride this morning to the conference site from some of the folks who run “The Seed” and related annotation and analysis servers.  I have written about them before but people really should check them out if you are interested in microbial genome analysis. 
#3 – Alex Worden is talking now about picoeukaryotes.  Alex does some of the coolest environmental microbiology out there and just happens to focus on groups of organisms that are frequently ignored.  She just said a key quote “Physiology is not a bulk or an average property” basically saying what I say which is that an environment is not simply a bag of genes.  That is we need to remember that there are real compartments in communities.  Alex just showed an interesting figure on rRNA sampling of uncultured eukaryotes from the Sargasso See (Not et al. EM 2007).   Another key point she has made is that microbial eukaryotes are barely sampled in terms of genomics
#4 – a ridiculously short break (the organizers of this meeting really really need to change the scheduling to have more time to talk to people in breaks).  
#5 – Oded Beja is talking now.  He is really one of the key people behind the entire metagenomics revolution as he was the lead on many of the papers from the Delong Lab onthe discovery of proteorhodopsin
#6 – Shannon Williamson is showing an incredibly cool contraption that she uses to take water samples and size fractionate them in the bottom of the ocean.  It is basically a series of filter systems that works on a platform that is run by a deep sea submersible … this allows them to sample large volumes of water in the deep sea (larger volumes than they could bring back up to the surface)
#7 – a little note — already many talks referring to using IMG, IMG/M and MG-RAST tools to help with annotation and analysis of genomes and metagenomes.  Clearly there is enormous demand for getting ones data analyzed by some public or semi-public tools …
#8 – Yuri Gorby — gave a talk about nanowires which are basically little mini cables that cells use to connect to other cells and shuttle electrons around.  This stuff is beyond cool — it is completely fascinating.
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Metagenomics Meeting — Competing with the Election

Well, I apologize but I am not going to post anything today about the metagenomics meeting in San Diego since I came late today as I wanted to be at home for the beginning of the election. But I made my way down to San Diego and made it to dinner. The dinner “entertainment” was a talk by one of the grand gurus of ocean microbiology – Steven Giovannoni. Alas, even he realized that he was competing with people wanting to know about the election and I confess I spent most of his talk hitting reload on my phone and surfing between sites. But So I have no notes to post about his talk. But I can say that I am happy about the election. And tomorrow I will try to post some notes about talks. But I may be still too happy to take notes …

((Note added later — in retrospect, I (and others I talked to) felt Steve G’s talk had way way too much detail for an after dinner talk so I spent the next day taking out much of the detail from my talk to lighten it up. What did this get me? After my talk and later after drinks Steve G. made it clear he thought it stunk because it was too light on details of something he thought should have been in it. Oh well, I guess this goes to show you cannot make everyone happy.)).

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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More about How I feel – from my iPhone

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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How I feel – drawn on my iPhone

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Charles Darwin Reiterates Endorsement of Obama

Charles Darwin has again spoken from the grave. In February I reported how Darwin endorsed Obama in the primary against Hilary Clinton (The Tree of Life: Charles Darwin Endorses Obama as the “Natural Selection”) (note – his candidacy took off immediately after the 2/5 endorsement). And Darwin is getting in his own November surprise for the election tomorrow. Darwin spoke through a variety of media (I am using this term in reference to the plural of medium – people who speak to the dead .. but I am not sure whether media or mediums is the plural) and said

“This one is such a complete no brainer. Obama is so far and away the fitter candidate. Plus if Palin and McCain do not believe in my greatest work, well they can …” (we cannot print the rest)

So there it is. Of course, most living well known scientists who have made public statements also endorse Obama, but getting Darwin’s support is an extra feather in his cap.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Conflict between religion and evolution? Not according to the Papal Conference on Evolution …

Not to beat a dead horse here, but some people out there still think there is a absolute conflict between religious beliefs and believing that evolution occurs.  And if you still think that, you might want to check out the schedule for the Vatican Conference on Evolution (and related topics) that is going on right now (see here for the PDF and here for an outline).  
Held at the Vatican from Oct 31 – Nov 4 and sponsored by the Pontifical Academy of Sciences is a conference on “Scientific Insights into the Evolution of the Universe and of Life.”  Among the speakers: Takashi Gojobori, Werner Arber, H.Em. Cardinal Christoph Schönborn, Martin Rees, Stephen Hawking, David Baltimore, Luca Cavalli-Sforza, Christian de Duve, Francis Collins (who is the only one of the speakers with God in the title of his talk) and Maxine Singer.  Sounds like a pretty good conference and I really wish I had been invited.  But suffice it to say that (1) the Pope has strong religious beliefs and (2) that the Pope and the Vatican are enthusiastic about evolution as a science.  
Too bad one of our VP candidates seems still stuck on the notion that we need to teach “the controversy” about evolution.  Just what controversy is that?
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Genome Technology Runs the Table on Open Access …

Wow.  Again, wow.  Genome Technology Magazine has dedicated in essence an entire issue to Open Access and they have a whole series on interesting things to say about it.  In addition they are making the issue available under a Creative Commons License so everyone can check it out.  Among the articles are:

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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