Category: Misc.

What’s Lurking in Your (Work) Basement

Well, sad as it may be I finally made it into the basement in the building where I have worked for five + years – the Genome and Biomedical Sciences Facility (GBSF) at UC Davis (the Genome Center is in the same building).  There, down in the basement they were having an Open House for the CMGI – the Center for Molecular and Genomic Imaging.  I knew of some of the stuff they did but had never been down to see their facility and their, well, toys.  And it was really cool.

https://picasaweb.google.com/s/c/bin/slideshow.swf

They also had a nice food spread upstairs on the first floor of our building that I discovered later.  The best part of this spread were the animal chocolates and carvings:

Anyway – just a little post here.  Oh, and they do some pretty cool science at the CMGI, including some interesting uses of CT, PET, SPECT, MRI, and more.   You just never know what you will find in the basement …

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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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Crosspost from microBEnet: Where is metagenomic analysis heading? Hopefully in directions suggested in this paper.

Figure 3 from Raes et al. Molecular Systems Biology 7 #473  doi:10.1038/msb.2011.6 

Just a quick post here.  I have been reading this paper: Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data by Jeroen Raes et al. in Molecular Systems Biology.  This integration they try to pull off in the paper is to me where we need to move as a field (i.e., microbial ecology) in order to make full use of metagenomic data.  The paper provides a nice overview of microbial biogeography too.  Definitely worth a read.

Am crossposting this from the microBEnet blog (microBEnet is the site for the microbiology of the built environment network that I am building):

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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.

——–

Microbiology for the public – Science at the Lesher in Walnut Creek Sponsored by DOE-JGI

Well, a month or so ago I asked people for help in planning a talk on microbes to a non sciency crowd.  I got some good suggestions and, well, I think it ended up OK.  The talk I gave was part of the JGI Science @ the Theater series in Walnut Creek.  The topic was “The Deal with Carbon: How the Earth’s Mighty Microbes Respond”  and my job was to introduce microbes to set up talks by Rachel Mackelprang (on permafrost melting) and Berkeley Lab’s Terry Hazen (on microbes and the gulf oil spill).  In the beginning, JGI debuted a short video about the carbon cycle and the Berkeley Lab Carbon Cycle 2.0 initiative, created in collaboration with Illumina Visual in Emeryville.

The best part of the whole thing was meeting John Fowler from KTVU TV.  He was great.  I have a ten minute chat with him before the talks started and he inspired and impressed me with his interest in both science and science communication (see his “Side Effects” blog here and his twitter feed here).  Another good part of this event was I got to meet Terry Hazen.  We have seen each other before at conferences but never really talked.  He is doing some very interesting work on bacteria and oil spills (see the video).  I note, I am not completely convinced by his conclusions regarding microbes being “primed” to degrade/eat the oil that was spilled into the gulf but his work is still fascinating and comprehensive.  I note – it is not just that he does interesting work.  I published a paper a few years ago with his daughter Tracy Hazen on plasmids from marine sediments and I always wanted to meet her dad.

Another good thing about the night was that some of my wife’s family came to the event.  That was inspiring in a way and kind of fun.  I think that was the first time they had seen me give a talk.

Anyway – I hope people like the talk I gave – it was my first real introduction to microbes and molecular studies of microbes to a non science audience.  So forgive me for some of the mistakes in there.

——–
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.

——–

Updated Again: Compilation of articles, news, blogs about the "arsenic bacteria" NASA study

Lots of new stuff on the arsenic-bacteria front.  For those interested I am compiling some of the more useful links here:

News stories:

Blogs:
  • A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus
    • Felisa Wolfe-Simon, 
    • Jodi Switzer Blum, 
    • Thomas R. Kulp, 
    • Gwyneth W. Gordon, 
    • Shelley E. Hoeft,
    • Jennifer Pett-Ridge, 
    • John F. Stolz, 
    • Samuel M. Webb, 
    • Peter K. Weber, 
    • Paul C. W. Davies,
    • Ariel D. Anbar, 
    • and Ronald S. Oremland

      • Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”

        • James B. Cotner and

          •  

        • Edward K. Hall

        Science 27 May 2011: 1201943Published online 27 May 2011

      • Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”

        • Rosemary J. Redfield

        Science 27 May 2011: 1201482Published online 27 May 2011

      • Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”

        • B. Schoepp-Cothenet, 
        • W. Nitschke, 
        • L. M. Barge, 
        • A. Ponce, 
        • M. J. Russell, 
        • and A. I. Tsapin

        Science 27 May 2011: 1201438Published online 27 May 2011

      • Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”

        • István Csabai and

          •  

        • Eörs Szathmáry

        Science 27 May 2011: 1201399Published online 27 May 2011

      • Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”

        • Stefan Oehler

        Science 27 May 2011: 1201381Published online 27 May 2011

      • Editor’s Note

        • Bruce Alberts

        Science 27 May 2011: 1208877Published online 27 May 2011

      • Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”

        • David W. Borhani

        Science 27 May 2011: 1201255Published online 27 May 2011

      • Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”

        • Steven A. Benner

        Science 27 May 2011: 1201304Published online 27 May 2011

      • Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”

        • Patricia L. Foster

        Science 27 May 2011: 1201551Published online 27 May 2011

      • A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus

        • Felisa Wolfe-Simon, 
        • Jodi Switzer Blum, 
        • Thomas R. Kulp, 
        • Gwyneth W. Gordon, 
        • Shelley E. Hoeft,
        • Jennifer Pett-Ridge, 
        • John F. Stolz, 
        • Samuel M. Webb, 
        • Peter K. Weber, 
        • Paul C. W. Davies,
        • Ariel D. Anbar, 
        • and Ronald S. Oremland

        Science 2 December 2010: 1197258Published online 2 December 2010

——–
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.

——–

Some general tips for how to keep up w/ American Society for Microbiology Mtg #ASM2011

https://picasaweb.google.com/s/c/bin/slideshow.swf

Well, I have arrived in New Orleans for the ASM General Meeting 2011.  Some quick notes here about how people might keep up with whats going on:

Watch this or other real time streams of twitter posts

http://widgets.twimg.com/j/2/widget.js
new TWTR.Widget({ version: 2, type: ‘search’, search: ‘#asm2011’, interval: 6000, title: ‘American Society for Microbiology General Meeting 2011’, subject: ‘#ASM2011 Twitter Stream’, width: 250, height: 300, theme: { shell: { background: ‘#8ec1da’, color: ‘#ffffff’ }, tweets: { background: ‘#ffffff’, color: ‘#444444’, links: ‘#1985b5’ } }, features: { scrollbar: true, loop: true, live: true, hashtags: true, timestamp: true, avatars: true, toptweets: true, behavior: ‘default’ } }).render().start();
Follow just my posts about the Meeting:

http://widgets.twimg.com/j/2/widget.js
new TWTR.Widget({ version: 2, type: ‘search’, search: ‘#asm2011 from:phylogenomics’, interval: 6000, title: ”, subject: ‘Jonathan Eisen at ASM2011’, width: 250, height: 300, theme: { shell: { background: ‘#8ec1da’, color: ‘#ffffff’ }, tweets: { background: ‘#ffffff’, color: ‘#444444’, links: ‘#1985b5’ } }, features: { scrollbar: true, loop: true, live: true, hashtags: true, timestamp: true, avatars: true, toptweets: true, behavior: ‘default’ } }).render().start();

Read up on some of my past reports from ASM meetings

——–
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.

——–

Freeing my father’s publications part 5: near completion of PDF collection at Mendeley (h/t @David_Dobbs)

Well, the story continues.  Yesterday marked a major achievement in my goal to free up the scientific publications of my father Howard J. Eisen, who passed away in 1987 when I was in college.  I have been working for the last 3+ years or so on collecting and sharing as much of his scientific work as possible.  I have documented this effort on a page on this blog: Freeing dads pubs.  That page contains links to various details about my effort here.

I have been doing this for many reasons.  And I could detail them all here.  But instead I point you to the amazing story written by David Dobbs that relates to this effort: Free Science, One Paper at a Time | Wired Science | Wired.com.  David is a science writer/blogger/scientist/journalist and about a year ago he was interviewing me for a story that he was working on about Mendeley.  It was good timing as right around then I was trying all sorts of different tools for sharing his publications, from Academia.Edu to web pages and so on.  And I had been looking at Mendeley too.  When Academia.Edu did not pan out, Mr. Gunn suggested in a comment on one of my posts that this might work in Mendeley.  So I set up a Mendeley page for my father which I diddled around with for a bit.  But inspired by the discussions with David I tried to beef up the Mendeley page and try to learn how to use the system.  And I managed to post many of my dad’s papers there and on my blog.  And I ended up telling David about the whole saga of trying to free up my dad’s papers.  David, being an insightful journalist, realized that this saga was a good story and he asked a lot of questions about it.

But then I got caught up in life and the effort to free my dad’s publications slowed down.  That was, until David’s blog post came out: Free Science, One Paper at a Time | Wired Science | Wired.com.  The piece moved me.  It scared me a bit at first, since there are some really personal details in there, but I realized when reading it why he had focused in on this story.  So, with his post out there – for all to read.  I realized, I had to get my shit together and redouble my efforts to free up my father’s publications.  So over the last week or so I have been scavenging around (with some help from people around the web) trying to dig up PDFs of as many of my father’s papers as possible.  Note – I generally would like to obtain these papers without having to pay for them but I am trying to not break any laws either.

I am writing today because I have nearly completed the task of getting PDFs of all of his papers.  And I have discovered that Mendeley is really a great way to share them.  So now on the Howard Eisen Mendeley page almost all of his papers are there for anyone to obtain.  And thanks to the social features of Mendeley, more and more people will see and have access to those papers, thus ensuring that they do not wallow in never never land but continue to have some potential impact on science and society.  Anyway – thanks David, for a wonderful article and for inspiring me to get moving on the “Freeing My Father’s Publications” effort.  And thanks to all the people who have supported me along the way including Linda Avey, Mr. Gunn, David Williams, and more.  It has been a slog but we are getting there.

Afterthought: some additional discussions of David’s story include:

——–
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.

——–

Symposium in Honor of the great Juergen Wiegel: Extremophiles: Key to Bioenergy? UGA 9/19-20

Well, this symposium announcement gets an extra few lines here from me so not just going to twitter:

Extremophiles Symposium. This symposium is in honor of my friend and colleague Juergen Wiegel, a professor at University of Georgia. He is one of my favorite people in all of microbiology: serious about his science, fun to be around, interested in a wide diversity of topics, and all around good guy. He has written some really fascinating and excellent papers including these relatively recent ones

——–
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.

——–

Wanted – OpenAccess figures on introductory molecular and cellular biology topics

Quick post here.  I am looking for OpenAccess figures on introductory topics in molecular and cellular biology like DNA, RNA, proteins, transcription, translation, etc.  I want these for multiple purposes including teaching, blog posts, etc.  Anyone out there know of a database of such things?

UPDATE
Some suggestions from Twitter

——–
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.

——–

iEVOBIO Call for Lightning Talks #Evolution #InOklahoma

Just got this email and thought I would repost:

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The Call for Lightning Talks is now open for the 2011 conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio), athttp://ievobio.org/ocs/index.php/ievobio/2011. See below for instructions.

Lightning talks are short presentations of 5 minutes. They are ideal for drawing the attention of the audience to new developments, tools, and resources, or to subsequent events where more in-depth information can be obtained. Please also see our FAQ for more information ( http://ievobio.org/faq.html#lightning). Lightning talks will be part of the more interactive afternoon program on both conference days.

Submitted talks should be in the area of informatics aimed at advancing research in phylogenetics, evolution, and biodiversity, including new tools, cyberinfrastructure development, large-scale data analysis, and visualization.


Submissions consist of a title and an abstract at most 1 page long.  The abstract should provide an overview of the talk’s subject.  Reviewers will judge whether a submission is within scope of the conference (see above). If applicable, the abstract must also state the license and give the URL where the source code is available so reviewers can verify that the open-source requirement(*) is met.

Review and acceptance of lightning talks will be on a rolling basis.  The deadline for submission is the morning of the first day of the conference (June 21). Note that the number of lightning talk slots is finite, and given the high volume of submissions we experienced for full talks, the Lightning Talks track may fill up early. We cannot accept lightning talks until the open-source requirements are met, and so waiting with that until the deadline risks that the track is full by that time.

We ask all submitters of lightning talks to be willing to also serve as reviewers of such, as described above.

Lightning talks are only 1 of 5 kinds of contributed content that iEvoBio will feature. The other 4 are: 1) Full talks (closed), 2) Challenge entries, 3) Software bazaar demonstrations, and 4) Birds-of- a-Feather gatherings. The Call for Challenge entries remains open (see  http://ievobio.org/challenge.html), and information on the Software Bazaar and Birds-of-a-Feather sessions is forthcoming.

More details about the program and guidelines for contributing content are available at  http://ievobio.org.  You can also find continuous updates on the conference’s Twitter feed athttp://twitter.com/iEvoBio.

iEvoBio is sponsored by the US National Evolutionary Synthesis Center (NESCent) in partnership with the Society of Systematic Biologists (SSB). Additional support has been provided by the Encyclopedia of Life (EOL).

The iEvoBio 2011 Organizing Committee:
Rob Guralnick (University of Colorado at Boulder) (co-Chair)
Cynthia Parr (Encyclopedia of Life) (co-Chair)
Dawn Field (UK National Environmental Research Center)
Mark Holder (University of Kansas)
Hilmar Lapp (NESCent)
Rod Page (University of Glasgow)

(*) iEvoBio and its sponsors are dedicated to promoting the practice and philosophy of Open Source software development (see  http://www.opensource.org/docs/definition.php) and reuse within the research community. For this reason, if a submitted talk concerns a specific software system for use by the research community, that software must be licensed with a recognized Open Source License (see http://www.opensource.org/licenses/), and be available for download, including source code, by a tar/zip file accessed through ftp/http or through a widely used version control system like cvs, Subversion, git, Bazaar, or Mercurial.

——–
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.

——–

UC Davis, home of "Explosive Evolution"

A semi quick one here.  I am writing this in part because it is really a lot of fun to be at UC Davis with all the excellent evolution and ecology stuff going on here.  Some links for those who might be interested in learning more about Evolutionary studies at UC Davis include:

There is more but that is a good start.  Anyway a recent press release from Davis caught my eye in part because I know the people involved and also in part because I was unaware of the details of what they have been working on.  The press release is titled “Explosive Evolution in Pupfish” and discusses some interesting research by a PhD student Chris Martin and his advisor, my colleague Peter Wainwright.  The work was published in Evolution and is entitled: “TROPHIC NOVELTY IS LINKED TO EXCEPTIONAL RATES OF MORPHOLOGICAL DIVERSIFICATION IN TWO ADAPTIVE RADIATIONS OF CYPRINODON PUPFISH” (DOI: 10.1111/j.1558-5646.2011.01294.x).  Alas it is not OpenAccess, but the paper is available on their lab web site here.

The work is a bit out of my arena, and I suppose I could critique the press release a bit, but I won’t right now. As a side note, I should mention I really love pupfish so that also caught my eye, and I have occasionally tried to convince Chris to look at the microbes in pupfish.  
Anyway, rather than bore people with my thoughts, I thought it might be nice to post some comments I got from Chris about the paper.  I got these is a series of emails and though they are a bit out of context, I am just going to post them here: 

Note that the press release is a bit confusing: there are other scale-eating fishes (has evolved at least 14 times independently), but this is the only scale-eating pupfish (and only scale-eater among all 1500 atherinomorphs). 

#2: Pupfish are indeed named after puppy dogs for their playful swimming behavior!

#3: I think the most exciting thing about this system is that it presents the opportunity to study the origins of ecological novelty in a very recent radiation (possibly as young as 8,000 years if we go by geographic dates of the lakes). This study leaves many outstanding questions that I hope to address in my future research.

For example, why does exceptional adaptive radiation occur on these two islands and nowhere else in the Caribbean? Is this due to lack of sampling, is there something unique about these two environments, or is there something unique about the founding populations in these two cases? Both lakes are large, isolated, productive environments with only 1 or 2 other competing fish species and this is surely part of the story. But, there are many other large lakes in the Caribbean, often with very similar fish communities. Further, note that the other competing fish species have not diversified at all: is this due to their time of arrival or is there something special about pupfishes? I’m currently planning to do broader sampling of pupfish populations and lake environments across the Caribbean to address these questions.

Second, what factors actually drive such dramatic rates of morphological diversification? I have just returned from a trip to San Salvador Island where I setup four field enclosures and added juvenile pupfish to estimate a fitness landscape for jaw morphology in this environment. Juveniles were F2 hybrids of the three species raised in the lab here at Davis in order to sample from the full spectrum of phenotypic variation. I will be returning in July to collect this experiment and I do hope my enclosures and some fish survive! This study should provide an estimate of the strength of selection on existing phenotypes as well as potentially unfit intermediate phenotypes.

Finally, why have different sets of resource specialists evolved in very similar environments? In particular, why has a specialized scale-eater failed to evolve in Mexico – there are obviously scales to feed on and the fish densities appear comparable. Scale-eating has evolved independently many times, but why don’t all fish communities contain scale-eating specialists?


Anyway, going to try to write more about Evolutionary studies at UC Davis in the future. I am always amazed at how much interesting work there is here.

——–
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.

——–