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.

Mina Bissell, another of my science heroes, returns to #UCDavis

Well, one of my favorite people Mina Bissell is coming to talk at UC Davis tomorrow "The Microenvironment and the Genome: How Do Tissue Architecture and Extracellular Matrix Inform Breast Cancer Therapy". I first met Mina through my activities in something called the Defense Science Studies Group (DSSG) which I was a member of in 2004-2005.  DSSG was an amazing program that introduced me (and others) to the various science activities going on in the defense, intelligence, security and related agencies of the US Government.  I wish I had had a blog during much of this because it would have been fun to write about it (well, the parts that were not classified of course).  Among the amazing things in that program, I got to meet Mina Bissell who was one of the program advisors.  What an incredible woman.  See her lab page here: Bissell Lab and more about her on Wikipedia Mina Bissell - Wikipedia, the free encyclopedia or here in a New York Times article by Gina Kolata Forty Years' War - Old Ideas Spur New Approaches in Cancer Fight .  Mina became a bit of an advisor to me when I was looking to move to California many years ago and every interaction with her is always rewarding.  So I am really looking forward to her coming to UC Davis tomorrow.  Hopefully I will not screw up like I did the last time she was here (see The Tree of Life: A eureka moment - but not of the good kind).

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:

• Debate over arsenic-based life enters a new chapter by Brian Vastag in the Washington Post
• Critics take aim at NASA 'arsenic life' study - CBC.ca
• NASA arsenic life study faces critics - USA Today
• Concerns Aired About Arsenic-Containing Bacteria - Science Now
• Arsenic-life debate hits a new level - Alan Boyle MSNBC
• Arsenic microbe study spurs scientific debate - SF Chron
• 
  

Blogs:

• Arsenic-based bacteria: Fact or fiction? - New Scientists blog
• Science Publishes “Arsenic is Life” Critiques. Game On - David Dobbs 
• RRResearch: Arseniclife: The formal critiques and the authors - Rosie Redfield
• How #arseniclife changed science. - Carl Zimmer

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

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:

• Search for the hashtag #ASM2011 on twitter. 
• Download the ASM Meeting App. 
• Check out ASM Live
• Search google news for any press releases and reports

Watch this or other real time streams of twitter posts

Follow just my posts about the Meeting:




Read up on some of my past reports from ASM meetings

• Slides and audio from my talk at #ASMGM
• A field guide to the microbes?
• You know the conference you are at is too big when ....
• ASM Phylogenomics Notes
• Yet another reason to avoid big meetings
• Fear and Loathing in Boston for the ASM Meeting

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:

• David Dobbs on the importance of open-source science
• Dewayne-Net Technology Weblog
• Four short links - 17 May 2011 - O'Reilly Radar - Journalist on ...
• Maschmeyer: Open Source Science
• Free Science…
• Links | Not Exactly Rocket Science | Discover Magazine

Unknown vs. Hawking? Seriously? I mean, I'm not looking to Hawking for faith lessons but not looking to Tyson either. #YAFPRBE

Just got this press release by email that pits a new author Scott Tyson against Stephen Hawking in some sort of "religion vs. science" debate.

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

• Extremophiles: from abyssal to terrestrial ecosystems and possibly beyond.
• Temperature and pH optima of extremely halophilic archaea: a mini-review.
• Biodiversity of poly-extremophilic Bacteria: does combining the extremes of high salt, alkaline pH and elevated temperature approach a physico-chemical boundary for life?
• Thermoanaerobacter uzonensis sp. nov., an anaerobic thermophilic bacterium isolated from a hot spring within the Uzon Caldera, Kamchatka, Far East Russia.
• Life at extreme limits: the anaerobic halophilic alkalithermophiles.
• Sporulation genes in members of the low G+C Gram-type-positive phylogenetic branch ( Firmicutes).

Anyway - just wanted to make a little post here to say how much I appreciate him and his contributions. 

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

• NCBI bookshelf (from jewmanchue)

Strange things at #PLoS; a public call to get rid of the constraints of describing author contributions

Well, am working with some others to submit a paper from a DARPA project to PLoS Computational Biology. And yet again, we have to fill out this form regarding author contributions. And yet again, I am baffled by this. PLoS can be so wise in some areas of publishing. But yet remarkably non creative in others. They ask for you to say which authors "Conceived and designed the experiments" which "Performed the experiments" which "Contributed reagents/materials/analysis tools" and which "Analyzed the data" which "Wrote the paper." This has always seemed completely inane to me. First of all, this just does not work for some types of scientific research. Plus it seems so forced and arbitrary.

Why not actually let the authors say who did what in their own words? You can, I note, sort of get around this by badgering the copy editors a bit (e..g, see in my PLoS ONE: Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees where we added some additional categories of "Ideas and discussion" "Built microbial genome database" "Analyzed sequences linked to RecA and RpoB clusters" and "Analysis of distributions of sequences in GOS data."

Even Nature lets the authors use their own words. For example, in my Genomic Encyclopedia paper published with Nature's Creative Commons license for genome papers we wrote:

Compiling a list of reporters who cover #microbiology stories well; suggestions wanted

Well, I got asked recently for examples of reporters who cover microbiology related stories well.  A few examples came to mind.

But before I biased anyone with those I thought I would snoop around the web and see if anyone else had written about this.  And in googling around I discovered something I probably should have known about - the American Society for Microbiology gives out a Microbiology Public Communication Award.  The list of past winners is very helpful. However, the ASM site does not have a lot of detail so I have tried to compile it here:

Year	Recipient	Highlighted story	Publisher
2010	Debora MacKenzie	An End to Flu?	New Scientist
2009	Ken Armstrong, Michael Berens	Culture of Resistance	Seattle Times
2008	Martin Enserink, Leslie Roberts	Combating Malaria	Science Magazine
2007	Kenneth Weiss, Usha McFarling	Altered Oceans	Los Angeles Times
2006	David Baron, Clark Boyd, Katy Clark, Orlando de Guzman	The Forgotten Plague: Malaria	Public Radio International’s “The World”
2005	Leslie Roberts	Polio: The Final Assault?	Science Magazine
2004	Martin Enserink, Dennis Normile	SARS In China	Science Magazine
2003	John Fauber, Mark Johnson	“A New Kind of Killer” and “The Hand of Man”	Milwaukee Journal Sentinel
2002	Jonathon Knight	Meet the Herod Bug	Nature
2001	Janet Ginsburg	Bio Invasion	Business Week
2000	Susan Okie	Science Races to Stem TB’s Threat	The Washington Post
1999	Richard Monastersky	The Rise of Life on Earth	National Geographic
1998	Rachel Nowak, Ian Anderson	Australia’s Giant Lab	New Scientist
1997	Andy Coghlan	Slime City: Where Bugs Build Skyscrapers	New Scientist
1996	David Baro	Living on Earth: Microbial Diversity	National Public Radio

Obviously there are many other great journalists dealing with microbial topics out there. But this is a pretty interest list.  Most of the others I know about I know through their blogs.  Examples of reporters who's microbiology writing I tend to like include:

• Carl Zimmer (seconded by John Logsdon)
• Ed Yong
• Maryn McKenna
• Hannah Waters
• Rita Rubin
• Brandon Keim
• Laurie Garrett

There are also many microbiology bloggers out there who are great.  For now I am focusing on those who do more traditional reporting (e.g., writing for newspapers or magazines).   

So - I am now asking - do people have any other reporters who have done good work on microbiology related topics to recommend out there?  I am certain I am missing a few.

-----------------------
Some additional names coming from out there in the internets (with some links to example articles):

• David Biello (self-recommended)
• Oil spill article
• Lizzie Buchen (recommended by Brendan Maher and endorsed by David Dobbs)
• Microbiology, the New Germ Theory
• Ewen Calloway (recommended by Brendan Maher)
• Paul Voosen (self-recommended)
• http://nyti.ms/b651qh
• http://nyti.ms/f3JY5q
• http://nyti.ms/igZIAP
• Gina Kolatta (suggested by Theresa Britschgi)
• Luke Timmerman (suggested by Mark Minie)

iEVOBIO Call for Lightning Talks #Evolution #InOklahoma

Just got this email and thought I would repost:

------------------------------------
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.

#DavisCA music video from Law Students

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:

• Evolution and Ecology | UC Davis
• Undergraduate Program in Evolution and Ecology
• UC Davis: Center for Population Biology
• Graduate Group in Ecology

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.

Kickstarter project: Xalts Open Source Text to Speech DB & Touch Screen App #autism #disabilities

A quick note here. For those out there who believe in the importance of open source, here is a project of great potential importance: Xalts Open Source Text to Speech Database & Touch Screen App by S David Jacobson — Kickstarter

The goal of the project is to develop "Xalts":

Xalts is a free, open source, picture exchange mode of communication that adds speech to visual language samples. Picture exchange (PECS) uses images to facilitate communication for individuals with expressive language deficits. Xalts is appropriate for those on the autistic spectrum and useful for learning a foreign language or dubbing film. Visual language samples can be comprised of any icons, symbols, photos, text or video. Xalts will associate the sample with whatever spoken definition you assign and then add it to our library. Users can store their vocabularies on a free web based account or download it to a personal device. Best of all you can share your vocabulary with others no matter what device they are using. Xalts’ open structure invites everyone to create, contribute and share. In short, we want to eliminate costs and wildly expand the PECS dictionary. We come at this project as parents, family members and friends of children with disabilities and our objective is to assure that these children have access to free and powerful tools for communication. There are more than 500,000 children in the United States who could benefit from this application, and globally there may be as many 25 million.

Please consider donating or publicizing in some way. I note, this project is partly run by a very good friend Saul Jacobson. He is completely committed to seeing this happen and has a great developer involved. They just need a bit of money to get going.