Eisen Lab Blog

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

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:

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.

PR Contact: Ginny Grimsley:

Why Hawking Was Wrong
To Discount Life After Death
Award-Winning Physicist Chastises Scientist
For Decrying Religion

Scientists make terrible theologians.

That’s the opinion of physicist and researcher Scott M. Tyson, who thinks colleague Stephen Hawking was wrong to dismiss the concept of life after death. Hawking recently explained in a newspaper interview his belief that there is no God and that humans should therefore seek to live the most valuable lives they can while on Earth.

“I have lived with the prospect of an early death for the last 49 years,” Hawking told The Guardian. “I’m not afraid of death, but I’m in no hurry to die. I have so much I want to do first. I regard the brain as a computer which will stop working when its components fail. There is no heaven or afterlife for broken down computers; that is a fairy story for people afraid of the dark.”

But Tyson believes that Hawking’s comments may serve to do more harm than good for both people of faith and people of science.

“I think that people in general believe that scientists don’t believe in God, and that’s just not true,” said Tyson, author of The Unobservable Universe: A Paradox-Free Framework for Understanding the Universe (www.theunobservableuniverse.com). “History is filled with scientists who were also men of faith, from Copernicus, Galileo, and Newton to Einstein. Now, I do also believe that there are other scientists who would like to prove that God doesn’t exist. These scientists might want to rain on everyone else’s parades with respect to God really, really badly. The problem is that one of the limitations of science is that science simply cannot prove the non-existence of objects and phenomena over the full spectrum of possibilities. So, while scientists may be able to prove in a scientific framework that there is no life after death, they cannot, nor should they even attempt to, prove it in a theological framework, which is the territory of faith. To do so creates unnecessary divisiveness that can serve no beneficial purpose. And that’s the line Dr. Hawking crossed – he essentially discounted the idea in both frameworks, and nothing good could come of that.”

Tyson’s concern is that Hawking’s comments deepen the rift between the scientific and religious communities, erecting hurdles that only diminish the prospects for potential good that science could do for humanity.

“Dr. Hawking is probably one of only a handful of scientists in the world who is a household name,” he added. “In many ways, he’s the captain of the team, he’s the quarterback, so when he speaks, millions of people believe he is speaking for scientists everywhere. That’s part of the weight of his celebrity on the scientific community as a whole. His comments are out of line and further complicate complex issues like stem cell research, in which faith effectively blocks the use of scientific discoveries that could heal people and ease their suffering – a concept not inconsistent with the tenets of most organized religions,” Tyson added. “But science oftentimes becomes blocked politically and socially not because the science contradicts religion, but because the argument is framed in an ‘us versus them’ context. We inadvertently challenge people to either believe in science or to believe in God, at the exclusion of the other. It’s an unreasonable and unnecessary position in which to place anyone.”

What’s worse, according to Tyson, is that people who believe in both science and faith get left out or, worse, placed into the difficult situation of needlessly choosing sides.

“Millions of people practice their faith but then also believe in the veracity of Darwin’s evolution,” he said. “Many in the scientific community view science through their faith, rather than in spite of it. When scientists discount theology in a wholesale fashion, they not only insult the faithful who discount science, but also the faithful who embrace it. It discourages and further polarizes the dialogue between the two disciplines and increases the challenges that science must overcome in its quest to better comprehend the nature of our world for the betterment of society, goals that I and many other scientists will continue to embrace.”

About Scott M. Tyson

Award-winning physicist, engineer, scientist and researcher, Scott M. Tyson graduated from Johns Hopkins University with an engineering degree, and then embarked on a career that included working at IBM’s VLSI Laboratory, Johns Hopkins University’s Applied Physics Laboratory, Sandia National Laboratories and Westinghouse’s Advanced Technology Laboratory. Responsible for the implementation of new microelectronics approaches for space, Tyson also served as an advisor to the Office of the Secretary of Defense on space computing technology development and planning, as well as for congressional delegations to accelerate the advancement of meaningful and effective space electronic solutions.

To interview Scott M. Tyson or request a review copy of The Unobservable Universe contact Ginny Grimsley

Ginny Grimsley
National Print Campaign Manager
News and Experts

Now – mind you – I am not a big fan of the “science is the only way of thinking” crowd and I am sympathetic to a diverse set of view points.  But I do not wear my opinions about this on my sleeve, so to speak.  Regardless of where I stand on some of these discussions, what I cannot stand is bad arguments on any side.  And the arguments in this PR piece are pretty bad I must say.  
For example, the PR states at the beginning “Scientists make terrible theologians.”  Certainly, some do.  But then the PR argues that scientists who discount religion leave out all the scientists who are religious and that that is not fair.  So – I guess scientists who are religious make good theologians while scientists who aren’t religious don’t?  I am lost here on the logic flow.
What really gets me here is the attempt to diss Hawking for misusing his fame as a great scientist but to then use the names of other great scientists who supposedly believed in God.  Which is it?  Is it OK to use fame / notoriety as a great scientist to support a point of view or not?
Another thing that gets me is the attempt to somehow elevate the author of this book into Hawking territory.  Hawking is referred to as a “colleague” of Tyson, like they routinely work together or something.  And Tyson is an award winning physicist.  What awards would that be (look here – I could not find any).  Out of curiosity you might ask – has Hawking actually won any awards?  Well, lets see – Wikipedia lists a few: 
  • 1975 Eddington Medal
  • 1976 Hughes Medal of the Royal Society
  • 1979 Albert Einstein Medal
  • 1981 Franklin Medal
  • 1982 Order of the British Empire (Commander)
  • 1985 Gold Medal of the Royal Astronomical Society
  • 1986 Member of the Pontifical Academy of Sciences
  • 1988 Wolf Prize in Physics
  • 1989 Prince of Asturias Awards in Concord
  • 1989 Companion of Honour
  • 1999 Julius Edgar Lilienfeld Prize of the American Physical Society
  • 2003 Michelson Morley Award of Case Western Reserve University
  • 2006 Copley Medal of the Royal Society
  • 2008 Fonseca Price of the University of Santiago de Compostela
  • 2009 Presidential Medal of Freedom, the highest civilian honour in the United States

Are we really trying to compare the two here?  Colleagues?  Seriously?   Hawking is a brilliant brilliant brilliant man.  Does that mean his thoughts should count for more than other people’s?  I don’t know.  But there is no doubt something he says will get my attention more than something Tyson says.  Doesn’t mean I think Hawking is right about everything.  But you have to give respect where it is due.  And he deserves it.  If Hawking announced that the color red was inherently better than the color blue I would want to know why he thought that.  He has earned that.  Tyson hasn’t really earned much of anything.  Not discounting his ideas per se.  But to try to take down Hawking while elevated himself, that kind of bothers me.  Makes me think that Tyson’s ideas may have trouble standing on their own merit.  If they were solid, he wouldn’t need to start off with an attack.

Again, this post is not about how I feel about religion and science or religion vs. science (I think the science vs. religion debate is unnecessary personally – but that is all I am going to say about it here).

This post is about how I feel about badly thought out arguments and YAFPRBE (Yet another press release by email).  I am sick of publicists sending me these emails.  Especially when they seem fundamentally flawed.

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

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

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:
“D.W. (rRNA analysis, gene families, actin tree, manuscript preparation), P.H. (selection of strains, analysis, manuscript preparation, project coordination), L.G. and D.B. (project management), R.P., B.J.T., E.L., S.G., S.S. (strain curation and growth), K.M., N.N.I., I.J.A., S.D.H., A.P., A.Ly. (annotation, genome analysis), V.K. (CRISPRs, actin), M.W. (whole genome tree), P.D., C.K., A.Z. and M.S. (actin studies), M.N., S.L., J.-F.C., F.C. and E.D. (sequencing), C.H., A.La., M.N. and A.C. (finishing), P.C. (analysis), E.M.R. (manuscript preparation), N.C.K. (selection of strains, annotation, analysis), H.-P.K. (strain selection and growth, DNA preparation, manuscript preparation), J.A.E. (project lead and coordination, analysis, manuscript preparation).”
Which is more useful? I think without a doubt, the constraints by the PLoS system obfuscate what people did. And it is so unnecessary. Here’s a public call for PLoS to get rid of this constraint. (I am sure some at PLoS will give me grief for a public call like this, but hey it is the Public Library of Science right?). It seems completely inconsistent with many other aspects of PLoS publishing. Let the author’s describe what they did in their own words.

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:

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):

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.


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.

#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:

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.