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).
Author: Jonathan Eisen
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
- 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
- The Tree of Life: NASA arsenic story – let’s lay off the personal …
- The Tree of Life: Arsenic revisited: discussing arsenic story with …
- Twitter / Jonathan Eisen: It’s not an arsenic-based …
- A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus
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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:
- 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
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 ReligionScientists 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
- 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
- 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).
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
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.”
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
———————–
Some additional names coming from out there in the internets (with some links to example articles):
- David Biello (self-recommended)
- Lizzie Buchen (recommended by Brendan Maher and endorsed by David Dobbs)
- Ewen Calloway (recommended by Brendan Maher)
- Paul Voosen (self-recommended)
- 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.
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.



