The Tree of Life

Worst new omics word award: diseasome (thx @steinsky @noahwilliamgray @mocost )

jonathan.eisen@gmail.com (Jonathan Eisen) — Thu, 16 Jul 2009 15:17:00 +0000

And the winner of the "worst new omics word award" is "diseasome."

Credit for pointing this one out goes to Noah Gray and MoCost on Twitter. See Mos first post here: Twitter / Mo: Diseasome project visualiz ...

And some follow up:

Amazingly, I missed this when the New York Times used it in a headline: "Mapping the Human 'Diseasome' - Interactive Graphic - NYTimes.com" and in many other reports (see Google search here).

What does diseasome actually mean? I do not know. And it does seem really unnecessary to me. And since I got blasted (justifiably) a bit by one of the people I gave my previous award to here is a clarification. I am not commenting here on the science behind the "diseasome" work. Just the word. And the word, I do not like.

Previous awards I have given:

On Friendfeed:

Deep subseafloor microbiology talk at #UCDavis raises questions about the definition of life

jonathan.eisen@gmail.com (Jonathan Eisen) — Tue, 14 Jul 2009 21:36:00 +0000

Wildly interesting talk here at Davis yesterday by Bo Barker Jorgensen Prof. Dr. Bo Barker Jørgensen

He talked about deep subseafloor microbiology and how many/most of the microbes there grow VERY VERY slowly or not at all.

His talk was part of a series here on "Major Issues in Modern Biology Seminar Series" funded by the Tracy and Ruth Storer Lectureship in the Life Sciences endowment

He did a great job of presenting the evidence for and possibly against whether these organisms that live in the deep subseafloor are alive and whether or not they grow really slowly (with doubling times of hundreds of years). He refers to these organisms as the "starving majority" because their main challenge appears to be getting energy.

The way they do much of their work is to take cores (from ships) of the deep subseafloor and to then characterize the microbes in the cores. They have found, for example, high #s of microbes (mostly bacteria and archaea) as far as 1000m down in the cores.

Among the things he discussed were

Paper by Whitman on estimating the number of prokaryotes (his word, not mine) in different places on the planet. This paper suggested most of the prokaryotes are in the subsurface (terrestrial and seafloor)
Paper by him in Science reviewing the starving majority.
Paper by Biddle et al on rRNA surveys of sedimentary subsurface that suggested that most of the microbes were archaea
Paper by Schippers et al (on which Jorgensen is the sr. author) that used qPCR and suggested that most of the microbes were bacteria
Paper by Biddle et al on metagenomics of subsurface microbes
Paper by Lipp et al in 2008 that looked at membrane lipids to estimate the amount of cellular carbon in the deep subsurface.
Various papers that suggest that radioactivity could be the indirect energy source fo these communities (note they are not proposing these are radiation-utilizaing microbes but rather that radiation can lead to the production of H2 which in turn is an energy source).
Various papers that suggest that the archaea found in these environments are phylgoenetically very novel
He did not mention it but he was a cuauthor on a cool PLOS Biology paper on giant bacteria.
At the dinner he discussed briefly one of my favorite topics - nano wires and mentioned one of my favorite scientists - Yury Gorby who is studying these nanowires. Nanowires appear to be mechanisms by which microbes can move electrons around and scanege for electrons

Anyway - the talk gave me lots to think about in terms of slowly growing organisms and how to determine if something was living or not.

Strong Letter of Support for Katehi from group of UC Davis faculty

jonathan.eisen@gmail.com (Jonathan Eisen) — Sat, 11 Jul 2009 20:13:00 +0000

There was a strong letter of support for UC Davis' incoming chancellor Linda Katehi published in the Davis Enterprise yesterday. Alas, the enterprise is not available free online so unless you have a subscription you may not be able to read the whole thing. The letter is written by some big shot faculty on campus:

J. Clark Lagarias, professor of cellular and molecular biology
Walter S. Leal, professor and former chair of the department of entomology
Alan Hastings, professor of environmental science and policy
James R. Carey, professor of entomology
Judith S. Stern, professor of nutrition and internal medicine
Robert Rucker, emeritus professor of nutrition
Tilahun Yilma, professor of pathology, microbiology and immunology
Gabrielle Nevitt, professor of neurobiology, physiology and behavior
Chris Calvert, professor of animal science
Carl Keen, professor of nutrition and internal medicine
Charles H. Langley, professor of genetics
Bruce D. Hammock, distinguished professor of entomology

And in it they say "Katehi’s selection and appointment electrified us"

I agree.

And they also discuss the overblown reports that she may have been involved in some impropriety in admission of students at U. Illinois. I have already written about this here and I agree too. Now I am not saying the news should not report on these stories but I do wish the reports were clearer about how little evidence there is that she did anything untoward. In contrast, there is abundant evidence that she has enormous potential to help out UC Davis in trying times. So I too would like to welcome Katehi as they do.

Help request - how does one block some DNA from being PCR amplified?

jonathan.eisen@gmail.com (Jonathan Eisen) — Sat, 11 Jul 2009 03:30:00 +0000

Dear world:

We need help.

We would like to use PCR amplification of rRNA genes to characterize rare bacteria in a sample where there are some very very dominant bacteria.

The problem is that we do not know what those rare bacteria are and would like to use "universal" rRNA PCR primers to amplify the rRNA genes from these organisms. Such universal primers will also amplify the rRNA genes from the dominant organisms.

If the rare organisms are, like, really rare, almost all the PCR products will be from the dominant organisms. We would like to obtain sequence data for the rRNA genes from the rare organisms without sequencing 1000s of the known rRNA genes from the dominant organism. How can we do this?

I know of attempts to block PCR amplification of specific DNAs and also attempts to digest away PCR products or bind ones to a column to get rid of them. But I do not know if any of these methods really work.

Anyone out there know methods that work to do this?

Added - here are the responses on FriendFeed

The White House - Press Office - President Obama Announces Intent to Nominate Francis Collins as NIH Director

jonathan.eisen@gmail.com (Jonathan Eisen) — Wed, 08 Jul 2009 20:48:00 +0000

The White House - Press Office - President Obama Announces Intent to Nominate Francis Collins as NIH Director

Not much else to say here. Collins is being nominated to run NIH. I personally think Collins will be perfectly capable of running NIH. I have mixed fellings however about whether he is the best pick for the job. What do others think?

Much ado about nothing - sniffing around for scandal with new UC Davis chancellor and not finding any

jonathan.eisen@gmail.com (Jonathan Eisen) — Mon, 06 Jul 2009 02:33:00 +0000

Well, it seems that despite the attempts of California State Senator Leland Yee nobody has found anything of any interest in the background of the incoming chancellor of UC Davis Linda Katehi. The worst that has been dug up so far is an email that she forwarded while provost at U. Illinois that could be interpreted as applying subtle pressure to get a child of a well connected person admitted to the school (see New UC Davis leader denies wrongdoing in inquiries about student in previous job - Sacramento News - Local and Breaking Sacramento News | Sacramento Bee). I guess we will just have to wait and see but I personally really hate corruption and abuse of power and would not want anyone to be the UCD chancellor if they seemed to be part of something untoward. But so far, all I can see if Sen. Yee trying to get publicity for himself by throwing mud and really very little if any of the mud seems to stick. This crusade of his is starting to sound like some of the right wing "holier than thou" crusades of recent times. A bit to vocal when nothing much seems to be there

The end of Science? (Or, the danger of having a video camera at the beach with my brother)

jonathan.eisen@gmail.com (Jonathan Eisen) — Sun, 05 Jul 2009 01:13:00 +0000

Really sick of Bentham Open Spam

jonathan.eisen@gmail.com (Jonathan Eisen) — Wed, 01 Jul 2009 06:46:00 +0000

Once again, I am getting sick of getting email after email from various Bentham Open Journals like the one below. This is basically a form of SPAM as they send these out to people no matter what the connection is to the journals field. I like how they now emphasize that "Please note that submission of a manuscript is not a guarantee for acceptance for publication"

This likely has something to do with the recent controversy over a Bentham Open journal accepting a nonsense paper .

Just goes to show you that just as their are annoying commercial journals and annoying society journals, there certainly are annoying open access journals. And many Bentham journals take the prize for being as annoying as they come. Perhaps not all Bentham journals are like this, but I get spam-like email from dozens of them ... and do not get any from other Open Access journals.

Dr. J.A. Eisen
Institute for Genomic Research Rockville MD 20850
United States

Dear Dr. Eisen,

I am writing to you in my capacity as the Editor-in-Chief of Current Molecular Pharmacology, which is a cutting-edge peer-reviewed journal published by Bentham Science Publishers. Bentham Science publishes more than 300 print and open access journals.

Current Molecular Pharmacology is in its second volume and is indexed by all major indexing media includingChemical Abstracts, EMBASE, Genamics JournalSeek, Scopus, etc. The journal's homepage may be viewed athttp://www.currmolpharm.org

The journal invites contributions for both comprehensive review articles and guest edited issues in all areas of cellular and molecular pharmacology with a major emphasis on the mechanism of action of novel drugs under development, innovative pharmacological technologies, cell signaling, transduction pathway analysis, genomics, proteomics, and metabonomics applications to drug action.

It is a great pleasure to invite you to contribute to Current Molecular Pharmacology. If you wish to submit your work to the journal, then please provide us the title and an abstract (up to 250 words) of your article by email toeditorial@currmolpharm.org You may submit the full article.

Please note that submission of a manuscript is not a guarantee for acceptance for publication, as all manuscripts will be subjected to peer review. Each prospective first-named (corresponding) author will receive a limited number of free reprints and PDF of the paper.

Please could you also refer the journal to your colleagues and other contacts in the field, including your librarian, for promotional purposes. I look forward to hearing from you soon.

Yours sincerely,

Nouri Neamati,
Editor-in-Chief CMP

Here are some comments from FriendFeed

Nature Biotechnology is auditing me?

jonathan.eisen@gmail.com (Jonathan Eisen) — Tue, 30 Jun 2009 20:20:00 +0000

Just got this mail - it says "Important Audit Material Enclosed"

Turns out, it is a subscription notice from Nature Biotechnology (which I get for free).

Annoying, to say the least. I really wanted them to audit me.

Cool open source software of the month - mothur - for microbial ecology

jonathan.eisen@gmail.com (Jonathan Eisen) — Sun, 28 Jun 2009 16:41:00 +0000

Anyone interested in microbial ecology informatics should check out the "mothur" software (Main Page - mothur) from Pat Schloss at U. Mass. Schloss, who has developed a lot of great software tools inlcuding for example dotur and sons, is now developing an open source modular sofwate system for microbial ecology studies. And the name of it is mothur (get the theme?). Here is some more detail about mothur:

This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. As of version 1.2.0 we have incorporated the functionality of dotur, sons, treeclimber, s-libshuff, and unifrac. In addition to improving the flexibility of these algorithms, we have added a number of other features including calculators and visualization tools. If you would like to contribute code to the project feel free to download the source code and make your own improvements. Alternatively, if you have an idea or a need, but lack the programming expertise, let us know and we'll add it to the queue of features we would like to add. Our current goal is to release a new iteration of the project monthly.

Anyway, thanks to my student Amber Hartman for pointing this out --- I will be perusing it but thought others should too. Hopefully, we can include some of the software from my lab such as AMPHORA, STAP, etc. into their code at some point.

Have money, would like to buy entrance to PhD program

jonathan.eisen@gmail.com (Jonathan Eisen) — Sun, 28 Jun 2009 16:10:00 +0000

Got this letter today. Thought I would share, with some specifics removed. I have never seen anything quite like this and I have gotten lots and lots of emails about jobs, positions, students, etc.

Subject: Application for Ph.D. studies

Dear Prof.

Hope for your best. I am working as lecturer, Department of XXXX, XXXX University, XXXX, Pakistan. I have completed my M.Phil (Biotechnology) from XXXX University XXXXX, Pakistan (Thesis title something about microbe interactions with plants). I have recently secured a fully funded scholarship for Ph.D studies (funding agency: Higher Education Commission, Islamabad, Pakistan). This scholarship includes living expenses, university fees and travel expenses etc. I wish to conduct my Ph.D studies at your esteemed university (in any area of biological sciences) . I will highly appreciate if you kindly send me an acceptance letter for Ph,.D studies under your esteemed supervision, so that I can proceed with my paper work with Higher Education commission, Islamabad. Please also find attached herewith my brief CV.

Best regards

XXXXXX

Lecturer

Department of XXXX

XXXX University, XXXX

Pakistan

Here are some comments from FriendFeed

Another reason to publish as Open Access - libraries hurting big time financially and they will be cancelling many subscriptions

jonathan.eisen@gmail.com (Jonathan Eisen) — Sat, 27 Jun 2009 16:11:00 +0000

If you need any more incentive to publish a paper in an Open Access manner if you have a choice - here is one. If you publish in a closed access journal of some kind, it is likely fewer and fewer colleagues will be able to get your paper as libraries are hurting big time and will be canceling a lot of subscriptions. (e.g., see this page from UC Davis system Library Collections: A Forum - About the Libraries - University Library - UC Davis).

From Friendfeed

Who should have acess to publications supported by federal money? Well, everyone. See Federal Research Public Access Act

jonathan.eisen@gmail.com (Jonathan Eisen) — Sat, 27 Jun 2009 16:05:00 +0000

Well, this is good news. Here is some information on the Federal Research Public Access Act S. 1373 introduced by Sen. Lieberman and Sen. Cornyn (information is mostly from this site: Alliance for Taxpayer Access | Federal Research Public Access Act). This is really important as it will expand the accessibility of papers to agencies outside NIH (e.g., NSF are you listening, DOE are you listening). To help with this see Call to action: Tell Congress you support the Federal Research Public Access Act

Every federal agency with an annual extramural research budget of $100 million or more will implement a public access policy that is consistent with and advances the federal purpose of the respective agency. Each agency must:

Require each researcher – funded totally or partially by the agency – to submit an electronic copy of the final manuscript that has been accepted for publication in a peer-reviewed journal.
Ensure that the manuscript is preserved in a stable digital repository maintained by that agency or in another suitable repository that permits free public access, interoperability, and long-term preservation. Agencies have the flexibility to choose the best suitable location for their repository.
Require that free, online access to each taxpayer-funded manuscript be available as soon as possible, and no later than six months after the article has been published in a peer-reviewed journal.

To whom this policy applies:

Any researcher employed by a federal agency with an annual research budget exceeding $100 million who publishes an article based on the work done for the funding agency in a peer-reviewed journal.
Any researcher funded by a federal agency with an annual research budget exceeding $100 million who publishes an article based on the funded research in a peer-reviewed journal.

What is not covered by this legislation:

The public access policy does not apply to laboratory notes, preliminary data analyses, author notes, phone logs, or other information used to produce the final manuscript.
The policy does not apply to classified research. Research that results in works that generate revenue or royalties for the author (such as books), or patentable discoveries are exempt only to the extent necessary to protect copyright or a patent.

Also see below from the Congressional Record (and Hat Tip to Heather Joseph from SPARC for pointing all of this out).

From June 25 Congressional Record: By Mr. LIEBERMAN (for himself and Mr. Cornyn):

S. 1373. A bill to provide for Federal agencies to develop public access policies relating to research conducted by employees of that agency; or from funds administered by that agency to the Committee on Homeland Security and Governmental Affairs

Mr. CORNYN. Mr. President, I rise to introduce the Federal Research Public Access Act. I am very pleased to be joined again by my good friend and colleague, Senator Joe Lieberman, who has remained dedicated to seeing this important legislation passed. This bipartisan bill is the same legislation we introduced in the 109th Congress. The purpose of this legislation is to ensure American taxpayers' dollars are spent wisely, which is even more important now in this time of fiscal tension.

To put things in perspective, the Federal Government spends upwards of $55 billion on investments for basic and applied research every year. There are approximately 11 departments/agencies that are the recipients of these investments, including: the National Institutes of Health, National Science Foundation, NASA, the Department of Energy, the Department of Defense, and the Department of Agriculture. These departments/agencies then distribute the taxpayers' money to fund research which is typically conducted by outside researchers working for universities, health care systems, and other groups.

While this research is undoubtedly necessary and is beneficial to America, it remains the case that not all Americans are capable of experiencing these benefits firsthand. Usually the results of the researchers are published in academic journals. Despite the fact that the research was paid for by Americans' tax dollars, most citizens are unable to attain timely access to the wealth of information that the research provides.

Some Federal agencies, most notably the NIH, have recognized this lack of availability and have proceeded to take positive steps in the right direction by requiring that those articles based on government- funded research be easily accessible to the public in a timely manner. I am proud to report that the NIH's public access policy has been a success over the past few years. By the NIH implementing a groundbreaking public access policy, there has been strong progress in making the NIH's federally funded research available to the public, and has helped to energize this debate.

Although this has surely been an encouraging and important step forward, Senator Lieberman and I believe there is more that can and must be done, as this is just a small part of the research funded by the Federal Government.

With that in mind, Senator Lieberman and I find it necessary to reintroduce the Federal Research Public Access Act that will build on and refine the work done by the NIH and require that the Federal Government's leading underwriters of research adopt meaningful public access policies. Our legislation provides a simple and practical solution to giving the public access to the research it funds.

Our bill will ask all Federal departments and agencies that invest $100 million or more annually in research to develop a public access policy. Our goal is to have the results of all government-funded research to be disseminated and made available to the largest possible audience. By speeding access to this research, we can help promote the advancement of science, accelerate the pace of new discoveries and innovations, and improve the lives and welfare of people at home and abroad.

Each policy that these departments and agencies develop will require that articles resulting from federal funding must be presented in some publicly accessible archive within six months of publication. In doing so, the American taxpayers will have guaranteed access to the latest research, ensuring that they do not have to pay for the same research twice--first to conduct it and then again to view the results.

This simple legislation will provide our government with an opportunity to better leverage our investment in research and in turn ensure a greater return on that investment. All Americans stand to benefit from this bill, including patients diagnosed with a disease who will have the ability to use the Internet to read the latest articles in their entirety concerning their prognosis, students who will be able to find full abundant research as they further their education, or researchers who will have their findings more broadly evaluated which will lead to further discovery and innovation.

While a comprehensive competitiveness agenda is still a work-in- progress, this legislation is good step forward. Providing public access to cutting-edge scientific information is one way we can encourage public interest in these fields and help accelerate the pace of discovery and innovation. In promoting this legislation, I hope to guarantee that students, researchers, and every American can access the published results of the research they funded.

Still hiring - despite budget issues

jonathan.eisen@gmail.com (Jonathan Eisen) — Thu, 25 Jun 2009 15:52:00 +0000

Recently I blogged about issues with the California budget possibly leading to major salary cuts/furloughs at UC campuses. Well, furloughs and salary cuts have been happening all around the country as many schools have had similar issues. But the good news is (1) if you are looking for a staff type position many people will have more money in their grants available since the people on the grants might get paid less and (2) many universities are not doing full faculty hiring freezes.

For example, the Center for Bioinformatics and Computational Biology - at U. Maryland is hiring faculty and post docs. UC Davis is continuing searches for faculty positions that are in progress (and we have some good candidates for people for the Genome Center). In evolution, a good place to look for job positings is Evoldir on the web or on Twitter.

And very shortly I will be posting ads for some bioinformatics related positions in my group - but have not finished writing the ads. Anyway - though the financial condition of many US Universities is less than ideal, those fields with a lot of government grant support seems to be doing OK.

Scientists getting antsy over possible salary reductions/furloughs at University of California

jonathan.eisen@gmail.com (Jonathan Eisen) — Tue, 23 Jun 2009 14:53:00 +0000

Just got this via email - a letter circulating at UC Santa Cruz about the possibility of furloughs/salary reductions at the University of California. Basically the issue is that UC is having some major financial trouble due mostly to getting less money from the state of California (due to California's financial problems). And the UC has circulated a memo saying that they are considering 4-8% pay cuts or furloughs that will reduce salary by 4-8% for ALL UC personnel.

This is a bit off putting to many since some personnel get their money from government grants not from the UC budget, but apparently to try and avoid inequality (which of course already exists) or to avoid hard decisions or for other reasons, UC is planning to have these cuts apply to everyone, even if that does not save UC money. I do find it strange that most of the people who work for/with me will get pay cuts which will lead to having extra $$ in my grants to spend. The extra weird thing is, if I cannot spend the money save from salary reductions, then UC loses money due to getting less indirect costs. I personally accept that the budget is in the toilet right now and UC needs to do some drastic things, but I am not sure if this across the board cut makes sense.

Anyway I thought the letter would be of interest to some.

We in the biomedical research community at the University of California, Santa Cruz are writing to express serious concerns about the salary budget cuts proposed as of 6/17/09. This letter represents the concerns of technicians, graduate students, postdoctoral scholars and fellows, research specialists, and project scientists in the departments of Molecular, Cell and Developmental Biology, Microbiology and Environmental Toxicology, Chemistry, Biomolecular Engineering, and Computer Engineering. We generally fall into the category of “staff”, and thus we understand that any staff salary cuts instituted in the future will affect all of us. However, it is important to understand that nearly all of us are paid by funds that do not come from the state of California, but rather from federal grants awarded by the National Institute of Health, the National Science Foundation, and grants awarded by many other public and private agencies. In many cases, the grant has been awarded to a Principal Investigator, and then is used by the Principal Investigator to pay us for our research work. In other cases, the grants are awarded directly to us to cover the salary necessary for our scientific training. So, as the majority of our salaries are not provided by the California state budget, a mandatory salary cut for our staff will not ease the University budget crisis, while it will indeed make our day-to-day living more difficult. Other effects of a mandatory reduction of our salaries are that: 1) This will actually reduce the amount of money the University receives in indirect costs from grants. 2) This will decrease the amount of income tax we pay to the state of California, further exacerbating the existing budget crisis. 3) The depletion of the funds coming into the University of California due to these salary cuts will make it increasingly difficult for the University to support its employees. 4) Lastly, the salary cut propos al may, in the longer-term, undermine confidence in the University of California system and lead talented people to move to states that are able and willing to support higher education and scientific research.

In summary, we strongly urge that no salary cut be instituted for University of California-affiliated personnel like ourselves whose salary is independent from the California state budget. Below you will find our signatures along with those of our supporting staff and Principal Investigators. Sincerely, The biomedical researchers of the University of California, Santa Cruz

Now this is my kind of meeting

jonathan.eisen@gmail.com (Jonathan Eisen) — Wed, 17 Jun 2009 04:21:00 +0000

Just got to Asilomar conference center for a meeting organized by
CIFAR on integrated microbial diversity

It is my Kind of meeting in every way

1. On the coast
2. Few talks with lots of discussion and free time
3. Really diverse with runs and bacteria and archaea and viruses covered
4 not all about genomics (some meetings I go to are)
5. Did I say it is on the coast?
6 ford Doolittle is supposed to be here . He is one of my science heroes
7. The meeting is VERY small but still seems great
8 My family came (little Kids and wife)
And already felt welcome
9 I do not know many of the people
10 Elio Schaechter of Small Things Considered is giving a special talk

This is such a contrast to the big ASM meeting .. Which was fun in
ways and useful but overwhelming

Looking forward to the week

----------------------------------

Note added after the fact -

Here are my tweets about the meeting (mostly mine) some by Rosie Alegado

rosiealegado Listening to Jonathan Eisen at #CIFAR talk about a genomic encyclopedia for bacteria & archaea. 2 days ago from Tweetie phylogenomics Huge % of talks at #CIFAR make use of Venter Sargasso or GOS metagenomic data 2 days ago from TwitterFon phylogenomics I am next at #CIFAR talking about a phylogeny driven genomic encyclopedia of bacteria and archaea 2 days ago from TwitterFon phylogenomics The one and only WF Doolittle is talking at #CIFAR about Thermotogales and lateral transfer 2 days ago from TwitterFon phylogenomics Rebecca Rundell is talking at #CIFAR about the amazing diversity of "meiofauna" (not big nor tiny) in marine samples 2 days ago from TwitterFon phylogenomics Nicole King at #CIFAR is talking about using choanoflagellate genomics/experiments to study the origins of multicellularity in animals 2 days ago from TwitterFon phylogenomics Barry Leadbetter at #CIFAR is using modelling/microscopy to study how choanoflagellates (single celled animal relatives) move/assemble 2 days ago from TwitterFon nthmost #ff @phylogenomics is live-tweeting some very interesting stuff from #CIFAR (Canadian Institute for Advanced Research): http://bit.ly/Eei6X 2 days ago from TweetDeck phylogenomics Michael Worobey at #CIFAR is telling how phylogenetics of archival samples helps resolve questions about the history of HIV movement 2 days ago from TwitterFon phylogenomics Michael Worobey at #CiFAR just told the story of how the brilliant WD Hamilton died after their trip to Africa to get chimp SIV samples 2 days ago from TwitterFon phylogenomics Michael Worobey who does fantastic "open science" flu work is talking at #CIFAR about HIV and swine flu origins 2 days ago from TwitterFon MicrobeWorld @phylogenomics Is there a site for this #CIFAR event? 2 days ago from web phylogenomics Relman at #CIFAR outlines benefits from microbes in gut: vitamins, digestion, infection protection, developmnt, immune training, etc 2 days ago from TwitterFon phylogenomics David Relman at #CIFAR is talking about humans as an ecological collective with microbes as an extension/component of self 2 days ago from TwitterFon CigarRadio @NetworkCacher Thanks, glad you enjoyed tghe show. #cigars #cifar #dogwatch 3 days ago from TweetDeck domonicmongello RT @phylogenomics Rob Beiko at #CIFAR is talking re: geospatial visualization of microbial diversity - genomics .. http://bit.ly/AYVEJ 3 days ago from twitterfeed aeroculus RT @phylogenomics Rob Beiko at #CIFAR is talking re: geospatial visualization of microbial diversity - genomics ecology geography - GenGIS 3 days ago from web phylogenomics Rob Beiko at #CIFAR is talking re: geospatial visualization of microbial diversity - merging of genomics, ecology and geography - GenGIS 3 days ago from TwitterFon phylogenomics Rebeeca Case is taking at #CIFAR about how marine algae also suffer from bleaching like coral 3 days ago from TwitterFon rosiealegado Listening to Kevin Carpenter #CIFAR. Learned a new word: ectosymbiont. 3 days ago from Tweetie phylogenomics Kevin Carpenter at #CIFAR is talking about and showing aamazing picture of microbes that live in termite and cockroach guts 3 days ago from TwitterFon phylogenomics Jan Janouskovec talking at #CIFAR about alveolate plastids "assessing the evidence" & how # of membranes are useful to know 4 days ago from TwitterFon phylogenomics Adrian Reyes-Prieto at #CIFAR is talking about plastid and chromatophore evolution 4 days ago from TwitterFon pathoadaptation @phylogenomics #CIFAR exactly the kind of meeting I need to get back to going to...must work harder to get out of my government 'hole'. 4 days ago from Tweetie phylogenomics Andrew Roger at #CIFAR is talking about the origin and evolution of mitochondria and related organelles 4 days ago from TwitterFon phylogenomics Joel Dacks at #CIFAR is talking about evolution of eukaryotic membrane traffiicking & how it is about "more than just eating" 4 days ago from TwitterFon JATetro @phylogenomics Will there be a proceedings or at least a review of the meeting? #CIFAR 4 days ago from Seesmic Desktop phylogenomics Tom Cavalier-Smith at #CIFAR is one of the few people who can really mix molecar phylogenetics and function/morphology for microbial euks 4 days ago from TwitterFon phylogenomics Listening to THE Tom Cavalier-Smith talking about eukaryotic evolution at #CIFAR - I don't always agree with him but he still rocks 4 days ago from TwitterFon phylogenomics Yan Boucher at #CIFAR is talking about "the life aquatic - vibrio an their mobile gene pool" - looking at lateral transfer & recombination 4 days ago from TwitterFon matthewherper RT @phylogenomics Alex Worden at #CIFAR communities of microbes are not a black box "physiology is not a bulk or an average property" 4 days ago from web matthewherper RT @phylogenomicsAlex Worden at #CIFAR communities of microbes are not a black box "physiology is not a bulk or an average property" 4 days ago from web phylogenomics Alex Worden at #CIFAR says we cannot treat communities of microbes as a black box "physiology is not a bulk or an average property" 4 days ago from TwitterFon phylogenomics Listening to Andrew Allen talk about phylogenomics, transposins, and gene transfer in diatoms at #CIFAR 4 days ago from TwitterFon phylogenomics Hearing Robert Morris from UW talking about proteomic studies of functions of bacterioplankton in Atlantic ocean at #CIFAR 4 days ago from TwitterFon phylogenomics Hearing Jennifer Foster discuss diatom bacterial symbioses and nitrogen fixation in oceans at #CIFAR microbial diversity meeting

Jonathan Losos wins E O Wilson award

jonathan.eisen@gmail.com (Jonathan Eisen) — Tue, 16 Jun 2009 01:08:00 +0000

Just got this in email

Harvard Biologist Jonathan Losos to Receive 2009 E. O. Wilson Naturalist
Award

The American Society of Naturalists is pleased to announce that Dr.
Jonathan B. Losos of Harvard University has been selected to receive
the 2009 E. O. Wilson Naturalist Award. The award, established in
recognition of Professor Wilson's lifetime contributions to ecology
and evolutionary biology, is given each year to a scholar who has made
significant contributions to the knowledge of a particular ecosystem
or group of organisms.

Dr. Losos is the Monique and Philip Lehner Professor for the Study of
Latin America, and Curator of Herpetology, Museum of Comparative
Zoology, Harvard University. His work with anole lizards in the West
Indies has contributed fundamentally to our understanding of the roles
of natural selection, competition, and niche evolution in shaping
assemblages of Anolis species.

Through the pioneering application of molecular phylogenetics and
comparative methods, he has thoroughly characterized the historical
biogeography and evolutionary radiation of anoles in the Caribbean,
including the roles of historical contingency and reiterated adaptive
evolution. His work on ecomorphology established early on the
relationship between morphology and ecologically relevant aspects of
behavioral performance, providing a foundation for work on
morphological evolution in the group. His experimental work with Tom
Schoener has demonstrated rapid selective impacts of introduced
predators, altered competition, and, by chance, hurricanes on Anolis
populations on tiny islands.

His work culminated this year in the publication of a major book on
the biology and adaptive radiation of the genus Anolis.

As Editor of The American Naturalist from 2002 to 2006, Dr. Losos
encouraged the publication of natural history observations in the
context of major issues in ecology and evolutionary biology.

"His enthusiasm as a colleague and mentor has inspired a generation of
biologists," said Dr. Robert Rickfels, a professor at University of
Missouri-St. Louis and chair of the award committee. "Dr. Losos's work
epitomizes the integration of natural history into scientific
investigation at the highest level."

The E. O. Wilson Naturalist Award was established in 1987, the year of
Professor Wilson's retirement from Harvard University. An appropriate
work of art and an honorarium of $2,000 will be presented to Dr. Losos
at the annual meeting of the American Society of Naturalists in June.

http://www.oeb.harvard.edu/faculty/losos/

Post Doc in quantitative modeling of viral dynamics and evolution

jonathan.eisen@gmail.com (Jonathan Eisen) — Sat, 13 Jun 2009 03:43:00 +0000

A postdoctoral position in quantitative modeling of viral dynamics and evolution is available under the direction of Prof. Joshua Weitz (School of Biology, Georgia Tech). The postdoc will work in an interdisciplinary research group of biologists, physicists, and computer scientists. The postdoc will collaborate on research focusing on bacteriophage dynamics and evolution, at the molecular and ecological scales. Specific project goals will be to develop gene regulatory models of viral exploitation and link intracellular dynamics to long-term changes in viral functional traits at the population scale. The postdoc will also have the opportunity to develop new research projects at the interface of systems biology, theoretical ecology & dynamical systems.

The position will provide competitive salaries and benefits. The postdoc will be based in the School of Biology at Georgia Tech, with a preferred start date of September 2009, though the start date is flexible. The initial appointment will be for one year, with renewal up to three years subject to satisfactory progress and mutual agreement.

REQUIREMENTS: (1) PhD in computational biology, physics, mathematics, microbiology, ecology or related area; (2) Demonstrated research excellence; (3) Strong quantitative skills; (4) Strong oral and written communication skills. Ideal candidates from the biological sciences should have experience with scientific programming. Ideal candidates from the physical/mathematical sciences should have prior exposure to research in the biological sciences. However, outstanding applicants looking to broaden their field of interest will also be considered.

TO APPLY: Applications should be emailed to jsweitz(at)gatech.edu and consist of (1) a cover letter describing your interest in the position, (2) the names and contact information for three references, (3) a curriculum vita (including publications). Applications will be reviewed upon receipt, and continue until the position is filled.

ABOUT THE GROUP: The Weitz group is supported by grants from the Burroughs Wellcome Fund, the James F. McDonnell Foundation, DARPA, and the National Science Foundation. For more information, consult the Weitz group website or contact Joshua Weitz: jsweitz(at)gatech.edu.

More information is available at: http://ecotheory.biology.gatech.edu/

Michael Ashburner or Francis Ford Coppola in the New York Times?

jonathan.eisen@gmail.com (Jonathan Eisen) — Tue, 09 Jun 2009 22:00:00 +0000

Imagine my surprise when I opened the New York Times a few days ago and saw a giant picture of Michael Ashburner the Drosophila genomics guru, open science advocate, and Won for All author. Now, Ashburner is one of my favorite people in all of science (see my posting from a while ago recruiting him top start a blog to which he even responded). I mean, sure, people I know are in the Times everyonce in a while but this was astonishing. Here he was in some sort of fashions of the Times type of section, shirt unbuttoned, lounging in some field.

Alas, closer examination and some google searching found the truth. This is alas not Ashburner, but actually Francis Ford Coppola and his daughter Sofia. But I mean - look at the pics of Ashburner below. It really could have been him. Oh well, maybe next time ...

Archaea get no respect from the New York Times

jonathan.eisen@gmail.com (Jonathan Eisen) — Sat, 06 Jun 2009 02:54:00 +0000

There was kind of funny and certainly interesting article in the New York Times on June 4: Greening the Herds - Trying to Limit Cows' 'Emissions'

The article by Leslie Kaufman discussed how there are attempts in some dairy farms in the US to change the diet of cows to reduce their methane output. The methane is a strong greenhouse gas and in total cows make a surprisingly large global contribution to greenhouse gases. The article states:

Cows have digestive bacteria in their stomachs that cause them to belch methane, the second-most-significant heat-trapping emission associated with global warming after carbon dioxide.

Alas, this is not correct. Yes, bacteria in the cow rumen contribute to the production of methane. But they do not make the methane. The methane is made by archaea (for those not in the know, archaea are a distinct group of organisms relative to bacteria - they resemble bacteria in many ways but are a separate branch on the tree of life). For those of us who study archaea this is a major slight. A diss. A taunt. A sad day. And all those other things. Not sure how we archaea fans will have our revenge but I swear we will. Too bad Carl Zimmer does not think that this is important enough to go on one of his newspaper fact chekcing investigations.

Children's Science Books from NY Times 5/10/09

jonathan.eisen@gmail.com (Jonathan Eisen) — Sat, 30 May 2009 23:35:00 +0000

Better late than never I guess. I missed the NY Times Children's Books section in teh 5/10 Book Review but my mother brought it with her and left it so I am posting a tiny bit about it.

They review/suggest a few books for kids and many of them have a theme related to this blog including:

Two books on Darwin. See "Darwin's Prenup" by Bruce Barcott in which he reviews Charles and Emma: The Darwins' Leap of Faith and Animals Charles Darwin Saw (Explorers (Chronicle Books)) Both sound good.

Three books on the oceans and Jacques-Yves Cousteau. See "Undersea Pioneer" by Lawrence Downes who reviews Manfish: A Story of Jacques Cousteau (which my kids love), The Fantastic Undersea Life of Jacques Cousteau and Down, Down, Down: A Journey to the Bottom of the Sea all of which also sound good.

Art-Science Fusion and Darwin's Face at Davis

jonathan.eisen@gmail.com (Jonathan Eisen) — Wed, 27 May 2009 23:25:00 +0000

ART/SCIENCE FUSION STUDENTS EXHIBIT PHOTOGRAPHY AND A CERAMIC MOSAIC MURAL, THE FACE OF DARWIN

The final student exhibition for "Photography: Bridging Art and Science," a Science and Society Program class taught by Terry Nathan as a part of the Art/Science Fusion series at the University of California, Davis (UC Davis), will be held at the Buehler Alumni and Visitors Center on the University of California, Davis campus beginning June 3 and continuing through July 3. The exhibit features over 50 student photographs exploring the conceptual connections between art and science and the role of art and science on the UC Davis campus. The opening reception, which is free and open to the public, is June 4 from 3-5 p.m.

Also included in the exhibition is a ceramic mosaic mural, The Face of Darwin, created by students and community members in a special Freshman Seminar entitled, “The Face of Darwin: Exploring the Art/Science Borderland”. In recognition of Darwin’s 200^th birthday, students from majors across campus studied Darwin’s life and the observations that led him to propose evolution by natural selection. Darwin’s face is formed by selections from his secret notebooks and the images of those organisms that influenced him most. With a beard of peppered moths, hair of barnacles and a coat of iguanas, finches, orchids and a host of other creatures, this mosaic is a profound learning experience in and of itself. The seminar was led by Diane Ullman and Donna Billick (co-directors of the Art/Science Fusion Program).

(this came in an email to me and am posting here)

Junk mail and trash associated with science

jonathan.eisen@gmail.com (Jonathan Eisen) — Wed, 27 May 2009 08:00:00 +0000

Just got back from the ASM Meeting that was in Philly last week. It was good and bad - and will write more about it soon.

But what I am writing about now relates to an annoying part of the meeting. It seems ASM has sold my name/address to various entities since I have been receiving a significant amount of junk/trash advertising things associated with microbiology. I am sure ASM gets some $$$ out of this, but at what cost to the world? The last thing I want is more trash and there seems to be no way to say no to this.

And on top of it, many science related publications also seem really keen on wrapping themselves in plastic.

In this case I am showing Nature Methods and the ASM Microbe and even the HHMI magazine wrapped in plastic. Bad Nature. Bad ASM. Bad HHMI. Sure there may be reasons for this (e.g., maybe they have an insert), but there must be non plasticy solutions. And fortunately the news from the JDRF has no plastic. Good JDRF. Here's to sciency publications getting a little greener.

Good science education resource: HHMI Cool Science

jonathan.eisen@gmail.com (Jonathan Eisen) — Sun, 24 May 2009 02:31:00 +0000

Just a quick one here. Was reading the HHMI Bulletin and saw a note about this web site they have set up on science education (see Cool Science: Home). It has all sorts of goodies for educators, kids, and others. Some of my favorite things there in looking so far include material from the Genome Consortium for Active Learning (GCAT) and the Biointeractive page. YAGTFH (Yet another good thing from HHMI).

Do not fall for SPAM pretending to be from Elsevier

jonathan.eisen@gmail.com (Jonathan Eisen) — Sat, 16 May 2009 20:19:00 +0000

Just got the email below (with some key parts blotted out). It is clearly (to me) fake (although it is kind of funny in a way given the recent news about Elsevier publishing fake journals). But just in case someone else out there got the same SPAM and did not figure out it was fake, I am posting this message here.

ELSEVIER:
BUILDING INSIGHTS; BREAKING BOUNDARIES
MANUSCRIPTS SUBMISSION

Dear Colleague,

On behalf of all the Editors-in-chief of Elsevier Journals, we wish to Communicate to you that we are currently accepting manuscripts in all Fields of human Endeavour.
All articles published will be peer-reviewed. The following types of papers are considered for publication:

• Original articles in basic and applied research.
•Critical reviews, surveys, opinions, commentaries and essays.

Authors are invited to submit manuscripts reporting recent developments in their fields. Papers submitted will be sorted out and published in any of our numerous journals that best Fits. This is a special publication procedure which published works will be discussed at seminars (organized by Elsevier) at strategic Cities all over the world. Please maximize this opportunity to showcase your research work to the world.

The submitted papers must be written in English and describe original research not published nor currently under review by other journals. Parallel submissions will not be accepted.

Our goal is to inform authors about their paper(s) within one week of receipt. All submitted papers, if relevant to the theme and objectives of the journal, will go through an external peer-review process.

Prospective authors should send their manuscript(s) in Microsoft Word or PDF format to XXXXX and should Include a cover sheet containing corresponding Author(s) name, Paper Title, affiliation, phone, fax number, email address etc.

Kind Regards,

XXXXXXXXX

PS: Pls. show interest by mailing XXXXXX if your Manuscript is not ready but will be ready soon.