Thursday, October 29, 2009

More on the PLoS Special Collection on the Genomic of Emerging Infectious Diseases

In case people have not seen in. There is a new collection out from PLoS on the Genomics of Emerging Infectious Diseases. The collection, edited by me and Catriona MacCalum, one of the PLoS Biology Editors. It was sponsored by Google.Org who have a growing interest in emerging infectious diseases. Also heavily involved were Carol Featherstone a freelance writer/editor and Maggie Brown the copy editor.

An Editorial by me and Catriona describing the collection is here: PLoS Biology: Genomics of Emerging Infectious Disease: A PLoS Collection

The papers in the collection are listed below. It truly is an amazing collection of papers all on genomics of emerging infectious diseases and all completely open. Take the material from these papers. Reprint it. Reuse us. Mash it up. Use the figures. And most of all, help in the fight against emerging infectious diseases. Thanks to all the authors, all the PLoS folks (especially Catriona) and all the Google.Org people for working on this. And also thanks to Dr. Kiki for handling the interview for the podcast about the series which is available here.

Some more on the series from the web:

Eisen, J., & MacCallum, C. (2009). Genomics of Emerging Infectious Disease: A PLoS Collection PLoS Biology, 7 (10) DOI: 10.1371/journal.pbio.1000224

Genomics Faculty Jobs at the Joint Genome Institute

Just got an email from Eddy Rubin the Director of the Joint Genome Institute (JGI) advertising faculty jobs in genomics at the JGI. Looks like this could be very nice. I have an Adjunct Appointment at JGI and do a lot of work there and am hoping that some great people apply for these jobs ...

Dear JGI User Community,
I would like to bring to you attention an elite early career faculty position presently available at the DOE Joint Genome Institute. The Divisional Fellow position that we are advertising (in Nature and Science, attached) is equivalent to a tenure-track faculty position at a university, and is appropriate for highly-qualified scientists with a Ph.D. or M.D. degree, who have completed post-doctoral training or equivalent experience. We are specifically seeking individuals to direct a genomics-based research program in the study of either plants, microbes, metagenomes or genome informatics. Divisional Fellows are appointed to five-year term, provided with research and salary support and an accelerated path for achieving promotion to Senior Scientist status at the end of this term.

I urge you to contact me directly if you have questions about the position while interested parties should submit CV, summary of research interests, and references to recruiter Bill Cannan:

For more information see:

Personal Medicine Panel Discussion at American River College

Genetics as a Consumer Good: The Personal Side of Medicine, What It Means,
and Who Should Know?
You can obtain a scan of your personal genetic code with just the internet and a credit card—
for as low as $100! Consumer Genomics can be part of your medical care in the 21st century.

• Will this information enable us to take charge of our own health?
• Is it a form of medical “self-malpractice”?
• How will Consumer Genomics affect patient privacy?

Explore these issues with leading experts in the field:

FREE Public Forum at American River College
Date & Time: Saturday, November 7, 2009 * 2:00 – 4:00 PM
Location: ARC Main Theatre * 4700 College Oak Dr. Sacramento
Free Parking in Lot D – Corner of College Oak Dr. & Myrtle Ave.

Speakers Include:
• Andro Hsu Ph.D.: Science and Policy Liaison, 23andMe (a pioneering Direct to Consumer
Genomics Company)
• Lynn Dowling, MA, MBA: Consultant to El Camino Hospital’s Genomic Medicine Institute (one of
the first hospitals to incorporate genetic analysis with traditional medical practice)
• Kelly Ormond, MS CGE: Program Director, Human Genetics and Genetic Counseling MS
Program, Stanford University (one of only four genetic counseling programs in the Western US)

For more information contact the North Valley Biotechnology Center at: (916) 484-8660

Wednesday, October 28, 2009

Job posting: Bodega Marine Reserve Manager #ecology #marine #UCDavis

Reserve Manager, Bodega Marine Reserve, Bodega Bay, California,
University of California - Davis

Principal Museum Scientist - Supervisor
Career position, 50% variable, full benefits
$4,024-$6,841/Mo. (minimum to midpoint of salary range)

For consideration, apply by November 10, 2009. Open until filled.

The Reserve Manager is responsible for all management of the University's Bodega Marine Reserve and coordination and support of all field programs at the site. Facilitates and implements the research, education and public service missions of the Natural Reserve System and supports field programs of the Bodega Marine Laboratory. Reviews proposals, develops policies for use of both terrestrial and marine habitats, supervises staff, administers budgets, and develops management plans. Gives lectures and leads field trips for classes and the public. Develops monitoring programs and databases, initiates invasive species control and re-vegetation programs.

Seeks supplemental funding through grants and contracts. Coordinates with local, state and federal agencies in matters of permits, land management, conservation and land use policies. Represents the Reserve and the University at public meetings, government hearings, and scientific meetings at the local and national level.

Qualifications include:
Background in ecology or related field, experience in land stewardship, skills to make sound scientific decisions while developing Reserve use and management policies, skills to develop and maintain effective working relationships with neighboring landowners, resource agencies, campus departments, administrative offices, and faculty, staff and students, and knowledge of invasive plant species, control methods, and re-vegetation techniques. Supervisory experience, experience at a field station or marine lab and skills in writing, preparing proposals and verbal communication/presentation are preferred.

Application Procedure:
To view the position and to submit an application on-line visit;
Number #03001704

Tuesday, October 27, 2009

Microbes, art, science all rolled into one - yum

A quick one here. Just got sent a link to this site - Microbial Art. It includes work art with microbes from "Dr. Niall Hamilton (New Zealand), Dr. T. Ryan Gregory and his students (Canada), Dr. Jeff Tabor and colleagues (USA), Dr. Ben Wise and his students (USA), Dr. Eshel Ben-Jacob (Israel), and various other contributors."

It has some nice stuff. Definitely worth checking out.

Sunday, October 25, 2009

A field guide to the microbes?

Here is a link to an article in Microbe Magazine (Genomic Analyses Could Lead to “Field Guide to Microbes”) discussing in part a session from last years ASM Meeting on the "1$ Bacterial Genome". The article includes a discussion of my proposal to create a "Field Guide to the Microbes." Also the article has a link to an audio interview of me by the article author Jeffrey Fox.

Audio interview with Jonathan Eisen

The article does not quite capture what I mean by a Field Guide to the Microbes (not the authors fault - my talk did not capture this either). But I will be writing more on this soon. Very soon. Stay tuned. Also here are the slides from that talk, which I posted to slideshare

Also see this talk I gave at the JGI User Meeting where I ended with my call for a Field Guide to the Microbes ...

Thursday, October 22, 2009

Science journals: asking for concision-good, restricting # of refs-bad

Once again, I am being driven crazy by some aspect of scientific publishing. And today it is arbitrary (or silly) restrictions some journals place in the number of references allowed. I have been dealing with this because I have a paper in Press in one such journal (alas not an open access journal, and not my first choice of journals, but the paper will be published under a CC license ...more on this in another post )

Anyway, on top of my own issues, I was reminded of the perils of length/reference restrictions by an email from Jean-Michel Claverie from CNRS. In the email he told me of a situation involving a recent paper in a high profile journal with a name that begins with the letter N. This paper did not cite some highly relevant earlier work of Claverie's in PLoS One and when he wrote to the author to politely point this out, he was told that the reference was basically removed for space reasons. I have seen this happen many times with a variety of journals and the explanation for some lack of reference to relevant work is always something like "oh yes, of course we knew about that, but had to leave it out for space reasons" or "well, you know, they only allow 30 citations, so we had to leave some things out".

Sure, in the past, when printing articles and keeping track of references was difficult, this may have made sense. But a HUGE part of science is giving and getting credit for work. And thus it baffles me why some journals enforce strict restrictions on the number of references allowed. Basically what this says is - it does not matter what type of work you did - it could only possibly have been built up the work of (insert # here) previous studies. This is just wrong in so many ways. One option to solve this would be for these journals to allow expanded reference lists in online material - and for these lists to somehow get picked up by citation indexing systems. But this is something they need to solve. And until then, people should be aware that by publishing in such journals you may indirectly be doing a disservice to the people whose work contributed to your own.

CSI-Miami could be renamed CSI Microbiology

The CSI shows have certainly done a lot for science, from the point of view of getting people to talk about science as it relates to forensics. Sure, much of the science in the show is a bit off kilter, but the show would basically suck if it showed the real science (e.g., things work really quickly in all the shows -- unlike much of science). But if we compare the science in CSI versus in the latest CNN/Fox yelling matches or the latest wife swapping show, CSI rules the day.

And all of the CSI-like shows (which can be viewed as a form of convergent evolution in ways), also have a decent chunk of science here and there (e.g., NCIS). What is most remarkable to me about all of this has been the number of shows with something about microbes. And the latest CSI- Miami is an example of this (see the recap here:CSI: Miami Recap: Bad Seed -

This episode had a mix of DNA based forensics of E. coli infections, as well as a smattering of microbe associated anti-GMO sentiment when an evil biotech company made some GMO corn that was designed to be carrying a cellulytic gene from a Clostridium species but instead some of the corn carried a toxin gene from Clostridium botulinum. And the winner from a microbial point of view was the brief mention of lateral gene transfer that was responsible for the cellulolytic species of Clostridium picking up some genes from the botulism bug.

No the science they showed was not perfect. But when a TV show starts discussing mechanisms of lateral gene transfer - they will get my attention.

Wednesday, October 21, 2009

What a waste in #Davis - a whole election & associated material for one vote

Well, however you feel about the Wildhorse Ranch vote in Davis, this whole election just seems absurd. A whole election just to vote on this one thing? And do they really need a multi-page color sample ballot? So if I could, I would vote to require these "special" elections about rezoning to only happen if there already was another important election going on. Even if the pro-Ranch crown pays for the election, it just seems like a waste ...

Walkscore - software for walkability of communities goes open source

Just got this email (see below) from WalkScore that I thought might be of interest to Davisites. Walk Score is one of several types of "software for civic life" from Frontseat. This systems allows one to evaluate the walkability of a community or address. And now they are looking to release the software for WalkScore at Walkscore.Org as an open source development. And they are trying to get more people involved in this - including asking for what new developments they should make. I have suggested previously that they should incorporate bikability. And if you agree, you should vote for it here.

Dear Jonathan,

You deserve a break. Take a sec to:

Also, we're thrilled to announce our Rockefeller Foundation grant (see below).

— The Front Seat Team

Vote on Walk Score improvements

We just launched — a new website where you can vote on Walk Score improvements. We're also releasing open source code for Walk Score on this site.

Friends with benefits

Can you help us get to 100 fans on Facebook so we can claim a URL for our Facebook page?

Let's create a Facebook group of people who support walkable neighborhoods.

Rockefeller Foundation grant

We're using our new grant from the Rockefeller Foundation to improve Walk Score and make it open source. Sign up on to get notified when the code is available.

Tuesday, October 20, 2009

#OPenAccess Week event at #UCDavis today 10/20: C. Mitchell from California Digital Library

“Take Control of Your Publications with eScholarship”

An Open Access Week Presentation

Catherine Mitchell

Director, CDL Publishing Group

University of California

Tuesday, October 20, 2009

1:00 p.m. – 2:30 p.m.

Shields Library, Second Floor Instruction Room

Friday, October 16, 2009

Want a qick $100,000 for infectious disease research - ask uncle Bill

Just got this email from Uncle Bill Gates
This is a reminder that the deadline for submissions to Round 4 of Grand Challenges Explorations is November 2, 2009, a $100 million initiative to encourage bold and unconventional global health solutions.

Anyone can apply, regardless of prior experience or institutional affiliation. Previous winners include graduate students, entrepreneurs at private companies, and creative thinkers from all fields of research.

Click here to apply now.

Initial grants will be $100,000 each, and projects showing promise will have the opportunity to receive additional funding of up to $1 million. Full descriptions of topics and application instructions are available at:

We look forward to receiving innovative ideas from scientists around the world and from all scientific disciplines. If you don't submit a proposal yourself, we hope you will forward this message to someone else who might be interested.

Thank you for your commitment to solving the world's greatest health challenges.

The topics are:
  • Create New Technologies for Contraception
  • Create New Ways to Induce and Measure Mucosal Immunity
  • Create Low-Cost Diagnostics for Priority Global Health Conditions
  • Create New Ways to Protect Against Infectious Disease

Thursday, October 15, 2009

Worst new omics word award #5: fermentome

I do not have access to the article but the abstract is all I need to give out my fifth "Worst New Omics Word Award"
Fermentation of undigested foods in the colon by its resident bacteria affects not only colonic health (protection against inflammation and tumour formation) but also influences metabolic health. Studying fermentation directly is difficult for lack of access. We hypothesise that the anatomical structure of the colon is suited to act as a fermenting chamber with the gaseous molecules (VOCs) emitted having direct effects on the colonocytes as well as gut neural and metabolic effects. We refer to this complex system as the ‘fermentome’, and further hypothesise that alteration in the ‘fermentome’ through dietary modification will have a direct impact on colonic as well as metabolic health and disease. The VOCs emitted may play a role in bacterial chemical signalling within the colon but importantly could also function as a ‘gas’ biomarker. Measurement of such VOCs through non-invasive methods would have important application as a hypothesis-generating tool with subsequent clinical application.

From an article titled "Colonic fermentation – More than meets the nose" in Medical Hypotheses, Volume 73, Issue 5, Pages 753-756 by R.P. Arasaradnama, M.W. Pharaoh, G.J. Williams, C.U. Nwokolo, K.D. Bardhana, S. Kumar

Not really much to say other than, this one is a stinker.
Hat tip to @steinsky for tweeting to me about this.

Help save viral ecology (or, when a corporate takeover can kill a field of science)

Just got this an interesting email below from a friend and colleague, Eric Wommack at U. Delaware. In the email, Eric discusses how the recent purchase of Whatman by GE Helathcare has apparently wreaked havoc on the field of viral ecology. You see, a key tool in many studies of viruses in the field turns out to be filters with really small pore sizes to collect the viruses. And, alas, apparently, GE Healthcare has decided to end sales of the filters that a lot of viral ecology researchers use and cannot replace.

So a seemingly small decision by GE Healthcare could severely harm viral ecology work. Eric (and others) are encouraging researchers to write to GE Healthcare to ask them to reconsider the discontinuation of these filters. I encourage you to do so. A person to wrote to at GE is listed in the email below

I'm writing in hopes that you can help the viral ecology research field build a grass roots campaign to convince GE Healthcare to reverse its decision to discontinue manufacture of all 0.02 µm Anodisc filters. GE Healthcare recently acquired Whatman the sole manufacturer of these filters. Presently, 0.02 µm Anodiscs are the only means of collecting direct counts of free virus particles by epifluorescence microscopy. All other types of filter membranes with suitably small pore sizes (sub 30 nm) simply do no work. Viral direct counts are a baseline inventory measurement throughout the field and the loss of these filters will effectively shut down all cutting-edge viral ecology research productivity.

The official word from GE Healthcare is that the company will fill existing orders and then discontinue the entire product line as of December. According to an openly honest Whatman tech support worker, who was entirely sympathetic with our plight, this decision is entirely financial. The irony is that the company has an effective monopoly in this niche so those labs who absolutely rely on these filters would find a way to pay whatever is necessary to make the product financially viable. The tech support guy said that Whatman actually manufactures Anodisks, so unless another company steps forward to adopt the technology viral ecology research will grind to a crawl over the next couple of years. I know this scenario sounds dramatic, but I've seen a nearly complete work stoppage on three projects since the Anodisc supply dried up in July.

Please mail the letters to:
Navin Pathirana, Ph.D., CChem
Regional Product Manager
Whatman, Inc.
GE Healthcare Bio-Sciences Corp.*
800 Centennial Avenue***
Building 1*
Piscataway**, NJ 08855 USA***
Here are some PLOS Open Access papers using these filters
Here are some links to papers found in Google Scholar that have used these things:

Wednesday, October 14, 2009

Bay Area Biosystematists: 10/15 w/ undergrads. on their research

Gotta love this - education, evolution, science, all rolled into one ...

Bay Area Biosystematists Meeting: Thursday, 15 October, 2009

at UC Berkeley, 2063 Valley Life Sciences Bldg.

Undergraduate Research in Evolutionary Biology

This will be a first-time-ever-for-BABS panel discussion led by undergraduates, focused on the research experience for undergraduates in evolutionary biology in the Bay Area. Several undergraduate researchers will speak informally about their research, the path they took to get into research, where they hope to go with it in the future, and what their hopes/fears are. Suggestions on how professors and departments could enhance the process will be featured; this should lead to a productive exchange between undergrads and professional researchers, and a chance for us all to examine this vitally important educational process.

Panel discussants include:
Elaine Fok, UCB (Mishler Lab)
Nairi Hartononi, UCB (Baldwin Lab)
Irene Liao, UCB (Specht Lab)
Brian Mahardja, UCD (May Lab)
Norma Pantoja, UCB (O'Grady Lab)

Schedule and venue:
5:30 - social gathering with beverages and informal pizza dinner:
cost ca. $10, to be collected at door, 2063 Valley Life Sciences Bldg.,
UC Berkeley campus.
7:00 - talk followed by discussion, in same room.

Please email reservations to your host, Gordon Bennett, at by Tuesday, Oct 13th

For a map of campus and view of VLSB, use the link below.

All are welcome, members or not. If you want to join the Biosystematists, a venerable yet exceptionally lively group that provides the only inter-institutional seminar/discussion forum addressing evolutionary topics in the Bay Area, sign up for our mailing list at:

Saturday, October 10, 2009

Open Access Week October 19-23, 2009

To broaden awareness and understanding of Open Access — Open Access Week - October 19-23, 2009

Hope everyone is going to do something ....

Adopt a GEBA genome program for education - from the DOE/JGI

The DOE Joint Genome Institute’s Education Program is providing opportunities for colleges and universities across the country to “adopt” bacterial genomes, such as those sequenced as part of the "Genomic Encyclopedia of Bacteria and Archaea" (GEBA project), for analysis. This “Adopt a GEBA Genome” Education Program makes available a selection of recently sequenced genomes for use in undergraduate courses. The organisms ideally provide a unifying thread for concepts across the life sciences curriculum. For example, students can analyze the six open reading frames for a given fragment of DNA, compare the results of various gene calling algorithms, assign function by sequence homology, and use gene ortholog neighborhoods for comparative genomics and annotate biochemical pathways, while learning the underlying biological concepts in a variety of science courses.

For more information, and to apply for the November 2, 2009 deadline, see:

For more on the GEBA project, which I am coordinating, see a video of a talk I gave about it at the JGI User meeting. Slides from that talk are on slideshare here.

Data fro the GEBA project is available at a dedicated IMG site here.

A much much much older talk, from when we just started the project is here:

3rd Annual Western Evolutionary Biology Meeting 12/5/09 at Berkeley

The 3rd Annual Western Evolutionary Biology Meeting will be at UC Berkeley. This is a meeting of the UC Network for Experimental Research on Evolution (NERE), attendees from the UC campuses will be present, other evolutionary biologists, researchers, teachers and writers are encouraged to participate as well.

When: Sat. 5 December FREE registration - deadline, 29 October 2009 Submit Abstracts - deadline 16 October 2009 - or present a poster

Where: On the UCB Campus in VLSB, see website for details NOMINATE: Western Evolutionary Biologist of the Year by 9 Oct. 2009

See website for details. Open to Researchers, Teachers, Writers.

Monday, October 05, 2009

Some tweets of mine with links about #PLoS papers by #Nobel winners

  1. #Nobel winner Blackburn's 2004 #PLoS Biology essay: Reason as Our Guide -
  2. #Nobel winner Greider's re #PLoS Genetics pub on telomeres in Primary and Tumor Cells -
  3. #Nobel winner Szostak has many #PLoSOne pubs
  4. Yippe - another Nobel Prize for work in Tetrahymena - see my #PLoS Biology paper on the genome here -
  5. The Greider Lab | Johns Hopkins Medicine - #Nobel
  6. Blackburn Lab Research -
  7. Szostak Lab: Home Page

Thursday, October 01, 2009

Worst new omics word award: Omnigenomics by (surprisingly) @Genomicron

Well, been taking a break from this award, as I am in over my head with teaching right now. But could not resist this one. Based on a tip from Marcio Pie in Brazil I checked out T. Ryan Gregory's recent posting (Genomicron: Omnigenomics) on his normally excellent Genomicron Blog. And he has clearly been overcome with H1N1 fever or something like that, as he discusses in this new posting, his desire to coin a catchy new omics word to describe his work on comparisons of genome size across species.

And he has chosen, get ready

Proposed neologism: "Omnigenomics"

Etymology: Latin "omnis" (all or everything) + genomics (study of genomes)

Sample usage: "What do you do?" / "Omnigenomics" / "What's that?" / "I study the total amount of DNA in different species of animals, which includes genes and all the other sequences, most of which are non-coding and..."
All I can say, as I did in the comments on his blog, is


And for this full slide down the slippery slope of omics words, T. Ryan Gregory is the recipient of my fourth "Worst New Omics Word Award." Check out previous winners:diseasome, ethomics, and Museomics. (I note if you look through Google results, domain names with omnigenomics in them have been registered previously and then allowed to expire. Those were good deaths. Hope the resurrection is short lived).

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