The Tree of Life

And the winner of 'most nimble new science journal web site' is mBio

2009-11-20T17:42:00.000-08:00

Kudos to mBio the recently announced new open access journal from ASM. I posted a little bit about it a few days ago. There was some back and forth in the comments w/ people involved in the journal and, impressively, they have already modified some sections of the web site to clarify some of the things I and others felt were unclear. A pretty rare thing in the world of journals as far as I know, to make changes quickly. Normally there would be some sort of deliberative, painfully slow, and annoyingly conservative process in response to comments/feedback. Good job Barbara Goldman and ASM. And happy to have ASM moving a bit more towards an Open Access future.

For $&%# sake, Bentham Open Journals, leave me alone

2009-11-19T23:59:00.000-08:00

For crying out loud, I am still getting crappy spammy mail from various "Bentham Open" journals. The most annoying part to me of Bentham Open is that they try to make it seem that anything published in an Open Access journal is better than anything published in a non Open Access journal. While I personally believe publishing in an OA manner is great, lying about the benefits of OA is not a good thing.

For example they ask and answer the following question "WHY PUBLISH IN OPEN ACCESS JOURNALS? " Their answers include:

Your article will obtain more citations.
Your article will be peer-reviewed and published very fast.
Your article can be read by potentially millions of readers, which is incomparable to publishing in a traditional subscription journal.
All published open access articles will receive massive international exposure and as is usually the case for open access publications, articles will also receive high citations.

Yes, that is right, the crappiest, most boring, most idiotic article in an OA journal will receive "massive international exposure" and "high citations."

I know, criticism of Bentham Open may seem biased coming from me, a PLoS insider. So, just in case you were not aware that just about everyone else out there cannot stand them, here are some reading assignments:

And so on.

Wanted - Bad New Omics Words

2009-11-18T12:34:00.001-08:00

Blogger in need of material while taking a little break for medical reasons needs help. Seeking bad new "omics" words to give "Worst New Omics Word Award" to. Junkome from PZ Myers already under consideration. Please post suggestions here.

Previous winners are

Biologists rally to sequence 'neglected' microbes : Nature News

2009-11-18T07:52:00.000-08:00

Nice little story in Nature News about the need to sequence "neglected" microbes.

Biologists rally to sequence 'neglected' microbes : Nature News

Quotes me and a few others. Love the fact that it quotes Steven Giovannoni in support of this notion:

"The broad brush strokes of microbial diversity are not adequately represented in that first thousand," says Stephen Giovannoni, a microbiologist at Oregon State University in Corvallis. "It's absolutely important that we sequence more."

I like this because Steve gave me enormous grief about this project at a conference last year. Though I argued with him and disagreed with him, his critiques helped guide much of our work on this project that helped make our paper on the work (which is in press) much better. Glad he generally is now in support of this type of project, though not sure what he thinks about our work in this area ...

Here are some of my quotes:

"There's no doubt to us that filling in the branches of the tree is going to be useful to lots of scientific studies that use genomic data," says Eisen. "There have been four billion years of evolution and we can really benefit from having some of that information in our databases."

All these new genomes should improve researchers' understanding of the evolution, physiology and metabolic capacity of microbes, says Eisen. They will also help match DNA sequences to their proper species from large-scale, high-throughput metagenomic studies from environmental samples, and ultimately contribute in the fields of synthetic biology and genetic engineering.

And the sling jaw wrasse makes it to ESPN

2009-11-17T00:53:00.000-08:00

OK - now this is really going viral. The slingjaw wrasse video from Peter Wainwright's lab at UC Davis (which I wrote about here) has now made it to ESPN.

See the SportsNation web site:

Weird Web Stories: Monday, Nov. 16 - SportsNation - ESPN

And on Twitter SportsNation says

The slingjaw wrasse has officially replaced the waiter monkeys as our favorite animals: http://bit.ly/34mMzE

ASM - launches new Open Access journal - w/ some aspects of #PLoS One and PNAS

2009-11-16T14:50:00.000-08:00

Just got this in an email announcement from the President of ASM

ASM’s first broad-scope, online-only, open access journal, mBio™ will begin accepting submissions in January 2010 in preparation for launch in May 2010. mBio™ will offer rapid review and publication of the best research in microbiology and allied fields. The scope of mBio™ will reflect the enormity of the microbial world, highly interconnected biosphere where microbes interact with living and non-living matter to produce outcomes that range from mutualism to parasitism, energy acquisition and conversion, climate change, geologic change, food and drug production, and behavioral change. “We will encourage authors to explain how their findings fit into the larger picture,” says Editor in Chief Arturo Casadevall. Find out more at http://mbio.asm.org.

Seems like they are trying to become a PLoS One for Microbiology. Actually, ~~they are going~~ one interpretation of their description is that they are going even further than PLoS One in terms of making review more streamlined (see below).

mBio™ will offer authors streamlined decisions. mBio™ editors will either accept or reject manuscripts, and will request only minor revisions; editors generally will not require authors to make extensive modifications or perform additional experiments. The philosophy behind this decision is a desire to break away from the current publication model where authors are often uncertain of whether their work will ultimately be acceptable when additional work is required. Authors of a manuscript rejected by mBio™ who choose to do additional experiments will have the option of resubmitting the paper to mBio™ or another ASM journal one additional time. The resubmission must be accompanied by a response to the prior decision letter. A rejection from mBio™ does not disqualify a manuscript from subsequent submission to another ASM journal.

NOTE - THERE ARE MULTIPLE INTERPRETATIONS OF THIS STATEMENT - COULD MEAN THAT EVERYTHING WILL BE SENT OUT FOR REVIEW AND THEN EDITORS WILL MAKE SIMPLE DECISIONS. ALTERNATIVELY EDITORS COULD JUST ACCEPT OR REJECT PAPERS WITHOUT SENDING THEM OUT. THE LATTER IS HOW I INTERPRETED THE ANNOUNCEMENT.
Not sure everyone is going to like the policy here of allowing editors to just accept papers. Also - seems like they are adopting a policy like PNAS where Fellows can submit their own papers. I note PNAS just ditched this policy, in part due to the problems with peer review of some such papers.

AAM Fellows also will be entitled to submit one paper per calendar year via a special, accelerated submission path. This path will require Fellows to obtain two reviews (from reviewers who are not recent collaborators, trainees, etc.) prior to submission, make any necessary modifications in response to the reviewers' comments, and communicate the paper plus reviewer feedback and author responses to mBio™. After the manuscript is received by the journal it will be assigned to a member of the Editorial Board (EB) for disposition. Although we anticipate that most manuscripts submitted by Fellows will be approved, the EB member will have the option of recommending modification, additional review, or rejection.

One other things to note - which I do not like by the way - ASM has created their own version of Open Access that they call ASM Access

The term “open access” can mean different things depending on the publisher. ASM has coined the term “ASM Access™” to describe the specific form of open access that applies to mBio™. Full text of mBio™ articles and supplemental materials will be freely available on the mBio™ website immediately upon publication. Full text of mBio™ articles also will be deposited in PubMed Central and will be freely available upon publication.
Authors of accepted papers will be asked to sign a license that grants ASM publishing rights and permits unrestricted non-commercial reuse. ASM will continue to require permission for commercial reuse of mBio™ content.
“ASM Access™” publications will fully meet the open access requirements of funding agencies such as NIH, HHMI, and the Wellcome Trust.

Worst new omics word award: material degradomics

2009-11-14T07:56:00.000-08:00

And the bad omics words just keep getting worse. This one really takes the cake. A story from BBC News Online (Sniff test to preserve old books)
discusses how

"Researchers report in the journal Analytical Chemistry that a new "sniff test" can measure degradation of old books and historical documents."

The work they are doing actually seems quite interesting. But alas, the way they describe it does not. They refer to this method as "material degradomics". I fortunately do not have access to the paper at home but a google search reveals some text from their paper

Through similarities with metabolomics,(15) we propose to define a new field of material degradomics (and related terms, Table 1).

I literally dread what is in table 1. For creating a new omics term that seems thoroughly unnecessary and distracting, I am giving Matija Strli and colleagues one of my coveted "Worst New Omics Word Awards." Hat tip to PaulBo who posted a comment about this on my "Fermentome" award post.

Holy Slingjaw Wrasse and the power of twitter

2009-11-13T16:05:00.000-08:00

OK I am now a bit blown away by twitter.

Last week I posted a tiny teeny itsy bitty entry on twitter:

"Peter Wainwright showed this crazy slingjaw wrasse video in our class at#UCDavis yesterday:http://tinyurl.com/ybqv429"

The video indeed is awesome:

And then a few others retweeted/commented on this.

Then Carl Zimmer blogged about it on "The Loom" in a post "The last thing the mosquitofish saw".

And that is really when the fish hit that fan.

On Tuesday, Tom Chivers at the Telegraph wrote about it "Weird feeding habits of the slingjaw wrasse" saying

"Almost 6,000 people have watched the YouTube footage of Epibulus insidiator, a strange predator found in tropical waters in the Pacific and Indian Oceans."

Little did he know what would happen next. It seems to have then gotten picked up by all sorts of web news sites around the world and KABOOM, like the fishes jaw, this video went crazy.

See for example

Now there have been 165,000 views. Completely deserving I must say. But pretty surprising too ...

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

And here are some more links:

1000 Complete Bacterial and Archaea Genomes -wow

2009-11-09T13:41:00.001-08:00

1000 Complete Bacterial and Archaeal Genomes in Genbank. Big MileStone. Good day for a microbial genome party. This whole thing is amazing to me. I moved to TIGR in 1998 in order to get in early on the "genome sequencing revolution" as we called it then. We were amazed when the 10th genome came out. We were then thrilled when TIGR sequenced its 20th genome. And now, there are 1000. Amazing.

And as Nikos Kyrpides just told me (he is sitting next to me right now) - actually if you go to GOLD (Genomes Online) (Nikos runs this DB) you can see there are actually a few more than 1K there. Even more amazing.

Posted using ShareThis

Bay Area Bioinformatics Group

2009-11-08T09:48:00.000-08:00

OK - so in the era of H1N1 it is definitely yucky to have REAL meetings with people, but this "Bay Area Bioinformatics" meetup group seems like a good idea. They have a meetup in Berkeley 11/14 at Cafe Strada. Folks can sign up here: BayBIFX (El Cerrito, CA) - Meetup.com

Seems like they are focused on East Bay but want to get Davis, and other people involved ...

Bay Area Biosystematists Mtg 11/10, #UCDavis, on Community Phylogenetics

2009-11-05T19:28:00.000-08:00

Bay Area Biosystematists Meeting: Tuesday, 10 November, 2009

at UC Davis, 1022 Life Sciences (LSA)

"Community Phylogenetics"

Featuring Jean H. Burns of the Center for Population Biology, UC Davis
Plus contributions from panel discussants:
Paul Fine, Integrative Biology, UC Berkeley
William Cornwell, Integrative Biology, UC Berkeley

Come and hear about this emerging synthesis of systematics and ecology that promises to transform the way we do both!

Schedule and venue:
5:30 - social gathering with beverages and informal pizza dinner:
cost ca. $12, to be collected at door, 1022 Life Sciences Bldg. (LSA),
UC Davis campus.
7:00 - talks followed by discussion, in same room.

Please email reservations to your host, Kristy Deiner, at alpinedna@gmail.com by Monday, Nov. 9th

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: https://calmail.berkeley.edu/manage/list/listinfo/babs-l@lists.berkeley.edu

For a map of this region of the UCD campus, use the link below.
http://www.cevs.ucdavis.edu/map/map_detail.cfm?centerTile=7_6

Posting Notes from NAS Microbes and Health Meeting here on my blog

2009-11-02T08:51:00.000-08:00

I am going to be posting notes on the NAS Meeting on Microbes and Health Here

Elaine Holmes at #NASMH studying metabolomics & microbes vs. human hypertension & BMI & type II diabetes - strong IDing signals

Vaughan at #NASMH using "Simulator of the Human Intestinal Microbial Ecosystem" aka SHIME Reactor

@DavidSela There goes my 30 minutes of twitter fame ...

Vaughan at #NASMH performing human 'intervention study' using tea & grape/wine polyphenols - each person is their own control

Keijser at #NASMH using microarray to survey rRNAs from oral samples - calls this the "OC" chip

Elaine Holmes #NASMH "dosed up post docs w/ Chamomile tea" & compared metabolites & microbes (hard to prevent EToH consumption though)

Elaine Vaughan from UNILEVER at #NASMH discussing bioconversion of dietary polyphenols by gut microbiota

RT @Scitable Cucumber genome published http://www.eurekalert.org/pub_rel... Guide to pumpkin, melon and plant vascular system #UCDavis

Bart Keijser at #NASMH talking about exploring oral microbiota in kids - using traveling "dental bus" - every kids nightmare

Keijser at #NASMH - w/ array get correlations betw. oral health status & certain organisms - these may be new targets for intervention

Vaughan at #NASMH looking at polyphenol metabolites from grape/wine extract & black tea - steps by microbiota vary greatly

Elaine Holmes at #NASMH trying to correlate specific metabolites w/ specific organisms - very difficult

Keijser at #NASMH using 454 rRNA sequencing to compare oral microbiota over time in permanent vs. "deciduous" teeth

Elaine Holmes at #NASMH is talking about metabolomics of microbes - see here home page here http://www1.imperial.ac.uk/medicin...
Monday from Twitter - Comment - Share – Edit

Elaine Holmes at #NASMH is talking about metabolomics of microbes - see here home page here http://www1.imperial.ac.uk/medicin...

Elaine Holmes at #NASMH looking at metabolites & microbes in model of bariatric surgery in rats

Elaine Holmes at #NASMH looking at metabolic profiles in different ethnic groups re; obesity epidemic

Elaine Holmes at #NASMH - using metabolomics of faecal H20 to compare normal & vancomycin treated mice

Elaine Holmes at #NASMH discussing study infecting germ free mice with microbiota from human babies http://www.nature.com/msb...

Elaine Holmes at #NASMH - metabolomics of urine from rats gives insight into gut microbiota (very cool)

Elaine Holmes at #NASMH - metabolomics of gnotobiotic (aka germ free) mice w/ and w/o colonization by microbes

R. Knight #NASMH discussing ecological "convergence" in microbial communities species assemblages

R. Knight #NASMH showing amazing study of microbes all over people's bodies (27 or so locations)

R. Knight #NASMH - comparison of mammal gut communities shows clustering by diet

R. Knight #NASMH "much as we love rRNA at Boulder we accept that we have to look at other parts of the genome"

R. Knight #NASMH - deep sequencing gives us samples of rare biosphere - though unclear what these rare organisms do

R. Knight #NASMH using 454 sequencing to survey microbial communities - expensive but saves money in long run

Knight #NASMH - UNIFRAC comparison of all communities suggests vertebrate gut communities are very unique

Getting reads for my talk at #NASMH

Knight at #NASMH says "hierarchical clustering as w/ microarrays" -good 2C my brother's work referred this way http://www.pnas.org/content...

Rob Knight at #NASMH discussing how UNIFRAC uses tree of life as organizing theme http://bmf2.colorado.edu/unifrac...

N. Moran #NASMH - aphid defense against parasitoids by H. defensa due to phage encoded toxins

Rob Knight - microbiome is good for personalized medicine b/c there is much variation between people

Rob Knight #NASMH discussing how van Leeuwenkoek was first to look at "Human Microbiome" using tooth scrapings

N. Moran #NASMH - many symbionts on border between bacteria & organelle - though more on the bacteria side

N. Moran #NASMH aphid resistance to parasitoid wasps due to presence of facultative symbiont H. defensa http://www.pnas.org/content...

# Rob Knight from CU-Boulder talking at #NASMH on 16s rRNA "enlightenment"

R. Knight #NASMH - was a major need for methods to compare rRNA data from different microbial communities

N. Moran #NASMH summary: symbioses major force in evolution, source of adaptation in changing envir, source of host constraints

N. Moran #NASMH comparing symbiont DNA repair genes: all missing some, some missing all, leads to incr. mutation rate & DNA biases

N. Moran #NASMH - once endosymbionts lose genes - never coming back b/c no lateral transfer - has profound effects on host ecology

R. Knight at #NASMH says next generation sequencing helps saves toothpicks previously used for colony picking

N. Moran #NASMH - accidental selection in lab for symbionts to lose heat shock response - see #PLoS Bio http://www.plosbiology.org/article...)

N. Moran #NASMH: organisms w/ small genomes lose non essential genes & also useful genes by drift b/c population sizes low

N. Moran #NASMH aphid resistance to parasitoid wasps due to presence of facultative symbiont H. defensa http://www.pnas.org/content...

# Rob Knight from CU-Boulder talking at #NASMH on 16s rRNA "enlightenment"

R. Knight #NASMH - was a major need for methods to compare rRNA data from different microbial communities

N. Moran #NASMH summary: symbioses major force in evolution, source of adaptation in changing envir, source of host constraints

N. Moran #NASMH comparing symbiont DNA repair genes: all missing some, some missing all, leads to incr. mutation rate & DNA biases

N. Moran #NASMH - once endosymbionts lose genes - never coming back b/c no lateral transfer - has profound effects on host ecology

Watching Nancy Moran, 1 of my favorite scientists, talk on symbioses at NAS Microbes&Health mtg (#NASMH) http://www.nasonline.org/site...

Nancy Moran at #NASMH: bacteria are incredibly diverse & plastic whereas animals are not so plastic & need some metabolic help

N. Moran #NASMH: in many symbioses host & symbiont phylogenetic trees are congruent -must be due to ancient associations

Nancy Moran defines symbiosis as I do: "members of more than 1 genetic lineage associate closely, often for mutual benefit" #NASMH

Nancy Moran: studies of symbionts used to be very hard b/c most cannot be cultured - molecular methods have revolutionized studies #NASMH

Nancy Moran is talking about symbioses

SHowing rRNA tree of life

Bacteria very diverse - in many ways - and very plastic and dynamic

Animals do not do this much

Essential roles of symbionts in animals - many examples

Giving props to Paul Buchner who documented associated involving bacteria buyt had not molecular methods and no culturing

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

2009-10-29T13:24:00.001-07:00

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.

Molecular Genomic Approaches to Infectious Diseases in Resource-Limited Settings in PLoS Medicine by Josephina Coloma and Eva Harris
Can an Infectious Disease Genomics Project Predict and Prevent the Next Pandemic? in PLoS Biology by Rajesh Gupta, Mark Michalski and Frank Rijsberman
The Role of Genomics in the Identification, Prediction, and Prevention of Biological Threats in PLoS Biology by W. Florian Fricke, David Rasko and Jacques Ravel
Discovering the Phylodynamics of RNA Viruses in PLoS Computational Biology by Eddie Holmes and Bryan Grenfell
Computational Resources in Infectious Disease: Limitations and Challenges in PLoS Computational Biology by Eva Berglund, Bjorn Nystedt and Siv Andersson
The Role of Medical Structural Genomics in Discovering New Drugs for Infectious Diseases in PLoS Computational Biology by Voorhis et al
The Key Role of Genomics in Modern Vaccine and Drug Design for Emerging Infectious Diseases in PLoS Genetics by Kate Seib, Gordon Dougan and Rino Rappuoli
Toward the Use of Genomics to Study Microevolutionary Change in Bacteria in PLoS Genetics by Dan Falush
The Application of Genomics to Emerging Zoonotic Viral Diseases in PLoS Pathogens by Bart Haagmans et al
The Role of Genomics in Tracking the Evolution of Influenza A Virus in PLoS Pathogens by Alice Mchardy and Ben Adams
The Past and Future of Tuberculosis Research in PLoS Pathogens by Inaki Comas and Sebastien Gagneux
Helicobacter pylori's Unconventional Role in Health and Disease by Dorer et al
Helminth Genomics: The Implications for Human Health in PLoS Neglectued Tropical Diseases by Brindley et al

Some more on the series from the web:

Bora writes about it here: Genomics of Emerging Infectious Disease PLoS Collection
From the Google.Org blog: Will genomics help prevent the next pandemic?

Genomics Faculty Jobs at the Joint Genome Institute

2009-10-29T07:47:00.001-07:00

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: WRCannan@lbl.gov.

For more information see: http://jobs.lbl.gov/LBNLCareers/details.asp?jid=23646&p=1

Personal Medicine Panel Discussion at American River College

2009-10-29T07:41:00.000-07:00

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

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

2009-10-28T08:08:00.000-07:00

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
http://www.employment.ucdavis.edu/applicants/Central?quickFind=53986;
Requisition
Number #03001704

Microbes, art, science all rolled into one - yum

2009-10-27T17:36:00.000-07:00

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.

A field guide to the microbes?

2009-10-25T17:28:00.000-07:00

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

Jonathan Eisen talk on 1$ Genome

View more presentations from phylogenomics.

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

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

2009-10-22T01:19:00.000-07:00

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

2009-10-22T01:08:00.000-07:00

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 - CBS.com)

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.

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

2009-10-20T08:37:00.000-07:00

“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

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

2009-10-16T10:12:00.000-07:00

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: http://www.grandchallenges.org/explorations

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

Worst new omics word award #5: fermentome

2009-10-15T16:17:00.000-07:00

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)

2009-10-15T07:40:00.000-07:00

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@ge.com
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:

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

2009-10-14T14:12:00.000-07:00

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 gbennett@nature.berkeley.edu by Tuesday, Oct 13th

For a map of campus and view of VLSB, use the link below.
http://www.berkeley.edu/map/maps/ABCD123.html

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: https://calmail.berkeley.edu/manage/list/listinfo/babs-l@lists.berkeley.edu