Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

NSF looking for grants on "Life in Transition" re:climate change

Just got this email from the National Science Foundation saying that NSF is looking for more grants relating to responses of organisms/ecosystems to climate change.

The Divisions of Integrative Organismal Systems (IOS) and Molecular and Cellular Biosciences (MCB) in the Directorate for Biological Sciences at NSF encourage submission of proposals that address the biochemical, molecular, cellular, genetic and/or organismal underpinnings of adaptation and biological feedbacks to climate change.  Interdisciplinary and systems level approaches to these problems are encouraged. A cross-divisional working group has been established to ensure that exciting proposals in this area receive adequate and appropriate attention. 

Life on earth contributes actively to the forces involved in troposphere climate and chemistry. Not only are organisms key participants in climate and chemistry forcing functions, they are also highly sensitive to changes in many climatic and chemical properties of the troposphere.  Research is needed to understand the limits of biological adjustments to such changes, and the feedbacks on climate and chemistry that will result. 

The Foundation has a rapidly growing commitment to research directed towards understanding the interplay between living organisms and the earth’s climate and surface chemistry.  In the Directorate for Biological Sciences, this was emphasized last year by the establishment of a special Life in Transition activity, as announced in an open letter to the research community, accessible at: http://www.nsf.gov/pubs/2008/nsf08078/nsf08078.jsp?org=NSF.

Please consider submitting proposals of this kind to IOS and MCB using the ‘LiT:’ title preface described in the Life in Transition ‘Dear Colleague’ letter referenced above.  A project summary and introduction that place the proposed  research in the context of global climate change will be most helpful in determining appropriate sources of funding within NSF. 

If you seek further information, queries sent to this return email address will be directed appropriately to insure a prompt reply.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Worst new omics word award: Negatome

Last week I asked for people to post suggestions for bad new omics words as candidates for my “Worst new omics word award”. And there were some great ones posted there by MAT kinase (physiomics, orfeomics), Mr. Gunn (degradomics, though he noticed it was already suggested), anonymous (incidentalome), Karl Broman (human connectome), Paul (splicome), blJOg (Systemomics), Farhat Habib (resourceome), Rosie Redfield (sewa-genomics), Marmaduke (Microbial paleomics), and many others.

But by far and away, the worst of the worst, the most negative of all new omics words I have seen in a while, is the negatome suggested by multiple people. Yes, indeed, a group ( Pawel Smialowski, Philipp Pagel, Philip Wong, Barbara Brauner, Irmtraud Dunger, Gisela Fobo, Goar Frishman, Corinna Montrone, Thomas Rattei, Dmitrij Frishman and Andreas Ruepp ) has written about, and even created a database for the negatome (for an excellent description about what the negatome is about, see The ‘negatome’ – a database of negative information… « mental indigestion (from Dr. Jim).

The concept of the negatome is good – it- “is a collection of protein and domain pairs that are unlikely to be engaged in direct physical interactions”. It is meant in many ways as a database for testing various interaction measuring methods. And it could end up being quite useful. See Dr. Jim for more on its uses at the link in the previous paragraph.

But the name. Oh the name. It hurts to see. It hurts to say.

And thus,
… as suggested by GenomeWeb “Just watch out for Jonathan Eisen’s Worst New Omics Award.”
…and Iddo Friedberg on Twitter (@phylogenomics is going to love this one. The Negatome. Actually, quite useful.)
…and PSI Wavefunction on my blog) …
…and contrary to the suggestion by Ed Winstead on twitter who misinterpreted my twitter post about Iddo’s post when he said “Liked “The ‘negatome’ – a database of negative information” http://bit.ly/5ht98d even got the nod from @phylogenomics”

…  Negatome the word is a winner of my coveted “Worst New Omics Word Award“.

Previous winners were:

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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My favorite evolution stuff 2. Charles Darwin Tobacco Card




In honor of Charlie D. I am posting one of my favorite Darwin items.  I got this from Ebay years ago.  It is a Darwin card – about 3 x 5 cm.  From Ogden’s Cigarettes, much like baseball cards.


Also see my previous “Favorite Darwin thing” – a post card from 1900 or so. 
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Going on pump is like going back to school

OK – been on the pump now for about 1.5 weeks. Been OK. A huge learning curve here after 25 years of taking insulin shots. It feels a bit like I am going back to school. So much to learn. So much to unlearn.

Anyway. I am getting to know a few people on pumps too and they are an invaluable resource. What I find most amazing so far is how my kids, 4.5 and 2.5 years old, take this completely in stride. My 4.5 year old daughter now asks which pocket I am carrying the pump in so she can sit on the other leg. And she has asked if it is nice to not be taking shots anymore. Completely casual. Completely normal.
So far – my biggest challenges have been figuring out how to carry the pump and inserting the infusion sets. Getting the hang of the infusion sets (I am using a Medtronic pump currently with the Silhouette infusion system). Still no clue about how to carry the pump in diverse situations, like riding my bike in the rain … but I guess I will learn.
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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

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.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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

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.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Wanted – Bad New Omics Words

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

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Biologists rally to sequence ‘neglected’ microbes : Nature News

UPDATE: Our paper on this topic is out and there has been a bit of news here and there about it (e.g., NyTimes).  For more see

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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.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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And the sling jaw wrasse makes it to ESPN

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


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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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

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.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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