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

What should be the next genome sequenced?

What should be the next genome sequenced? Olivia Judson has turned this question into an analog of Fantasy Baseball. Submit your suggestions to her/the world at The Fantasy Genome Project – Olivia Judson Blog – NYTimes.com

Or submit them here. For microbes it is so cheap that there is no point in doing this type of competition (e.g., for a bacterial isolate it would cost ~ 1-2000$$$ to do the shotgun sequencing for most species and then if you want to finish it would cost more, but still not very much)

My suggestion for a bigger genome to do that would be fun, interesting and important — the blue whale. Biggest animal on the planet. Ever. Just must have its genome.

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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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#PLoS Currents is live, in case you missed it …

PLoS Currents is live (as of last week). Check out the blog posting by Harold Varmus:A new website for the rapid sharing of influenza research | Public Library of Science

I am very excited by this — it seems to be a new step on Open Science.

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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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Ted Kennedy in Pubmed Central #openaccess

For those interested in open access and/or Ted Kennedy, you might be interested to know that Kennedy has a few articles available in PubMed Central – all available for free …

Quality, Affordable Health Care for All Americans
Edward M. Kennedy

Am J Public Health. 2003 January; 93(1): 14.

PMCID: PMC1449947

Health care reform: workers beware.
E M Kennedy

Public Health Rep. 1996 Jan–Feb; 111(1): 11.

PMCID: PMC1381734

The congress and national health policy. Fifth Annual Matthew B. Rosenhaus Lecture.
E M Kennedy

Am J Public Health. 1978 March; 68(3): 241–244.

PMCID: PMC1653906

National leadership in confronting bioterrorism: 2.
E M Kennedy

Public Health Rep. 2001; 116(Suppl 2): 116–118.

PMCID: PMC1497282
| Summary | PDF–32K |

Discussions
Edward M. Kennedy

Bull N Y Acad Med. 1972 January; 48(1): 146–156.

PMCID: PMC1806655

1974 Yale Medical Student Council Lectureship: Partners or protagonists-Congress and the Academic Medical Centers.
E. M. Kennedy

Yale J Biol Med. 1975 March; 48(1): 1–7.

PMCID: PMC2595194

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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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UC asking for people to write letter to government

For those interested in supporting the University of California and encouraging the California government to increase the budget next year here is a link for you:

UC for California – a dynamic advocacy support network for the University of California

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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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Good move or not? – UC decides faculty furlough’s will not be

Just received this email (also attached letter)

Colleagues:

After speaking at length with all of you and a number of other people with an interest in the issue, we have decided that faculty furlough days will not occur on instructional days (days for which a faculty member is scheduled to give lectures, lead classes or workshops, have scheduled office hours, or have other scheduled face-to-face responsibilities for students).

The furloughs that have been necessitated by the severe University underfunding by the State are causing significant problems for faculty who have restrictions on research and service as well as increased teaching workloads; employees who have fewer days to do their work and sometimes fewer colleagues to help them; administrators who have reduced staff and budgets to accomplish their complex tasks; on top of lower salaries for everyone. Students too will suffer the effects of the underfunding–larger and fewer classes, and increased fees, as were imposed for this fall instruction period, among other burdens. In such difficult times, I believe that we must do everything we can to ensure that the students continue to receive all of their instruction. Asking the faculty to carry a full teaching load during furloughs is a large request, but in my mind is justified by the University’s paramount teaching mission. Research is permitted on furlough days, but for many faculty this extra research will not be remunerated unless they have grants in which there are funds that can be reallocated to pay for increased effort. And since furlough days are not “service days”, they can be used for outside professional activities that may be remunerated.

We understand that the furlough plan will cause hardships for the entire University family. As such, the President and the Regents are committed to do everything possible to ensure that the plan ends after 12 months.

We will continue to work closely with faculty, students, staff and administrators to find the most efficient and thoughtful way to address the problems that will arise this year. You have my pledge that we will make the University as effective and productive as we can under the current budget problems, after which we will help you all plan for better times ahead.

Best wishes,

Lawrence H. Pitts

Interim Provost and Executive Vice President

Academic Affairs

I am sure many of my colleagues will disagree with this decision by UC. The debate around campus here has basically been about whether there should be some teaching “consequences” to all the cuts being placed on faculty. I accept that it could be useful for there to be some pain and that teaching less would be a way to show that the cuts have real impact on education. But I think personally this would be a horrible political move right now. California’s budget could still go down next year and there could be more cuts. UC needs as much good will as possible in Sacramento and around the state and having faculty cut teaching days does not seem to be the best maneuver.
What do other people think? I propose we slash committees, meetings, and other “service” activities like that. Many of them won’t be missed by anyone.

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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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YARFOS: Yet another reason for #OpenScience – getting useful input from reviewers

This is in the YARFOS (Yet another reason for open science) category.

A bit old here but was cleaning out my email inbox and just found a message about a cool Open Science story.

Seems Ivan Baxter and others had submitted a paper to PLoS Genetics (it is published now – see here). As described in his Ionomics Blog (yes, another omics, but we will let than slide here):

We just got the reviews back from Plos Genetics for our esb1 paper. There were many constructive suggestions and helpful suggestions, which is what we have come to expect from Plos Genetics (and why we submit many of our manuscripts there).

One of the reviewers actually came to Piims and retrieved some of the data that went into the paper to make the point that we should comment on the Mg effect of the mutation. Specifically, the reviewer pointed out that the mutation doesn’t affect Mg, even though it affects Ca. They even included a figure of the data! I am posting the figure here, Blue is the mutant, and pink is the wild-type.

Go check out his post to see the figure. In the end, by putting their data out in the open, and by having a good intentioned reviewer, they got a really useful suggestion for their work …

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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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RIN/NESTA open science case studies project

Just got this email ….

RIN/NESTA open science case studies project

The Research Information Network (RIN) and the National Endowment for Science, Technology and the Arts (NESTA) are looking to fund a series of case studies which will look at what motivates researchers to work in an open way with their data, results and protocols, and whether there are advantages to working this way. The case studies will also examine the disincentives and barriers to such ‘open science’ methods. The RIN and NESTA are making available up to £15,000 for this project, which is intended to run from October 2009 until January 2010.

Expressions of interest are sought, in the form of an outline statement, on not more than a single sheet of A4, indicating the scope and rational of the proposal, the research methodology likely to be used and suggestions of case studies to be examined. The deadline is 9 September 2009. For more information visit http://www.rin.ac.uk/open-science

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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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Thanks ASM for your offer of a Credit Card with APR of up to 17.99%

I had been growing somewhat fond of the American Society for Microbiology (ASM) recently.  I had a decent time at the annual meeting.  I am chair elect for Division R (Evolutionary and Genomic Microbiology) within ASM. And though their journals are not fully open access, they at least are making efforts to put material into Pubmed Central pretty rapidly.  But the amount of crap I get in the mail courtesy of ASM is really astounding.  And today could be the proverbial straw.  I got an offer for an ASM Credit Card via Bank of America with an APR that can be raised to more than 27% with one late payment.  Umm, thanks but no thanks.  And note to anyone out there thinking of signing up for ASM or their meetings – get ready for a massive waste of paper when your name and address get sold to marketers and annoying junk mail.  Fun fun fun.

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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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Fun w/ web ads: Science words banned by @carlzimmer featured in his ads

Carl Zimmer has recently been writing about words that should be banned from scientific communication. Originally, I thought this notion was hokie but then I read his postings about it and am starting to warm to the idea. In essence he is railing against jargon. Words and phrases he thinks are to be avoided include

  • Breakthrough
  • Captive observation
  • Demographic leveling
  • Marine environment
  • Material properties
  • Morphology
  • Phylogenetics

When I was browsing his posting something pretty funny started to happen. Ads popped up making use of the banned terms. The best is shown in the one below:

This features an ad from Phizer for its “Big Think/ Breakthroughs” campaign to “explore medical science at the cutting edge.” I guess Zimmer has not yet set up an ad blocker system which will keep out ads that use the banned terms …

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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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Petition to Support the Redesign of Fifth Street in #Davis CA

Make Davis even more bicycle friendly. Sign the petition regarding 5th street redesign. See

Petition to Support the Redesign of Fifth Street Petition : [ powered by iPetitions.com ]

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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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