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

#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.

——–

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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More phishing pretending to be from Elsevier …

I got another bizarre phishing email with the lure being something to do with Elsevier journals. Note to any gullible people out there – if Elsevier were recruiting people to do something (e.g., write papers, be editors, etc) my guess is the request would come from an Elsevier.Com email address.

Anyway here is some of the latest:

BREAKING BOUNDRIES

The Editorial Policy and Practices Of The Elsevier Journals

1. The Editorial Board

Elsevier journals are headed by Editors and an Editorial Board Members. The Editors and Editorial Board is appointed by the Publication Committee of Elsevier Journals. Editors serve a 3-year term and Editorial Board members also serve a 3-year term. Board members are chosen based on the journal’s need for representation from a particular subject area in conjunction with the individual’s commitment to maintaining high journal standards as illustrated in objective and prompt reviews.

An Editorial Office Team is also appointed by the publication committee to directly assist the editors and editorial board members.

II. The Review Process

The Elsevier Journals editorial office policy requires each manuscript be reviewed by individuals who are highly competent and recognized in the particular field of the submitted manuscript. The editorial office contacts those reviewers that have been identified as qualified and/or recommended by the authors. Authors are also encouraged to submit in their cover letters names of individuals whom they feel are appropriate and qualified to review their manuscript. Once potential reviewers agree to read a manuscript they are given a one-week time-frame to complete the review

When the reviews are completed, a decision is made to either accept the paper or give the authors the opportunity to revise according to reviewers’ suggestions or to reject the paper based on the reviewers’ criticisms and the editors’ opinion of the paper. In some instances it is necessary to seek the opinion of other reviewers if further comment is necessary to make a final decision. When an editor has completed his decision on a manuscript, the decision letter and reviewers’ comments are sent to the author. Any questions or concerns regarding the editorial decision on any manuscript must be made directly to the Elsevier Journals editorial office. Revised manuscripts are evaluated to determine if the author(s) have adequately addressed and answered the critiques of the reviewers and editors. Depending upon this evaluation, manuscripts may be accepted, returned for further revision, or rejected. If a paper is accepted, the paper is immediately sent to the publication office and slotted for the next available issue. Elsevier journals tries to complete the review cycle in one week. This time, however, may vary depending on the amount of revision work that needs to be completed before the manuscript is acceptable.

111. Grounds for Declining a Manuscript

Elsevier Journals will decline a manuscript after it has completed the review process. Manuscripts that do not meet the standards of the journal are returned to authors with substantial comments describing the basis for the decision. Manuscripts may be rejected if it is felt that the findings are not sufficiently novel, do not provide sufficient new insights, do not contain enough new information, or are too preliminary to warrant publication.

V1. Guidelines

1. Obligations of an Editor

  • The editor should give unbiased consideration to all manuscripts offered for publication, judging each on its merits without regard to race, gender, religious belief, ethnic origin, citizenship, or political philosophy of the author(s).
  • The editor should process manuscripts promptly.
  • The editor has complete responsibility and authority to accept a submitted paper for publication or to reject it. The editor may confer with reviewers for an evaluation to use in making this decision.
  • The editor and the editorial staff should not disclose any information about a manuscript under consideration to anyone other than reviewers and potential reviewers.
  • The editor should respect the intellectual independence of authors.
  • Editorial responsibility and authority for any manuscript authored by the editor and submitted to the journal should be delegated to some other qualified person. The editor should avoid situations of real or perceived conflicts of interest. If the editor chooses to participate in an ongoing scientific debate within his journal, the editor should arrange for some other qualified person to take editorial responsibility.
  • The editor should avoid situations of real or perceived conflicts of interest. Such conflicts include, but are not limited to, handling papers from present and former students, from colleagues with whom the editor has recently collaborated, and from those in the same institution.
  • Unpublished information, arguments, or interpretations disclosed in a submitted manuscript should not be used in an editor’s own research except with the consent of the author.
  • If the editor is presented with convincing evidence that the main substance or conclusions of a paper published in the journal are erroneous, the editor should facilitate publication of an appropriate paper pointing out the error and, if possible, correcting it.

2. Obligations of Reviewers of Manuscripts

  • Inasmuch as the reviewing of manuscripts is an essential step in the publication process, every scientist has an obligation to do a fair share of reviewing.
  • A chosen reviewer who feels inadequately qualified or lacks the time to judge the research reported in a manuscript should return it promptly to the editor
  • A reviewer of a manuscript should judge objectively the quality of the manuscript and respect the intellectual independence of the authors. In no case is personal criticism appropriate.
  • A reviewer should be sensitive even to the appearance of a conflict of interest when the manuscript under review is closely related to the reviewer’s work in progress or published. If in doubt, the reviewer should return the manuscript promptly without review, advising the editor of the conflict of interest or bias.
  • A reviewer should not evaluate a manuscript authored or co-authored by a person with whom the reviewer has a personal or professional connection if the relationship would bias judgment of the manuscript.
  • A reviewer should treat a manuscript sent for review as a confidential document. It should neither be shown to nor discussed with others except, in special cases, to persons from whom specific advice may be sought; in that event, the identities of those consulted should be disclosed to the editor.
  • Reviewers should explain and support their judgments adequately so that editors and authors may understand the basis of their comments. Any statement that an observation, derivation, or argument had been previously reported should be accompanied by the relevant citation.
  • A reviewer should be alert to failure of authors to cite relevant work by other scientists. A reviewer should call to the editor’s attention any substantial similarity between the manuscript under consideration and any published paper or any manuscript submitted concurrently to another journal.
  • Reviewers should not use or disclose unpublished information, arguments, or interpretations contained in a manuscript under consideration, except with the consent of the author
  • Reviewers should respond promptly, usually within one week of receipt of a manuscript. If reviewers need more time, they contact the editor promptly so that authors can be kept informed and, if necessary, assign alternate reviewers

There is a letter attached to it and also the procedures on how to fill the form

We would appreciate if you contact us as soon as possible because we are updating our data sheet for reviewers and editors which we want to upload in our website soonest. Thank you for your co-operation. Please reply to board.elsevier@gmail.com

Please note that you are to pay $100, for more details please read the letter attached below.

Best regards

Chief editor

————————————————————

Then the form asks for:

Please read the letter carefully before filling the form.
Before filling this form you have to accept the conditions stated regarding the payment and on our own part we are to pay you for each work sent to you.
Payment is done only when you are accepted to become a member.

Name of Editor
Date of Birth
Area of Specialization
Degree
No. of Articles Published

Name of Reviewer
Date of Birth
Area of Specialization
Degree
No. of Articles Published

And a separate PDF says

Dear colleague,
Elsevier publishes the largest journals online which is a close access
system. Each year we organize a routine test for all our reviewers
and editors to ascertain their level of research in the reviewing and
editing of articles before publication. We would like to know if you are
interested in serving as a member of our reviewing and editorial
board. You are required to pay $100 to enable us include your
name on our website. Successful candidate will be paid $30 per
page of manuscript given to review or edit. Please fill the form
attached.

——–
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.

——–