Tag: Misc.

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 …

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 ]

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.

Funny use of a “Tree of Life” in the New York Times book review section from a few months ago (The New York Times:Natural Selections)

In this, they overlay onto a somewhat strange Tree of Life, the images used for various book publishers and what types of organisms they use. They say that this represents a fair amount of biodiversity, but really only because they draw the tree in a skewed manner. Basically, there are animals and plants in the logos and the way they draw the tree makes this look like it is a lot of biodiversity … but really it is a small component compared to the whole tree of life. I also like that they put robots on the insect branch and they have mythology as a VERY deep branch in the tree.

A bioinformatics engineer position is available on a microbial metagenomics project called iSEEM (http://openwetware.org/wiki/ISEEM) under the direction of

Jonathan A. Eisen (UC Davis) http://128.120.136.15/mediawiki/index.php/Main_Page

Jessica L. Green (U Oregon) http://biology.uoregon.edu/people/green/

Katherine S. Pollard (Gladstone Institutes at UC San Francisco) http://docpollard.com

The engineer will work in an interdisciplinary research group of evolutionary biologists, ecologists, and statisticians. Applicants should have substantial experience with genome-scale bioinformatics, including comparative genomics, analysis of protein families, multiple sequence alignment, and phylogenetic analyses. Familiarity with SQL, Perl/Python, and standard bioinformatics tools are essential. Typical responsibilities for this position may include designing and managing an in-house MySQL database of metagenomic sequence data; running BLAST, HMMER, and AMPHORA on the Global Ocean Survey and other large metagenomic data sets; identifying OTUs (operational taxanomic units) based on 16S rRNA or proteins; writing Perl scripts to query databases, process data, or run simulations; distributing data, scripts, and information to project members on all three campuses. Strong project management skills are essential.

We will offer a generous salary and benefits commensurate with experience. The position is available immediately, and the initial appointment will be for one year. The engineer would ideally be located at UC Davis, although other arrangements will be considered.

TO APPLY: Applications should be submitted at

http://jobs.genomecenter.ucdavis.edu/start_app.php?job_id=78

and consist of (1) a cover letter describing your interest in the position, (2) the names and contact information for three references, (3) a curriculum vita (including publications). Applications will be reviewed upon receipt, until the position is filled.

Sure, James Watson has been known, especially recently, to say some outrageous things. But here is something I think everyone, scientists and the public should read – an opinoin piece in the NY Times today by Watson ( Op-Ed Contributor – To Fight Cancer, Know the Enemy – NYTimes.com)

This piece is worth reading because it contains some critical ideas and wisdom which has been missing in discussions of the fight against cancer.

First, Watson discusses the critical importance of basic science and says that when he expressed this importance to the National Cancer Institute advisory board many years ago, he was eventually booted off.

Second, he discusses how we have only recently begun to understand the basic biology of cancer (he also mentions how the human genome project has helped in this). The genome project will, he says, allow for the determination of most/all of the major genetic changes that occur in cancer cells.

Third, he discusses some limitations of the FDA drug approval process that limit the ability to test combinations of drugs which Watson believes will be needed in the fight against cancer.

Fourth he suggests that the National Cancer Institute should help support small biotech companies in the development of new drugs since venture capital has dried up for such endeavors.

As usual, Watson would not be Watson if he did not say something potentially controversial. In this, the most controversial thing is probably how he discusses that the National Cancer Institute has become a “a largely rudderless ship in dire need of a bold captain who will settle only for total victory. ” Now, I do not have any opinion about this since I have not followed NCI or its leadership. But it is certainly worth considering Watson’s opinion here.

In the end, Watson says the time is now to reinvigorate the “War on Cancer.” Despite misgivings about many things he has been up to recently, I found myself agreeing with almost everything he said in this piece. Again, definitely worth a read.

Absolutely terrifying and intriguing story in the New York Times yesterday (Ghostwriters Paid by Wyeth Aided Its Drugs )

In the article Natasha Singer reports on how Wyeth commissioned the writing by a communication firm of a series of “draft” articles that were then published under the names of various medical professionals. It seems from the article that in some if not many cases the articles were in essence written by this company and then names of authors were placed on the papers which were then submitted to various journals and were published (they were generally review papers, and shockingly supported the use of Wyeth manufactured products).

The issues here are as always complex. But in the end, the articles did not disclose the role Wyeth played in paying for the writing of drafts and/or nearly complete forms of the papers and certainly should have. For more detail, read the Times article.

Interestingly, the documents that helped uncover the full details of the practice were obtained after a “a request in court from PLoS Medicine, a medical journal from the Public Library of Science, and The New York Times.” For more detail on this see the PLoS Medicine blog here. Kudos to PLoS Medicine for getting involved in this and for pushing hard for more disclosure in medical publishing.

All I can say is the practice of ghostwriting medical and scientific articles should stop. Getting help with editing a paper is one thing. But putting your name on a paper conceived of and written by someone else is unacceptable.