Eisen Lab Blog

Workshop of Interest: 7 Secretes of Highly Successful PhDs and Masters Students

The 7 Secrets of Highly Successful PhDs and Masters Students

March 1, 2012 12-2:30 PM

UC Davis: Internship and Career Center.

 

 

New openaccess paper from my lab on "Zorro" software for automated masking of sequence alignments

A new Open Access paper from my lab was just published in PLoS One: Accounting For Alignment Uncertainty in Phylogenomics. Wu M, Chatterji S, Eisen JA (2012) Accounting For Alignment Uncertainty in Phylogenomics. PLoS ONE 7(1): e30288. doi:10.1371/journal.pone.0030288

The paper describes the software “Zorro” which is used for automated “masking” of sequence alignments.  Basically, if you have a multiple sequence alignment you would like to use to infer a phylogenetic tree, in some cases it is desirable to block out regions of the alignment that are not reliable.  This blocking is called “masking.”

Masking is thought by many to be important because sequence alignments are in essence a hypothesis about the common ancestry of specific residues in different genes/proteins/regions of the genome.  This “positional homology” is not always easy to assign and for regions where positional homology is ambiguous it may be better to ignore such regions when inferring phylogenetic trees from alignments.

Historically, masking has been done by hand/eye looking for columns in a multiple sequence alignment that seem to have issues and then either eliminating those columns or giving them a lower weight and using a weighting scheme in the phylogenetic analysis.

What Zorro does is it removes much of the subjectivity of this process and generates automated masking patterns for sequence alignments.  It does this by assigning confidence scores to each column in a multiple seqeunce alignment. These scores can then be used to account for alignment accuracy in phylogenetic inference pipelines.

The software is available at Sourceforge: ZORRO – probabilistic masking for phylogenetics.  It was written primarily by Martin Wu (who is now a Professor at the University of Virginia) and Sourav Chatterji with a little help here and there from Aaron Darling I think.  The development of Zorro was part of my “iSEEM” project that was supported by the Gordon and Betty Moore Foundation.

In the interest of sharing, since the paper is fully open access, I am posting it here below the fold. UPDATE 2/9 – decided to remove this since it got in the way of getting to the comments …

——–
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.

——–

Symposium of possible interest: UC Davis Law School on Scientific Evidence

The UC Davis Law School is having a symposium on scientific evidence. Information can be found here: UC Davis School of Law – News & Events – Events.

I have copied text from the announcement below:

Law Review Symposium “The Daubert Hearing – From All the Critical Perspectives”

Friday, March 2

Kalmanovitz Appellate Courtroom

March 2, 9:00 a.m. – 4:30 p.m.

Free – MCLE CREDIT provided (approx. 6 hours)

Come and learn from the experts about the tactical use of scientific evidence in litigation. On March 2, 2012, the UC Davis Law Review will host a symposium in two parts. In the first half, a federal judge and two experienced attorneys will conduct a Daubert hearing on a controversial type of expert testimony. During the second segment, our expert academic panel will comment on scientific evidence and discuss the law and tactics of Daubert hearings.

This symposium is designed to help scientists and litigators better produce and evaluate scientific evidence.

The Supreme Court’s celebrated 1993 decision in Daubert v. Merrell Dow Pharmaceuticals, Inc. adopted a new empirical validation test for the admissibility of scientific evidence.

In criminal cases, defense counsel started challenging the prosecution’s forensic evidence identifying the accused as the perpetrator. In civil tort cases, defense counsel filed motions attacking the plaintiff’s evidence on general causation. When counsel won these motions, the opposition lacked sufficient evidence to go to trial. The hearing on the pretrial Daubert motion became the centerpiece of the litigation.

The participants are:

Hon. James Rosenbaum, a distinguished former federal District Court judge in Minnesota who has lectured widely on the subject of expert testimony;

Mr. Bert Black from Minnesota, a leading plaintiff’s attorney who coauthored one of the leading articles on Daubert in Texas Law Review;

Mr. Robert Smith, a veteran defense attorney from Maryland who specializes in major cases involving expert testimony;

Dr. William Toscano, Professor and Division Head of Environmental Health Sciences at the University of Minnesota;

Dr. Sander Greenland, Professor of Epidemiology and Professor of Statistics at UCLA.

After the demonstration, all of the participants will deliver remarks, giving their perspective on the law, strategy, and tactics of Daubert hearings. In addition, there will be expert academic commentary by Professor David Faigman of U.C. Hastings School of Law, the lead author of the popular treatise, Modern Scientific Evidence. The moderator will be Professor Edward Imwinkelried of U.C. Davis, the coauthor of Scientific Evidence (with Giannelli).

There will be a complimentary breakfast spread, lunch, and post-event hors d’oeuvres and wine/coffee.

EVENT: The Daubert Hearing Symposium – UC Davis Law Review

TIME: March 2, 2012. 9:00 a.m. – 4:30 p.m.

LOCATION: UC DAVIS School of Law, 400 Mrak Circle Drive, Davis, CA. King Hall Room 1001 (Kalmanovitz Appellate Courtroom)

COST: FREE MCLE CREDIT (approx. 6 hours)

RSVP: lawreview@law.ucdavis.edu

Fun visit to the #UCDavis Bohart Entomology Museum w/ my daughter’s Daisy Troop (led by my wife)

Kudos to the UC Davis Bohart Museum of Entomology for the tour they gave to the Daisy Troop my daughter is in (which is run by my wife and a friend of hers). I got there a little late and embarrassed myself by thinking one of the dads was one of the museum workers and introducing myself (even though I know the dad pretty well).  Oh well, live and let learn.  The visit went great – the kids got to play with bugs, got to open the stacks and even pull out drawers of various bugs (note – the general term, not the Homoptera).  The museum staff were wonderful and the museum itself is very nice.  A great kids activity in Davis and good for adults too.  Always great to see passionate science education and outreach.

——–
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.

——–

Next up for Science in Congress: HR3433 – the Grant Reform and Transparency Act

Just got pointed to this by Mark Martin. There is a new bill making its way through congress – HR 3433 – the Grant Reform and New Transparency Act of 2011. It has a subtitle apparently of “To amend title 31, United States Code, to provide transparency and require certain standards in the award of Federal grants, and for other purposes.”
The full text of the bill and other information is available here.
I personally don’t know much about this bill but found some discussion of it here:
I have not formed an opinion of the act but thought I would share the information since it does not seem to be getting much attention but seems like it could have impact.  I note – one group that I respect deeply supports the act: the Sunlight Foundation which involves people like Ester Dyson and Lawrence Lessig.  Any opinions or insight on the bill would be welcome.
——–
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.

——–

Stop deifying "peer review" of journal publications:

Peer review.  It is a critical part of scientific research and scientific progress.  Without it, science as a field might look like Fox News Stories or postings on Jenny McCarthy’s web site, where ideas people have are given gravitas regardless of how ludicrous they are.  But somehow, many in the public and press, and many many scientists alas, have deep misconceptions about peer review.

The most recent example of such misconceptions involves the arsenic life saga.  If you are not familiar with this story – here is a summary (for some fine scale details on the early parts of the story see Carl Zimmer’s post here).

In November 2010 NASA announced that in a few days they would hold a press conference discussing a major finding about life in the universe.  On December 2, 2010, they held their press conference and discussed a paper that was in press in Science from multiple NASA funded authors including Felisa Wolfe-Simon.  The paper was of interest because it claimed to have shown that a bacterium was able to replace phosphate in its macromolecules, including its DNA, with arsenic.  The press conference made claims that were very grandiose, like that textbooks would have to be rewritten, and the study of life on Earth and elsewhere would have to be completely rethought.

After a few days of mostly very glowing press reports, a few critiques began to emerge including in particular one from Rosie Redfield, a microbiologist at the University of British Columbia.  The critiques then snowballed and snowballed and the general consensus of comments appeared to be that the paper had fundamental flaws.  Some of the critiques got way too personal in my opinion and I begged everyone to focus on the science not personal critiques.  This seemed to work a little bit and we could focus on the science, which still seemed to be dubious.  And many, including myself, expressed the opinion that the claims made by the authors in the paper and by the authors and NASA in the press conference and in comments to the press, were misleading at best.

Now critiques about new findings are not unusual.  We will get back to that in a minute.  But what was astonishing to me and many others, was how NASA and the authors responded.  They said things like:

… we hope to see this work published in a peer-reviewed journal, as this is how science best proceeds.

and

It is one thing for scientists to “argue” collegially in the public media about diverse details of established notions, their own opinions, policy matters related to health/environment/science. 

But when the scientists involved in a research finding published in scientific journal use the media to debate the questions or comments of others, they have crossed a sacred boundary [via Carl Zimmer]

and the kicker for me was a letter Zimmer posted

Mr. Zimmer, 

I am aware that Dr. Ronald Oremland has replied to your inquiry. I am in full and complete agreement with Dr. Oremland’s position (and the content of his statements) and suggest that you honor the way scientific work must be conducted. 

Any discourse will have to be peer-reviewed in the same manner as our paper was, and go through a vetting process so that all discussion is properly moderated. You can see many examples in the journals Science and Nature, the former being where our paper was published. This is a common practice not new to the scientific community. The items you are presenting do not represent the proper way to engage in a scientific discourse and we will not respond in this manner. 

Regards,
Felisa

This was amazing since, well, they were the ones who held the overhyped press conference.  And then I (and others) found it appalling that they in essence would not response to critiques because they were not “peer reviewed.” I told Zimmer

Whether they were right or not in their claims, they are now hypocritical if they say that the only response should be in the scientific literature.

Zimmer had a strong defense of scientists “discussing” the paper:

Of course, as I and others have reported, the authors of the new paper claim that all this is entirely inappropriate. They say this conversation should all be limited to peer-reviewed journals. I don’t agree. These were all on-the-record comments from experts who read the paper, which I solicited for a news article. So they’re legit in every sense of the word. Who knows–they might even help inform peer-reviewed science that comes out later on.

(I note – yes I am quoting a lot from Zimmer’s articles on the matter and there are dozens if not hundreds of others – apologies to those out there who I am not referencing – will try to dig in and add other references later if possible).

And so the saga continued.  Rosie Redfield began to do experiments to test some of the work reported in the paper.  Many critiques of the original paper were published.  The actual paper finally came out.  And many went about their daily lives (I keep thinking of the Lord of the Rings whisper “History became legend. Legend became myth. And for two and a half thousand years, the ring passed out of all knowledge.”  Alas, the arsenic story did not go away.

And now skipping over about a year.  The arsenic story came back into our consciousness thanks to the continued work of Rosie Redfield.  And amazingly and sadly, Wolfe-Simon’s response to Rosie’s work included a claim that they never said that arsenic was incorporate into the bacterium’s DNA.  (I have posted a detailed refutation of this new “not in DNA” comment here).

But that is not what I am writing about here.  What is also sad to me are the continued statements by the paper’s authors that they will not discuss any critiques or work of others unless they are published in a peer reviewed article.

For example, see Elizabeth Pannisi’s article in Science:

But Wolfe-Simon and her colleagues say the work on arsenic-based life is just beginning. They told ScienceInsider that they will not comment on the details of Redfield’s work until it has been peer reviewed and published.

So – enough of an introduction.  What is it I wanted to write about peer review?  What I want to discuss here is that the deification of a particular kind of journal peer review by the arsenic-life authors is alas not unique.  There are many who seem to have similar feelings (e.g., see this defense of the Wolfe-Simon position).  I believe this attitude towards peer review is bad for science.  Fortunately, many others agree (e.g., see this rebuttal of the defense mentioned above) and there is a growing trend to expand the concepts of what peer review is and what it means (see for example, David Dobbs great post about peer review and open science from yesterday).

Though much has been written about peer review already (e.g., see Peer review discussion at Nature as one example), I would like to add my two cents now – focusing on the exalted status some give to peer reviewed journal articles.  I have three main concerns with this attitude which can be summarized as follows

  1. Peer review is not magic
  2. Peer review is not binary
  3. Peer review is not static.

I suppose I could stop here but I should explain.

Regarding #1 “Peer review is not magic.”. 
What I mean by this is that peer review is not something that one can just ask for and “poof” it happens.  Peer review of articles (or any other type of peer review for that matter) frequently does not work as sold – work that is poor can get published and work that is sound can get rejected.  While it may pain scientists to say this (and brings up fears of FoxNews abusing findings) it is alas true.  It is not surprising however given the way articles get reviewed.

In summary this is how the process works.  People write a paper.  They then submit it to a journal. An editor or editors at the journal decide whether or not to even have it reviewed.  If they decide “no” the paper is “sent back” to the authors and then they are free to send it somewhere else.  If they decide “yes” to review it, the editors then ask a small number of “peers” to review the article (the number usually ranges from 2-3 in my field).  Peers then send in comments to the editor(s) and the editor(s) then make a “decision” and relay that decision to the authors.  They may say the paper is rejected.  Or they may say it is accepted.  Or they may say “If you address the comments of the reviewers, we would consider accepting it”.  And then the authors can make some revisions and send it back to the editors.  Then it is reviewed again (sometimes just by the editors, sometimes by “peers”).  And it may be accepted or rejected or sent back for more revisions.  And so on.

In many cases, the review by peers is insightful, detailed, useful and in the best interests of scientific progress.  But in many cases the review is flawed.  People miss mistakes.  People are busy and skim over parts of the paper.  People have grudges and hide behind anonymity.  People can be overly nice in review if the paper is from friends.  People may not understand some of the details but may not let the editors know.  Plus – the editors are not completely objective in most cases either.  Editors want “high profile” papers in many cases.  They want novelty.  They want attention.  This may lead them to ignore possible flaws in a paper in exchange for the promise that it holds.  Editors also have friends and enemies.  And so on.  In the end, the “peer review” that is being exalted by many is at best the potentially biased opinion of a couple of people.  At worst, it is a steaming pile of … Or, in other words, peer review is imperfect.  Now, I am not saying it is completely useless, as peer review of journal articles can be very helpful in many ways.  But it should be put in its rightful place.

Regarding #2: “Peer review is not binary”
The thumbs up / thumbs down style of peer review of many journal articles is a major flaw.  Sure – it would be nice if we could apply such a binary metric.  And this would make discussing science with the press and the public so much easier “No ma’am, I am sorry but that claim did not pass peer review so I cannot discuss it” “Yes sir, they proved that because their work cleared peer review.”  But in reality, papers are not “good” or “bad”.  They have good parts and bad parts and everything in between.  Peer review or articles should be viewed as a sliding scale and not a “yes” vs. “no.”

Regarding #3: “Peer review is not static”
This is perhaps the most important issue to me in peer review of scientific work.  Peer review of journal articles (as envisioned by many) is a one time event.  Once you get the thumbs up – you are through the gate and all is good forever more.  But that is just inane. Peer review should be – and in fact with most scientists is – continuous.  It should happen before, during and after the “peer review” that happens for a publication.  Peer review happens at conferences – in hallways – in lab meetings – on the phone – on skype – on twitter – at arXiv – in the shower – in classes – in letters – and so on.  Scientific findings need to be constantly evaluated – tested – reworked – critiqued – written about – discussed – blogged – tweeted – taught – made into art – presented to the public – turned inside out – and so on.
Summary:
In the end – what people should understand about peer review is that though it is not perfect, it can be done well.  And the key to doing it well is to view it as a continuous, nuanced activity and not a binary, one time event.  

UPDATE 3: some twitter comments

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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.

——–

Seminar of interest – Stephen Kowalczykowski 2/8 4:10 PM

Dr. Stephen Kowalczykowsk

“So, How Does RecA Find Homologous DNA Sequences?”

Wednesday, February 8, 2012

4:10pm

1022 Life Sciences

Interesting new metagenomics paper w/ one big big big caveat – critical software not available "

Very very strange.  There is an interesting new metagenomics paper that has come out in Science this week.  It is titled “Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota” and it is from the Armbrust lab at U. Washington.

One of the main points of this paper is that the lab has developed software that apparently can help assemble the complete genomes of organisms that are present in low abundance in a metagenomic sample.  At some point I will comment on the science in the paper, (which seems very interesting) though as the paper in non Open Access I feel uncomfortable doing so since many of the readers of this blog will not be able to read it.

But something else relating to this paper is worth noting and it is disturbing to me.  In a Nature News story on the paper by Virginia Gewin there is some detail about the computational method used in the paper:

“He developed a computational method to break the stitched metagenome into chunks that could be separated into different types of organisms. He was then able to assemble the complete genome of Euryarchaeota, even though it was rare within the sample. He plans to release the software over the next six months.”

What?  It is imperative that software that is so critical to a publication be released in association with the paper.  It is really unacceptable for the authors to say “we developed a novel computational method” and then to say “we will make it available in six months”.  I am hoping the authors change their mind on this but I find it disturbing that Science would allow publication of a paper highlighting a new method and then not have the method be available.  If the methods and results in a paper are not usable how can one test/reproduce the work?

——–
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.

——–

2010 "Arsenic found in DNA", 2012 "We never claimed arsenic was in the DNA" WTF?

Unbelievable.  Check out this news story on some new results relating to the “Arsenic Life” story.  The story discusses a paper from Rosie Redfield that has been deposited in arXiv.  Rosie has been persistent in doing tests on the strain GFAJ-1 that Wolfe-Simon had isolated.  One of their new results is that they cannot detect arsenic/arsenate in the DNA from this strain.  Amazingly, in this news story Wolfe-Simon is reported to have said that they never claimed that arsenic was getting into the DNA:

Wolfe-Simon, who says she can’t comment in detail until Redfield’s results appear in a peer-reviewed journal, wrote in an email that her original paper never actually claimed that arsenate was being incorporated in GFAJ-1’s DNA, but that others had jumped to that conclusion. “As far as we know, all the data in our paper still stand,” she wrote. “Yet, it may take some time to accurately establish where the [arsenic] ends up.”

Wow.  I recommend people go check out the original paper and see for themselves.  And also check out the press conferences and news stories.  The whole thing was about their claim that the arsenic was ending up in the DNA. 
In their abstract, for example:

Our data show evidence for arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins. Exchange of one of the major bio-elements may have profound evolutionary and geochemical importance.

In their conclusions:

We report the discovery of an unusual microbe, strain GFAJ-1, that exceptionally can vary the elemental composition of its basic biomolecules by substituting As for P. How As insinuates itself into the structure of biomolecules is unclear, and the mechanisms by which such molecules operate are unknown.

I personally am hoping beyond hope that Wolfe-Simon was misquoted in the new story, but I am guessing that that is unlikely.  As I have said before, I feel some sympathy towards Wolfe-Simon and I was one of the first people to call for the community to stop the personal attacks against her and to focus on the science and her claims about the science.  And I still think we need to do this.  But this does not mean we should to not criticize her claims and the almost ludicrous path she is leading some people down with her comments. The notion that they never claimed arsenic/arsenate was getting into the DNA of the strain they isolated is beyond absurd. 

Hat tip to Rosie Redfield for alerting me to this news story.

UPDATE: See these other stories on the new work

UPDATE2: Here are some additional quotes from the original paper to consider:

These measurements therefore specifically demonstrated that the purified DNA extracted from +As/–P cells contained As.

Our NanoSIMS analyses, combined with the evidence for intracellular arsenic by ICP-MS and our radiolabeled 73AsO43– experiments, indicated that intracellular AsO43– was incorporated into key biomolecules, specifically DNA

Therefore, our x-ray data support the position of AsO43– in a similar configuration to PO43– in a DNA backbone or potentially other biomolecules as well

UPDATE3: Some quotes from older news stories

From the Christian Science Monitor 12.2.2010

“So far we’ve showed that it can do it in DNA, but it looks like it can do it in a whole lot of other biomolecules” as well, says Wolfe-Simon, a NASA research fellow in residence at the USGS in Menlo Park, California. 

“It is the first time in the history of biology that there’s been anything found that can use one of the different elements in the basic structure,” says Paul Davies, the director of BEYOND: Center for Fundamental Concepts in Science at Arizona State University in Tempe, Arizona.

 From CNN 12-2-2010

“We’ve discovered an organism that can substitute one element for another,” said NASA scientist Felisa Wolfe-Simon. “Nothing should have grown. Put your plant in the dark, it doesn’t grow.” 

The bacterium not only grew but also incorporated the arsenic molecules into its DNA, in place of phosphorus, she said 

“We’ve cracked open the door to what’s possible elsewhere in the universe,” Wolfe-Simon said during a press conference Thursday.

UPDATE 4: Here is the text of one of the original press releases entitled “Get Your Biology Textbook…and an Eraser!”

One of the basic assumptions about life on Earth may be due for a revision thanks to research supported by NASA’s Astrobiology Program. Geomicrobiologist Felisa Wolfe-Simon has discovered a bacterium in California’s Mono Lake that uses arsenic instead of phosphorus in its DNA. Up until now, it was believed that all life required phosphorus as a fundamental piece of the ‘backbone’ that holds DNA together. The discovery of an organism that thrives on otherwise poisonous arsenic broadens our thinking about the possibility of life on other planets, and begs a rewrite of biology textbooks by changing our understanding of how life is formed from its most basic elemental building blocks. Astrobiology Magazine has the story. 

Wolfe-Simon’s research is supported by NASA’s Exobiology and Evolutionary Biology (Exo/Evo) Program and the NASA Astrobiology Institute. Among the goals of these programs is determining the evolution of genes, metabolic pathways, and microbial species on Earth in order to understand the potential for life on other worlds. Wolfe-Simon’s discovery represents the first time in the history of biology that an organism has been found to use a different element to build one of its most basic structures. The paper appears in today’s issue of “Science Express“ and will subsequently be published in the journal Science.

UPDATE 5: In 2010 for the press conference about the arsenic story NASA even released a video showing how arsenic could replace phosphorus in DNA.

UPDATE 6: A video of the original press conference shows Wolfe-Simon introducing the video as a model of how they think arsenic replaces phosphorus in the DNA.

UPDATE 7: In a blog post relating to the arsenic life story, Brian Krueger suggests we should in essence discount some new work by Rosie Redfield on the topic because it has not “been properly reviewed.” – see his full post here: A peril of “Open” science: Premature reporting on the death of #ArsenicLife

I tried to comment there but something did not work so I figured I would post my comments here. I think his point is completely and thoroughly wrong. What I had tried to post there I thought might be useful to share here:

I cannot disagree more with your post here. You vastly overvalue what happens in peer review. Peer review should not be considered a thumbs up / thumbs down process as you are suggesting here. And it should not be considered a one time event. It should be considered a continuous process and a sliding scale. Some things that get through the normal peer review process for papers are end up being retracted and many things that are presented prior to traditional peer review are fundamental new insights. Scientific results can be evaluated before, during and after the review that happens for a publication. Scientists do this all the time already – at conferences – in hallways – in lab meetings – on the phone – on skype – on twitter – at arXiv – in the shower – in classes – in letters – and so on. It is actually a disservice to science to annoint “peer review” as applied at some journals into something it is not.

Also see Zen Faulkes’ post in response to Brian’s: Reporting on that non peer reviewed stuff.  Hat tip to @boraz for pointing me to it.

UPDATE 8: Some links to additional stories coming out

UPDATE 9: Found a video of the whole press conference

UPDATE 10: some more links and news stories

UPDATE 11: July 7, 2012: lots of new things since March when I did the last update

UPDATE 12: Storify of Redfield’s talk at Evol2012 and related tweets


    ——–
    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.

    ——–

    Q & A about Elsevier, my blog retraction, and #OpenAccess

    Jop de Vrieze has written an article related to the Elsevier boycott for ScienceInsider:

    Thousands of Scientists Vow to Boycott Elsevier to Protest Journal Prices

    In the article, one of the things he discusses is my blog post (which I then “retracted) suggesting people ignore any papers published in Elsevier Journals: Boycotting Elsevier is not enough – time to make them invisible (UPDATED/RETRACTED).

    In his article he wrote:

    One scientist who strongly supports the boycott is Jonathan Eisen, a microbial genomicist at the University of California, Davis, and the Academic Editor-in-Chief of PLoS Biology, an open access journal. On Tuesday, Eisen urged readers of his blog to go one step further, by no longer paying attention to research published by Elsevier. “In essence, ignore them – consider them dead – make them invisible,” he wrote. But after readers protested that no paper should be ignored just because of where it’s published, Eisen quickly retracted the entire post, which he said had been written “at midnight, with a cat on my lap.” “The response to my post helped make me realize that the semi-sarcastic attempted tone was not coming through correctly,” Eisen writes in an e-mail to ScienceInsider.

    de Vrieze did a good job of representing my point of view.  But I thought it might be useful to all of the Q&A in the email with him.  Fortunately, he said this was OK to do so … here are my full answers to his questions:

    If you would have adjusted your blog, what would have been the main points your would have reconsidered?

    Oh – my blog post was really just a thought question written in anger in the middle of the night. I could have written it better but in the end, the idea behind the post was wrong-headed. Any scientific publication or presentation, no matter where it is made, should be considered a contribution to science. The name of the journal or the
    publisher does not matter (nor from my point of view does it matter if something is in a journal per se). Thus even though I was being a bit tongue in cheek in the post suggesting we ignore publications in Elsevier journals – clearly my tone was not coming through and I decided to retract the post.

    I note – following the recommendation of Ivan Oransky who runs the Retraction Watch site I left up the original post (though I changed it
    to strikethrough font) and posted an explanation for the retraction.
    I also tried to chase down twitter and blog and Google+ discussions of my post to say I was “retracting” the post and to explain why and what I had been trying to say.

    I also note – I had sense knocked into my head on this by people on twitter like @drugmonkey -so the response to my post helped make me realize that the semi-sarcastic attempted tone was not coming through correctly

    For your article you might want to check out the discussions happening on Google+ and on Drug Monkey’s blog.

    https://plus.google.com/u/0/103101121348859087349/posts/B8f1XyuY7Gk

    https://plus.google.com/u/0/106772544387169323774/posts/TszquaTKeoA

    What do you think is the value of this petition?

    I support the petition. I think scientist’s and others (humanities too …) need to take a stand against some of the publishing policies and political actions (e.g., support of the RWA) of Elsevier. I note – I already do not review for or publish in or edit for any of their journals. And I think if 1000s of scientists really followed through on this Elsevier might be forced to change their policies.

    What do you think needs to change in the system?

    I should note – I am personally not against for profit companies and not agains the notion that people can make a profit off of publishing.

    The problem I have is really two fold.

    1. I think that research and publications that are supported by taxpayer money should be made available broadly to the public. 
    2. I think there is abundant evidence that more openness in science is beneficial to the progress of science – open data (e.g., Genbank) has revolutionized certain fields. True open access publishing frees up the literature so that not only can anyone access it but also allows anyone to remix and utilize the literature in creative ways (and potentially make a profit from doing so). Open release of software is critical for cases where software is used in scientific publications. And so on. Openness aids in the progress of science.

    Thus with #1 and #2 above, I think it is imperative that we move towards more openness. The challenge is – how do we get there? And how do we pay for it? (Note – I am not saying above that being open has no cost – I am saying it is beneficial and politically wise). The problem with Elsevier in my mind is they take government subsidies that pay for journal charges, salaries of their reviewers and editors, and subscription fees for libraries – and in return – amazingly – they generally take ownership of the literature. This seems to be an unsound trade.

    So – the question is – can we become more open and afford it? Yes, I think it is pretty clear that there is more than enough money being spent currently on publishing broadly that could be reallocated to open publishing. The success of PLoS and Biomed Central and the move of some societies to release publications rapidly (e.g., ASM) indicates that this is possible (though I note – Science still lags in this area).

    I think we are still figuring out exactly how to set up a new system – but the old system of signing over the ownership and / or publishing rights for papers is no longer needed and it is not helpful to scientific progress.

    Who should take the first, or most important steps? Scientists? Publishers? Libraries? Institutions?

    Everyone. We all need to work together to come up with a system that retains the good things in the old system (e.g., scientific societies, good peer review, paper editing, etc) while being more open. We need to change hiring policies, library subscription systems, peer review, journal search algorithms, and so on.

    What, if publishers like Elsevier would disappear, would give scientists a mark of quality or relevance of scientific publications?

    Well – the name of a publisher and the name of a journal is a crude mark of quality at best. What should be measured is the ACTUAL quality of publications not a surrogate for quality. Certainly, everyone is busy and surrogates of quality end up being used a lot. But we need to develop systems that measure article quality better and also help people find the right articles for them. There are many examples of things in the works to help do this. The PLoS commenting system was/is an attempt at this. So is Faculty of 1000. I think post-publication peer review is going to be critical. The cream should rise to the top and the more we can do to make sure this happens quickly the better.

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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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