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

Results of #UCDavis Faculty Resolutions released re: Katehi, Pepper Spray, #OccupyUCDavis

Just received the three emails below regarding results of three UC Davis Faculty Senate Resolutions regarding the pepper spray incident from November and thought they might be of some interest.  See this post for a little background.  

REPORT OF THE DAVIS DIVISION OF THE ACADEMIC SENATE COMMITTEE ON ELECTIONS, RULES AND JURISDICTION

On December 20, 2011, a petition bearing the signatures of at least 50 members of the Davis Division of the Academic Senate of the University of California was submitted asking that the following Motion Concerning Police Actions be voted on by the membership of the Davis Division (tenure/tenure-track faculty of the UC Davis Campus):


Motion:


Be it resolved that that the Davis Division of the Senate of the University of California hereby (1) condemns both the dispatch of police and use of excessive force in response to non-violent protests on November 18, 2011;
(2) opposes violent police response to non-violent protests on campus;
(3) demands that police deployment against protestors be considered only after all reasonable efforts have been exhausted and with direct consultation with Academic Senate leadership.


The Davis Division membership was notified on February 3, 2012 that on-line balloting was open and would be closed on February 17, 2012, at 5:00 PM.  The on-line ballot results were reviewed by the Committee on Elections, Rules and Jurisdiction on February 17, 2012 after 5:00 PM and are reported as follows:


Total eligible voters:                               2,693


Required to pass:                               Majority


Vote received:
      Yes:                                                     635
      No:                                                      343


Invalid Ballots:                                             0


The Motion was therefore declared approved and the University of California, Davis Division of the Academic Senate does support the Motion Concerning Police Actions.


Respectfully submitted,


Committee on Elections, Rules and Jurisdiction
G.J. Mattey, Chair
James Fadel
Mark Grismer

REPORT OF THE DAVIS DIVISION OF THE ACADEMIC SENATE
COMMITTEE ON ELECTIONS, RULES AND JURISDICTION




On December 15, 2011, a petition bearing the signatures of at least 50 members of the Davis Division of the Academic Senate of the University of California was submitted asking that the following Five-Resolution Vote of Confidence be voted on by the membership of the Davis Division (tenure/tenure-track faculty of the UC Davis Campus):


Resolution:


Be it therefore resolved that the Davis Division of the Academic Senate:


1)     Condemns both the dispatch of police in response to non-violent protests and the use of excessive force that led to the deplorable pepper-spraying events of November 18, 2011.
2)     Opposes all violent police responses to non-violent protests on campus.
3)     Demands that police deployment against protesters be considered only after all reasonable administrative efforts to bridge differences have been exhausted, including direct consultation with the leadership of the Davis Division of the Academic Senate.
4)     Accepts Chancellor Linda Katehi’s good faith apology.
5)     Expresses confidence in Chancellor Linda Katehi’s leadership and efforts to place UC Davis among the top 5 public universities in the nation.


The Davis Division membership was notified on February 3, 2012 that on-line balloting was open and would be closed on February 17, 2012, at 5:00 PM.  The on-line ballot results were reviewed by the Committee on Elections, Rules and Jurisdiction on February 17, 2012 after 5:00 PM and are reported as follows:


Total eligible voters:                               2,693


Required to pass:                               Majority


Vote received:
      Yes:                                                     586
      No:                                                      408


Invalid Ballots:                                             0


The Motion was therefore declared approved and the University of California, Davis Division of the Academic Senate does support the Five-Resolution Vote of Confidence.


Respectfully submitted,


Committee on Elections, Rules and Jurisdiction
G.J. Mattey, Chair
James Fadel
Mark Grismer

REPORT OF THE DAVIS DIVISION OF THE ACADEMIC SENATE
COMMITTEE ON ELECTIONS, RULES AND JURISDICTION




On December 6, 2011, a petition bearing the signatures of at least 50 members of the Davis Division of the Academic Senate of the University of California was submitted asking that the following Motion Concerning the Chancellor’s Judgment be voted on by the membership of the Davis Division (tenure/tenure-track faculty of the UC Davis Campus):


Motion:  In light of the events on the quadrangle of the UC Davis campus on the afternoon of Friday November 18, 2011, in light of Chancellor Linda Katehi’s email to faculty of November 18 in which she admitted that she had ordered the police to take action against the students who were demonstrating on the quadrangle and said that she had had “no option” but to proceed in this way, and in light of the failure of Chancellor Katehi to act effectively to resolve the resulting crisis in the intervening days,


Be it therefore resolved that the Davis Division of the Senate of the University of California lacks confidence in the leadership of Chancellor Katehi, and


Be it also resolved that the result of the vote on this motion be communicated to the Board of Regents and the President of the University of California.


The Davis Division membership was notified on February 3, 2012 that on-line balloting was open and would be closed on February 17, 2012, at 5:00 PM.  The on-line ballot results were reviewed by the Committee on Elections, Rules and Jurisdiction on February 17, 2012 after 5:00 PM and are reported as follows:


Total eligible voters:                               2,693


Required to pass:                               Majority


Vote received:
      Yes:                                                     312
      No:                                                      697


Invalid Ballots:                                             0


The Motion was therefore declared defeated and the University of California, Davis Division of the Academic Senate does not support the Motion Concerning the Chancellor’s Judgment.


Respectfully submitted,


Committee on Elections, Rules and Jurisdiction
G.J. Mattey, Chair
James Fadel
Mark Grismer

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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.

——–

Calling on AAAS to Deposit all Archives of Science in Pubmed Central

Much has been written recently about a call to boycott Elsevier due to their outrageous policies regarding academic publishing.  I support the boycott but I also agree with many others who have said it perhaps unnecessarily singles out one publisher over others who also have publishing policies that could, well, use a bit of work.  And one such publisher is AAAS – the American Association for the Advancement of Science.

Today, the annual meeting of AAAS begins today in Vancouver.  I was supposed to be there by now, but thanks to some technical problems at Alaska Airlines, I am back in Davis for the day.  AAAS has some policies regarding openness that I believe are unnecessary and not in the general interest of scientific progress.  One is the strange “talk embargoes” I have written about recently.  Another, which is much more problematic, is the fact that Science Magazine (published by AAAS) does not deposit archival content in Pubmed Central.  Now, mind you, I think all scientific publishing funded by taxpayer money should be openly and freely available immediately. But that is not going to happen immediately.

One helpful tool in making scientific literature freely available is Pubmed Central.  Most scientific societies I know of deposit published material in Pubmed Central after some initial delay of 3-6-12 months.  But for reasons that are not entirely clear (to me at least, or to a Google search), AAAS clings to their archival material making it only available through their own web site.  Sure – they do allow authors to deposit their version of their manuscripts in Pubmed Central after a delay.  But most alas do not do this.  And I note – this option is only open to NIH and Wellcome Trust funded work.  So much material cannot be deposited anyway.

AAAS’s policy seems unnecessarily closed accessy and limits the impact and spread of the knowledge contained within papers in Science.  I note – this policy is yet another reason to not publish in Science and to instead choose either fully open access journals or ones that at least release their stranglehold on the papers after a short delay.

Today I call on AAAS to make archival literature from Science Magazine available in Pubmed Central.  And I call on others out there, such as those at the AAAS meeting, to pressure AAAS to do this.  Write blog posts.  Call and email AAAS members and leadership.  Email AAAS.  And so on.

Ideally everyone would just publish in fully open access journals and the journals would deposit material in archives.  But until that happens, we need to make every effort to increase the amount of literature getting into Pubmed Central and other archives.  So – pressure AAAS.  And while everyone is at it, please deposit whatever you can in preprint servers, in various repositories and in Pubmed Central.  Every little bit helps.

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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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Calling all phylogeneticists: Encyclopedia of Life Phylogenetic Tree Challenge

Just got an email from Todd Vision about this. Definitely seems worth checking out: EOL Phylogenetic Tree Challenge – Encyclopedia of Life
The challenge is summarized on their web site and I quote it here
“A prize is offered to the individual or team that can provide a very large, phylogenetically-organized set(s) of scientific names suitable for ingestion into the Encyclopedia of Life as an alternate browsing hierarchy.

  • Names must be provided in Darwin Core Archive1 format.
  • Extinct organisms may be treated but are not required.
  • Ranks are not required for names but may be included.
  • Internal nodes need not all have formal Linnaean names but require a label which can be arbitrary. Leaf nodes also need not have formal names but ideally most will overlap with current EOL species pages.
  • For the purpose of this contest, metrics and source of node support, branch lengths, vernaculars, and synonyms are not required. These may be included; not all are currently displayable on EOL.
  • Trees must be rooted. Multiple, overlapping hierarchies may be submitted as a set (e.g. to handle reticulation)
Among other factors, the total number of uniquely named nodes, node/leaf ratios and tree height may be used to compare entries so contestants should consider how they wish to trade off strict consensus versus other methods of reflecting the state of phylogenetic knowledge.
Problems to solve include 1) how to assign labels to unnamed nodes, 2) how to fill in gaps so that the set of taxa included is as comprehensive as possible, even if trees are not fully resolved or all taxa have not been analyzed, 3) how to handle competing hypotheses, 4) how to update the hierarchy at least annually.
The winning submission must be available to EOL and others under an acceptable CC license if it is under copyright. The tree need not be previously published in peer-reviewed form.
Questions about the challenge may be asked in the Phylogenetic Tree Challenge community on EOL.”

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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.

——–

Leaked insider docs from Heartland Institute goal: "dissuading teachers from teaching science" (ps hey Scholarly Kitchen do you support this?)

Yesterday I worried about the deceptive climate change related writings and work of one of the authors at the Scholarly Kitchen blog: Something rotten in the Scholarly Kitchen?
Basically, I wrote about how one of the authors at the Scholarly Kitchen – David Wojick – has been involved in some groups that have taken a decidedly deceptive anti-science stance on the issue of climate change.
I did not translate all of my worries into words because they were not completely formed. One of the reasons for my concern was the feeling that Wojick might be using his position in a apparently scholarly group to boost his authority in some way. Note – he has no apparent record of working on climate science yet he has written about it extensively with attempted authority.
Well, my unformed thoughts have hit me smack in the face today. Alexy Merz pointed me to this article published today:INTERNAL DOCUMENTS: The Secret, Corporate-Funded Plan To Teach Children That Climate Change Is A Hoax | ThinkProgress
The article quotes internal documents from the “Heartland Institute” discussing the development by one David Wojick of a “global warming curriculum for elementary schoolchildren that presents climate science as ‘a major scientific controversy.’ “
And more disturbing, the internal papers imply that they believe Wojick’s curricula have great potential for spreading because of his connections to organizations involved in “producing, certifying, and promoting scientific curricula.” So, in a way I think it is not a stretch to interpret his involvement in the Scholarly Kitchen as a way to boost his “authority” in academic circles even in the absence of any expertise in climate science.

And then as the evening progressed I found out more detail from the internal documents of the Heartland Institute that are even more disturbing:

Mind you, I generally try to avoid mixing writing about science and politics – and I am pretty open to diverse political points of view. But this is different.  The Heartland Institute and Wojick and others are using the same strategy used by Intelligent Design advocates. They want to “teach the controversy” and they want to make equivalent the thoughts of a few people with actual research by 1000s of scientists. I am all for freedom of speech and think anyone should be able to express their beliefs and opinions in a free and open manner.

The ultimate to me is in this leaked document:

Development of our “Global Warming Curriculum for K-12 Classrooms” project. Principals and teachers are heavily biased toward the alarmist perspective. To counter this we are considering launching an effort to develop alternative materials for K-12 classrooms. We are pursuing a proposal from Dr. David Wojick to produce a global warming curriculum for K-12 schools. Dr. Wojick is a consultant with the Office of Scientific and Technical Information at the U.S. Department of Energy in the area of information and communication science. His effort will focus on providing curriculum that shows that the topic of climate change is controversial and uncertain- two key points that are effective at dissuading teachers from teaching science. We tentatively plan to pay Dr. Wojick $100,000 for 20 modules in 2012, with funding pledged by the Anonymous Donor.

Let me repeat one part:

His effort will focus on providing curriculum that shows that the topic of climate change is controversial and uncertain – two key points that are effective at dissuading teachers from teaching science.

http://storify.com/phylogenomics/scholarly-kitchen-bloggers-response-to-questions.js?template=slideshow[<a href=”http://storify.com/phylogenomics/scholarly-kitchen-bloggers-response-to-questions” target=”_blank”>View the story “Scholarly Kitchen Bloggers response to questions” on Storify</a>]
UPDATE 4: More stories

UPDATE 5: 2-15 Kent Anderson, head of The Scholarly Kitchen blog responds and says actions of Wojick are irrelevant to his blog.
@phylogenomics @drs1969 it’s an irrelevant topic to this blog. It’s not a science blog, it’s a publishing blog.
Incredible. So – apparently being paid to deceive about the science behind studies of climate change is not relevant to a blog about publishing which has a big emphasis on peer review and science.

UPDATE 6: 2-15 8 PM More stories

UPDATE 7 with even more links:
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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.

——–

Some of the more interesting papers in Pubmed Central that reference Valentine’s Day

Earlier this AM I posted to twitter a brief comment about articles in Pubmed Central that reference Valentine’s Day.

//platform.twitter.com/widgets.js

Kay Thaney’s response caught my eye b/c she called attention to some of the more interesting papers from my link:

//platform.twitter.com/widgets.js

So I thought I would post a few of the links here:

Enjoy …
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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.

——–

Paper out from the "Evolution in the Deep Biosphere" workshop I went to #OpenAccess

Just picked up this paper in one of my automated Google searches for, well, my own name: Prospects for the Study of Evolution in the Deep Biosphere.
The paper is the result of a workshop I went to at the USC Wrigley Marine Station on Catalina Island. See my notes on the trip here: A “work” trip to Catalina Island: USC, Wrigley, C-DEBI, dark energy biosphere, Virgin Oceanic, Deep Five, & more. I note – the group of people at the meeting worked on their paper after the meeting and invited me to be a co-author on it. However, I was busy and I felt like I could not contribute to it in a way that would qualify for authorship. So I sent them comments here and there and had also given them some ideas while at the meeting. And now I am happy to report their paper is out.

I note – the paper is in “Frontiers in Extreme Microbiology” one of the new Open Access journals in the Frontiers series.  Not sure yet what to think of all these Frontiers journals.  But they do have a suite of journals in “Microbiology” so I will keep an eye on them …

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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.

——–

Something rotten in the Scholarly Kitchen? (Climate Change Denialism is Everywhere)

I never not previously paid much attention to the “Scholarly Kitchen” site before.  Every once in a while I have noticed their posts and usually have found them off in some way.  But then my brother Michael decided to respond to a recent posting from someone named Kent Anderson there.

I wrote about this briefly here: Trolls and flames discuss #NotSoFunny satire at the Scholarly Kitchen.

And the twitter had quite a bit too.  So, of course, I made a “Storification” of this:

http://storify.com/phylogenomics/scholarly-kitchen-rwa-parody-dissected.js[<a href=”http://storify.com/phylogenomics/scholarly-kitchen-rwa-parody-dissected” target=”_blank”>View the story “Scholarly Kitchen RWA \”Parody\” Dissected” on Storify</a>]

But that is not what I am here to discuss.  What I am here to discuss is something that I discovered from a tweet of my brother’s.

//platform.twitter.com/widgets.js
And I clicked on the link but the details were not there.  So I sniffed around a bit and did some googling (I could have just called my brother I guess …).

And I discovered that one of the contributors to the Scholarly Kitchen David Wojick does indeed appear to be a pretty extreme climate change denialist.  Some information reported to be about him and his anti-climate-change ways can be found at these sites

Apparently Wojick has been affiliated with places like the Heartland Institute (see more on them here) and the Greening Earth Society which are relatively notorious in their “climate change is not happening” points of view.

Sniffing around the web I found some publications which appear to be by him that certainly are, well, extreme:

Not sure what this means exactly about the Scholarly Kitchen site but it smells a bit like their power went out and stuff is rotting in their fridge.
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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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Cool paper from DerisiLab on viruses in unknown tropical febrile illnesses #metagenomics #viroarray

Quick post:

Figure 3. Circovirus-like
NI sequence coverage and phylogeny.

Cool new paper from Joe Derisi’s lab: PLoS Neglected Tropical Diseases: Virus Identification in Unknown Tropical Febrile Illness Cases Using Deep Sequencing

Full citation: Yozwiak NL, Skewes-Cox P, Stenglein MD, Balmaseda A, Harris E, et al. (2012) Virus Identification in Unknown Tropical Febrile Illness Cases Using Deep Sequencing. PLoS Negl Trop Dis 6(2): e1485. doi:10.1371/journal.pntd.0001485

They used a combination of a viral microarray and metagenomic sequencing to characterize viruses in various samples from patients with febrile illness.  And they found some semi-novel viruses in the sample.  Definitely worth a look.

Note – here are some other posts of mine about Derisi:

See some follow up discussion on Google+ here.

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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.

——–

Trolls and flames discuss #NotSoFunny satire at the Scholarly Kitchen

Bit of a tiff going on over at the Scholarly Kitchen over a “satire” someone named Ken Anderson wrote related to the Research Works Act. The piece was about the “Restaurant Works Act” — Someone pointed me to the post and I found the satire to be, well, unfunny so I chose to ignore it. My brother alas could not ignore it, nor could some others and there is some discussion going on there now.

I will skip commenting on the discussion itself – go read it. But a few things there annoyed me. One of these is that Anderson has resorted to criticizing the punctuation of some of his critics there. That is pretty lame.  See start of thread below

Alex Merz wrote 

The inappropriateness of the analogy was clear by the end of paragraph 2. For the rest: TL;DR

To which Anderson responded

For those of us not as hip as Alex, TL DR means “too long, didn’t read.” I won’t comment on the inappropriateness of the semicolon in his Urban Dictionaryesque construction. The post is about 850 words, by the way

To which Alex re-responded

It is sad when an overly serious someone attempts a grammar or usage flame, and fails. 

“Too long; didn’t read” is both proper usage and a more effective construction than “too long, didn’t read.” 

Bryan Garner: “Fourth, the semicolon sometimes appears simply to give a weightier pause than a comma would. This use is discretionary. A comma would do, but the writer wants a stronger stop—e.g.: “There is never anything sexy about Lautrec’s art; but there also is never anything deliberately, sarcastically anti-feminist in it.” Aldous Huxley, “Doodles in the Dictionary” (1956), in Aldous Huxley: Selected Essays 198, 206 (1961).” 

Don’t be sad, though. Like you, a lot of smart people don’t know their way around a semicolon. 

If you’re too timid to wade into Fowler, Strunk & White, or Garner, there is help:
http://theoatmeal.com/comics/semicolon

 

To which Anderson responded

Nice try, but you don’t have any reason to use a semicolon there. In any event, I think you’re just covering up a typo with sophistry, so let’s move on.

To which Merz responded

You attempt a punctuation flame. When your own-goal is pointed out (with reference to authoritative sources) you mumble that your flame was correct (though it wasn’t), and you indicate that we should drop the discussion of punctuation that *you initiated.* 

Do you have *any* idea that makes you look? 

I’m guessing that you don’t: http://en.wikipedia.org/wiki/Dunning–Kruger_effect

and so on …

And before the folks at Scholarly Kitchen accuse me of having no sense of humor about such things – I suggest they look at my history of making fun of EVERYONE in publishing all the time.  The key to me is to be funny first and if you have some political comments you want to make, make them in that context.  I found the cooking / food RWA story to just not be funny so I did not pay any attention to its other messages.  Though clearly those messages bothered some folks, like my brother.

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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.

——–

Storification of Fake Science Publishing @fakeelsevier @fakeplos @realelsevier @fakeeisen @closedaccessj

So – I have been enjoying all the Fake Scientific Publishing Posts on Twitter from @fakeelsevier @fakeplos @realelsevier @fakeeisen @closedaccessj and others.  Now I understand why some people think I am behind some of these (e.g., here are some of my Fake Science News posts).  But alas though I WISH I was behind some of these accounts, I am not.  Anyway – I created a storification of the beginning of some of these postings if you want to see some of the origins of the fakery.

http://storify.com/phylogenomics/fake-scientific-publishing.js[<a href=”http://storify.com/phylogenomics/fake-scientific-publishing” target=”_blank”>View the story “Fake Scientific Publishing” on Storify</a>]

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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.

——–