Eisen Lab Blog

Dean Robert Post 3/14/14 The Constitutional Dimensions of Academic Freedom

Posting this announcement I got:

Dear UC Davis Faculty, Staff, Students and Community Members,

We would like to remind you that the next event in the Provost’s Forums on the Public University and the Social Good, which is co-sponsored with the  Academic Senate’s Committee on Academic Freedom and responsibility, will be held on Friday, March 14, 2014.

Robert Post, Dean and Sol & Lillian Goldman Professor of Yale Law
School will speak on the topic of “The Constitutional Dimensions of
Academic Freedom”.  After his talk, he will be joined by a panel
comprised of Ralph Hexter, Provost and Executive Vice Chancellor at UC
Davis, Roberta Rehm, Associate Professor in the Department of Family
Health Care Nursing at UC San Francisco, and Henry Reichman, Professor
Emeritus of History at CSU Easy Bay and First Vice President of the
AAUP and its Committee A on Academic Freedom and Tenure.Prior to assuming his position as Dean of the Yale Law School, Dean
Post spent twenty years as a professor at the UC Berkeley School of

Law. His areas of expertise include constitutional law, First
Amendment law, legal history, and equal protection. He has written and
edited numerous books, including, For the Common Good: Principles of
American Academic Freedom (2009), and more recently Democracy,
Expertise, Academic Freedom: A First Amendment Jurisprudence for the
Modern State (2012).The event will begin at 2 p.m. in the Vanderhoef  Studio Theatre at
the UC Davis RobertMondavi Center. It is free and open to the general public. There will
be a reception with light refreshments directly following the lecture
in the Yoche Dehe Grand Lobby of the Mondavi Center.

If you are unable to attend this event, videos of all Provost’s Forums
lectures are available to the public and can be found on the official
Provost’s Forums website

(http://provost.ucdavis.edu/initiatives-and-activities/activities/future/past-events.html).

Our most recent lecture, “The Public University: What Should We Be
Doing on Climate Change?”  featuring Professor Naomi Oreskes, is now
available for viewing along with all of the 2013-2014 season lectures.For more details and information on this event, please see the
attached flyer, visit our website: The Provost’s Forum on the Public
University and the Social Good (http://provost.ucdavis.edu/initiatives-and-activities/activities/future/index.html), or contact Casey Castaldi (cvcastaldi@ucdavis.edu).

In addition, please forward this information to any interested parties, as all events are open to the public. We hope to see you at this important event!

Robert Post 3.14 Flyer.pdf

What to do when kicked out of my own lab meeting?

Thought some would enjoy a bit of comic relief.

//storify.com/phylogenomics/kicked-out-of-my-own-lab-meeting/embed//storify.com/phylogenomics/kicked-out-of-my-own-lab-meeting.js[View the story “Kicked out of my own lab meeting” on Storify]
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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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A must read: How to Level the Playing Field for Women in Science by Mary Ann Mason

This is a must read for anyone interested in Science / Academia: How to Level the Playing Field for Women in Science – Advice – The Chronicle of Higher Education.  By Mary Ann Mason, who is a professor at UC Berkeley and has extensive experience on studying issues relating to women in science and academia.  She details in this article four key things that can be done to reduce the “baby penalty”:

  • Better (and more) child-care options
  • Effective dual-career policies
  • Childbirth accommodations
  • Compliance with Title IX 
Definitely worth reading.  And worth checking out some of the web material from her including
(Thanks to Madhu Katti – who posted this to Facebook)
——–
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.

——–

Another Mostly Male Meeting from UCSD- should be called "Food and Fuel for the 19th Century"

Well, just when I thought meeting organizers from UCSD had learned their lesson regarding mostly male meetings – this comes along.  Check out “Food and Fuel for the 21st Century” (I was pointed to this by a comment on a blog post of mine). The speakers are

That a ratio of 18:2 or 10% female.  
Not that I know the cause of this but here are some other pieces of information to consider.
The Food and Fuel for the 21st Century Program lists 5 people on their Executive Committee.  Any guesses on the # of these that are men?  Well it is 5.
Fortunately they have an Advisory Committee too and that must have some women on it right?  Nope.

Reminds me a bit of the QBio meeting from 2013 organized by many from UCSD which I wrote about last year: Q-Bio conference in Hawaii, bring your surfboard & your Y chromosome because they don’t take a XX.  I note – this years Q-Bio meeting is much better.  But one can ask – does nobody at UCSD think about these issues when planning conferences and Advisory / Executive Committees.  I personally don’t think one should choose women to just choose women.  But as with the Q-Bio meeting from last year, I think there are an enormous number of highly qualified women working on topics directly related to “Food and Fuel for the 21st Century” and thus I am both surprised and disturbed by the gender ratio of this meeting and this organization.

UPDATE 3/4 7:21 AM

It took me a bit but I found details on the 2013 symposium from the same group.  The web site for the 2013 meeting is not active as far as I can tell.  However it is available in the Internet Archive.  For example, here is a snapshot from June 1, 2013.  From that snapshot here are the listed speakers

  • David Kramer, Michigan State University
  • Susan Golden, University of California, San Diego
  • Julian Schroeder, University of California, San Diego
  • Stephen Mayfield, University of California, San Diego
  • Steven Briggs, University of California, San Diego
  • Matteo Pellegrini, University of California, Los Angeles
  • Donald Weeks, University of Nebraska–Lincoln
  • Michael Burkart, University of California, San Diego
  • Chancellor Pradeep Khosla, University of California, San Diego
  • Farzad Haerizadeh, Life Technologies
  • Ben Hueso, California State Assembly
  • Bill Gerwick, Scripps Institution of Oceanography
  • Eric Mathur, SG Biofuels
  • James Van Etten, University of Nebraska–Lincoln
  • Fred Tennant, Heliae
  • David Dunigan, University of Nebraska–Lincoln
  • Xuemei Bai, Cellana
  • George Oyler, University of Nebraska–Lincoln
  • Gerry Mackie, University of California, San Diego
  • Mark Hildebrand, Scripps Institution of Oceanography
  • Lawrence Johnson, Salim Group
  • Craig Behnke, Sapphire Energy
  • Rebecca White, Sapphire Energy

For a ratio of 20:3.

——–
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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Nice wrap up from Anna Sharman on Science Publishing topics in February

Definitely worth checking out this post from Anna Sharman: February highlights from the world of scientific publishing | sharmanedit.  It covers many topics of relevance including new journals, the PLOS Data Policy kerfuffle, and misc. links of interest.

Save the dates / preliminary program for Lake Arrowhead Microbial Genomes Meeting

UPDATE 3/13/14 – Official Web Site now up

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Preliminary information for the The Lake Arrowhead Microbial Genomes – which is going to be great (note – I am on the planning committee) is below.  Registration information and Abstract Submission details will be coming soon.


Preliminary Program of Confirmed Speakers
Lake Arrowhead International Microbial Genomics Conference
September 14-18, 2014
Keynote Speaker: 
  • Julia A. Segre, National Human Genome Research Institute, NIH, Bethesda, MD (skin microbiome; tracking outbreaks through genomic sequencing)
Mirobial Communities I: Microbiomes
  • Peter Turnbaugh, Harvard University, Cambridge, MA (human microbiome)
  • Noah Fierer, University of Colorado, Boulder, CO (human microbiome; soil microbial communities)
  • Sarkis K. Mazmanian, California Institute of Technology, Pasadena, CA (gastrointestinal microbiota)
  • Andrew Goodman, Microbial Diversity Institute, Yale University, West Haven, CT (human microbiome; pathogens)
Microbial Communities II, Metagenomics, Biodiversity, Natural Products, Evolution
  • Nancy Moran, University of Texas, Austin Texas (Symbiosis between multicellular hosts and microbes)
  • Tanja Woyke, DOE Joint Genome Institute, Walnut Creek, CA (metagenomics; single cell genomics)
  • Eric J. Alm, Massachusetts Institute of Technology, Cambridge, MA (evolution of microorganisms)
  • Michael Fischbach, UCSF, San Francisco, CA (Insights from a global analysis of secondary metabolism: Small molecules from the human microbiota)
  • Jessica Green, University of Oregon, Eugene, OR (metagenomics; built environment)
  • Karyna Rosario Cora, University of South Florida, St. Peterburg, FL (Exploring the viral world through metagenomics)
  • Susannah Green Tringe, DOE Joint Genome Institute, Walnut Creek, CA (Microbial communities and the carbon cycle)
  • Nicole Perna, University of Wisconsin, Madison, WI (Evolution of the response to oxygen availability in enterobacteria: a complex trait in a model family)
  • Katie Pollard, UCSF, San Francisco, CA (Metagenomics; evolutionary genomics)
  • Jenna Morgan Lang, University of California, Davis, CA (Citizen microbiology)
Pathogens, Antibiotic Resistance
  • Julian Parkhill, Welcome Trust Sanger Institute, Cambridge, UK (genomics of pathogens; tracking outbreaks through genomic sequencing)
  • Lance B. Price, George Washington University, Washington, D. C. (foodborneurinary tract infection studies)
  • Gautam Dantas, Washington University, St. Louis, MO (reservoirs of antibiotic resistance)
  • Jeffrey T. Foster, Northern Arizona University, Flagstaff, AZ (genomic epizootiology of white-nose syndrome in bats)
  • Timothy D. Read, Emory University School of Medicine, Atlanta, GA (S. aureus antibiotic resistance genomics)
  • Evgeni Sokurenko, University of Washington, Seattle, WA (Pathoadaptive mutations in microbial genomes)
  • Jennifer Gardy, University of British Columbia, British Columbia, Canada (Genomics and epidemiology)
  • Ashlee Earl, The Broad Institute of Harvard and MIT, Cambridge, MA (Pathogen and Comparative Genomics)
Systems Biology, Metabalomics, Synthetic Biology
  • Fiona Brinkman, Simon Fraser University, Greater Vancouver, British Columbia, Canada (Using genomics and network analysis to characterize disease outbreaks)
  • Mallory Embree, University of California, San Diego, CA (Deciphering dynamic community interaction using systems biology)
  • Fuzhong Zhang, Washington University, St. Louis, MO (producing biofuels and pharmaceuticals with synthetic biology)
  • Sri Kosuri, University of California, Los Angeles, CA (synthetic biology, TBA)
  • Michele C. Chang, University of California, Berkeley, CA (expanding fluorine chemistry of living systems by genetic engineering)
Some of my posts about previous Lake Arrowhead Meetings can be found below:

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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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When to "defend" on Twitter and when to listen #scio14 #scicomm

So – by Friday morning I was dying for the weekend to come. It had been a rough week.  Without getting too much into my saga, suffice it to say that “The saga of my pancreas..feet..microbiome ..blood.. liver – part 1” is not turning out so well right now and medical issues are on my mind a lot. With a little help from my family, friends, colleagues, and cats I have been getting by.

//platform.twitter.com/widgets.js And as Friday went by things were not getting better. And then another medical issue and I had to head home early. Fun. I was just starting to recover, getting ready to watch a movie with my wife and kids when, well, the Twitter world intervened. I started to see some posts from Science Online 2014 making not so positive comments about the SpaceMicrobes project in which I am involved. Oh – and they were coming from people like Madhu Katti, who I deeply deeply respect.

//platform.twitter.com/widgets.js It took me a few minutes to figure out that there was a microbial swabbing “event” going on at Science Online connected to the Space Microbes project. And there were many many questions being posted to the Twittersphere about the project by Madhu and a few others (e.g., see one below).

//platform.twitter.com/widgets.js Hmm. This did not look good. But for perhaps the first time in a very very long time I felt like somehow I should not respond online. I am not sure why I felt this. I think partly I felt that, since the Space Microbes project is a collaboration in which many people from my lab are involved (and help run) that somehow I should let this play out without my “interference”. I think somehow I thought that once I got involved it could become more about me and not about how the people involved handled the questions in real time. Now – I say “I think” and “somehow” and such because this was going on while I was reading books to my son (my phone was just sitting next to me, and I really did not want to look at it or follow what was going on). So – anyway – I did not do anything directly, but I sent an email to some of the people from my lab who are involved in the SpaceMicrobes project. It included an intemperate title line and the following text:

You should look at Twitter What exactly is happening at Science Online? Who is doing sampling there and what is the purpose?

Anyway – after I wrote this it was about time for movie night to start with my wife and kids and things were getting complex. My son did not want to watch the same movie as my daughter. Important decisions had to me made. And now I was getting sucked into Twitter. And I started to try to answer some of the questions Madhu and DocRicky and others had. Madhu made a Storify of much of the exchange.

Now – I personally believe that we can answer all the questions Madhu and others had about the project. And I started to try and explain some of the goals and aims of the project and the reason things were done in the way they were done. However, I was also explaining bits of Star Trek II to my son.  And I started thinking – was “defending” the project really the right thing to do here? I thought not actually.  And I decided that this was an important moment to listen and learn (and step away from the keyboard a little) and not to defend. The event that was happening (or happened – I was not sure if it was live or after the event) was what it was. If the people there could not answer the questions coming up, and if our materials on the web and in the handouts could not answer the questions, then we had, well, failed. And my explaining things on Twitter was, in a way, a cheat only made possible because I was willing to ignore family time and be online.

So – I did not completely put away the keyboard but I stopped trying to explain it all away and started trying to just listen and to accept that things had gone a bit awry. Anyway – clearly those of us involved in SpaceMicrobes need to do a better job in multiple areas. I will not try to defend or explain or justify everything here either. But I will say – thanks. To the people who are willing to ask questions and have high expectations. I will just end this post with a few of my last Tweets

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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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Tanja Woyke talk at UC Davis on Single Cell Genomics

Quick post.  Tanja Woyke – a friend a colleague from the DOE-JGI gave a talk at UC Davis a few days ago.  Some notes via Storify:

//storify.com/phylogenomics/talk-by-tanja-woyke-of-doe-jgi-at-ucdavis-on-singl/embed//storify.com/phylogenomics/talk-by-tanja-woyke-of-doe-jgi-at-ucdavis-on-singl.js[View the story “Talk by Tanja Woyke of @DOE_JGI at #UCDavis on “Single Cell Genomics”” on Storify]
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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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Microbial forensics and phylogenetics go hand in hand

Interesting story in Nature today: Science in court: Disease detectives : Nature News & Comment.  It details a bit of the history and current approaches to forensics associated with microbes and has quotes from many of the key players in the field.  It discusses anthrax, HIV, the FBI, Bruce Budowle, David Hillis, and more.  Definitely worth a look for anyone interested in either microbial diversity of phylogenetics.  I have been interested in this topic for a very long time – pretty much since I was recruited to apply to work at the FBI many many years ago.

I have been to a few recent meetings on the topic organized by the White House OSTP and the FBI and I think there is lots of interesting work that can happen in this area.  The development of Phylosift in my lab was funded by a grant from DHS (to myself and THE Aaron Darling who has since left to a large island near New Zealand) largely in relation to microbial forensics.

See some related posts:

In particular people might want to check out the Mendeley Group collection of references on the topic I have made: Microbial Forensics | Mendeley Group

//www.mendeley.com/groups/1147121/microbial-forensics/widget/29/3/

Microbial Forensics is a group in Biological Sciences, Law on Mendeley.

——–
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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Shocked – shocked to hear that some fake papers got published in CLOSED ACCESS journals

Oh no.  This world.  It vexes me.  I am vexed.  I thought that only Open Access journals published papers that were fake science.  Now it turns out – closed access journals also sometimes have no peer review and overzealous pulsing pressures: Publishers withdraw more than 120 gibberish papers : Nature News & Comment.  How can I go on?  I thought peer review was perfect and all journals were honorable.  Oh well.  Back to 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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