New preprint from the lab on “Network analysis to evaluate the impact of research funding on research community consolidation”

We (me and David Coil) have a new preprint out on analysis we did in collaboration with Daniel Hicks and Carl Stahmer also from UC Davis. The paper is an analysis of the Microbiology of the Built Environment program funded by the Alfred P. Sloan Foundation via analysis of publications from within and outside the program. We would love feedback …


Network analysis to evaluate the impact of research funding on research community consolidation. Daniel J Hicks, David A Coil, Carl G Stahmer, Jonathan A. Eisen.


In 2004, the Alfred P. Sloan Foundation launched a new program focused on incubating a new field, “Microbiology of the Built Environment” (MoBE). By the end of 2017, the program had supported the publication of hundreds of scholarly works, but it was unclear to what extent it had stimulated the development of a new research community. We identified 307 works funded by the MoBE program, as well as a comparison set of 698 authors who published in the same journals during the same period of time but were not part of the Sloan Foundation-funded collaboration. Our analysis of collaboration networks for both groups of authors suggests that the Sloan Foundation’s program resulted in a more consolidated community of researchers, specifically in terms of number of components, diameter, density, and transitivity of the coauthor networks. In addition to highlighting the success of this particular program, our method could be applied to other fields to examine the impact of funding programs and other large-scale initiatives on the formation of research communities.

Storify of Future Proofing Law symposium at #UCDavis #futureproofinglaw #AI #algorithms #robots #CRISPR

This may be of interest to some here.  I made a Storify of the Tweets from the “Future Proofing Law” symposium that was at UC Davis yesterday and the day before.  There were multiple scholarly publishing related sessions and presentations as well as discussions of many topics connected to ICIS in various ways such as open scholarship, intellectual property, publishing and more.

Matt Hahn @3rdreviewer talk at #UCDavis – pen and paper notes

Matt Hahn was at UC Davis giving a talk yesterday.

// I did not have my laptop available so took notes with – gasp – a pen and paper.  I thought it was quite a nice talk so am posting my notes here.  More about Matt and his work can be found here:

And now for some good news from UC Davis – teaching and research awards

And now for some good news from UC Davis

On my evolving thoughts on the #UCDavis saga involving Chancellor Linda Katehi

Still trying to wrap my brain around the controversy at UC Davis involving our Chancellor (the head of the University) Linda Katehi (see some of these news stories if you are not aware of what is going on).  In some sense I could just watch this all from the sidelines and see what happens.  But that is not in my nature.  And, over the last month I have gotten a near endless stream of comments and suggestions (some in private, some in public) about the topic.  Some say I need to be more vocal in condemning Chancellor Katehi (e.g., a student in my lab told me the other day that they have talked to faculty who are wondering why I am being so hesitant to condemn Chancellor Katehi).  Other people (many) say any negative posts about Katehi are damaging UC Davis.  Still others say and and all actions of Katehi must be considered in the context of overwhelming sexism against female leaders.  And so on.  In total I have probably gotten dozens of private comments and even more public comments about the case with suggestions for what I should be doing here.

For those who know me or know about me, I assume you know I am not exactly shy about expressing my opinions on topics like behavior of academics or academic institutions.  For example, just after joining UC Davis I wrote a post that was shared widely, condemning a UC Davis Vice Provost over her misuse of her position in support of Closed Access publishing: Vice Provost of U. C. Davis on the wrong side of Open Access.

I give out all sorts of snarky awards on my blog to friends, colleagues, and other folds in the world for doing things I think are inappropriate (e.g., see this STAT story). Sometimes I go overboard in this, but certainly I am not hesitant at expressing thoughts when I think there has been something untoward going on.  I try as much as possible to turn my microscope on myself and UC Davis too.  For example, see this post from a few weeks ago: UC Davis Storer Lecture series – since 1963 87% of speakers are male.

Again, I know I overdo this sometimes but I am certainly not hesitant to make my feelings know.

But the case of Chancellor Katehi leaves me on the fence and with my fingers unclear what to type somewhat.  And so I thought I would try to write up what my thoughts are here, even if they are muddled.  I wonder what other people think of the situation and would love feedback (as always) on this post.

So – what is so complex here?  What am I trying to wrap my brain around?  I think my challenge here comes down to the following: I don’t know whether some of the responses (including mine) to Chancellor Katehi’s actions are tinged with bias, especially sexism.  Or, in other words, are the actions and inactions of Chancellor Katehi “firing offenses” or have they been overblown by biased and sexist points of view.

And honestly, I do not know exactly how to figure this out.  On the one hand, I accept that there are massive amounts of sexism in society and certainly in regard to how we judge women in power.  On the other hand, I think the actions and inactions of Chancellor Katehi and her administration have been serious (in a bad way).  I note – one thing I have done to try and better understand my own feelings and actions in this saga is to compile all my posts and communications as best I can and go through them.

This has helped me sort out my thoughts and also helped show me at least that I was certainly not going easy on the UC Davis administration over these cases.  I also re-examined my posts about the Pepper Spray incident and aftermath from 2011 which has many parallels to the current situation and also involved Chancellor Katehi. See here for those: posts about the UC Davis Pepper Spray Incident and Aftermath.

Below is a discussion based in part on going through the news stories and posts of others and posts of mine.

Maybe it is best to start with this.  A few weeks ago I was pondering the fate of Chancellor Katehi and I wrote a detailed post about this The #UCDavis Chancellor’s Board Positions and the Need for a More Public, Open and Early Disclosure System.

I also included in that discussion some possible conflicts of interest of my own that might be clouding my judgment.  Those are relevant to this post too and I encourage people to read them.  Anyway, this post was written at the beginning of the latest controversy when all that had been disclosed was her acceptance of a set of outside Board positions that were controversial.  I had written many mini posts and Tweets about the situation such as those below:


And I also had started to see some calls for her to be fired and such and made a point to say I did not feel things were that far along and I also linked to some of those posts.







Anyway I discussed all of this in the longer post linked above. In the post, I concluded two things at the time.  First, the Board positions were not good ideas and second, that her actions in regard to these Board positions did not raise to the level of firing or asking for her to resign.

And I note – all of this was not just a remote discussion for me.  I was part of the story in relation to one of her Board positions. And I got grief and support from people about my comments about this (even though I was clear to say to everyone I did not know anything about the Chancellor’s interactions with this university).

I confess, I found the responses of the “Pro-Katehi” people really disappointing in this story.  The Board positions seemed clearly to be bad ideas – riddled with potential or real conflicts of interest and poor judgement about what the response would be to these positions.  And I wrote publicly as such. For example:


But I still tried to temper my positions and thoughts to give Chancellor Katehi the benefit of the doubt.  And also a student protest began in response to the initial stories and eventually the students “occupied” the Chancellor’s main office.  I don’t have the time in this post to cover the protests, the response to the protests and the response to the responses.  But it got ugly.  And this made things extra complex.  But the protests were quite important in keeping attention on the stories and in revealing both the good and bad sides to some of the critical responses to the Chancellor’s actions.

Since that time much else has happened.  First, it was revealed that UC Davis had a set of contracts with outside agencies to do damage control PR of various kinds.  This literally exploded into a PR nightmare for UC Davis with news coverage from across the globe and massive criticism on social media.  I was one of the people throwing out negative comments.  I was angry and embarrassed and wrote about this extensively.

And I went out of my way to share critical posts about the administration and to also share some past posts of mine about the pepper spray incident.



// And I just decided that I felt the need to post about it a lot. For example:



But for both of the above stories alternative more supportive narratives were being presented by the UC Davis administration and by various friends and colleagues of mine (and even myself).  These supportive narratives basically took four forms:

  • First, many suggested that many of these actions were perfectly acceptable normal behavior by a university and its leader.  UC Davis and many others kept saying things like that the PR campaign was just about promoting good things UC Davis did.  
  • The second form of supportive narrative was that even if these actions were wrong, there were minor infractions.  
  • The third form of supportive narrative, which I myself discussed and struggled with, was that the Chancellor had done many good or great things and that evaluating her actions should be done with the big picture in mind.
  • The fourth form of supportive narrative, which was not shared much publicly at first, was that the response to Chancellor Katehi’s role in these actions was tinged with sexism. 

I did not buy the first two supportive narratives (that this was normal behavior and that the infractions were minor) and still do not. And I posted about this repeatedly. See for example:

And the third supportive narrative was complicated.  After all just liking what people have done in some area is not enough to grant them a pass on transgressions.  We needed to examine the current actions in detail to figure out just how bad they were.  But the fourth supportive narrative struck a cord with me.  Why?  Well, because I have worked for years with Chancellor Katehi on some issues in bias against women.  And I have become actively involved in fighting implicit and explicit bias against women in academia and it is pervasive.  And I deeply respect the people who kept bringing up this issue.

So as the story continued to evolve it came to a head early last week.  Various emails were circulating around campus suggesting that UC President Napolitano had asked Chancellor Katehi to step down.  And some were happy about this.  But others were not.  I was asked to sign a letter to Napolitano about the case and on first read it simply seemed to be saying “Back off and give the case some time” and so I signed it.  But then I reread it and felt it was too supportive of Chancellor Katehi’s actions (and made some statements for which I did not know of any evidence) so I removed my name.  And then an email came which included a letter written by a colleague of mine Linda Bisson who I believe is very level headed and fair and reasonable. The letter was to President Napolitano and it discussed possible sexism in the responses to Chancellor Katehi’s actions.  And even though I was not sure how I felt about the letter, I felt that it had to be shared publicly.  So I asked – and Linda Bisson allowed me to post it on my blog: Letter from #UCDavis Profs to Janet Napolitano about possible sexism in responses to Chancellor Katehi’s activities.

Just sharing the letter itself generate some heated discussions.  I again note – I was not endorsing the letter.  I just felt the ideas in the letter needed to be brought into the discussion even if I was not sure how I felt about the letter.

The more I think about it the more I realize that sexism is clearly a part of the response to Chancellor Katehi’s actions.  Egregious actions of other UC leaders who are male have not been met with the same level of response.  Repeatedly.  This just seems unfair in many ways.  And also the reaction from President Napolitano seemed pretty extreme and overly personal and reactionary (e.g., some of the charges in it were not part of the current discussion).

And so I went back an reexamined the first three supportive narratives I outlined above trying to consider how they could be viewed in the face of sexism. Regarding the first supportive narrative I guess a question to ask is – what do other universities and university leaders do?  But even if things are done by others I don’t think that justifies them.  I think the PR campaign was massively misguided.  I think the Board positions were unwise and riddled with potential and real conflicts of interest.  So regardless of what others do I think these were missteps.  They show a lack of foresight in thinking about what others would think about these activities.  And the leader of a major university needs to use such foresight and use it well.

Regarding the second supportive narrative, I think this is more complicated.  At first it seemed the Chancellor and her staff were defending all of her actions (the first narrative) which I found unseemly.

But then she did (sort of) apologize and said she would work to fix any mistakes.  I found the apology unconvincing to be honest but was happy to see it.  So she was accepting some responsibility for mistakes and thus I could in a way cross of the first narrative.  Thus we could now discuss whether these mistakes were enough to lead to firing / stepping down.  At that point after consulting many colleagues, I decided that I was still displeased with the Chancellor and her administration in many ways, but that I was hoping that we could move forward in some way.

I think the third narrative (that I felt she had done many good things for UC Davis) played a big role in my thoughts here.

But then, just thereafter there came some new revelations.  And these ones I think rewrite the situation a bit.  First, President Napolitano had apparently asked Katehi to resign (as mentioned above).  And Katehi apparently decided not to.

And then the hammer came down from President Napolitano including various new accusations.  And also the Sacramento Bee revealed further details about the recent social media “listening campaign” paid for by the UC Davis Administration.


These two stories together were particularly distressing to me.  And most distressing they revealed a side of the story I have not discussed move above which was there throughout.  This involves the communications from Chancellor Katehi and her administration about all of these topics.  Napolitano,  for example, was angry about the possible misleading statements about Chancellor Katehi’s role in the PR contracts.  And though I think the Napolitano letter has some problems (e.g., no consolation consultation of anyone from UC Davis apparently before taking this action) I also did feel that some of the communications from the UC Davis administration were misleading.  The UC Davis Administration had been trying to say in regard to these PR and social media contracts that they were all about promoting UC Davis and not about watching or trying to clean up the reputation of Chancellor Katehi.  But if you look at the listening reports published by the Sacramento Bee – they are all about Katehi.  And even more disconcerting, they included a lot of material about me and my brother and many colleagues.  It just smelled really off to me.  And so I got angrier and angrier.  And less forgiving.
And the fact that the reports published by the SacBee included a lot of material about me and my brother and close friends and colleagues really threw me into a bit of a rage.


And these were just the latest examples of disastrously bad or misleading or inaccurate communications coming from the UC Davis Administration.  The press releases they had been putting out were pretty awful. The statements they made were frequently incomplete or downright misleading.  And they seemed to never really get the seriousness of any of the situations.  I had been pointing this out along the way but it just never got better.  It just got worse.  A good summary of the communications problems has been discussed by Marcos Breton in a series of articles in the Sacramento Bee.  For example:

So after all the saga, after all the rehashing of my prior responses, I feel torn still.  I get that there is real sexism in how women and women leaders are treated.  I have been fighting such sexism for years and been inspired by how Chancellor Katehi fight’s fights such sexism with action.  But I think even in the face of this, there are real and distressing mistakes that Chancellor Katehi and her administration have made and keep making.  And these mistakes are doing damage to my beloved UC Davis.  In addition, and also very important,  I worry deeply about unfair charges of sexism against critics of Chancellor Katehi. There are real and valid criticisms of Chancellor Katehi and her actions and her administration and discounting them all just because some aspects of the situation involve sexism is also damaging.

In the end, am I willing to wait for the results of the planned investigation by the University of California into Chancellor Katehi’s actions?  Yes I am.  Do I think she will be absolved of the more serious charges?  I do not know but I truly hope so.

But regardless of the results of this investigation, I am deeply worried about how the entire situation impacts UC Davis.  Yes, Chancellor Katehi deserves to be treated fairly.  And yes, she has done some very good things for UC Davis.  And yes I like her personally. And yes there is a great deal of subtle and not so subtle sexism in the world and likely some in the response to her actions.  But I am unable to stop coming back to the series of clear mistakes that have been made.  Of actions and inactions that have shown poor judgment.  And of repeated, baffling, and damaging poor communications in response to the ongoing situation.  I have given as much benefit of the doubt as I am able to give I guess.  And at this point in time I have just really had enough. I hope we can move UC Davis back to a better path as soon as possible.  Maybe this could happen with a rapid (very rapid) and complete and open investigation of Chancellor Katehi and of her being cleared of all major accusations.  I hold out hope for that to happen.  However, it seems to me that the most obvious way forward, unless something else drastically changes, is going to be with a new Chancellor.

Some responses and comments



// UPDATE May 4, 2016. 9 PM. After a lot of thought and discussions with many many many people about this post and about Chancellor Katehi I have come to the conclusion that we need a new Chancellor at UC Davis. I have come to this conclusion for many reasons which I will try to write about as soon as possible.

Letter from #UCDavis Profs to Janet Napolitano about possible sexism in responses to Chancellor Katehi’s activities

The current Chair of the UC Davis Division of the Academic Senate forwarded an email to UC Davis faculty today.  This email included a letter that had been send from from Linda Bisson (past Chair of the UC Davis Division of the Academic Senate) and Rachael E. Goodhue (Chair Elect of UC Davis Division of the Academic Senate) to the President of the University of California Janet Napolitano.  The letter’s overall message is concern about possible sexism in how the Chancellor of UC Davis is being treated in regard to recent events at UC Davis. 
I note – I have received many (over a dozen) private messages also expressing concern that some of the reaction to Chancellor Katehi’s activities may be sexist.  Mind you – most of these people are not defending the activities of the Chancellor but are concerned about the responses to her activities.  I think it is important for these expressions to be more widely viewed and thus I asked Linda Bisson if I could post it here and she said yes. 

From: Linda Bisson
Date: Sun, Apr 24, 2016 at 6:43 AM
Subject: Letter to President Napolitano

Dear President Napolitano:

We want to express grave concern over a pattern of negativism in the press and social media regarding women Chancellors and senior administrative leaders. There are strong parallels between the singularly intensive criticism of our Chancellor Linda Katehi and that previously of Chancellors Fox (UCSD) and Denton (UCSC), and of UC Vice President Greenwood. Yet, the activities that are being criticized clearly fall within the standards of UCwide practice. This pattern is exemplified by a 2006 LA Times article that criticized compensation practices for senior UC executives: those singled out for criticism for “extravagant pay practices, perks and privilege for top executives” are all women ( The intensity of the criticism at the time ended in tragedy for Chancellor Denton. Chancellor Fox’s term was equally framed as fraught with turmoil, turmoil apparently not experienced by her male colleagues who were facing identical issues due to budget cuts and lack of diversity and inclusion. In an article in the San Diego Union Tribune written on Chancellor Fox’s decision to step down ( leaving-ucsd/?#article-copy), she is described in terms steeped in implicit gender bias such as the quote ascribed to former President Atkinson: “She handled that as well as she could have handled it” – not as well as anyone could have handled it or as well as it could have been handled.

Women in leadership positions are often the victims of intense implicit bias and, as a consequence, of the phenomenon of “single storyism” – the reduction of their actions to a simple narrative that appeals to the biases of a broad section of society, in this case implicit gender bias and women being incompetent for their position. Whatever they say or do in response is twisted to fit the “single story.” We think the LA Times article listed above illustrates perfectly the problem of the single story experienced by senior women administrators at UC. If the LA Times story were rewritten today, Chancellor Katehi’s name is likely the only one that would be added to the list.

All of UC is richer because of the participation of women and underrepresented groups at all levels. We know you and your leadership team share this belief. We are concerned that UCOP does not recognize that senior administrators who are identified with an underrepresented identity vital to our diversity are subject to vilification in the press simply because of that identity. We are also concerned, as recent press regarding our Chancellor Katehi demonstrates, that Chancellors and other senior administrators are not well-equipped to deal with single storyism, nor is there the recognition that others, such as UCOP, must step in to address the criticism as well.

The absence of factual information on UC policies and practices with respect to external compensation for all senior administrators has led to speculative and negative public debate regarding a single senior woman, when the practice of external involvement is widespread. We would like to request clear articulation from UCOP of both the formal policies and the informal practices as they pertain to executive compensation (e.g., have senior managers been encouraged to participate in activities outside UC). We note that legislators are calling for the same review. UCOP’s understanding of the broader issues involved is essential to informing these external discussions. The need for UCOP to take action is urgent.

We thank you for considering this request.

Linda F. Bisson, Former Chair, Davis Division of the Academic Senate, 2006-2008 & 2011-2012
Rachael E. Goodhue, Chair Elect, Davis Division of the Academic Senate 2016-2018

UC Davis Storer Lecture series – since 1963 87% of speakers are male

I wrote this blog post a while ago but never published it partly out of fear for upsetting some of my colleagues.  I try to be brave about such things, but I guess I just did not quite get up the poxy.  Well, today something came up that stimulated me to write the post.

I got an email announcement for a talk that seems potentially quite interesting. The problem is not the talk.  The problem is with the endowed Lectureship that this talk is connected to.  So here is the post I have worked on on and off over the last year or more.

UC Davis has an endowed lecture series- the Storer Lectureship in the Life Sciences.  It has been running since the 1960s and is a relatively big deal on campus here.  The speakers come in, usually give one or two talks (one for the public and one for researchers).  They usually have a big dinner (I have gone to a few of these) and the speakers get a decent honorarium (a few thousand dollars) and some sort of gift.

Most years I have been here, I have received a request from the organizers for suggested speakers and every once in a while I have made suggestions, some of which have even led to invitations.  Recently, I had suggested a famous colleague who is also a UC Davis alum.  Alas, she could not come.  The organizers asked if I had any other suggestions and I sent them a list of a few candidates who are both very good, well known and do something related to microbes.  The organizers really liked one of the suggestions and asked if I would be willing to invite this person.

So I started drafting a letter.  And as part of drafting a letter I wanted to give examples of past speakers to show how great a set of speakers we had for this series.  So I Googled “Storer” and
UC Davis” or something like that and got to the page:

Storer Lectureship in the Life Sciences

And that is when I got a bit heartbroken.  The speakers have been, well, very male.   I note I spent a while looking at descriptions of each speaker that I did not know to try and determine their gender, looking at their web sites if available, or how they were described (e.g., what pronouns were used).  I am pretty confident in the assignments though I realize this is an error prone approach.  Here is the full list as far as I have put together with the males labelled in yellow and females in green.

Oct 5-16, 1963 Ernest W. Caspari University of Rochester
Oct 17-31, 1966 Vincent G. Derhicr Univesity of Pennsylvania
May 7-20, 1967 Ernst Mayr Harvard University
Nov 3-15, 1968 Elizabeth C. Crosby Univesity of Michigan
Jan 3-15, 1969 W.D. Billings Duke University
Apr 13-23, 1969 Frank Fenner Australian National University,
Apr 5-19, 1970 A. Frey-Wyssling Eidgenossiche Tcchnische Hochschule
Nov 11-23, 1970 Carl L. Hubbs Scripps Institution of Oceanography
Feb 1-12, 1971 H.L. KornBerg University of Leicester, England
Nov 22-Dec 3, 1971 Hilary Koprowski University of Pennsylvania
Jan 17-28, 1972 George Beadle University of Chicago
Jan 17-28, 1972 Muriel Beadle University of Chicago
May 1-12, 1972 Sterling Hendricks Agriculture Research Service, U.S.D.A
Oct 16-27, 1972 George Gaylord Simpson The Simroe Foundation
Feb 23-Mar 9, 1973 Sir Alan S. Parkes The Galton Foundation
Apr 9-20, 1973 Peter R. Marler The Rockefeller University
May 7-18, 1973 George C. Cotzias, M.D. Brookhaven National Laboratory
Nov 6-13, 1973 Eugene E. Odum University of Georgia
Nov 12-16, 1973 Peter Alexander Royal Marsden Cancer Hospital
Mar 4-15, 1974 Davis A. Hamburg, MD. Stanford University School of Medicine
Apr 1-15, 1974 Kent V. Flannery University of Michigan
Nov 4-15, 1974 Garrett Hardin University of California, Santa Barbara
Mar 30-Apr 9, 1975 Kenneth J. Carpenter University of Cambridge
Apr 20-May 2, 1975 Murray S. Blum University of Georgia
Oct 20-31, 1975 Bert W. O’Malley, M.D. Baylor College of Medicine,
Apr 12-23, 1976 Sydney Brenner Division of Cell Biology of the Medical Research Council Laboratory of Molecular Biology, Cambridge, England
May 17-28, 1976 Peter S. Carlson Michigan State University,
Nov 22-Dec 3, 1976 Roger Y. Stanier Pasteur Institute,
Jan 24-Feb 4, 1977 Peter Albersheim University of Colorado
Feb 22-Mar 4, 1977 *Jere Mead, M.D. Cecil K. and Philip Drinker Harvard University
Apr 11-12, 1977 S. J. Singer University of California, San Diego
Nov 20-30, 1977 James D. Ebert Marine Biological Laboratory
Feb 8-15, 1978 Sir Kenneth Blaxtcr Rowen Research Institute
Apr 5-12, 1978 Eric H. Davidson California Institute of Technology
Oct 9-20, 1978 Jutgen Aschoff Max-Planck Institute for Behavioral Physiology
Feb 20-22, 1979 *Burt L. Vallee, Paul C. Cabot Harvard Medical School
Apr 24-26, 1979 Carl R. Woese University of Illinois, Urbana Champaign
Nov 5-16, 1979 Daphne J. Osborne Oxford University
Februarv 4-15, 1980 John F. Eisenberg Smithsonian Institution.
Apr 16-18, 1980 George E. Palade, M.D. Yale Medical School
May 5-16, 1980 Jerre Levy University of Chicago
Oct 27-30, 1980 Colin Blakemore Oxford University
Jan 21-27, 1980 Pierre Dejours CNRS
Feb 26-Mar 5, 1981 Richard Alexander  University of Michigan
Oct 20-27, 1981 Alfred F. Harper  University of Wisconsin Madison
May 11-19, 1982 Glenn W. Burton USDA-SEA
Oct 11-18, 1982 Richard F. Leakey National Museums of Kenya
Jan 6-11, 1983 Eric R. Kandel, M.D. Columbia University,
Oct 12-18, 1983 Donald S. Farner University of Washington
Feb 13-15, 1984 Daniel Branton Harvard University
Apr 24-26, 1984 J. Michael Bishop University of California, San Francisco
Dec 3-6, 1984 Maurice Fried National Research Council
Apr 3-8, 1985 John Krebs Edward Grey Institute of Field Ornithology
May 8-14, 1985 Geoffrey M. Ole Maloiy University of Nairobi
Oct 8-10, 1985 Michael P. Hassell Imperial College, London
Apr 21-24, 1986 John Maynard Smith University of Sussex.
Dec 1-4, 1986 Aldo Carl Leopold Boyce Thompson Institute
Mar 2A, 1987 Gerald Edelman The Rockefeller University
Nov 10-12, 1987 Jean-Claude Chcrrnann Pasteur Institute, Paris France
Jan 15-20, 1988 Jean-Pierre Changeux Pasteur Institute, Paris France
Apr 11-15, 1988 John I. Harpcr University College of North Wales
Oct 17-21, 1988 Rudiger Wehner University of Zurich
Oct 23-26, 1989 John C. Torrey Harvard University
Feb 26-Mar 2, 1990 Heinz Saedler Max-Planck-Institute
Nov 5-7, 1990 Francis Crick The Salk Institute
Jan 28-31, 1991 Thomas A. McMahon Harvard University
May 28-30, 1991 Lynn Margulis University of Massachusetts
Nov 18-21, 1991 Richard C. Lewontin Harvard University
Feb 4-6, 1992 Philip Leder Harvard Medical School
Apr 13-16, 1992 Patrick Bateson University of Cambridge
Nov 16-19, 1992 Melvin I. Simon California Institute of Technology
Feb 1-5, 1993 Anne McLaren Wellcome/CRC Institute
Apr 13-16, 1993 Judah Folkman Harvard Medical School
Jan 24 -27, 1994 Philippa Marrack National Jewish Center
Feb 28-Mar 3, 1994 Stephen O’Brien National Cancer Institute
Apr 18-21, 1994 Roy M. Anderson University of Oxford
Oct 31-Nov 2, 1994 Michael J. Berridge The Babraham Institute
Feb 6-10, 1995 Hal Hatch CSIRO Division of Plant Industry
May 1-5, 1995 Elaine Fuchs The University of Chicago
Oct 16-19, 1995 Peter Ellison Harvard University
Mar 4-8, 1996 Gottfried Schatz University of Basel, Switzerland
Apr 8-10, 1996 Daniel Hillel University of Massachusetts at Amherst
Feb 3-6, 1997 Peter R. Grant Princeton University
Apr 14-17, 1997 William J. Lennarz State University of New York
May 5-7, 1997 Carolyn W. Slayman Yale University School of Medicine
Apr 20-22, 1998 Floyd Bloom The Scripps Research 1nstitute
May 18-20, 1998 Ian Wilmut Roslin Institute
Jan 11-13, 1999 Leroy E. Hood University of Washington
Apr 26-28, 1999 Patricia Goldman-Rakic Yale University School of Medicine
Jan 30-31, 2001 Charles Arntzen Arizona State University

University of Oxford
Mar 4-6, 2002 Jan H. Hoeijmakcrs  Erasmus University
Apr 11-12, 2002 Fred H. Gage The Salk Institute
May 6-7, 2002 Phillip A. Sharp Center for Cancer Research, MIT
Jan 13-15, 2003 George M. Martin, M.D. University of Washington
Mar 10-11, 2003 Kim A. Nasmyth Vienna Biocenter
Apr 28-29, 2003 Tim Flannery Director of the South Australian Museum
Dec 1-2, 2003 William Greenough University of Illinois
Feb 18-19, 2004 Bruce Ames Children’s Hospital, Oakland Research Institute
Nov 29-30, 2004 Hans Herren International Centre of Insect Physiology and Ecology
Apr 26-27, 2005 H. Robert Horvitz Massachusetts Institute of Technology
May 9-10, 2005 Steven Chu Lawrence Berkeley National Laboratory
Jan 24-25, 2006 Cynthia Kenyon University of California, San Francisco
Mar 14-15, 2006 Thomas D. Pollard Yale University
Oct 23-24, 2006 Mimi Koehl University of California, Berkeley
Dec 4-5, 2006 Simon A. Levin Princeton University
Apr 5-6, 2007 Sir Peter Crane, FRS University of Chicago
Apr 23-24, 2007 Stephen Quake Stanford University
May 14-15, 2007 Pasko Rakic Yale University
Mar 23-24, 2009 Sean Carroll University of Wisconsin
Apr 20-21, 2009 H. Allen Orr University of Rochester
May 19-20, 2009 John Doebley University of Wisconsin
Mar 11-12, 2010 Elliot Meyerowitz California Institute of Technology
May 17-18, 2010 Robert Langer Massachusetts Institute of Technology
May 11-12, 2011 Nina Federoff Pennsylvania State University
Jan 11-12, 2012 Jane Lubchenco NOAA
Apr 24-25, 2012 Ilkka Hanski University of Helsinki
May 30-31, 2012 Loren Rieseberg University of British Columbia
Oct 2-3, 2012 Ed Delong MIT
Nov 15, 2012 Jordi Bascompte Estación Biológica de Doñana
Nov 19, 2012 Simon Boulton London Research Institute
Jan 16, 2013 Ary Hoffman University of Melbourne
Jan 31, 2013 Jonathan Losos Harvard
Mar 18, 2013 Gloria Coruzzi NYU
Apr 10-11 2013 Peter Agre Johns Hopkins Malaria Research Institute
May 6, 2013 Richard Wrangham Harvard
May 16, 2013 Sue Carter RTI International
May 28, 2013 Larry Gold CU Boulder
June 4, 2013 Eric Schadt Mount Sinai
June 05, 2013 Nancy Moran Yale
Oct 28-29, 2013 Walter Bodmer University of Oxford
Dec 4-5, 2013 Ronald Kaback UCLA
Feb 24, 2014 Patricia Wright Stony Brook
Mar 5-6, 2014 Steve Carpenter University of Wisconsin
Apr 9-10, 2014 Jerry Coyne University of Chicago
May 20-21, 2014 May Berenbaum University of Illinois
May 28-29, 2014 Joel Cohen Rockefeller University
Oct 28-29, 2014 Charles Rice The Rockefeller University
Nov 19-20, 2014 Rolf Zinkernagel University of Zurich
Apr 15-16, 2015 Tim Clutton Block University of Cambridge
Oct 7-8, 2015 Richard Lenski Michigan State
April 22, 2016 Steve Nowicki Duke University

The total numbers come to 19 females out of 142 speakers or ~13% female and 87% male.  Ugh.

And the person I had suggested to invite was male.  So I wrote back to the organizers and I wrote:

From: Jonathan Eisen 

Sent: Thursday, June 11, 2015 11:34 AM 


Subject: Abyssmal gender ratio of speakers in the Storer Lectureship series 


With sincere apologies but … 

In preparing a letter of invitation for XXX I decided to include some examples of previous Storer Lecturers. And therein lies the problem On the web site my count, there are 121 past speakers listed. Of these, 15 appear to be female (from my estimate). That comes to 12%. That is embarassaingly low. I hope my calculations here are wrong. 

Can you tell me if the Storer Lectureship has any policies regarding diversity of speakers? If yes, can you provide me with those details.

If no, I recommend you implement one as soon as possible. Either way, I refuse to have my name affiliated with this series, and will not invite anyone to talk in it, without further information and without some serious attempt to figure out how to do a better job representing the diversity of biologists who could give such talks. 


They wrote back with a very detailed response and were very supportive of the concept of increasing diversity of speakers.  And they explained some of the efforts they had made in this regard.  And they really seem to be trying in some ways.  But in the end, their main justification for the lack of diversity was that they were trying to invite already recognized, in essence famous, biologists.  People who had won a Nobel or were in the National Academy of Sciences or were HHMI investigators.  And this pool, that they had chosen, was skewed in gender balance.

So I wrote back to them June 18:

Thanks very much for the response.

I understand you have some constraints and greatly appreciate that you are committed to trying to improve the diversity of speakers.  However, the end result is truly not acceptible in my mind and therefore I believe more needs to be done, urgently, to improve the situation.

What are some possible ways to improve the situation?

Well, the number one recommendation I would make would be to not constrain the pool to honorific groups that themselves have severe skews.  No we cannot solve those skews and there are many causes for them.  But I believe it is a major mistake to use the diversity of those groups (NAS, Nobel, HHMI) as a target.  Either invite people to represent diversity well even from a constrained pool, or, open up to a broader pool (there are plenty of incredible scientists who have not gotten HHMI, NAS, or Nobels).

In addition to opening up the pool and not aiming at such a low bar, there are many things one can do to improve the diversity of speakers.  I have written about this extensively as have many others.  I can point the committee to some of these articles if interested.

In the end, whatever the reasons are, the Storer series has ended up with extremely biased gender ratio of speakers.  I think it is up to the committee to fix this with a combination of actions.  But the first thing I would recommend is to not use the diversity of a set of pools you have chosen as an excuse.  We can and should do better and if the pools are the reason, the pools from which you sample need to be changed.


They wrote back, saying they were really committed to achieving better gender balance in the future writing “we are totally committed to the same goals as you in terms of gender balance now and in the future.” And they also wrote that they expected “the final lineup to reflect at least 30 percent or more female” as long as one additional woman (the person I had originally recommended) would come (though I had told them she said she could not).  And then they asked if I would reconsider inviting the man who I had been about to invite that had started this whole discussion.

So I wrote back again July 14:

Thanks again for the response. And though I do not want to continue beating a dead horse, I am not convinced we are doing enough in this area. For example, what explains the “at least 30 percent” and how close to 30% will that be. This is important as, for example, the National Science Foundation will not support their people attending meetings if female speakers are at < 33%. I think 30% is, to be honest, just not acceptable in biology. So beofre contributing any more to this series I need to know exactly what is meant by "we are totally committed to the same goals as you in terms of gender balance now and in the future.”

For example, here are some questions I would like to know the answers to:

  • Are you committed to achieving gender balance in the speaker series or just saying you are being more even than before?
  • Are you committed to researching and using diverse options to ensure diversity of speakers beyond just focusing on who is invited?
  • Are you interested in understanding why the series has been so undiverse in the past and addressing this directly or just moving forward?
  • Are you willing to address the lack of diversity in the past publicly and also discuss efforts to improve the diversity? 

I would very much like to know more detail about how serious you are to having a diverse series and what you plan to do to achieve this. 

With apologies, but in regard to inviting XXX or XXX. I am sorry but given the past record of this series, which as I said is among the worst I have seen anywhere, I am just not willing to be involved in any way until I see a stronger and more public committment to diversity. 

I am happy to help with the series and to help improve the diversity of speakers. But this should be done openly and publicly and forcefully. And without evidence of this, I am unable and unwilling to be involved.

And, well, I have not heard from them again.  So, I am writing this.  For many reasons.  But a key one is, I think we need to be more public about such issues.  And we just need to fix things that are broken.

So today I decided to make the post live.  I wish I had done this earlier.

Some responses




The #UCDavis Chancellor’s Board Positions and the Need for a More Public, Open and Early Disclosure System

So, I assume by now many people out there have heard about the controversy going on at UC Davis over the board positions taken by the UC Davis Chancellor Linda Katehi.  If you have not – here is a brief summary.

  • In late February, Chancellor Katehi accepted a board position at the for profit educational company Devry but then steeped down after complaints.  See for example this story by Diana Lambert in the SacBee for details.  Note – she has admitted that her accepting of this position prior to getting approval from the UC President was a violation of UC policy.
  • Chancellor Katehi received $420,000 in compensation for serving on the board of John Wiley and Son’s from 2012-2014.  See this SacBee story by Diana Lambert and Dale Kasler for more detail.  In relation to this report, Chancellor Katehi has apologized and has said she will donate “all the stock proceeds” she made from Wiley to a Scholarship fund for UC Davis students.
  • Chancellor Katehi served on the International Advisory Board of King Abdulaziz University in Saudi Arabia for a year.  This is the same University that has been strongly critiqued for its practice of paying highly cited scholars to become adjunct faculty in order to boost its ratings. It has been reported that she did not attend any of the board meetings in person and did not receive any compensation for this.  See this and this for more detail.  
There have been many responses to these revelations including:

The situation does not appear to be letting up.  I note – in the description above I have tried to be as objective as possible in describing the situation.  And I have been thinking a lot about what I think should happen now.  Do I think the Chancellor should resign?  Should she be fired?  Do we need more faculty to come out in support of her?  What is the best path forward for UC Davis?  I certainly have thoughts on these questions and related topics.  And I assume many people who know me know that I am not exactly shy about expressing my thoughts in public.

But … there is one major thing that gives me pause here.  And it relates to the comment above about trying “tried to be as objective as possible” here.  The reason this gives me pause here is because one of the key issues at play relates to “Conflicts of Interest” – both real and perceived – in the Chancellor’s board positions.  Many critics have argued that each of these board positions comes with major conflicts of interest in the Chancellor’s job as the head of a major public university.  The Chancellor’s supporters have argued that these board positions at worst involved the appearance of a possible conflict and not any real conflict.

Why I am digging into this conflict of interest topic?  Because I think one key way to help people assess whether there are any real or possible conflicts of interest in one’s activities is to fully disclose as much as possible about one’s activities.  And I think the UC in general and the Chancellor of UC Davis could do a much much much better job in terms of disclosures.  And I have a proposal for that.

But before we get into that I think it is necessary for me to make some disclosures.  Here are some:

  • I am a Professor at UC Davis
  • I have worked on a few projects with the UC Davis Chancellor Linda Katehi directly and indirectly and I have always had positive interactions with her).
  • I have worked on the UC Davis ADVANCE Project ( to increase the participation and advancement of women in academic science and engineering careers) for which Chancellor Katehi is the lead. 
  • I don’t always agree with actions taken by Chancellor Katehi but I do believe she is truly committed to improving UC Davis
  • I have worked for many years on “open access” to scholarly literature (and a little bit to textbooks) and have occasionally been at odds with the John Wiley and Son’s company.
  • I was involved in an exposé of what I believe to be unethical behavior of King Abdulaziz University a few years ago in their attempts to buy rankings by trying to have scholars change their institutional affiliations on publications and in citation databases.  See for example this and this and this.  I note – I was threatened by one of the people from KAU who I helped expose.  I am NOT A FAN of KAU.
  • I spent almost two months writing about the pepper spray incident and follow up in 2011 in an effort to help save the image of UC Davis, which I love.  See some of my posts about this here.  The whole incident and the aftermath was very traumatic for the University and many individuals associated with the University, including myself.  There were calls for Chancellor Katehi to resign then.  And there were statements of support by deans and faculty.  I refused to sign either.  I thought she and the UC Davis admins made many mistakes and did not by any means deserve endorsements.  But I also thought it was unclear if their mistakes were enough for them to be pushed out. 
  • Other disclosures of mine are here:
I have listed these disclosures because I am not sure I can be objective about this story.  And I want everyone reading this to have this information so that you can make your own decision as to whether you think my possible conflicts of interest might cloud my judgement in various ways.  I tried to be objective in outlining what I think the current state of the situation is above, but I understand that not everyone may agree.  And if people think my view of the situation is too biased, well, they probably will not care too much about what I think we should do now.  And I am OK with that.  What I want most is for people to know now just what my positions are, but what might have affected what my positions are.

OK – so that is a way longer introduction than I had imagined in getting to the question of “what should we do now?” 

A reader who thinks I am not completely compromised might ask – what do I think about the situation and what do I think should happen now?  Here are some comments:

  • I personally think that accepting each of these board positions was really not wise.  Yes, the Chancellor may have accepted them with the best of intentions.  And yes, she may not have done anything inappropriate in her time on the two on which she served (Wiley and KAU).  But I think it would not have been that hard to imagine how these board positions might be perceived – especially by UC Davis students.  And that alone I think should have led to turning down these board positions.  She has admitted Devry was a mistake. She has not admitted (as far as I know) that Wiley was a mistake but has hinted that she can see how some people may not like it.  She has not admitted at all that KAU was a mistake as far as I can tell (and has defended it as being in the interest of promoting diversity), but given that it was known in 2011 widely that they were buying ranking in a seemingly unethical manner, this should have raised some red flags.  I do wonder a bit whether my really unpleasant interaction with KAU has made me more judgmental about this board position than maybe I should be (hence why I thought it was important to disclose this above).
  • Despite the above comments, I do not think that the board positions taken by the Chancellor are enough of a problem to call for her firing or resignation.  There are two major reasons for this.  My min reason for this is that I think one has to weigh the board position issue against all she has done as Chancellor and overall I believe she has done many very good things as Chancellor and that she is truly and deeply committed to UC Davis.  I understand that other people do not agree with this.  So I think in a way how people respond to this board position issue may relate largely to how good a job they think she has been doing as Chancellor.
  • I think a key mistake in this whole situation involved a poor job of disclosure.  More on this below.
  • I think another key mistake has been the slow and minimal communication with UC Davis and the public in response to these issues.  I really wish Chancellor Katehi and UC Davis administrators would hold some town halls or the like to discuss these issues and to explain to us why these board positions were taken.
So in summary – I think the Board positions were mistakes but I do not think they rise to the level of calling for the Chancellor to be fired or to resign.  I do think we should use this situation to completely revisit the topic of conflicts of interest, disclosure, and outside activities of the UC Administrators.  There have been calls, for example, to greatly limit if not stop entirely outside activities, especially at for profit entities, by the UC Chancellors and other higher ups.  I am not sure what I think about these calls, but they are definitely worth considering.  However, I think as a first step the UC could tackle one key issue – Disclosure.  

In general I think disclosures of possible conflicts of interest are done really poorly in academia.  So poorly that before this whole issue cropped up at UC Davis I made a proposal that scholars add disclosures to a centralized universal scholarly ID system known as ORCID.  See Improving Ability to Identify Possible Conflicts of Interest of Scholars 1: Adding a Disclosure Field to ORCID.  This would certainly help when on sees a paper by someone (say, Eric Lander) and would allow one to get more information about their possible conflicts of interest (say, billions of dollars in possible royalties for the institute one runs).  I think such a system would be very useful.  But it is not really enough for the issue at hand here.

So in order to at least get the UC started down a better path in terms of conflicts of interest and activities by UC administrators I propose the following simple steps (and I note – this are just some ideas and thoughts, not a well formulated system at this point).

Proposed Public, Open, and Early Disclosure System for UC Administrators.

  • This system should be applied to all top UC Administrators (UC President, Chancellors, Provosts, Deans, and possibly others)
  • Disclosures of outside activities and potential conflicts of interest must be made publicly available in a centralized location. 
    • This would include Form 700s and other declarations.
    • I have been told such forms are available for all UC Admins.  They are certainly not readily available.
    • UC Administrators should be required to update such disclosures quarterly
  • The disclosures need to be referenced and linked readily and widely:
    • The disclosures should be provided at the administrator’s profile pages 
    • Disclosures or links to them should accompany all official communications of these administrators (much in the way disclosures should accompany scholarly publications).
  • Administrators should be required to submit proposed outside activities to the public PRIOR to commencing those activities. 
    • There should be a public commenting period regarding these proposals
    • The specific activities and compensations must be included in all proposals
    • The proposals should include a discussion of the putative benefits to the UC for such activities.
    • There should be a more public, more formal review process for determining if the proposed activities are in the best interest of the UC
  • These disclosures should happen whether or not any other regulations about outside activities happen.
I understand this will not solve all the issues associated with outside activities, conflicts of interest, and such.  But I think one big step would be for the UC to adopt a more open, public, early, easy to find, and widely share disclosure system for outside activities of UC Administrators.  And perhaps, just perhaps, requiring such open, public, and early disclosure system would lead some UC Administrators to think more carefully and clearly about what outside activities they choose to do – or propose to do.

Update 3/23: some other links of relevance

Been attempting to get for 700s for the Chancellor (as an exercise, not to dig into them in any detail). Writing about it in a seagate post.

Janelle Ayres talk at #UCDavis on host-microbe-microbiome interactions

Evolution of DNA sequencing talk 2015 version

Crossposted from microBEnet

Every year for the last few years I have given a talk on the “Evolution of DNA Sequencing” at the “Workshop in Applied Phylogenetics” at Bodega Bay Marine Lab. I just did the talk and thought I would post the slides here. I note – I also added an evolutionary tree of sequencing methods which I include here as a separate animated gif too.


I note I posted a request to Twitter the day before the talk pointing to last years slides and I got lots of helpful suggestions from people about what to add or change. I included links to Tweets in the talk and thanked those people on the slides. But I would like to thank everyone here too. Published originally on March 10, 2015.  Updated  10/20/15 with information below and republished. Finally posted the video of the talk (recorded using Camtasia) to Youtube.  It is imperfect (there are a few things I said that came out wrong .. it was late at night).  But since it may be helpful to people I am posting it.