Endosymbiosis Animations for "Biodiversity and the Tree of Life"

So I am in the midst of co-teachign a very large introductory biology course at UC Davis "BIS2C - Biodiversiy and the tree of Life". I cover much of microbial diversity in this class and also the large scale structure of the Tree of Life. 

As always, I spent a lot of time working on slides and such for this class and recently posted some animations based on these slides to Twitter and Facebook and thought I would share some of them here. For today, I am sharing the animations I made on Endosymbiosis. I posted a first version of this to Twitter last week. Note - I added music - Mussorgsky - Night on Bald Mountain for drama ... I also posted it to Facebook:

  

And boy am I glad I did. Because multiple people commented and pointed out parts that were, well, not correct. I had lecture too soon to fix them so I told my students about this and that I would update the slides. I then spent a day updating everything and made a new version which I think is much much better.

 

My talk for the @ucdavis Advance Awards Symposium

I gave a talk Thursday as part of the UC Davis Advance Awards Symposium in Sacramento. I am crazy busy right now so don't have a lot of time to write here about the talk but I did post about it to Twitter in a long thread.

Here are the slides for the talk:



Here is the first Tweet in a long thread I posted annotating the slides.



He is a Wakelet with some Tweets about the Symposium.

Four days of microbial phylogeny at #UCDavis #Asgard #Phylogenomics #MAGs

So - I did a guest appearance in a UC Davis Microbiology class run by a colleague / friend of mine - Renee Tsolis and I thought I would just post the details here.

Class: MIB200A - Biology of Prokaryotes

Four days of microbial phylogeny oriented around discussions of papers.  So to do this I picked four topics, really organized around papers.  See below for details.  I have posted the slides though I note they are pretty boring since most of them are just figures / text from the papers.

Class 1: rRNA and the Tree of Life

Papers
Slides





Class 2. Phylogeny

Slides:




Class 3: A New View of the Tree of Life

Paper:
Slides:




Class 4: Asgaard Archaea

Paper:

Slides:


Four days of microbial phylogeny at #UCDavis #Asgard #Phylogenomics #MAGs

So - I did a guest appearance in a UC Davis Microbiology class run by a colleague / friend of mine - Renee Tsolis and I thought I would just post the details here.

Class: MIB200A - Biology of Prokaryotes

Four days of microbial phylogeny oriented around discussions of papers.  So to do this I picked four topics, really organized around papers.  See below for details.  I have posted the slides though I note they are pretty boring since most of them are just figures / text from the papers.



Class 1: rRNA and the Tree of Life

Papers
Slides








Class 2. Phylogeny

Slides:






Class 3: A New View of the Tree of Life

Paper:
Slides:




Class 4: Asgaard Archaea

Paper:

Slides:


Gatekeeper training at UC Davis focused on student mental health and illness and everything in between

I went to a really useful training yesterday at UC Davis focusing on mental health and illness off students.  I posted a bunch to Twitter during it.  See the tweet below and the thread linked to it.


Also see this Twitter moment I made: https://twitter.com/i/moments/1154119660377239552?s=13.




Storify of Day 1 of "An open digital global south meeting" at #UCDavis

I made a Storify of Tweets and some pictures from the "An open digital Global South" meeting that I am a co-organizer of. This was organized by my "ICIS project and was, to be honest, really put together by other people on the project (I helped, but definitely was not one of the major organizers). Much of the credit should go to Michael Wolfe and Alexandra Lippman. See more in the Storify below.


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: http://www.indiana.edu/~hahnlab/.
















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 (http://articles.latimes.com/2006/feb/16/local/me-cap16). 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 (http://www.sandiegouniontribune.com/news/2011/jul/05/fox- 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