Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

Letter from Chancellor Katehi to #UCDavis Community #OccupyUCDavis

I received this by email last night:
Dear UC Davis Community,

I want to thank everyone for attending the recent student and then faculty and staff town hall meetings.   I sincerely appreciated the opportunity to not only share my thoughts, but also hear from you.
There are a number of investigations underway that will help us truly understand what happened on November 18.  As you know, I requested that the UC Office of the President investigate this matter; the goal was to ensure an independent review.  We have also launched our own internal investigation.  More details on these and other independent investigations can be found in the fact sheet which was posted on our website on Tuesday:

As Chancellor, I feel accountable for everything that happens on this campus and deeply regret what happened on Friday, November 18.  We were all shocked by the pepper spray incident on our quad and wish that it had never happened.  But it did, and now our community needs to come together, to heal and move forward.  I promise to redouble my efforts to engage in a positive meaningful dialogue with everyone that is a part of the UC Davis community.

Meetings with the various colleges are underway and more are being scheduled.  Following winter break, I am also planning to meet with students in the dorms and at other locations throughout the campus. I will also be talking to our parents and alumni about our campus’ plans going forward.  Lawmakers in Sacramento will hear from me about our shared concerns with rising cost of education.  I’ve given a great deal of thought on various ways we can continue to engage in a positive, meaningful dialogue.  More details can be found in my remarks at the recent faculty and staff town hall:

Your input is critical to making this process a success, and I look forward to continuing our conversations.  Thank you for your strength and commitment to our UC Davis community.

Sincerely,

Linda P.B. Katehi
Chancellor
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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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Top 10 reasons to still consider attending #UCDavis #OccupyUCDavis

I am sure I will get in trouble for this but here goes …

Top 10 reasons to still consider attending UC Davis

1. Performance art spreading throughout campus

2. Chancellor will be doing student laundry for next five years
3. Buy a van with a satellite dish, get free parking anywhere on campus
4. Work study program has many alternative career paths including sign makers, tent cleaning, socialism club treasurer, etc. 
5. Our logo found on more artwork than any school in country
6. Free housing in the quad
7. Students determine which professors get tenure
8. Police nowhere to be found, even for huge parties

9. New majors in “Crisis Mismanagement” and “Silent Movie Making”

10.  Like a building – it is yours.

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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.

——–

The evil Pecoses

P206 P211 P209 P207 P205 P210 P208 P212 P204

See the full gallery on Posterous

p213.mov Watch on Posterous

Friends who went to Pyle Junior High may appreciate this story more than other people. A few years ago I told my kids a story about throwing up on the Vice Principal of Pyle – Mr Pecos. They got me to tell this story over and over and then one day a new kind creature appeared in their play stories – the evil “Pecoses”. And now Pecoses are everywhere. Here are some pics and a video of some Pecoses

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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.

——–

Well #occupyevolution Eisen lab meeting in UCDavis quad has begun #occupyucdavis

P189
P187 P190 P188

See the full gallery on Posterous
——–
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.

——–

Well #occupyevolution Eisen lab meeting in UCDavis quad has begun #occupyucdavis

P189 P187 P190 P188

See the full gallery on Posterous

——–
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.

——–

Charles Vest Seminar "The 21st century university: Purpose, problems & promise" wrap up

Here is a wrap up, via my twitter posts and responses to them, of the seminar yesterday by Charles M. Vest, ex head of MIT and current head of the National Academy of Engineering. I know it is a bit lazy not to rewrite a summary but I think the tweets do an OK job …

UPDATE – some new links regarding the talk

Here are my tweets:

phylogenomics
Awaiting seminar by CHarles Vest, Pres. of US Natl. Acad. Engineering, past pres. of MIT #UCDavis
11/30/11 4:07 PM

phylogenomics
Vest seminar “The 21st Century Research University Purpose, Problems and Promise” #UCDavis
11/30/11 4:08 PM
phylogenomics
Charles Vest http://t.co/NlxrgeeE says Linda Katehi is an admired educational leader throughout the country #UCDavis
11/30/11 4:10 PM
phylogenomics
Charles Vest: two main challenges for universities now are globalization and access (i.e., access to education)
11/30/11 4:13 PM
phylogenomics
Charles Vest: currently trend to “brain interaction” across the globe, but need to work on how to connect people & computers better
11/30/11 4:14 PM
phylogenomics
Vest: FoldIt tool is evidence for “collective intelligence” – the researchers involved weren’t just integrating computers but brains
11/30/11 4:15 PM
phylogenomics
Vest discussing book A New Culture of Learning by Douglas Thomas and John Seely Brown “www.newcultureoflearning.com/”
11/30/11 4:16 PM
phylogenomics
Vest says location of universities still matter for many reasons incl. people need to be together and universities are embedded in cultures
11/30/11 4:17 PM
phylogenomics
Vest: purpose of research universities is “to create opportunity” (1) for graduates, (2) for business/industry (3) nations/regions
11/30/11 4:19 PM
phylogenomics
Vest: though research universities have many purposes, must be patient b/c hard to predict when benefits will occur
11/30/11 4:20 PM
phylogenomics
Vest: MIT and Stanford work very well b/c research is side by side w/ applications
11/30/11 4:21 PM
phylogenomics
Vest: few people understand that research universities are central to innovation (e.g., computing, laser, internet, gennomics)
11/30/11 4:22 PM
phylogenomics
Note – I might disagree with Vest’s claim that Universities drove genomic innovation
11/30/11 4:23 PM
phylogenomics
Vest: virtually every job in America depends on one or more university based innovations
11/30/11 4:23 PM
phylogenomics
Vest six lessons including (1) teaching and research must be intimately intertwined and are inseparable
11/30/11 4:24 PM
phylogenomics
Vest lesson 2: quality of research university is determined by quality of its faculty
11/30/11 4:25 PM

oldivory
@phylogenomics I’ve quit telling kids to interview the faculty when applying to colleges. Parents don’t get it either. Ah, well.
11/30/11 4:29 PM

phylogenomics
@oldivory good idea …
11/30/11 4:30 PM
phylogenomics
Vest: need in particular young faculty to grow up through rising w/in university
11/30/11 4:26 PM
phylogenomics
Vest lesson 3: science can flourish only in an open environment #herehere
11/30/11 4:26 PM
phylogenomics
Vest lesson 4: young faculty must be free to study and teach what they believe is important (e.g., should not be assistants to Sr. faculty)
11/30/11 4:27 PM

KSBruno9
@phylogenomics so not the European model.
11/30/11 5:11 PM
phylogenomics
Vest lesson 5: competition engenders excellence in universities (drives improvement in research, teaching, ideas, facilities, etc)
11/30/11 4:28 PM

rmtakata
@phylogenomics @carloshotta Mild competition. Wild competition could lead to cheating, forgery, distrust, sabotage…
11/30/11 4:32 PM

phylogenomics
@rmtakata @carloshotta he did not say it was perfect, just that it can be useful
11/30/11 4:34 PM
phylogenomics
Vest Lesson 6: fundamental scholarship and research must be equal w/ applied research and innovation
11/30/11 4:29 PM
phylogenomics
Vest: there is a danger in focus on applied issues that we ignore search for truth – must not be too utilitarian
11/30/11 4:30 PM

phylogenomics
Vest says “never in his lifetime has it been so hard to hang onto his optimism” b/c Washington is broken
11/30/11 4:32 PM

tjsharpton
As a young researcher, this concerns me RT @phylogenomics Vest says “never in his lifetime has it been so har… (cont) http://t.co/eZwvMurX
11/30/11 5:23 PM
phylogenomics
Vest: v. concerned w/ financial pressures on universities especially as it affects access & this started even before recent financial issues
11/30/11 4:33 PM
phylogenomics
Vest: in the last decade real per student state appropriations have dropped >20% while costs have risen
11/30/11 4:35 PM
phylogenomics
Vest: response to financial issues will be cut back on low demand classes, fewer low/middle $$ students, decr. in merit based aid & all bad
11/30/11 4:36 PM
phylogenomics
Vest: the favorite solution to State university financial problems is to seek out of state students; this spirals out of control
11/30/11 4:37 PM
phylogenomics
Vest: cites U. Michigan slogan from 19th century “an uncommon education for the common man”
11/30/11 4:37 PM

jim_croft
nice… but also woman? RT @phylogenomics: Vest: cites U. Michigan slogan from 19th century “an uncommon education for the common man”
11/30/11 4:43 PM

phylogenomics
@jim_croft I was not endorsing – just reporting
11/30/11 4:44 PM

jim_croft
@phylogenomics of course – the sentiment is perfect, the wording is excellent, for its time, just a little dated in some circles today.
11/30/11 4:49 PM
phylogenomics
Vest references Vannevar Bush’s vision “Science The Endless Frontier” for research & for access http://t.co/9n1Q0LAF
11/30/11 4:39 PM
phylogenomics
Vest references Vannevar Bush Quote on education access http://t.co/LmE1bTF7
11/30/11 4:42 PM
phylogenomics
Vest: we must be good citizens of the world and contribute to and learn from increasing globalization of education
11/30/11 4:43 PM
phylogenomics
Vest: all regions of the world are more/more linked/integrated w/ shared environment, challenges, resources, knowledge, humanity
11/30/11 4:45 PM
phylogenomics
Vest: modern research universities concept was developed from Humboldt University in Germany in 1800s -> JHU in US -> others in US -> global
11/30/11 4:46 PM
phylogenomics
Vest says he has a hard time contemplating scale of educational expansion in China and India
11/30/11 4:46 PM
phylogenomics
Vest: the Yin and Yang of Universities are Competition and Collaboration
11/30/11 4:47 PM
phylogenomics
Vest: people everywhere need opportunity from universities and thus MIT developed “Open Courseware” for anyone to use anywhere/anytime
11/30/11 4:48 PM

phylogenomics
Vest: Open Courseware movement has spread globally – and it (and related initiatives) are a revolution
11/30/11 4:49 PM

mikedelic
@phylogenomics I’ve taken free courses from Stanford and MIT that imwoudlnt have been able to back in the day. Love open source education
11/30/11 5:07 PM

mikedelic
@phylogenomics my favorite was Robert sapolsky’s behavioral biology course from Stanford
11/30/11 5:08 PM
phylogenomics
Vest: openness is the true spirit of education, democratization and empowerment
11/30/11 4:49 PM
phylogenomics
Vest refs: “Unlocking the Gates” and “Abelard to Apple” – books about open education
11/30/11 4:50 PM
phylogenomics
Vest: in 21st century we are observing the early emergence of a “Meta University” via open materials and platforms
11/30/11 4:51 PM
phylogenomics
Vest: must rekindle spirit of research university as provider of opportunity while also promoting openness
11/30/11 4:52 PM
phylogenomics
Here is more form Charles Vest on the “meta university” http://t.co/tJ0fNSqo
11/30/11 4:53 PM
phylogenomics
Vest: analog of Tip ONeil’s “all politics is local” need outreach to get people locally to understand importance of research universities
11/30/11 5:03 PM
phylogenomics
Questioner asks Vest how to best export notion of democracy/ access
11/30/11 5:09 PM
phylogenomics
Vest in response to question expresses dismay at how anyone could support the “Dream Act” http://t.co/FpwekBzu
11/30/11 5:09 PM


(NOTE – I GOT THIS WRONG SOMEHOW – HE CLEARLY SEEMS LIKE THE TYPE WHO WOULD SUPPORT THE ACT). SEE OTHER POSTS …)

lukedones
@phylogenomics Dismay that anyone would *support* the DREAM Act? Why?
11/30/11 5:12 PM

phylogenomics
@lukedones do you mean why would anyone be dismayed that some support the act?
11/30/11 5:15 PM

lukedones
@phylogenomics Yes. Just wondering whether he gave a reason.
11/30/11 5:21 PM

phylogenomics
@lukedones not that I remember
11/30/11 5:21 PM

phylogenomics
@lukedones sorry – in looking at the Dream Act I am wondering if he misspoke and meant he supported it … no longer sure what he said
11/30/11 6:24 PM

VoteBothell
@phylogenomics why no support for Dream Act?
11/30/11 7:01 PM


phylogenomics
Sorry all; MAJOR error tweeting Charles Vest talk; I wrote he was against Dream Act; I think he/I got that backwards & must be for it
11/30/11 7:19 PM

phylogenomics
@VoteBothell sorry – I think he must be for it – so either he or I got it backwards
11/30/11 7:20 PM

VoteBothell
@phylogenomics Great, got it. Enjoy your tweets. I’ve been following you since the pepper spray. My support and thoughts are with UC Davis.
11/30/11 7:22 PM
lukedones
@phylogenomics Thanks – I expected an academic would be for the Dream Act.
11/30/11 7:26 PM
phylogenomics
Vest: we need more experimentation with how research is funded to try to find other ways
11/30/11 5:21 PM
phylogenomics
Vest: should keep systems at basic science agencies but should try new approaches like ARPA-E
11/30/11 5:22 PM
phylogenomics
Vest views Open Courseware as a new form of publication not really as “classes” per se, b/c not interactive
11/30/11 5:25 PM
——–
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.

——–

California Aggie (#UCDavis student newspaper) also doing great job w/ #OccupyUCDavis Coverage

The California Aggie, the UC Davis student newspaper is also doing a great job with covering the Occupy UC Davis saga.  Here are some links of interest:

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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.

——–

Davis Enterprise really doing a rocking job covering #OccupyuUCDavis Story

The Davis Enterprise has really come through in the clutch with diverse coverage of the pepper spraying incident as well as diverse, interesting and sometimes unusual letters and comments.  Here are some links from them of interest:

News Stories


Some other articles:


Letters





——–
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.

——–

My brothers dream come true: baseball meets bioinformatics

James Fraser & Michael Eisen: Baseball Meets Biology

——–
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.

——–