BIS002C "Biodiversity & the tree of life" Lecture2&3 more on phylogeny & trees

Well, tomorrow is going to be a bit crazy for me.  I teach four lectures tomorrow for “BIS002C – Biodiversity and the Tree of Life” and UC Davis.  Well, actually, I do each of two lectures twice.  This happens for two reasons.  First, there are two sections for the class and the way we do it, each faculty gives each lecture for which they are responsible twice.  Second, on Mondays, we do two lectures for each section.  In total there are four lectures per week and our schedule is as follows

Section A:  MWF 11-12 M 6-7
Section B: MWF 3-4 M 7-8

So tomorrow at 11 AM I give Lecture 2 for the class to Section A.  Then at 3 PM I give Lecture 2 to Section B.  Then at 6 PM I give Lecture 3 to Section A.  Then at 7 PM I give Lecture 3 to Section B.  Well, enough trying to make it seem like I am working hard.  Especially after PZ Myers gave me a little grief about this on twitter since, well, my teaching load is not actually that big compared to many.

Anyway – back to the class.  I am going to be posting about the class here as much as I can.  To give people an idea of the whole course this is the general highly simplified schema:

Lectures 1-5 Phylogeny (me)
Lectures 6-13 Microbes (Bacteria, Archaea, microbial euks) (me)
Lectures 14-21 Plants and relatives (Jim Doyle)
Lectures 22-24 Fungi  (Jim Doyle)
Lectures 25-36 Metazoa (Susan Keen)
Lectures 37-38 Wrap up, symbioses, etc (Susan Keen)

I do Lectures 1-13 and possibly 37-38.

For the first week or so I am introducing the students to various aspects of phylogeny and phylogenetic trees.  We do this in part because the rest of the class is oriented around using phylogenies and phylogenetic trees so it is important that the students really understand them.

To that end, tomorrow here is the plan:

Lecture 2 will focus on (a) the components of a phylogenetic tree and what they mean plus (b) taxa and groups in trees.  Among the topics we will cover are rooted trees, rotating trees (e.g., vertical vs. horizontal), rotating branches in trees, monophyletic groups/clades, non monophyletic groupings, outgroups vs. ingroups and more.  Oh in addition we will show the awesome Tree of Life movie that we did not get to on Friday. See below

Lecture 3 will then focus on characters and on tracing character evolution on trees.  Among the topics we will cover include traits vs states, homology, ancestral vs. derived, synapomorphies, and the many faces of homoplasy.  Am planning to start posting slides from the class after lecture hopefully starting soon.  But I keep refining them so not going to post before I am close to done ….

Any comments or suggestions welcome …

Quick Tip: if you want someone to share job ads, announcements, etc, send links to web sites not attachments

OK I have had it. I have had it with people who send me job ads and meeting announcements and other things they want me to “share” with colleagues or students. I got six such requests today – two for job ads, two for course announcements and two for meeting announcements.

But this rant may not be what you think. I am not annoyed that they want me to share something. I actually like doing this. What I am annoyed with is how people do this. 95% of the time people send these email requests with an attachment and expect me to forward this on to all who might be interested. And much of the time these attachments are big files, sometimes written in programs that only some people can open.

Does this work some of the time? Sure. Do I sometimes forward these on? Sure. But that approach is so 2005. Here in 2010 there are better ways than email blasts to people who mostly just click delete. In my opinion, the best way to get someone to share something like this is to post your announcement on the web somewhere and then send people a link to the web site. Include a brief summary in the email you send around and if people want more information they can go to the web site. Not only does this save some bandwidth and not clutter up peoples email servers, but it also allows those of us who share via Twitter and Friendfeed and Facebook and so on to more easily send the announcement around. I am sure many people prefer the attachments, but I for one get 50+ attachments a day, almost all of which do not get looked at.

UPDATE 9/23/2012
So – the post above was written two years ago, almost to the day.  And not much has changed.  Excepted perhaps the way people share links (I mention Friendfeed above — I guess I that could be replaced by Google+).

What is an easy way to post a document and then send people a link?  There are many ways to do this including

  • Post as a Google Doc/Presentation in Google Drive and send the link
  • Upload to Dropbox or another such site and, well, share the link
  • Post as a blog post (if you have a blog) or friggin start a blog and post it there
And of course many many other ways.  But please please please stop sending all these files around.  For a while I was posting them to my blog (I can autopost by forwarding email messages to the right address).  But I am sick of doing this for other people and am going to stop.

Probiotic use spreading, lots of money being made, known benefits still murky

A little news report from last week prompted me to write this mini post.  The report (Global probiotics market approaching $30bn by 2015: Report) indicates that the use (and purchase) of probiotics is spreading globally.

I find the whole thing pretty interesting actually. I personally think that at some point we will be able to figure out how to use “good” microbes to manipulate and manage human health and performance in all sorts of ways.  And there is more and more evidence that in some cases probiotics can have positive effects.  So in a way it is not surprising that more and more people are buying and using probiotics.

On the other hand, the evidence showing that probiotics are actually beneficial is still limited.  I note, this is why I have started giving out an “Overselling the microbiome and probiotics award” here.  So far, the best simple site I have found discussing probiotics is from NCCAM – the National Center for Complementary and Alternative Medicine.  This may come as a surprise to some (as it did to me), since NCCAM has been severely criticized by many for its support of pseudoscience (e.g., see here).  I note I am not even remotely trying to defend much of what NCCAM does here.  I am simply pointing out that they have a decent resource on probiotics.

For more on the science of probiotics see “Probiotic Microbes: The Scientific Basis” from ASM.  The report references above clearly seems to overstate the potential of probiotics by suggesting that they are being targeted for use in all sorts of health situations without presenting the caveats that these health benefits are not that well established.

Anyway, given that the evidence for benefits of probiotics is still pretty sparse, the fact that their use is spreading very rapidly is I guess a little bit disconcerting.  I would be willing to wager that a lot of the spread has to do with deceptive marketing practices by probiotic suppliers.  But there is a silver lining to this.  I think over the next few years we will see many new discoveries relating to where and when probiotics can help people and animals and such.  And the fact that the notion of “good microbes” is spreading is a good thing since we certainly need to reduce the “kill all microbes” mentality that has pervaded in some circles (consider the use of antibiotics in all sorts of materials).

Anyway, just a little post here about the spread of probiotic purchasing.  One thing I will end with – the report referenced above mentions that probiotics are being put into all sorts of new foods including “chocolates, cheese, muffins, and sausages”.

Can’t wait for this meeting on Microbial Communities as Drivers of Ecosystem Complexity

I truly can’t wait for this meeting: Keystone Symposia Conference | Microbial Communities as Drivers of Ecosystem Complexity – Program

Organizers: Jacques Ravel, Vincent B. Young, Mitchell Sogin and Trina McMahon. March 25 – 30, 2011 • Beaver Run Resort  •  Breckenridge, Colorado

The current program is listed below.  Still time to register.  Oh, and it is in Breckenridge, CO, which is kind of nice.  If you are interested in microbial communities, especially molecular studies of said communities, this could be the place to be …

  • Norman R. Pace, University of Colorado at Boulder, USA 
    Molecular Analysis of Microbial Communities – Historical Perspective
  • Mitchell Sogin, Marine Biological Laboratory, USA Long-Tailed Microbial Communities
  • Susan Lynch, University of California, San Francisco, USA Microbial Community Analysis Using the PhyloChip
  • Jonathan A. Eisen, University of California, Davis, USA Phylogenetic and Phylogenomic Approaches to Metagenomic Analysis
  • Joseph Petrosino, Baylor College of Medicine, USA Sequencing Technologies Applied to Studying Microbial Ecology
  • Patrick D. Schloss, University of Michigan, USA Developing and Validating Tools for Computational Microbial Ecology
  • Rob Knight, University of Colorado, USA Quantitative Insights into Microbial Ecology
  • Jed Alan Fuhrman, University of Southern California, USA Integrating Molecular and Environmental Data to Evaluate Community Patterns
  • John Heidelberg, University of Southern California, USA Metagenomic Analysis of Marine Microbial Communities
  • Peter J. Turnbaugh, Harvard University, USA Metagenomic Analysis of the Human Gut
  • Susannah Tringe, DOE Joint Genome Institute, USA Bioenergy Metagenomics
  • Stanislav Dusko Ehrlich, Institut National de la Recherche Agronomique (INRA), France A Human Gut Microbial Gene Catalogue Established by Metagenomic Sequencing
  • Trina McMahon, University of Wisconsin-Madison, USA Functional Genomics of Polyphosphate Accumulating Bacteria: ‘Eco-Systems’ Biology for Wastewater Treatment
  • Gregory J. Dick, University of Michigan, USA Talk Title to be Determined
  • Robert L. Hettich, Oak Ridge National Laboratory, USA A Proteogenomic Approach for Characterizing the Molecular Activities of Gut Microbiomes
  • Brendan Bohannon†, University of Oregon, USA Environmental Microbial Ecology
  • Claire Horner-Devine, University of Washington, USA Biogeography of Microbial Communities
  • Thomas Schmidt, Michigan State University, USA Ecologic Strategies of Environmental Microbes
  • Margaret Riley, University of Massachusetts Amherst, USA Antibiotic-Induced Changes in the GI
  • Jacques Ravel, University of Maryland School of Medicine, USA The Temporal Dynamics of the Vaginal Microbiota
  • Forest Rohwer, San Diego State University, USA RNA Virus Communities Associated with Human
  • Zoe G. Cardon, Marine Biological Laboratory, USA Soil Microbial Ecology
  • David A. Stahl, University of Washington, USA Metabolic Modeling of a Mutualistic Microbial Community
  • Jay P. Tiesman, Procter & Gamble, USA Microbial Community Analysis from a Systems Biology Perspective
  • Edward F. Delong, Massachusetts Institute of Technology, USA Systems Biology of Planktonic Marine Microbial Communities
  • David A. Relman, Stanford University, USA Perturbation of the Human Microbiome: Unrest at Home
  • Julie Segre, NHGRI, National Institutes of Health, USA The Skin Microbiome
  • Vincent B. Young, University of Michigan, USA Integrating Human Microbial Ecology in a Clinical Setting

A complete summary (probably TMI) about my time at the human #microbiome meeting #HMP2010

Well, I am writing this on my flight heading back from St. Louis after going to the “Human Microbiome Research Conference”

I have already posted some summaries of the meetings Day 1 and Day 2  and will soon do one about Day 3.  And you can find out more about the meeting from multiple other sources such as here, here, here and here.  But what I thought I would do here is give some of the story behind the meeting – why I went and what it was like behind the scenes, at least for me.  Note – I know this is very long – but hopefully it will give people a feel both for some of the science, some of the behind the scenes, and some of (my) history relating to this meeting.

Some prelude to the meeting

I headed out to the meeting from Davis on the afternoon on the Monday the 30th.  I was originally planning on only going to the meeting for the last day, Thursday. that was because, well, the 31st was my birthday, and I wanted to spend it with my family.  normally, I reserve important family events and do not travel or schedule things that conflict with them.  So, when George Weinstock invited me to give a talk at the meeting, I told him that I could probably only come for the last day.  So that is when he scheduled my talk.

But then as the meeting approached I changed my mind.  You see, in the last few months I have gotten more and more interested in the human microbiome as a research area.  I had done some work on the human microbiome.  For example, my lab was involved in a collaboration with Michael Zasloff at Georgetown University in which they were conducting human ileal transplants and we looked at the microbial recolonization of the ileum after transplantation.   This project was headed by a stellar student, Amber Hartman, who just finished her PhD in my lab.  Her paper was published recently in PNAS (which I note, we paid for the Open Access option there and really wish more people would do similarly).

Anyway, that project had been my main foray into human microbiome studies.  However, I have led or been involved in dozens of studies looking at the genomics of symbioses (good and bad) between animals and microbes (e.g., see these Open Access papers on Wolbachiasharpshooter nutritional symbiontsdeep sea worm epibiontsa cellulolytic symbiont of shipworms).  In fact, I have been moving more and more towards studies of communities of microbes that live in or on animals and plants.  And I have been writing on and off about the microbiome in my blog including the following posts:

And I guess as the meeting approached I realized I really do want to do more human associated studies.


Day 1, August 30, 2010: Getting there

So, given the above desire to go to the meeting, I changed my flight, and then headed on out on Tuesday PM.  As I was posting to twitter along the way and during the meeting, I am going to use my tweets to give some feel for what I was thinking as things were happening:

Tour de Lance

The trip getting there was OK … I got into Phoenix, my connection city and bumped into, of all people, Lance Price at the airport.  He had a cold, and I avoided him after a brief hello, and then got the good news that I was upgraded to first class. Imagine my surprise when who was in the seat next to me it the man with the cold, Lance Price.  This was funny in a way because I had been pondering a recent interaction I had with Price via my blog.  A while back I had written a post pointing to an interesting paper by Price on the penis microbiome and circumcision.  However, I was not completely happy with the paper, since the press release that came with it was quite misleading.  The press release had made some unfortunate statements that gave the impression that the study had direct implications for the transmission of HIV.  The paper had nothing directly to do with HIV – it was mostly a comparison of the microbes found on the penis of circumcised and uncircumcised males. Sure, this could in theory be connected to HIV since other studies had started to make connections between HIV transmission and circumcision and it was possible that the transmission differences were due in some way to microbiome differences.  But they did not show is in any way and it was inappropriate really to have any suggestion that their study was directly connected to the HIV-circumcision story.  So I said is in the blog and amazingly to me, Price, who happened to be the lead author, got the press release taken down and changed in a VERY short period of time.  Anyway, you can read more about that on my post.

So there he was, in the flesh, with a cold of some kind, sitting next to me.  It was actually quite entertaining …. We had a great time talking about penises and vaginas and anthrax and the FBI and all kinds of other nasty things (this makes me want to say – “and everything was fine until the flight attendant came over and had some paper in his hand, held it up and said” … but people might not get that if they have not heard of Alice’s Restaurant by Arlo Guthrie).  I am certain some of the others in first class were wondering WTF was wrong with us.

  • Sat next to Lance Price on flight to #microbiome mtg – am still impressed w/ his response to blog of mine months ago http://ff.im/-pWTaU
  • Passengers near me & Lance Price on way to #microbiome mtg got earful: anthrax, penises, vaginas, wounds, microbes everywhere

Stranded Landed in St. Louis

We landed around 11:30 PM local time and I asked a flight attendant what time zone we were in she said Eastern.  This meant that it would, be 8:30 PM at home.  So while taxiing I called my wife in the hope I could talk to my kids as they went to sleep to say good night.  But alas, it turns out St Louis is on Central Time and the kids were asleep.  We got off the plane and Price and I headed downstairs … He had checked a bag and after discussing it I decided to not wait and share a cab with Dr. Sniffly.  So I took a cab to the hotel. The hotel the meeting was at (and thankfully where my room was) was the Park Chase Hotel. It was perfectly nice, and my room was enormous.  There were some issues, like the proliferation of pillows on the beds, and the strange key card system in the elevators that did not work well, and the 12$ beers in the lobby bar, and the fact that they kept the conference rooms at something like 60°F but it was still an OK place to have a conference.

No food for you

Anyway, I checked in, dropped my stuff in my room and went out to try and find a place to eat.  On the way out of the hotel, I bumped into Ashlee Earl and Bruce Birren who were working on something on the computer in one of the common areas.  I would have lingered longer, since I have known Ashlee for many years as used to collaborate with her when she worked on one of my favorite organisms Deinococcus radiodurans in John Battista’s lab (see our paper on gene expression in Drad here). But since it seemed I was interrupting some important work, I headed out to look for food since I had missed dinner (note to self, getting upgraded on US Air is certainly better than coach but nothing special – no food except chips).

I headed into the streets to a place directed by the hotel front desk people.  Alas, even though they promised the place would be serving food at 12:10 am, it was not.  So I grabbed some simple thing at a cafe and then went to my room to crash, on what was now, my birthday.

Day 2: Start of the meeting

On the morning of the meeting start, I got up a bit late and rushed downstairs to the conference area.

  • Well, I am late to the human microbiome conference this am – I hate meetings that start at 8 am, especially when not on west coast

I got my conference material and ID badge – I had missed the general introduction by George Weinstock and Jane Peterson and Larry Shapiro.  The current speaker was (I think) Jim Versalovic and I was standing in the way back trying to figure out whether to go get some coffee or get a seat.

The talk ended and then I saw that Bruce Birren was up.  Well, as Bruce does some good/interesting stuff and as I had seen him working away earlier that AM, I figured I should stay.  So I grabbed a seat in the way back, and got out my iPad to start tweeting.  I saw that some others were tweeting the meeting and had settled upon a hashtag of #HMP2010, so I started firing away.  I note I like to live tweet meetings for a variety of reasons, including that I think it is a good way to let people have a feel for a meeting as it is happening.  But I also do it to take notes and force myself to pay attention.

Alas, sometimes you do not always write things out perfectly.  Here are my tweets from his talk:

  • Well, I made it … To catch Bruce Birren from Broad starting his talk on 16s surveys and developing high throughput approaches 
  • The human microbiome meeting #HMP2010 is quite packed – microbes rule http://twitpic.com/2jynzt
  • Bruce Birren says that they developed a 454 rRNA sequencing pipeline that has been tested & is accurate across centers; #HMP2010
  • Birren used a mock community to test rRNA PCR methods – wonder if he has read our mock metagenomics paper http://bit.ly/cPaIKF #HMP2010
  • Bruce Birren testing diversity estimators from rRNA PCR – for simulation got many more OTUs back than they put in #HMP2010 #sequencingerror
  • Birren – given that they trust their PCR, now comparing many human samples – seems like they are way behind the field here #hmp2010
  • Birren presenting clustering of samples based on rRNA analysis – but could do much better referencing prior lit on this #HMP2010
  • Interesting question after Birren’s talk re: archiving samples & informed consent – key things to think about in this type of work #HMP2010

Anyway, more later about the mini firestorm that my tweets about his talk created.  I was moving on to other things at the time.  Like responding to my brother’s Michael’s Happy Birthday wishes, which he surprisingly sent through twitter, which he rarely uses.

Next up speaking was Ian Lipkin.  Lipkin is another one of the people at the meeting I first interacted with through my blog, though with him it was a bit more awkward than with Lance Price.  A few years ago now I had written a post about a paper from Lipkin on colony collapse disorder (CCD).  The post I wrote was not positive, let’s put it that way.  And one of the coauthors of the paper, wrote to me and basically told me I was a jackass and I was wrong about what I had written in the post.

Alas, they were right.  And so I did what I thought any good scientist would do if they published something that was wrong – I retracted the blog post and put out an apology (this will be a recurring theme here) and gave myself a new “genomic jerk award”.  Plus I wrote a new post discussing their paper.   And then I was stunned – Lipkin called me up to thank me for apologizing and retracting the post.  Since then I have interacted with Lipkin on and off over the years and have followed his work with some fascination as in a way he is an old school microbe hunter.

Anyway, here is what I wrote during his talk:

  • Ian Lipkin now up discussing microbe hunting in the 21st century #HMP2010 – mentions problems with Koch’s postulates at start
  • Ian Lipkin talking about emerging infectious diseases – says we have only scratched surface of sampling viral diversity #HMP2010
  • Lipkin showing world wide air traffic to scare us (rightly so) about how fast EIDs can spread #HMP2010
  • Ian Lipkin referring to Edgar Allen Poe and cryptography in trying to sort through Metagenomic data#HMP2010 #binningishard
  • Lipkin talking about nothing controversial: autism and MMR and microbes #HMP2010
  • Lipkin has looked at microbial diversity in biopsies of people w/ &; w/o autism – found microbes associated w/ autism #hmp2010
    • apoorva_nyc asked: @phylogenomics what sort of microbes? that’s all this field needs, more gut/autism theories
    • I wrote back: @apoorva_nyc he simply said that there are differences in the microbial diversity in patients with autism – not claiming causal
  • Really like how Lipkin caveated his autism work by saying “this is one study in one place” & then asked for others to test if real #HMP2010
  • Ok Ian Lipkin has won me over forever . He just quoted Yogi Berra and Neils Bohr in one sentence #HMP2010

Coffee with a Tiger

In the first break, I headed out to get coffee, as I was starting to drag.  I bumped into none other than Owen White, who also was going to get coffee.  Owen was one of the people who helped convince me to take a faculty job at TIGR in 1998.  He was the PI on the project to sequence the genome of Deinococcus radiodurans, the most radiation resistant organism known, and I was at the time working on the evolution of DNA repair and radiation resistance.  One of my first projects at TIGR involved helping Owen analyze the Deinococcus genome and write a paper on our analysis.  I note, look at the figures in that and other TIGR genome papers very very carefully and you will see some secrets Owen, I and others put in there.  For example, in the Deinococcus paper, search for “strangelove.”

I worked at TIGR for eight years before moving to Davis in 2005 and Owen and I worked together on many many projects.  Owen and I did not always see eye to eye on various things while I was at TIGR but I both respect his work enormously and still consider him a friend so it was great to see him from my point of view.

We went to the hotel cafe and got there just before all the others from the meeting since we snuck out just as questions were starting for the last talk.  And then we wandered back to the mixing area outside where the talks were and I bumped into an array of people I knew.  The meeting really was a “who’s who” of microbial genomics and human microbial studies including many of my old TIGR colleagues (most of whom were ow at either UMD or the J. Craig Venter Institute – JCVI).

More talks

Talks started up again I went back to my live tweeting.  I note, it was also interesting to see who else was tweeting the meeting and eventually to meet them in the flesh.  After the break there were four talks:

  • Roger LaskenJohannes Goll discussed metagenomic projects at the J. Craig Venter Institute.  They did a tag team talk with Roger focusing on whole genome amplification (which he was one of the pioneers of) and Johannes discussing the JCVI metagenomic analysis tools.  Here is what I wrote:
    • Roger Lasken from the J Craig Venter Institute now talking about whole genome amplification w/ MDA to get at uncultured organisms’ #hmp2010
    • Roger Lasken: phylogenetic analysis can help assess MDA samples – note work done by Jonathan Badger who used to work in my lab #HMP2010
    • Johannes Goll discussing Metarep – JCVI metagenomics analysis tool #HMP2010 – now available / published http://ff.im/-pYRF7
    • Lasken: shallow 454 sequencing with barcoding – 50-100 MDA reactions to verify 16S classification of HMP samples #HMP2010
    • Best place to find out about Human Microbiome Project?: probably The HMP DACC #HMP2010 #somecoolthingshttp://ff.im/-pYTFo
    • For software geeks: The MetaREP software is open source & uses CAKEPHP, Solr, MySQL mix to do rapid indexing and searching #HMP2010
  • Makedonka Mitreva from Wash. U. then discussed various microbiome projects going on there.
    • Makedonka Mitreva from Wash U Genome Center: shotgun metagenomics of 54 people x 5 body sites: oral, skin, gut, vagina, nasal #HMP2010
    • Mitreva – the big problem in analyzing human microbiome metagenomics data is computational time –#HMP2010 #weneedbettermethods
    • Ugh: Mitreva referred to “lower eukaryotes” – maybe she says this because the podium is high above the meeting hall? #HMP2010
    • Mitreva: current tools for analyzing metagenomic data mostly die (my word, not hers) when analyzing massive new data sets #HMP2010
  • Owen Whitethen gave an overview of the Human Microbiome Project Data Analysis and Coordination Center, which he runs. His talk was quite good – a good mix of detail about what they are doing and big picture commentary about the state and future of this type of activity.
    • Next up Owen White on the HMP Data Analysis and Coordination Center that he runs #HMP2010http://www.hmpdacc.org/
    • White: one of their goals is to have a nice, easy to use website to coordinate information about HMP #HMP2010see http://www.hmpdacc.org/
    • White: major goal is to provide ease of access to certain types of HMP data #HMP2010
    • Key issue: open data is important but ease of access and use of open data also critical #HMP2010
    • Best place to find out about past & ongoing microbial genome projects?: definitelyhttp://www.genomesonline.org/ #HMP2010
    • I almost said same thing: RT @mikethemadbiol#HMP2010 *I* care if we sequence another E. coli genome 😉 Though metadata ARE critical
    • Key issue: genome and metagenome data is not very useful without metadata about samples, methods, etc#HMP2010
    • White: some challenges in downloading data from short read archive from NCBI #HMP2010
    • White: DACC putting together virtual machines to run all sorts of microbiome/metagenomic analyses – can run locally or on cloud #HMP2010
    • White: his goal is to teach community to fish not give them food (i.e., to give community tools, rather than run things for them) #HMP2010
  • Eric Alm gave the final talk in the session.  His was not about human microbiome work but instead about population genomics of Vibrio strains.   
    • And now for something completely different but very
      relevant: ocean microbes and genome evolution from Eric Alm#HMP2010
    • Eric Alm discussing Fred Cohan’s ecotype model for species formation in bacteria and archaea #HMP2010
    • Eric Alm describing how microbial samples are collected from ocean water; me: informatics people need to understand these things #HMP2010
    • Alm: comparing 75 genomes of strains of Vibrio species; note all of these are in essence same OTU/species but lots of differences #HMP2010
    • A questioner asked about something relating to “higher primates” – come one everyone – stop the evolution bogusness #HMP2010
    • Alm, in response to my question, says that much of their evolution analyses done on incomplete genomes but he thinks it works fine #HMP2010

Lunch and PM talk burnout

And then it was time for the herd of scientific sheep to go to lunch.  The mechanisms for getting up to the 11th floor for lunch were awkward. Two-three elevators, no stairs, and nobody sure exactly where to go. But people made it on up to a freezing cold room on the top with a nice view of the park nearby the hotel.  I had a relatively quick lunch, went outside on the balcony to get some air, and then it was time for the PM sessions.

I was now a bit burned out. Too many talks I think.  And it is a bit hard to tweet all the talks and not just space out for a while.  But I soldiered through, and tweeted some more,

Much of the PM talks are a bit blurry to me now, but here is what I wrote on twitter:

  • Ruth FarrellRichard Sharp, both bioethicists from the Cleveland Clinic talked about ELSI issues in the human microbome project
    • Oops … Missed the first part of the talk on ELSI issues associated with the human microbiome project#HMP2010 #importantstuff
    • Issues relating to microbiome ethics: genetic discrimination, GMOS, release of probiotics to world, gene therapy #HMP2010
    • Richard Sharp discussing how patients seem willing to use GMO probiotics even if they don’t like GMO foods#HMP2010
    • Sharp: patients may be susceptible to aggressive marketing of probiotics #HMP2010
    • Sharp saying that we should not oversell the microbiome project – he should read my bloghttp://bit.ly/ahXB4n #HMP2010
  • Jo Handelsman discussed some of her work on looking for antibiotic resistance encoding genes in microbes in the environment
    • Jo Handelsman, one of my favorite scientists, now up talking about finding antibiotic resistance genes in the environment #HMP2010
    • Jo Handelsman refers to the “resistome” – collection of antibiotic resistance genes in a community;#badomics word? – probably #HMP2010
    •  I note, Jo Handelsman coined the word metagenomics many years ago #HMP2010 – this omics word seems OK to me
  • Vincent Denef discussed population genomics in the human microbiome
    • Vincent Denef from Jill Banfield’s lab discussing “how deep does the rabbit hole really go?” #HMP2010
    • Denef now explaining his talk title – lots of closely related organisms and may have to distinguish at very fine scale #HMP2010
    • Denef now giving homage to the red pill blue pill choice from the Matrix #HMP2010#Toldyoumetagenomicswascool #geekytoo
    • Denef discussing metagenomic studies of preterm infant gut -using similar methods as in acid mine drainage studies #HMP2010
    • Denef – looking at population shifts over time using metagenomics -getting to correlating pop. changes with specific allelic diffs #HMP2010
    •  Denef showing how proteomics can be used in environmental studies – Banfield lab does v. cool stuff in this area #HMP2010
    • A main worry re: metagenomic studies: like GWAS, lots of genetic variation but w/ few variables, will always find correlations #HMP2010

In the next break I bumped into Ian Lipkin and we agreed to go to dinner together.  Then the next session seemed to begin way too fast but it was good.

  • David Relman was up first.  I note, before I got accepted to graduate school I had an offer to work in Relman’s lab on rRNA PCR studies (I do not think we ever met, but I am not sure anymore).  I wonder how my career would have ended up if I had joined his lab then …           
    • David Relman is w/o a doubt the Philosopher of the Microbiome – always discussing deep questions #HMP2010
    • David Relman discussing single cell genomics and other approaches to studying single cells in communities#HMP2010
    • Relman: reagents in molec. biology freq. contaminated w/ DNA; this impacts many amplification studies when DNA levels low; #HMP2010   
  • Margaret-McFall-Ngai who I have interacted with on and off over the years and love her approach to studies of symbioses.
    • Margaret McFall-Ngai : vertebrates are a very old group & likely been associated w/ microbes for hundreds of millions of yes #HMP2010
    • McFall-Ngai: humans are not the pinnacle/crown of evolution; me: just YAV (yet another vertebrate) #HMP2010
    • RT @TheGenomeCenter McFall-Ngai: most human genes are old; most genes associated with human disease are also old#HMP2010 
    • McFall-Ngai’s talk is so far an homage to model organisms and how they will be relevant to human microbiome studies #HMP2010
    • McFall-Ngai encouraging everyone to study circadian rhythms of host-symbiont interactions #HMP2010
  • Mihai Pop who I used to work with when we were both at TIGR.  He discussed metagenomic assembly methods.
    • Mihai Pop says his talk on Metagenomic assembly will be very short b/c it is impossible #HMP2010
    • Alas Pop didn’t end his talk, says one can make (somewhat) useful assemblies from metagenomic data; utility depends on goals #HMP2010
    • Pop showing challenge in assembly by showing assembly of A Tale of Two Cities; repeats Ike “it was the” can confuse things #HMP2010
    • Pop: genome assembly is hard b/c of 1) repeats 2) low coverage 3) sequencing errors – gets even harder for metagenomics #HMP2010

A bloggable dinner?

After the last talk that PM I got a drink in the bar and was hanging out talking to people when I realized I was late to meet Ian and I headed over to the lobby and off we went.  We found a place and sat down outside – good to not be in a freezing cold room for a while.  Mike the Mad Biologist of ScienceBlogs wandered by and we invited him to join us (not sure if his real name is public knowledge so not posting it here).  We had a good dinner and Lipkin even got the restaurant to bring out a candle for my birthday after dinner.

Drinks and criticism and bedtime stories

Afterward, we went back to the hotel,  I dropped off my stuff and headed down to the bar to get a birthday drink, and bumped into a crowd of people from the Broad, JCVI and UMD coming from a dinner they had for the sequencing centers involved in the HMP.  I skipped out for a fun 30 minutes to tell bedtime stories to my kids over the phone (I really wonder what the hotel staff lurking nearby thought while listening to me tell a crazy invented story about submarines, polar bearskin, whales, and strange activities).

Anyway I returned to the bar, got some complaints from the Broad and JCVI people about something I tweeted about Bruce Birren’s talk and then went to my room. The comments about my tweet led me to relook at what I had written and especially in light of having been thinking about the Lipkin blog retraction.  So after fretting a bit, I decided I probably was a bit over the top in some of my comments on his talk.  So I wrote up a mini apology and clarification on my blog at night when I wrote up notes on day 1.  In summary what I said in that post I quote here, in part to make this a very very long post, but also b/c I think it is relevant:

As I have tweeted many meetings I guess I am used to various aspects of such activities but many out there clearly are not.  Live tweeting a meeting is a rough thing in many ways, at least for me.  I want to give people a feel for the meeting, as it happens.  I want them to know what I actually think about talks, at least within some reasonable limits.  But alas sometimes, hopefully not too often, I get things wrong.  And sometimes I post something obnoxious.  And sometimes I miss key points.  To me, this is analogous to the conversations people have about talks all the time.  Overall, I think mostly I do an OK job tweeting meetings.  But occasionally I write something that does not sit right with others or myself.  And alas, today has one such tweet (well, only one I know of right now).

It happened during Brice Birren’s talk.  Birren, from the Broad, was discussing a few different things including studies done by the Broad in which they have tried to compare and contrast and use rRNA PCR studies done at different centers associated with the HMP.  Much of what he was discussing was technical details of the control experiments they did to assess how variable the results were between centers.  I felt at the time that he was placing this work in enough of the context of other rRNA studies of the human microbiome.  And I tweeted this feeling.

  • phylogenomics Birren presenting clustering of samples based on rRNA analysis – but could do much better referencing prior lit on this #HMP2010
  • phylogenomics  Birren – given that they trust their PCR, now comparing many human samples – seems like they are way behind the field here #hmp2010

But in the end, after discussions at the bar later, I think I may have missed the point of his talk.   I thought at the time that he was discussing solely new findings and new analysis tools that they developed.  To me, I did not like that he did not spend much time discussing other analysis tools nor how their work compared to other studies of the human microbome.  And that gnawed at me.

But in retrospect, I think perhaps he was focusing more specifically on the comparison across the centers.   In that context, the way he laid out his talk and what other work he referenced makes more sense.  I think perhaps he could have still placed things in a broader context but my comments in retrospect were a bit over the top and unnecessary.  As I said above, I think it is useful to try and post what I am actually thinking at the time.  I try to filter this if I know what I am thinking is rude, biased, obnoxious, etc; but I do post critiques if they seem relevant.  But my filtering was a bit off here.  Alas, now Bruce (if he reads twitter) probably wants to dump a beer on my head and people from Broad think I am a putz (well, some may have thought that before). I guess I may have to change the tuning on my filter a bit … but I still will try and post what I think at the time.  It is a fine balance I do not always do precisely … off to sleep and in the AM – Day 2 plus time to make some in person apologies …

In the end, I accept that live tweeting is a bit risky in the way I do it, where I try to not just say what people are saying but try to say what i think about what they are saying.  Sometimes my comments are overreactions or rude or wrong.  But I always try to correct them or clarify when something was off.  From the emails and tweets out there I know a lot of people follow along when I am tweeting a meeting and they seem to like it … Just got to try and be careful to not be over the top.

Other notes on Day 1 on the meeting.

In addition to my comments about the Birren tweet, I thought it might be of interest to post here what else I said about Day 1.

Well, Day 1 of the Human Microbiome Project meeting is over.  And overall, I think it was quite good.  So now for a Day 1 wrap up.

First, a bit about the meeting.  The meeting is formally called the “Human Microbiome Research Conference” and more information about it can be found here. It is directly tied to the NIH “Human Microbiome Project“, also known as the HMP, which has been in operation for a few years now.  The HMP is one of a small number of NIH “Roadmap” initiatives (these are also known as NIH Common Fund Projects).  These are cross cutting projects that are funded outside of the normal NIH departments/centers.  The HMP started a few years ago and is focused on studies of the communities of microbes that live in and on humans.  The HMP has so far funded a wide array of projects including some big scale and some smaller scale.  This meeting is I think the first to try to cover the diversity of different projects funded by the HMP at once.

Day 1 covered a bit of introduction and then a diversity of HMP related and some not so related (but good) talks.  The talks were perhaps a bit too reviewy for my liking, but I think actually, all of them were interesting.  Some lessons I got from today include the following:

  1. The human microbiome is becoming a fascinating area of research with an ever growing set of data to look at
  2. The data for the HMP seems to be openly available, which is good. Reference genomes can be found here. Some rRNA data can be found here. Strains of microbes are available too.  Not sure where the metagenome data.
  3. Ease of access and use of data is more important than just access to data; the HMP DACC is doing a decent job with helping access data.
  4. As important as access is metadata about samples. Not sure how much of this is available right now nor how easy the metadata is to make sense out of.
  5. As with most (all?) large scale, top down projects, there are multiple areas where improvements could be made in communication and engagement with the broader community.  It seems like the HMP is working hard on this issue.
  6. There are some possible complicated issues around release of microbiome data and medical records from people
  7. There is still a big risk in overselling the potential benefits of microbiome research
  8. Correlations ≠ causation.  Sorry I had to put that here.  See #7 above.
  9. Analyzing and making sense of metagenomic data is still very very hard
  10. We desperately need more ecology driven studies of the microbiome
  11. To me, the HMP should really try to mimic the human genome project and focus on producing reference data (genomes, metagenomes, and rRNA) for everyone to use.  Trying to do complex scientific/clinical studies in this project seems inappropriate.  We all need the baseline to do the science.
  12. As with every meeting, the best stuff that happens is in between talks.
  13. Having the meeting room be something like 40 °C is probably not the best idea nor use of resources (hotel issue, not HMP issue).

Those are some of the lessons I am thinking about now, a few hours after the last talk.  But if you want to get a “real time” feel for the talks, the best way to do this, if you weren’t here, is to look at twitter posts about the meeting.  If you do not know, the common practice these days is to use a code within twitter specific for the meeting called a hashtag.  For this meeting the hashtag is #HMP2010 and you can find the tweets about the meeting easily by searching twitter for this code.  There were other twitter posts about the meeting, but may be somewhat hard to find b/c they did not use this code.  Such is life I suppose.

Anyway, if you want to see all the tweets from the first day of the meeting with this hash tag I have appended them at the bottom of this email.  This includes anyone who may have reposted (aka retweeted) these tweets to their twitter feed. 



Day 3 of trip, Day 2 of meeting.

Anyway, since I was up so late working on the blog post, I overslept and missed the first few talks,  I was really really bummed about this because one of the ones I missed was from Floyd Dewhirst who does some absolutely fascinating stuff.  I also missed a talk by Susan Haake.  Bummer.  But talks did start really early.

Fortunately, I got there in time for most of Jeff Gordon’s talk.  I simply am in awe of Jeff Gordon.  He is to me, the grand guru of the field of human microbiome research.  He has in particular specialized in making studies of germ free animals a key part of work on the microbiome.  I have always had very positive interactions with him, although I think he may still want to get back at me for including him in my April Fools joke about Craig Venter sequencing his own microbiome.

  • Jeff Gordon discussed his current work on using germ free animals to study function and ecology of microbial communities
    • RT @TheGenomeCenter Next talk Jeff Gordon from @wustl on the marriage of comparative metagenomics and gnotobiotics#HMP2010
    • RT @TheGenomeCenter Gordon: took fecal microbe community from healthy donor and graft it into gut of germ-free mice successfully #HMP2010
    • After brief delay now at #HMP2010 – Jeff Gordon up: creating artificial communities of many species & introducing to germ free animals
    • Gordon: using defined communities of microbes to test microbiota response to different diets#HMP2010 – track changes in abundance, txn, etc
    • Gordon : using RNAseq to track gene expression patterns in model microbial communities #HMP2010
    • Gordon: Goal .. use “personal” culture collections isolated from people to get a collection that has coevolved w/ each other #HMP2010
    • Gordon – much of OTU diversity in human gut microbes can be captured via culturing #HMP2010; though this ignores w/in species diversity
    •  Jeff Gordon has electrified the crowd w/ his discussion of model organisms & model communities#HMP2010 #modelorganisms
  • Liping Zhao discussed microbes associated with metabolic syndrome
    • Now Liping Zhao from Shanghai Center of Systems Biomedicine on re-eng. gut microbiota with TCM foods to prevent metab. syndrome #HMP2010
    • Zhao: multiple models could explain connection between microbes and obesity #HMP2010
    • Zhao: who is right? Grandma: you are what you eat; Geneticists: you are your genes #HMP201
    • Good to sea some old school TFLP Data here from Zhao mixed in with sequence data #HMP2010
    • Zhao: what is connection between diet, microbiome and longevity? Doing experiment in mice over four years #HMP2010
    • Zhao: diet / excercise differences -> lifespan differences + microbiota differences; though I note just correlations right now #HMP2010
    • Zhao emphasizes benefits of having reference genomes to sort through metagenomic data #HMP2010
    • Zhao wants to encourage marriage of metagenomics and metabolomics in gut studies #HMP2010

Then there was a brief break and then more talks.  Much of this has blurred together now so I think my tweets will be the best record of what happened from my point of view.

  • Joe Petrosino discussed metagenomic projects at Baylor
    • Now Joseph Petrosino from Baylor on improved metagenomic sequencing and analysis for healthy and diseased individuals #HMP2010
    •  Joe Petrosino from Baylor giving overview of role of Baylor in HMP #HMP2010
    • Petrosino – reminds people that not only is HMP producing data and science, but also spin off benefits akin to space program #HMP2010
    •  Petrosino: key ?s: what are biases, how do new sequencing platforms perform, what is gained/lost from assemblies #HMP2010
    • Petrosino has interesting results on sequencing mock community, I note we have study like this in PLoSonehttp://bit.ly/cPaIKF #HMP2010
    • Petrosino doing some interesting analysis of the risks/benefits of assembly in metagenomics #HMP2010
    • Note of caution: For statement “X manipulations of microbes help treat X ailments in X people X of the time”: X=”some” NOT “all” #HMP2010
    • Petrosino working on a viral metagenomic sequencing pipeline including isolation, concentration strategies#HMP2010
  • Phil Tarr discussed microbes associated with necrotizing enterocolitis
    • Next up – Philip Tarr on the infant microbiome and necrotizing einterocolitis #HMP2010
    • I have created a PaperLi newspaper on the human microbiome meeting tweets – seehttp://www.paper.li/tag/HMP2010 #HMP2010
    • Phil Tarr telling a very sad story of a premature infant dying of necrotizing enterocolitis – which is alas very common #HMP2010
    • Phil Tarr doing “massively parallel stool collection” for necrotizing enterocolitis study “all stools all the time” #HMP2010
    • Tarr: high throughput, barcoded, quick collection of all stools of premies in hospital, then if some get NEC will do sequencing #HMP2010
    • Tarr doing a great job of saying who did the analysis for which he presents results #HMP2010#willtrytodothisbetter
  • Vincent Young
    • Next up Vince Young on the role of gut microbiota in ulcerative colitis, IBD #HMP2010
    • Young: many studies suggesting possible connection between microbes and IBD; but emphasizes these are associations not causal proof #HMP2010
    • Young: complexities in IBD microbe studies incl. lack of time zero, diversity of host history/genetics, no info on microbe function #HMP2010
    • Young looking at “pouchitis” to develop in IBD patients who get inflammation of diverting intestinal pouch#HMP2010
    • Those interested in IBD/microbes might want to look at ileal transplant study from my lab/Georgetown http://bit.ly/XFRWf #HMP2010
  • J. Dennis Fortenberry
    • Dennis Fortenberry: urethral & coronal sulcus microbiome studies of adolescent males; offers caution for sexual nature of talk #HMP2010
    •  Fortenberry “for those of you who have not been thinking about male sexual anatomy this morning, here is a primer” #HMP2010
    • RT @TheGenomeCenter Fortenberry: multiple microbiomes of the penis – in areas where pass urine and areas used during sex#HMP2010
    • Fortenberry discussed scanner image of MF sex, how microbes could exchange, ended w/ “don’t how how they got them in scanner” #HMP2010
    • Fortenberry on difficulty studying microbe-sexual activity connection in teens “These are free-ranging adolescents” #HMP2010
    • Fortenberry: need to train teens “amazing the things teenage males will do with specimen cups that does no involve peeing in cup” #HMP2010
    • Fortenberry discussing ethical issues w/ genomic research on young people; especially on sexual behavior #HMP2010

Then lunch.  I sat again with some people from JCVI including Granger Sutton and Shibu Yooseph.  And I tried to get out of there quickly to get a bit of time to walk around, but it was hard to escape.

Then came the concurrent sessions which made me write this:

  • Oh no – #HMP2010 has concurrent sessions – where to go? Where to go?

Here are some of my notes from the concurrent session talks I went to:

  • Gail Rosen discussed metagenomic binning methods
    • Listening to Gail Rosen talk about naive bayesian classifiers for metagenomic data #HMP2010
    • @ianholmes yes i think kmer classification though got in late
      • @phylogenomics “naive Bayesian classifiers for metagenomics” = clustering using k-mer composition of reads?
    • Here is a link to Gail Rosens Naive Bayesian Classifier tool for metagenomics analysishttp://nbc.ece.drexel.edu/ #HMP2010
    • Here is a link to Gail Rosens Naive Bayesian Classifier tool for metagenomics analysishttp://nbc.ece.drexel.edu/ #HMP2010
  • Tom Schmidt discussed culturing microbes 
    • Tom Schmidt now up talking about culturing the human microbiome #HMP2010
    • Schmidt: Great Plate Count Anomaly misinterpreted to mean most microbes are unculturable – means most don’t grow in one condition #HMP2010
    • Schmidt – cultured organisms very valuable for working on functions in communities #HMP2010
    • Schmidt discussing nice trick for tracking oxygen in tissues – GFP only fluoresces win essence of oxygen#HMP2010
    • Schmidt: to study microbes in colon they developed methods to do colonoscopies on unprepped people so microbes not flushed out #HMP2010
    • Schmidt: in trying to culture from human microbiome have to switch methods and samples often to continue to recover new things #HMP2010
  • Anthony Fodor discussed CF infections
    • Anthony Fodor: how do infections in CF patients respond to antibiotics? Followed CF patients during exacerbation events #HMP2010
    • Fodor pronounces T-RFLP “Tee R Flip” while I and I think others usually say “Tee Riff Lip” – I think I like his more #HMP2010
    • Fodor – OTU diversity (i.e., number of bacterial species) is lower in severe CF infections #HMP2010 though he notes small sample size
  • Diane E. Hoffmann discussed federal regulation of probiotics
    • Listening to a Diane Hoffman discussing federal regulation of probiotics – there is lots of misleading stuff out there #HMP2010
    • Hoffman: for most probiotics we know very little about effectiveness, safety, mechanisms and other key parameters #HMP2010
    • Hoffman: whether/how to regulate probiotics depends on health claims, whether in food or not, etc.#HMP2010
    • Many probiotics sellers make structure/function claims like “x promotes intestinal health” – these are less regulated #HMP2010
    • Hoffman: FDA regulates health claims probiotics though FTC can also be involved if claims in media#HMP2010
    • Hoffman: some think probiotics overregulated (making research harder); others think underregulated (bogus stuff out there) #HMP2010

The worst part of the concurrent sessions was that the schedules somehow got switched in some of them and I missed talks by both Rob Knight and Jeroen Raes.  Completely bummed about this as both are great.  Rob Knight apparently discussed his push for an Open Microbiome Project which I think is brilliant.

After the concurrent sessions I had coffee with a post doc candidate from Wash. U and then wandered back over to the hotel lobby to see if I could find someone who wanted to go to dinner.  I saw Peer Bork and Jeroen Raes having a beer and sat down with them with a plan to go to dinner in a bit. Dusko Ehrlich eventually sat down with us too as did a few others.  Eventually, Peer and Dusko headed off I think to work on their talks for the next day and Jeroen and I wandered off for dinner.  We bumped into Gail Rosen and one of her students and we all went to a pub, had dinner, and eventually I headed back to the hotel to do my bedtime stories activity with my kids again.

Then I wrote up a post on notes from Day 2 of the meeting, which is always good to do while things are fresh in ones head.  Here is what I wrote

Well, Day 2 is over now for the Human Microbiome Meeting.  See my previous post for information about the meeting and about Day 1. I enjoyed Day 2, though some things are starting to wear me down a little bit.  In particular, the fact that the meeting starts at 8 AM, or 6 AM California time, has been really rough.  I missed the first 1.5 talks today because of that.  Not to organizers of meetings everywhere – don’t start meetings so early.  And don’t have too many talks in one day.  It is better, far better, to just have fewer talks, than it is to wear people out.  Also not to meeting organizers – do not change the order of talks in concurrent sessions at the last minute.  Very bad idea.  Anyway – onwards.

As with Day 1, I think the best way to get a feel for the meeting would be to look at Twitter posts with the hashtag #HMP2010.  Unlike what I did with my post for Day 1 I am going to put only my tweets below, not everyones.

Today was split up into one series of talks in the AM and then concurrent sessions in the PM.  What lessons did I learn today?  Well here are a few, with some overlap to those on Day 1 but that is OK by me.

  1. Again – correlations ≠ causation.  Those of you out there who do not get this should GTF out of science.
  2. For statement “X manipulations of microbes help treat X ailments in X people X of the time”: X=”some” NOT “all”
  3. Seems like we are really on the cusp of publications of 100s of clinical studies of microbes and their association with health status
  4. Some of these studies are even starting to get at causation
  5. It should be remembered that all of the methods used in microbiome studies are just methods; none are per se better than others; it is the science that should be judged not the tools themselves
  6. With some effort it seems one can culture many more organisms from a system than might be expected
  7. Cultures have many many uses
  8. But culture based studies do not really get at population genetic frequencies and relative abundance information very well
  9. Be wary of those who stick relentlessly with one idea or method
  10. Very strange how few pharma reps there were here (more on this in my next post)
  11. Please please please do not confuse data with knowledge.  Data can be very very useful and I completely support some projects that just are focused on generating data sets.  But knowledge comes from thinking about the data, and carefully analyzing it.
  12. Microbes, I think, run our lives much more than we would like to believe

Anyway – that is a brief update.  Back to preparing my talk for later this AM …

Finally, I got to work on my talk.  Wow that took a while.  I was up until about 3 am.  Finally I got to sleep a bit worried about missing my alarm ..

Day 4: My talk and heading home

Got up with plenty of time to spare, worked a bit on my talk, got my stuff together, grabbed a coffee, and went to set up my presentation. Peer Bork was already there getting his set up. The AV guy was not pleased that we all wanted to present off of our laptops. He said “We have a mac you can use”. I asked if they had keynote and they did not. Not very useful. Got myself set up and then paced around waiting for the lovely 8 am start. And then we were on.  Here are my tweets from just before my talk:

    • Attn Apple Keynote experts: anyone know how to hide the flashing volume bar when using “record slideshow” option?
    •  In relation to my upcoming talk at #HMP2010 I thought I would share this 2007 April Fools story about microbiomes http://ff.im/-q6t01
    • Next up at #HMP2010 Jonathan Eisen, aka, me: the Genomic Encyclopedia of Bacteria & Archaea & the dark matter of the genomic universe

I note, I tried to record my talk but that did not work for some reason.  I did post my slides on slideshare here.  And I think I can embed them in this post

Here are my notes on the rest of the talks in that AM session.

  • Peer Bork: Towards Microbial Markers for the Human Gut Microbiome
    • Now Peer Bork from EMBL on microbial markers for the human gut #microbiome #HMP2010
    • Peer Bork now discussing covariation of gene families within Metagenomic data sets #HMP2010
    • Bork: analyzing metahit data on metagenomics of the human gut #HMP2010
    • Bork: developed a metagenomics pipeline called SMASH which should be available soon #HMP2010
    • Bork: does some interesting comparisons of phylogenetic vs. Functional composition in Metagenomic samples; #HMP2010
    • Bork: tries to remove vagrants (e.g., organisms in food) from Metagenomic data sets by looking at habitat of reference genomes #HMP2010
    •  Bork: w/ small sample get three distinct clusters of co-ocurring gene families within human Metagenomic samples #HMP2010
    • Bork: then went to analyzing newer Metagenomic Illumina data w/ more samples – get three major clusters of coocurring genes again #HMP2010
    • Bork – also sees three distinct clusters of coocurring rRNA types in human samples #HMP2010 – he now calls these enterotypes
    • Bork – can find specific functional categories that correspond to the three distinct Metagenomic types#HMP2010
    • Bork – can find specific functional categories that correspond to the three distinct Metagenomic types#HMP2010
    • Bork: shows cool pathway analysis iterated along fine scale transecting in hypersaline samples, showing as pathways shift #HMP2010
    • Bork : we need better databases of pathway-gene mapping in diverse organisms and diverse phenotypes#HMP2010
  • Dusko Ehrlich discussed the metahit project 
    • Next: one of most entertaining people in field: S. Dusko Ehrlich discussing the MetaHit approach to relation between microbes & us #HMP2010
    • Ehrlich: discussing the BGI/MetaHit Nature metagenomics paper which I personally found fascinating#HMP2010
    • Ehrlich: in gut metagenomes, a high fraction of all genes are shared between people; same true for species#HMP2010
    • Ehrlich: much of the variation between people in metagenome is in relative abundance not in presence/absence of genes or species #HMP2010
    • Ehrlich: comparing metagenome of 177 Danish people; 67 lean, 110 obese, deep Illumina sequencing#HMP2010
    •  Ehrlich: Identifying some microbial genes associated with host body mass index #HMP2010
    • Ehrlich: the major differences between metagenome in obese vs. lean people are genes from Firmicutes#HMP2010
    • Ehrlich shown a cool graph that he calls the Metahit barcode – 4 species x genes in rows, samples in columns ordered by BMI #HMP2010
    • Here is link to the MetaHit human metagenome paperhttp://www.nature.com/nature/journal/v464/n7285/full/nature08821.html #HMP2010
    • Ehrlich also doing metagenome analysis of IBD, says there are correlations but cautions we do not know causal vs. consequence #HMP2010
    • Ehrlich now showing that his metahit barcode can potentially be used for strain level differences #HMP2010
    • Ehrlich: we are on brink of having diagnostic tests, possibly better treatments, possibly novel treatments for health states #HMP2010
    • Ehrlich ends by saying you should follow @metahit #HMP2010
    • Excellent suggestion from crowd after Ehrlichs talk: we should look at microbiome in non industrialized populations #HMP2010
  • Kanitsak Boonanantanasarn discussed oral cancers
    • Boonanantanasarn looking at microbes associated with oral cancers #HMP2010
    • Boonanantanasarn: see increase in archaea in samples from oral cancer vs. normal #HMP2010 #archaearule
  • Heidi Kong discussed atopic dermatitis
    • Now up Heidi Kong on the skin microbiome, atopic dermatitis and immunodeficiency #HMP2010
    • Kong: how to move from correlation to causation?; using longitudinal studies, selective alteration of microbes, mouse models #HMP2010
  • Yuzhen Ye discussed metagenomic informatics
    • Awesome: Yuzhen Ye just used a drawing by her four year old w/ cryptic writing to discuss difficulty in Metagenomic analysis #HMP2010
    • Ye now discussing her FragGeneScan Metagenomic gene finderhttp://omics.informatics.indiana.edu/FragGeneScan/ #HMP2010
    •  Ye: working on assembling genes from within metagenomics data (and thus not doing assemblies of everything) #HMP2010
    • Ye: has a metagenomic binner called abundancebin which not surprisingly using abundance information to bin #HMP2010
    • Uploaded my slides for my #HMP2010 talk tohttp://slidesha.re/cQQkws
    • Ye: describing SWIFT a fast protein similarity search method using reduced alphabet suffix arrays #HMP2010
  • Daniel Haft, who I used to work with a little bit when we were both at TIGR then discussed protein family analysis
  • Cindy M. Liu
    • Next and last: Cindy Liu talking about the sinus microbiota in health and disease #HMP2010
    • Liu discussing chronic rhinosinusitis – effects millions and costs lots (though kills very few) “We should help them” she says #HMP2010
    • Liu discussing need for ecological models of stable states in human microbiome studies #HMP2010
    • And #HMP2010 is done; overall I enjoyed it; will post thoughts on day 3 later

And then, just like that, the meeting was a wrap. I checked out, chatted a bit with a few people, and then off to the airport and home.  If you have gotten this far in this post, I am impressed …  I am going to hold off a few days before writing up a summary of what I learned from the meeting overall but I think the lessons learned from Day 1 and Day 2 are a good place to start.  Thanks for reading.

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Also here are some other links of relevance to the meeting

Live from the Human Microbiome Meeting #HMP2010

For those interested, I and some others are posting live from the Human Microbiome Meeting in St. Louis

Perhaps the best place to find these posts is on Twitter using the hashtag #HMP2010 here

Will post a few more links here in a bit .. Listening to talks right now

Who owns UCDavis (& other University Names) in various Web Domains?

Well, this is awkward.  But apparently, some domain name registrars in China think I am the person to write to regarding UC Davis domain name issues.  Am I that high up in web searches somehow?  Perhaps I am if you do not use google, or maybe even if you do (I guess, perhaps most of the high hits to UC Davis are not people … just web sites).  Anyway this is the email I just got:(If you are not the person who is in charge of this, please forward to the right person/ department, as this is urgent, thank you.) 

Dear CEO,

We are the department of registration service in China. we have something which needs to confirm with you. We formally received an application on  August 26h  2010. One company called “Napa International, Inc.” is applying to register “ucdavis     ” as Brand name and domain names as below:

 ucdavis.asia     

 ucdavis.cn     

 ucdavis.com.cn     

 ucdavis.com.hk     

 ucdavis.com.tw     

 ucdavis.hk     

 ucdavis.in     

 ucdavis.tw  

After our initial checking, we found the Brand name and domain names being applied are as same as your company! So we need confirmation with your company. If the aforementioned company is your business partner or your subsidiary, please DO NOT reply us, we will approve the application automatically. If you don’t have any relationship with this company, please contact us within 5 workdays. If over the deadline, we will approve the application  submitted by “Napa International, Inc ” unconditionally.

Best Regards

Rensis Ho

Not sure if this is a scam of some sort or not so I figured I would post.  Anyone seen anything like this before?  If it is not a scam, does this mean they really think I am the CEO of some UC Davis brand?  

Another question is – if this is not a scam – can places register a domain name using someone else’s trademark?  What is the protection for domain names outside the US?

Anyway – am forwarding this to people at UC Davis who I hope can answer the email … but am wondering how much I can sell the UC Davis brand name for in various places … could be a good fund raising opportunity

Interesting take on peer review & openness from outside the sciences in @nytimes

I assume many supporters of open science may have seen this already but if not it is worth a look.  The New York Times had an interesting article on Monday by Patricia Cohen: For Scholars, Web Changes Sacred Rite of Peer Review.

The article starts off with a familiar refrain

For professors, publishing in elite journals is an unavoidable part of university life. The grueling process of subjecting work to the up-or-down judgment of credentialed scholarly peers has been a cornerstone of academic culture since at least the mid-20th century.

It follows with a very important discussion focusing on how the web can transform scholarly publishing.  For example:

… scholars have begun to challenge the monopoly that peer review has on admission to career-making journals and, as a consequence, to the charmed circle of tenured academe. They argue that in an era of digital media there is a better way to assess the quality of work. Instead of relying on a few experts selected by leading publications, they advocate using the Internet to expose scholarly thinking to the swift collective judgment of a much broader interested audience.

This likely will sound very familiar to those who have read my blog, those who follow the discussions on peer review, or those with a pulse in the scientific community.  But there is a catch that caught me off guard here and might surprise many of you.  This catch is highlighted by the fact that the article was in the Arts section of the Times.  You see, the article was about transformation in the humanities.  Seems as though there is an almost completely parallel universe there where peer review and publishing and sharing are all getting re-evaluated.

This is yet another case of why we need more cross talk between the arts/humanities and the sciences.  For example, the article discusses how the journal Shakespeare Quarterly is becoming the first humanities journal to “open its reviewing to the World Wide Web.” They even recently conducted an experiment in fully open review where four preprints were posted on the web and feedback was solicited.  The feedback was then used by editors to guide the revision of the preprints to become published articles.  Sounds a lot like Biology Direct.  Note however, that they are not talking about publishing the final articles in an open access manner (see discussion of this on BigThink here) – but more about engaging the broader audience in commentary before an article is published.

The article does suggest that perhaps the humanities are lagging a bit behind the sciences in experimenting with new forms of peer review but I think that is OK.  We desperately need new experiments and ideas in this arena.  Peer review, at least the way it operates right now, has many problems.  I think there must be many better ways to go about things.  And thus cross pollination across fields from arts and humanities to economics to physics to life sciences is a good thing.

Interestingly Cohen identifies what she considers to be the most daunting obstacle to opening up review:

peer-review publishing is the path to a job and tenure, and no would-be professor wants to be the academic canary in the coal mine.

I think this is the same main obstacle in the sciences.  That is, it is our system of promotion and tenure and hiring that is the main roadblock.

Finally, I note that though the article was focusing mostly on opening up peer review, it does have some interesting bits on openness in general. In particular, there is a great line at the end from Dan Cohen from George Mason

“There is an ethical imperative to share information,” said Mr. Cohen, who regularly posts his work online, where he said thousands read it. Engaging people in different disciplines and from outside academia has made his scholarship better, he said.

I could not agree more.  Seems like the arts and humanities and sciences actually have much much more in common that many might think.

For some related posts from the web see

Some recent web stuff on peer review in the sciences

New Stem Cell ruling trickle down effects: changes in NIH grant review/submission

Just got this email from UC Davis administration that I thought might be of interest

Dear UCD Research Community:

Pursuant to a court order issued on August 23, 2010, NIH is not accepting submissions of information about human embryonic stem cell lines for NIH review.

If you are currently preparing a proposal to NIH that includes stem cell research and NIH has not pulled the RFP, please continue preparing your proposal and Sponsored Programs will submit to Grants.gov.

Per the Council on Governmental Relations (COGR):

In a press briefing today August 24, 2010,  Francis Collins, Director of NIH, described the impact of the preliminary injunction prohibiting NIH from funding embryonic stem cell research under the NIH Guidelines on current and pending grants.    A NIH Guide notice will be issued shortly containing greater detail. 

 

In short, NIH consulted with the Department of Justice to make the following determination:

 

·                    Current grantees – those who have received their award already – may continue with their research;

 

·                    NIH will freeze the funds for the current grants due for annual renewal (non-competing renewals) by September 30, 2010;

 

·                    Grants in the review process – initial peer review or recommended for consideration by the advisory council – will be pulled from further consideration at this time.

 

We expect to receive additional information shortly, which we will share when received.

When Universities Grow in the Wrong Places

A bit of a rambling post here but here goes anyway …

Well, normally I have avoided digging in to UC Davis too much here on my blog.  Mostly because it does not really fit with the themes of evolution, open access, microbiology, genomics, etc.  Plus, overall, I really really like Davis and UC Davis.  The town is very pleasant – simple – but very nice.  I lived on my bike in the Washington DC area, taking my life into my own hands, and now living in bike town USA is great.  In fact, I even have a blog about life in Davis.  And UC Davis is overall a great place to be for me, especially with its strengths in evolution and ecology, population biology, and various aspects of microbiology.

But alas, now all is perfect here in blissville. And one thing that drives me crazy is the mind numbing complexity of the bureaucracy.  I note, I moved to Davis from The Institute for Genomic Research (TIGR), a small non profit research institute that helped lead the genomics revolution.  And mostly I have suffered annoyances of the crazy giant complex system here in silence (except for with a few colleagues here and there).  However, I have been planning to start to discuss some of these issues in public more.  And just as I was thinking about this, it seems that others are also discussing some issues with the need to reform some UC Davis admin activities.

You see, last year we got a new Chancellor (the name they use here for the head of the University).  The new Chancellor is Linda Katehi.  I have met her a few times and overall I am very impressed.  Perhaps the thing that impresses me most is that in times of somewhat bad financial struggles she has decided to take on the bloat in the administrative side of things as one of her first activities.  And it seems this is not all talk.  For example our great local newspaper, the Davis Enterprise has been running a series of articles, most by Cory Golden, on some reports and announcements from UC Davis suggesting that Katehi really will be trying to change things around here.  Alas, the Davis Enterprise is not available for free on the web for all to read.  If you want to get some really insightful stories about UC and UC Davis, you should subscribe.  It is not much and if you have any connection to Davis it is worth the money.

Fortunately for me, and perhaps for you, the Davis Enterprise has agreed to let me post extensive quotes from their articles especially as they relate to UC Davis.  I will delay a bit in posting to try and respect their need for subscribers (unlike with scientific publications, which should all be open and freely available, I do not feel that way about private enterprises like newspapers).  Anyway – I am posting below two stories by Cory Golden of relevance to the UC Davis attempts to change the way things are done here.  One is about reorganization of some administrative functions.  And one is about an outside evaluating group that just wrote a report on some of the challenges for research at UC Davis.  A third is about a campus “vision” statement put out by Katehi.

The main gist is, that UC Davis has enormous potential that is being impeded by some bureaucratic complexities and inefficiencies.  Some good quotes include:

Those included “overstaffing, ineffective personnel and playing ‘lawyer games’ to be sure that no risks threaten the organization.”

“Over many decades Davis has developed a culture that permeates its institutions and people, one that can best be described as risk-averse, modest and insular.”

And Katehi seems like she is going to try and fix many of them.  No – the plans are not exactly what I would do.  But more on that later.  The direction things are moving is very appealing to me.  I was not inspired by the previous leadership of UC Davis.  I am much more hopeful now and am awaiting these changes very impatiently.

Anyway – thanks to the Davis Enterprise for allowing me to post here.  And please consider subscribing to the paper.  That way you will get stories as they come out …

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Reorganization ramps up at UCD

By Cory Golden

August 18th, 2010

Enterprise staff writer

UC Davis leaders have OK’d in spirit a plan to cut up to $16 million in staff positions while rolling campus information technology, human resources and finance offices into a single shared services center.

An all-staff forum about the reorganization is set for Thursday at 10:30 a.m. in the UCD Conference Center Ballroom.

Chancellor Linda Katehi said last week that her goals for the effort, dubbed the “Organizational Excellence Initiative,” are to redirect money to academics, student services and other priorities while improving the service given to the campus.

For now, staff members are left with questions and union leaders have growing concerns.

Among them: how many jobs will be eliminated, how positions in the proposed new center willbe filled, how fast UCD will make the changes and how much money the campus will invest in technology intended to increase efficiency.

Some answers may come from a meeting of the chancellor’s cabinet Aug. 31.

At its last two-hour meeting, last week, the cabinet decided to move forward on the outlines of recommendations made by the Atlanta-based consulting firm ScottMadden, based on more than three months of on-site assessment.

About 6,500 finance, HR and IT employees would be affected by the first phase of the project, as drawn up by the consultant.

“On the amount of savings projected, what percentage of that is from staff positions?” asked a woman in the audience during a presentation Monday to employees of administrative units that would be part of the proposed center.

Answered Karen Hull, associate vice chancellor for human resources, “Those savings reflect staff positions.”

Just how many would be cut, she said she didn’t know.

“We don’t know that for a couple of reasons,” Hull said. “One is that we don’t know for sure whether the cabinet will support the recommendation that ScottMadden has made, so that’s one big variable.

“(It) would be very misleading to connect the (estimated savings) to actual positions,” she added. “There’s a lot of dynamic changes that occur. We have natural attrition every year. We have natural turnover. We have retirements. We will not be wanting to fill any of those positions while we are forming the shared service center.

“I know that it sounds alarming — and it is alarming. These are your jobs, but I think that when we get the picture painted in a more detailed manner it will be more clear as to what will be the potential job loss.”

The consultant found that, at a core cost of $54 million a year, the campus’ human resources, information technology and finance staffing exceeded those of similarly sized organizations.

Among its recommendations: creating a shared structure with one director, improving the use of technology for timekeeping, purchasing, accounting and other tasks, and simplifying policies and processes.

The report pegged one-time or recurring costs, much of it from computer software systems, at about $19.5 million. If UCD follows its suggested timeline, the report says the university should begin saving money in less than three years.

Under the proposed model, about 80 percent of faculty, staff and student questions would be handled through self-service, either through a web portal or interactive phone system.

In what’s likely to be a controversial recommendation, the consultant suggests that the campus create job descriptions for the shared services center, then have employees apply for those positions.

“They recommend kind of an open slate. Everyone has an opportunity, and you compete for those jobs,” Hull explained, adding that the administration may yet choose another way to staff the center.

Among existing problems the consultant’s report pinpointed: large amounts of the same or similar work being done by multiple departments, excessive reviews, delayed service and multiple IT help desks. It also found “manual data collection, transcription of data, high error rates and significant rework.”

One employee at UCD might process about 1,065 invoices per year, working on paper with a long approval process. At Johns Hopkins University, which uses a shared service center model and automated system, one employee can process 45,000, the report says.

Union leaders interviewed Tuesday wondered aloud if the reorganization was an attempt to weed out their members.

Dorie Decosta, president of UCD’s chapter of the Coalition of University Employees Local No. 7, said there was a “general feeling of unrest and discomfort” among staff.

The prospect of automation replacing personalized customer service “sounds like hogwash,” she said.

“You need that element of continuity and what UCD says it stands for: caring about students, caring about staff, caring about faculty.”

Wrote Susan McCormick, president of the University Professional and Technical Employees Local No. 6, in an e-mail message, “I am getting the feeling that UC is finding ways to eliminate the highest-paid employees. They are eliminating at the top of the pay scales, those at UC the longest and those with the most knowledge.”

ScottMadden’s contract calls for a fee of $350,000, plus up to $70,000 in expenses.

The proposed reorganization comes as UCD continues to grapple with an unprecedented $150 million in state budget cuts since 2008-09. It has cut 1,062 positions: 459 layoffs or employees who had hours cut, the rest through attrition or voluntary separation.

The campus has cut 30 percent of its administration’s core budget, compared to a 15.4 percent cut for academic units.

UCD faces another $38 million to $78 million shortfall depending on the outcome of state budget talks this year.

— Reach Cory Golden at cgolden@davisenterprise.net. Track him at http://twitter.com/cory_golden.

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Reports rap UCD research
By Cory Golden
August 15th, 2010

Enterprise staff writer
If UC Davis is to continue its climb in national status, it has its work cut out for it, according to a blunt assessment by an outside consultant.
While the campus has its share of advantages, including its broad research portfolio and location, it has been stymied by a risk-averse culture and a bottleneck in its research support structure, according to the Washington Advisory Group.
The advisory group, led by Eric Bloch, a former director of the National Science Foundation, interviewed more than 100 people on campus, from senior administrators to graduate students, over three days.
Many of the themes its 74-page assessment sounded were echoed in recently completed reports by two in-house “blue-ribbon” committees, one each on research and technology transfer. In an interview last week, Chancellor Linda Katehi said the campus would begin making changes in response to the three reports this academic year.
UCD ranked 36th among U.S. universities in the 2009 Academic Ranking of World Universities.
Despite state general fund cuts that could total more than $228 million since 2008, depending on the outcome of state budget talks, UCD “knows what it has to do,” the consultants write, to improve to a rank of between 20th and 30th. That group includes Northwestern University, UC Santa Barbara and the University of North Carolina, Chapel Hill.
Katehi has set a new goal of $1 billion in outside research support. UCD more than doubled such funding from $295 million in 2001 to a preliminary estimate of $679 million for 2009-10.
Claire Pomeroy, the chair of the blue-ribbon committee on research and dean of the School of Medicine, called it “a new era” for research.
“There’s a pent-up desire among the faculty and the staff and the students to really optimize how our research enterprise is functioning and a recognition that we have some work to do in that area,” she said.
“The statement that we made in the blue-ribbon report on research that UC Davis is ‘less than the sum of its parts’ reflects the idea that we have incredible excellence here, and if we can just bring it together and support the people and give them the administrative support and infrastructure support, then we can really propel this university up to the next level.”
Campus culture
To reach such heights, UCD will need to undergo a personality change, the advisory group writes:
“Over many decades Davis has developed a culture that permeates its institutions and people, one that can best be described as risk-averse, modest and insular.”
While collegiality can result in the interdisciplinary research that UCD touts, it “can also have negative consequences when events and behaviors are tolerated that in other similar institutions would cause friction and result in remedies. The prime example we heard about is tolerating decision-making delays that at times may have dire consequences.”
The university has been slower than its peers to embrace partnerships with industry, described by the consultant’s report as “frowned upon by former administrations as counter to what a university is all about.”
A lack of aggressiveness has sometime been costly in other ways, the advisory group writes. For instance, UCD “seems to have missed the opportunity to expand programs in human genetics, genomics and other ‘omics at a time of explosive growth in funding in these fields. This problem must be rectified swiftly.
“UCD and its accomplishments are not as well-known as they deserve to be, in large part because of some of the cultural traits discussed,” the report says.
Andrew Hargadon, chairman of the blue-ribbon committee on tech transfer and professor of technology management at the Graduate School of Management, said he did not think the campus suffered from “collegiality to the point of complacency.” However, he acknowledged “a long history of cultural conditioning” on the campus: feeling forever overshadowed by UC Berkeley and UCLA.
“We had such a huge growth of faculty in the last decade, and the increase of research dollars as a result,” Hargadon said. “When you look at the faculty we’ve got — they weren’t there in the ’50s and ’60s; they weren’t there when that identity was being shaped.
“They would very much like to have an impact, even if it comes at the cost of driving their agenda forward.”
Research support
The main target of the complaints that the advisory group heard: the Office of Research.
Those included “overstaffing, ineffective personnel and playing ‘lawyer games’ to be sure that no risks threaten the organization.”
The office is made up of three sections: sponsored programs, which submits thousand of grant applications; institutional review boards, which govern protocols for clinical trials; and technology transfer and business development, which handles applications for patents and royalties and acts as a broker between researchers and the corporate world.
Those interviewed by the advisory group said the sponsored research group is often “overbearing,” “dictatorial” and “prone to almost missing filing dates for proposals, thus jeopardizing the opportunity to participate in important competitions,” the report reads.
The blue-ribbon committee on research, in its own 20-page reported submitted Thursday, writes that its members are “greatly concerned that UC Davis, including its research administration, has become overly bureaucratic and risk-averse, and is too narrowly focused on compliance with rules and constraints. This risks frustrating creative researchers and reducing the level of scholarly creativity and productivity.”
Said Pomeroy, “We need to find the right balance between, of course, emphasizing safety and research quality and research compliance with being at the cutting edge of discovery. I think there has been a desire to minimize risk, sometimes at the expense of efficiently processing some of the research applications.”
Additions like expanded use of technology can help speed the process, she said.
The 12-page report by the tech transfer committee recommends creating a new office that would concentrate decision-making authority for technology licensing and industry research agreements. It also urges the establishment of standards for transparency, timeliness and accountability of patenting, licensing and processing industry research agreements.
The advisory group also found that area sorely lacking: “We did not get the impression that UCD has taken this general subject of intellectual property rights and technology transfer very seriously.”
UCD doesn’t have a long tradition of spinning off businesses, Hargadon said. That means that while there are faculty who have started a business, they aren’t great in number. So those who aspire to do so must lean on the tech transfer office for help.
“There’s no hard and fast rules on tech transfer. There’s no clear value with any intellectual property,” he said. “There’s a lot of clear-cut ways to go wrong, in terms of the legality of contracts and conflicts of interest, but there’s not clear-cut ways to go right.
“It would have taken a lot of strong leadership and vision to get the process to one where the university could make bold bets and make a claim that a particular patent would have more impact if it got out than if it got out with some sort of onerous revenue obligation associated with it. As a result, the office, without that sort of leadership vision, ended up weighing compliance and weighing risk mitigation higher than was really good for the system.
“Basically, we spent more time trying to stay out of trouble than trying to launch companies.”
Increased workload
The doubling of research funding has meant a greater workload for staff. That money has increasingly come from the federal government, which has steadily imposed more stringent regulations and reporting guidelines.
At the same time, the office’s staff has been trimmed from about 90 to about 75, said outgoing Vice Chancellor for Research Barry Klein.
He said of his staff, “These are very good people working very hard for the university, but very good people working hard doesn’t mean there aren’t ways to make our organization better; there are.
“If you look across the country at organizations that have these sort of hot-button service roles as we have, they are always subject to criticism. It’s impossible to be perfect,” Klein added.
“The faculty are like thoroughbreds. They want to win the race. It’s a mad dash to the finish line, but that causes a lot of tension and getting things in at the last minute and quickly, so there’s always this dynamic tension with the research office.”
Klein said being less “risk-averse” will increase the risk of violations and fines, but his staff would oblige.
“The people in my office don’t make the rules, they implement the campus culture,” he said. “And if it’s a culture that’s emerging now where you’re putting more things back to individual responsibility — having less oversight of details and assuming the departments and colleges and individuals will follow the rules — staff will move in that direction as well.”
One of the longest-serving vice chancellors for research in the UC system, Klein was due to step down in June 2009 but he said he stayed on to smooth the transition for the new chancellor, who arrived last August. His return to the physics department, announced last December, was a joint decision with Katehi.
“I was ready for a change and it was good for her to bring in some fresh blood,” Klein said.
Other findings
Among the other findings in the advisory group’s report, UCD:
** Lacks a five-year strategic financial plan;
** Needs a new strategy for technology transfer and business development;
** Suffers high student-faculty ratios in some areas;
** Should invest in technology on par with peer institutions;
** Needs a well-organized campaign to make itself and its faculty more visible if it’s to become a household name; and
n Faces a space crunch, including a lack of Biosafety Level 3 and 4 containment facilities, and should build them elsewhere if the community is opposed.
The advisory group also found that school- and college-level strategic plans were “meaningful and well-documented” but that “an institution as complex and broad as Davis requires a five- or 10-year strategy, plan and budget. No such interlinking documents exist today.”
Katehi recently unveiled a vision statement for the campus. Next, units will set out plans to meet those newly stated goals and, sometime next year, UCD will begin funding those priorities, the chancellor said.
The advisory group found it worrying that it received different financial information about research depending on who provided it.
“One wonders: What are the numbers that are at the chancellor’s disposal?” the report asks.
The advisory group also received complaints of “bloated” administration generally, despite recent cuts. UCD is rolling out a new effort this month to further reduce and reorganize its administration.
UCD paid the Washington Advisory Group $226,000, plus up to $30,000 in expenses.

— Reach Cory Golden at cgolden@davisenterprise.net. Track him at http://twitter.com/cory_golden

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Katehi details campus vision
By Cory Golden
July 30th, 2010

Enterprise staff writer
UC Davis Chancellor Linda Katehi and other campus leaders have crafted a “Vision of Excellence,” 10 months in the making, to guide the campus for the next 10 years.
The 17-page document combines many of the themes Katehi has sounded since her arrival last year, about the campus’ readiness for greater national and international prominence, with long-standing notions of UCD’s land-grant identity.
Released last week, the vision statement received a warm response from faculty, staff and student leaders reached for comment for its positive tenor, even against a backdrop of ongoing financial turmoil.
“To transform our university, we must chart a new course of action, an equally transformative vision to guide our actions and define our future,” Katehi writes in the document. It lays out goals like “foster a vibrant community of learning and scholarship” and “champion health, education, access and opportunity.” The document also describes how progress toward each goal will be assessed.
Bob Powell, chair of the Academic Senate, said the vision statement spells out change in ways both big and small.
“Before, it was about collaboration and now it’s about leadership,” he said. “It’s one thing to say you’re going to develop joint or international programs to enhance UC Davis, but this, to me, is a step above anything we were talking about before.”
Powell read one line aloud: “UC Davis will provide an efficient, professional administrative organization that is committed to serving and advancing the university’s academic mission.”
“From the outside, people would say, ‘Isn’t that obvious?’ Well, I’ve been here 26 years and it’s never been obvious,” he said. “To have that as an explicit statement is really important.”
Powell said he believed the document would go a long way toward building “grassroots support” when it falls to the colleges, schools and divisions to flesh out corresponding goals and plans to realize them.
An example of the document’s approach is its emphasis on increasing UCD’s international reach.
UCD will seek to increase the number of faculty, scholars and students from abroad and the number of students and faculty who pursue academic experiences overseas, the document says.
To accomplish those goals it will evaluate its needs in attracting, retaining and supporting international students; develop joint, collaborative international graduate programs; launch academic and clinical health research projects that tackle global challenges; strengthen and expand international alumni and global business ties; and provide the technological tools, cultural programs and student services to expand international dialogue.
Linda Bisson, professor of viticulture and enology and past chair of the Academic Senate, said the “solid” document is important for what it includes — and what it does not.
“It is different than what we’re used to because it has metrics,” Bisson said. “Typically, these kinds of vision statements are kind of just platitudes stuck together.
“This is going to sound weird,” she added, “but the change of focus that I see is that we’re not apologizing for who and what we are. Previously, things like this have read like we’re apologizing for not being (UC) Berkeley, the jewel of the UC crown.
“But this says, this is our value internationally: We’re problem-solvers — we’re a different kind of animal than Berkeley. It says we are very strong and proud of what we do — and that we’re not going to chase esoteric things when there are real things to be addressed.”
Though talk of breakthrough discoveries and spinning off research into new businesses can sometimes leave those in the humanities left wondering where they fit in, Margaret Ferguson, a professor of English and former chair of her department, said in an e-mail message that she felt that was not the case here.
“Im thrilled to say that this vision statement does speak to many of the questions that preoccupy those of us in the humanities, arts and humanistic social sciences,” she said. “These areas are mentioned early on as among the comprehensive research universitys ‘core disciplines,’ and the vision statement includes among its goals some that will particularly excite those students and faculty whose work focuses on deepening and expanding our understanding of past cultures as well as on creating new ideas for the future.”
She said she also was happy to see the goal of increasing need- and merit-based financial aid for both undergraduate and graduate students — which is “especially important for humanities graduate students, who are rarely supported by federal grants.”
Dan Wilson, chair of the Academic Federation, praised the vision statement’s emphasis on collaboration across disciplines, its promise of incentivizing success and its commitment to UCD’s land-grant role in improving the fates of the state and region.
Money, of course, remains the $228 million question mark. That may yet be the size of state cuts, dating back to July 1, 2008, depending on the outcome of the stalled state budget.
Bruno Nachtergaele, chair of the mathematics department, said in an e-mail message that he and many of his colleagues felt the document took into account their goals while also showing “the personal vision and commitment of the chancellor.”
“The recession we all suffer through is a hurdle, but not one that will stop her from promoting this vision and the long-term project of making UC Davis into the best university it can be,” Nachtergaele said.
Chair Peter Blando said in an e-mail message that the Staff Assembly was “extremely pleased to see a positive campus vision that takes us beyond the near daily concern over our job security and the university budget.
“While both are important,” he added, “staff morale is helped by providing any positive vision of the campus.”
Jack Zwald, president of the Associated Students of UC Davis, said he liked what he read, too, but was left wondering how Katehi would manage to increase the size of the university’s endowment while expanding programs. Likewise, he had questions about how UCD will be able to expand need- and merit-based aid to students.
“I think they’re going to give it a shot, but do I think it’s going to get done? I’m not overly optimistic it’s going to happen,” he said.
Wilson said the chancellor was right not to set the university’s sights lower because of the financial crisis.
“We don’t want to crawl into a shell — we want to move forward as a university,” he said.
To read the full document, see http://vision.ucdavis.edu.
— Reach Cory Golden at cgolden@davisenterprise.net. Track him at http://twitter.com/cory_golden