Jonathan Eisen

Human microbiome project meeting (HMP2010) Day 1 wrap up w/ mea culpa

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:

The human microbiome is becoming a fascinating area of research with an ever growing set of data to look at
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.
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.
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.
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.
There are some possible complicated issues around release of microbiome data and medical records from people
There is still a big risk in overselling the potential benefits of microbiome research
Correlations ≠ causation. Sorry I had to put that here. See #5 above.
Analyzing and making sense of metagenomic data is still very very hard
We desperately need more ecology driven studies of the microbiome
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.
As with every meeting, the best stuff that happens is in between talks.
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.

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 …

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Here are the tweets from Day1: The start with the most recent at the top, so if you want to start from the beginning, scroll to the end. I am going to try and post a prettier version of this ASAP but working on some html pasting issues …

Molecularbond
Quickly catching up on the Human Microbiome Meeting news before lecture starts. Thanks to @phylogenomics for good tweet action! #HMP2010 about 7 hours ago via Twitter for iPhone
TheGenomeCenter
Thanks to @GenomeScience, @phylogenomics, @westr, @genomeresearch and others for the retweets! #HMP2010 about 8 hours ago via TweetDeck
TheGenomeCenter
Pop: Bambus 2 software http://bit.ly/cxuKzk that can be used with output from most assemblers #HMP2010 about 8 hours ago via TweetDeck
TheGenomeCenter
Mihai Pop: repeat detection difficult in metagenomics since depth of coverage different in organisms (some abundant, some not) #HMP2010 about 8 hours ago via TweetDeck
TheGenomeCenter
Mihai Pop: assembler must work well for clonal data (handle repeats, errors, low coverage) and deal w/ polymorphisms #HMP2010 about 8 hours ago via TweetDeck
phylogenomics
Pop: genome assembly is hard b/c of 1) repeats 2) low coverage 3) sequencing errors – gets even harder for metagenomics #HMP2010 about 8 hours ago via Twitterrific
mndoci
RT @phylogenomics: Mihai Pop says his talk on Metagenomic assembly will be very short b/c it is impossible #HMP2010 about 8 hours ago via Tweetie for Mac
TheGenomeCenter
Mihai Pop: not having coverage may obscure true assembly and sequencing errors make everything more difficult #HMP2010 about 8 hours ago via TweetDeck
widdowquinn
RT @phylogenomics: Pop showing challenge in assembly by showing assembly of Tale of Two Cities; repeats:”it was the” confuse things #HMP2010 about 8 hours ago via TweetDeck
phylogenomics
Pop showing challenge in assembly by showing assembly of A Tale of Two Cities; repeats Ike “it was the” can confuse things #HMP2010 about 8 hours ago via Twitterrific
TheGenomeCenter
Mihai Pop: assembly in general is hard since have repeat regions #HMP2010 about 8 hours ago via TweetDeck
phylogenomics
Alas Pop didn’t end his talk, says one can make (somewhat) useful assemblies from metagenomic data; utility depends on goals #HMP2010 about 8 hours ago via Twitterrific
pathogenomenick
hah! RT @phylogenomics: Mihai Pop says his talk on Metagenomic assembly will be very short b/c it is impossible #HMP2010 about 8 hours ago via Seesmic Desktop
phylogenomics
Mihai Pop says his talk on Metagenomic assembly will be very short b/c it is impossible #HMP2010 about 8 hours ago via Twitterrific, 3 Retweets
TheGenomeCenter
Mihai Pop from U Maryland on assembling short reads from metagenomics – will be short since metagenomics assembly is impossible! #HMP2010 about 8 hours ago via TweetDeck
fionabrinkman
@bffo Yes, I worry bias is forming – archaeal human microbiome is sometimes neglected. Need to ensure whole microbiome is studied #HMP2010 about 8 hours ago via web in reply to bffo
1 Retweet
TheGenomeCenter
McFall-Ngai: looking at first changes in host gene expression when interact w/ symbiont #HMP2010 about 8 hours ago via TweetDeck, 1 Retweet
phylogenomics
McFall-Ngai encouraging everyone to study circadian rhythms of host-symbiont interactions #HMP2010 about 8 hours ago via Twitterrific
TheGenomeCenter
McFall-Ngai: squid-vibrio symbiosis -the two converse through their genes #HMP2010 about 8 hours ago via TweetDeck, 1 Retweet
phylogenomics
McFall-Ngai’s talk is so far an homage to model organisms and how they will be relevant to human microbiome studies #HMP2010 about 8 hours ago via Twitterrific, 1 Retweet
TheGenomeCenter
McFall-Ngai: cancer genes arose w/ 1st cellular orgs =caretaker genes; then when cell-cell interaction started =gatekeeper genes #HMP2010 about 8 hours ago via TweetDeck, 1 Retweet
TheGenomeCenter
McFall-Ngai: most human genes are old; most genes associated with human disease are also old #HMP2010 about 8 hours ago via TweetDeck
4 Retweets
phylogenomics
McFall-Ngai: humans are not the pinnacle/crown of evolution; me: just YAV (yet another vertebrate) #HMP2010 about 8 hours ago via Twitterrific
TheGenomeCenter
McFall-Ngai: humans not the pinnacle of evolution, just a recent outcome #HMP2010 about 9 hours ago via TweetDeck
phylogenomics
Margaret McFall-Ngai : vertebrates are a very old group & likely been associated w/ microbes for hundreds of millions of yes #HMP2010 about 9 hours ago via Twitterrific
TheGenomeCenter
Margaret McFall-Ngai from U Wisc on host-microbe interaction through animal evolution #HMP2010 about 9 hours ago via TweetDeck
TheGenomeCenter
Relman: use digital MDA (Multiple Displacement Amplification) on E. coli gDNA fragments – more sensitive than digital PCR #HMP2010 about 9 hours ago via TweetDeck
phylogenomics
Relman: reagents in molec. biology freq. contaminated w/ DNA; this impacts many amplification studies when DNA levels low; #HMP2010 about 9 hours ago via Twitterrific, 1 Retweet
TheGenomeCenter
Relman: commercial approaches for quantifying small samples of DNA – digital PCR gives advantage by quantifying single molecs #HMP2010 about 9 hours ago via TweetDeck
bffo
@fionabrinkman Bruce Birren mentioned archae in that they were missed by the standard primers used for 16S … not much more 😦 #hmp2010 about 9 hours ago via TweetDeck in reply to fionabrinkman
TheGenomeCenter
Relman: microfluidics reduces enviro contamination, improves detection of rare microbes, increases speed of single cell selection #HMP2010 about 9 hours ago via TweetDeck, 1 Retweet
TheGenomeCenter
Relman: single cell #genomics, microfluidics and the human #microbiome #HMP2010 about 9 hours ago via TweetDeck, 1 Retweet
phylogenomics
David Relman discussing single cell genomics and other approaches to studying single cells in communities #HMP2010 about 9 hours ago via Twitterrific, 1 Retweet
phylogenomics
David Relman is w/o a doubt the Philosopher of the Microbiome – always discussing deep questions #HMP2010 about 9 hours ago via Twitterrific, 1 Retweet
a2binny
Dave Relman opened up by pointing out that the number of people in the room is much larger than it would have been 5 years ago #HMP2010 about 9 hours ago via AOL Lifestream
TheGenomeCenter
David Relman from Stanford on the human #microbiome ‘one cell at a time’ #HMP2010 about 9 hours ago via TweetDeck
emergentnexus
oddly, none of my afternoon microblogging seems to be on twitter yet. catch it at http://friendfeed.com/human-microbiome #HMP2010 about 10 hours ago via web
fionabrinkman
@phylogenomics If you can, do mention if there’s anything said about Archaea in the human microbiome. #HMP2010 about 10 hours ago via Echofon
phylogenomics
A main worry re: metagenomic studies: like GWAS, lots of genetic variation but w/ few variables, will always find correlations #HMP2010 about 10 hours ago via Twitterrific, 1 Retweet
fionabrinkman
Thx @phylogenomics for human microbiome meeting tweets (Agenda: http://bit.ly/9FyDlu) #HMP2010 about 10 hours ago via Echofon
phylogenomics
Denef showing how proteomics can be used in environmental studies – Banfield lab does v. cool stuff in this area #HMP2010 about 10 hours ago via Twitterrific
phylogenomics
Denef – looking at population shifts over time using metagenomics -getting to correlating pop. changes with specific allelic diffs #HMP2010 about 10 hours ago via Twitterrific
phylogenomics
Denef discussing metagenomic studies of preterm infant gut -using similar methods as in acid mine drainage studies #HMP2010 about 10 hours ago via Twitterrific, 1 Retweet
a2binny
Denef presents interesting results showing two distinct strains of Citrobacter “fighting it out” in the newborn gut #HMP2010 about 10 hours ago via AOL Lifestream
a2binny
Vincent Denef has been roped into studying necrotizing enterocolitis in preterm infants #HMP2010 about 10 hours ago via AOL Lifestream
TheGenomeCenter
Denef: preterm infant gut colonization shows how functional microbial community emerges #HMP2010 about 10 hours ago via TweetDeck, 2 Retweets
phylogenomics
Denef now giving homage to the red pill blue pill choice from the Matrix #HMP2010 #Toldyoumetagenomicswascool #geekytoo about 10 hours ago via Twitterrific
TheGenomeCenter
Denef: The Matrix movie gave red/blue pill option – choose your reality – studying microbial ecology similar – what level to study? #HMP2010 about 10 hours ago via TweetDeck
phylogenomics
Denef now explaining his talk title – lots of closely related organisms and may have to distinguish at very fine scale #HMP2010 about 10 hours ago via Twitterrific
TheGenomeCenter
Denef: linking genotypic traits to microbial ecology #HMP2010 about 10 hours ago via TweetDeck
phylogenomics
Vincent Denef from Jill Banfield’s lab discussing “how deep does the rabbit hole really go?” #HMP2010 about 10 hours ago via Twitterrific
TheGenomeCenter
Next up Vincent Denef from UC Berkeley on studying microbial ecology using community #genomics #HMP2010 about 10 hours ago via TweetDeck, 1 Retweet
ASA_CSSA_SSSA
RT @TheGenomeCenter: Jo Handelsman from Yale on antibiotic resistance in soil and the human #microbiome #HMP2010 about 10 hours ago via HootSuite
TheGenomeCenter
Handelsman: kanamycin resistance genes from soil are similar to ea. other (even over a distance) but differ from humans #HMP2010 about 10 hours ago via TweetDeck
OmicsKnowmics
Not #badomics word 4 me as refers 2 a subset of genomes: MT @phylogenomics: “resistome” = collection of antibiotic resistance genes #HMP2010 about 10 hours ago via TweetDeck
TheGenomeCenter
Handelsman: found streptomycin resistance gene from human #microbiome that modifies the antibiotic #HMP2010 about 10 hours ago via TweetDeck
TheGenomeCenter
Handelsman: found kanamycin resistance genes from human #microbiome – all methyltransferases modifying the target of the antibiotic #HMP2010 about 10 hours ago via TweetDeck, 1 Retweet
a2binny
Handelsman: soil-derived kanamycin resistant determinants are different than clinically significant ones #HMP2010 about 10 hours ago via AOL Lifestream
phylogenomics
I note, Jo Handelsman coined the word metagenomics many years ago #HMP2010 – this omics word seems OK to me about 10 hours ago via Twitterrific, 1 Retweet
TheGenomeCenter
Handelsman: use functional metagenomics to find new antibiotics by cloning DNA from uncultured samples from soil and humans #HMP2010 about 10 hours ago via TweetDeck, 1 Retweet
TheGenomeCenter
Handelsman: hard to culture microbes from soil – ~99% can’t be cultured #HMP2010 about 10 hours ago via TweetDeck
HankCampbell
RT @phylogenomics: Richard Sharp discussing how patients seem willing to use GMO probiotics even if they don’t like GMO foods #HMP2010 about 10 hours ago via TweetDeck
TheGenomeCenter
Handelsman: resistant Acinetobacter in Iraq could come from soil #HMP2010 about 10 hours ago via TweetDeck
phylogenomics
Jo Handelsman refers to the “resistome” – collection of antibiotic resistance genes in a community; #badomics word? – probably #HMP2010 about 10 hours ago via Twitterrific, 1 Retweet
TheGenomeCenter
Handelsman: resistome – collective resistance genes in the environment to understand where resistance comes from #HMP2010 about 10 hours ago via TweetDeck, 1 Retweet
TheGenomeCenter
Handelsman :“we’re facing one of the worst health crisis in decades” – drug resistance #HMP2010 about 10 hours ago via TweetDeck
phylogenomics
Jo Handelsman, one of my favorite scientists, now up talking about finding antibiotic resistance genes in the environment #HMP2010 about 10 hours ago via Twitterrific
TheGenomeCenter
Jo Handelsman from Yale on antibiotic resistance in soil and the human #microbiome #HMP2010 about 10 hours ago via TweetDeck, 1 Retweet
phylogenomics
Sharp saying that we should not oversell the microbiome project – he should read my blog http://bit.ly/ahXB4n #HMP2010 about 11 hours ago via Twitterrific, 2 Retweets
TheGenomeCenter
Tweeting from the Human #Microbiome Conference in St. Louis http://bit.ly/b3ZLKD also check out microblog at http://bit.ly/aEtRXl #HMP2010 about 11 hours ago via TweetDeck, 1 Retweet
phylogenomics
Sharp: patients may be susceptible to aggressive marketing of probiotics #HMP2010 about 11 hours ago via Twitterrific, 1 Retweet
phylogenomics
Richard Sharp discussing how patients seem willing to use GMO probiotics even if they don’t like GMO foods #HMP2010 about 11 hours ago via Twitterrific, 1 Retweet
a2binny
data presented that people would be willing to take GM probiotics, when they wouldn’t eat GM food #HMP2010 about 11 hours ago via AOL Lifestream
TheGenomeCenter
Sharp: Patients don’t see GM probiotics in same way as GM foods – may shun GM foods but accept GM probiotics if dr.-approved #HMP2010 about 11 hours ago via TweetDeck, 1 Retweet
TheGenomeCenter
Sharp: Patients may be weary of manipulating gut #miccrobiome (i.e. probiotics) as a form of gene therapy #HMP2010 about 11 hours ago via TweetDeck
phylogenomics
Issues relating to microbiome ethics: genetic discrimination, GMOS, release of probiotics to world, gene therapy #HMP2010 about 11 hours ago via Twitterrific
a2binny
The ethical, legal and social issues (ELSI) of micro biome research are being discussed #HMP2010 about 11 hours ago via AOL Lifestream
TheGenomeCenter
Rich Sharp from Cleveland Clinic on why do Ethical, Legal, and Social Issues (ELSI) Research #HMP2010 about 11 hours ago via TweetDeck
phylogenomics
Oops … Missed the first part of the talk on ELSI issues associated with the human microbiome project #HMP2010 #importantstuff about 11 hours ago via Twitterrific
TheGenomeCenter
Ruth Farrell from Cleveland Clinic talks about ethical challenges in the clinical applications of the Human #Microbiome Project #HMP2010 about 11 hours ago via TweetDeck
emergentnexus
wrapping up morning session #HMP2010 about 12 hours ago via web
phylogenomics
Alm, in response to my question, says that much of their evolution analyses done on incomplete genomes but he thinks it works fine #HMP2010 about 12 hours ago via Twitterrific
phylogenomics
A questioner asked about something relating to “higher primates” – come one everyone – stop the evolution bogusness #HMP2010 about 12 hours ago via Twitterrific
TheGenomeCenter
Eric Alm: bacteria from same habitat tend to share more ‘flexible’ (changing) genome blocks #HMP2010 about 12 hours ago via TweetDeck
mikethemadbiol
#HMP2010 Alm: 25 ecotypes of what is basically one species of Vibrio. In four species of seawater! about 12 hours ago via web, 1 Retweet
TheGenomeCenter
Eric Alm: looking at loci to determine ecological split of bacterial strains from zooplankton #HMP2010 about 12 hours ago via TweetDeck
GenomeScience
more info re: CloVR & cloud computing w/ DACC – http://www.cloudbook.net/university-maryland-baltimore-research #HMP2010 about 12 hours ago via web
TheGenomeCenter
Alm: dvlping tool ‘Starry Nights’ that takes genome sequences and divides into blocks consistent with single phylogenetic tree #HMP2010 about 12 hours ago via TweetDeck
phylogenomics
Alm: comparing 75 genomes of strains of Vibrio species; note all of these are in essence same OTU/species but lots of differences #HMP2010 about 12 hours ago via Twitterrific, 1 Retweet
phylogenomics
Eric Alm describing how microbial samples are collected from ocean water; me: informatics people need to understand these things #HMP2010 about 12 hours ago via Twitterrific
TheGenomeCenter
Alm: Model system is vibrio bacteria; found could partition resources in ocean #HMP2010 about 12 hours ago via TweetDeck
phylogenomics
Eric Alm discussing Fred Cohan’s ecotype model for species formation in bacteria and archaea #HMP2010 about 12 hours ago via Twitterrific
TheGenomeCenter
Eric Alm from MIT on ocean microbes #HMP2010 about 12 hours ago via TweetDeck
phylogenomics
And now for something completely different but very relevant: ocean microbes and genome evolution from Eric Alm #HMP2010 about 12 hours ago via Twitterrific
phylogenomics
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 about 12 hours ago via Twitterrific, 1 Retweet
phylogenomics
White: DACC putting together virtual machines to run all sorts of microbiome/metagenomic analyses – can run locally or on cloud #HMP2010 about 13 hours ago via Twitterrific
TheGenomeCenter
White: CloVR – Clouid Virtual Resource tool- bunding diff analysis pipelines on virtual machine that you could run on your computer #HMP2010 about 13 hours ago via TweetDeck, 2 Retweets
emergentnexus
CloVR: Cloud Virtual Resource bundles analysis pipelines into virtual machines #HMP2010 re: http://ff.im/pZ7b9 about 13 hours ago via FriendFeed
emergentnexus
DACC has subversion repositories #HMP2010 re: http://ff.im/pZ7b9 about 13 hours ago via FriendFeed
bffo
Owen White keeps saying “GenBank” when I think he sometimes means NCBI … not the same! #microbiome #hmp2010 about 13 hours ago via TweetDeck
phylogenomics
White: some challenges in downloading data from short read archive from NCBI #HMP2010 about 13 hours ago via Twitterrific, 1 Retweet
jacobnix
@phylogenomics Key issue: genome and metagenome data is not very useful without metadata about samples, methods, etc #HMP2010 about 13 hours ago via web
emergentnexus
dbGaP provides patient phenotype information #HMP2010 re: http://ff.im/pZ7b9 about 13 hours ago via FriendFeed
phylogenomics
Key issue: genome and metagenome data is not very useful without metadata about samples, methods, etc #HMP2010 about 13 hours ago via Twitterrific, 2 Retweets
TheGenomeCenter
Owen White: DACC w/ NCBI has set of recommendations for how to describe and present your data most clearly #HMP2010 about 13 hours ago via TweetDeck
phylogenomics
I almost said same thing: RT @mikethemadbiol #HMP2010 *I* care if we sequence another E. coli genome 😉 Though metadata ARE critical about 13 hours ago via Twitterrific
TheGenomeCenter
White: Partner w/ JGI to make Img tool 2 look at metabolic profiling – at http://www.hmpdacc-resources.org/cgi-bin/img_hmp/main.cgi #HMP2010 about 13 hours ago via TweetDeck, 1 Retweet
kshameer
RT @phylogenomics: Best place to find out about past & ongoing microbial genome projects? http://bit.ly/aOxFhV #HMP2010 #genomics about 13 hours ago via TweetDeck
emergentnexus
img/hmp website: http://www.hmpdacc-resources.org/cgi-bin/img_hmp/main.cgi #HMP2010 re: http://ff.im/pZ7b9 about 13 hours ago via FriendFeed
phylogenomics
Best place to find out about past & ongoing microbial genome projects?: definitely http://www.genomesonline.org/ #HMP2010 about 13 hours ago via Twitterrific
GenomeScience
O. White from IGS: 1 goal – a nice, easy to use website to coordinate info re: HMP #HMP2010 http://www.hmpdacc.org/ via @phylogenomics about 13 hours ago via web
MetaHIT
RT @phylogenomics: Key issue: open data is important but ease of access and use of open data also critical #HMP2010 about 13 hours ago via HootSuite
mikethemadbiol
#HMP2010 *I* care if we sequence another E. coli genome 😉 Though metadata ARE critical about 13 hours ago via web
phylogenomics
Key issue: open data is important but ease of access and use of open data also critical #HMP2010 about 13 hours ago via Twitterrific, 2 Retweets
phylogenomics
White: major goal is to provide ease of access to certain types of HMP data #HMP2010 about 13 hours ago via Twitterrific
TheGenomeCenter
White: making a better website to make HMP data available http://bit.ly/cO6Maq #HMP2010 about 13 hours ago via TweetDeck, 1 Retweet
phylogenomics
White: one of their goals is to have a nice, easy to use website to coordinate information about HMP #HMP2010 see http://www.hmpdacc.org/ about 13 hours ago via Twitterrific, 1 Retweet
emergentnexus
Website: http://www.hmpdacc.org #HMP2010 re: http://ff.im/pZ7b9 about 13 hours ago via FriendFeed
TheGenomeCenter
White: DACC tries to keep data traffic rolling #HMP2010 about 13 hours ago via TweetDeck
phylogenomics
Next up Owen White on the HMP Data Analysis and Coordination Center that he runs #HMP2010 http://www.hmpdacc.org/ about 13 hours ago via Twitterrific, 1 Retweet
TheGenomeCenter
Owen White from U Maryland Data Analysis and Coordination Center (DACC) for HMP #HMP2010 about 13 hours ago via TweetDeck, 1 Retweet
emergentnexus
Owen White: A Data Analysis Coordination Center for the Human Microbiome Project #HMP2010 http://ff.im/pZ7b9 about 13 hours ago via FriendFeed
TheGenomeCenter
Mitreva: shout out to @TheGenomeCenter – more info at http://bit.ly/bQVuvk #HMP2010 about 13 hours ago via TweetDeck
mikethemadbiol
#HMP2010 Either need to go to cloud computing or we’re going to need a lot more blades… about 13 hours ago via web
phylogenomics
Mitreva: current tools for analyzing metagenomic data mostly die (my word, not hers) when analyzing massive new data sets #HMP2010 about 13 hours ago via Twitterrific, 1 Retweet
emerlyyy
follow @phylogenomics for updates on the Human Microbiome meeting! #HMP2010 about 13 hours ago via web, 2 Retweets
TheGenomeCenter
Mitreva: looking at how community profile differs based on shotgun seq vs. 16 s data – #HMP2010 about 13 hours ago via TweetDeck
phylogenomics
Live from the Human Microbiome Meeting #HMP2010 http://ff.im/-pZ5F6 about 13 hours ago via FriendFeed, 2 Retweets
TheGenomeCenter
Mitreva: sequence similarity analysis to compare communities without relying on ref genomes; look at seq composition of every comm. #HMP2010 about 13 hours ago via TweetDeck
emergentnexus
Metarep: http://www.jcvi.org/metarep “an open source tool for high-performance comparative metagenomics” #HMP2010 re: http://ff.im/pYQBa about 13 hours ago via FriendFeed
emergentnexus
Johannes Goll: The J. Craig Venter Institute’s update on the HMP #HMP2010 http://ff.im/pYQBa about 13 hours ago via FriendFeed
TheGenomeCenter
Mitreva: are looking at metabolic profiling of communities – in oral, nasal, gut, vaginal sites #HMP2010 about 13 hours ago via TweetDeck
TheGenomeCenter
Mitreva: can separate different body sites based on breadth and depth of coverage of reference genomes #HMP2010 about 13 hours ago via TweetDeck
emergentnexus
Makedonka Mitreva: Shotgun Metagenomic Sequencing and Analysis at the Washington University Genome Center #HMP2010 http://ff.im/pYWdT about 13 hours ago via FriendFeed
emergentnexus
greatest challenges computational: takes >2 months to analyze data that took 0.3 months to produce #HMP2010 re: http://ff.im/pYWdT about 13 hours ago via FriendFeed
TheGenomeCenter
Mitreva: id’d many taxonomies/species in only 6 body sites to indicate common and unique species in a body site #HMP2010 about 13 hours ago via TweetDeck
phylogenomics
Ugh: Mitreva referred to “lower eukaryotes” – maybe she says this because the podium is high above the meeting hall? #HMP2010 about 13 hours ago via Twitterrific
TheGenomeCenter
correction – Mitreva – use publicly available CLOUD computing (not sure what loud computing would be!) #HMP2010 about 13 hours ago via TweetDeck
phylogenomics
Mitreva – the big problem in analyzing human microbiome metagenomics data is computational time – #HMP2010 #weneedbettermethods about 13 hours ago via Twitterrific
TheGenomeCenter
Mitreva: takes over 2 months to analyze data; to accelerate this, use alt algorithms, publicly available loud computing #HMP2010 about 13 hours ago via TweetDeck
bffo
#hmp2010 #microbiome it is rep, not rap 🙂 METAREP http://bit.ly/c1VIGz about 13 hours ago via TweetDeck
TheGenomeCenter
Mitreva: @TheGenomeCenter sampled 54 adults and 16 body sites – nasal, skin, gut etc. – 346 samples = 4 terabases of data #HMP2010 about 13 hours ago via TweetDeck
phylogenomics
Makedonka Mitreva from Wash U Genome Center: shotgun metagenomics of 54 people x 5 body sites: oral, skin, gut, vagina, nasal #HMP2010 about 13 hours ago via Twitterrific, 1 Retweet
TheGenomeCenter
Makedonka Mitreva from @TheGenomeCenter on our shotgun metagenomic sequencing activities #HMP2010 about 13 hours ago via TweetDeck
bffo
Johannesburg Goll from JCVI on METAREP, published as a 2 pager in Bioinformatics #OA #micro biome #hmp2010 http://bit.ly/c1VIGz about 13 hours ago via TweetDeck
phylogenomics
For software geeks: The MetaREP software is open source & uses CAKEPHP, Solr, MySQL mix to do rapid indexing and searching #HMP2010 about 13 hours ago via Twitterrific, 3 Retweets
TheGenomeCenter
Goll: Can use METAREP to compare datasets with more intuitive visualization and scaling capabilities #HMP2010 about 13 hours ago via TweetDeck
bffo
Johannesburg Goll from JCVI on METARAP, published as a 2 pager in Bioinformatics #OA #micro biome #hmp2010 http://bit.ly/c1VIGz about 13 hours ago via TweetDeck
phylogenomics
Best place to find out about Human Microbiome Project?: probably The HMP DACC #HMP2010 #somecoolthings http://ff.im/-pYTFo about 13 hours ago via FriendFeed 6 Retweets
eurogene
so how many $ spent on these trials worldwide now? MT @TheGenomeCenter: MMR vaccine and autism-Columbia trial found no correlation #HMP2010 about 13 hours ago via TweetDeck
TheGenomeCenter
METAREP: to compare two samples e.g. from healthy and diseased individuals; analyze pathways, enzyme presence, search/filter data #HMP2010 about 13 hours ago via TweetDeck
phylogenomics
Johannes Goll discussing Metarep – JCVI metagenomics analysis tool #HMP2010 – now available / published http://ff.im/-pYRF7 about 13 hours ago via FriendFeed, 2 Retweets
GenomeScience
Next up: Johannes Goll from JCVI – on METAREP high throughput #metagenomics tool #HMP2010 via @WashU about 14 hours ago via web
TheGenomeCenter
Goll – METAREP tool is at http://bit.ly/9kvX2r #HMP2010 about 14 hours ago via TweetDeck, 1 Retweet
TheGenomeCenter
Next up: Johannes Goll from JCVI – on METAREP high throughput metagenomics tool #HMP2010 about 14 hours ago via TweetDeck
GenomeScience
RT @phylogenomics FYI, agenda for the #HMP2010 human microbiome mtg is here http://bit.ly/9FyDlu http://fb.me/wxpn12gE about 14 hours ago via web
TheGenomeCenter
Lasken: HMP samples submitted to BEI http://bit.ly/9nw8ue #HMP2010 about 14 hours ago via TweetDeck
TheGenomeCenter
Lasken: shallow 454 sequencing with barcoding – 50-100 MDA reactions to verify 16S classification of HMP samples #HMP2010 about 14 hours ago via TweetDeck, 1 Retweet
phylogenomics
Roger Lasken: phylogenetic analysis can help assess MDA samples – note work done by Jonathan Badger who used to work in my lab #HMP2010 about 14 hours ago via Twitterrific
TheGenomeCenter
@phylogenomics For those interested the agenda for the #HMP2010 human microbiome meeting is here http://bit.ly/9FyDlu http://fb.me/wxpn12gE about 14 hours ago via Facebook
MetaHIT
RT @phylogenomics: For those interested the agenda for the #HMP2010 human microbiome meeting is here http://bit.ly/9FyDlu about 14 hours ago via HootSuite
phylogenomics
For those interested the agenda for the #HMP2010 human microbiome meeting is here http://bit.ly/9FyDlu about 14 hours ago via Twitterrific 5 Retweets
TheGenomeCenter
Lasken on Multiple Displacement Amplification (MDA) used to amplify smaller DNA samples and sequencing from single cells #HMP2010 about 14 hours ago via TweetDeck, 1 Retweet
emergentnexus
Roger Lasken: The J. Craig Venter Institute’s update on the HMP #HMP2010 http://ff.im/pYKwf about 14 hours ago via FriendFeed
phylogenomics
Roger Lasken from the J Craig Venter Institute now talking about whole genome amplification w/ MDA to get at uncultured organisms’ #hmp2010 about 14 hours ago via Twitterrific
TheGenomeCenter
Roger Lasken from JCVI update on Human #Microbiome Project #HMP2010 about 14 hours ago via TweetDeck, 1 Retweet
MetaHIT
#HMP2010 feed integrated to our dashboard dedicated to the Human Microbiome http://ow.ly/2xmNL about 14 hours ago via HootSuite, 1 Retweet
emergentnexus
I am microblogging #HMP2010 on FF; comment tweets showing up w/o hashtag. Follow me to see them! about 14 hours ago via web
MetaHIT
RT @MikeyJ: Glued to the tweets from Human Microbiome meeting #HMP2010 about 14 hours ago via HootSuite
MikeyJ
Glued to the tweets from Human Microbiome meeting #HMP2010 about 14 hours ago via Tweetie for Mac
mikethemadbiol
#HMP2010 Would note about Sutterella that I looked at human data & Sutterella found in ~30% ofadults; might be associated w/stomach illness about 14 hours ago via web
mikethemadbiol
#hmp2010 Would note about Sutterella that I looked at human data & Sutterella found in ~30% ofadults; might be associated w/stomach illness about 14 hours ago via web
TheGenomeCenter
Lipkin: Looking in cave in Spain, found novel filovirus – intermediate between Marburg and Ebola #HMP2010 about 14 hours ago via TweetDeck
phylogenomics
Ok Ian Lipkin has won me over forever . He just quoted Yogi Berra and Neils Bohr in one sentence #HMP2010 about 14 hours ago via Twitterrific, 1 Retweet
TheGenomeCenter
Lipkin: in last 9 months discovered over 300 viruses due to change in technology #HMP2010 about 14 hours ago via TweetDeck
mikethemadbiol
#hmp2010 Lipkin-1 series of gut samples from autistic kids & controls suggests elevated levels of Sutterella were associated w/autistic kids about 14 hours ago via web, 1 Retweet
phylogenomics
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 about 14 hours ago via Twitterrific, 1 Retweet
phylogenomics
Lipkin has looked at microbial diversity in biopsies of people w/ & w/o autism – found microbes associated w/ autism #hmp2010 about 14 hours ago via Twitterrific, 1 Retweet
phylogenomics
Lipkin talking about nothing controversial: autism and MMR and microbes #HMP2010 about 15 hours ago via Twitterrific
TheGenomeCenter
Lipkin: Identified disease of farmed salmon – unable to swim since gills don’t work; used high-thruput seq #HMP2010 about 15 hours ago via TweetDeck
phylogenomics
ian Lipkin referring to Edgar Allen Poe and cryptography in trying to sort through Metagenomic data #HMP2010 #binningishard about 15 hours ago via Twitterrific
TheGenomeCenter
New Aussie virus isolated from tissues extracted from women – found only 14 out of 100,000 sequences were from virus (vs. host) #HMP2010 about 15 hours ago via TweetDeck, 2 Retweets
GenomeScience
Now common protocols, benchmarked data accuracy, new tools & control data sets, better at defining variants #HMP2010 via @WashU #microbiome about 15 hours ago via web
TheGenomeCenter
Ian Lipkin: found a novel rhinovirus – HRV C – implicated in pneumonia, asthma using multiplex sequencing methods #HMP2010 about 15 hours ago via TweetDeck
phylogenomics
Lipkin showing world wide air traffic to scare us (rightly so) about how fast EIDs can spread #HMP2010 about 15 hours ago via Twitterrific, 3 Retweets
phylogenomics
Ian Lipkin talking about emerging infectious diseases – says we have only scratched surface of sampling viral diversity #HMP2010 about 15 hours ago via Twitterrific, 1 Retweet
phylogenomics
Interesting question after Birren’s talk re: archiving samples & informed consent – key things to think about in this type of work #HMP2010 about 15 hours ago via Twitterrific, 1 Retweet
mikethemadbiol
#HMP2010 B. Birren-E. coli K-12 can be assembled into 1 scaffold for hundreds of $s with Illumina seq & new jumps about 15 hours ago via web
phylogenomics
Ian Lipkin now up discussing microbe hunting in the 21st century #HMP2010 – mentions problems with Koch’s postulates at start about 15 hours ago via Twitterrific
emergentnexus
Ian Lipkin: Microbe Hunting in the 21st Century #HMP2010 http://ff.im/pYdKG about 15 hours ago via FriendFeed
mikethemadbiol
At #HMP2010 mttg. No fireworks yet, but liked Apollo metaphor by WashU science dean-I’ve used it myself; good 2 see I’m not only crazy about 15 hours ago via web
TheGenomeCenter
Ian Lipkin from Columbia U on microbe hunting #HMP2010 about 15 hours ago via TweetDeck, 1 Retweet
phylogenomics
Thanks to @GenomeScience for giving me the hashtag #HMP2010 for the Human Microbiome meeting I am at … about 15 hours ago via Twitterrific, 1 Retweet
TheGenomeCenter
Now have common protocols, have benchmarked data accuracy, created new tools and control data sets, are better at defining variants #HMP2010 about 15 hours ago via TweetDeck
phylogenomics
Birren presenting clustering of samples based on rRNA analysis – but could do much better referencing prior lit on this #HMP2010 about 15 hours ago via web
phylogenomics
Birren – given that they trust their PCR, now comparing many human samples – seems like they are way behind the field here #hmp2010 about 15 hours ago via web
pgspicer
At #HMP2010 in St. Louis about 15 hours ago via Twitter for iPhone
phylogenomics
Bruce Birren testing diversity estimators from rRNA PCR – for simulation got many more OTUs back than they put in #HMP2010 #sequencingerror about 15 hours ago via Twitterrific, 1 Retweet
TheGenomeCenter
Hashtag for Human Microbiome Conference in St. Louis is #HMP2010 – follow the conference going on right now! about 15 hours ago via TweetDeck, 2 Retweets
phylogenomics
Birren used a mock community to test rRNA PCR methods – wonder if he has read our mock metagenomics paper http://bit.ly/cPaIKF #HMP2010 about 15 hours ago via Twitterrific, 1 Retweet
TheGenomeCenter
21 bacteria with finished references used as positive control to test 16S 454 sequencing accuracy and determine data variability #HMP2010 about 15 hours ago via TweetDeck, 1 Retweet
OmicsKnowmics
I have starting to accept that microbes ARE cool (HOT!) RT @phylogenomics: The human microbiome meeting #HMP2010 is packed – microbes rule about 15 hours ago via TweetDeck
EdwardWinstead

Follow #HMP2010 for tweets from the Human Microbiome Conference in St Louis about 15 hours ago via TweetDeck, 2 Retweets

phylogenomics

Bruce Birren says that they developed a 454 rRNA sequencing pipeline that has been tested & is accurate across centers; #HMP2010 about 15 hours ago via Twitterrific, 1 Retweet

phylogenomics

The human microbiome meeting #HMP2010 is quite packed – microbes rule http://twitpic.com/2jynzt about 15 hours ago via Echofon

TheGenomeCenter

Bruce Birren from Broad on 16S sequencing in human metagenomics #HMP2010 about 15 hours ago via TweetDeck

emergentnexus

Bruce Birren: High throughput 16S sequencing in human metagenomics #HMP2010 http://ff.im/pXX52 about 15 hours ago via FriendFeed

GenomeScience

sample sites for human #microbiome project: oral cavity, skin, nasal, gi tract, vaginal, blood & serum #HMP2010 via @TheGenomeCenter about 16 hours ago via web

TheGenomeCenter

sample sites for human #microbiome project: oral cavity, skin (behind ear, elbow), nasal, gi tract, vaginal, blood and serum #HMP2010 about 16 hours ago via TweetDeck

emergentnexus

apparently the hashtag is #HMP2010 re: http://ff.im/pXTTj about 16 hours ago via FriendFeed

TheGenomeCenter

@TheGenomeCenter is tweeting from the Human Microbiome Conference in St. Louis #HMP2010 about 16 hours ago via TweetDeck

TheGenomeCenter

@GenomeScience – great suggestion! Human Microbiome Conference in St. Louis hashtag = #HMP2010 about 16 hours ago via TweetDeck, 2 Retweets

GenomeScience

@TheGenomeCenter – how about a hashtag for HMP mtg? #HMP2010 – does that work for you? about 16 hours ago via web

Clarification to Overselling Microbiome Award to Marshall Protocol: Critique of some claims by supporters, not protocol per se

OK time for a bit of a clarification.

Recently I gave out a somewhat aggressive “Overselling the microbiome award” to supporters of what is called the Marshall Protocol. I have started this award because I feel that many working on microbiomes have been overselling the potential for these studies to lead to cures and treatments for all sorts of ailments. And certainly,, some associated without the Marshall Protocol are making what I consider to be extremely overstated claims about this particular treatment.

But after talking to a supporter of the protocol here at the microbiome meeting I should clarify here that I was not actually critiquing the protocol itself. I was criticizing some of the claims of supporters of the protocol. In a way I erred in the same way that critiques of genomics have erred – where some have said genome sequencing is not useful because some promoters of genome sequencing oversell it. So I should have been more careful .. I should have focused on the claims about the protocol by some supporters. I stand by my criticism of some of these claims. The protocol seems to have no, or very littke, evidence that it works. And thus I did not like the claims that it cured all sorts of ailments.

But overselling the protocol by some supporters does not mean that the protocol does not work (though, again, I see no evidence that it does work). And overselling by some also does not mean that all supporters oversell it. It seems clearly that some of the supporters are sincerely interested in testing whether it works. In fact the person I talked to said they will work very hard to make sure that claims without evidence are removed from the Knowledge Base web site associated with the group supporting the protocol. I hope that is true. I am still skeptical about the activities of some supporters of the Marshall Protocol and whether the protocol can work. But at least some of the supporters really want to do clinical trials and use science to test the Protocol.

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

Science Conference SPAM: ICEME2011 on all of engineering & metaengineering

Well this one really really takes the cake. I got an email today that I think I simply have to post the entire thing because of its awesomeness:

Dear J. Eisen:

We invite you to submit a paper/abstract to The 2nd International Conference on Engineering and Meta-Engineering: ICEME 2011 (March 27th – 30th, 2011 – Orlando, Florida, USA): http://www.2011iiisconferences.org/ICEME. If you have any colleagues who might be interested in making a submission to the conference, please feel free to forward this e-mail to them. Below are the deadlines for ICEME 2011:
Papers/Abstracts Submission and Invited Session Proposals: September 22nd, 2010
Authors Notifications: November 22nd, 2010
Camera-ready, full papers: December 15th, 2010

Technical keynote speakers will be selected from early submissions because this selection requires an additional evaluation according to the quality of the paper, assessed by its reviewers, the authors’ CV and the paper’s topic. All Submitted papers/abstracts will go through three reviewing processes: (1) double-blind (at least three reviewers), (2) non-blind, and (3) participative peer reviews. These three kinds of review will support the selection process of those papers/abstracts that will be accepted for their presentation at the conference, as well as those to be selected for their publication in JSCI Journal.

Pre-Conference and Post-conference Virtual sessions (via electronic forums) will be held for each session included in the conference program, so that sessions papers can be read before the conference, and authors presenting at the same session can interact during one week before and after the conference. Authors can also participate in peer-to-peer reviewing in virtual sessions

Submissions for Face-to-Face or for Virtual Participation are both accepted. Both kinds of submissions will have the same reviewing process and the accepted papers will be included in the same proceedings

Authors of accepted papers who registered in the conference can have access to the evaluations and possible feedback provided by the reviewers who recommended the acceptance of their papers/abstracts, so they can accordingly improve the final version of their papers. Non-registered authors will not have access to the reviews of their respective submissions.

Registration fees of an effective invited session organizer will be waived according to the policy described in the web page (click on ‘Invited Session’, then on ‘Benefits for the Organizers of Invited Sessions’), where you can get information about the ten benefits for an invited session organizer. For Invited Sessions Proposals, please visit the conference web site, or directly to http://www.2011iiisconferences.org/iceme/organizer.asp
Authors of the best 10%-20% of the papers presented at the conference (included those virtually presented) will be invited to adapt their papers for their publication in the Journal of Systemics, Cybernetics and Informatics.
Best regards, ICEME 2011 Organizing Committee

There are so many parts of this that are incredible. Like that it covers all of Engineering and Meta-engineering (whatever that is) in one conference. And that authors CV will be used to decide if submissions are accepted. And that all papers will be reviewed by three distinct review processes including double blind and non blind.

But the best, by far and away the best, comes when you go to the conference site. I dare ANYONE to try and read the beginning description out loud to someone else without laughing:

Purpose

Engineering and Meta-Engineering is what synergistically relate Science and Industry. Two cybernetic loops are based on an adequate combination of different kinds of knowledge creation and two other cybernetic loops related to wealth creation. Both creations are produced by Engineering and Meta-Engineering which synergistically bridge Science and Industry/Business. Details regarding this issue can be found at http://www.iiis.org/Engineering-and-

Meta-Engineering

Consequently, the purpose of the ICEME 2011 Organizing Committee is to bring together researchers and professionals from the Academic, Industrial and Public sectors with Engineering and Meta-Engineering problems and/or solutions and/or technological innovations in order to share their knowledge and experience in the context of a Multi- and Inter-Disciplinary forum.

The site then goes on to define meta-engineering. I could post it all here but the site has some nice figures to look at too. This is the best example of Conference SCAMs/SPAM that I have yet seen, and I have seen a lot.

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.

Overselling the microbiome award #2: The Marshall Protocol

Wow – until I started sniffing around actively, I never realized how much crap was out there in regard to the microbiome. But there is so so much. Certainly, the human microbiome (the microbes that live in and on people) is more important than people used to think. The microbes in and on us show some interesting correlations relative to disease and health states. And almost certainly changes in the microbiome likely cause some alterations in health state. Recent studies on fecal transplants, for example, suggest even that altering the microbiome is both possible and could be helpful in some cases. But we are really early in the work here.

But right now, for many health and disease states
(1) we don’t know if the altered microbiome is a cause or an effect or not related at all and
(2) even if there were a causal relationship between microbes and various health/disease states, there will also be enormous complexities relating to history and genes that will be very hard to sort out
(3) even if we knew a causal relationship this would not mean we would know how to change the trajectory (e.g., what microbes are there) in a useful way

Because there is so much iffy stuff out there relating to the microbiome and because some are starting to use studies of the microbiome to indirectly lend credence to their crap, I have decided to start giving out an “Overselling the microbiome award”. I gave out the first one a few days ago: Overselling the microbiome award: Stephen Barrie on pre and probiotics at the Huffington Post

Interesting, Barrie posted a comment on the blog trying to defend his post, but I was not convinced. I think he did not understand my point about correlation vs. causation but am not sure.

Anyway, after I wrote the response to Barrie I looked around the web for others using the term microbiome in what seemed to be unsavory ways. And I found a really painful one. This is something called the “Marshall Protocol Knowledge Base.” This so called knowledge base is a web site set up to promote, you guessed it, the Marshall Protocol. The Marshall Protocol is “a curative medical treatment for chronic inflammatory disease.” In turn this protocol is based on the Marshall Pathogenesis which is “A description for how chronic inflammatory diseases originate and develop.” It follows that this Marshall Pathogenesis “posits that chronic diseases (termed Th1 illnesses), are the result of infection by an intraphagocytic, metagenomic microbiota of chronic bacterial forms that are often referred to as the Th1 pathogens.” I have read the last sentence dozens of times and I still do not know what it means. What is a metagenomic microbiota? I just do not know.

Anyway, I am sure everyone will be shocked to find out that the Marshall Protocol Knowledge Base, the Marshall Protocol and the Marshall Parthogenesis are being promoted by someone named, well, Marshall (Trevor Marshall) who seems to be the head of the Autoimmunity Research Foundation which is the place promoting the Marshall Ps (I swear, I will not call it the Marshall Plan, I will not, I will not).

Based upon what appears to be little if any actual published research, the Marshall Protocol promotes the treatment of all sorts of ailments with in essence long term
high dose
cocktail of multiple antibiotics at apparently low dosage and a long term attempt to alter Vitamin D levels by treating in part with very high doses of a drug called olmesartan. Among the ailments that this protocol is claimed to help are Crohn’s, Type I diabetes, Multiple Sclerosis, Psoriasis, Rheumatoid Arthritis, Celiac Disease, and many many more. (I note they say “The Phase II clinical trial conducted from 2002-2008 by the Autoimmunity Research Foundation has demonstrated applicability of this antibacterial therapy to a wide range of chronic Th1 immune illnesses ” and then cite a powerpoint presentation).

I could go on and on. But it seems clear to me that they are both making mistaken claims about what we know about the effect of microbes on health as well as making almost absurd claims about how one treatment system can cure a series of diseases by fixing ones microbial content. Note I am NOT saying microbes have no connection to these ailments – studies are supporting the microbial diversity in people with these ailments is different than in people w/o the ailments. Nor am I saying that Vitamin D is unimportant. In fact, it is becoming clear that Vitamin D is much MORE important than people realized. But importance alas, is different that saying we know exactly WTF is going on. And certainly the treatment outlined by the MP folks here is not as far as I can tell supported by any evidence of effectiveness not is it obvious how it connects to scientific knowledge about microbes and vitamin D.

Fortunately, others have taken on the MP folks here and have written about how it appears to be a scam of sorts, and a potentially dangerous one at that. See for example:

I know, there are lots of medical scams out there. But this is the first one I have seen discussing metagenomics and the microbiome. And for that, I am giving the Marshall Protocol and the folks behind it, my second “Overselling the microbiome award“.

UPDATE 7/18/2012 – some stories worth looking at

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

Bad omics word of the day: waveomics

Let’s just cut to the chase. The Bad Omics Word of the Day is Waveomics. Suggested to me by SeaSaver.

On the one hand, I really like that people in biology related fields are putting out preprints in places like Nature Precedings. On the other hand, this one is a bit painful from the omics terminology point of view: Waveomics: bringing experimental data to online collaboration : Nature Precedings

Well, the term is really just, well, awful. Here is a key phrase about it:

A Robot is introduced here, waveomics, which provides the first example of allowing experimental data from multiple sources to be queried and shared in the Google Wave environment.

The concept is not so bad in principle – the author Neil Swainston (who has done some cool things – check out his blog and his slideshare presentations and his Academia.Edu page for some detail) was trying to design tools for streaming genomics data in Google Wave. So this is not a critique of Neil or his work, just of the word waveomics.

Thankfully, in many ways, Google Wave is going extinct. I guess we should wave good bye to waveomics too.

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