Thursday, February 25, 2010

Genome Sequencer FLX Bay Area Regional User Group Meeting

Just got this email - may be of interest to some:

Genome Sequencer FLX Bay Area Regional User Group Meeting

Roche 454 Life Sciences invites you to the Bay Area Regional Genome Sequencer FLX User Group meeting which will be held at Roche Diagnostics in Pleasanton, CA on March 8th and 9th.

We will kickoff the meeting the afternoon of March 8 with interactive sessions with our BioInformatics Specialist Teri Mueller and Regional Applications Consultant Shamali Roy. Bring any questions or ideas you may want to address. Teri will present on the most recent upgrades to our Data Analysis software and Shamali will be available for experimental design advice. This will be a user driven question and answer event scheduled from 1:00-4:00 pm.

Tuesday will feature local scientists presenting their 454 Genome Sequencer FLX work for a variety of applications. Presentations will begin at 10:00 am and conclude at 4:00 pm.

Speakers for the event include

Robert Shaffer, MD – Associate Professor of Medicine and Pathology, Stanford University

Feng Chen, PhD – Group Lead, Technology and Applications, US DOE Joint Genome Institute

Matt Ashby, PhD – President and Chief Scientific Officer, Taxon Biosciences

Henry Erlich, PhD – Vice President Discovery Research, Roche Molecular Systems

This meeting is designed to allow GS FLX users to share experiences and knowledge about the platform, creating a community of users where tips and tools can be shared. Other than a brief introduction by Roche 454, this will be a Science for Scientists event. Please feel free to share this invitation with colleagues.

Come and network with other researchers using Roche 454 technology as well as learn tips ranging from sample management to base calling to whole genome analysis, and much more. This event is free of charge and is open to everyone with an interest in using this exciting technology for accelerating your research and discovery. Lunch will be provided on March 9.
Space is limited and registration is required. To register for the event please RSVP to either courtney.brady@roche.com or goli.shariat@roche.com Please indicate if you will be attending March 8th or 9th or both days.

The address for the event is Roche Diagnostics, 4300 Hacienda Drive, Pleasanton, CA 94588. There is a BART station nearby and shuttles to Roche can be arranged.

Visit to #UCDavis Bohart Museum of Entomology

For those of you who know me, and for those of you who do not, you may not know that I am generally a fanatic about bugs.  And in this case, I do not mean microbes (which I also love).  I mean insects and their relatives.  So it was with great pleasure that yesterday I finally got to go to the UC Davis Bohart Museum of Entomology.  I have been meaning to go for a while but it just never happened.  And then, a graduate student in my lab, Lizzy Wilbanks, asked for suggestions for activities that might be interesting to do with Jared Leadbetter who was the speaker the Microbiology Graduate Students were hosting here at Davis.  Now, I know Leadbetter a tiny bit and know that he really likes bugs too (both kinds ...).  So I suggested - why not see if you can get a tour of the museum. And like magic, Lizzy arranged it.  Any yesterday, Marc Facciotti and I took Leadbetter over the the museum after he had lunch with students.  And it was very cool.

I will try to write up more about the museum at a later point but here are some pictures.



For details on Leadbetter's talk see my Friendfeed posts below:

Wednesday, February 24, 2010

Letter from #UCDavis Chancellor Katehi on "Rallies in support of higher education"

Just got a letter from UC Davis Chencellor Katehi addressed to the UC Davis community (so presumably this went out to 1000s) regarding some upcoming rallies in support of higher education and I thought it might be of interest to share it here because it may be of interest to some who did not receive it:
Dear UC Davis Community Members:

Next week's rallies in support of public higher education provide us with another opportunity to work together on behalf of the University of California and in support of the California Master Plan for Higher Education -- a visionary plan forged in 1960 that viewed higher education as a collective good and as the primary engine of social mobility.

That plan is threatened today with the state's steady and steep disinvestment in UC, in California State University and in the California Community Colleges. I know you feel the impact of that disinvestment in very real, very personal ways.

The Governor's January budget proposal offers us some hope, but it's critical that we persuade lawmakers to make public higher education a funding priority. Together, we can help our state to re-prioritize.

Three advocacy opportunities are fast approaching. While on-campus responsibilities must always come first, I'm hopeful that, with attentive planning, you'll be able to help deliver the message to Sacramento that our public colleges and universities need greater state investment.

On Monday, March 1, the UC Student Association will hold a march, rally and press conference at the State Capitol between 11:30 a.m. and 2 p.m. UCSA leaders have asked UC President Mark Yudof and several regents and chancellors to join them in meetings with key legislative leaders throughout the day. I am pleased to do so, and am looking forward to accompanying our students to Sacramento. If you're able, I hope you will join us and add your voice to others advocating for keeping our public university truly public. If you need transportation, our Government and Community Relations Office is working with student leaders to coordinate UC-provided buses.

On Thursday, March 4, a national day of action in defense of public higher education is being planned by a coalition of K-14 and UC and CSU students, employees and other education stakeholders. Rallies are planned at the State Capitol and throughout the state.

And on Tuesday, April 27, another advocacy day at the State Capitol is being planned by a coalition of UC, CSU and California Community Colleges advocates throughout the state. It's hoped that a broad alliance of public higher education supporters will participate, including students, parents, alumni, faculty, staff, business leaders and community organizers.

I hope we can continue to work together on the university's behalf, raising issues and raising our voices effectively and respectfully. Together, we can make our best case for preserving affordable, accessible and world-class public higher education. That was the state's vision in 1960, and that must remain its commitment today. Please join me in carrying that message to the State Capitol and ensuring that the principles of the California Master Plan endure.

Sincerely,

Linda P.B. Katehi
Chancellor

New #UCDavis Open Science Group & OpenWetWare page

Just got an email about this group from Carl Boettiger and thought I would help spread the word. If interested in open science and affiliated with Davis please sign up:

I just met some students recently who were talking about creating an Open Science group at UC Davis. Thought you might be interested in joining their mailing list: openscience@ucdavis.edu

email listproc@ucdavis.edu with
subscribe openscience firstname lastname
in the body.

Some more info here: http://openwetware.org/wiki/UC_Davis_Open_Science

Tuesday, February 23, 2010

Evolution word of the week: bislagiatt (& check out WSJ evolution article too)

Normally I spend some time here criticizing bad words used in various areas of science in which I work. Today I am praising a word. The word is bislagiatt and I had never seen it until reading a Wall Street Journal article today. The article (Blame Evolution for Disease - WSJ.com) has some good and bad moments. It presents some arguments for why some human diseases today are in essence side effects of historical natural selection that no longer applies well. Many of the arguments seem OK but smell of adaptationism in reverse - just so stories that may not have a lot of evidence on their side. But the article overall is good and has some nice figures with it. But the best part of the article is the introduction of a new word

"And some body parts that provided a benefit at some time in human history pose challenges today—a phenomenon Texas Tech University geneticist Lewis I. Held Jr. calls "bislagiatt," an acronym for "but it seemed like a good idea at the time.""


Now that is a perfectly good evolution term. And though I have never seen it used anywhere else, the use in this article I think will lead to it being used more commonly in the field. And thus today I am giving out a new award "Best new evolution word" to "bislagiatt" and to Dr. Lewis Held for at least using it here if not coining it.

Wednesday, February 10, 2010

Funny Mobio ad "No microbe will be left unsequenced" #DNA #genomics

Funny ad from Mobio on their web site and YouTube "No Microbe Will be Left Unsequenced." Perhaps they are familiar with my obsession to create a Field Guide to the Microbes (e.g., see here and here) and my obsession with creating a Genomic Encyclopedia of them? Who knows? But I do know my lab uses lots of MoBio kits - they are quite nice.

Tuesday, February 09, 2010

Call me a curmudgeon but I do not do "reciprocal links" on my blog

Arrg.  I am so sick of getting emails from people hawking some blog site saying "We like your blog ... if you link to us we will link to you."  Here is an examply I just got
Saw the “The Tree of Life” blog and thought it was great. I wanted to introduce our blog to you. The XXX Blog (http://www.XXXX.com/blog/) has been created as a place where blah blah blah. Would you be interested in reciprocal linking? We will link to you on the XXX Blog http://www.xxxx.com/blog/ and our other blog the xxxxx http://xxx.wordpress.com/. If you are interested feel free to contact us xxx@xxxx.com .
Here is another one:
Greetings:      
My latest site is dedicated to xxxxx. If you would like to exchange links I would be more than happy to trade my link in exchange for a reciprocal link on your site. If you agree, please place my link: 
TEXT: xxxx                       
URL: http://www.xxxx.com
Desc. (optional): The top xxxx xxx xxx for your xxx xxx. .  
Send link placement and your link information to wrap up the exchange
Thanks  
I am sorry but I put up links that I find interesting.  And I do not post links in exchange for others posting links to me.  Am I somehow missing out on something?  I know people are trying to game google hits but I want nothing to do with it.

Sunday, February 07, 2010

Bad omics word of the day: religionome

And so they go - on and on.  I am addicted to bad omics words.  They are a bit fascinating ion that the spread of the ome suffix is astonishing.  And here is one that is both funny and a bit sad: religionome.  Not that new.  But out there.  And winner of today's "Bad omics word of the day." Not sure exactly where it started but here is one of the first uses I could find:
We have a lot of new data we are working on, and one of the thoughts I’ve come up with recently is can we create something similar to the human genome – perhaps we can call it the religionome – with which we can begin to look at all of the different beliefs and practices and traditions and try to evaluate and understand them not just from a spiritual perspective or a subjective perspective, but from physiological and biological and social and cultural perspectives as well
This is from a transcript of a conference involving Andrew Newberg from U. Penn.

Some other things on this include:

Saturday, February 06, 2010

Oldy but baddy: bad omics word of the day - "speechome"

I know I swore to quit but I could not help myself here. I was going through old draft blog posts that I never finished and found this link to an article about the "Human Speechome Project" BBC NEWS | Science & Environment | Big brother untangles baby babble

Basically, the idea is they are recording everything a particular child hears and says and categorizing it all to create "the Human Speechome project"
"Just as the Human Genome Project illuminates the innate genetic code that shapes us, the Speechome Project is an important first step toward creating a map of how the environment shapes human development and learning," said Frank Moss, the director of MIT's Media Lab at the time.
In some ways - the project is eerily fascinating. But in many ways it is more on the creepy side of things. Regardless of whether one likes the project or not, the word "speechome" has just got to go. So, quite a few months late - I am still giving this my "Bad Omics Word of the Day" award.

Friday, February 05, 2010

Received my first soliciation regarding "Broader Impact" reqs for grants

Got an interesting email the other day:
What do the following research programs have in common?

1. Lost Ladybug Cornell (Cornell University, NY)
2. Museum of the Earth (Ithaca, NY)
3. Crossing Boundaries (Hobart and William Smith Colleges, NY)
4. High School Polar Outreach Project (Charleston, SC)
5. Go Inquire Project (George Mason University, VA)
6. Project Wetkids (University of Southern Mississippi)

Answer: They decided to hire Next Interactives to develop a highly engaging research website to help fulfill their Broader Impact and Outreach requirements.

Sound interesting? Simply reply to this email for a free website consultation.

Regards,
XXXX

Outreach Project Manager
Next Interactives LLC
Our portfolio: www.nextinteractives.com
This seems to be focused specifically on the "Broader Impact" requirement in National Science Foundation grants.  I have never received a solicitation like this before.  Anyone else out there get anything like this?  What do people think?  I think it is possibly a good thing that some companies are thinking there is a niche for them in Broader Impact and outreach assistance.

Thursday, February 04, 2010

A eureka moment - but not of the good kind

Well, today I had one of those eureka moments that scientists all around the world crave.  You know, where all of a sudden you find out something that causes you to re-evaluate all sorts of aspects of the world you thought you knew.  I have had some of these, here and there before.  Sometimes even about my own work.  More often, when I read a paper or go to a talk that presents some major breakthrough that you just know is going to win a Nobel Prize one day.

I spent part of Thursday talking to some people about this exact type of thing in science.  I was answering some questions from some high school students about why one likes doing research and I said one reason is that such eureka moments can happen (mostly I said science was just fun but also said there are some big discoveries that happen too).

Well, 30 minutes ago this happened to me.  Alas, it was not about science per se.  But more about about how one's assumptions can cloud one's judgement and cuase one to miss what is right in front of you.  You see, I just got back, a few minutes ago, from driving through the pouring rain to get to one of the better restaurants in Davis, Osteria Fasulo, where alas I have never been.  I was going there to have dinner with the amazing, brilliant and fascinating Mina Bissell. Mina is a "Distinguished Scientist" at Lawrence Berkeley National Laboratory and a well known cancer researcher (see a great profile of her by Gina Kolata from the 12/28/09 New York Times here).

Anyway - I have known Mina for many years since I was involved in something called the Defense Science Studies Group (aka DSSG - though be careful when you search the web for this term ...).  Mina gave a seminar here at UC Davis today in the Cancer Center.  And a week or so ago, her host invited me to go to dinner with Mina and I said yes (after my standard delay due to being behind in email all the time).

Alas, I was unable to go to the seminar because it was at 9 AM in Sacramento (about 20 minutes from Davis - most of the UC Davis medical school including the Cancer Center is there) and I had kid duties in the morning.  But I was looking forward all day to having dinner with Mina and to meeting some other cancer researchers at UC Davis who I did not know.  Plus her host had called me Wednesday to make sure I was coming to dinner - she wanted to know because one of the other participants wanted to know how much special wine to bring.  (It was a little weird that she called Wednesday to make sure I was going to dinner Thursday since the message she left me sounded urgent but whatever). It all sounded good - Mina, colleagues I had not yet met, good restaurant I had not been to, fancy wine.

So today at work I left a little early to buy some dinner for my wife and kids who have all been sick - and I dropped it off at home and got ready to go to the dinner.  And then I headed out - through the driving rain to the restaurant nestled within "Village Homes"  in Davis.  I got to the restaurant at just about the meeting time, went in, and ... nobody was there.

The host of the restaurant said there was no reservation for 6:15 but that there was one for 7:30.  But he said - maybe they made a mistake - and he sat me at a table and gave me some sparkling water to drink.  And then I decided to get out my phone to just double check about the dinner.  And that's when I decided to look at Mina's itinerary to see when her last meeting was before dinner so I could guess when they would really arrive.  And that is when I saw it.  Dinner was Wednesday night.  I literally said something I will not print here out loud.  So I missed the dinner.  Turns out they waited for me for a while, tried to call me (they should have sent me email I guess .. or posted something to twitter), and then went ahead without me (I found out about this b/c I called Mina's host to find out if maybe she was still around Davis but she had left at 5 PM).

So I know a long story not really about science.  But here is the reason I am writing it.  I had set myself up for getting the date wrong by a series of assumptions.  I assumed Mina would just come to Davis for the day since she lives 1 hour away in Berkeley.  And since she was talking Thursday, I just assumed the dinner would be Thursday. But alas she came the night before her talk.  All of a sudden - everything made sense in hindsight.  Her host calling me Wednesday and leaving an urgent message about the dinner.  The comment by another one of her hosts that if I could not come to the dinner I could always see her afterwards (I thought he meant go to Berkeley).  And a few other things ... Oh man, what an idiot.  Anyway - I am sure I should not confess to being such a doofus on my blog - but I had planned on writing about Mina when I got back from dinner.  I even brought Rebecca Skloot's amazing "The Immortal Life of Henrietta Lacks" to show Mina, and wanted to know what she thought of the whole HeLa story.  Oh well. Maybe next time.

End (at least for while) of the bad omics word awards

Well this is it. I am declaring that I am (mostly) done with the posts about bad omics words. I will on occasion I am sure rail about one word or another with my Worst New Omics Word Award, but I will try to let ome words rest in peace, at least for a while. Mostly this is because the task is too overwhelming.  There are simply too many bad omics words out there.

I would like to note however, that as I have browsed around, I have noticed many other bloggers doing similar occasional snarky complaints about omics words here and there. That was good to see. But most amazing was that there is in fact published literature on the topic of bad omics words. See for example The Wholeness in Suffix -omics, -omes, and the Word Om and apparently[The odd omes and omics] (which is in Finnish) and many others.

My favorite published rant even has rant in the title "A rant against jargon and neologisms". It is definitely worth a read and is free in Pubmed Central. In it, Simon Young says many things I agree with. In particular the ending
This does not mean that these terms are not useful. However, as with all new terms, they will help to promote knowledge and ideas only if their precise meaning becomes known to a broad range of researchers. Only time will tell what will become a useful scientific term and what will remain the jargon of a subgroup of researchers.
The best discussion I have seen of the issue is by none other than the great Joshua Lederberg (may he rest in peace) who wrote 'Ome Sweet 'Omics — A Genealogical Treasury of Words with Alexa McCray. In it they discuss the history of the word genomics, among others. They also quote Roland Brown author of "Composition of Scientific Words"
"words, when they make their debut in scientific or literary society ... should be simple, euphonious, pure and mnemonically attractive."
Clearly many of the new omics words do not meet this criteria but I am going to leave that for others to (help) judge. If you personally want to see some lists of the every growing number of omics words, check out any/all of the following:

Wednesday, February 03, 2010

Carnival of Evolution #20! is out and it's got some good stuff ...

Just a quick post here to suggest people check out the Carnival of Evolution (#20) being hosted at Skeptic Wonder (see Skeptic Wonder: Carnival of Evolution #20!).
It's has some juicy evolution posts discussed and (perhaps) best of all has a "phylogenetic" tree based on the postings. I recommend everyone check it out ...

Story behind the science: #PLoS Genetics "Evolutionary mirages" paper

ResearchBlogging.org

So there is this cool new paper out in PLoS Genetics: Evolutionary Mirages: Selection on Binding Site Composition Creates the Illusion of Conserved Grammars in Drosophila Enhancers. and I have wanted to write about it for a week or so. You see, the paper is about something I have been interested in for most of my career - how the particular processes by which mutations occur can sometimes be biased (i.e., some types of mutations are more common than others) and that these biases can create highly ordered patterns in genomes and in turn that observation of these ordered patters can sometimes be misinterpreted as being the result of adaptation. Mistaken claims of adaptation in genomics are a favorite topic of mine - and let me to create (with tongue in cheek) a new omics word - Adaptationomics.

Anyway - so I really really like this paper. But there is a week bit of a problem in writing about it. You see, it is by my brother, Michael Eisen, a Prof. at UC Berkeley (and a student in his lab Richard Lusk). And, well, I don't want to say anything wrong or stupid about the paper since, well, my brother will be pissed off. And so I have not written about it yet. But then I realized the best way to write about this one is to simply ask my brother for the "Story behind the science" for the paper, as I have been doing for some other recent papers.

If you want a summary of the paper, here it is in their own words:
Authors summary: Because mutation is a random process, most biologists assume that apparently non-random features of genome sequences must be the result of natural selection acting to create and preserve them. Where this is true, genome sequences provide a powerful means to infer aspects of molecular, cellular, and organismal biology from the signatures of selection they have left behind. However, recent analyses have shown that many aspects of genome structure and organization that have traditionally been attributed to selection can often arise from random processes. Several groups—including ours—studying the sequences that specify when and where genes should be produced have identified common, seemingly conserved, architectural features, based on which we have proposed new models for the activity of the complex molecular machines that regulate gene expression. However, in the work described here we simulate the evolution of these regulatory sequences and show that many of the features that we and others have identified can arise as a byproduct of random mutational processes and selection for other properties. This calls into question many conclusions of comparative genome analysis, and more generally highlights what Michael Lynch has called the “frailty of adaptive hypotheses” for the origins of complex genomic structures.
Conclusions: Lynch has eloquently argued that biologists are often too quick to assume that organismal and genomic complexity must arise from selection for complex structures and too slow to adopt non-adaptive hypotheses. Our results lend additional support to this view, and extend it to show that indirect and non-adaptive forces can not only produce structure, but also create an illusion that this structure is being conserved. We do not doubt that many aspects of transcriptional regulation constrain the location of transcription factor binding sites within enhancers. Indeed a large body of experimental evidence supports this notion, and we remain committed to identifying and characterizing these constraints. But if this process is to be fueled by comparative sequence analysis, as we believe it must be, it is essential that we give careful consideration to the neutral and indirect forces that we now know can produce evolutionary mirages of structure and function.
I must say I love the title lead in "Evolutionary mirages" which is another but much better way of saying "Adaptationism is a bad thing".

Anyway, before I get in any more trouble, here are some words about the paper from the Senior Author, Michael Eisen, my brother. Questions by me (I know, not very creative ones - but they will have to do):


Tuesday, February 02, 2010

Worst new omics word & bad omics word of the day: receptorome

Well, I really want to quit with this "Worst New Omics Word Award" and with the new "bad omics word of the day" theme I started a few days ago. But I just can't quit. Today's reason for not quitting is a new PLoS One paper: Psychedelics and the Human Receptorome. Even though the word is not defined in the paper, it is alas, defined elsewhere. Wikipedia says
The receptorome, is a concept analogue to the genome and proteome, but also to other sets of structural or functional units such as the proteasome and connectome.
In analogy with the genome, where the genome is the total set of genes, the receptorome can be considered the total set of genes giving rise to receptors or receptor molecules. It could also be seen as the total number of receptor proteins in a certain organism.
There is even, receptorome.org.
I do not know the origins of the word. I do know, however, that it is a bit much. A key question for this and many other omics words is - is it needed? How much trouble would it be to say what we actually mean "all the receptors" or something like that. Recepterome gives too much formality to something that does not seem to be a concrete entity. Proteosomes - they are real things. Proteome - possibly annoying to some, but a straightforward concept independent of functional properties of proteins. Recepterome just is not a good analog of these terms.

And though at some level I do not want to thank them - I guess I should thank those who pointed this out to me: Bora in an email, mocost on twitter and PSI-Wavefunction in a comment. Thanks all - for for pointing out this new omics word ... so that I can give it today both by Bad Omics Word of the Day and Worst New Omics Word Award, even though it may not be so new. At some point I guess I should merge these awards. Then maybe I will call it the "Awardome.

Monday, February 01, 2010

Bad omics word of the day: vaccinomics

The more I look at the litany of omics words, the more I fret. So let's just get straight to the point. Todays bad omics word is "Vaccinomics" which was defined as follows:
Vaccinomics encompasses the fields of immunogenetics and immunogenomics as applied to understanding the mechanisms of heterogeneity in immune responses to vaccines
I do not like this word but if you want to learn more I guess you could look here. Not really much more to say.