Best new omics word: the beardome - absolutely brilliant

Not much to say other than that this is awesome: The Beard-ome : Oscillator: "Christina Agapakis".

Hat tip to Bora

WANTED: Used Roche GS FLX sequencer; ready to buy

Well, I have been looking around on the web for a bit and figured I should just post to my blog. We are in the market for a used Roche GS FLX sequencer. Anyone know of one for sale? We had planned to buy a new one but with the 3rd generation sequencers coming out soon it seems unwise to spend 500K on a new machine. But I like the current capabilities in the Roche GS FLX, as well as the apparently soon to be released ~1000 base pair reads. So we still would like to have the technology here at UC Davis. So if you know of one for sale, please let me know.

Looking to open access (preferably w/ CC licenses) review papers covering introduction to phylogenetic trees and methods

I am teaching a class this spring and as part of the class am having one lecture on "Phylogenetic trees and methods." I would like to link to (and be able to mix and match material from) some review paper on this topic. So I am searching for something that is Open Access and preferably with a broad Creative Commons license. Anyone know of anything good?

JGI User Mtg Day3 notes (coming up Rita Colwell, ex head of NSF)

Here are links to the Friendfeed Notes for today

And the Joint Genome Institute's User Meeting Begins (posting notes/feeds here)

Will be posting my notes and feeds (e.g., Friendfeed) here - so stay tuned if you want to hear about the JGI User Meeting

Pictures here:



FriendFeed Notes on Talks here:

CA Proposition 16: PG&E's outrageous, offensive, misleading initiative

Just heard an ad on the radio from the Vote Yes on Proposition 16 campaign here in California.  And got a heads up from a friend about it too. Just to cut to the chase before getting into detail - this initiative is horrendous and deceptive.  Here are some details 


From Ballotpedia.Org:
"The proposed constitutional amendment would require a two-thirds majority vote of local voters before a local government could:

• Establish a Community Choice Aggregation (CCA) program.
• Use public funding to implement a plan to become a CCA provider
• Expand electric service to new territory or new customers.^[3]

It is being pushed by promoters as the "Californians to Protect Our Right to Vote." bill.  But really what this is a move by PG&E to help it make more money.  Some comments/questions


1. Why is the only major donor to the Vote Yes campaign PG&E?  See here for more detail on donors, where as of today the top donors are all PG&E. 


2. Every editorial I could find came out vigorously against it:

• San Jose Mercury News
• Contra Costa Times
• Sacramento Bee
• Fresno Bee
• Modesto Bee
• Long Beach Press Telegram

3. Not surprisingly, many other utilities have come out against this, as it clearly favors PG&E, aka the status quo.  I am not overly sympathetic to the opinions of these other utilities but it seems that the initiative is more about reducing competition than in favoring democracy.

4. One thing that really annoys me is the component of the proposition that a two-thirds majority vote will be required before local communities can change their energy plans.  To then say that this initiative is about protecting our right to vote is just absolutely offensive.  What this is a way to try and make change of any kind very very difficult.  In this day and age, with energy becoming more and more of an issue, we should have as much flexibility as possible.  What we do not need is an initiative that requires a 2/3 majority to make changes.

5. The most astonishing aspect of the proposal has been some of the words from the head of PG&E, as reported in the Mercury News

Asked why the company was sponsoring the initiative, Darbee referred to the 2006 battle in which it spent more than $11 million to prevent Davis, Woodland and West Sacramento from defecting to the Sacramento Municipal Utility District.

"So it was really a decision about could we greatly diminish this kind of activity for all going forward rather than spending $10 (million) to $15 million a year of your money to invest in this," Darbee told the shareholders. "The answer was yes."

So basically this is there way to limit the choices of cities by putting this on a statewide ballot.  In essence, whether liberal or conservative, Democrat or Republican, I can't see why anyone would support this Proposition.  A conservative could easily see this as  PG&E trying to be the big hand of government to take away taxpayer choice.  A liberal could see this as a company using their money to buy votes and prevent choice in energy usage.  I really cannot see any potential upside in this for anyone but PG&E.  Lovely

Simple solution.  Vote No on Proposition 16.  More comprehensive solution would be to actually punish PG&E for the audacity and idiocy of this measure as well as the misleading nature of all of their ads and claims about it.  Not sure how to do that but boy do they deserve it.

UC Regents 3/24 public/ustream discussion of recent "intolerance" issues

Just got this announcement:


"The UC Board of Regents, at its March 24 meeting, will hold an extended public comment period and discussion of recent incidents of campus intolerance and UC's efforts to address them.

The Office of the President will provide live streaming video of the discussion, available to members of the public and the UC community at:
http://www.ustream.tv/regentsmeeting

The public comment period begins at 8:30 a.m., Wednesday March 24. Following that 40-minute period, President Mark Yudof, Regents Chairman Russell Gould, Interim Provost Lawrence Pitts, Senior Policy Advisor Christopher Edley and select chancellors will discuss the recent events and the actions they are taking to ensure that these types of incidents do not occur in the future.

For employees who are unable to watch the proceedings live, an archived tape will remain available at the same web address:
http://www.ustream.tv/regentsmeeting "

Phyloseminar.Org 3/29 Streaming talk by Jens Lagergren on Gene Family evolution

Just got his email from the organizer of Phyloseminar.Org:

On March 29th, phyloseminar.org will present Jens Lagergren speaking

on "Probabilistic analysis of gene families with respect with gene

duplication, gene loss, and lateral gene transfer." Abstract below.

NOTE: the seminar will begin at 10h PST, which is three hours earlier

than the previous seminars.

This is 13h Eastern Standard Time, 19h Central European Time, and 6h

in Christchurch and Auckland!

Here's the abstract:

Incongruences between gene trees and corresponding species trees are

common. Gene duplication, gene loss, and lateral gene transfer are

three types of evolutionary events that can cause such incongruences.

I will first describe a probabilistic process that contains standard

models of nucleotide substitutions (i.e., such that underly

probabilistic methods for phylogenetic tree reconstruction) as well as

gene duplication and gene loss. This process takes place in a given

species tree and can be used to reconstruct a gene tree for a gene

family of interest and simultaneously reconcile the gene tree with the

species tree. I will describe the algorithms available for this model

and also describe how they perform on biological data compared to

competing methods. Finally, I will describe an extension of this model

that also contains lateral gene transfer and show how it performs on

synthetic data.

Hope to see you there!

Bad omics word of the day: Bibliome

(Note - this was supposed to be published tomorrow but clicked the wrong button - so we will have two today - yay)

And here is a doozy.  The bad omics word of the day is ... Bibliome. See for example, the source of all knowledge (Wikipedia): Bibliome - Wikipedia, the free encyclopedia Which also refers to some other related omics words the literaturome and the textome.  Now, every one at once, 1,2, 3, groan.

Back to the bibliome which is described in Wikipedia as follows:

"The bibliome is the totality of biological text corpus. This term was coined around 2000 in EBI (European Bioinformatics Institute) to denote the importance of biological text information. 

The first uses seem to be in and around 2001. See this article from Nature Reviews Genetics in 2001 Mining the bibliome.  And another one with a very similar title in EMBO in 2002: Mining the Bibliome (with some other words in the title).  And another one in Pharmacogenomics entitled Mining the bibliome. 

And though I would have thought and hoped that it would not get used much it has shown up here and there for a while (see for example Ten thousand views of bioinformatics: a bibliome perspective.). 

So here is a question - what exactly is "the totality of biological text corpus"?  And does this thing, whatever it is, need an omics word?

Hat tip to @rdmpage and others for pointing this one out.

Bad omics word of the day: epitehliome epitheliome

The Bad Omics Word of the Day: Epitheliome. Not really much to say. See for example:

The epitheliome: agent-based modelling of the social behaviour of cells. [Biosystems. 2004 Aug-Oct] - PubMed result

Hat tip to Steve Koch on Friendfeed for this.

Bad omics word of the day: nutriome

And the winner is ...

The Bad Omics Word of the Day is "Nutriome".

From: Dietary reference values of individual micronutrients and nutriomes for genome damage prevention: current status and a road map to the future -- Fenech, 10.3945/ajcn.2010.28674D -- American Journal of Clinical Nutrition

From the abstract "strategies to determine dietary reference values of single micronutrients and micronutrient combinations (nutriomes)"

As with my last Bad Omics word, I have no real clue what that means. But it seems this author has been using the term for a while.

Some other papers have defined it more concisely such as "Nutriomic analysis is a postgenomic-based study of nutritious components (nutriome)."

Yuck yuck and double yuck is what I say.


Hat tip to @nutrigenomics and @larry_parnell and @eurogene for pointing this one out. 

Bad omics word of the day: transactome

Hat tip again to Rami Aziz for pointing this out on twitter

The Bad Omics word of the day is "Transactome". Used recently in the following paper: PLoS ONE: Time-Dependent c-Myc Transactomes Mapped by Array-Based Nuclear Run-On Reveal Transcriptional Modules in Human B Cells

From the abstract: "The definition of transcriptional networks through measurements of changes in gene expression profiles and mapping of transcription factor binding sites is limited by the moderate overlap between binding and gene expression changes and the inability to directly measure global nuclear transcription (coined “transactome”)."

I have no real clue what that means.

I confess, going to skip this paper.  So I will not figure out if there is some clearer meaning. But here's a guess - the word is unnecessary.

Bad omics word of the day: N-terminome

Yes indeed. Someone has used N-terminome.

Nature Protocols: System-Wide Proteomic Identification of Protease Cleavage Products by Terminal Amine Isotopic Labeling of Substrates

From the introduction:

"The sequence and nature of all the protein amino-termini (N-termini) within the proteome (the N-terminome) provides valuable functional annotation, since translation start sites, N-terminal isoforms, modifications and truncations determine the cellular localization, activity and fate of most proteins"

Prediction: will not get widespread use.

But they will get an award today: the Bad Omics Word of the Day.

Hat tip to @mglo for this one.

Good words on bad omics words: "A crisis in postgenomic nomenclature" from 2002

Just got pointed to a fun paper from 2002 "A Crisis in Postgenomic Nomenclature by Stanley Fields and Mark Johnston" by Mark Johnston himself. Their paper, in Science, is available for free on Stanley Fields website here. It is actually a hilarious tongue in cheek read where they proceed from arguing for more specificity in omics names (e.g., they go so far as to propose a EC# like system with things such as the "4.7.5.3.8ome" and also that conditions should be specified like the "37°-7.4-G1-Golgi-N-but-not- 63 O-linked glycosylome".  And they end with a proposal to replace the term "the cell" with either the someone or the omesome.  It is definitely worth a read.

Bad omics word of the day: miRNAome

Hat tip to Rami K. Aziz on Twitter for this.

The winner of today's Bad Omics Word of the Day is a paper in PLoS One: PLoS ONE: Characterization of the Melanoma miRNAome by Deep Sequencing

They even slipped the word into the title. I do not think the word was coined by them as I found some older references going back at least to 2005: MicroRNA Gene Expression Deregulation in Human Breast Cancer in Cancer Research.

Given that there were only 847 google hits as of today, the word clearly has not taken off, which is good.  But alas it is still being used, even in titles.  As far as I can tell, what they mean by the term is "All the miRNAs in a particular cancer class" --- unclear to me why that needs an ome.

Bad omics words of the day: modomics and tRNomics

Well, just was browsing through a paper on the non coding RNAs of the model halophile Haloferax volcanii, which I study. The paper BioMed Central | Full text | RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes is quite useful. However, the terminology is icky. They use two omics terms I have never seen before, but I guess should have known were out there: tRNomics (all the tRNAs in an organism, or something like that) and modomics (the pattern of RNA modifications). These are really not needed are they? And since they are both in the same paper, today we are giving out a linked "Bad omics word of the day" award to both of these terms.

Wildhorse Ag Buffer and Burrowing Owls

Just thought I would post some pics here from a walk on the Ag Buffer trail behind WildHorse gold course. Lots of burrowing owls out there these days.

Bad omics word of the day: variome

OK - I am back. I cannot resist. The Bad Omics Word of the Day is Variome. I am not even completely sure what people mean by this, but I guess if you want to know you can go to this meeting: 3rd HVP Meeting � Paris

On the web site the seem to define this project as an attempt to "collect variation causing disease (mutations) in all genes world wide" so I guess that is what variome means to them. So - I wonder here - what is wrong with "polymorphisms"??????

HT to @ivanoransky and @boraz for pointing this out to me (by feeding my other people's tweets).

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:

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

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.

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.

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.

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:

• Is there a “religionome” and can it be mapped?
• Always put one in the brain « The Immanent Frame
• brain - Business & Financial News, Breaking US & International ...

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.

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.

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:

• Omes_and_Omics
• Omes Table, Gerstein Lab
• The best place is "Alphabetically ordered list of omes and omic words" at omics.org

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

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):

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.

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.

Bay Area Biosystematists Meeting: w/ Quenton Wheeler - Feb 9

Announcement below:

Bay Area Biosystematists Meeting: Tuesday, 9 February, 2010

at UC Berkeley, 2063 Valley Life Sciences Bldg.

"Biodiversity Discovery"

Featuring Quentin Wheeler from Arizona State University
Plus contributions from additional panel discussants TBA

Quentin Wheeler is a well-known insect systematist interested in biodiversity discovery, phylogenetics, and species concepts. He is University Vice President and Dean of the College of Liberal Arts and Sciences at Arizona State University. He was also one of the founders of the International Institute for Species Exploration at ASU (http://species.asu.edu/index), producers of the great You Tube video "Planet Bob" (http://www.planetbob.asu.edu/index.html), which uses humor to focus attention on biodiversity and taxonomy (and won a 2008 Webby Award).

Schedule and venue:
5:30 - social gathering with beverages and informal pizza dinner:
cost ca. $10, to be collected at door, 2063 Valley Life Sciences Bldg.,
UC Berkeley campus.
7:00 - talk followed by discussion, in same room.

Reservations required for beverages and dinner (but not the talk). Please email reservations to your host, Brent Mishler by Sunday, Feb. 7th

For a map of campus and view of VLSB, use the link below.
http://www.berkeley.edu/map/maps/ABCD123.html

All are welcome, members or not. If you want to join the Biosystematists, a venerable yet exceptionally lively group that provides the only inter-institutional seminar/discussion forum addressing evolutionary topics in the Bay Area, sign up for the mailing list at: https://calmail.berkeley.edu/manage/list/listinfo/babs-l@lists.berkeley.edu

Bad omics word of the day: connectome

Well, I have decided that I need to look beyond just new omic words to snark about here (I have been giving a "Worst New Omics Word Award" every once in a while"). So I am now going to post, as often as I can, a little ditty about any bad omics word that is out there. Yesterday's winner was "phenogenomics" which I posted only to twitter.

Today's winner is "connectome" (see for example NIH Launches the Human Connectome Project to Unravel the Brain's Connections, July 15, 2009 News Release - National Institutes of Health (NIH)). I think it's first major use was here but not sure. It even has a wikipedia entry which says:

A connectome is a detailed map of the full set of neurons and synapses within the nervous system of an organism. The production and study of such a map is known as connectomics.

Now I am not the first to be a bit annoyed by this word (e.g., see the Neurochannels blog post "Review of Seung's talk at SFN":

Incidentally, 'connectomics' is a cheesy mouthful of a word. Some words just weren't meant to be biologized with the -omics suffix, and 'connect' is one of them. 'Genomics,' cool. 'Proteomics,' a little annoying and not very creative. 'Connectomics,' stop the bus I want to get off. At the very least let's reserve the -omics for molecular biology. Thank goodness Bialek didn't try to pull us into the world of 'infomics.

Hat tip to Karl Broman for pointing this one out in comments here.

As with posts about other omes and omics words, I am not saying anything really at all about the science behind the word here. Just the word.

Wanted:Feedback on Importance of Finishing (Microbial) Genomes

To all

I am writing because I am working on a project to evaluate the importance of finishing microbial genomes. I know there has been lots of talk about this out there on the web and in papers, etc but I think a fresh discussion is useful. To get people up to speed below is a summary of the issue as I see it.

1. Shotgun sequencing: Genome sequencing relies generally on the shotgun method at the beginning of a project where DNA fragments from an organism of interest are sequenced in a highly random manner.
2. Assembly: After shotgun sequencing, the genome is assembled as best as possible into larger pieces (called contigs) and ordered sets of contigs (called scaffolds). All of this put together can be called an "assembly"
3. Gaps: After the assembly phase, there are almost always gaps in the assembly. These generally come in two forms:
• sequencing gaps (where we know two contigs go together in some orientation but where we do not know the sequence of the DNA in between the contigs)
• physical gaps (where we have sets of scaffolds but do not know how the connect to each other).
4. Quality: After the assembly phase, different components of the assembly can have different "qualities" where from example, some sections are somewhat ambiguous and others are highly reliable
5. Finishing: Using any combination of laboratory, computational and other analyses one can both fill in gaps in the assembly and improve the quality of the assembly. This can generally be called "finishing"
6. Quality of final product: Depending on the end quality of the assembly we could assign it to one of a few categories of "completeness" as outlined in a paper by Patrick Chain et al. In essence, you can consider the post to be a follow up to their paper and their work.
   

We plan to try to measure what one gains by the finishing steps. We need to know this because we would like to make intelligent decisions about how to allocate resources. If one gains a lot from finishing then it would make sense to allocate significant resources to it. I note, I and some colleagues wrote a paper about this issue "The value of complete microbial genome sequencing (You get what you pay for)" that was published in 2002. This is without a doubt not the only discussion of the topic but I just wanted to point out I have been involved in this debate before. Despite that, I think we simply do not know right now what the benefits might be in the new sequencing landscape.

------------------------------------------

So the question I am asking here is:

What do people think are the potential benefits that could come from finishing?

------------------------------------------

Here are some possible answers to get the discussion going:

1. Gene discovery (e.g., there may be interesting/important genes in missing/low quality data)
2. Esthetics of completeness (as in, it just feels better to have a finished genome)
3. Improved analysis of genome organization (in particular from having contigs oriented correctly)

Also - I note there has been some discussion of this for animals, plants etc (e.g., see recent paper by Eric Green and others on vertebrates) Many of the issues are similar but they are different enough that I think a microbe focused discussion is useful.

Other links of interest:

• Discussion on Friendfeed to question from Michael Barton
• LANL finishing in the future meeting
• Scivee talks from 2009 LANL meeting

Blakesley, R., Hansen, N., Gupta, J., McDowell, J., Maskeri, B., Barnabas, B., Brooks, S., Coleman, H., Haghighi, P., Ho, S., Schandler, K., Stantripop, S., Vogt, J., Thomas, P., Comparative Sequencing Program, N., Bouffard, G., & Green, E. (2010). Effort required to finish shotgun-generated genome sequences differs significantly among vertebrates BMC Genomics, 11 (1) DOI: 10.1186/1471-2164-11-21

Fraser, C., Eisen, J., Nelson, K., Paulsen, I., & Salzberg, S. (2002). The Value of Complete Microbial Genome Sequencing (You Get What You Pay For) Journal of Bacteriology, 184 (23), 6403-6405 DOI: 10.1128/JB.184.23.6403-6405.2002

Chain, P., & et al. (2009). Genome Project Standards in a New Era of Sequencing Science, 326 (5950), 236-237 DOI: 10.1126/science.1180614

Friendfeed discussion of this post:

Cool paper, & winner of "worst new omics word award": Predatosome

And the bad new omics words keep streaming in. Today's winner of the "Worst New Omics Word Award" is going to Carey Lambert, Chien-Yi Chang, Michael J. Capeness and R. Elizabeth Sockett from Nottingham for their use/ invention of "Predatosome". They use this term in the title of their new PLoS One paper: The First Bite— Profiling the Predatosome in the Bacterial Pathogen Bdellovibrio. Here is the very long sentence where the define it:

The gene products required for the initial invasive predatory processes have not been extensively studied but the genome sequencing of B. bacteriovorus HD100 [1] revealed a genome of 3.85Mb, including a core genome similar to that of non-predatory bacteria and some 40% of the genome comprising a potential predicted “predatosome” of genes, encoding both hydrolytic products that may be employed in prey degradation, and genes that may be required specifically for host predation and thus are not conserved across the Proteobacteria.

The paper is actually quite interesting. They use genomic approaches to characterize a fascinating organism - the bacterial species Bdellovibrio bacteriovorus. This bug is a predatory organism - eating other bacteria. Since it eats them from the inside out, some, including these authors, refer to this organism as a pathogen of other bacteria and their is some discussion here and elsewhere for its potential to serve as a "living antibiotic" in much the same way people are trying to use bacterial viruses (a.k.a. phage).

The paper overall is quite nice on first read. They used microarray studies to characterize gene expression patterns in different phases of the life cycle (see Figure above for the life cycle outline). They backed up this work by quantitative PCR studies and regular RT PCR. And based upon their analysis they found some genes that are "Up-Regulated in Predatory, but Not HI" phase (HI stands for host-independent). And here is where they really tell us what they mean by predatosome:

This category of 240 genes are very interesting as they potentially exclude those genes simply involved with release from attack-phase into growth, namely they should be part of the “predatosome” of predatorily specific genes.

It seems to me this terminology is completely unnecessary. All they need to do is say they are studying the genes related to the predatory phase. To assign these genes to the "predatosome" is a bit much. They continue in the paper to report some really interesting stuff. For example, they also examine another predatory bacterial species, and look at whether there are genes conserved in the process between species. They made some really nice figures by the way about the different phases of hte life cycle in this organism and which genes are expressed:

Anyway - the science in the paper is nice. However, the invention of yet another omics word is a bit much. And thus Lambert et al. are winners of the highly coveted "Worst New Omics Word Award" for their invention of "predatosome". Details on the paper are below - and that is where the figures come from too. (Hat tip to Bora for letting me know about the paper, and the word).

Lambert, C., Chang, C., Capeness, M., & Sockett, R. (2010). The First Bite— Profiling the Predatosome in the Bacterial Pathogen Bdellovibrio PLoS ONE, 5 (1) DOI: 10.1371/journal.pone.0008599

Friendfeed comments below:

ISI - late to index #PLoS One but now marketing that they do so

Well, just a mini post here. In case you did not know - PLoS One is now being indexed by ISI (see their announcement: PLoS ONE and see the PLOS blog post here
and see Erik Svensson's blog post for an interesting take) and will get an impact factor and be in their Citation Index and all such things. Now mind you, I think "Impact Factor" is a silly thing overall in that we should evaluate papers not journals per se.

So why am I writing this - because I find it pretty funny that despite being slow to recognize PLoS One ISI is now promoting the fact that they are indexing PLoS One on their home page. See the screen capture above.

GlaxoSmithKline opening up malaria data a wee bit, but more needed

Robert Langreth in an article at Forbes.Com on January 20 (GlaxoSmithkline's Malaria Plan: Limit Profits, Open Labs) reports that Glaxo Smith Kline is becoming a bit more open with their data on malaria drug/vaccine development.  Apparently, they plan to open up their labs and some of their data to non profit collaborators such as Emory University.  Sounds like this could be a good first step.  But if they really want to advance malaria vaccine research, perhaps they should release their data to everyone? I get that they want/need to make a profit, but if they want to try and get credit for being open, I think they really should jump into the deep end and do something radical.  Just sharing bits and pieces of data with a few labs is not a particularly stunning move.