Friday, September 28, 2012

Some arguments for why Carl Woese (and probably Norm Pace) deserves a Nobel Prize

Compiling posts and articles discussing why Carl Woese deserves a Nobel Prize.  Will be writing a new article on this but felt like I should share the articles in case I don't get done in time

I note I do not think Woese should win a Nobel for discovering the archaea.  That was a groundbreaking finding but it does not fit well with the Nobel Prize categories.  I think he should win it for the concept of molecular classification of microorganisms and applying this in general to the microbial world around us.  This concept (expanded by Norm Pace and colleagues to uncultured microbes) revolutionized our approach to studying single microbes in the environment, to studying single microbes infecting people and to studying communities of microbes in and on people.  And thus Woese and Pace in my opinion deserve the Nobel Prize for Medicine.  I will be expanding on this in a future post ...

Thursday, September 27, 2012

American Chemical Society not winning any blogging friends these days

Wow - just got an email from a colleague with details on a scientific publishing saga.  Here is the summary:

Stage 1: Jenica Rogers wrote a blog post expressing a bit of frustration with the American Chemical Society and their publishing system: Walking away from the American Chemical Society

Stage 2: The Chronicle for Higher Education wrote a story about it: As Chemistry Journals' Prices Rise, A Librarian Just Says No

Stage 3: The Director of Public Affairs for the ACS responded to questions and was quoted with the following
“We find little constructive dialogue can be had on blogs and other listservs where logic, balance and common courtesy are not practiced and observed,” Glenn S. Ruskin, the group’s director of public affairs, said in an e-mail message. “As a matter of practice, ACS finds that direct engagement via telephone or face-to-face with individuals expressing concern over pricing or other related matters is the most productive means to finding common ground and resolution."
Then he attempted to clarify some details of the quote in that he claimed that the following got left off the end of the quote "Therefore, we will not be offering any response  to this blog posting or the conversation that has ensued." but when doing this he got a bit personal and nasty:
The individual responsible for the above cited blog certainly has the right to her opinion, but that does not excuse rude behavior or her use of profanity and vulgarity in addressing ACS or its employees. While not evident in the most recent postings, I won’t repeat what she has posted in the past.  But I think you would agree that vulgarity and profanity postings do not lend themselves to meaningful, productive and civil discourse, thus our decision not to engage any further with her on this topic
And the discussion continued on various blogs like Chembark.  The most disturbing part to me of the whole thing is that it is hard to find anything particularly extremely vulgar in writings by Jenica Rogers (I note - I only googled around for a minute or so so I may have missed things but Walk Walt at Random has more detail on this and also did not find any serious vulgarity).  Generally I find the response of ACS to be extremely distasteful.  They don't like what she wrote.  So they go after her character.  Brilliant.

For other takes on this story see

Headline says it all "Opera singer grows algae on her face by feeding it w/ her breath & then the audience eats it"

Wow.  I am always on the lookout for microbe-themed art.  In most cases, when I see such art, I think "wow - that is an interesting way of embedding microbes into a traditional form of art".  You know - painting with microbes or art with microbes in it or such.  Well, in this new case I can say this is the most unusual and most creative use of microbes in art I have ever seen: Opera singer grows algae on her face by feeding it with her breath and then the audience eats it

You see, an opera singer work a "head-mounted, face-clinging device" which contained within in some algae in water.  And then the algae was fed by the opera singer's breath.  This is part of something called the "Algae Opera".  The most amazing part of this is described in the io9 article
"Because the algae's growth is dependant on the amount of CO2 it receives, the singer controlled her pitch and volume to alter various characteristics of the algae, including taste (what they called "sonic enhancement"). Depending on the way she sang, the different pitches and frequencies could make the food taste either bitter or sweet"
And then at the end of the performances the audience was invited to sample some of the algae. Yum.  Certainly a bit weird.  But kudos on the creativity index.

Wednesday, September 26, 2012

Diabetes and the microbiome - some hype and some caution - in the same stories

A new paper is getting some press on a link between type II diabetes and the microbiome.  The paper is here.  The abstract of the paper reads:
Assessment and characterization of gut microbiota has become a major research area in human disease, including type 2 diabetes, the most prevalent endocrine disease worldwide. To carry out analysis on gut microbial content in patients with type 2 diabetes, we developed a protocol for a metagenome-wide association study (MGWAS) and undertook a two-stage MGWAS based on deep shotgun sequencing of the gut microbial DNA from 345 Chinese individuals. We identified and validated approximately 60,000 type-2-diabetes-associated markers and established the concept of a metagenomic linkage group, enabling taxonomic species-level analyses. MGWAS analysis showed that patients with type 2 diabetes were characterized by a moderate degree of gut microbial dysbiosis, a decrease in the abundance of some universal butyrate-producing bacteria and an increase in various opportunistic pathogens, as well as an enrichment of other microbial functions conferring sulphate reduction and oxidative stress resistance. An analysis of 23 additional individuals demonstrated that these gut microbial markers might be useful for classifying type 2 diabetes.
Seems pretty reasonable.  All they say there is that they found associations between bacteria and diabetes.  That is interesting but they do not seem to present any evidence about a causal connection.  Perhaps people who get type II diabetes end up then having their microbiome shift.  Perhaps a shift in the microbiome causes type II diabetes.  Or perhaps something else (e.g., excessive inflammation) causes both type II diabetes and microbiome shifts.  Who knows.

But alas a bit of hype crept into some of the the news stories.  And it seems that the scientists behind the study are responsible for some of this hype.  For example, consider the article Changes in Intestinal Bacteria Linked to Type 2 Diabetes - US News and World Report.  One quote is a bit much for me:
"I think our study provides many targets for disease prevention and treatment through gut microbiotia in the near future," said study senior author Jun Wang, executive director of the Beijing Genomics Institute in Shenzhen, China.
Fortunately the reporter who wrote this story does a very good job of providing cautious interpretations.  See for example:
"There's no way right now that you can say there's a cause-and-effect relationship. It could be that the patients with diabetes were treated with drugs that changed their gut flora. Or maybe they ate differently? This is an interesting hypothesis -- that gut bugs could influence diseases states -- but it's far from proven," said Dr. Stuart Weinerman, associate chief of the division of endocrinology at North Shore University Hospital/Long Island Jewish Medical Center in New Hyde Park, N.Y.
Also see stories like Gut bacteria could cause diabetes from Science Codex.  The title alone makes me want to cry.  Some quotes as well as discussion in that article also seem, well, not cautious enough.
The research, which was recently published in the scientific journal Nature, also demonstrated that people with type 2 diabetes have a more hostile bacterial environment in their intestines, which can increase resistance to different medicines.
Definitely not buying this "hostile" environment claim.  Fortunately as with the US News story, there is some caution presented
"It is important to point out that our discovery demonstrates a correlation. The big question now is whether the changes in gut bacteria can affect the development of type 2 diabetes or whether the changes simply reflect that the person is suffering from type 2 diabetes."
 So - the stories seem to actually be doing an OK job with the correlation vs. causation issue I have complained about many times.  And though some of the scientists may be pushing a bit of overinterpretation the reporters and even the press releases have some decent cautionary statements.

Fecal transplants in the news

CNN has a story on a fecal transplant case: Little-known fecal transplant cures woman's bacterial infection -  It is worth a look and if you want to laugh (sometimes in pain, sometimes for jokes) read the comments. Some other recent stories on this topic include
And the CNN story got picked up by Reddit
As many know - I have been talking / writing about such treatments a bit recently.  I discussed it in my Tedmed talk (which is now on Ted).

And I have a blog post with background and links on the topic.

Monday, September 24, 2012

Eisen Lab Paper.Li Magazine

Playing around with Paper.Li. Took feeds from the blogs and Twitter profiles of people in my lab. Seems to come out OK ...

Saturday, September 22, 2012

Lake Arrowhead Microbial Genomes Meeting 2012 Speaker Gender Ratio #LAMG12

Got some questions about the Lake Arrowhead Microbial Genomes 2012 Meeting in regard to gender ratio of speakers and organizers, after I have been complaining about ratio at other meetings.  Here is the full list of speakers and organizers for this meeting.  Women in bold.

  1. Jeffrey H. Miller
  2. Jonathan Eisen
  3. Ashlee Earl
  4. Lisa Raleigh
So the organizers are a 50-50 split.

Speakers (in order)
  1. Jonathan Eisen
  2. Nina R. Salama
  3. Frederic Bushman
  4. Kristine Wylie
  5. Janet K. Jansson
  6. Forrest Rohwer
  7. Curtis Huttenhower
  8. Tanja Woyke
  9. Maomeng Tong
  10. Jeffrey Cox
  11. Susannah Tringe
  12. Julian Parkhill
  13. Rustem F. Ismagilov
  14. Gautam Dantas
  15. Pamela Yeh
  16. Mike Gilmore
  17. Lance B. Price
  18. James Meadow
  19. Jason E. Stajich
  20. Laura Sauder
  21. Tara Schwartz
  22. Susanna Remold
  23. Bernhard Palsson
  24. Anca Segall
  25. Trent Northern
  26. Rick Morgan
  27. Beth Shank
  28. Morgan Langille (added)
  29. Anthony Fodor (added)
  30. Peter Karp
  31. Tatiana Tatusova
  32. Timothy Harkins
  33. Katrine Whiteson
  34. Mallory Embree
  35. Varum Mazumdar
  36. Abigail McGuire
  37. Ee-Been Goh
  38. Shota Atsumi
  39. Howard Xu

So 37 39 speakers, 16 of which are women.  So that comes to 43.2 41%.

Storify for Lake Arrowhead Microbial Genomes #LAMG12 Meeting

Meeting went well.  Here is a storification of it:

Friday, September 21, 2012

Google Scholar has search by date option - a good thing

Woohoo.  Just discovered a cool (I think new) thing.  Was looking for a link to a new publication of mine.  And I searched Google Scholar

That gets my publications but they are sorted by citation number which alas does not pull up new publications.  So I went to click on the "Since 2012" button I usually click on

And I noticed something I have not noticed before (and that I think must be pretty new):

Woohoo - a full sort by date option.  And so I clicked it and indeed it did work.

This will make Google Scholar much more useful for certain purposes.  This - along with other new features such as the Google Scholar "Updates" system is giving me hope that Google will continue to expand the tools/features of Google Scholar.

Fun science art example: Jennifer Welsh on Zachary Copfer glowing microbe drawings

Microbiology art pops up again.  This time in this story from Jennifer Welsh: Galaxies And Faces Drawn With Glowing Bacteria - Business Insider .  For more see the artist Zachary Copfer's website here:  Other stories about Copfer are popping up too - not sure if their is some publicity blitz going on or not but see below for examples:

ut whatever is going on the art is worth checking out.

Wednesday, September 19, 2012

Upcoming on phyloseminar "Inferring macroevolutionary processes based on phylogenetic trees"

See home for more detail.
Next talk
Inferring macroevolutionary processes based on phylogenetic trees"
Tanja Gernhard Stadler (ETH Zurich)

Phylogenetic trees of present-day species allow inference of the rate of speciation and extinction which led to the present-day diversity. Classically, inference methods assume a constant rate of diversification, or neglect extinction. I will discuss major limitations of this null model and will present a new framework which allows speciation and extinction rates to change through time (environmental-dependent diversification), with the number of species (density-dependent diversification), and with a trait of a species (trait-dependent diversification). For the latter model, particular focus is given to the trait being the age of a species. Issues arising in empirical data analysis, such as incomplete taxon sampling, model selection, and confidence interval estimation, will be discussed. The methods reveal interesting macroevolutionary dynamics for mammals, birds and ants, and can easily be applied to other datasets using the R packages TreePar and TreeSim available on CRAN.

West Coast USA: 10:00 (10:00 AM) on Wednesday, September 19
East Coast USA: 13:00 (01:00 PM) on Wednesday, September 19
UK: 18:00 (06:00 PM) on Wednesday, September 19
France: 19:00 (07:00 PM) on Wednesday, September 19
Japan: 02:00 (02:00 AM) on Thursday, September 20
New Zealand: 05:00 (05:00 AM) on Thursday, September 20

Monday, September 17, 2012

The best writing in science papers part 1: Vladimir Nabokov in Notes on Neotropical Plebejinae (Lycaenidae, Lepidoptera)

I have been wanting to start a new series here on my blog about examples of great writing in scientific publications.  There is a lot out there on great science writing.  But that is not what I am writing about here.  I mean actual scientific research papers where the writing itself is exceptional.  And todays example, which may be a bit unfair, comes from the one and only Vladimir Nabokov.  For not only was he a great writer of literature, he was also a lepidopterist.  He was for some time the curator of leps at the Harvard Museum of Comparative Zoology.

I note - I first discovered this when I got a work-study job shelving books at a library at Harvard only to discover that that library had on display a collection of Nabokov's butterflies.  I got little shelving done when nobody else was around).

Anyway, I had read some of his short stories and book in high school but was not aware of his butterfly obsessions.  What amazed me most was they had some of his butterfly research papers on display too and they were simply amazing to read.  The writing in them is just awesome.

So thus we get to todays's example of great writing in science papers: Notes on Neotropical Plebejinae (Lycaenidae, Lepidoptera).  Thankfully, somehow, Hindawi publishers have come into possessing of the rights to the back issues of the journal Psyche where this was published and it is freely available as a PDF.  The paper is not perfect mind you - some parts are written more eloquently than others.  But there are sparks in there of what I think are wonderful (for a science research papers).  Some of my favorite parts are quoted below:
The results proved so unexpected and interesting that it seems worth while to publish the present paper despite its rather superficial and incomplete nature.

In a way the initial blunder was Swinhoe’s who while correctly giving a subfamilial ending to the group which Tutt’s intuition and Chapman’s science had recognized ("tribe" Plebeidi which exactly corresponds to the Plebefine of Sternpffer) as different from other "tribes" (i.e., subfamilies) within the Lyccenidce, failed to live up to the generic diagnoses which he simply copied from Chapman’s notes in Tutt and tried to combine genitalic data he had not verified or did not under- stand with the obsolete "naked v. hairy eyes" system (which at Butler’s hands had resulted in probably the most ludicrous assembly of species ever concocted, see for example Butler 1900, Entom. 33: 124), so that in the case of several Indian forms which Chapman had not diagnosed, Swinhoe placed intra-
generically allied species in different subfamilies and species belonging to different Tuttian "tribes" in the same subfamily. [[ YES - THIS IS ONE SENTENCE]]
The arrangement proposed in the present paper needs to be prefaced by a few words on taxonomic units. The strictly biological meaning forcibly attached by some modern zoologists to the specific concept has crippled the latter by removing the morphological moment to a secondary or still more negligible position, while employing terms, e.g., "potential interbreeding," that might make sense only if an initial morphological approach were presupposed. 
I am sure there are other Nabokov papers with other choice sections ... will be looking for those later.  If anyone has suggestions for other great writing in science papers, please post comments ..

Friday, September 14, 2012

A must read for those interested in "Spin" of science by press releases & in papers

A new paper in PLoS Medicine is of great interest to me: PLOS Medicine: Misrepresentation of Randomized Controlled Trials in Press Releases and News Coverage: A Cohort Study.  Bad press releases drive me crazy.  And it has been shown that press releases can frequently be a source of scientific misinformation in the press.  Interestingly this paper concludes that spin in the papers themselves is correlated to spin in press releases ... So in other words, the scientists are partly to blame ... Not shocking but interesting ...

Thursday, September 13, 2012

Quick post: nice #openaccess review: Insights from Genomics into Bacterial Pathogen Populations

Just a quick post here.  There is a new review/commentary that may be of interest: PLOS Pathogens: Insights from Genomics into Bacterial Pathogen Populations.  By Daniel Wilson from the Wellcome Trust Centre at Oxford.

Full citation: Wilson DJ (2012) Insights from Genomics into Bacterial Pathogen Populations. PLoS Pathog 8(9): e1002874. doi:10.1371/journal.ppat.1002874

It is a nice and useful review ...

Some quick comments on "Giant viruses coexisted w/ the cellular ancestors & represent a distinct supergroup"

Got asked on Twitter about this paper:

BMC Evolutionary Biology | Abstract | Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya

I answered briefly
Don't have time for a detailed blog post but here are some quick comments:

1. Giant viruses are fascinating and cool

2. I have done work connected to the topic of this paper and thus might not be considered fully objective.  For example see

3. I see no evidence that the type of analysis that they do on protein folds is a robust phylogenetic method.  Phylogeny from sequence alignments (which is what we focus on in my lab) have been tested and tweaked for some 50 years.  There are 100s to maybe 1000s of papers on methods alone - not to mention the 1000s of papers using alignments for phylogenetics.  I am not convinced that the analysis being done here of FFs and FSFs is particularly robust.  It seems interesting, certainly.  But is it sound?  I mean, I could build phylogenetic trees from cell size, from shape, from eye color, and from all sorts of other features.  Those would all suck for certain.  Protein folds - not sure about them.  They almost certainly are prone to convergent evolution and I do not see any attempt in this analysis to deal with that issue.

4. The authors of the current paper do not show any taxa names on their trees - just colors for large groups of taxa (bacteria, archaea, eukaryotes and viruses).  It is really not good practice to remove the taxon names.  If they were there the first thing I would do is to look at the patterns within the groups they highlight.  Do all the major phyla / kingdoms of eukaryotes, for example, come out looking as one would expect based upon other studies.  Or are they all over the place?  Same for bacteria and archaea.  Not including taxa makes it nearly impossible to judge this paper positively.  I could not find this information in supplemental data either.

5. They really should have released the data tables they used for the phylogenetic analysis.  Don't know why they did not.

6. In Figure 3 with the rooting they have, either viruses are a subgroup of archaea or archaea are not monophyletic.  Not a good thing in a paper trying to claim viruses represent a fourth grouping on the tree of life.

Anyway - got to do some other things but just wanted to get some comments out there.

UPDATE 9/19 - some prior stories about the "fourth domain" and ancient viruses - to counter notion in the press release for this paper that their findings "shake up the tree of life".  Even if their specific inferences about viral evolution are correct, such inferences / conclusions have been made before.

Wednesday, September 12, 2012

NASA personnel ignore planetary protection guidelines and risk putting microbes on Mars

Many years ago I served on a NASA sponsored committee for a series of meetings about the handling of samples collected from Mars.  One of the key points of discussion at those meetings was "planetary protection".  The involved protecting Earth from possibly strange life forms that in theory could exist on Mars.  And it also involved protecting Mars from microbes and other life forms that could come from space ships/landers.  I even posted all the materials from these meetings a few weeks ago: Notes and materials from MARS Sample Handling Workshops 2000 ....

It is thus with great distress that I read an LA Times article that reveals that some of the people involved in launching Curiosity decided to ignore some of the planetary protection guidelines and made some hands on modifications that may have contaminated some of the drill bits on Curiosity with microbes from people.  See: If the Mars rover finds water, it could be H2 ... uh oh! -

The LA Times reports that some NASA personnel opened a box of drill bits that had been sterilized and - in clean but not sterile conditions - installed one of these drill bits in a drill on Curiosity prior to launch.  Apparently they were worried that a rough landing could prevent the bits from being installable in the drill which would make the drill not be of any use.  And they appear to have now risked the sterility of the entire operation by doing this.  Well crap.  That just plain sucks.  So much effort by "planetary protection officers" and others.  That effort might all go down the drain because of this.  I get that some times things seem urgent and that sure - if the drill was useless people would be pretty upset too.  But this seems to me to be a serious error in judgement.

In a small way I helped develop the guidelines that were put in place to protect Mars from human induced contamination.  And now that seems to have been a wasted effort as the guidelines were ignored.  Not good.

Note - for those interested I have posted links below to the documents from my days at the NASA Mars Sample Handling Workshops.  Most/all are public domain materials but not all are easy to find so I thought I would post them here.  Note – I have done no clean up of scans – will do so at some point. Enjoy

UPDATE 9/13 - some more stories on this
UPDATE 2: 9/13 - UC Davis Prof. Dawn Sumner (who is involved with the Curiosity mission) disputes notion that opening the drill bit box is an issue

Tuesday, September 11, 2012

Q-Bio conference in Hawaii, bring your surfboard & your Y chromosome b/c they don't take a XX

Wow.  Just wow.  And not in a good way.  Just got an email invitation to a meeting.  The meeting is
"THE FIRST ANNUAL WINTER Q-BIO MEETING: Quantitative Biology on the Hawaiian Islands. February 18-21, 2013."  
Well, I mean - who wouldn't want to go to Hawaii for a meeting.  And a meeting that 
"brings together scientists and engineers who are interested in all areas of q-bio."  
"Each year, the meeting will rotate on the Hawaiian Islands with a different thematic focus within q-bio."
So I could go to Hawaii each year.  Cool.  And 
"The focus for the meeting this year will be Synthetic Biology, with about half of the invited speakers chosen as renowned experts in this area."  
I like synthetic biology and, well, sometimes I like experts, so still good

But then, OMG, then, the confirmed speaker list and the conference organizers.
  1. Jim Collins, Boston University
  2. Johan Elf, Uppsala University
  3. Michael Elowitz, California Institute of Technology
  4. Timothy Elston, UNC Chapel Hill School of Medicine
  5. James E. Ferrell, Stanford University 
  6. Martin Fussenegger, ETH Zurich
  7. Leon Glass, McGill University
  8. Terry Hwa, University of California, San Diego
  9. Roy Kishony, Harvard Medical School
  10. Galit Lahav, Harvard University
  11. Andre Levchenko, Johns Hopkins University
  12. Wendell Lim, University of California, San Francisco
  13. Andy Oates, The Max Planck Institute, Dresden
  14. Bernhard Palsson, University of California, San Diego
  15. Gurol Suel, UT Southwestern Medical Center
  16. Chao Tang, Peking University
  17. John Tyson, Virginia Tech
  18. Craig Venter, The J. Craig Venter Institute
  19. Chris Voigt, Massachusetts Institute of Technology
  20. Ned S. Wingreen, Princeton University  
  1. Bill Ditto, University of Hawaii 
  2. Jeff Hasty, UC San Diego 
  3. Bill Hlavacek, University of New Mexico
  4. Alex Hoffmann, UC San Diego
  5. Brian Munsky, New Mexico Consortium 
  6. Lev Tsimring, UC San Diego 
That is a 25:1 ratio.  Pathetic.  Embarrassing.  The sponsors - UC San Diego's Division of Biological Sciences and BioCircuits Institute, San Diego Center for Systems Biology, the University of Hawaii and the Office of Naval Research - should all be ashamed.

For other posts on this topic see

UPDATE - I have now submitted an abstract to the meeting.  The abstract I submitted is available here and posted below

The probability of having one out of twenty six participants at a scientific meeting be female

A quantitative analysis of gender bias in quantitative biology meetings 
Jonathan A. Eisen
University of California, Davis

(Note - new title suggested by John Hogenesch)

Scientific conferences have key participants which I define to be the speakers and the organizers. Such key participants can be divided into two main classes based on gender: male and female, which I denote here as M and F, respectively (I realize there are other gender classes and I regretfully am not including them here). The number of key participants (which I denote as KP) for conferences varies significantly. For this analysis I focused on meetings with KP = 26. This value was selected for multiple reasons, including (a) that it is the number of letters in the English alphabet (b) that its factors include the number 13 which I like, and (3) because in email announcements for this meeting KP= 26. I sought to answer a relatively simple question - what is the probability that, for a meeting with KP=26, that F = 1. I chose this because this seemed extreme and because F=1 in the email announcements for this meeting. Using the probability mass distribution formula as below:

which becomes

n = NP = number of participants
k = f = the number that are female
p = percentage of f in population being sampled

I have calculated Pr (F=1) for KP = 26. Assuming for the moment that p = 0.5 (i.e., that the population to be sampled is 50:50 male vs female) then Pr (F=1) = 3.8743E-07. This is highly unlikely by chance alone. However the assumption of p = 0.5 is certainly off in some fields. I therefore calculated P (F=1) for different frequencies of F in the population (i.e., what is the expected ratio of females to sample from).

Thus for a meeting with NP = 26, only when the frequency of F is ~0.16 does P (F=1) exceed 0.05. So a question is then, what should we use for p for this meeting? An informal survey (John Hogenesch, posted to Facebook at ) suggests that in qBio the percentage is about 20%. However that may not be an ideal estimate since this meeting is specifically about synthetic biology, I do not have a any estimate of p for this field. However, examination of key meetings in the field (e.g., see for a list) reveals a percentage of perhaps a bit higher. For example at SB5 the ratio was about 35%. I conclude that it is likely that p > 20% in Synthetic Biology. Given that for p = 0.2 the Pr (F=1) < 0.05 I therefore conclude that the null hypothesis (that having one female out of 26 key participants) can be rejected - and that this meeting has a biased ratio of males: females.

UPDATE 2: Here is the full email I received, just for the record


Quantitative Biology on the Hawaiian Islands
February 18-21, 2013

The Winter q-bio meeting brings together scientists and engineers who are interested in all areas of q-bio. Each year, the meeting will rotate on the Hawaiian Islands with a different thematic focus within q-bio. The focus for the meeting this year will be Synthetic Biology, with about half of the invited speakers chosen as renowned experts in this area.

SPONSORED BY:UC San Diego's Division of Biological Sciences and BioCircuits Institute
San Diego Center for Systems Biology
University of Hawaii
Office of Naval Research

Jim Collins, Boston University
Johan Elf, Uppsala University
Michael Elowitz, California Institute of Technology
Timothy Elston, UNC Chapel Hill School of Medicine
James E. Ferrell, Stanford University
Martin Fussenegger, ETH Zurich
Leon Glass, McGill University
Terry Hwa, University of California, San Diego
Roy Kishony, Harvard Medical School
Galit Lahav, Harvard University
Andre Levchenko, Johns Hopkins University
Wendell Lim, University of California, San Francisco
Andy Oates, The Max Planck Institute, Dresden
Bernhard Palsson, University of California, San Diego
Gurol Suel, UT Southwestern Medical Center
Chao Tang, Peking University
John Tyson, Virginia Tech
Craig Venter, The J. Craig Venter Institute
Chris Voigt, Massachusetts Institute of Technology
Ned S. Wingreen, Princeton University

Bill Ditto, University of Hawaii
Jeff Hasty, UC San Diego
Bill Hlavacek, University of New Mexico
Alex Hoffmann, UC San Diego
Brian Munsky, New Mexico Consortium
Lev Tsimring, UC San Diego

Registration fee covers conference venue, opening reception, banquet, coffee & snacks.

EARLY BIRD ($450.00) REGISTRATION DEADLINE: December 1, 2012


HOTEL: A block of rooms have been reserved for registered conference participants available for a negotiated rate of $199 per night at the Hilton Hawaiian Village in Waikiki. The rooms are available on first come first serve basis and will be available soon, so book early!

CONTRIBUTED TALKS: If you wish to present your work at the conference, either as an oral talk or a poster, you must submit an abstract through the conference website by the September 15th deadline. Abstract guidelines and submission information at:

ABSTRACT DEADLINE: September 15, 2012
Accepted abstracts will be announced October 31, 2012.

We encourage you to forward this message to any colleagues that may be interested in taking part in this exciting event.

Questions should be emailed to:

UPDATE 4:  (9/18/12)

Plus some links that may be of relevance

UPDATE 6: 9/23/12

Some more links on the recent PNAS paper on gender bias and evaluating scientists

UPDATE 7:  9/23/12

Interesting article on gender and invitations to write major reviews

UPDATE 8: More follow up to the Gender Bias study from PNAS 9/26

UPDATE 9: Other posts on gender bias of interest

UPDATE 10: 11/21/13

Just got this in my email.  Kudos to the people behind qBio for adding more women to their planning committee and adding a many women to the speaker list.


UPDATE:  In response to participant interest, the submission deadline has been extended to December 2, 2013.  This year 15 contributed talks will be selected from the submitted abstracts to be presented with the invited talks during the plenary sessions.  Contributed talks will also be selected for parallel breakout sessions which commence in the late afternoon.

Quantitative Biology on the Hawaiian Islands
February 17-20, 2014

The Winter q-bio meeting brings together scientists and engineers who are interested in all areas of q-bio. The venue for 2014 is the Hilton Waikoloa Village, which is located on the Kohala Coast of Hawaii’s Big Island. The resort lets you experience breathtaking tropical gardens, abundant wildlife, award-winning dining, world-class shopping, art and culture, and an array of activities. The Island of Hawaii is the youngest and biggest in the Hawaiian chain, providing a vast canvas of environments to discover--home of one of the world’s most active volcanoes (Kilauea), the most massive mountain in the world (Maunaloa), and the largest park in the state (Hawaii Volcanoes National Park).

UC San Diego BioCircuits Institute and the San Diego Center for Systems Biology
The University of Hawaii at Manoa
UC San Diego Divisions of Biological Sciences and Engineering
The Office of Naval Research

Naama Barkai, The Weizmann Institute of Science
Sangeeta Bhatia Massachusetts Institute of Technology
Hana El-Samad, University of California, San Francisco
Zev Gartner, University of California, San Francisco
Taekjip Ha, University of Illinois
Shigeru Kondo, Osaka University
Arthur Lander, University of California, Irvine
Andrew Murray, Harvard University
Steve Quake, Stanford University
Petra Schwille, Max Planck Institute
Christina Smolke, Stanford University
Aleksandra Walczak, Laboratoire de Physique Théorique

Kevin Bennett, University of Hawaii at Manoa
William Ditto, University of Hawaii at Manoa
Hana El-Samad, University of California, San Francisco
Jeff Hasty, University of California, San Diego
Alexander Hoffmann, University of California, San Diego
Galit Lahav, Harvard University
Eva-Maria Schoetz-Collins, University of California, San Diego
Chao Tang, Peking University
Lev Tsimring, University of California, San Diego

Registration fee covers conference venue, registration reception, banquet, coffee & snacks.

EARLY BIRD REGISTRATION ($500/$425 Student) DEADLINE: December 20, 2013
REGULAR REGISTRATION ($600/$525 Student) DEADLINE: January 31, 2014
LATE REGISTRATION ($675/$600 Student) After January 31, 2014


HOTEL:  A block of rooms has been reserved for registered conference participants at a negotiated rate of $199 per night at the Hilton Waikoloa Village. The rooms will be available soon on a first-come, first-served basis, so book early!

CONTRIBUTED TALKS:  If you wish to present your work at the conference, either as an oral talk or a poster, you must submit an abstract through the conference website by the November 5th deadline. Abstract guidelines and submission information at:

ABSTRACT DEADLINE: EXTENDED UNTIL MONDAY, December 2, 2013 (Extended due to large volume of interest!)
Accepted abstracts will be announced by December 6, 2012.  You may submit your abstract now and if accepted, still register by the early bird registration deadline of December 20, 2013.
Abstract guidelines and submission information at:

We encourage you to forward this message to any colleagues that may be interested in taking part in this exciting event.

Questions should be emailed to:

Monday, September 10, 2012

Thanks Google Scholar Updates for new article to read .. wish you had an #openaccess only setting

I have a new friend in Google Scholar Updates

I have written about the Updates system before and if you want more information please see this post: The Tree of Life: Wow - Google Scholar "Updates" a big step forward ...

Alas, it is imperfect in my mind for I went to try to read this article and boom - $32 for a day's access

Now I am really wishing Google Scholar had an "show me only open access" articles option.

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Gave my 1st ever talk about Yolo Bypass and my 1st ever talk about Nature Photography. Here it is ...