Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

Microbes and hyenas and smells

So when this press release about microbes and hyenas came out: Microbes help hyenas communicate via scent I wanted to write about it.  But I could not figure out what I thought about the story.  Still don’t know what I think but it is interesting and worth sharing.  Also see the original paper:

Kevin R. Theis, Thomas M. Schmidt, Kay E. Holekamp. Evidence for a bacterial mechanism for group-specific social odors among hyenas. Scientific Reports, 2012; 2 DOI: 10.1038/srep00615

For some possible related papers see

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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 …

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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 …

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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

//platform.twitter.com/widgets.js I answered briefly

//platform.twitter.com/widgets.js 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.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Coming to #UCDavis – THE Ed Delong #Microbes #Metagenomics #Oceans #Alumni

Ed Delong is coming to #UCDavis -and will give two talks. See the email I received below:

“Attached, you will find the flyer for the upcoming Storer Lecture speaker, Dr. Edward DeLong. Please post and distribute.

Note: Dr. DeLong will receive the 2012 Outstanding Alumni award from the College of Biological Sciences. The Alumni Awards celebration will take place immediately following his October 4 lecture. If you would like to attend, please RSVP by September 21 to rsvp. Space is limited, so be sure to reserve your spot early. Visit http://biosci.ucdavis.edu/alumni_and_friends/alumni_awards_2012.html for more information.”

 

Ed DeLong flyer FN.PDF

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! – latimes.com.

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

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

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.”  

Plus 

“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.

2013 CONFIRMED SPEAKERS:

  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  

CONFERENCE ORGANIZERS:

  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 https://www.facebook.com/jonathaneisen/posts/10151208978630767?comment_id=24634832&offset=0&total_comments=15 ) 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 http://syntheticbiology.org/Conferences.html 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

ABSTRACT SUBMISSION DEADLINE 09/15/12http://w-qbio.org/abstracts.html

THE FIRST ANNUAL WINTER Q-BIO MEETING
Quantitative Biology on the Hawaiian Islands
February 18-21, 2013http://w-qbio.org/

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

2013 CONFIRMED SPEAKERS:
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

CONFERENCE ORGANIZERS:
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 NOW OPEN***
Registration fee covers conference venue, opening reception, banquet, coffee & snacks.

EARLY BIRD ($450.00) REGISTRATION DEADLINE: December 1, 2012
REGULAR REGISTRATION ($550) DEADLINE: February 5, 2013

REGISTER NOW: http://w-qbio.org/abstracts.html

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:http://w-qbio.org/guidelines.pdf

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: coordinator@w-qbio.org

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.
***ABSTRACT SUBMISSION DEADLINE EXTENDED TO MONDAY, DECEMBER 2, 2013***
http://w-qbio.org/abstracts/

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.

THE SECOND ANNUAL WINTER Q-BIO MEETING
Quantitative Biology on the Hawaiian Islands
February 17-20, 2014
http://w-qbio.org/

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).

SPONSORED BY:
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

2014 CONFIRMED SPEAKERS:
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

CONFERENCE ORGANIZERS:
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 NOW OPEN***
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

REGISTER NOW: http://w-qbio.org/

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: http://w-qbio.org/abstracts/

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: http://w-qbio.org/abstracts/

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: coordinator@w-qbio.org

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

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.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

I can’t keep up so here are some unfiltered links on obesity and microbiomes

I just can’t keep up.  These seem like they might be worth reading.  But no time to blog about them.  So here are some possible things to look at if you care about obesity and its possible connection to the microbiome.

Blogs

News stories:

And I am sure there is a lot more ….
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Overselling the microbiome award: MedicalDaily on Effects of Sugary Drink

There is a news article of possible interest in Medical Daily: Sugary Drinks Increase Bad Bacteria in Gut, Risk of Diabetes : Consumer News  This article reports on a paper in Obesity Reviews.  Alas the paper is not freely available. But the PhD thesis from one of the authors is.  The thesis is fascinating – I have read much of it now and skimmed other parts and it has the article as Chapter 2.  There are a few differences in the abstract – for example the Obesity Reviews paper does not start off with “The saying “you are what you eat” is no longer pure folklore but is scientifically substantiated by recognition of host-microbe interactions promoting digestion, absorption and metabolism.” which is in the thesis chapter.  But my guess is the published article is very similar to the thesis chapter.

The news article really goes overboard in hyping what appears to be little more than a correlation.  Among the issues I have:

  • Title:  Sugary Drinks Increase Bad Bacteria in Gut, Risk of Diabetes
    • Whew.  It is a doozy.  No evidence that the bacteria found are “bad” as far as I can tell.  No evidence that sugary drinks specifically cause the increase.  The paper is a review paper outlining a lot of prior work and some theories hypothesizing connections between fructose and sweeteners and the microbiome and obesity.  But I don’t see any evidence of specific increases in bad bacteria in the gut.
  • Byline: Sugary drinks help bad microbes grow in the human gut. This increase leads to many health complications like obesity and metabolic syndrome, raising risk of diseases associated with metabolic syndrome like diabetes.
    • Wow.  Even worse than the title.  Sugary drinks help the bad microbes grow.  And this leads to many health complications.  No evidence is presented for this.

In this case it is certainly much better to go to the source than to read the news story since the source (the PhD thesis and presumably the review paper) is quite thorough and interesting.  It has some fascinating ideas about sugar and sugar substitutes and their potential effects.

Mind you, I think microbes play a role in obesity too.  But the simple “sugary drinks CAUSE growth of bad bacteria which CAUSES health problems” well, if only it were so.  So for their overselling the effects of sugar and the microbiome without evidence I am giving the Medical Daily a highly coveted “overselling the microbiome award“.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–