Monday, March 26, 2012

Hey Nature Publishing Group - When are you going to live up to your promises about "free" genome papers? #opengate #aaaaaarrgh

This is just ridiculous.  Nature Publishing Group in 2007 announced that they were making all papers in their journals that reported genome sequences would be made freely available and would be given a Creative Commons license: Shared genomes : Article : Nature.

About a year ago I posted to twitter (using the hashtag #opengate) and my blog about how Nature Publishing Group was not following through on their promises.  See for example
and more including some from others
Amazingly, and pleasantly, I note, in my complaining I exacted some responses from people from Nature Publishing Group who swore that these were just oversights and they would fix them.  Well, alas, the money collecting machine of Nature Publishing Group is back.

Saturday, March 24, 2012

12 hours of me: Slideshows w/ audio from "BIS2C: Biodiversity & the Tree of Life" at #UCDavis

Well, it has taken a few months of processing but I have finally gotten my lectures from the introductory biology course I teach uploaded in some way to share.  The course is "BIS2C: Biodiversity and the Tree of Life" and it is the third quarter of a three quarter introductory biology series at UC Davis.  Each year some 2300 or so students take this series which means that we at UC Davis have to offer each of the courses (BIS2A, BIS2B, and BIS2C) each quarter.   Every fall I co-teach BIS2C.  Alas we do not have a lecture hall big enough for 700 students, so we do the course in two sections.  The way we teach it each of the faculty double up and teach their part of the course to each section.  The course also has a weekly lab.  It is a machine of sorts.

This fall I taught 13 lectures for the course.  I covered basically phylogenetic methods, the big picture of the tree of life, and microbial diversity.  I used the Apple presentation program Keynote for slides for my lectures and I used the "Record Slideshow" option to record audio in synch with the slides.  After a bit of pain, I managed to convert these recordings into video and then posted them to Youtube.  And today I am sharing them with you.  There are imperfections of course.  But I thought some might find them useful.  Plus I have made a YouTube playlist for all the lectures if you want to just sit down and enjoy 12 hours or so of me.  Now if only Youtube would allow me to change the thumbnail image for each lecture ...  Plus I note - next year I will be doing much more interactive learning in class so this may be the last record of some of these lectures ...

Lecture 1: Introduction to Course and the Tree of Life


Lecture 2: Trees, Taxa and Groups




Friday, March 23, 2012

And now I have a billion plus infinity dollars

P72

Just a typical Friday in #davisca - printing our own money

P58

Just grand -Donald Williamson published more crap on larval "evolution" - this time in one of the #OMICS journals

Well this is great.  Just great.  Donald Williamson has a new paper "The Origins of Chordate Larvae" published in Cell and Developmental Biology - a spammy journal from the OMICS publishing group.  Don't know who Williamson is?  Well consider yourself lucky.  For more on him and his horrendous history of publishing crap see:

And many many more.  Short summary - he has a theory regarding larval forms of organisms having a separate evolutionary history from adult forms.  He has no evidence for this.  And he keeps finding new ways to publish his theory.  Uggh.  I guess this serves as a reminder to everyone out there - crap does get published.  It is too bad.  But it does happen and will continue to.  We need to call out the crap as much as possible so that as few people as possible out there end up getting deceived.  So this is my contribution to that notion.  Google search engines pay attention. Donald Williamson really publishes some horrible stuff.

Thursday, March 22, 2012

OMG - Without a doubt the worst omics word ever - The Sexome

I really have nothing to say here.  I just got pointed to a new paper by Thiago Venancio.  The paper is - I kid you not: Understanding the Sexome: Measuring and Reporting Sex Differences in Gene Systems.  I don't have access to the paper but here is the abstract which is all you need
The current male bias in biomedical research should be eliminated. The large sex differences in incidence and progression of diseases mean that sex-biased factors are an untapped source of factors that protect from disease. Greater understanding will come from intensified study of the "sexome," which is the sum of sex-biased effects on gene networks and cell systems. The global search for sites and mechanisms of sex-specific regulation in diverse tissues will provide unanticipated insights into physiological regulation and targets for novel therapies.
That is without a doubt the worst omics word I have ever seen.  All my previous posts about bad omics words pale in comparison (though I encourage you to read them: Worst New Omics Word Award and bad omics word of the day).

Calling all computational biologists - do as C. Titus Brown does - submit your pubs to arXiv

Can I just express my love/respect for C. Titus Brown?  Not only is he into openness in science and metagenomics and such.  But he practices what he preaches.  For example see - Daily Life in an Ivory Basement : /mar-12/diginorm-paper-posted in which he describes his new submission to arXiv and some background.  I know I am big on Open Access and all, but even we have been lame about submitting things to preprint servers like arXiv.  Gonne do my best to fix that and try and copy Titus.

Lenses in Biology collection from Nature Outlook: free (for now at least) & worth a look

Some nice long features in Nature Outlook on various topics plus interviews with the authors.  Summed up in Lenses on Biology.  All freely available though I think that is only for this collection and not in general for Nature Outlook.

Wednesday, March 21, 2012

Notes (from me and mostly others) from the JGI User Meeting #JGIUM7

OK, so the DOE Joint Genome Institute User Meeting is underway. Day 2 just finished. And I have been there for much of it but alas, not in some of the talks since I can't seem to get past the hallway/gathering area outside the talks. There are way way too many people there who I have not talked to or seen in a while ... So ... apologies to those who thought I might be live tweeting the whole meeting ... it just hasn't happened. But I did use the Storify web tool to make a "storification" of posts to twitter from the meeting - most of which were from other people. Here is the story in slideshow format.



I will update the storification tomorrow. If you want to see the full details in a scrolling winder see below

Tuesday, March 20, 2012

OMICS Driven Microbial Ecology ...

Quick post here.  Just discovered a nice review paper by Suenaga on targeted metagenomics: Targeted metagenomics: a high-resolution metagenomics approach for specific gene clusters in complex microbial communities - Suenaga - 2011 - Environmental Microbiology

This "Special Issue" on "OMICS Driven Microbial Ecology" has a series of papers, all of which seem to be freely available, of potential interest to readers of this blog including:

and more

Oh, and a paper of mine (with Alex Worden and other members of her lab as well as multiple others)

Google Wage or Google Wave? I am interested in Google Wage if they are still offering ...

Just got this email

Google Wage wave-noreply@google.com

12:24 AM (4 minutes ago)

Dear Wavers,More than a year ago we announced that Google Wave would no longer be developed as a separate product. Back in November 2011, we shared the specific dates for ending this maintenance period and shutting down Wave. Google Wave is now in read-only mode. This is reminder that the Wave service will be turned off on April 30, 2012. You will be able to continue exporting individual waves using the existing PDF export feature until the Google Wave service is turned off. We encourage you to export any important data before April 30, 2012.

If you would like to continue using Wave, there are a number of open source projects, including Apache Wave. There is also an open source project called Walkaround that includes an experimental feature that lets you import all your Waves from Google. This feature will also work until the Wave service is turned off on April 30, 2012.

For more details, please see our help center.

Yours sincerely,

The Wave Team

© 2012 Google Inc. 1600 Amphitheatre Parkway, Mountain View, CA 94043
You have received this mandatory email service announcement to update you about important changes to your Google Wave account.

Notice anything unusual? How about that it is from "Google Wage?" I assume this is either a really bad typo or a really funny prank from inside Google.

This is both crazy and completely brilliant: The Microbial Academy Of Sciences

Oh My God.  This is so wild and crazy I can't just write OMG - I have to write the whole thing out: The Microbial Academy Of Sciences: What Bacteria Can Discover That We Can't | Co.Exist: World changing ideas and innovation

The article describes an art exhibition in San Francisco in which one part involves giving microbial cultures access to images from space.  The reason for this is possibly captured in this quote
"Because cyanobacteria can perform photosynthesis," Keats says, "they’ll be able to detect patterns of starlight just as human scientists do with their eyes. The difference will not be in their methodology, but rather in the conclusions they reach."
and even better
But in all those eons, bacteria have never been given observatory access, to study the cosmos for themselves. … My observatory is built to address that unfortunate oversight, providing the resources for colonies of bacteria to research a theory of everything, reconciling cosmic and quantum observations in their own bacterial way."
I know some hard core scientists may object to this and some of the other lines by the artist but I personally think this is brilliant (in a devious way but brilliant nevertheless).   Everyone out there should read this article by Morgan Clendaniel.  And I for one and going to try to go to the exhibit ASAP.  I personally cannot believe I have not heard of this yet since it seems to have opened in January ...

Saturday, March 17, 2012

The Axis of Evol: Getting to the Root of DNA Repair with Philogeny


The Axis of Evol: Getting to the Root of DNA Repair with Philogeny 

In 2005 I wrote an essay about my time in graduate school that was potentially going to be included in a special issue of Mutation Research in honor of my PhD advisor Phil Hanawalt.  Alas, publishing my essay ran into complications in regard to the closed access policies of this journal.  So in the end, my essay was not published.  I had forgotten about it mostly until very recently.  And so I decided to convert the essay to a blog post.  The essay is sort of about what I did in grad. school and sort of about Phil ...

Abstract:
Phylogenomics is a field in which genome analysis and evolutionary reconstructions are integrated. This integration is important because genome data is of great value in evolutionary reconstructions, because evolutionary analysis is critical for understanding and interpreting genomic data, and because there are feedback loops between evolutionary and genome analysis such that they need to be done in an integrated manner. In this paper I describe how I developed my particular phylogenomic approach under the guidance of my Ph.D advisor Philip C. Hanawalt. Since I was the first to use the term phylogenomics in a publication, I have decided to rename the field (at least temporarily) Philogenomics.

1. Doctor of Philosophy
When I went to Stanford for graduate school, I was interested in combining evolutionary analysis and molecular biology in a way that would allow me to study molecular mechanisms through an evolutionary perspective. Although I had gone to Stanford ostensibly to work on butterfly population genetics, within two days of starting a rotation in Phil’s lab, I knew that that was where I wanted to work. This decision was somewhat traumatic, since the work on butterflies included spending the summers at 10,000 feet in the Rocky Mountains and possibly chasing butterflies like a Nabakov wanna-be all over the mountain ranges of the world. As an avid outdoor person, this was quite appealing. Nevertheless, I chose to spend 99% of my graduate work in the dingy confines of Herrin Hall, studying DNA repair. The choice of joining Phil’s lab did have one very positive affect – and that was on my relationship with my grandfather on my mother’s side. Benjamin Post was in many ways like a father to me, especially after my father passed away. He was a physicist from the “old school” and thought that most of biology was completely useless. Needless to say, when I told him I was going to graduate school in California (which he considered already one strike against me) to study butterflies, he decided I was simply a lost cause. Despite all his talk of Einstein and computers and math when I was a child, I might as well have been a poet from his point of view. To make matters worse, my grandfather was a crystallographer, and my brother was getting his Ph.D in crystallography at Harvard. When I informed my grandfather that I was going to be working on DNA repair, he seemed somewhat interested. And then I told him, my advisor, Phil Hanawalt, is relatively well known, and actually used to be considered a biophysicist. Then my grandfather really perked up. He said, “Hanawalt – is he related to Don Hanawalt?” It turns out, that my grandfather worked in the same field as Phil’s father (they both did powder diffraction) and knew him. So my grandfather said “You may not be doing real science, but at least you are doing it with the relative of a real scientist.” Thankfully, I was no longer the black sheep in the family. So, with my grandfather’s approval, I embarked on a career in DNA repair.

Friday, March 16, 2012

Want more research funding? Time to give your study organism a better nickname

People who work on pathogens, especially really nasty ones, have built in marketing and fundraising tools. They have nicknames (for the organism, the disease, or both): Good ones. Like "black death" "flesh eating bacteria" "bone break fever" any "wasting disease" any "hemorrhagic fever" "male killer" and more. Now - there are a few non pathogens with good nicknames, like "Conan the bacterium" for Deinococcus radiodurans. But I think we really need to work on better nicknames for non pathogenic microbes. So here are a few proposals:

Any halophilic archaea -> "salt monsters"
Prochlorococcus -> The carbon eater
Rhizobium -> The fixer
Any methanogen -> Fartilicious
Myxococcus xanthus -> The stalker
Nanoarchaeum -> The Hobbit
Tetrahymena thermophila -> The hymenator

Come on everyone.  Let's get some better nicknames.

Thursday, March 15, 2012

Evolution rap: 3.5* til infinity #music

Well, after a rough day I am in need of some lightness. And thanks to Eric Lowe, an undergrad. working in my lab, I got a giggle out of this:

Elaine Mardis rocks: nice talk on "Next generation sequencing"

I wish I had seen this before I gave my first lecture on Next Gen Sequencing Methods on Monday.  I will post mine later but here is a really really nice talk by Elaine Mardis from Washington University on the same topic:

Wednesday, March 14, 2012

Diabetes & H.pylori - a correlation but no known causation despite authors claims


Am having a hard time right now with the comments from the authors of this new paper showing a correlation between H. pylori presence and both type II diabetes and blood glucose levels.  As far as I can tell, the paper does not show any causal connection.  That is, they do not determine if H. pylori infection is a cause of blood sugar issues or a consequence of blood sugar issues.

Yet the authors of the paper, one of whom (Martin Blaser) is a very respected H. pylori expert are saying things like
This study provides further evidence of late-in-life cost to having H. pylori,
And they suggest that antibiotic treatment for the elderly may help prevent diabetes.

This to be seems to be a bit over the top.  Yes, it makes sense that H. pylori could cause these issues.  And they have a model for how it might.  But they really should be more careful with their words until a causal connection is established.  After all, we have many well known negative effects of antibiotic overuse, including some shown by Blaser.  The last thing we need is people going out and dosing up on antibiotics in the hope that it will prevent type II diabetes.  But I can guarantee that is what will happen if this story gets overplayed.

At least a few sources report on the lack of anything showing a causal connection (e.g. see US News and World Report):
An expert not involved with the study said that while it did not show a cause-and-effect relationship between the bacterium and diabetes, the findings suggest certain possibilities
But I am worried that that is not enough skepticism to counteract the claims of the authors here. The study is certainly interesting.  And their model for a causal connection is fine.  But they probably need to do a little bit of toning down of their claims here.

UPDATE: 3/17/13

After some people asked me questions about this study at a few recent meetings I dug a little deeper.  And I am a bit startled to find out what the basis is for Chen and Blaser to claim a causative association between H. pylori and type II diabetes/ glucose levels.  Here is a summary of their logic:
Helicobacter pylori is acquired almost exclusively in childhood [8], and there is no clear mechanism for how glucose intolerance present only after the age of 18 would increase risk of H. pylori colonization. It also is unlikely that H. pylori positivity and high levels of HbA1c levels share a mutual antecedent cause because there is no diathesis to both acquire H. pylori and to cause glucose intolerance.
They go on to discuss other lines of indirect evidence for why they think their conclusion is correct.  And some of this is very suggestive.  But "likely" and "suggestive" is not proof.  There are many possible issues with their conclusion.  In particular I think it is easy to come up with a scenario whereby something about the host (either their genetics or their history of exposure or even their micro biome) could influence both whether or not they get colonized by H. pylori or even whether or not they get colonized by particular strains of HP.  And the same factor could influence microbiome interactions later in life.  I see no evidence to indicate that H. pylori is the causative agent here.  And for them to then basically recommend prophylactic antibiotics for elderly with HP seems dangerous at best.


California Breast Cancer Research Fund Tax Checkoff; wondering about Open Access policies

Just got this email below about what seems to be a worth cause:
March 8, 2012 
Dear UC Colleagues, Throughout California and UC, researchers are developing new approaches to prevent, treat and cure cancer. I am writing you to share important information with those of you who will soon file your California state tax return. At the end of California Tax form 540, there is a section in which you can donate to two highly regarded cancer research programs that are administered by the UC Office of the President.

Tuesday, March 13, 2012

Not sure what to make of this new "Datasets.Com" effort from Hindawi

Just got this email and I thought I would share.  Not sure what to make of this effort.  I do support the sharing of data sets but I am think we probably do not need a whole new cadre of data journals to handle this data.

But there is a spread of what some have called "Predatory" open access publishers (see http://metadata.posterous.com/83235355 for example).  Hindawi, who is behind this, seems to have a mix of good and predatory tendencies and this seems like it may fit into the more predatory categorization.  And I just thought it would be good to bring this a bit more into the open to discuss it.

Dear Dr. Eisen,

My name is Safa Tahoon and I am a Journal Developer for the Hindawi Publishing Corporation. We are in the process of launching a new peer-reviewed, open access journal titled Dataset Papers in Genetics, which will publish Dataset Papers in all areas of genetics research, and I am writing to invite you to join the Editorial Board of this new journal.

Sunday, March 11, 2012

Wanted - opinions/details on online systems for annotation of genomes and metagenomes

Doing a little survey/snooping around.  Trying to compile a list of available online tools for annotating microbial genomes and metagenomes.  And I am also trying to get comments on what people think of the various tools.  There are some obvious candidates to think about
But given that there are certainly many many more out there I decided to post a request to Twitter and Google plus and got some responses.


  • Jonathan Eisen ‏ @phylogenomics
    • Researching blog post on free/online microbial genome/metagenome annotation services - looking for examples beyond IMG & RAST
  • Mick Watson @BioMickWatson
  • Ewan Birney ‏ @ewanbirney 
  • Mick Watson ‏ @BioMickWatson 
    • @ewanbirney @phylogenomics @EBImetagenomics needs illumina support, and support of assemblies :/


And from Google Plus where I asked "Researching blog post on free/online microbial genome/metagenome annotation services - looking for examples beyond IMG & RAST ":




Saturday, March 10, 2012

Worst new omics word award: circomics - running circles around my head

Wow - this is really not a good "omics" word.  Check out this paper title and it's abstract Circular DNA genomics (circomics) exemplified for g... [Virology. 2012] - PubMed - NCBI
Circomics was coined to describe the combination of rolling circle amplification (RCA), restriction fragment length polymorphism (RFLP) and pyro-sequencing to investigate the genome structures of small circular DNAs. A batch procedure is described using 61 plant samples from Asia, South America and Central America which revealed 83 contig sequences of geminiviral DNA components and 4 contig sequences of DNA satellites. The usefulness of this approach is validated for the Brazilian begomoviruses, and the sequence fidelity is determined by comparing the results with those of conventional cloning and sequencing of Bolivian begomoviruses reported recently. Therefore, circomics has been proven to be a major step forward to economize costs and labor and to characterize reliably geminiviral genomes in their population structure of the quasi species.
This definitely fits the category of a "bad omics" word which I have history of complaining about but had been ignoring for a bit.  But I am back.  I am giving "Circomics" a "Worst New Omics Word Award" here because, well, it seems completely unnecessary and distracting.

Hat tip to AJ Cann for pointing this one out on Google Plus.

Friday, March 09, 2012

Who is hiring research fellows and/or instructors in microbiology?

A colleague emailed me the following question
 "A good friend of mine is looking for a position as a research fellow or instructor in microbiology with an emphasis on teaching. While she's exploring options herself I figured it couldn't hurt asking; I usually know who is hiring in [my area of expertise] but this is way outside my usual networks, and from what I've been learning positions with an emphasis on teaching are surprisingly rare. Any pointers to departments or groups that might be hiring would be highly appreciated (as are tips on how to find such a position)." 

And alas I did not have a good answer. So, with this person's permission I am reaching out to the blogosphere to see if anyone has suggestions for good places/sources of information about job openings in teaching and/or research fellow positions in microbiology.

Social Biology of Microbes 2012 #SocialMicrobes12 wrapup via Storify


Meeting details: 

Welcoming remarks: 

  • David Relman (presentation) (audio)
  • James Hughes (audio)
  • Lonnie King (audio)
  • KEYNOTE: 
Sociomicrobiology: 

  • Quorum sensing, biofilms, and territoriality (presentation) (audioE. Peter Greenberg, University of Washington
  • Moderator: David Relman DISCUSSION (audio)
SESSION I: Formation and Function of Microbial Communities

  • Moderator: Jacque Fletcher
  • Symbiont community complexity 
    • The fungal gardens of leafcutter ants
      • (presentation) (audio)
      • Cameron R. Currie, University of Wisconsin Madison
    • The role of oxygen in shaping the structure and function of microbial communities
      • (presentation) (audio)
      • Thomas M. Schmidt, Michigan State University
  • Source-sink dynamics: 
    • Marine invertebrate-associated and free-living chemosynthetic symbionts
    • Colleen Cavanaugh, Harvard University DISCUSSION (audio)
SESSION II: Factors Contributing to Community Stability 

  • Moderator: David Relman
    • Social evolutionary theory, cooperation, and the expression of virulence in microbial communities
    • (presentation) (audio)
  • Sam Brown, University of Edinburgh
    • Ecological factors and processes during evolutionary transitions in Darwinian individuality
    • (presentation) (audio)
  • Paul Rainey, New Zealand Institute for Advanced Study & Max Planck Institute for Evolutionary Biology
    • Evolution of cooperation and control of cheating in the social amoeba:
  • Dictyostelium discoideum
    • (presentation: part 1 part 2) (audio)
    • Joan E. Strassmann, Washington University\
  • Swarming bacteria as freight haulage systems (presentation) (audio)
    • Colin J. Ingham, Wageningen University
    • Emergence and robustness of multicellular behavior in bacteria (presentation) (audio)
  • Joao Xavier, Memorial Sloan-Kettering Cancer Center
    • Mathematical and computational challenges in the study of complex adaptive systems
    • (presentation) (audio)
  • Simon A. Levin, Princeton University
    • DISCUSSION (audiopage2image12752 page2image12912 page2image13072 page2image13232 page2image13392 page2image13552 page2image13712 page2image13872 page2image14032 page2image14192 page2image14352 page2image14512 page2image14672 page2image14832
DAY 2: WEDNESDAY, MARCH 7, 2012
]
SESSION III: 

  • Summary of Day One: David Relman (presentation) (audio)
  • Edith Widder, Ocean Research & Conservation Association
    • KEYNOTE: Glowing corpses & radiant excrement: The role of bioluminescence in microbial communities
    • (presentation) (audio)
    • Moderator: Lonnie King DISCUSSION (audio)page3image6024 page3image6184 page3image6344 page3image6504
  • Jo Handelsman, Yale University
    • Interspecies interactions among rhizosphere and soil bacteria (presentation) (audio
    • Moderator: David Rizzo
  • David Low, University of California - Santa Barbara
    • Contact dependent mechanisms of communication in bacteria (presentation) (audio)
  • Vanessa Sperandio, The University of Texas Southwestern Medical Center 
    • Interactions between symbiotic microbes, their mammalian host, and invading pathogens
    • (presentation) (audio)
    • Moderator: Carole Heilman
  • Jonathan Eisen, University of California - Davis
    • Phylogenetic and phylogenomic approaches to studies of microbial communities
    • (presentation) (audio)
SESSION IV: What More Do We Need to Know about Microbial Community Dynamics?
page3image14888 page3image15048 page3image15208 page3image15368 page3image15528 page3image15688

  • DISCUSSION (audio
  • Jared R. Leadbetter, California Institute of Technology
    • Discovery and applications of the metabolic diversity of microbial communities
    • (presentation) (audio)
    • Statistical tools for integrating community networks, spatial and clinical data (presentation) (audio)
  • Jill Banfield, University of California - Berkeley
    • Microbial community assembly and dynamics: From acidophilic biofilms to the premature infant gut
    • (presentation) (audio)
  • David A. Relman, Stanford University
    • Human-microbe mutualism in health and disease (presentation) (audio)
  • DISCUSSION (audio
  • Concluding Remarks (audio


Just got back from a meeting on the "Social Biology of Microbes". Here are some notes from my trip and from the talks at the meeting, done via Storify. Here it is as a slideshow:

And here it is a a full scrollable presentation

Thursday, March 08, 2012

Interesting upcoming conference Exploring Human Host-Microbiome Interactions in Health and Disease

Interesting upcoming conference:

Exploring Human Host-Microbiome Interactions in Health and Disease.

8-10 May 2012 Wellcome Trust Conference Centre
Wellcome Trust Genome Campus
Hinxton, Cambridge, UK

See WT Scientific conferences for more detail.

A day of field guides at #UCDavis and @Wired

Well, how perfect is this.  Today Wired ran a follow up "Birds, Poop and Roadkill: A field guide to Field Guides" to an article that came out last week about my drive for a full field guide to the microbes.  Last weeks article was "Book of Germs: The Quest for a Field Guide to Microbes."  It is by Daniela Hernandez and was a follow up on my talk at AAAS on "A Field Guide to the Microbes" which you can see on YouTube here.  I wrote a blog post with more detail on my obsession with field guides and microbes here.

While Daniela was writing the article I told her about how I collected field guides.  And I sent her a link to a private album I had made of me and my field guides which I am now making public:




For the follow up Daniela and a photographer from Wired Jon Snyder came to my office and lab and took some pictures of me and my field guides (with assistance from Russell Neches in my lab to help set up some of the "scenes).

Here are some pics from their visit.







And now today, the Wired article came out and and amazing coincidence happened.  I was taking a walk around campus with Misha Angrist who is giving a talk at UC Davis today.  And on the walk first we saw a collection of turkeys wandering around campus:


So my birding sense was turned up.  And then we walked across to the UC Davis Arboretum along Putah Creek and bumped into a "birding tour" of the Arboretum.  In six years here I have never seen one of these.  There were some teachers and kids carrying around field guides looking for particular species of birds.




And I note - one even had a field guide I do not have - the "Birds of Northern California" which I will be getting very very soon.  I think today will only serve to boost my obsession with field guides, but that is OK by me.

I note - I love the Wired photo spread of my field guides and my lab.  I particularly am happy that they includes some of the funnier field guides out there like "Flattened Fauna." And I am glad they got in Betsy Dyer's Field Guide to Bacteria because it is one of my favorite field guides of all time.  Thanks to Russell Neches for helping out with it and Daniela Hernandez and Jon Snyder for their work.


Monday, March 05, 2012

Social Biology of Microbial Communities

Off to DC for a meeting on the "Social Biology of Microbial Communities" and I thought people out there might like to see the schedule.  Going to try to live blog/tweet so stay tuned ...


Sunday, March 04, 2012

Yes, Virginia, Cell Phones Have Bacteria on Them ... And this means????

A new report is out with a discussion of microbes on cell phones: Study: Cellphones can be more germ-infested than toilet handle | News - Home. Not sure what was done in the study but regardless it seems to be focused on culture based work. And as is usually, the finding of some microbes related to ones known to cause disease leads to the inevitable conclusion that we must kill everything on the phones.

It seems to me that we need a bit more detail on what microbes are found on cell phones before bringing out the cleaners and the irradiation and such.

Playing w/ Google Scholar's "Citations" system - some nice features but in need of a little fine tuning

Been playing around with Google Scholar's Citations system that allows anyone to create a mini page with their publications.  Here is a link to mine: Jonathan Eisen.  I recommend that everyone out there who has any publications create a Scholar Citations page for themselves. Instructions can be found here.

I quite like the simplicity yet informativeness of the Scholar Citations front page:


Yet there are many other things I wish were there.  For example, I really wish the "Institution" part was an active link and led to other people at UC Davis.  Alas, not so.  So I had to use the search function to pull out other people from UC Davis (searching for UC Davis in the search for Authors in the box in the upper right from my home page).



The list comes out in order of numbers of citations, which is good and bad.  Here are some of the top people from the list:

Friday, March 02, 2012

And now Spam from Elsevier - thanks - but no thanks

Just got an email from Elsevier for something called "Reviewers' Update" which starts off:
Dear Dr Eisen,

As a valued contributor to Elsevier's journals we thought you may be interested in receiving the Reviewers' Update - our free quarterly e-update for reviewers - which contains advice for reviewers, updates on how Elsevier supports the peer review process as well as information which we hope proves useful to you when reviewing manuscripts.

Click on the headings below for access to a selection of articles in Issues 8 and 9, or browse through the full archive on the Reviewers' Update homepage.

Would you like to receive the next issue of Reviewers' Update as well as future reviewer updates?

If so, please register here.

Kind regards,

Andrea Hoogenkamp-O'Brien, PhD
Communications Manager, Elsevier

That leads me to wonder - just what did I do to become a valued contributor?  I cannot for the life of me remember the last time I reviewed for any Elsevier journal.   And the last time I was an author on a paper in an Elsevier journal was 2006 and that was only because I did not really realize that is where collaborators were submitting a paper.  Thanks Elsevier, but I will skip registering for this service.


Thursday, March 01, 2012

Some answers to "Wanted-good simple guide to the statistics of sampling design for field ecology studies"

I asked a question on twitter "Wanted - good simple guide to the statistics of sampling design for field ecology studies" and got some useful answers, which I have "storified" below. Any additional suggestions welcome.

Full list of 2012 American Academy of Microbiology Fellows Announced

Just got this email and well, I thought I would share.  I would share even if I was not on the list since, well, I love microbes and microbiology.  Note the list is also available on the AAM Web site here.

The American Academy of Microbiology is honored to welcome these new Fellows, elected in recognition of their records of scientific achievement and original contributions that have advanced microbiology:
  • James B. Anderson, Ph.D., University of Toronto, Mississauga, ON, Canada
  • Dan I. Andersson, Ph.D., Uppsala University, Sweden

My obsession with a Field Guide for Microbes

Recently I gave a talk at the AAAS Meeting in Vancouver on my dream of having "A Field Guide to the Microbes".  The talk was part of a session on the "Earth Microbiome Project" organized by Jack Gilbert and others.

You can see a slideshow with audio of my talk below:




It seems that my talk has sparked a lot of interest as I have been interviewed by various people and publications about this concept.

For example, Holly Menninger recently interviewed me for a blog post for the "Your Wild Life" blog:
Is a Field Guide for Microbes in Our Future? Q & A with Microbiologist Jonathan Eisen.

And today a wonderfully illustrated piece came out at Wired.Com by Daniela Hernandez titled "Book of Germs: A Quest for a Field Guide to Microbes."

If you are interested in some more background on what I have been thinking about a Field Guide to the Microbes here are some previous things I have written or said or commented on relating to this topic:
And if you want to check out some "Field Guide" like books on the topic of microbes I am posting some recommendations on an Amazon Page. My favorite is "A Field Guide to Bacteria" by Betsey Dyer.  

Wednesday, February 29, 2012

Task force investigating #UCDavis Pepper Spray Incident report to be released 3/6

Just got an email from UC Communications


"Former California Supreme Court Associate Justice Cruz Reynoso, chair of the task force investigating the pepper-spray incident on November 18, 2011, said today the task force is working toward public release of findings and recommendations on Tuesday, March 6, at a time and location on the UC Davis campus to be determined. 

Additional information will be provided as soon as it is available."

Guest post from Russell Neches @ryneches, PhD student in my lab "Blogging his qualifying exam"

Below is a guest post from Russell Neches a PhD student in my lab.


Blogging my Qualifying Exam

Because this seems to be my default mode of organizing my thoughts when it comes to research, I've decided to write my dissertation proposal as a blog post. This way, when I'm standing in front of my committee on Thursday, I can simply fall back on one my more more annoying habits; talking at length about something I wrote on my blog. Or, since he has graciously lent me his megaphone for the occasion, I can talk at length about something I wrote on Jonathan's blog.

Introduction : Seeking a microbial travelogue
Last summer, I had a lucky chance to travel to Kamchatka with Frank Robb and Albert Colman. It was a learning experience of epic proportions. Nevertheless, I came home with a puzzling question. As I continued to ponder it, the question went from puzzling to vexing to maddening, and eventually became an unhealthy obsession. In other words, a dissertation project. In the following paragraphs, I'm going to try to explain why this question is so interesting, and what I'm going to do to try answer it.

About a million years ago (the mid-Pleistocene), one of Kamchatka's many volcanoes erupted and collapsed into its magma chamber to form Uzon Caldera. The caldera floor is now a spectacular thermal field, and one of the most beautiful spots on the planet. I regularly read through Igor Shpilenok's Livejournal, where he posts incredible photographs of Uzon and the nature reserve that encompasses it. It's well worth bookmarking, even if you can't read Russian.

The thermal fields are covered in hot springs of many different sizes. Here's one of my favorites :



Each one of these is about the size of a bowl of soup. In some places the springs are so numerous that it is difficult to avoid stepping in them. You can tell just by looking at these three springs that the chemistry varies considerably; I'm given to understand that the different colors are due to the dominant oxidation species of sulfur, and the one on the far left was about thirty degrees hotter than the other two. All three of them are almost certainly colonized by fascinating microbes.

The experienced microbiologists on the expedition set about the business of pursuing questions like Who is there? and What are they doing? I was there to collect a few samples for metagenomic sequencing, and so my own work was completed on the first day. I spent the rest of my time there thinking about the microbes that live in these beautiful hotsprings, and wondering How did they get there?


Extremophiles are practically made-to-order for this question. The study of extremophile biology has been a bonanza for both applied and basic science. Extremophiles live differently, and their adaptations have taught us a lot about how evolution works, about the history of life on earth, about biochemistry, and all sorts of interesting things. However, their very peculiarity poses an interesting problem. Imagine you would freeze to death at 80° Celsius. How does the world look to you? Pretty inhospitable; a few little ponds of warmth dotted across vast deserts of freezing death.

Tuesday, February 28, 2012

Nice #openaccess review on the ecology of chemosynthetic symbioses from @chicaScientific & Guus Roeselers

Figure 1 from 10.1007/s00253-011-3819-9. Sediment cross section 
exposing the characteristic Y-shaped burrow dug by S. velum. 
Positioning itself at the triple junction of the Y, the bivalve alternates
 between actively pumping oxygenated water from the upper arms of
 the burrow through the mantle cavity and across the gills and 
accessing reduced sulfur compounds diffusing up from the anoxic 
zones below and pumped through a ventral incurrent opening in the 
mantle. Scale bar equals 2.5 cm

For those who do not know, I got my first taste of microbiology research when I was an undergrad at Harvard and I did my senior/honors research project in the lab of Colleen Cavanaugh. Colleen studied (and in fact still studies) symbioses between invertebrates and chemosynthetic bacteria. The bacteria basically allow these invertebrates to function like plants in many ways. Some of these invertebrates (like the giant tube worms in hydrothermal vents) have lost their mouths and digestive systems and basically live by bringing in high energy chemicals for their symbionts which then make sugars, vitamins, amino acids and other goodies for the host.

Monday, February 27, 2012

My favorite new thing/site on the web: Download The Universe

I am completely fascinated by this new site: Download The Universe. It is a group effort from (so far) some 16 science writers. The main goal of the site is summarized in a post from Carl Zimmer who appears to be the instigator in chief of this effort:

"... It is still tough for readers to discover new science ebooks. Traditional book reviews limit themselves to works on paper. Some ebooks may appear in computer magazines, but buried in reviews of laptops and printers. In between, we need a community.

Download the Universe is a step towards that community. It is the work of a group of writers and scientists who are deeply intrigued by the future of science books. (You can find our names and links to our web sites on the right.) Here we review science ebooks--broadly defined, except for ebooks that are just spin-offs of print books. We hope to build up a library of titles that curious readers can browse. Some reviews will be positive, others negative. We welcome your own judgments, and we look forward to vibrant (but civilized) discussions in the comment threads. We will also write essays from time to time about the changes that publishing is undergoing.

As we continue to build Download the Universe, we may change our minds about the scope of its mission. We can't say what those changes will be. We can only be sure they will be here before too long."

I confess - I have never read an ebook of any kind - science or not. And I really really love "real" books - I have collected them for years and years. But I think I am going to start on the ebooks thing. And this site is giving me some ideas for what to start with ... This site is definitely worth checking out, and keeping an eye on ...

In case you didn't hear - #openness WON - Research Works Act shelved

See this story from infojustice.org: Research Works Act Shelved by Sponsors

This is just awesome news. The act was completely inane.

Hooray for Open Access and Open Science and Openness in general.

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