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

Nice wrap up from Anna Sharman on Science Publishing topics in February

Definitely worth checking out this post from Anna Sharman: February highlights from the world of scientific publishing | sharmanedit.  It covers many topics of relevance including new journals, the PLOS Data Policy kerfuffle, and misc. links of interest.

Save the dates / preliminary program for Lake Arrowhead Microbial Genomes Meeting

UPDATE 3/13/14 – Official Web Site now up

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Preliminary information for the The Lake Arrowhead Microbial Genomes – which is going to be great (note – I am on the planning committee) is below.  Registration information and Abstract Submission details will be coming soon.


Preliminary Program of Confirmed Speakers
Lake Arrowhead International Microbial Genomics Conference
September 14-18, 2014
Keynote Speaker: 
  • Julia A. Segre, National Human Genome Research Institute, NIH, Bethesda, MD (skin microbiome; tracking outbreaks through genomic sequencing)
Mirobial Communities I: Microbiomes
  • Peter Turnbaugh, Harvard University, Cambridge, MA (human microbiome)
  • Noah Fierer, University of Colorado, Boulder, CO (human microbiome; soil microbial communities)
  • Sarkis K. Mazmanian, California Institute of Technology, Pasadena, CA (gastrointestinal microbiota)
  • Andrew Goodman, Microbial Diversity Institute, Yale University, West Haven, CT (human microbiome; pathogens)
Microbial Communities II, Metagenomics, Biodiversity, Natural Products, Evolution
  • Nancy Moran, University of Texas, Austin Texas (Symbiosis between multicellular hosts and microbes)
  • Tanja Woyke, DOE Joint Genome Institute, Walnut Creek, CA (metagenomics; single cell genomics)
  • Eric J. Alm, Massachusetts Institute of Technology, Cambridge, MA (evolution of microorganisms)
  • Michael Fischbach, UCSF, San Francisco, CA (Insights from a global analysis of secondary metabolism: Small molecules from the human microbiota)
  • Jessica Green, University of Oregon, Eugene, OR (metagenomics; built environment)
  • Karyna Rosario Cora, University of South Florida, St. Peterburg, FL (Exploring the viral world through metagenomics)
  • Susannah Green Tringe, DOE Joint Genome Institute, Walnut Creek, CA (Microbial communities and the carbon cycle)
  • Nicole Perna, University of Wisconsin, Madison, WI (Evolution of the response to oxygen availability in enterobacteria: a complex trait in a model family)
  • Katie Pollard, UCSF, San Francisco, CA (Metagenomics; evolutionary genomics)
  • Jenna Morgan Lang, University of California, Davis, CA (Citizen microbiology)
Pathogens, Antibiotic Resistance
  • Julian Parkhill, Welcome Trust Sanger Institute, Cambridge, UK (genomics of pathogens; tracking outbreaks through genomic sequencing)
  • Lance B. Price, George Washington University, Washington, D. C. (foodborneurinary tract infection studies)
  • Gautam Dantas, Washington University, St. Louis, MO (reservoirs of antibiotic resistance)
  • Jeffrey T. Foster, Northern Arizona University, Flagstaff, AZ (genomic epizootiology of white-nose syndrome in bats)
  • Timothy D. Read, Emory University School of Medicine, Atlanta, GA (S. aureus antibiotic resistance genomics)
  • Evgeni Sokurenko, University of Washington, Seattle, WA (Pathoadaptive mutations in microbial genomes)
  • Jennifer Gardy, University of British Columbia, British Columbia, Canada (Genomics and epidemiology)
  • Ashlee Earl, The Broad Institute of Harvard and MIT, Cambridge, MA (Pathogen and Comparative Genomics)
Systems Biology, Metabalomics, Synthetic Biology
  • Fiona Brinkman, Simon Fraser University, Greater Vancouver, British Columbia, Canada (Using genomics and network analysis to characterize disease outbreaks)
  • Mallory Embree, University of California, San Diego, CA (Deciphering dynamic community interaction using systems biology)
  • Fuzhong Zhang, Washington University, St. Louis, MO (producing biofuels and pharmaceuticals with synthetic biology)
  • Sri Kosuri, University of California, Los Angeles, CA (synthetic biology, TBA)
  • Michele C. Chang, University of California, Berkeley, CA (expanding fluorine chemistry of living systems by genetic engineering)
Some of my posts about previous Lake Arrowhead Meetings can be found below:

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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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When to "defend" on Twitter and when to listen #scio14 #scicomm

So – by Friday morning I was dying for the weekend to come. It had been a rough week.  Without getting too much into my saga, suffice it to say that “The saga of my pancreas..feet..microbiome ..blood.. liver – part 1” is not turning out so well right now and medical issues are on my mind a lot. With a little help from my family, friends, colleagues, and cats I have been getting by.

//platform.twitter.com/widgets.js And as Friday went by things were not getting better. And then another medical issue and I had to head home early. Fun. I was just starting to recover, getting ready to watch a movie with my wife and kids when, well, the Twitter world intervened. I started to see some posts from Science Online 2014 making not so positive comments about the SpaceMicrobes project in which I am involved. Oh – and they were coming from people like Madhu Katti, who I deeply deeply respect.

//platform.twitter.com/widgets.js It took me a few minutes to figure out that there was a microbial swabbing “event” going on at Science Online connected to the Space Microbes project. And there were many many questions being posted to the Twittersphere about the project by Madhu and a few others (e.g., see one below).

//platform.twitter.com/widgets.js Hmm. This did not look good. But for perhaps the first time in a very very long time I felt like somehow I should not respond online. I am not sure why I felt this. I think partly I felt that, since the Space Microbes project is a collaboration in which many people from my lab are involved (and help run) that somehow I should let this play out without my “interference”. I think somehow I thought that once I got involved it could become more about me and not about how the people involved handled the questions in real time. Now – I say “I think” and “somehow” and such because this was going on while I was reading books to my son (my phone was just sitting next to me, and I really did not want to look at it or follow what was going on). So – anyway – I did not do anything directly, but I sent an email to some of the people from my lab who are involved in the SpaceMicrobes project. It included an intemperate title line and the following text:

You should look at Twitter What exactly is happening at Science Online? Who is doing sampling there and what is the purpose?

Anyway – after I wrote this it was about time for movie night to start with my wife and kids and things were getting complex. My son did not want to watch the same movie as my daughter. Important decisions had to me made. And now I was getting sucked into Twitter. And I started to try to answer some of the questions Madhu and DocRicky and others had. Madhu made a Storify of much of the exchange.

Now – I personally believe that we can answer all the questions Madhu and others had about the project. And I started to try and explain some of the goals and aims of the project and the reason things were done in the way they were done. However, I was also explaining bits of Star Trek II to my son.  And I started thinking – was “defending” the project really the right thing to do here? I thought not actually.  And I decided that this was an important moment to listen and learn (and step away from the keyboard a little) and not to defend. The event that was happening (or happened – I was not sure if it was live or after the event) was what it was. If the people there could not answer the questions coming up, and if our materials on the web and in the handouts could not answer the questions, then we had, well, failed. And my explaining things on Twitter was, in a way, a cheat only made possible because I was willing to ignore family time and be online.

So – I did not completely put away the keyboard but I stopped trying to explain it all away and started trying to just listen and to accept that things had gone a bit awry. Anyway – clearly those of us involved in SpaceMicrobes need to do a better job in multiple areas. I will not try to defend or explain or justify everything here either. But I will say – thanks. To the people who are willing to ask questions and have high expectations. I will just end this post with a few of my last Tweets

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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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Tanja Woyke talk at UC Davis on Single Cell Genomics

Quick post.  Tanja Woyke – a friend a colleague from the DOE-JGI gave a talk at UC Davis a few days ago.  Some notes via Storify:

//storify.com/phylogenomics/talk-by-tanja-woyke-of-doe-jgi-at-ucdavis-on-singl/embed//storify.com/phylogenomics/talk-by-tanja-woyke-of-doe-jgi-at-ucdavis-on-singl.js[View the story “Talk by Tanja Woyke of @DOE_JGI at #UCDavis on “Single Cell Genomics”” on Storify]
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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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Microbial forensics and phylogenetics go hand in hand

Interesting story in Nature today: Science in court: Disease detectives : Nature News & Comment.  It details a bit of the history and current approaches to forensics associated with microbes and has quotes from many of the key players in the field.  It discusses anthrax, HIV, the FBI, Bruce Budowle, David Hillis, and more.  Definitely worth a look for anyone interested in either microbial diversity of phylogenetics.  I have been interested in this topic for a very long time – pretty much since I was recruited to apply to work at the FBI many many years ago.

I have been to a few recent meetings on the topic organized by the White House OSTP and the FBI and I think there is lots of interesting work that can happen in this area.  The development of Phylosift in my lab was funded by a grant from DHS (to myself and THE Aaron Darling who has since left to a large island near New Zealand) largely in relation to microbial forensics.

See some related posts:

In particular people might want to check out the Mendeley Group collection of references on the topic I have made: Microbial Forensics | Mendeley Group

//www.mendeley.com/groups/1147121/microbial-forensics/widget/29/3/

Microbial Forensics is a group in Biological Sciences, Law on Mendeley.

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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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Shocked – shocked to hear that some fake papers got published in CLOSED ACCESS journals

Oh no.  This world.  It vexes me.  I am vexed.  I thought that only Open Access journals published papers that were fake science.  Now it turns out – closed access journals also sometimes have no peer review and overzealous pulsing pressures: Publishers withdraw more than 120 gibberish papers : Nature News & Comment.  How can I go on?  I thought peer review was perfect and all journals were honorable.  Oh well.  Back to work

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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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Wanted – participants and helpers for a "Women in Science" Wikipedia Editathon at #UCDavis March 4 – UC Davis ADVANCE

I wrote a post on the UC DAVIS ADVANCE Blog recruiting people to participate in a Wikipedia Editathon regarding Women in Science: Wanted – participants and helpers for a “Women in Science” Wikipedia Editathon at #UCDavis March 4 – UC Davis ADVANCE

And Phoebe Ayers from the UC Davis Physical Sciences and Engineering Library has volunteered to host the event there.

See her post about this.   Please consider signing up to participate if you are around UC Davis at that time …

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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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At #UCDavis today: – Storer Speaker: Dr. Patricia Wright: Lessons from the Lemurs: Senescence in Madagascar

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Patricia Wright flyer 1.pdf

Seminar at #UCDavis 2/24 C. Titus Brown: Genomics And Bioinformatics In Non-Model Organisms: Where Is The Data Tidal Wave Bringing Us?

Good Morning,

Dr. Titus Brown, Candidate for Assistant/Associate/Full Professor of Genetics, Department of Population Health and Reproduction, will present a seminar titled, “Genomics And Bioinformatics In Non-Model Organisms: Where Is The Data Tidal Wave Bringing Us?” on Monday, February 24, 2014, 3:10-4:00pm in 1041 Valley Hall.

Thank You,

Brown Seminar Presentation Announcement.pdf

Antidiscriminatism – a new religion for the good people of Arizona

Am so disturbed by the new Arizona bill that proposes to allow people to discriminate against others if someone about the others violates their religious beliefs.  I wanted to declare a boycott of all Arizona academic institutions if the bill passes, but I thought better of that (for now).  And so instead I am in the process of creating a new religion that would allow good people of Arizona to discriminate against discriminators.  I know this is not fully thought out but I just had to share something …

Antidiscriminatism

When in the course of human events, it becomes necessary for the people to dissolve the political bands which have connected them with the State of Arizona, a decent respect to the opinions of hummankind requires that they should declare the causes which impel them to the separation.  Alas, despite a previous well-known Declaration in 1776 that “all … are created equal” and “endowed by their Creator with certain unalienable Rights, that among these are Life, Liberty and the pursuit of Happiness.” the State of Arizona threatens to ignore this declaration and to hide under the guise of religious freedom to declare that some people are less equal than others.  In every stage of these oppressions many have petitioned for redress in the most humble terms, yet, our repeated petitions have been answered only by repeated injury. Nor have we been wanting in attentions to our Arizonian brethren. We have warned them from time to time of attempts by their legislature to extend an unwarrantable jurisdiction over free people. We have reminded them of the circumstances of our emigration and settlement here. We have appealed to their native justice and magnanimity, and we have conjured them by the ties of our common kindred to disavow these actions, which, would inevitably interrupt our connections and correspondence. They too have been deaf to the voice of justice and of consanguinity. 

We, therefore, the citizens of the rest of United States of America, declare the creation of a new religion to counter the discrimination found both in Arizona and throughout the land.  This religion shall be known as Antidiscriminatism.  The main tenets of this religion are below:

  • The creator of the world created many different people’s among which are found many diverse appearances, skills,  behaviors, preferences and other traits.
  • Discrimination against any of these people for any reason – whether explicit or implicit – whether justified by religious texts or by word of mouth – is hereby declared to be evil and is forbidden.
  • Any association with those who discriminate is an indirect support of evil and is forbidden.
  • Any payment of taxes or fees to any institution (government or otherwise) that supports discrimination shall be forbidden.
  • Any verbal or written or other support for discrimination is hereby forbidden.
  • Any association with any who have expressed verbal, written or other support for discrimination is herby forbidden.
  • Only one kind of discrimination shall be allowed – discrimination against those who discriminate.

Given the tenets outlined above, if the people of Arizona or any other state declare that discrimination will be allowed for religious reasons we free people of the United States of America declare that we shall make use of such laws to not associate in any way with those who discriminate. 

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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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