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

Yes, I am a #RedSox & #PLoS fan; & this video sort of is proof #BenFranklinAward #OpenScience

Just saw this posted on Youtube.  Did not know it was coming … but am happy they recorded it

And here are the slides I used.  Will try to synch

Ben Franklin Award Slides

For more on this award 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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How about this? Wash your hands. Please. (Nice video from SLV Health)

Saw this news story a while ago: Videos help spread word of bacteria, other health issues | Deseret News but only just got to watching the video from Salt Lake Valley Health. 

I note – my post originally said “Wash you hands” and my 6 year old daughter was snooping at my computer and said “Daddy, it says ‘wash you hands’ not ‘wash your hands.'” Well, I think I found a new blog editor.

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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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Opening up one’s eyes to other fields (cross-posting from #microBEnet)

Cross-posting this: Opening up one’s eyes to other fields which I posted originally on the microBEnet blog.

I spend most of my time working on biology.  I like to think I cover lots of breadth within biology and I probably do – microbes, evolution, ecology, human health, pathogens, symbioses, forensics, genomics, bioinformatics, and more.  But nothing like really looking at other fields to realize how narrowly focused one is.

And that is what has happened to me since I took on the “microBEnet” project trying to foster communications and collaborations on microbiology of the built environment. I now pay much more attention to anything that might have a connection to “Building Science” in one way or another.  Not only did I just go to an Indoor Air meeting, but I keep discovering more and more stuff right near home that I was not aware of before.  For example – I just got sent this news link from Aaron Darling in my lab: UC Davis News & Information :: History of sciences in architecture subject of Mellon Foundation winner’s study.  Previously, I would definitely not have been paying much attention to architecture and history of science.  But now seeing other people at UC Davis working on the Built Environment just makes me think about how I can build connections with them and talk to them about buildings (and other built environments) and possibly, one day, about the microbes that are in them.

Which brings me to another story.  At the Indoor Air meeting earlier in the week in Austin, Texas, when heading to the conference center I got into a conversation with someone looking for the registration desk.  After showing her where to go she asked where I was from and I said “UC Davis.”  And it turns out – she was too.  Turns out, this was Deborah Bennett, who I had heard mentioned the evening before but had not heard the whole name.  I just knew someone else at the meeting was from Davis.   Deborah is at the UC Davis School of Public Health and works on some really interesting stuff.  And since UC Davis is so big (some 2500 or so faculty I think) – it is not always easy or simple to find people even if you might have a connection to them.

So anyway, just a little commentary on how I find it fascinating to see for the first what was in a way right before my eyes.

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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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Fun with Ligercat: pubmed word clouds

I have been having enormous fun over the last hour playing with LigerCat.  I was searching for ways to build tag clouds for papers in Pubmed and this came up: LigerCat: Using “MeSH Clouds” from Journal, Article, or Gene Citations to Facilitate the Identification of Relevant Biomedical Literature.   And they have a web site to do searches: LigerCat Literature and Genomics Resource Catalogue

So, of course, like many others, the first thing I did was search for myself:

Eisen JA

http://ligercat.ubio.org/articles/1365086.cloud

I then repeated the search, but excluded articles from the SIGS journals, since I have about 100 of those articles that are in essence “Genome sequencing reports”:

http://ligercat.ubio.org/articles/1365087.cloud

So this was fun. So then I played around with a variety of other searches

Phylogenomics

http://ligercat.ubio.org/articles/1364022.cloud

Indoor Microbiology

http://ligercat.ubio.org/articles/1365091.cloud

University of California[Affiliation] Davis[Affiliation]

http://ligercat.ubio.org/articles/1365093.cloud

Haloarchaea

http://ligercat.ubio.org/articles/1365095.cloud

Wolbachia

http://ligercat.ubio.org/articles/1365097.cloud

GFAJ-1

http://ligercat.ubio.org/articles/1365099.cloud

Some things did not work for some reason(microbiome, metagenomic) but overall this is a useful quick way to get a feel for topics covered in some area.

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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 update (pics, twitter feed) on #IndoorAir2011 in Austin, TX #microBEnet

Here are some pics from my trip to the Indoor Air 2011 meeting. I am going to post more detail about the meeting later.

https://picasaweb.google.com/s/c/bin/slideshow.swf

If you want some information about what happened at the meeting, best place right now is probably twitter

http://widgets.twimg.com/j/2/widget.js
new TWTR.Widget({ version: 2, type: ‘search’, search: ‘#IndoorAir2011’, interval: 6000, title: ”, subject: ‘Indoor Air 2011’, width: 250, height: 300, theme: { shell: { background: ‘#8ec1da’, color: ‘#ffffff’ }, tweets: { background: ‘#ffffff’, color: ‘#444444’, links: ‘#1985b5’ } }, features: { scrollbar: true, loop: false, live: true, hashtags: true, timestamp: true, avatars: true, toptweets: true, behavior: ‘all’ } }).render().start();

Also see the microBEnet blog which has some recent posts on this.

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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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Worst new omicsword, perhaps ever, the Dispensome #awful #badomics #reallybad #uggh

Well, I do not even have any idea what to say. I got pointed to this paper: PLoS Genetics: Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis by KamounLab on twitter. The authors of the paper include colleagues at the DOE-Joint Genome Institute so it is possible that they are baiting me to get some attention. But YHGTBFKM – the dispensome? Defined by them as “The dispensable chromosomes collectively comprise the dispensome and showed extreme plasticity during sexual reproduction.” Now, I have seen my share of bad omics words (and which I write about often with, for example, my Worst New Omics Word Award and Bad Omics Word of the Day). But this is the first case where the word, and the excessive use of it in the paper is distracting (as suggested by KamounLab) to the science. Is this word really necessary? Could they not just say “dispensable chromosomes” (which I note, I might still have problems with since they would only be known as dispensable under certain conditions)? But “dispensome” is unnecessary, distracting, and, well, not a good word. Thus in this case I have decided to not even give them an award per se but to simply say that I think this is possibly the worst omics word I have ever seen. I note – I am not criticizing the science (nor endorsing it mind you) they did here. But the word, oh the word. It hurts me. It really does.
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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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I like this pic of me so much it gets a whole post – "Apple Love" by Rhonda Roman

Apple Love by Rhonda Roman
 So a few Saturday’s ago I was at the Davis Farmer’s Market and Steve Smit from Mt. Moriah Farm’s showed me this pic that a photographer had given him.  Steve is one of my favorite people anywhere.  I don’t know why really.  But I go to the Farmer’s Market many times just to see him/buy stuff from him.  He is funny, warm, interesting, social, etc.  And apparently a photographer caught one of our interactions from earlier this year.  

Fortunately, she put her name on the back of the picture and a little googling and I found her photo collection on flickr.  Her name is Rhonda Roman and I really like her collections there.  But in particular I love this picture she took of me and Steven and others at the Market.  It captures everything really about my interactions with Steve.  Thanks Rhonda.  A picture is worth way way more than 1000 words.

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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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#UCDavis to partner with the Beijing Genome Institute (BGI)

Well, it is now formal so I guess I can post about it here.  UC Davis is officially developing a genomics partnership with the Beijing Genomics Institute (BGI).

For more on this breaking news see

Not much detail there I know – but in essence the plan is to build a partnership between UC Davis and BGI with BGI provided genomics and informatics expertise and capabilities and Davis providing biological expertise and diversity (of course, Davis has some genomics chops too and BGI does some biology but you probably get the point). 
For those who do not know, BGI is a relative newcomer on the block in terms of large scale genomics research institutes.  But by being new they have had a massive advantage in a way in that they are really the first to be developed as a “Second-generation Genome Center” having been built / developed with the new second generation sequencing systems at its core.  Thus while other large centers around the world have tried to adapt to the new second generation sequencing systems, BGI started from scratch and could build it’s enterprise around the new systems.  
I am excited about the possible connections with BGI though I confess I do not know a whole lot about the plans.  There have been lots of whisperings here at Davis about building a partnership with BGI and people have been a bit nervous about word getting out too early.  So, though I have heard some details I have not been an active part of the discussions.  However, whatever the plans are I am looking forward to interactions with BGI.  They are really pushing the frontiers of genome sequencing in many ways.  And despite the moans and groans from many people, I do not think genome sequencing is on a downward slope in any way.  For example, as a tool in studying microbes, genome sequencing still has many many years of use – after all there are hundreds of millions of microbial species that have yet to be studied and each one has lots of intraspecific diversity (e.g., across geography) to be characterized.  
And as a UC Davis faculty member I think BGI picked a great place to work with.  Davis has an almost unprecedented diversity of faculty working on some area in the life sciences – and these faculty come from across campus from the College of Biological Sciences, School of Medicine, Viticulture and Enology, School of Veterinary Medicine, College of Agriculture and Environmental Sciences, College of Engineering, School of Nursing, and College of Letters and Sciences.  In fact, you could say – in a way – UC Davis is a campus more dedicated to Life Sciences than almost any other place in the world.  
This development is just one of many that make me impressed with the new UC Davis Administration.    Ever since Chancellor Katehi came on board I have been pleased with almost every major initiative and development and administrative hire on campus.  Sure – the budget cuts from the California government hurt.  But in challenging times, you need great leadership.  And we certainly have it at UC Davis these days.  And if you think I am just sucking up, you should read some of the things I wrote about our previous administration.  I really am impressed here.  
I do not know what will happen with the BGI – UC Davis partnership.  Right now it is just a plan.  But I will do what I can to help it succeed and I am looking forward to interactions with BGI and the bright future at UC Davis. 
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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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Off to #IndoorAir 2011 in Austin, TX – to discuss and promote http://microbe.net #microBEnet

Well, off to Austin for a meeting I would not have imagined going to a few years ago. Indoor Air 2011. Why am I going? Because a few years ago I began to discuss studying the microbiology of the built environment with Paula Olsiewski, from the Alfred P. Sloan Foundation. You see, the Sloan Foundation has a new program in this area “The Indoor Environment“. Eventually, after much discussion I applied for a grant in their program. My grant is a bit unusual (for me and for others probably) in that it focuses on communication, coordination, networking, collaboration, etc.
My project is called “microBEnet” – which stands for “microbiology of the Built Environment network”. The BE is purposefully capitalized to emphasize the Built Environment part and we figure, since microbes are small, the m should be lower case. For more on the project see: Microbiology of the Built Environment Network | Site for the microBEnet project. As part of this project, a collaborator (Hal Levin) and I are doing many activities and I will post more about them over time. Among our activities are a new blog, and a diversity of resources.

Which brings me to Indoor Air 2011.  We are also starting to organize or help organize some meetings and workshops to bring together the various folks who might be interested in microbiology of the built environment.  And for Indoor Air we have helped the meeting organizer Rich Corsi plan some sessions on microbiology of the built environment.  The sessions take place Wednesday and Thursday and should be great.   Looking forward to going to Austin, maybe seeing some friends at UT and nearby (hint hint Dr. Hillis, Sheril K, etc) and learning about the built environment.

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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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Apparently, my own local paper hates my blog

I mean, I knew evolution was controversial and that I can be a bit snarky at times.  But does my own local paper -the Davis Enterprise have to have a whole article about how they hate me and my blog?

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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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