Eisen Lab Blog

All Nobel Prizes in 2014 Will be Microbially Themed: The Microbes Guarantee It

So – last year I secretly created a microbiome based spying system that can transmit the thoughts and emails of people who they colonize.  I introduced this community into all the people on the various Nobel Prize committees in order to get information in advance about their plans for the Nobel Prizes. After getting such information, and discovering that the Nobel’s this year were NOT focused on microbes, I then created a microbiome-behavioral manipulation system and re-infected the Nobel committees with this community.  This community forces their host to think about microbes all the time.  All microbes.  All the time.  And thus I am nearly 100% certain that all the Nobel’s this year will be about microbes in some way.

Given that, here are my predictions for the All-Microbial Nobel Prizes.

Medicine:
The Human Microbiome and Methods for Studying Microbial Communities.  Should go to Norm Pace and some other people.  Possibly Jeff Gordon.  Possibly Jo Handelsman.  Possibly others.  Depends on how much the microbes in the committees emphasize themselves versus all microbes.

Physics:
Vera Rubin for her work on “Dark Matter” since we all know that the key dark matter in the universe is “microbial dark matter”.

Chemistry:
Discovery and characterizing of the mechanisms of CRISPRs.  No clue who will get this but it likely could include Jennifer Doudna and Emmanuelle Charpentier and others.

Peace:
Bill and Melinda Gates and their foundation for their work on global health, especially on protecting from infectious diseases.

Literature: Ursula K. Le Guin in particular for her Wrinkle in Time series and its emphasis is on mitochondria.

Economics:
Well, since microcredit has already won an Economics prize, I am not sure how this will play out but certainly it will involve some type of microeconomics.  Definitely NOT macroecnomics. I think the most likely winner here is Esther Duflo because of her work on both microeconomic topics and microcredit.

Me: Will survey results be published openly. Them: yes. Me: OK – will do survey. #opensurveys

Got this email:

Dear Jonathan, 

Your peers at the University of California, Riverside, Stanford University, and the Coachella Valley Association of Governments are seeking participation in a survey designed to explore the relevancy and perceptions of basic natural history knowledge and skills among professionals and graduate students in environmental science-related fields.
Professionals and Faculty (including post-doctoral researchers) may access the survey through the following link:https://stanforduniversity.qualtrics.com/SE/?SID=SV_9XmYW9WipZ0JGm1 

If you cannot complete the entire survey all at once, you can return to the survey within 30 days to complete it at your convenience. 

This survey will be distributed at universities, organizations and agencies state-wide, and we would greatly appreciate your participation! All responses will be kept completely confidential. The information collected will be used to provide summary statistics and form the basis of a peer-reviewed publication. 

Please feel free to forward this survey link to peers within California that may be interested in participating. Thank you for your assistance! 

****************************************************************************** 

Should you have questions about this study please contact us: natural.history.survey@gmail.com

Michelle Murphy-Mariscal, M.S. (Center for Conservation Biology, UC Riverside)Cameron W. Barrows, Ph.D. (Center for Conservation Biology, UC Riverside)Rebecca Hernandez, Ph.D. (Stanford University, Carnegie Institution for Science)Kathleen Fleming, M.S. (Coachella Valley Association of Governments)

—————————————–
I wrote back

Thanks for the invite.

Can you tell me more about what will happen to the results from the survey? I only participate in surveys if the data and publications from the survey will be released in an open access manner.

Jonathan Eisen


And then got a very pleasing response:

Hi Jonathan, 

Yes, the results and data of the survey will definitely be published. Attached is a previous, survey-based study and we published the data set in Dryad (an online data repository that you are probably familiar with). The survey that my group and I are doing currently will follow the same format and strict adherence to open access. 

Thank you very much for your participation. 

Warmly,
Rebecca

And then I did the survey and sent this email:. 

Thanks so much for the response and I so pleased with your commitment to openness. I will now gladly participate and share w/ California colleagues.

Why I Tweet and Blog: Captured by Beryl Lieff Benderly

You know, many people ask me – why do I talk to science reporters so often.  They ask this and then claim that science reporters are just all kinds of evil because they always get quotes and facts and concepts wrong.  Well, that has really not been my experience.  Sure, I have my examples of problems.  But overall, I have been impressed and pleased more often than not.  And here is a great example. I was interviewed a while back by Beryl Lieff Benderly about my somewhat obsessive experimentation with social media for communicating science.  And then, of course, I forgot about it.  So I was exceptionally pleased when I saw the story come out today: To tweet or not to tweet? | Science Careers.  Beryl did a remarkably good job in capturing the essence of my thoughts about Tweeting, Blogging, social media, and science communication.

If you want to know what I think about how to not get overwhelmed with Twitter, how to not spend too much time on social media, and what I think abotu aboutb social media, you don’t need to wait for me to try to write my thoughts on the topic down.  Read what Beryl wrote.

Sexism in Science

“Are you going to church before your oral exam?”. That was the question I’d asked my friend jokingly when I saw her dressed in a funny looking attire, which I can only describe as a floral print, beige colored, raincoat. Except it wasn’t waterproof.
“No, I’m wearing it to the oral exam”, was her simple response. Something didn’t seem right here. This is a girl who is very fashion conscious and in a city like Davis, where T-shirt and jeans/shorts is the norm she can sometimes standout as well dressed.
She doesn’t just wear clothes that are “expected” of a female grad student, but she also wear skirts, dresses and a menagerie of clothing articles for which I don’t even know the names. She dresses nice because she like to. That’s her individuality and freedom of expression. So I probed her some more.

She said, “One of my committee member had given me a review on one of my previous talks. It said, Please don’t treat these seminars as a fashion show. It distracts the people away from your work”.

Safe to say I was not only stunned but riled up. It was incredibly sexist.
And then she pointed out that she also sewed another button to make sure that this dress can’t be considered even revealing. A beige color floral dress with puffy shoulders going below the knees that could be adorned by septuagenarian.
How can someone say that? This is not appropriate. This is was my second hand encounter was with sexism in science.
No one would ever say such a thing to me. Not that I dress very fashionably, but to any man. No one points out a guy’s baggy jeans mopping up the university buildings. Or comments on the unkempt male grad students who might be spreading more than their “usual” skin microbiota around. And trust me, there are plenty of those in Davis. That’s a ok. But we are judging a woman’s clothes because she decides to “dress up”. And to make it worse, we are blaming her of distracting people from her talk/seminar/work. Where have I heard that before. Ohh, here or here or here.
I know it’s taking it to extreme, but this is where is begins. One that needs to be distracted at a science talk can always look at the guy sleeping in the front row, or the loud whisperers in the back. They don’t need to look at a speaker’s clothes for that.

But the cake isn’t finished without the icing.

After her exams, I met up with her to congratulate. I asked about what all happened in the exam. She said something to the tune of “Towards the end, the person who’d commented earlier was apologetic for clothing remarks. But.”
There was a but.
“But when reviewing my transcript the committee laughed about how come I played varsity basketball. And as I was leaving another committee member tried to explain that they weren’t laughing about my basketball career because I was short, but because I wore a dress”.
Listening to it my jaw dropped. Are you f…ing kidding me? They’re incredulous towards her sports career. And made an effort to explain that’s not because of her below average height but the fact she wore a dress. I didn’t realize that for a girl to be taken seriously as an athlete she has to wear Tee, shorts and sneakers. Even three-four years after the fact. And these are “well educated” scientists from a renowned university we’re talking about.

How is that we have seminars and counseling available on sexual harassment and ethics in science, but nothing on sexism, another widespread scourge in the STEM fields. It should be part of the sensitivity training. It might be possible that the university offers it now, but I don’t remember being mandated to take one. They could also be useful for the international students like myself, where the cultural differences may require one to get acquainted with the local customs and the knowledge of “Acceptable or not acceptable”. It is about time we realize and break the stereotypes that were created decades (if not centuries) ago. No one deserves to be mistreated and (mis)judged because of their genitalia. We need an environment which supports science from men and women equally. Gone are the days when universities had only men’s room, today’s scientists should be free to do science in a supportive environment, free of sexism and gender discrimination.

Disclaimer
As a promise to her, I’ve kept certain details confidential and will not be divulged.
My PI is one of the campaigners for the women’s right and #STEMwomen and had no influence on this post. It is my own rant.

Rob Pringle – EVE seminar speaker at #UCDavis today 4 PM –3 Kleiber Hall

Got this in email and thought it would be of interest to many .. should be worth going to.

Rob Pringle from Princeton is the first seminar speaker of the Ecology and Evolution seminar series. Rob is a very versatile ecologist with many interests and passions. (http://www.princeton.edu/eeb/people/display_person.xml?netid=rpringle)
His interests in his own words:

I seek to understand how direct and indirect species interactions (predation, herbivory, competition, mutualism) combine with abiotic factors (climate, habitat heterogeneity) to determine the diversity and abundance of species at multiple scales. My method is rooted in natural history and manipulative field experiments and supplemented by whatever computational, isotopic, molecular, remote-sensing, and social-scientific approaches are necessary to understand the mechanisms underlying phenomena in nature. Most of this work is done in the savannas of eastern and southern Africa.

My current work focuses on three interrelated sets of questions. First, what are the functional roles of large mammals in savanna systems, how are these functional roles contingent upon climate, and what are the ecological consequences of large-mammal extinction? My lab is working on these questions in central Kenya (where since 2008 we have been excluding different large-herbivore species from a series of 1-ha plots replicated across a rainfall gradient) and Mozambique’s Gorongosa National Park, where large-mammal populations are recovering following near-extinction of many species from 1977-1994.

Second, how does self-organized spatial pattern arise in landscapes, and what are the consequences of this patterning for animal behavior and ecosystem functioning? Throughout much of Africa, termite mounds occur in strikinglyoverdispersed spatial patterns. We know that these patterns are ubiquitous and ecologically important, yet we have limited understanding of how they arise and what emergent effects they have at the ecosystem scale. Work here is also concentrated in Kenya and Mozambique.

Finally, I am using small experimental islands in the Bahamas to extend classic work about how invasive predators and competitors affect the behavior, population dynamics, and coexistence of Anolis lizards, and how interactions among lizards propagate to influence island food webs more generally.

Michi Taga at #UCDavis today: Corrinoids in Communities: Nutrient Sharing in the Microbial World

MIC 291: Selected Topics in Microbiology

Work-in-Progress Seminars

Dr. Michi Taga
(UC Berkeley)

"Corrinoids in Communities: Nutrient Sharing in the Microbial World"

Wednesday, October 1, 2014

4:10 pm

1022 Life Sciences

Taga 10-01-14.doc

Crosspost from microBEnet: Some interesting new papers on functional analysius of metagenomics

Crossposting from microBEnet:

Some new papers that may be of interest to people:

Crosspost from microBEnet: Collection of papers on "The Science of Science Communication"

Crossposting this from microBEnet 

 Just got pointed to this by Sharon Strauss, the chair of the Evolution and Ecology department here at UC Davis: The Science of Science Communication II Sackler Colloquium.  This is a collection of papers from a colloquium held in Septment 2013.  Slides and videos of the talks are available online. The papers and links (copied from the PNAS site) are listed below.  There are many papers here of relevance to work done at microBEnet and are also likely of general interest to many:

  • Select this article
  • Select this article
  • Select this article
  • Select this article
  • Select this article
  • Select this article
  • Select this article
  • Select this article
  • Select this article
  • Select this article
  • Select this article

Today on "Express Yourself" Teen Radio – me – being interviewed about #Microbes & #OpenScience

Just a little self-centered plug.  I was interviewed recently for Express Yourself! | VoiceAmerica™ teen radio show.  The teens interviewing me included Henna Hundal who worked in my lab this summer as an intern on our “Seagrass Microbiome” project. See a post from Cassie Ettinger about Henna’s work.  Also see:

//platform.twitter.com/widgets.js
It was a fun interview and I love the idea of teens doing a science radio show.   From their site

Science is everywhere. From the stars that light the night sky to the intricate patterns on a butterfly’s wings, science is at play in all parts of our world and is continually making our lives so great. Hosts Henna Hundal and Courtney Chung discuss how science shapes our perspective on life from cell phones to lawn mowers, from cures for diseases to prosthetic limbs. Global Youth Talk reporter, Ryan Sim, talks about science careers in the United Nations, and how this international community is looking at science innovation to create solutions for the next generation. Special guest Dr. Jonathan Eisen,a Full Professor at the University of California, Davis, with appointments in the UC Davis Genome Center, the School of Medicine, and the College of Biological Sciences focuses on communities of microbes and how they provide new functions – to each other or to a host. Dr. Eisen is entertaining with his study systems of boiling acid pools, surface ocean waters, agents of many diseases, and the microbial ecosystems in and on plants and animals. In Health with Henna, Henna Hundal reports on how we can prevent the negative effects of prolonged sitting. It’s important to take those “stretch breaks” every hour. Whether it’s writing scientific articles, thoughtful science reporting, or even talking about science on the radio, integrating humanities with science is key to reaching a mass audience.

So – I recommend everyone listen …12 noon Pacific Time on VoiceAmerica Kids Channel. Express Yourself! | VoiceAmerica™

.

Personalized Medicine World Conference 2015: 55 speakers 7 of which are women #YAMMM #StemWomen

Well, umm, Ralph Snyderman, despite the email invitation I will not be attending PMWC 2015 Silicon Valley.  Why not?  Well how about the fact that you have 55 speakers listed, only 7 of which are women.

Previous year’s meetings are not much better.  For example, for the 2014 Meeting in Silicon Valley the Track 1 session (which they call the premier session or something like that) has a ratio of 52:5 Male:Female.