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

Biomedical Ph.D. Career Development Trends, Wed 10/22 @ 3 pm at #UCDavis

well, this could be intersting :

This announcement is sent on behalf of Associate Dean John Harada

Biomedical Ph.D. Career Development Trends: Implications for Workforce Development & Diversity

· Wednesday, October 22, 2014 at 3:00 – 4:00 PM

· Location: Memorial Union, MUII room (2nd floor)

· Target Audience: STEM faculty, postdocs, and students

· Recent biomedical workforce policy efforts have centered on the twin challenges of enhancing career preparation for graduate students and postdocs, and increasing diversity in the research workforce & professoriate. Dr. Gibbs will discuss results of his work that has focused on the graduate and postdoctoral training experiences and career-decision making of recent Ph.D. graduates, and whether/how these differ across lines of race/ethnicity and gender. Specifically, Dr. Gibbs will share from a focus group study, and national survey of 1500, recent biomedical PhD graduates (including 276 from URM backgrounds).

· Speaker: Kenneth Gibbs, Jr., PhD, is a Cancer Prevention Fellow at the National Cancer Institute (NCI). Dr. Gibbs conducts policy-relevant research aimed at strengthening the research enterprise.

· For more info and to RSVP: http://goo.gl/forms/IScrjZUBrE

flyer – Biomedical PhD Career Pathways.pdf

Aspen Center for Biophysics: Workshop on Microscale Ocean Biophysics

Just got this from the Moore Foundation ..

Dear colleague,

The MMI team would like to apprise you of the following meeting on microscale ocean processes. Please share with potentially interested colleagues; the application deadline is quickly approaching — October 15, 2014. Further information can be found at http://www.aspenphys.org/physicists/winter/winterapps.html and tinyurl.com/MicroAspen.

Workshop on Microscale Ocean Biophysics

At Aspen center for physics

11-16 January 2015

Application deadline: 15 October

This highly interdisciplinary meeting will focus on how physical processes affect aquatic organisms at small scales, and thereby the global processes in oceans and lakes that microorganisms overwhelmingly govern. Over the past two decades, there has been a growing realization that the ecology of these organisms depends not only on the bulk environmental conditions, but also crucially on small-scale biophysical interactions and microscale heterogeneity in the physical and chemical conditions. It is becoming clear that physical processes play a fundamental role in shaping the microscale landscapes that form the arena in which these organisms forage, reproduce and encounter each other. A key goal of this meeting is to help advance our understanding of aquatic ecosystems by replacing current statistical and heuristic descriptions with a mechanistic understanding of the component processes. This cannot be achieved without a strong appeal to small-scale fluid physics, mass transport, active suspensions, turbulence, and mechanics in general. The result is a rich landscape of opportunities for physicists, mathematicians, chemists and engineers to be involved in oceanographic and environmental problems, and for oceanographers, biologists and ecologists to inspire and utilize physical concepts and approaches more pervasively. The vision underpinning this meeting is that the interdisciplinary application and advancement of these topics in the context of oceanographic processes will greatly improve our understanding of how organism life is constrained and has evolved to exploit the fundamental laws of physics.

Deadline to apply is October 15, 2014

Apply here:

http://www.aspenphys.org/physicists/winter/winterapps.html

Organizers:
Roman Stocker (MIT)
Stuart Humphries (University of Hull)
Thomas Kiørboe (Technical University of Denmark)
Lee Karp-Boss (University of Maine)
Justin Seymour (University of Technology, Sydney)

At #UCDavis Leonid Chindelevitch, 10/09/14 “Probing Networks to Understand Nature”

Department of Computer Science Colloquium Seminar Series

Speaker: Leonid Chindelevitch

Harvard, MIT

Host: Dan Gusfield

WHEN: Thurs. Oct 9, 2014 3:10pm

WHERE: 1131 Kemper Hall

Title: Probing Networks to Understand Nature

Abstract: Networks are a fundamental tool for understanding the intricate interconnections that govern biological systems. This talk will describe two ways in which networks, in combination with mathematical models and algorithmic techniques, can yield valuable biological insights.

Causal regulatory networks help reveal the hidden regulators of gene expression patterns. To facilitate their analysis we established an efficient method for evaluating the significance of the overlap of ternary signals, which generalizes Fisher’s exact test. We used this method to analyze a large-scale causal regulatory network and uncovered new regulators of cardiac hypertrophy.

Metabolic networks help identify novel drug targets. We uncovered structural features of these networks that had been missed by previous researchers, and developed a theoretical framework based on duality for analyzing them in a consistent fashion. We used this theoretical framework to create a new metabolic network for Mycobacterium tuberculosis by algorithmically merging two existing networks, and identified several putative drug targets.

Bio: My research interests lie primarily in the modeling of infectious diseases, both on the molecular level (using approaches from computational and systems biology) as well as on the population level (using approaches from epidemiology and biostatistics). I am particularlly interested in the interactions between science, medicine and policy as they relate to improving patient outcomes, especially in low-income, low-resource settings.

Session on microbial interactions at ASLO 2015 in Spain

Email just received:

Dear colleagues,

This is just to remind you that the deadline for abstract submission (October 10) for the ASLO Aquatic Sciences Meeting in Granada, Spain, 22-27 February 2015 is coming closer. We would like to invite you to participate in our session "MICROBIAL INTERACTIONS ACROSS THE DOMAINS OF LIFE" (# 058). We are looking forward to your contributions on microbial interactions, as well as evolutionary studies related to understanding microbial ecology. Please find more details in the flyer attached.
Feel free to pass this on to other colleagues who might be interested.

Thank you,
Susanne, Valeria & Alex

Deadline for Abstract Submissions: October 10, 2014
http://sgmeet.com/aslo/granada2015/

Session058_AquaticSciencesMeeting_Granada_Spain_Feb2015.pdf

Workshop at #UCDavis: Overcoming Imposter Syndrome with Valerie Young #UCDAdvance

Please forward to graduate students and postdocs (flyer):

How to Feel As Bright and Capable As They “Think” You Are

Why Smart People (including Graduate Students and Postdocs!) Suffer from the Impostor Syndrome
and How You Can Thrive In Spite of It


Thursday, October 9, 2014
2:00-4:00pm | Conference Center, Ballroom A&B
Please Register: http://tinyurl.com/OverComingImpostorSyndromeF14

· Do you secretly worry that others will find out you’re not as intelligent and competent as they seem to think you are?

· Do you often dismiss your accomplishments as a “fluke” or “no big deal?”

· Do you think, “If I can do it, anyone can”?

· Do you sometimes shy away from taking on even greater challenges because of nagging self-doubt?

· Are you crushed by even constructive criticism, taking it as evidence of your ineptness? If so, join the club!


Key Take Aways

§ Why the impostor syndrome is not “just low self-esteem”

§ Creative ways “impostors” discount or minimize their success

§ Perfectly good reasons why smart people feel like frauds

§ How your personal Competence Type may be setting you (or your students) up to fall short

§ Procrastination, holding back and other unconscious coping strategies “impostors” use to avoid being found out

§ The role of academic culture in fueling self-doubt

§ Why women are both more susceptible to and held back by impostor feelings

§ Practical steps to help yourself, your students, or high achieving children to interrupt the impostor syndrome and end needless self-doubt

You’ll walk away with practical strategies for interrupting the Impostor Syndrome that you can start using immediately. By applying these simple but powerful techniques you’ll finally be able to begin to see yourself as the bright, competent person you really are!

Dr. Valerie Young is an internationally known speaker and the author of the award-winning book The Secret Thoughts of Successful Women: Why Capable People Suffer from the Impostor Syndrome and How to Thrive in Spite of It (Crown/Random House) now available in five languages including Russian. Valerie has addressed such diverse audiences as Chrysler, Intel, IBM, P&G, Boeing, Merck, McDonalds (Europe), Society of Women Engineers, American Women in Radio and Television, and faculty and students at over 60 other colleges and universities including Harvard, Stanford, Cornell, MIT, and Princeton. Her work has been cited in such publications as The Wall Street Journal, USA Today Weekend, O magazine, Entrepreneur, Kiplinger’s, Inc., The Chicago Tribune, Sydney Morning Herald, More, The Globe & Mail, Woman’s Day, Redbook, and the Irish Independent.

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.

——–
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.

——–

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.

——–
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.

——–

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.

——–
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.

——–

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