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

iEvoBio Applications open for iEvoBio 2012 Travel Awards

From Hilmar Lapp

The 2012 conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) is offering limited funds for travel expenses for the 2012 iEvoBio meeting in Ottawa, Canada. Preference will be given to participants lacking sources of funding for meeting attendance, such as graduate students, emerging professionals, and participants from underrepresented groups and countries. Please explain in an attached document the need for funding, the benefit that attending iEvoBio will afford you and how you will contribute to the meeting (max 350 words). We are looking for do-ers! A brief letter of support from your advisor, supervisor, or professional mentor should be submitted to the organizing committee (electronically), together with the application headed by the information below, to travelaward by the deadline of 15 April 2012.

Participants are required to make all their own travel arrangements, including visas and lodging, if required.

Application format:

Name:
Contact information (address/phone/email):
Academic Institution:
Role (student, researcher, etc.):
Origination of travel (if different from home institution) and estimated travel expenses:
Explain the benefit that attending iEvoBio will afford you and what you will bring to the meeting (350 words or less):

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:

——–
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.

——–

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:

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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.

——–

Phyloseminar: David Liberles speaks March 28th on “Protein Structural, Biophysical, and Genomic Underpinnings of Protein Sequence Evolution”

"Protein Structural, Biophysical, and Genomic Underpinnings of Protein
Sequence Evolution"
David Liberles (U Wyoming)

Common models for amino acid substitution assume that each site
evolves independently according to average properties in the absence
of a genomic, protein structural or functional context. Two
characterizations of amino acid substitution will be presented. One
approach extends a population genetic model to inter-specific genomic
data and a second approach evaluates the effects of selection for
protein folding and protein-protein interaction on sequence evolution.
Several take home lessons include the importance of considering
linkage independent of protein structure, the importance of negative
pleiotropy (or not statements in folding and binding), and the nature
of the co-evolution of sites and how it links standard substitution
models with covarion models when binding function is conserved and
when it changes.

West Coast USA: 13:00 (01:00 PM) on Wednesday, March 28
East Coast USA: 16:00 (04:00 PM) on Wednesday, March 28
England: 21:00 (09:00 PM) on Wednesday, March 28
France: 22:00 (10:00 PM) on Wednesday, March 28
Japan: 05:00 (05:00 AM) on Thursday, March 29
New Zealand: 09:00 (09:00 AM) on Thursday, March 29

http://phyloseminar.org/

BABS Special March BABS at Fairfield Osborn Preserve, March 31

Bay Area Biosystematists Meeting: Saturday, 31 March, 2012

at Fairfield Osborn Preserve, Sonoma State University

Capturing Biological Diversity at Northern California Nature Preserves

Northern California is a biologically rich environment where many lineages of organisms from diverse origins have come together and have rapidly diversified. It is also a populated region with diverse land uses, an environment-conscious population, and many invasive species that threaten native ecological communities. Environmental change models offer differing predictions about future conditions in the region. Our speakers will describe the coverage of topographic and biological diversity found in the North Coast region, especially in nature preserves. They will also describe current efforts to document long-term changes in the environment.

Program organized by Nathan Rank and Claudia Luke of Sonoma State University.

Speakers:

Claudia Luke, Sonoma State University Nature Preserves– Introduction to topic and speakers.

Lisa Micheli, Pepperwood Preserve– Ground up development of a network to quantify biotic and environmental change in the North Coast region.

Stuart Weiss, Creekside Center for Earth Observation, Think Big, Connect More: The Bay Area Conservation Lands Network.

Schedule and venue:

2:00 – Guided tour of Preserve trails. We will explore ponds and creeks and visit an overlook with chapparal vegetation. We will also observe invertebrate and amphibian diversity in Preserve wetland habitats.

5:30 – Pizza, salad, and beverages at Fairfield Osborn Preserve Education Center (6544 Lichau Road, Penngrove CA) cost approx. $12.

6:30 – talks followed by discussion.

Please email RSVP to Nathan Rank, rank by Sunday Mar 25. Please specify whether you wish to come on the Preserves guided tour at 2:00 or just to the pizza and talks.

For directions, enter the address above into Google Maps or download directions at (http://www.sonoma.edu/preserves/docs/application/osborn_directions.pdf). Parking is free, carpooling encouraged.

All are welcome, members or not. If you want to join the Biosystematists, a venerable yet exceptionally lively group that provides the only inter-institutional seminar/discussion forum addressing evolutionary topics in the Bay Area, visit our website at: http://www.biosystematists.org/ to sign up for our mailing list.

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.

——–
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.

——–

ABGG Seminar: Maxine Zylberberg, Friday at 12:10 in 6 Olson Hall

This week’s Animal Behavior Graduate Group seminar (last of the quarter):

Dr. Maxine Zylberberg

California Academy of Sciences

ABGG Exit Seminar: Disease Defense Strategies: Linking Behavior, Immune Function and Disease Ecology in Galápagos Finches and House Finches

Friday, March 16, 12:10 in 6 Olson Hall

Coffee and cookies will be available

From Maxine’s website:

Research Interests: I take a multi-disciplinary approach to the study of disease ecology, drawing from the fields of ethology, behavioral ecology, and immunology to inform my study of disease dynamics in wild bird populations. I am particularly interested in how host behavior at both the individual and group level affects disease dynamics across a variety of geographical and temporal scales, from seasonal disease dynamics, to small and large scale geographic variation in disease prevalence, to evolution of pathogen virulence. My dissertation work focused on the ecology of avian pox in Galapagos finches, in particular annual variation in prevalence and recovery rates, and the importance of both behavior and immunology as underlying drivers of disease dynamics. In addition, I used house finches as a model system to study the relationship between individual behavior and immune function in captivity. I have participated in a number of collaborative projects in the fields of disease ecology and conservation, examining seasonal variation in the physiology of a nomadic species (red crossbills) and parasite load, the ecological correlates of long term variation in malarial parasites of mountain white-crowned sparrows, the inclusion of local experts in biological research, and best methods in conservation management practices.

Publications:

Wang D, Coscoy L, Zylberberg M, Avila PC, Boushey HA, Ganem D, DeRisi JL. Microarray-based detection and genotyping of viral pathogens. (2002) Proc Natl Acad Sci U S A 99(24), 15687-92

Cornelius J. M.; Zylberberg M.; Breuner C. W.; et al. 2006 Reproductive status and hematozoan parasite load in the opportunistically breeding and nomadic red crossbill, Loxia curvirostra. Integrative and Comparative Biology, Volume: 46: E182-E182

Cornelius J. M.; Zylberberg M.; Breuner C. W.; et al. 2009. Stress physiology and parasite burden differ during winter and summer breeding in a north-temperate zone temporal opportunist, the red crossbill Loxia curvirostra Integrative and Comparative Biology, 49: E37-E37

Elbroch, L., Mwampamba, T., Santos, M., Zylberberg, M., Liebenberg, L., Minye, J.,Mosser, C.,Reddy, E. 2011. The value, limitations and challenges of employing local experts in conservation research. Conservation Biology, 25: 1195-1202

Santos, M., Zylberberg, M., Reddy, E. Testing for conservation transferability in the Cape Floristic Region, South Africa. (submitted) Biological Conservation

Deiner, K., Forrester, T.,Grof-Tisza, P., Santos, M. J., Souza, L., Wilkerson, M. L., Zylberberg, M., Schwartz, M. W. Conservation management frameworks: the what, where and how of managing biodiversity. (submitted). Journal of Environmental Management

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.

If you go to line 405, you can contribute to the California Breast Cancer Research Fund and if you go to line 413, you can contribute to the California Cancer Research Fund.

No contribution is too small, and 95 percent of contributions to these two programs via this tax check-off go directly to cancer research or community-based education.

Donations from line 405 go to our California Breast Cancer Research Program, which is renowned not only for its cutting-edge research, but also for working with community advocates and health care providers in targeting the issues and needs of patients and families, especially the underserved.

In recent years, donations from line 405 have supported critical research including: identifying environmental factors that potentially cause breast cancer; developing targeted therapies to block breast cancer from spreading to other organs; and improving support networks to empower patients as they maneuver the health care system. See this website for more information: http://cabreastcancer.org/taxcheckoff/

Donations to line 413 go to the California Cancer Research Fund, which is helping to provide prevention and awareness programs in communities disproportionately affected by cancer. One major ongoing project is increasing the understanding of the impact of tobacco use and cancer on vulnerable populations. This research could lead to reduced smoking, increased cancer awareness and strengthened prevention programs.

I wanted to be sure you were aware of this means of investing in research that can serve all Californians and our communities.

Sincerely,

Lawrence Pitts, M.D. Provost and Executive Vice President University of California, Office of the President

However, I wonder about the open access requirements of the fund. I sniffer around at their web site http://cbcrp.org/about/ and could not find anything about guaranteeing access to the results of the work supported by this fund. That is too bad – this seems to be a great case where openness could be both a good thing and a useful marketing tool (to get people to chip in money from their taxes).

——–
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.

——–

GGG evolutionary genetics seminar series

evol_flyer.pdf

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.

Dataset Papers in Genetics is part of a new journal platform that Hindawi is developing called Datasets International (http://www.datasets.com). The main objective of Datasets International is to help researchers in all academic disciplines archive, document, and distribute the datasets produced in their research to the entire academic community. In addition to publishing a series of journals devoted to the dissemination of Dataset Papers, Datasets International hosts the underlying data behind these Dataset Papers and makes it accessible to all researchers worldwide.

The journal will be run using a collaborative editorial model which is designed to provide a fast peer review process for all submitted manuscripts. The journal will be edited by a distributed Editorial Board, and it aims for an average review time of 4 weeks from submission until a final decision has been reached.

Manuscripts that are submitted to the journal will be sent to a number of Editorial Board Members (typically each manuscript will be sent to at least 5 Editors), who will have two weeks to provide either a recommendation for the publication of the manuscript, along with a written commentary detailing any improvements that the authors should make to their manuscript, or a written critique of why the manuscript should not be published.

After the two-week period has elapsed, if the majority of the editorial evaluations recommend the manuscript be rejected, the manuscript will be rejected. If all the editorial evaluations that are received recommend that the manuscript be accepted for publication, the manuscript will be accepted. Otherwise, the editorial evaluations will be anonymously communicated to all of the Editors who participated in the peer review process. Each Editor will be given an additional week to review the feedback of the other Editors and to either confirm or revise their earlier editorial recommendations. If the majority of the editorial evaluations that are received by the end of this second round of review recommend the manuscript be accepted for publication, the manuscript will be accepted. Otherwise, the manuscript will be rejected. If the manuscript is accepted for publication, the names of the Editors who recommended the publication of the manuscript will be published alongside the ma!
nuscript. More information on the journal is available on the following web pages:

http://www.datasets.com/ (Datasets International Home Page)
http://www.datasets.com/journals/genetics/ (Journal Home Page)
http://www.datasets.com/journals/genetics/workflow/ (Editorial Workflow)
http://www.datasets.com/journals/genetics/editors/ (Editorial Board)

The journal will be published using an open access model, which allows disseminating scholarly articles by removing the access barriers imposed by the subscription model, in order to make the full-text of all published articles freely available for any interested reader. In this model the publication costs of an article are covered in the form of Article Processing Charges, which are publication fees paid from the research budget of accepted authors. In this model authors retain the copyright of their work, and we make every possible effort to ensure that the full-text of every published article is both visible and accessible to all potential readers.

Manuscripts that are submitted by the members of the Editorial Board of Dataset Papers in Genetics to the journal will automatically receive a 50% reduction in their Article Processing Charges.

Please do visit the web pages above and let me know if you have any questions or comments. We hope you will accept to join the Editorial Board of the journal and I will be looking forward to hearing from you soon.

Best regards,

Safa Tahoon

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Safa Tahoon
Journal Developer
Hindawi Publishing Corporation
http://www.hindawi.com/
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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.

——–