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

Online phylogenetics seminar 2/5 9 AM PST: Fiona Jordan "Testing hypotheses about cultural evolution"

From phyloseminar.org home. Online phylogenetics seminar 2/5: Fiona Jordan “Testing hypotheses about cultural evolution”

From the website:
Anthropologists had a name for the non-independence-of-species-problem way back in the 1880s. Solving “Galton’s Problem”, and the promise of comparative methods for testing hypotheses about cultural adaptation and correlated evolution was a major catalyst for the field of cultural phylogenetics. In this talk I will show how linguistic, cultural, and archaeological data is used in comparative phylogenetic analyses. The “treasure trove of anthropology” – our vast ethnographic record of cultures – is now being put to good use answering questions about cross-cultural similarities and differences in human social and cultural norms in a rigorous evolutionary framework.

West Coast USA:
09:00 (09:00 AM) on Tuesday, February 05

East Coast USA:
12:00 (12:00 PM) on Tuesday, February 05

UK:
17:00 (05:00 PM) on Tuesday, February 05

France:
18:00 (06:00 PM) on Tuesday, February 05

Japan:
02:00 (02:00 AM) on Wednesday, February 06

New Zealand:
06:00 (06:00 AM) on Wednesday, February 06

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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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The books of science online 2013 #scio13

Took pics of the books on display at Science Online 2013.

Here they are

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

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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.

——–

Cool new paper from DeLong lab: Pattern and synchrony of gene expression among sympatric marine microbial populations

Definitely worth looking at this paper if you are interested in uncultured microbes: Pattern and synchrony of gene expression among sympatric marine microbial populations.  From Ed Delong and team, it is published under the “Open” pathway in PNAS.

Also see press release here: Scientists track ocean microbe populations in their natural habitat to …

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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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Worth a read: The Sieve Hypothesis: Clever Study Suggests an Alternate Explanation for the Function of the Human Stomach | Guest Blog, Scientific American Blog Network

Quick post here pointing people to an interesting blog post by Rob Dunn: The Sieve Hypothesis: Clever Study Suggests an Alternate Explanation for the Function of the Human Stomach | Guest Blog, Scientific American Blog Network. Definitely worth checking out.

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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.

——–

Save the Date* IOM public workshop on “Microbial Ecology in Health and Disease ” 3/18-19 in DC

INSTITUTE OF MEDICINE

*SAVE THE DATE*

The Forum on Microbial Threats is pleased to announce a public workshop on:

Microbial Ecology in States of Health and Disease

March 18-19, 2013

Keck Building, Room 100

500 Fifth St., NW

Washington, DC 20001

Investigations of microbial ecology in a variety of organisms and contexts have begun to illuminate the properties of host-associated microorganisms. These observations have revealed a complex and dynamic network of interactions across the spectrum of “host”, “microbe”, and “environmental” niches that may influence states of health and disease. Alterations in the composition and dynamics of the human microbiota have been associated with a variety of complex diseases –including such chronic conditions as cardiovascular disease, obesity, and the inflammatory bowel diseases. This ‘ecologically’ informed view is a paradigm shift away from the conventional “one-microbe, one-disease” perspective of infection and may lead to new insights for health maintenance, disease prevention, and treatment approaches in humans, animals, and plants.

On March 18 and 19, 2013 the Institute of Medicine’s Forum on Microbial Threats will host a public workshop, in Washington, D.C., to explore the scientific and therapeutic implications of microbial ecology in states of health and disease. Topics to be explored may include: host-microbe interactions in humans, animals, and plants; emerging insights into how microbes may influence the development and maintenance of states of health and disease; the impacts of environmental change(s) on the formation, function, and stability of microbial communities; and research challenges and opportunities for this emerging field of inquiry. This meeting is an update of topics discussed at a 2002 Forum workshop: The infectious etiology of chronic diseases.

The workshop is free and open to the public, but registration is required. A DRAFT Agenda for this meeting is attached for your information.

Click here to register.

Click here for the Meeting Website.

Rediscover the IOM at our new website, www.iom.edu.

DRAFT AGENDA-March 2013 Microbial Ecology Workshop-012913.pdf

IBM will save the planet with this magical hydrogel – NOT

Well, press releases can drive me crazy.  And this one is one of the worst I have seen in a while: IBM News room – 2013-01-24 IBM and The Institute of Bioengineering and Nanotechnology Develop New Antimicrobial Hydrogel to Fight Superbugs and Drug-Resistant Biofilms – United States

This new fangled gel they have made they are very proud of.  That is good.  Pride in ones work is a good thing.  But getting the science wrong and making misleading statements is not.  Some statements I have issues with include

  • Able to colonize on almost any tissue or surface, microbial biofilms – which are adhesive groupings of diseased cells present in 80% of all infections – persist at various sites in the human body, especially in association with medical equipment and devices.
    • Huh?  Diseased cells?  What does this even mean?
  • When applied to contaminated surfaces, the hydrogel’s positive charge attracts all negatively charged microbial membranes, like powerful gravitation into a blackhole.
    • Again – huh?  How is this like gravitation in a black hole?
  • However, unlike most antibiotics and hydrogels, which target the internal machinery of bacteria to prevent replication, this hydrogel kills bacteria by membrane disruption, precluding the emergence of any resistance.
    • This is the killer statement.  They have apparently invented a treatment that no organism can resist.  It is therefore perfect.  Sort of like, well, penicillin?  Oh no, wait.  Sort of like chloroquine.  Oh no, wait.  I mean, sort of like streptomycin right?  Sorry – I meant tetracycline.  No no – I meant …. aaaaaaaaaaarrg.
I could go on.  Sounds like a possibly interesting new development.  But when you make absurd claims about it, and get the science all messed up, it does not give me that warm fuzzy feeling.  Annoyingly some news sources are basically just quoting from the PR with no skepticism.  For example, see this Daily Mail article. And this blip in The Star.  At least this in “The Conversation” has some comments on this being possibly overblown.  Anyway, shame on IBM for being more about hype than science.
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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.

——–

Lecture at #UCDavis by Sir Andrew McMichael, 2013 Nelson Scientific Lecturer 2/6

Forwarding this

Oxford immunologist to discuss the potential of HIV vaccines

Lectures scheduled Feb. 6 at noon in Davis and 5 p.m. in Sacramento
Professor Sir Andrew McMichael of the Weatherall Institute of Molecular Medicine at the University of Oxford in the United Kingdom will be the UC Davis School of Medicine’s 2013

There are two opportunities to hear McMichael’s address, which is titled “T-cell immune responses against HIV-1: Can they be harnessed by vaccines?” He will speak on Wednesday, Feb. 6, at noon in the auditorium of the Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, at UC Davis, and at 5 p.m. in the Matsui Lecture Hall of the Education Building, 4610 X St., in Sacramento.

Both lectures are free and open to the public. To reserve a seat, e-mail specialevents or call 916-734-9101.

Continue reading “Lecture at #UCDavis by Sir Andrew McMichael, 2013 Nelson Scientific Lecturer 2/6”

One way to keep up with new genome sequence publications – SIGS compilation

This is a very very helpful thing to keep up with new genome sequence releases/publications: Genome sequences published outside of Standards in Genomic Sciences, October-mid November 2012 | Nelson | Standards in Genomic Sciences.  From Oranmlyan Nelson and George Garrity in the SIGS Journal.  It is a bit mind boggling how many genome sequences are being determined and published.  Fun.  But mind boggling.  Anyway – good to have someone trying to keep track.  Also see GOLD: Genomes OnLine Database.

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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.

——–

1/25 11 AM at #UCDavis “Moving from Technical Operations to Serial Entrepreneur” Brock Siegel

Forwarding this announcement:

MCB/ECH 294
SEMINAR

“Moving from Technical Operations to Serial Entrepreneur”

Brock Siegel, PhD
Director: Life Science Angels, Ruubix Inc., Moleculo Inc., Rapid Diagnostek Inc., San Francisco

Friday, January 25, 2013
11:00am* 1022 Life Sciences

Continue reading “1/25 11 AM at #UCDavis “Moving from Technical Operations to Serial Entrepreneur” Brock Siegel”

Email from Biomed Central pointing to ways to get #altmetrics for recent sFAMS paper

Just received from Biomed Central and thought some people might be interested in some of the ways they try to help you gather metrics about your papers.

Dear Prof Eisen,

We thought you might be interested to know how many people have read your article:

Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource
Thomas J Sharpton, Guillaume Jospin, Dongying Wu, Morgan GI Langille, Katherine S Pollard and Jonathan A Eisen
BMC Bioinformatics, 13:264   (13 Oct 2012)
http://www.biomedcentral.com/1471-2105/13/264

Continue reading “Email from Biomed Central pointing to ways to get #altmetrics for recent sFAMS paper”