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

12 hours of me: Slideshows w/ audio from "BIS2C: Biodiversity & the Tree of Life" at #UCDavis

Well, it has taken a few months of processing but I have finally gotten my lectures from the introductory biology course I teach uploaded in some way to share.  The course is “BIS2C: Biodiversity and the Tree of Life” and it is the third quarter of a three quarter introductory biology series at UC Davis.  Each year some 2300 or so students take this series which means that we at UC Davis have to offer each of the courses (BIS2A, BIS2B, and BIS2C) each quarter.   Every fall I co-teach BIS2C.  Alas we do not have a lecture hall big enough for 700 students, so we do the course in two sections.  The way we teach it each of the faculty double up and teach their part of the course to each section.  The course also has a weekly lab.  It is a machine of sorts.

This fall I taught 13 lectures for the course.  I covered basically phylogenetic methods, the big picture of the tree of life, and microbial diversity.  I used the Apple presentation program Keynote for slides for my lectures and I used the “Record Slideshow” option to record audio in synch with the slides.  After a bit of pain, I managed to convert these recordings into video and then posted them to Youtube.  And today I am sharing them with you.  There are imperfections of course.  But I thought some might find them useful.  Plus I have made a YouTube playlist for all the lectures if you want to just sit down and enjoy 12 hours or so of me.  Now if only Youtube would allow me to change the thumbnail image for each lecture …  Plus I note – next year I will be doing much more interactive learning in class so this may be the last record of some of these lectures …

Lecture 1: Introduction to Course and the Tree of Life

Lecture 2: Trees, Taxa and Groups

Lecture 3: Characters

Lecture 4: Phylogenetic Inference

Lecture 5: Phylogenetic Inference

Lecture 6: The Tree of Life

Lecture 7: The Three Domains

Lecture 8: Three Domains and Microbial Diversity

Lecture 9: Microbial Diversity

Lecture 10: Endosymbioses and Lateral Gene Transfer

Lecture 11: Endosymbioses and Lateral Gene Transfer

Lecture 12: Extremophiles

Lecture 13: Human Associated Microbes

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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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And now I have a billion plus infinity dollars

P72

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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.

——–

Just a typical Friday in #davisca – printing our own money

P58

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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.

——–

Call for abstracts: Automated Function Prediction, 2012

Call for abstracts: Automated Function Prediction, 2012

Locale: Long Beach, California USA
Date: July 14, 2012 (Just before ISMB 2012)
URL: http://biofunctionprediction.org

Important dates:

April 18, 20112: Deadline for submitting abstracts.

May 9, 2011: Notifications for accepted abstracts e-mailed to
corresponding authors

May 16, 2011: Deadline for presenters to confirm acceptance of
invitation to speak.

July 14, 2011: AFP SIG preceding ISMB 2012

An ISMB Special Interest Group Meeting

Automated Protein Function Prediction

Sequence and structure genomics have generated a wealth of data, but
extracting meaningful information from genomic information is becoming
an increasingly difficult challenge. Both the number and the diversity
of discovered sequences are increasing, while the fraction of genes
whose function is known is decreasing.In addition, there is a need for
annotation which is standardized so that it could be incorporated into
function
annotation on a large scale. Finally, there is a need to assess the
quality of the function
prediction software which is out there.

For these reasons and many more, automated protein function prediction
is rapidly gaining interest among computational biologists in academia
and industry.

The AFP SIG has been part of ISMB since 2005.
We call upon all researchers involved in gene and protein function
prediction to submit an abstract to the AFP meeting. Authors of select
abstracts will be invited to give a talk and/or present a poster.

This year, AFP is delighted to have Jonathan Eisen from the University of
California, Davis as its keynote speaker. Prof. Eisen is a pioneer in the
field of function prediction.

>From his lab page:
http://bobcat.genomecenter.ucdavis.edu/mediawiki/index.php/Main_Page

"Dr. Eisen has published more than 200 scientific papers and is a co-author
of a relatively recently published Evolution
Textbook<http://evolution-textbook.org/>.
Dr. Eisen is also a strong proponent of the Open Access movement in
scientific publishing and is Academic Editor in Chief of PLoS
Biology<http://www.plosbiology.org/>.
Dr. Eisen is also an active and award winning science blogger (see his Tree
of Life blog here <http://phylogenomics.blogspot.com/>). For recent news
see http://twitter.com/phylogenomics" <http://twitter.com/phylogenomics>

For further instructions on how to submit abstracts to AFP 2012, please go
here:

http://biofunctionprediction.org/node/415

We are looking forward to seeing you in Long Beach, California!

Iddo Friedberg on behalf of the AFP organizing committee

Just grand -Donald Williamson published more crap on larval "evolution" – this time in one of the #OMICS journals

Well this is great.  Just great.  Donald Williamson has a new paper “The Origins of Chordate Larvae” published in Cell and Developmental Biology – a spammy journal from the OMICS publishing group.  Don’t know who Williamson is?  Well consider yourself lucky.  For more on him and his horrendous history of publishing crap see:

And many many more.  Short summary – he has a theory regarding larval forms of organisms having a separate evolutionary history from adult forms.  He has no evidence for this.  And he keeps finding new ways to publish his theory.  Uggh.  I guess this serves as a reminder to everyone out there – crap does get published.  It is too bad.  But it does happen and will continue to.  We need to call out the crap as much as possible so that as few people as possible out there end up getting deceived.  So this is my contribution to that notion.  Google search engines pay attention. Donald Williamson really publishes some horrible stuff.
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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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Ecology & Evolution Seminar Series UPDATED Flier – Spring 2012

Spring 2012 schedule for the Ecology & Evolution seminar series, ECL 296 (CRN 70181) / PBG 292 (CRN 44948). Seminars will be held each Thursday, 4:10-5:30PM in 1003 Giedt Hall.

We’re still waiting for one title and will send an updated flier as soon as it’s received. In the interim, can you please share this information with your students and anyone else who may be interested.

The most current listing of speakers and titles will be posted at http://www.des.ucdavis.edu/EcologyEvolutionSeminars.aspx.

EESeminar-Spring2012.pdf

Agilent Lunch & Learn on 3/27

From Agilent:

I wanted to let you know that Agilent will be hosting a Next Generation Sequencing Lunch & Learn next Tuesday, March 27th, from 11:00-1:00 in GBSF – Room 4202, which we’d like to invite you, and your lab, to attend. We will be covering all of our target enrichment technologies (SureSelect, HaloPlex and Methyl-Seq) as well as discussing a new addition to our electrophoresis portfolio, the TapeStation. We hope you and your colleagues can attend! Please let me know if you have any questions.

Kind regards,

Jamie

Jamie Andalis

Davis Lunch Learn Flyer (3).pdf

OMG – Without a doubt the worst omics word ever – The Sexome

I really have nothing to say here.  I just got pointed to a new paper by Thiago Venancio.  The paper is – I kid you not: Understanding the Sexome: Measuring and Reporting Sex Differences in Gene Systems.  I don’t have access to the paper but here is the abstract which is all you need

The current male bias in biomedical research should be eliminated. The large sex differences in incidence and progression of diseases mean that sex-biased factors are an untapped source of factors that protect from disease. Greater understanding will come from intensified study of the “sexome,” which is the sum of sex-biased effects on gene networks and cell systems. The global search for sites and mechanisms of sex-specific regulation in diverse tissues will provide unanticipated insights into physiological regulation and targets for novel therapies.

That is without a doubt the worst omics word I have ever seen.  All my previous posts about bad omics words pale in comparison (though I encourage you to read them: Worst New Omics Word Award and bad omics word of the day).

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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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Calling all computational biologists – do as C. Titus Brown does – submit your pubs to arXiv

Can I just express my love/respect for C. Titus Brown?  Not only is he into openness in science and metagenomics and such.  But he practices what he preaches.  For example see – Daily Life in an Ivory Basement : /mar-12/diginorm-paper-posted in which he describes his new submission to arXiv and some background.  I know I am big on Open Access and all, but even we have been lame about submitting things to preprint servers like arXiv.  Gonne do my best to fix that and try and copy Titus.

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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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Lenses in Biology collection from Nature Outlook: free (for now at least) & worth a look

Some nice long features in Nature Outlook on various topics plus interviews with the authors.  Summed up in Lenses on Biology.  All freely available though I think that is only for this collection and not in general for Nature Outlook.

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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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