Eisen Lab Blog

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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Notes (from me and mostly others) from the JGI User Meeting #JGIUM7

OK, so the DOE Joint Genome Institute User Meeting is underway. Day 2 just finished. And I have been there for much of it but alas, not in some of the talks since I can’t seem to get past the hallway/gathering area outside the talks. There are way way too many people there who I have not talked to or seen in a while … So … apologies to those who thought I might be live tweeting the whole meeting … it just hasn’t happened. But I did use the Storify web tool to make a “storification” of posts to twitter from the meeting – most of which were from other people. Here is the story in slideshow format.

http://storify.com/phylogenomics/jgi-user-meeting-day-1-2.js?template=slideshow[<a href=”http://storify.com/phylogenomics/jgi-user-meeting-day-1-2″ target=”_blank”>View the story “JGI User Meeting Day 1-2” on Storify</a>]

I will update the storification tomorrow. If you want to see the full details in a scrolling winder see below

http://storify.com/phylogenomics/jgi-user-meeting-day-1-2.js[<a href=”http://storify.com/phylogenomics/jgi-user-meeting-day-1-2″ target=”_blank”>View the story “JGI User Meeting Day 1-2” on Storify</a>]

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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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OMICS Driven Microbial Ecology …

Quick post here.  Just discovered a nice review paper by Suenaga on targeted metagenomics: Targeted metagenomics: a high-resolution metagenomics approach for specific gene clusters in complex microbial communities – Suenaga – 2011 – Environmental Microbiology

This “Special Issue” on “OMICS Driven Microbial Ecology” has a series of papers, all of which seem to be freely available, of potential interest to readers of this blog including:

and more
Oh, and a paper of mine (with Alex Worden and other members of her lab as well as multiple others)
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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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Google Wage or Google Wave? I am interested in Google Wage if they are still offering …

Just got this email

Google Wage wave-noreply@google.com

12:24 AM (4 minutes ago)

Dear Wavers,More than a year ago we announced that Google Wave would no longer be developed as a separate product. Back in November 2011, we shared the specific dates for ending this maintenance period and shutting down Wave. Google Wave is now in read-only mode. This is reminder that the Wave service will be turned off on April 30, 2012. You will be able to continue exporting individual waves using the existing PDF export feature until the Google Wave service is turned off. We encourage you to export any important data before April 30, 2012.

If you would like to continue using Wave, there are a number of open source projects, including Apache Wave. There is also an open source project called Walkaround that includes an experimental feature that lets you import all your Waves from Google. This feature will also work until the Wave service is turned off on April 30, 2012.

For more details, please see our help center.

Yours sincerely,

The Wave Team

© 2012 Google Inc. 1600 Amphitheatre Parkway, Mountain View, CA 94043
You have received this mandatory email service announcement to update you about important changes to your Google Wave account.

Notice anything unusual? How about that it is from “Google Wage?” I assume this is either a really bad typo or a really funny prank from inside Google.

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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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This is both crazy and completely brilliant: The Microbial Academy Of Sciences

Oh My God.  This is so wild and crazy I can’t just write OMG – I have to write the whole thing out: The Microbial Academy Of Sciences: What Bacteria Can Discover That We Can’t | Co.Exist: World changing ideas and innovation

The article describes an art exhibition in San Francisco in which one part involves giving microbial cultures access to images from space.  The reason for this is possibly captured in this quote

“Because cyanobacteria can perform photosynthesis,” Keats says, “they’ll be able to detect patterns of starlight just as human scientists do with their eyes. The difference will not be in their methodology, but rather in the conclusions they reach.”

and even better

But in all those eons, bacteria have never been given observatory access, to study the cosmos for themselves. … My observatory is built to address that unfortunate oversight, providing the resources for colonies of bacteria to research a theory of everything, reconciling cosmic and quantum observations in their own bacterial way.”

I know some hard core scientists may object to this and some of the other lines by the artist but I personally think this is brilliant (in a devious way but brilliant nevertheless).   Everyone out there should read this article by Morgan Clendaniel.  And I for one and going to try to go to the exhibit ASAP.  I personally cannot believe I have not heard of this yet since it seems to have opened in January …

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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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