Month: May 2009

Worst new omics word award: ethomics

Well, look at what I just saw on twitter:

tlemberger omics mania: ‘ethomics’ http://is.gd/wOcg – should be added to http://omics.org/ but perhaps also nominated for this http://is.gd/g2Bc

That is from Thomas Lemberger and so I followed the last link first, since I thought I might be to, well me. And indeed it was a link to my “Worst new omics word award” for museumomics.

And so then I went to the link on ethomics: High-throughput ethomics in large groups of : Drosophila : Abstract : Nature Methods.
And indeed they use “ethomics” – what is clearly a quite new omics word (only 62 google hits as of this PM). I confess, I stopped reading at the abstract because it was just too much:

We present a camera-based method for automatically quantifying the individual and social behaviors of fruit flies, Drosophila melanogaster, interacting in a planar arena. Our system includes machine-vision algorithms that accurately track many individuals without swapping identities and classification algorithms that detect behaviors. The data may be represented as an ethogram that plots the time course of behaviors exhibited by each fly or as a vector that concisely captures the statistical properties of all behaviors displayed in a given period. We found that behavioral differences between individuals were consistent over time and were sufficient to accurately predict gender and genotype. In addition, we found that the relative positions of flies during social interactions vary according to gender, genotype and social environment. We expect that our software, which permits high-throughput screening, will complement existing molecular methods available in Drosophila, facilitating new investigations into the genetic and cellular basis of behavior.

For trying to extend omics to ethogram and beahvioral plots I am giving my second coveted “worst new omics word award” to Kristin Branson, Alice A Robie, John Bender, Pietro Perona & Michael H Dickinson. Here is a prediction – ethomics will not become widely used – not soon – not ever. Thanks for pointing this one out Thomas.

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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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Worst new omics award: ethomics

Oops – posted this to the wrong blogspot blog.  Please go to my Tree of Life blog to see this post here.  
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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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Oops. Seems like Davis, CA does not have the swine flu, yet.

See :
Probable swine flu cases in Yolo County found to be human flu – Daily Democrat Online
and News 10 and KCRA

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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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Should evolutionary biologists "debate" creationists/ID advocates?

Last week I received an email also sent to a group of other local evolutionary biologists asking if one of us would be willing to participate in a “debate” with a creationist who was coming in to town to give some sort of talk.  The email said, among other things:

… we have a creationist (who holds to the 6-literal day creation and young earth 6,000 year position), (name deleted), coming on our campus challenging someone to debate him. 

And, well, I ignored the email as did the others apparently.  Then we all got a second email a few days later:

Dear Professors, 

The Creationist side is offering $300 for accepting the challenge! And another $250,000 to anyone presenting any empirical evidence for macro evolution! 

Why has this offer been out there for years? Where are the experts??? Where is the evidence?? How is  this possible?

If you are convinced that Darwin was right, if you accept it, if you teach it to students, as a career, then WHY DO YOU REFUSE TO DEBATE?!

You betray the students that look up to you!! Come on, Creationist don’t bite!

Sorry for this sarcastic tone, but it doesn’t make sense. If you teach it in class you must be the first ones defending it.

We have a philosophy graduate wanting to debate, no science professors yet, especially Biology and Anthropology.

Please respond to this email asap!

Clearly, they people organizing this were trying to get someone to do the debate.  But this strategy just convinced me that debating creationists was an absurdly silly thing.  So I wrote back:

The issue is pretty simple to me.  There is nothing really to debate.  Creationism is not science.  It is a religion driven position that pretends (and does so poorly) to be about science.  I for one have perfectly pleasant interactions with many creationists and I understand their beliefs at least at some level.  But just as I would not encourage physicists to debate with those who deny gravity, and just as I would not encourage chemists to debate with those who claim the periodic table is invented, I think it is inappropriate to evolutionary biologists to “debate” with creationists in this type of setting.  Discussing creationism – fine.  Discussing criticism of evolutionary hypotheses – fine.  Having a reasonable panel discussion of science and religion – fine.  Meeting with creationists to discuss their ideas about evolution – ok too.  But engaging in a “debate” and thus even for a second implying that creationism stands on the same ground as evolution – completely ludicrous.  
Sincerely
Jonathan Eisen

Alas, the people doing the inviting were not particularly impressed with my answer:

You Sir, are a COWARD.
If it is so easy in your mind to refute Creationist’s arguments, why don’t you do it publically? FOR MONEY?! 
Your words do nothing to change the standing offer of $250,000 for evidence of Macro-Evolution. How about Actions, not Words only?

By denying there is a challenge, and at the same time refusing to accept the challenge you tell us that you’re unable to defend your position.
We know why you are fine with a panel discussion: because there is no Looser or Winner, you are afraid to loose, that is the real reason behind your rhetoric.

your answer is a nonanswer

Try again.

I guess they did not get my point.  But anyway – I am asking readers out there – what do you think one should do?  Should one debate creationists/ID supporters?  

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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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More on Swine Flu in Davis from the Davis Enterprise.

There is a mini update on the swine flu incidence(s) in Davis at the Davis Enterprise.

Basically it appears the city of Davis is backing off some of the extreme quarantine type measures that were reported yesterday.

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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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GIS mapping of bike accidents in Davis

A PhD student in my lab has generated a nice GIS mapping of auto and bike accidents in Davis, CA.  Worth browsing …

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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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Swine Flu Hits Davis?

Seems like Swine Flu (aka H1N1) has hit Davis.  See here. 

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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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Swine Flu Hits Davis?

Seems like Swine Flu (aka H1N1) has hit Davis.  See here. 

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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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Open Access Pioneer Award: Rick Prelinger, Image Access

Just saw an interesting article in the UC Davis “Dateline” newsletter about Rick Prelinger who is the founder of the Prelinger Library in San Francisco (and see their blog here). He gave a talk at Davis and thus they wrote an article about him here.

Some good lines from the article include

Rick Prelinger’s biggest thrill is “mainstreaming” historical documents for public consumption.

But getting history into the hands of the average citizen is no easy task, the archivist says.

Overbearing copyright issues and rampant commercialism, he argues, threaten the free exchange of information on which a knowledge society — especially its libraries — depends.

…

Rather than concern themselves with rigid lending policies or copyright protections, library systems should focus on “more product, less process” to better serve patrons, Prelinger said.

…

“If the Google book deal is approved without any changes, we could soon lose 100 million books that society doesn’t know what to do with,” said Prelinger, referring to “orphan works,” or works under copyright, but whose owner is not known.

….

On the other hand, archives are empowering, Prelinger said. “Let’s open up the past. Interesting things happen when we do so.”

In general since Prelinger has been pushing for more openness in libraries and in images, I am giving him an “Open Access Pioneer Award“.  Sorry I missed the talk but glad I read the article.  

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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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Open Flu: Up to date Open analysis of Human/Swine A/H1N1 Influenza

Just got a pointer to a fantastic site with detailed up to date analyses of flu (e.g., swine flu) data. The site is http://tree.bio.ed.ac.uk/groups/influenza/. The site says

These pages are to allow the rapid dissemination of results and analysis of genetic data from the ongoing Influenza A/H1N1 outbreak attributed to swine flu.

And there is some great stuff there posted by among others, Andrew Rambaut, Oliver Pybus, Nicholas Grassly, Mike Worobey and Gavin Smith. Definitely worth checking out. Hat tip to Eddy Holmes for pointing this 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.

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