Tag: science

Hmm .. apparently I am not supposed to be posting about #UCDavis in "social media" (SEE UPDATE AT BOTTOM)

At the suggestion of a colleague I have been browsing through the UC Davis Policy and Procedure Manual – Chapter 310, Communications and Technology Section 40, University Communications: Publications, Graphic Standards, Marketing, and Media Relations.

Much of it is straightforward but much of it seems to basically be discouraging any direct social media posts or interaction with the press. See for example:

The News Service unit in University Communications is the exclusive source for developing and disseminating news about UC Davis to the general public via newspapers, radio, television, magazines, and the World Wide Web, including social media and related channels. The News Service unit determines the newsworthiness of significant developments and activities in academic research; administrative programs; accomplishments of faculty, staff, or students; events; and other campus matters. It conducts or coordinates direct contact with news media representatives, and assures that media relations are timely, accurate, comprehensive, and of broad public interest.

and

Generally, the news media will contact the News Service to find a source for a story. If a reporter contacts a source directly, that faculty member, staff member, or student shall notify the News Service

Hmm … so ..  when I was contacted by multiple reporters about the pepper spray incident and for my comments on it and on the handling of it by UC Davis I was supposed to notify the UC Davis News Service.  I suppose I could have done that.  But how about this – I communicate with dozens if not 100s of reporters on Twitter about all sorts of things.  Should I notify the news service about each contact?  That would actually be kind of fun.  They would block my emails very soon thereafter I am sure.
I am also wondering about the role of the News Service as the “exclusive source for developing and disseminating news” “via newspapers, radio, television, magazines, and the World Wide Web, including social media and related channels.”  So is this saying I am no longer supposed to write about UC Davis on social media?   No more blogging?  No more Twitter?  How does this jibe with all the retweets and reposts I get by official UC Davis groups/people?  
In the end I can imagine that the UC Davis administration would say this wording is not quite what they mean.  But it is there.  And technically, I am supposed to follow it.  Oh well, off to kill all my social media accounts.  Yeah, right.

UPDATE: Barry Shiller – UC Davis Communications Chief Guru has responded with clarifications that this policy is NOT intended to suppress any communications but is about coordination with the News Service

I’m replying directly and publicly as an expression of transparency, and professional respect for you.

You indeed misinterpret the policy. It was, and is, intended to optimize coordination with the media – not, as is inferred by your post, to inhibit anyone. Coordination, by the way, is as beneficial to the media as anyone. They appreciate knowing their go-to points of contact. That said, reporters contact faculty, staff and students without interference or inhibition. All the time. 

It may be that this policy fails to clarify or contemporize the distinction between “reporters” and social media content creators, including bloggers. If so, we will take a look at it; I’d welcome your input. 

But let me be clear: as you well know, many university constituents actively blog, tweet, post, opine. (I’m among them.) In this age, it is an important ingredient in telling our story. The policy is not intended to discourage that


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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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Interesting new metagenomics paper w/ one big big big caveat – critical software not available "

Very very strange.  There is an interesting new metagenomics paper that has come out in Science this week.  It is titled “Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota” and it is from the Armbrust lab at U. Washington.

One of the main points of this paper is that the lab has developed software that apparently can help assemble the complete genomes of organisms that are present in low abundance in a metagenomic sample.  At some point I will comment on the science in the paper, (which seems very interesting) though as the paper in non Open Access I feel uncomfortable doing so since many of the readers of this blog will not be able to read it.

But something else relating to this paper is worth noting and it is disturbing to me.  In a Nature News story on the paper by Virginia Gewin there is some detail about the computational method used in the paper:

“He developed a computational method to break the stitched metagenome into chunks that could be separated into different types of organisms. He was then able to assemble the complete genome of Euryarchaeota, even though it was rare within the sample. He plans to release the software over the next six months.”

What?  It is imperative that software that is so critical to a publication be released in association with the paper.  It is really unacceptable for the authors to say “we developed a novel computational method” and then to say “we will make it available in six months”.  I am hoping the authors change their mind on this but I find it disturbing that Science would allow publication of a paper highlighting a new method and then not have the method be available.  If the methods and results in a paper are not usable how can one test/reproduce the work?

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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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Is stupidity important in scientific research?

Just got sent this article which came out in 2008 but I do not remember seeing previously: The importance of stupidity in scientific research.  The title seems a bit trite and in some ways the article is.  But it has a resonance with many people and I thought I would at least post the link here.  Some comments about it I found on the web include:

I can see why it resonates with people even though I am not sure I personally agree with the sentiments.  It is definitely worth a read.
Hat top to Melanie Melendrez for pointing it 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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Draft post cleanup #16: Science and Title IX

Yet another post in my “draft blog post cleanup” series.  Here is #16 from July 2008.

I had seen an article that surprised me: Findings – John Tierney – Science Has Become the New Frontier for Title Nine – NYTimes.com

In the article Tierney discussed how the Title IX statute which forbids discrimination based on gender in education and has been applied extensively to athletic endeavors was beginning to be applied to science.  Not sure what has become of this over the last 3+ years — if anyone knows more please post …

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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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Woohoo – my kids are doing their 1st chemistry experiment (well 1st formal one)

Image
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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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Top 10 Humorous Science Videos of the Year

I was starting to compile a Top 10 list of best humorous Science-related videos of the year.  And I got stuck on #1 because it is so so so good.  But I was able to find some others I liked (and listed them in no particular order)… so here goes.  If you know of other good ones please post/tweet …

1. Bad Project video from the Zheng lab.  This is simply awesome.

2. Top 10 quirky science tricks for parties.  I found out about this from Twitter … and it is very good.

3. Cracked.Com has some funny spoofs, though usually not about science.  Here is one I found about science, sort of.

4. The Onion has some great science spoofs of course.  I found this one but there are many more.

http://www.theonion.com/video_embed/?id=26842
Brooke Alvarez Has All The Answers, Even About Particle Physics 

5. Colbert has some brilliant Science spoofs.  This one however takes the cake in a way: Colbert nuclear explosion

6. Robotic Operation (which I found through http://www.sciencehumor.org/category/videos/)

7. OK – so it’s very very long.  But there are some funny parts – the 2011 Ig Nobel Award Ceremony

8. Abby Harrison is very funny. … I first saw here microorganism stand up stuff but I think this one is better.

9. OK so this is not the funniest video with Brian Malow but it give some background on “The Science Comedian”

10. And perhaps my favorite – from the Daily Show — Science – What’s it up to?

Please suggest 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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Some links worth checking out regarding suppressing publishing and bioterrorism

Just a quick one here with some links worth checking out regarding the recent discussion of suppressing some parts of a paper on engineering flu viruses
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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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Blast from the past: 1997 Walter J. Gores Teaching Awards at Stanford w/ Condoleezza Rice

Just got this digitized. One of my proudest moments. In 1997 I received the Walter J. Gores Award for excellence in teaching for my work on the “SME Core” at Stanford. The SME Core was a new way to teach Science, Math and Engineering for non science majors.

 

The SME Core was an initiative coordinated in part by then Stanford Provost Condoleezza Rice.  I worked with her office on and off for 3 years to help get the SME Core program up and running.  (I note – whatever you think of her now – at the time I really really liked her – she was great to interact with, brilliant, and I think inspired in pushing this SME program).


For more on the SME Core see

It seems the SME Core may have gone away after I left Stanford.  But I think it was a great program – full year integrated courses that covered science, math and engineering on a specific topic.  I ended up helping design a course on Heart Disease (and was head TA).  And the faculty in the course changed my life – in particular interactions with David Botstein, Rick Myers and David Cox who were three of the four instructors – that is what got me into genomics.  But also – working on designing the course – and helping run it for two years – was an amazing experience.  By tracking / interacting with undergrads for a full year I got to know students at a level not possible in single quarter courses.  I will try to write more about the SME Core at some point but I was very proud to have received Stanford’s biggest teaching award – the Walter J. Gores Award for my work on the program.  So I am posting the video of the presentation because – well – I like it …
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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.

——–

Updated Again: Compilation of articles, news, blogs about the "arsenic bacteria" NASA study

Lots of new stuff on the arsenic-bacteria front.  For those interested I am compiling some of the more useful links here:

News stories:

Blogs:
  • A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus
    • Felisa Wolfe-Simon, 
    • Jodi Switzer Blum, 
    • Thomas R. Kulp, 
    • Gwyneth W. Gordon, 
    • Shelley E. Hoeft,
    • Jennifer Pett-Ridge, 
    • John F. Stolz, 
    • Samuel M. Webb, 
    • Peter K. Weber, 
    • Paul C. W. Davies,
    • Ariel D. Anbar, 
    • and Ronald S. Oremland

      • Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”

        • James B. Cotner and

          •  

        • Edward K. Hall

        Science 27 May 2011: 1201943Published online 27 May 2011

      • Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”

        • Rosemary J. Redfield

        Science 27 May 2011: 1201482Published online 27 May 2011

      • Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”

        • B. Schoepp-Cothenet, 
        • W. Nitschke, 
        • L. M. Barge, 
        • A. Ponce, 
        • M. J. Russell, 
        • and A. I. Tsapin

        Science 27 May 2011: 1201438Published online 27 May 2011

      • Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”

        • István Csabai and

          •  

        • Eörs Szathmáry

        Science 27 May 2011: 1201399Published online 27 May 2011

      • Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”

        • Stefan Oehler

        Science 27 May 2011: 1201381Published online 27 May 2011

      • Editor’s Note

        • Bruce Alberts

        Science 27 May 2011: 1208877Published online 27 May 2011

      • Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”

        • David W. Borhani

        Science 27 May 2011: 1201255Published online 27 May 2011

      • Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”

        • Steven A. Benner

        Science 27 May 2011: 1201304Published online 27 May 2011

      • Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”

        • Patricia L. Foster

        Science 27 May 2011: 1201551Published online 27 May 2011

      • A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus

        • Felisa Wolfe-Simon, 
        • Jodi Switzer Blum, 
        • Thomas R. Kulp, 
        • Gwyneth W. Gordon, 
        • Shelley E. Hoeft,
        • Jennifer Pett-Ridge, 
        • John F. Stolz, 
        • Samuel M. Webb, 
        • Peter K. Weber, 
        • Paul C. W. Davies,
        • Ariel D. Anbar, 
        • and Ronald S. Oremland

        Science 2 December 2010: 1197258Published online 2 December 2010

——–
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.

——–