The DNA Network

The search for August [Discovering Biology in a Digital World]

Posted: 09 Aug 2008 08:20 PM CDT

Instead of enjoying a sunny summer day today, or partying with SciBlings in New York, I'm staring out my window watching the rain. Inspiration hit! What about searching for August?

Folks, meet the HFQ protein from E. coli. I found this lovely molecule by doing a multi-database search at the NCBI with the term 'August'.

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Hyperbole of the Week [Mary Meets Dolly]

Posted: 09 Aug 2008 11:31 AM CDT

The unabashed exaggeration surrounding embryonic stem cell research never ceases to amaze me. Especially when it comes from our elected officials who should know better.

Democratic congresswoman Diana DeGette has written a book called Sex, Science and Stem Cells: Inside the Right Wing Assault on Reason in which I am sure is all the tired rhetoric about how George Bush is ruining the world. (DeGette's daughter was diagnosed with Type I diabetes when she was 4 years old.) It sounds like I am the on hyperbolizing until you read this quote from Rep. DeGette:

"That's why it angers me to think of George W. Bush sitting up there in the White House, deciding that the welfare of a bunch of frozen embryonic cells is somehow more important than the welfare of my child -- or any child for that matter," DeGette writes. "There are thousands and thousands of parents just like me, whose kids have diabetes or cancer or muscular dystrophy, who feel the same way; and, there are thousands and thousands of adult children whose parents have Alzheimer's or Parkinson's or a stroke. Together we're counting on those embryos to see us through and take some of that weight off our shoulders and set our world right once again."

Oh boy where do I start:

1. The "cells" of note here are not just "cells." They are EMBRYOS. Complete human organisms that no one thinks are MORE inmportant than DeGette's daughter. They need to be valued the SAME as all human organisms no matter what stage of development. Which means we do not rip them open while they are still alive and harvest the parts we are interested in.

2. Adult stem cells are already producing the insulin her daughter needs. There are no human trials even underway with embryonic stem cells for diabetes.

3. So if DeGette is "counting on those embryos to see us through" she is going to be waiting a VERY long time. Possibly decades.

4. The fact that she thinks that ripping open frozen human embryos is going to "set our world right once again" just shows that she is the one who needs a dose of reason. Reality check please.

Campus Open Access Policies: The Harvard Experience and How to Get There (SPARC) [The Tree of Life]

Posted: 09 Aug 2008 10:48 AM CDT

SPARC has a nice set of talks online about Harvard's move towards a University wide open access system (see Campus Open Access Policies: The Harvard Experience and How to Get There (SPARC))

From the web site
"This spring, Harvard's Faculty of Arts and Sciences voted to enable open access to their scholarly articles in an institutional repository. This vote granted the university the rights necessary to archive and make freely available on the Internet articles written by Arts and Sciences faculty members. It is the first time the faculty of a U.S. university has voted for an open access directive and the first time a faculty has granted permission to the university to make its articles available through open access. It is because of this vote, and the efforts leading up to it, that the Harvard FAS was named as the SPARC Innovators for June 2008.

The forum offers an exploration of the motivations behind the Harvard policy, the groundwork invested in its creation, reactions and outcomes to date, and the broader implications of this historic step. Headlining the event is Stuart M. Shieber, professor of computer science at Harvard, director of the Center for Research on Computation and Society, faculty co-director of the Berkman Center for Internet and Society, and the key architect of the policy.

Shieber is joined by Catherine Candee, executive director, Strategic Publishing and Broadcast Initiatives, from the office of the president of the University of California, who relates similar activity in the UC system; and by Kevin L. Smith, JD, scholarly communications officer at Duke University, who suggests legal considerations for institutions following the open access policy path."

Hat tip to Michael Rogawski from U. C. Davis for pointing this out. In particular, he and I are very interested in the discussion by Catherine Candee about why the UC system did not do this before Harvard (we are hoping to get the UC to do something like this). Rogawski has also pointed me in the direction of some nice tools for sharing my publications through the UC system (see his BE Press site here).

Happy Birthday Anna Eisen 8-8-8 at 8:08 PM [The Tree of Life]

Posted: 08 Aug 2008 10:08 PM CDT

Happy Birthday Anna Eisen (my niece)

8/8/08 at 8:08 PM

Flip flop [business|bytes|genes|molecules]

Posted: 08 Aug 2008 09:05 PM CDT

While cleaning out my feed reader, I ran into a post by Jeff Jonas entitled Smart systems flip-flop. He had my attention on line #1

Certainty often shifts with observations over time. And this is good

How true!!!

He argues that the intelligence of an organization can be directly related to the net sum of its perceptions. The part about perceptions is critical. As scientists our perceptions are/should be driven by our understanding and interpretation of available data. The key part is being smart about the data and converting the data at our fingertips into meaningful observations and eventually perceptions. We must be smart about how we get there.

Given recent kerfuffle’s around the petascale era, the following should be made mandatory reading.

But smarts requires much more than just available data and good correlation.

What do we require? According to Jeff, we need an ability to make assertions based on new data points and an ability to use these new data points to reverse earlier assertions. In my speak, this means we need to be able to make new models (if that’s what the new data leads us to). The problem we have today is that we have a lot of data, but that has actually led to more holes in our understanding. We know more than we used to, but what we used to know did a decent job of explaining the data we had. Now we just don’t have all the information required to make meaningful models, so we try and use statistics, heuristics and many other approximations.

Read the article, and the rest of Jeff’s writing. Talking to him over breakfast at Scifoo last year was one of the best things I ever did.

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