The Books of Science Online 2012 #scio12 #bookporn #sciencerocks cc: @avflox

Well, I am a book geek.  While others took pictures of all the tatoos, people, and more — the #1 thing I took pictures of were the books on display … (UPDATE – made a mini Amazon Store with all the books here).

UPDATE 2: August 2013.  Posterous is dead so deleted the links to the book pictures from Posterous below.  Changed it to Picasa.

https://static.googleusercontent.com/external_content/picasaweb.googleusercontent.com/slideshow.swf

Draft post cleanup #21: Tracking progress on the vertebrate tree of life

Yet another post in my “draft blog post cleanup” series. Here is #21; from March 2010:

A very interesting paper came out recently from colleagues of mine at UC Davis:  Rapid progress on the vertebrate tree of life.  I did not know they were working on this but perhaps should have.  It has some fun/interesting analysis of the accumulation of phylogenetic knowledge over time.  For example see Figure 1

Cumulative phylogenetic information amassed for the last 16 years. The accumulation of sequences for vertebrates in GenBank (a), papers using the term ‘phylogeny’ or ‘phylogenetics’ in the Web of Science database (b) and phylogenetic resolution (measured as the proportion of nodes with at least 50% bootstrap support) in the vertebrate tree of life resulting from these research efforts (c). In all cases, the data are cumulative from the start of each analysis. Phylogenetic resolution is calculated as in Table 1. Trend lines are exponential in (a), and second order polynomial in (b) and (c).

The rest of the paper is worth a look.

And alas I stopped there … I think I wanted to get Brad Shaffer and Bob Thomson’s comments on the paper but never got around to it.  Two years later the paper still is worth a look …

Nice walk to #scio12 – now on o the virtual world

UC going smoke free sometime soon apparently

Just got this email:

UC Davis community members,
I am writing to share with you the attached letter 
from President Mark G. Yudofto chancellors regarding the University’s recent decision to make all campuses tobacco-free by 2014. The new policy direction will prohibit the smoking and chewing of tobacco, as well as the sale of tobacco products, and aligns with practices already in place at UC medical centers and many other universities.
As the President’s letter indicates, each campus will soon be developing plans for implementing this decision, and we will have more information about what this new policy process will entail for our community as the UC Davis plan takes shape. We will, of course, consult with a broad range of our campus community as we develop mechanisms to implement this new policy direction.
Sincerely,
John Meyer

Vice Chancellor, Administrative and Resource Management

Draft post cleanup #19: Spam and biased spam at that

Yet another post in my “draft blog post cleanup” series.  Here is #19 from September 2011:

I am sure many others out there who blog have gotten this kind of message:

We at Onlinephdprograms.com recently came across your blog and were excited to share with you an article “15 Fictional Professors We Wish Were Real” was recently published on our blog and we hoped that you would be interested in featuring or mentioning it in one of your posts.

(http://www.onlinephdprograms.com/15-fictional-professors-we-wish-were-real/)

Either way, I hope you continue putting out great content through your blog. It has been a sincere pleasure to read.

Thanks for your time,
Liz Nutt

I assume that these posts that are written for this, and various other sites, are all about driving up Google Search ranking somehow.  So I normally avoid writing about them.  But I thought I would in this case because, well, their post annoyed me because of the 15 functional professors they wrote about, only one is female.  Really, that is the best they could do?  In three minutes of web surfing (e.g., browsing this site and this one) I have come up with a list of fictional female professors who certainly could have been included in their list.  And many are much more interesting than some they wrote about.  Here are some examples:

  • Eleanor Arroway – Jodie Foster’s character in Contact
  • Susan Calvin – character in Isaac Asimov’s I Robot series
….
But then I stopped because I was disappointed I could not find more functional female professors to add to my list.  I do think the list posted by the OnlinePhD site could certainly have had more women on it … but I never posted the post because I had a hard time coming up with a lot of examples … but now that I am trying to revive draft posts … well … I will put this out there even if it is an incomplete thought

Request for input – are there any rules regarding posting text of one’s own NSF (or other) grant proposals?

In response to a series of posts from Karen James (who is a biologist now in Maine and is director of the HMS Beagle Project) on Twitter, I am posting here to ask for input from the crowd.  On Twitter, Karen has been discussing her putting together an NSF proposal and was then celebrating a few days ago when it was done.

I have posted some of the twitter conversation below.  But to get directly to the point the question I have for everyone here is – are there any rules at the National Science Foundation that would prevent one from sharing with others a grant proposal that one has submitted?  Are there any rules against this at any agency?  I think there are none but apparently some are telling Karen otherwise.

Any information on this would be useful. Some of the twitter conversation is below:

kejames
So, @phylogenomics and others, with whom is it appropriate to share a submitted NSF proposal? Anyone? No one? Something in between?
1/12/12 6:15 PM

phylogenomics
@kejames what do you mean by “appropriate”
1/12/12 6:15 PM

johnhawks
@kejames If I were you, I’d share the whole thing in public and make the reviews public as well. But I’m a minority view.
1/12/12 6:16 PM

kejames
@johnhawks Thanks, I’ve thought of that, actually. It is a federal agency after all. I’d need to redact confidential budget info, though.
1/12/12 6:18 PM

johnhawks
@kejames Yes, and possibly key personnel. My attitude is the success rate is so low, it can’t hurt and might draw visibility pre-review.
1/12/12 6:19 PM

kejames
@phylogenomics Best practice. My instinct is to share it with colleagues, collaborators and associates I think might be interested in it.
1/12/12 6:16 PM

phylogenomics
@kejames what is the potential reason to not share?
1/12/12 6:17 PM

kejames
@phylogenomics That’s what I’m asking. Is there any rule or custom that prohibits sharing it far and wide?
1/12/12 6:19 PM

phylogenomics
@kejames none that I know of – only reason not to is if you are worried about people “stealing” your ideas
1/12/12 6:19 PM

kejames
@phylogenomics Not worried about that in the slightest. If anything sharing it widely establishes it as “my” idea. Thanks.
1/12/12 6:20 PM

kejames
@johnhawks Or I could ask the key personnel if they’re okay w/ it. I think it would be nice to include them if they want to be included.
1/12/12 6:21 PM

phylogenomics
@kejames I think Rosie Redfield posts hers on her blog http://t.co/g73Xb2Yz
1/12/12 6:25 PM

kejames
@phylogenomics Thanks for that. I notice she just posts the project description itself, none of the other “stuff”and doesn’t list names.
1/12/12 6:28 PM

DoctorZen
@kejames NSF proposals are your choice who to share with. Probably not best to post publicly, though.
1/12/12 6:25 PM

kejames
@DoctorZen Why not? As @phylogenomics notes, @RosieRedfield posts her grant proposals on her lab’s website: http://t.co/peWEmnvs
1/12/12 6:29 PM

kejames
Anyone else besides @phylogenomics @doctorzen @johnhawks want to weigh in on how broadly I should share my just-submitted NSF proposal? 1/2
1/12/12 6:31 PM

kejames
@rdmpage @RosieRedfield @DoctorZen @johnhawks @phylogenomics @kzelnio So I asked the collaborators on the proposal. One replied… 1/2
1/13/12 4:50 AM

kejames
@rdmpage @RosieRedfield @DoctorZen @johnhawks @phylogenomics @kzelnio 2/2…”Sharing not wise! Could disqualify proposal.”
1/13/12 4:51 AM

rdmpage
.@kejames @rosieredfield @doctorzen @johnhawks @phylogenomics @kzelnio In other words fear of what grant agency will do trumps being open 😦
1/13/12 5:10 AM

DoctorZen
@rdmpage I support being open; not sure every step always needs to be public. @kejames @rosieredfield @johnhawks @phylogenomics @kzelnio
1/13/12 5:18 AM

rdmpage
.@DoctorZen @kejames @rosieredfield @johnhawks @phylogenomics @kzelnio I agree, it’s not that it HAS to open, but that it COULD be
1/13/12 5:27 AM

phylogenomics
@kejames @rdmpage @RosieRedfield @DoctorZen @johnhawks @kzelnio WTF? As far as I know there are NO NSF issues w/ sharing a proposal
1/13/12 7:00 AM

phylogenomics
@kejames @rdmpage @RosieRedfield @DoctorZen @johnhawks @kzelnio Yes, need to discuss w/ collabs & get permission but not angst any rules
1/13/12 7:02 AM

phylogenomics
@rdmpage @DoctorZen @kejames @rosieredfield @johnhawks @kzelnio agree w/ Rod – issue was whether it could be posted, not if it had to be
1/13/12 7:04 AM

kejames
@phylogenomics I’m following up w/ him to find out what he meant He’s a seasoned NSF grantee and reviewer. Have also contacted NSF directly.
1/13/12 7:08 AM

Storification of Tweets from talk by Jane Lubchenco at #UCDavis

Jane Lubchenco, head of NOAA, gave a talk at UC Dav is yesterday and I made a “Storify” version of some tweets from it. I am putting it below the “fold” here since it takes up a lot of space and I cannot figure out how to put the “click here for more” feature in the middle of a storify embed.
http://storify.com/phylogenomics/jane-lubchenco-head-of-noaa-talk-at-ucdavis.js[<a href=”http://storify.com/phylogenomics/jane-lubchenco-head-of-noaa-talk-at-ucdavis” target=”_blank”>View the story “Jane Lubchenco, head of NOAA, talk at #UCDavis” on Storify</a>]

Letter from Chancellor Katehi to #UCDavis Community

Posting this email I received for those interested.  Not sure what will happen this quarter in terms of Occupy UC Davis actions and related issues … but will post as things develop.

Dear UC Davis Community,


Happy New Year! I am writing to welcome everyone back to campus and to share my thoughts about the coming year at UC Davis.



The many conversations we’ve had about the events of last November affirm that our pursuit of academic excellence can succeed only if our campus remains a safe and welcoming place for all voices and forms of expression.


As we work to ensure this, we must not forget the understandable frustration that has fueled protests. After repeated cuts in state support for California’s public universities and a near doubling of tuition the past four years, many of our students and their families have reached a breaking point. Rising student debt and a still-struggling economy have only made things worse. Students have every right to expect that we will stand with them in fighting to reverse these very troubling trends.


In the coming year, I will personally and persistently advocate for additional state and federal investment in our university to help ease this financial burden and make UC Davis more available and accessible to deserving students. We also will steward our resources wisely, seek to protect academic programs to the extent possible, and do everything possible to fund more student scholarships and fellowships.


Ours is a preeminent public university. As we all strive to enhance its many qualities and distinctions, let us be proud of what is taking place every day in our classrooms, laboratories, health centers and other centers of excellence. All of you, in some way, are benefiting our region, state, nation and world. All great universities place students at the center of their work. We cannot and will not rest until we provide our students the best learning environment and services possible.


I also am committed to focusing on the positive role of UC Davis in economic development and its positive impacts on communities, our state and beyond. A stronger regional, state and global economy will provide our graduates with the career and service opportunities they deserve.


In support of this goal, I have initiated an extensive effort involving faculty, students and staff to assess and evaluate our 2020 Initiative. Central to that task is our ability to convert this concept into a plan that is implementable, aligns well with and supports our values and principles as a land-grant university.


The 2020 Initiative can be a bold blueprint for UC Davis to meet its financial challenges while broadening access to California students and allowing our university to become an even more vital engine of economic development.


Much work lies ahead. We expect to receive in coming weeks the results of various inquiries regarding the events of last November. We will receive critical reports regarding the future of UC Davis athletics. And we will hear the concerns and ideas generated by the fifty faculty, staff and students helping to study and shape the proposed 2020 Initiative.


I look forward to sharing and discussing these important subjects with you.


Sincerely,


Linda P.B. Katehi

Draft post cleanup #14: Video of Talk of mine from 2005

Yet another post in my “draft blog post cleanup” series.  Here is #14 from July 2010.

Embedded here is a video of a talk I gave in 2005 at the NIH  entitled “More Questions Than Answers Insights into DNA Repair Processes from Genome Sequencing Projects”

http://videocast.nih.gov/embed.asp?file=12774

OK – testing "threaded commenting" on my blog

Just saw this post from Blogger and am testing it here – seems like it could be a better commenting system — Engage with your readers through threaded commenting | Blogger Buzz

Let me know if there are any opinions on the matter …