March 2012 Archives

Student conference on conservation science

| No Comments | No TrackBacks
Share |
From my inbox:

STUDENT CONFERENCE ON CONSERVATION SCIENCE-NEW YORK (SCCS-NY)
American Museum of Natural History, New York City
October 10-12, 2012
$100 USD 

The conference is designed for graduate students, post-doctoral fellows, and early-career professionals pursuing or considering the field of conservation science. (Undergraduate students conducting thesis-level research may also apply.)

ALL DISCIPLINES ARE WELCOME!
Whatever your focus--biology, sociology, medicine, economics, architecture, the law--if it has a relevance for conservation, we want to hear your perspective!  Join fellow conservation students and conservation professionals from around the world to network, exchange ideas, and receive feedback from leaders in science, policy, academia, and management at one of the world's preeminent scientific and cultural institutions. 

MONDAY, APRIL 2: ABSTRACT SUBMISSION DEADLINE for Talks, Speed Talks, and Posters
Non-presenting attendees may register until September.

The Student Conference on Conservation Science was created in 2000 by the University of Cambridge, and is currently held annually in Cambridge, New York, and Bangalore, India. The 2012 SCCS-NY is hosted by the Center for Biodiversity and Conservation at the American Museum of Natural History. Collaborating institutions include Cambridge University, Columbia University Earth Institute,Yale School of Forestry and Environmental Studies, and Princeton University.  

To learn more, visit the SCCS-NY site or follow us on Facebook.

Plants move too

| No Comments | No TrackBacks
Share |
If you don't believe me, watch this video.



The sensitive plant, Mimosa pudica, moves quickly in response to touch, but to me the most fascinating part of the video is watching the time-lapse recovery.

Follow up - Nature, genomes, and access

| No Comments | No TrackBacks
Share |
I mentioned a couple of days ago that there was a problem with access to genome papers at Nature Publishing Group. Grace Bynes from Nature Publishing Group replied, and I'm pleased to report that the access problem was apparently a technical glitch. Here's a bit of her reply:

All of these articles should now be restored to being free to access (under a Creative Commons license). We're also checking that this hasn't happened to other papers in Nature and the Nature research journals.

This was a technical error, for which we apologize.
Thank you, NPG, for fixing the problem.

It's worth noting that the Creative Commons Attribution-NonCommercial -ShareAlike license that NPG uses for papers "publishing the primary sequence of an organism's genome for the first time" applies only to Nature and Nature research journals. Journals published for societies by NPG, like Heredity for which I used to be an editor, may follow NPG's policy or not at their discretion. If you are a member of a society whose journal is published by NPG, I urge you to call on your society's leadership to follow NPG's policy.

Creating jobs

| No Comments | No TrackBacks
Share |
Regulations kill jobs, right? Not according to Josh Bivens, acting research and policy director at the Economic Policy Institute:

Textbook macroeconomics indicates that, from the perspective of job creation, the best time to enact regulations that may require costly investments is precisely when the economy is depressed.
Huh? Isn't that exactly the opposite of what we've been hearing? Well, I'm not an economist and Wikipedia refers to the Economic Policy Institute as a "liberal, non-partisan think tank" (emphasis added), but Bivens arguments make sense to me. Here they are in a nutshell:

  1. When the economy is functioning well, the effect of environmental regulation on job growth is roughly neutral. It creates jobs in industries that supply equipment and services necessary to comply with regulations even as jobs in industries affected by the regulations may be lost.

    Generally, these direct influences cancel each other out. Even if they don't, the second reason for regulation's neutral effect on jobs comes into play: the central bank. In an effort to hit its overall inflation and unemployment targets, a nation's central bank - in the US, the Federal Reserve - will simply sterilise any change in job growth stemming from regulatory changes by adjusting interest rates to spur or slow economic activity.

  2. When the economy isn't functioning well, environmental regulation creates jobs because:
    1. The investment necessary to respond to regulations wouldn't happen otherwise. It's the opportunities to invest that are limited, not the financial capital.
    2. Increases in costs aren't likely to be passed on. Consumers can't afford them.
    3. The employment boost won't be neutralized by the Federal Reserve.
The parts of this argument that seem likely to be contentious are the claims that (a) direct influences of regulation cancel each other out when the economy is functioning well and (b) opportunities to invest rather than financial capital are what's limiting in a recession. Both of those claims seem plausible to me, but as I said, I'm not an economist. I'm willing to be persuaded that they're implausible.


Making knowledge powerful

| No Comments | No TrackBacks
Share |


Color, size, orientation, and twinkle. I'd avoid twinkle in scientific graphics, but color and size can be extremely useful. I wish I were as talented at telling stories visually as some of my colleagues. I am improving, but as any of you who have seen me give a presentation can attest, I have a long way to go.



Nature, genomes, and access

| 1 Comment | 1 TrackBack
Share |
A little over 4 years ago, the editors of Nature had this to say:

In the continuing drive to make papers as accessible as possible, NPG is now introducing a 'creative commons' licence for the reuse of such genome papers. The licence (see http://www.nature.com/authors/editorial_policies/license.html) allows non-commercial publishers, however they might be defined, to reuse the pdf and html versions of the paper. In particular, users are free to copy, distribute, transmit and adapt the contribution, provided this is for non-commercial purposes, subject to the same or similar licence conditions and due attribution.
The editorial announced a laudable move to formalize what had been an informal arrangement before then.

Jonathan Eisen (@phylogenomics on Twitter) points out that there are a lot of genome papers published in Nature Publishing Group journals that seem not to be accessible. Here's hoping that his effort to shame them into living up to their own words has some effect.

A better approach to citation analysis

| No Comments | 2 TrackBacks
Share |
Many people use the impact factor of a journal as a quick and dirty assessment of its quality, in spite of its many limitations.1 Some administrators use the impact factor of journals in which an author's work appears as a quick and dirty assessment of the quality of that author's work. A better index would probably be how often that work is cited, but sometimes work becomes so broadly influential and so taken for granted that it's simply common knowledge and no longer cited. Who cites Darwin, On the Origin of the Species (1859), when they refer to the theory of evolution by natural selection, for example? Still, counting citations gives us some indication of the influence an individual has had on their field, but it's far from perfect.

It is a slightly more robust measure, but it is still silly because 90% of citations are shallow: most authors haven't even read the paper they are citing. We tend to cite famous authors and famous venues in the hope that some of the prestige will get reflected. (Daniel Lemire)
Unlike me, Daniel Lemire doesn't just point out the inadequacy of citation counting. He proposes to do something about it.

We have the technology to measure the usage made of a cited paper. Some citations are more significant: for example it can be an extension of the cited paper. Machine learning techniques can measure the impact of your papers based on how much following papers build on your results.
He's starting a project to develop such an approach, but he needs your help (if you've published one or more scientific papers). He needs you to head over to his site and fill out a short form that will give him and his collaborators the data they need to start building textual analysis tools that will allow for automated analysis of which papers have the largest influence on how a field develops. Please head over and help him out.

In case you want to see the link before you click on it, here it is:

http://lemire.me/blog/archives/2012/03/20/from-counting-citations-to-measuring-usage-help-needed/


Where I've been

| No Comments | No TrackBacks
Share |
IMG_0159.jpg
A week ago I got on a plane to Chicago at about 7:30am. A little less than twenty-six hours later, I got off another plane in Nanjing (after transfers in Chicago and Beijing). I've been visiting Nanjing Normal University for the past week. My host, Xiao-Yu Ding, put me up in a very nice hotel, where I had free Internet access,1 but I didn't have time to make any postings while I was away.

Over the course of my visit I gave three talks: one on estimating and interpreting FST, one on the demography of Dicerandra frutescens,2 and one on evolution of white proteas, as pictured in the poster to the left. (Click on it for a full-size image that will be easier to read.) My hosts found the story I had to tell about the white proteas especially fascinating. I was delighted that they found the story so interesting. I'm prejudiced of course, but I find it fascinating, too.

That being said, I have to point out that I really can't take credit for how interesting that story is. I am fortunate to be associated with some very talented people. Once again, they made me look much smarter and more talented than I am --  "they" in this case being Jane Carlson and Rachel Prunier, who did all of the real work on the white protea project. They collected the samples, they set up the experimental gardens, they scored the microsatellites, and they measured all of the traits. I simply kibbitzed from the side, ran a few stats, and now I get to bask in their glory.

Dimensions of biodiversity

| No Comments | No TrackBacks
Share |
Protea_obtusifolia-De_Hoop.jpg

Protea obtusifolia in the De Hoop Nature Reserve, Western Cape, South Africa
Photograph by Kent Holsinger
Click on the image for a high-resolution image in a new window.

I've mentioned before the Dimensions of Biodiversity project in which I am involved, Parallel radiations in Protea and Pelargonium. We'll be heading off again in mid-late June for our second season of field work. While the Pelargonium group and the community ecology group will continue to focus their work on sites in the western Cape and the karoo, the Protea group will probably spend a couple of weeks in Mpalunga and KwaZulu-Natal filling in some of the "non-Cape" species we wouldn't otherwise be able to collect. Stay tuned for updates as they develop.

In the meantime, the National Science Foundation just released a new Abstract Book with brief descriptions (and stunning photographs) for all of the projects funded so far. You can download it from the NSF website at http://www.nsf.gov/pubs/2012/nsf12053/nsf12053.pdf.

When you do, you'll find descriptions of projects ranging from the microbiota of amphibian skin to functional and taxonomic diversity in freshwater plankton to speces, trait, and genetic diversity of ants to energy metabolism, carbon fixation, and colonization of deep-sea vents to ecosystem function and plant-microbe symbioses to functional, genetic, and taxonomic diversity of plant-fungal interactions to the microbiota of bee guts to our very own Protea and Pelargonium project. Enjoy!

Spam conferences

| No Comments | No TrackBacks
Share |
All of us are familiar with e-mail spam. A few months ago, a couple of the folks I follow when I remember to log onto Twitter mentioned spam conferences. A spam conference is a conference clearly designed simply to make money. Here's an example of what I mean. It might look legitimate until you notice that the conference I'm being invited to attend is a forum on pathology. That's about as far from my interest and expertise as any subject could be and still be in biology.

Here's the text of the invitation:

Dear Dr. Kent E Holsinger, 

 

It is my great honor and pleasure to invite you to attend the 2012 Montreal International Forum on Pathology and present your most recent research achievements and ideas at this meeting. This event will take place in Montreal, Quebec, Canada during April 26-27, 2012. Please visit our website at www.epsworldlink.com for program details.

This Conference will broaden the scientific scope and give us all possibilities to new and exciting insights in the field of pathology. This meeting will include oral, poster and video presentations. The Organizing Committee has prepared a stimulating and informative scientific program, which covers a wide range of topics and pressing issues in various aspects of pathology. We will involve worldwide well-known scientists and physicians with expertise in diagnostic and research. This event will provide the participants a unique networking platform with chief professionals.

This event is organized and hosted by EPS Inc., a Canada-based biomedical consultant agency. Please check the following website for EPS Inc. introduction and the list of upcoming conferences:

http://www.epsworldlink.com/images/brochures2012/EPSConference2012.pdf .

The conference venue is in Montreal, the second-largest city of Canada. This city is well-known worldwide for its unique French-style characteristics of culture and city life. The various and colorful activities around the conference and the charming winter setup will make your journey an enjoyable and memorable experience.

Your participation in the forum would greatly contribute to the success of this unique event, and we look forward to meeting you in Montreal.

Warmest regards,

Organizing Committee of 2012 Montreal International Forum on Pathology

EPS Inc.

1625 Maisonneuve Ouest

Suite 305, Montreal

Canada, H3H 2N4


More on Google Scholar citations

| No Comments | No TrackBacks
Share |
Jonathan Eisen has been playing with Google Scholar citations. I'm not sure yet what the advantage of inviting co-authors is, but I've invited a couple. If they accept, maybe I'll begin to see the advantage and invite a few more.

On a more personal note, if you compare Jonathan's h-index (65) to mine (37), you'll see why I regard myself as clearly in the 2nd or 3rd rank of evolutionary biologists, not among the leaders.


Two Michaels and academic freedom

| 1 Comment | No TrackBacks
Share |
Almost a year ago, Ken Cuccinelli (the Attorney General of Virginia) filed suit asking that the University of Virginia turn over documents relating to research Michael Mann did while he was on the faculty there. Mann, of course, was the lead author on the famous "hockey stick" paper, which has attracted an enormous amount of attention since it appeared in 1998. Even one of Mann's most vigorous critics called Cuccinelli's actions a "witch hunt". The Virginia Supreme Court may not have used the words "witch hunt", but they agree that Cuccinelli's demand was not reasonable.

The Virginia Supreme Court said Friday that Attorney General Ken Cuccinelli II does not have the authority to demand records related to a former University of Virginia climate researcher's work. (source)
Most of the concern about the case came from organizations like the American Association for the Advancement of Science, the American Association of University Professors, and the American Council on Education, which saw Cuccinelli's suit as an attack on principles of academic freedom.

While many academics have worried about the academic freedom implications of Cuccinelli's information demands, the decision by the Virginia Supreme Court was a technical one that did not address academic issues at all. Cuccinelli's demands for the records from the University of Virginia were based on the Virginia Fraud Against Taxpayers Act, and the court ruled that this law was intended to give the attorney general power to obtain information, in certain cases, from individuals. The University of Virginia is not a person, and so not covered by the act, the court said. (source)
While it would have been nice to have the court reaffirm protections provided by academic freedom, the narrow grounds on which the decision was based ensure that it is the final decision. There can be no appeal.

Robert M. O'Neil, general counsel for the AAUP (and a former University of Virginia president), said in an interview Friday that he was not disappointed that the Virginia Supreme Court did not address the academic freedom issues. Had the ruling relied on First Amendment protections of academic freedom, he said, the attorney general might have appealed it to the U.S. Supreme Court. The ruling, however, is entirely based on Virginia law, so it must be final. (source)
Score another one for Michael Mann.


Letterpress

| 1 Comment | No TrackBacks
Share |
Some people think that I'm a geek, but they're wrong. I'm either a nerd or a dork (depending on whether or not you think I'm intelligent). So far you know that I get excited about peculiar things like fountain pens, statistics, and even LaTeX. Just a couple of weeks ago, I linked to a post illustrating how much better LaTeX is at typesetting than Microsoft word.

Long, long ago in graduate school, I had a chance to print some herbarium labels with a simple letterpress. I've long been fascinated by printing, but that's the only chance I had to work with metal type. This video shows from the Rhode Island School of Design shows how letterpress printing is done. I wish I had the time (and a good reason) to do some letterpress printing. Working with ink and paper would be very satisfying.1

LetterPress - Printing Kahlil Gibran from Callil Capuozzo on Vimeo



On the origin of chocolate

| No Comments | No TrackBacks
Share |
You may know that chocolate was domesticated in Mesoamerica, but you may not know why or how long ago it happened. Here's a short video in which Patrick McGovern, scientific director of the Biomolecular Archaeology Laboratory at the University of Pennsylvania Museum, describes vessels dating back to 1400 B.C.E. that were used for fermenting the pulp of Theobroma cacao. He also describes an alcoholic drink derived from the fermented pulp, and it may have been for the alcohol that Theobroma cacao was domesticated -- not the chocolate.


 Subscribe in a reader

Pages

OpenID accepted here Learn more about OpenID

Technorati

Technorati search

» Blogs that link here

Nature Blog Network
Creative Commons License
This blog is licensed under a Creative Commons License.

About this Archive

This page is an archive of entries from March 2012 listed from newest to oldest.

February 2012 is the previous archive.

April 2012 is the next archive.

Find recent content on the main index or look in the archives to find all content.

Trending content