January 2011 Archives

College degrees and swearing

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swearing.pngcollege-degrees.png

If I had the data underlying these figures, I could make a a very interesting graph relating the number of college degrees per county (on the left; data from 2005-2009) and the number of tweets with profanity (on the right; data from March/April 2010). Since I don't have the raw data, all I can do is to eyeball the maps, I can't tell whether there's a relationship or not. You won't be able to either with the size of the images in this post, but if you click on them, you'll get popup images that are much larger. Maybe then you'll be able to see what's going on. If you want a really good view head to the original sites:

Not the way to express disagreement

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A California university professor has been charged with peeing on a colleague's campus office door.
Read the whole thing at sfgate.com.

Another Desmodium paper

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Another of the papers from Krissa Skogen's dissertation has just appeared:

Skogen, K. A., L. Senack, and K. E. Holsinger. 2010. Dormancy, small seed size and low germination rates contribute to low recruitment in Desmodium cuspidatum (Fabaceae). Journal of the Torrey Botanical Society 137:355-365.
http://dx.doi.org/10.3159/10-RA-003.1

There will be more. We're currently working up results from her demographic modeling of Desmodium cuspidatum populations in New England. I'm especially pleased that the Journal of the Torrey Botanical Society is a BioOne journal.1 Unfortunately, the University of Connecticut doesn't subscribe to BioOne.2 -- yet. Only BioOne.1.

Debunking irreducible complexity II

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If you enjoyed last week's video on irreducible complexity, you'll also enjoy this one. Arguments for irreducible complexity reduce to an argument from lack of imagination.

USA Science & Engineering Festival

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Last October thousands of people gathered on the Capitol Mall for the first ever USA Science & Engineering Festival. In 2012,

[T]he 2nd USA Science & Engineering Festival will inspire the next generation of scientists and engineers with school programs and nationwide contests throughout the 2011/2012 school year and a finale Expo in Washington DC in the Spring of 2012. The Expo is the nation's largest celebration of all things science & engineering and features over 1500 hands-on activities and over 75 performances on multiple stages. The 2010 Festival attracted over 500,000 people of all ages and had strong support from the White House and Congress. (from the Festival website).

AIBS responds to the State of the Union

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In an e-mail this morning from Rob Gropp, Director of the Public Policy Office for the American Institute of Biological Sciences (AIBS):

AIBS APPLAUDS PRESIDENT'S CALL TO ACTION ON SCIENCE, SCIENCE EDUCATION
 
Washington, DC -- During the 2011 State of the Union Address, President Obama challenged the nation to recommit to a spirit of innovation.  The President noted that the nation must invest the resources needed to improve science education and drive the scientific research that will answer our most pressing questions in health, the environment, and energy. 
 
"The President has repeatedly expressed his commitment to scientific discovery, innovation, and education.  AIBS is pleased to see that his commitment remains strong."  Said Dr. Richard O'Grady, AIBS Executive Director. 
 
AIBS Public Policy Director, Dr. Robert Gropp, applauded the President's remarks on science.  "We were heartened to hear that President Obama plans to submit to Congress in the coming weeks a budget that would continue to make investments in scientific research.  I look forward to seeing the details." 
 
"Science can not move forward and respond to our grand challenges in an environment of uncertainty.  The nation must make sustained and predictable investments in research and development."  Said O'Grady.
 

Celebrating the life of an extraordinary botanist

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volunteer_training.jpg

Les training IPANE volunteers (from the IPANE website)

It's been a little more than a month since we lost Les Mehrhoff. Those of you who knew him will share my deep sense of loss, and we will best honor Les through acts of kindness to the natural world and through celebrating his life.

Olga and Jessie have scheduled a celebration of Les' life at the Storrs Congregational Church. Here are the details:

Date: Saturday, 12 March 2011
Time: 11:00am


Location:
Storrs Congregational Church
2 North Eagleville Road (corner of Route 195 and North Eagleville Road)
Storrs, CT

The ultimate climate change FAQ

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Mean surface temperature change for the period...

Image via Wikipedia

The Guardian has put together a very valuable resource on climate change -- the ultimate climate change FAQ. There you can find answers to questions like:

Head over and take a look for yourself. The Guardian focuses on reporting the consensus among climate scientists.

If you're not sure what to think of the claims some dissenters make, head over to Skeptical Science, where all of the major debates (and many of the minor ones) are discussed.

Presidential medals for mentoring in science, engineering, and mathematics

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Last Friday President Obama announced the 2011 recipients of the Presidential Awards for Excellence in Science, Mathematics, and Engineering Mentoring. From the OSTP press release:

The Presidential Awards for Excellence in Science, Mathematics, and Engineering Mentoring, awarded by the White House each year to individuals or organizations, recognize the crucial role that mentoring plays in the academic and personal development of students studying science or engineering--particularly those who belong to groups that are underrepresented in those fields. By offering their expertise and encouragement, mentors help prepare the next generation of scientists and engineers while ensuring that tomorrow's innovators reflect the full diversity of the United States.
The recipients are:

  • Richard L. Cardenas, St. Mary's University, TX
    Anthony Carpi, John Jay College of
  • Criminal Justice, City University of New York, NY
  • Isaac J. Crumbly, Fort Valley State University, GA
  • Jo Handelsman, Yale University, CT
  • Douglass L. Henderson, University of Wisconsin-Madison, WI
  • Bruce A. Jackson, Massachusetts Bay Community College, MA>br />
  • Marigold L. Linton, University of Kansas, KS
  • Maja J. Matarić, University of Southern California, CA
  • Gerard F. R. Parkin, Columbia University, NY
  • Julio J. Ramirez, Davidson College, NC
  • Michelle A. Williams, University of Washington, WA
  • Center for Innovation in Engineering and Science Education, Stevens Institute of Technology, NJ
  • Baccalaureate and Beyond Community College Mentoring Program, State University of New York, Purchase College, NY
  • Grinnell Science Project, Grinnell College, IA
  • Women in Science and Engineering Mentoring Initiatives, Center for Research on Women and Gender, University of Illinois-Chicago, IL

The scale of the universe

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Everything from 10-35m to 1027m -- the entire scale possible in our universe. Head over to Primax Studio for an interactive version that slides from the smallest to the largest.

universe-scale-small.pnguniverse-scale-large.png

My buttons

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If you stop by regularly1 and if you were paying very close attention, you will have noticed that two new buttons appeared in the middle column awhile ago.

The one for Twitter is pretty self-explanatory. Yes, Virginia, I have finally joined Twitter, and you can follow me there (@keholsinger) if you're so inclined.

The second one for Mendeley is less obvious. Mendeley makes sharing bibliographies easy. If you click on the link, you'll go to my profile where you'll see a list of recent publications (with links to online versions of some of them). You'll also see that I'm a member of two groups: Population genetics and Statistical phylogeography. Those are groups I created. The population genetics group is a list of references derived from notes I've prepared for my graduate course in population genetics. The statistical phylogeography group is for a graduate seminar I'm running this spring. Desktop versions of Mendeley for Windoze, Mac OS X, and Linux are available, and there's a version available for iPad.

Debunking irreducible complexity

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Intelligent design creationists are fond of the idea that some biological systems are irreducibly complex. From this they infer that those systems didn't evolve. The YouTube video below does an excellent job of explaining why they're wrong. It shows clearly that the argument from irreducible complexity is really just a failure of imagination.


2011 is starting off well

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"Remembering a beloved botanist"

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Connecticut Public Radio

Image via Wikipedia

That's the title of the piece on yourpublicmedia.org remembering Les Mehrhoff. If you're not able to listen to WNPR today during Morning Edition or All Things Considered when the piece will be broadcast (at about 7:30am and 5:30pm, as I recall), follow the link to yourpublicmedia.org, where you can read the story, including a personal note from Nancy Cohen1 that was not part of the broadcast.

If you're impatient, just click here, and a new window in your browser will open and play the audio for you.

Not good

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The White House issued guidelines for scientific integrity in late December. I'll admit that I haven't read them yet, but many of the reports I read about them found them disappointing. Recently, an environmental journalist, Joseph A. Davis, published a scathing series of articles analyzing the policy at Climate Science Watch.

Since I haven't studied the guidelines, and I've only read Part I of the series, I can't vouch for the accuracy of Davis's claims, but the, unfortunately, seem plausible. Certainly, Andy Revkin thinks so.


Radio remembrance of Les Mehrhoff

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Connecticut Public Radio

Image via Wikipedia

We lost our good friend and colleague, Les Mehrhoff, a little less than a month ago. Olga and Jessie are planning a celebration of his life, and I will post information about it when it is available for those who are able to attend. I recently spoke with a reporter from WNPR about Les, and I recently received an e-mail from her saying that a piece about Les is scheduled to appear on WNPR at 7:33am and 5:44pm on Wednesday, 19 January.1 You should be able to pick up the live stream at http://www.cpbn.org/listen-live, and it will also be published to the web at http://www.yourpublicmedia.org.2

More pain at UC

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UC Berkeley will lay off nearly 150 employees this year, Chancellor Robert Birgeneau said Thursday.

Some of the workers have already been notified, university spokeswoman Claire Holmes said, and most will be let go by June. About the same number of jobs will be eliminated through other means, such as retirements and voluntary departures.

About a quarter of the 280 or so positions have salaries of $100,000 or above, Birgeneau said in a letter to the campus. The job losses are expected to save the university about $20 million.

No faculty positions will be cut, but other layoffs will come from all areas of the campus. ("UC Berkeley to lay off nearly 150 employees," Matt Krupnick, San Jose Mercury News)

Will the UC administrators who want pension benefits calculated on their whole salary, not just the first $245,000, withdraw their demands? I hope they will, not because it will save enough money to make much difference in the grand scheme of things, but because it is unseemly for them to seek such benefits for themselves when their institutions are suffering so severely.


The Science Hall of Fame

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Adrian Veres and John Bohannon are curators of the new Science Hall of Fame. It's a database derived from the frequency with which scientists's names appear in books published from 1800 to 2000.1 Here are the top 25.

SHoF.pngI'm pleased that Charles Darwin outranks Albert Einstein, and it's interesting to see that Carl Sagan slips in at number 25, just behind Rachel Carson.

Publishers withdraw from HINARI

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From the HINARI web page:

The HINARI Programme, set up by WHO together with major publishers, enables developing countries to gain access to one of the world's largest collections of biomedical and health literature. More than 7,500 information resources are now available to health institutions in 105 countries, areas and territories benefiting many thousands of health workers and researchers, and in turn, contributing to improved world health.
From HINARI's about page:

HINARI was launched in January 2002, with some 1500 journals from 6 major publishers: Blackwell, Elsevier Science, the Harcourt Worldwide STM Group, Wolters Kluwer International Health & Science, Springer Verlag and John Wiley, following the principles in a Statement of Intent signed in July 2001. Since that time, the numbers of participating publishers and of journals and other full-text resources has grown continuously. Today more than 150 publishers are offering more than 7,500 information resources in HINARI and others will soon be joining the programme.
I'm proud to say that BioOne is part of HINARI (and AGORA, OARE, and eIFL). It's an important part of our mission:1

BioOne sees sustainable scholarly publishing as an inherently collaborative enterprise connecting authors, nonprofit publishers, academic institutions, research libraries, and research funders in the common goal of maximizing access to critical research.
That's why I was so saddened yesterday when I ran across a piece in BMJ reporting that 2500 journals have been withdrawn from access through HINARI in Bangladesh. The explanation?

Kimberly Parker, programme manager at HINARI, said that the decision to withdraw free access was not unusual practice once publishers start to secure "active sales" in a country. 
Look, I understand that it cost money to publish journals. And I don't begrudge any company the chance to make a decent return on their investment. But the publishers who have withdrawn are Elsevier, Springer, the American Association for the Advancement of Science (AAAS), and the American Society for Animal Science (AAS). According to their annual report Reed Elsevier had an adjusted operating profit of £1.57 billion in 2009, up from £1.379 billion in 2008. Springer's earnings declined over the same period, from €285 million to €275 million. As for Bangladesh, it had a GDP of $1600 per person in 2009 and ranked 197th in the world ($94 billion for the entire country; figures from the CIA factbook).

I am saddened that Elsevier and Springer withdrew their journals, and I'm ashamed of AAAS and AAS. Surely we are better than that.

I got a kick out of this

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OK. I admit it. I'm a little vain.1 Sometimes I Google myself just to see what comes up. This time when I got to the second page I found this:

falk-holsinger-google.pngI like to think that Falk and Holsinger has been useful. I hope there aren't many people who agree with Google that it's fiction.

This may not look like much

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CONN00108476.JPG

Switchgrass (Panicum virgatum) from the University of Connecticut Herbarium

That humble grass to the left won't like like much to most of you,1 but we2 are rather proud of it. It's not that it's a particularly rare species, or that it's from a particularly important place. It's not because switchgrass (Panicum virgatum) has been touted as an important biofuel. It's because of who collected that specimen.

You'll have to squint if you try to read the label from the image to the left. But if you click on the image and zoom in, you can probably read it without too much difficulty. Still, clicking on that image and zooming in is a bit of a bother, so let me make it a little bit easier on you.




Here's a close-up of the collection label in the lower left corner.

CONN00108476-label.jpg

Click on the image if you want a closer look, but you read that name right: "H. D. Thoreau", and yes, it is that H.D. Thoreau. The H.D. Thoreau who wrote Walden, A Week on the Concord and Merrimack Rivers, and Civil Disobedience, and who was a friend of Ralph Waldo Emerson.

It's one of two Thoreau specimens in our herbarium. The database listings for them are here. If you click on the camera icons, you'll see high resolution scans, and by high resolution, I mean high resolution -- 7295 x 10160 pixels.

I've heard rumors about Thoreau specimens in our herbarium for a long time, but they were only recently found -- and I'm delighted. The Hartford Courant has a nice article about their re-discovery.

A new paper on Protea

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CarlsonHolsingerPrunier_cover.jpg

Photo by Jane Carlson (from the cover of Evolution 65:1; 2011).

One way of making yourself look good is to hang out with talented people. If I've been looking good lately, it's because I've been hanging out with a couple of very talented people for the last several years, Jane Carlson and Rachel Prunier. They are co-authors with me on a very nice paper in the January issue of Evolution.1



That's Protea aurea, one of our study species, pictured above.

"A moment of bipartisan joy"

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"You're witnessing a moment of bipartisan joy," said Assemblyman Tim Donnelly, R-San Bernardino, vice chairman of the Higher Education Committee. "I'm ashamed that I didn't think of this myself." (source)
And why is a Republican Assemblyman from San Bernadino so happy about a bill introduced by a Democrat, Jerry Hill, from San Mateo? Because the bill would cap pension benefits of highly paid employees at the University of California. Instead of calculating benefits based on a percentage of their full salary, they would be based on a percentage of the first $245,000.

"They really need to come down from their ivory tower and see and feel what real people are going through," [Assemblyman Hill] said.
As I said, honorable executives wouldn't be demanding these benefits when California and the University of California system are facing such enormous financial shortfalls.

Related articles

Electronic publication in plant taxonomy

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The International Code of Botanical Nomenclature requires that new names of all plant taxa be distributed in printed publications. The Code is revised every six years at an International Botanical Congress. The next IBC will be held in Melbourne later this year. After two unsuccessful attempts to allow electronic publication (at the Congresses in St. Louis [1999] and Vienna [2005]) a third Special Committee on Electronic Publication was established and is proposing a new set of changes to the code that would amend the code, allowing electronic publication after 1 January 2013 provided that:

While there are still significant problems associated with long-term archiving of electronic documents, I'm pleased to see that some plant taxonomists are willing to accept that electronic publication is here to stay and to make accommodations for it.

Having said that, if they'd asked my advice, I would have argued for one change to the proposals. I would have argued for requiring that the PDF be automatically generated from an underlying XML document and that the XML document would be regarded as the "gold standard" for authentication. I understand that few people are able to manipulate XML and only a few more have the expertise needed to make it human readable. PDF is much better in that regard, but the real promise of electronic publication comes with the automation that follows, and the structure of XML lends itself more readily to automated extraction of taxonomic information than PDF.

The concern may be that small publications lack the expertise necessary to produce XML, while they can produce PDF. That's a reasonable argument, and it might have persuaded me, but I don't see a discussion of this issue in the Report of the Special Committee.

Some people just don't get it

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University of California

Image via Wikipedia

The University of California system raised tuition by 32% for this academic year. It will increase by another 8% in fall 2011. Faculty and staff have been forced to take unpaid furloughs as UC grapples with a massive deficit. In addition to the shortfall on current expenses, the system faces $21.6 billion in unfunded pension liabilities. Neither UC nor its employees have paid into the pension fund since 1990.1 To eliminate that gap, "UC is trying to ... reduc[e] benefits for future employees, rais[e] the retirement age, requir[e] employees to pay more into UC's pension fund and boost tuition" (source).

Pretty awful, isn't it? Yet there are at least 36 highly paid administrators at UC2 who are demanding more pension benefits than they are getting now.

In fairness, the executives may have a legal right to the additional benefits. The executives want their pensions calculated on their entire salary, not just the first $245,000. The UC Regents agreed to this calculation in 1999, and the IRS granted UC a waiver to pay the additional pensions in 2007.

But having a legal right to something doesn't make asking for it a reasonable thing to do. UC may have no choice but to honor the demands, but honorable executives wouldn't have made the demands.


Michael Oppenheimer

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The Steven Schneider lecture at the meetings of the American Geophysical Union in December, 2010.


View on the AGU website.

Anthropology and arsenic-based life

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James Holland Jones applies lessons from the arsenic-based life controversy to anthropology. His conclusions?

  1. [W]e need to have scientific theories that are sufficiently robust that they can generate testable predictions that transcend the particularities of time and place. Results generated in one population/place/time can then be challenged by testing in other populations/places/times.
  2. [W]e need to be scrupulous in our documentation of our results and the methods we employ to generate these results.
  3. [W]e need to be willing to share our data.
If those sound like reasonable, unobjectionable conclusions, they are. You may be surprised to learn that there is controversy within anthropology about whether these precepts should be followed, because there's debate about whether anthropology should be a science.1

Climate science and arsenic-based life

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Shortly after the report of arsenic-based life appeared, I pointed out that several scientists were skeptical of the claim. I used the debate as an example of how science works and compared it to the "debate" about intelligent design:

Compare that lengthy, tortuous process of debate and review among experts to the "debate" that intelligent design creationists want to have in high school textbooks. Which process do you think is most likely to help kids understand their world?
Much the same could be said about climate science. In fact, the folks at RealClimate have a post showing how the debate about arsenic-based life demonstrates three things:

  1. Major funding agencies willingly back studies challenging scientific consensus.
  2. Most everyone would be thrilled to overturn the consensus.
  3. Scientists offer opinions based on their scientific knowledge and a critical interpretation of data.
Here's the money paragraph:

This is the key lesson to take from this incident, and it applies to all scientific disciplines: peer-review continues after publication. Challenges to consensus are seriously entertained - and are accepted when supported by rigorous data. Poorly substantiated studies may inspire further study, but will be scientifically criticized without concern for funding opportunities. Scientists are not "afraid to lose their grant money".
But you should go read the whole thing.


Death of a climate bill

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From Dave Roberts, Thomas Pitilli, and Warp Graphics on Grist (click on that link to see all six panels):

death-of-a-climate-bill.pngI particularly like the conclusion:

etch-a-sketch.png


Communicating climate change

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I learned recently that the Intergovernmental Panel on Climate Change (IPCC) is looking for a Communications and Media Relations Manager to be employed by the World Meteorological Organization in Geneve, Switzerland.

The incumbent will direct and manage the media and outreach services of the IPCC in collaboration with key partners, in particular, governments, academics, inter-governmental and non governmental organizations. S(he) will contribute to the formulation of IPCC's overall communication strategies and policies, and advises all stakeholders on matters pertaining to the IPCC's communication priorities and issues, in addition to acting as spokesperson. The incumbent will ensure that communication and outreach on programmed activities are carried out in a timely manner and all outputs produced meet required standards. S(he) will advise and coach IPCC experts on when and how to interact with the media and the public in general. S(he) will oversee information activities of the different working groups and guide their communication experts and will propose and implement initiatives to strengthen the IPCC relations with governmental and intergovernmental partners. The incumbent will explore new cooperation and partnerships, including fund raising. S(he) will direct and supervise all web information of the IPCC Secretariat, will maintain and strengthen liaison with the media and will lead the development of communication and outreach programmes, including the social media (twitter, facebook, blogs, etc.).
As David Wogan argues,

The conservative bloc of scientists would argue that hard science and data are all that is necessary, which is expected: silos are hard to break down. But in a world where decisions are made by folks without technical backgrounds, having scientists that can talk to the rest of the world is the glue that holds everything together.
It is our responsibility as scientists to make our work accessible to the public and to share it with them. When the science is as complicated as climate science, we need help from professionals, and I'm delighted to see that the IPCC has recognized that.


Congratulations to Carl Zimmer

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Choice, the journal of record for academic librarians,1 just released its list of outstanding academic titles for 2010. What does this have to do with Carl Zimmer?

His The Tangled Bank: An Introduction to Evolution is on it! I have to confess to not having a copy yet, but when I teach evolution again next year, I'm going to have to take a careful look at it.2

Democracy and science

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Several weeks ago I mentioned a really bad idea that Adrian Smith (R-Nebraska) proposed. He asked people to search the NSF database of award abstracts and identify frivolous projects that shouldn't have been funded. As I wrote then:

It makes perfect sense for politicians to decide how much the federal government should invest in basic research through the National Science Foundation. That's what governing is all about. Making choices. Setting priorities. But having politicians make decisions about individual research grants makes as little sense as letting them decide whether to build a bridge to nowhere.
A little while after I posted that entry, Dan Hind published an opinion piece in The New Scientist, Time to democratise science. Diandra takes exception to Hind's suggestion for reasons that seem similar to mine:

Science should be open to anyone who wants to make the effort to understand it and how it works.  But asking people to do a blind search on a handful of terms and then make a determination as to the 'value' of the research is absurd. Does Dan Hind really think that the average person who was enjoying living in a house they couldn't actually afford and watching their property values soar would have seen a need to fund the small fraction of economists who were warning the bubble was near burst stage?  Or that the outcome of democratic science is going to be anything other than people advocating for research money to spent in areas that have touched them personally?
I wrote "seem similar" on purpose. While some parts of Diandra's critique are spot on, notably her emphasis on the quality of evidence supporting opinions and on the qualifications of those who express them, she throws out the baby with the bathwater here. She makes a mistake that many of us make, confusing democracy with voting.

There is an alternative conception of democracy -- deliberative democracy -- and in a deliberative democracy there is clearly a role for non-scientists to play.


An interactive guide to IPCC AR4

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Changes in radiative forcings between 1750 and...

Image via Wikipedia

The fourth assessment report of the Intergovernmental Panel on Climate Change was released in 2007. It's a long, complex document. But now there's an online guide to help you dig deeper into the science. It includes links to the primary literature cited in the reports, data on the journal cited (titles and numbers of citations), and data on authors cited in the reports.

The guide is not for the faint of heart. It's for those who really want to dig into the science, but it's great to have this resource available.

If you're interested in a shorter version, take a look at the Synthesis Report for Policymakers.

The joy of stats

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Who says statistics is boring?



Hat tip: Revolutions

I have to brag a little

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I wear a Garmin 405CX when I run, whether I'm running outdoors or on a treadmill.1 Then I upload the results to Garmin Connect where it keeps track of them for me. One of the things Garmin Connect allows me to do is to produce reports like this one, showing my totals for 2010. I'm pretty proud of that distance total - more than 1000 miles!

Kent's-exercise-2010.png


Greening Kansas

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Greensburg, Kansas was leveled by a Tornado on May 5, 2007. Residents decided to rebuild - and to rebuild green. They now have a higher density of LEED certified platinum buildings than anywhere else in the world. In Salina, Kansas residents don't accept the evidence for global warming, but they are ruthless when it comes to saving energy. Seems that folks in the heartland understand a few things that the rest of us don't.



For more information about Greensburg, visit http://www.greensburggreentown.org/.

For more information about climate and energy in Kansas, visit http://www.climateandenergy.org/

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This page is an archive of entries from January 2011 listed from newest to oldest.

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