December 2010 Archives

New Dimensions solicitation available

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National Science Foundation (NSF) Logo, reprod...

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NSF announced the new solicitation for its Dimensions of Biodiversity program.

Carl Schlichting, Cindi Jones, John Silander, Justin Borevitz, Andrew Latimer, and I were lucky enough to be funded the first time around. We're just getting started. Seeds of Pelargonium scabrum have been collected, and seeds of Protea repens will be collected starting in March. We'll get our experimental gardens started in May. We'll be posting news and updates on the project wiki. Please stop by if you're interested.

Something new on Kindle

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One drawback to e-books is that they're difficult to lend. That's now changed with Amazon's Kindle. Now I can lend books I've bought to a friend/colleague for 14 days. They don't even have to own a Kindle. All they need to do is to download the free Kindle app for their computer, smartphone, or iPad and read away. I won't be able to read the book for the 2 weeks while its lent out, but that's fair. If I lent someone a copy of a book on my bookshelf, I couldn't read it until it was returned.

Lending books on Barnes & Noble's Nook has been possible for awhile.

I'm glad to see Amazon.com picking up on the idea. eBooks are starting to resemble paper books more and more. No wonder sales of eBooks are growing rapidly.

Visualizing data

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tourists-in-sf-575x374.png
Displaying complicated data in a way that's easy to understand isn't easy. I mentioned Hans Rosling and Gapminder.org a couple of weeks ago. Over at FlowingData, they've identified what they regard as the top 10 visualizations in 2010.

The image at the left took top honors. It shows where Flickr users took photographs in and near San Francisco. Tourist photos are marked in red. Resident photos are marked in blue. Those that couldn't be identified are marked in yellow. If you want a closer look at the map, you can click on the image at the left. If you want a really close look, head over to Flickr. The original image is 6137x6137 pixels. You can find similar maps for London, New York, and many other places on in Eric Fischer's Locals and Tourists set.

If you're interested in visualizing data, a quick trip to FlowingData is well worth your time. The other featured visualizations are also quite striking. I especially like "Driving shifts into reverse."

And for a much simpler visualization, head over to Andrew Gelman's blog and take a look at his "Graph of the year".

Ken Robinson on education

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I

In this TED talk, Ken Robinson complains about the state of education. There are things in this presentation that are sure to make people angry.1 But he also has some useful observations, among them that the current educational system was largely designed during the Englightenment and Industrial Revolutions, that its structure matches that of a factory with standardized manufacture of products (students) in batches (grades), and that the current system privileges abstract, "academic" thinking over other kinds of knowledge.

I can't argue with much of his diagnosis.2, but in the end I have to agree with Punctuated Equilibrium at The Guardian:

Basically, Sir Ken Robinson whinges about the educational system without presenting even one creative, usable solution to the problems that he reports -- problems that every one of us is acutely aware of. Anyone can criticise the system but few can (or will, apparently) fix it.
I wish Robinson had not only diagnosed the disease, but also told us how to cure it.

Related articles

Mohammed Noor on the iPad

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Behold the iPad in All Its Glory

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Mohammed gets it exactly right. I've had my iPad a little longer than he has, I am a Mac person,1 I use some different apps than those that Mohammed mentions, and I still like paper and pen for notes at seminars [but not at meetings], but his advice matches the advice I've given to several people when they ask me about my iPad.

I got my iPad in early October. Even though I don't use a Mac, I love it- not just as the "new techy trendy toy" (which I fully acknowledge it is that too!) but as a functional part of my work and play. Let me say upfront- I don't think iPads are for everyone. It's neither a laptop replacement nor a smartphone replacement, and yes, no one "needs" to have one- we all got by last year without them. But here's how I use mine and why I like it, primarily in the context of my job.
Bingo! No one needs it, and you shouldn't get one if you're looking for a laptop replacement. But if you're looking for an easy way to take documents to meetings, take notes, read books (I love Kindle reader),2 sketch ideas, send short e-mails, and surf the web conveniently (no Adobe Flash), it's very handy. I wouldn't call it "magical" the way Steve Jobs did, but I use mine all the time. The New York Times, the Washington Post, and The Economist all look great on the iPad, and the NPR and PBS apps are pretty nice too.

As a Mac person, I should add Papers is great for organizing PDFs of scientific articles, and it syncs wirelessly with Papers on my iPad. Very nice!

Climate one-liners

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climate-one-liners.pngI just ran across a very useful resource over at Skeptical Science. It's a series of one-line responses to over 100 arguments climate change contrarians often use. The current top 5 are displayed above. You can also click on any of the one-liners to get more detailed information (basic, intermediate or advanced).

Photos from China

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5294270286_8535bc29ed_o.jpgI visted Beijing for a few days last August, and I finally got around to posting a few photos from the trip to Flickr. I'm afraid the photos of the Forbidden City aren't very good. It was raining hard that day, and there's only so much you can do with Photoshop. The photos of the Badaling section of the Great Wall and of the Olympic Park are better. The photo above is a Chinese "Keep off the grass" sign on the Olympic Park grounds. Click on the image to see a larger version.

Statistics and the filibuster

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cloture-by-congress.pngEzra Klein pointed out that Senate.gov provides a lot of historical data on the composition of the Senate and its procedures. One of the pieces of data it provides is the number of cloture motions filed in every congress since the 66th (1919-1920). I've plotted the data (in black dots) in the graph to the left. The red dots show the fit of a statistical model to the data in which the number of cloture motions is elated to the session in which they were filed, the proportion of Democrats in the Senate, and an indicator of whether the president is a Democrat or a Republican. As you can see, the model fits the data pretty well. (See the next page if you're interested in more details.)

As Klein points out, the number of cloture motions filed is an imperfect measure of how frequently the filibuster is used. For example, Senators often threaten filibusters and don't have to follow through. Still, the dramatic increase in the number of cloture motions filed over the last four decades must reflect a dramatic increase in the number of times bills have been filibustered in the Senate. There's a hint of an increase in the number of filibusters up to the 91st, but since then the number of filibusters has increased dramatically.

If you're thinking that's a Watergate effect, I'm afraid the timing isn't quite right. The dramatic increase in the number of cloture motions files occurs in the 92nd Congress (1971-1972) - pre-Watergate. I'm sure some political scientist has noticed this before and has a good explanation for why there was such a break with tradition in 1971-1972. It also can't be associated with the change in rules reducing the margin necessary to invoke cloture from 2/3 to 3/5. That rules change happened in 1975. If someone has a good explanation, I'd be delighted to hear it. In fact, the dramatic increase may not be so dramatic after all. Read on for an explanation.

Google body browser

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google-body.png
You'll need a browser with WebGL support to use the Google body browser, but if you have one, it's pretty amazing. The thumbnail at the left is a snapshot of the muscle layer looking at the right side of a human body. (Click on the image for a full-size screenshot captured with Google Chrome.)

You can zoom in, rotate, focus on muscles, organ systems, the circulatory system, or the nervous system. You can turn on labels (as I have here) or leave them turned off. If you ever want to see where your teres minor is (top left in this image), now you can find it.

Enjoy.



Remembering Les Mehrhoff

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volunteer_training.jpg

Les training IPANE volunteers (from the IPANE website)

I first met Les Mehrhoff almost 25 years ago, when I interviewed for my current job at the University of Connecticut. He and Greg Andeson picked me up for breakfast one morning. We talked about plant systematics over eggs and bacon at Friendly's. I remember thinking to myself at the time, "Wow! This guy has an incredible knowledge of natural history. There aren't many people like him." After I got to UConn I soon learned that I was wrong. There wasn't anyone like him.

Writing that last sentence about Les in the past tense was hard. I learned yesterday that Les suffered from a massive, fatal heart attack Wednesday night. Now the world doesn't have anyone like him, and I have lost a friend and colleague.

Les wasn't just a remarkable natural historian, though he was that. He didn't just know the flora of New England down to every variety, subspecies, forma, and synonym, though he knew all of that. He seemed to know every individual plant (and frog and salamander and mushroom and bird) in New England, and he didn't just know them as acquaintances. They were all his close friends. He cared passionately about them, and he devoted his life to protecting them.

Over the last 25 years, I got to know Les pretty well, first as the chief botanist for the Connecticut Department of Environmental Protecton, then as a collections manager for the biological collections in my department, then as the energy and life force behind the Invasive Plant Atlas of New England (IPANE).1 In all of these roles Les worked tirelessly to ensure that New England's natural heritage is protected for generations to come, and he did so with generosity, humility, and good humor.

When Les was at DEP his focus was on protection of rare and endangered plants. Because he knew I was interested in plant conservation, he got me involved with the Science and Stewardship Committee of the Connecticut Chapter of The Nature Conservancy. But he didn't stop there. He also recruited me to become an early part of the New England Plant Conservation Program, and he encouraged me to form the (now defunct) Connecticut Biodiversity Forum. His enthusiasm and passion were so infectious that when he asked you to do something, you couldn't turn him down.

In recent years, Les' passion has been directed at reducing the spread and impact of invasive exotic plants. In addition to his involvement with IPANE, he was a founding member of the Connecituct Invasive Plants Council and he provided expert advice on invasive plants to programs throughout the United States.

The world is a better place for all that Les did. And those of us who knew him have lost a wonderful friend and colleague.

Why biodiversity matters

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David Suzuki Foundation

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A wonderful short video from the David Suzuki Foundation



Hat tip: Robert Janssen

The UN and biodiversity

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Last June, delegates to an international convention in Busan, South Korea approved a resolution recommending to the General Assembly of the United Nations that it form an Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES). On Tuesday, the General Assembly accepted that recommendation. Here are a couple of paragraphs from the United Nations Environment Program's press release:

The new body will bridge the gulf between the wealth of scientific knowledge on the accelerating declines and degradation of the natural world, with knowledge on effective solutions and decisive government action required to reverse these damaging trends.

Its various roles will include carrying out high-quality peer reviews of the wealth of science on biodiversity and ecosystem services emerging from research institutes across the globe in order to provide gold standard reports to governments.
No countries met the 2010 target for stemming biodiversity loss. Let's hope that IPBES is more effective.

Molecular insights into classic examples of evolution

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Every year the American Institute of Biological Sciences1 (AIBS) and the National Evolutionary Synthesis Center (NESCent) co-sponsor a symposium at the annual meetings of the National Association of Biology Teachers. This year's symposium was held on 5 November and featured

  • Edmund "Butch" D. Brodie, III - Time to change the channel: predator-prey arms races and the evolution of toxin resistance in snakes
  • Allen G. Rodrigo - Rapidly evolving viruses: studying molecular evolution in real time
  • Hopi E. Hoekstra - From mice to molecules: the genetics of color adaptation
  • Sean Carroll - How bugs get their spots: genetic switches and the evolution of form
You can find videos of all presentations at the NESCent web site. Unfortunately, the embedding code doesn't seem to be working, so I can't post any of them here, but if you click through to NESCent, you'll see that they're much better than a typical YouTube video of a PowerPoint presentation. In addition to the videos, educational staff at NESCent have collected a variety of other materials that will be useful to any teachers who want to use these material in class (or to any students who want to do a little bit of extra studying).

Felisa Wolfe-Simon gives an interview

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Arsenic-based life has garnerd a lot of attention over the last few weeks. After the initial press conference, Felisa Wolfe-Simon and her collaborators have declined requests to respond to criticisms of their paper except in the peer-reviewed literatrue. A few days ago I wrote:

By holding a press conference to announce a new finding, scientists invite a broader audience to hear what they have to say. They also invite a broader audience to hear what their critics have to say.
I'm not conceited enough to think that Wolfe-Simon even read that post, but I was pleased to learn Monday evening that she did accept an interview request from Elizabeth Pennisi at Science. As I read the interview, Wolfe-Simon is blaming NASA for hyping the results. She also describes the press conference as a "complicated sort of situation where we didn't have enough time...it was really about representing this is what we found, this is the observations we made, in a way that a community could understand." She didn't see it as a scientific paper and wasn't prepared to answer questions about the data at the news conference. As for not responding to critics,

[W]e didn't want to answer it in a way, or respond to it in a way, that we thought would not give us the opportunity to think as deeply as we might need to. I was under a lot of pressure, and I'll be honest, I was exhausted. I really wanted to get back home and back into the lab.
Wolfe-Simon goes on to answer a variety of questions about tests that could have been done and about making samples available to other scientists. Head over to the Science web site and read the whole interview if you want to know more about that. Read on if you're interested in what I have to say about "science by press conference".

A note on comments

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This blog gets very few comments, so there won't be many of you who notice this change, but I've had to change the comment policy here. Only authenticated commenters will now be able to post. You can authenticate yourself through Google, Facebook, or several other sites, but I've had to institute this because darwin (my server) has been getting slammed with comment spam over the last few days. I know that requiring authentication makes this site less friendly, but I didn't have any choice.

Sorry.

Once again, a few miscreants make the world a less pleasant place for the rest of us.

The end of men

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Hannah Rosin presents data showing that women are coming to play a dominant role in many parts of western society. Women are the majority of the American workforce. Over 50 percent of managers are women. All but two of the 15 professions projected to grow most in the next decade are dominated by women. In short,

This is really just about the facts of this economic moment that we live in. the 200,000-year period in which men have been top dog is truly coming to an end, believe it or not, and that's why I talk about the end of men.

For more on Hannah Rosin's views about "the end of men", watch her TED presentation below. You may also want to click trhough to the TED website, where you can read the transcript of her presentation.1




88 and counting

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Those of you who know me know that I don't follow sports, but even I couldn't help but notice this headline on the Hartford Courant website this afternoon:

88-and-counting.pngFrom the article in the Courant:

NEW YORK -- Tiffany Hayes scored 26 points and Maya Moore had 22 as the No. 1 UConn women beat No. 11 Ohio State 80-50 at the Maggie Dixon Classic on Sunday afternoon at Madison Square Garden. The Huskies' 88th consecutive victory tied the UCLA men's NCAA Division I basketball record set in 1971-74.
What can I say but "Go Huskies!"

Bayes theorem and WikiLeaks

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Nate Silver provides an interesting perspective on the charges against Julian Assange at FiveThirtyEight.com. It's a nice example of a real-world application of Bayes' theorem. His conclusion? You should really read the whole column, but here it is:

[T]he fact that the charges are (apparently) politically motivated is indeed a reason to regard them skeptically, and they make it less likely -- perhaps much less likely -- that Mr. Assange is guilty of them. (Although he may be guilty of being a creep even if he is not guilty of a crime.)

Nevertheless, I have come across a number of analyses that try to evaluate the merits of the charges without regard to this political context, or which otherwise seem caught up in debating their salacious details. That is likely a mistake: in a world of limited information, the political motivation behind the charges might be the most important clue we have in evaluating their merit. (emphasis added)
Go read the whole column to understand why.

The story of health and wealth over 200 years

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You may have run across the visualization work done by Hans Rosling. If you haven't, you owe yourself a trip to Gapminder.org. The data that are available there on the health and wealth of nations and the tools that are available to visualize them are truly amazing. But even if you've been to Gapminder and you know about Hans Rosling's work. this short video will blow you away. His conclusion? "It's entirely possible that everyone can make it to the healthy, wealthy corner.



He's right isn't he? It's a pretty neat visualization, too. I wish I could pull something like this off. Talk about communicating science.

Arsenic-based life and public science

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WASHINGTON, DC - DECEMBER 02:  (L to R) Felisa...

Image by Getty Images via @daylife

When Felisa Wolfe-Simon and her colleagues announced that they had found a bacterium that could replace phosphorous with arsenic, they published a paper in Science. But NASA also scheduled a press conference to announce the findings:

nasa-press-conference.pngAs you know if you've seen my previous posts on arsenic-based life, that claim has been met with a lot of skepticism. The skeptics have posted detailed critiques on blogs in addition to submitting letters to Science questioning the results.

But Wolfe-Simon and her colleagues refuse to respond to their critics. They want the debate to play out in the pages of peer-reviewed journals. Funny. They were more than willing to share their claims with a broad public audience, but they aren't wiling to defend their claims against critics in the same venue. They want the critiques to be peer reviewed. Here's part of what the editors of Nature say in response.

Formal peer review does give criticized authors time to think critically and carefully, and it is a good way to filter out rubbish. But in this case, much of the criticism was already coming from the researchers' peers. And it should be remembered that peer review as conducted by journals is itself full of differing opinions, and is not the only way to crystallize truth from such disputes. In this instance, a prompt and explicitly provisional response from the authors would have been a better approach, particularly given the way they encouraged the original attention.

...

In the end, the scientific truth will prevail, as it usually does. In the meantime, researchers must accept some harsh truths about the speed and spread of digital criticism.
Blogging is no substitute for peer review. But peer review doesn't stop when a paper is published. If they're any good, papers are argued about in graduate seminars, in hallways, and at conferences. None of those discussions are peer reviewed, though they may lead to experiments or observations that are peer reviewed. By holding a press conference to announce a new finding, scientists invite a broader audience to hear what they have to say. They also invite a broader audience to hear what their critics have to say.


Science and writing

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A quick glance at the category archive listing in the far right column of this page makes one thing abundantly clear. I've written a lot about science communication, more than about any other topic1 That's because I think it's our responsibility as scientists to make our work accessible to the public and to share it with them.. For reasons Philip Kitcher explains well in the concluding chapter of Science, Truth, and Democracy, that obligation derives from our obligations as citizens of a democracy to contribute to its orderly functioning, and part of that orderly functioning depends on citizens being well informed.

I mention this because I just ran across a project that I'm going to have to learn more about,

NeuWrite is a collaborative working group for scientists, writers, and those in between: graduate, post-doctoral and faculty researchers, fiction and non-fiction writers, as well Journalism and MFA students at Columbia. The group serves as a writing and science resource for members pursuing their own projects, and as a forum for collaborative work. (source)
In particular, one of the projects linked to from neuwrite is the NeuroJournalism Mill, a "site dedicated to sifting the wheat from the chaff of popular media reporting on news about the brain". It looks like a very worthwhile project. If there are readers of this blog interested in trying something similar on environmental reporting, drop me a line. I'd like to "talk" with you about whether an EnviroJournalism Mill would also be worthwhile.

Michael Behe in the Quarterly Review of Biology

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When the table of contents for the December, 2010 issue of Quarterly Review of Biology appeared in my e-mail box, I noticed a paper by Michael Behe, Experimental evolution, loss-of-function mutations, and "the first rule of adaptive evolution". If the name "Michael Behe" rings a bell, it's probably because he's a proponent of intelligent design creationism who happens to be on the faculty at Lehigh University.1 It's unusual to see a paper written by Behe in a major biological. I've been meaning to sit down, read it, and offer a few thoughts about it. I still plan to read it, but instead of offering my own thoughts about it, let me quote a small part of Jerry Coyne's take on it:

While Behe's study is useful in summarizing how adaptive evolution has operated over the short term in bacteria and viruses in the lab, it's far less useful in summarizing how evolution has happened over the longer term in bacteria or viruses in nature--or in eukaryotes in nature.  In this sense it says nothing about whether new genes and gene functions have been important in the evolution of life.
If you want a more complete analysis, head over to Jerry's site and read the whole review.

Tracking arsenic-based life

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Logo of the British newspaper The Guardian

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There is far more web activity on the recent reports about arsenic-based life than I can possibly follow. If you want to keep up, head over to the Guardian where they have set up a "Story tracker" page where Alok Jha and James Kingsland are trying to keep up.

Dennis Overbye has more in Tuesday's ScienceTimes.

More on arsenic-based life

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If you'd rather listen to a discussion about arsenic-based life than read the blog posts and articles referred to in my last post, head over to The Guardian for the Science Weekly podcast. This week's edition gathers a group of scientists together to discuss the claims and the evidence. If you don't want to go to The Guardian's website for some reason, here's a direct link to the MP3 of the podcast:

Science Weekly podcast, 13 December 2010.

Related articles

Arsenic-based life and the nature of science

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ResearchBlogging.orgIf you read this blog, you probably read about the report in Science describing a claim that scientists had isolated a bacterium from Mono Lake in California that

substitutes arsenic for phosphorus to sustain its growth. Our data show evidence for arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins. (from Wolfe-Simon et al.; reference below; click through at the bottom)

In an accompanying news article, Elizabeth Pennisi quotes two scientists commenting on the report:

"This is a very impressive and exciting discovery," says Barry Rosen, a biochemist at Florida International University in Miami. "The implication of this work is that life can be quite different from what we know," agrees [Clara] Chan, [a geomicrobiologist at the University of Delaware.
To understand which the discovery would be so impressive, if it turns out to be right, just remember that the backbone of DNA is composed of bonds between phosphorous atoms. The claim that Wolfe-Simon and her collaborators make is that phosphorous can be replaced with arsenic in DNA. In fact, if that claim turns out to be right, it won't be merely "impressive" or "exciting". It will be truly astounding.

So why did I qualify what I wrote? Why did I write "if it turns out to be right" instead of simply writing "to understand why the discovery is so impressive..."? Click through for more of the story.

Carl Rettenmeyer and army ants

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A photograph of a trail of Eciton burchellii a...

Image via Wikipedia

Several weeks ago, I mentioned that the BBC had an article on its website featuring Carl and Marian Rettenmeyer's work on army ants and their guests. The technical article describing their work just appeared in Insectes Sociaux. Here's the abstract:

As possibly two of the last true naturalists, Carl Rettenmeyer and his wife Marian dedicated their lives to the study of army ants and their associates. Over the course of 55 years, the Rettenmeyers went on numerous field trips mainly to the Central American tropics and analyzed hundreds of self-collected samples and those sent by a multitude of other scientists, who were inspired by Carl's enthusiasm. It comes as no surprise that Carl Rettenmeyer became the world's leading expert on army ant associates. This paper, which the Rettenmeyers nearly completed before Carl's death in 2009, gives the first comprehensive list of animals known to be found in the company of a single army ant species: Eciton burchellii. The 557 recorded associates range from birds to insects and mites and comprise the largest described animal association centering around one particular species. Although some of these associates may be opportunistic encounters, we are confident that approximately 300 of the recorded species depend on the ants, at least in part, for their existence. The extinction of E. burchellii from any habitat over its vast area of distribution is likely to cause the extinction of numerous associated animals at that site. This overview will hopefully inspire researchers throughout the world to follow in the Rettenmeyers' footsteps and continue the investigation of army ants and their associates.

Adapting to climate change

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There are currently no technological quick fixes for global warming. Our only hope is to change our behavior in ways that significantly slow the rate of global warming, thereby giving the engineers time to devise, develop, and deploy technological solutions where possible. Unless large numbers of people take appropriate steps, including supporting governmental regulations aimed at reducing greenhouse gas emissions, our only options will be adaptation and suffering. And the longer we delay, the more unpleasant the adaptations and the greater the suffering will be.

Sooner or later, we will all deal with global warming. The only question is how much we will mitigate, adapt, and suffer. (Thompson, L. G. 2010. Climate change: the evidence and our options. The Behavior Analyst 33:153-170.)
The Behavior Analyst is is the official publication of the Association for Behavior Analysis International. Lonnie Thompson is Distinguished University Professor in the School of Earth Sciences and a Research Scientist in the Byrd Polar Research Center at The Ohio State University. His article appears in a special issue of The Behavior Analyst devoted to climate change.1

What is nature worth?

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Another bad idea

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cbo-budget-projection.png

Projected federal revenues and expenses as a fraction of gross
domestic product (from the Congressional Budget Office).

The federal budget deficit is projected to exceed $1 trillion in 2011 according to the Congressinal Budget Office.1 The total U.S. debt is estimated at $14.6 trillion. Given such enormous numbers, it's not surprising that many people are worried about the size of the federal deficit and are interested in finding ways of reducing it. I count myself among them

Eric Cantor, majority leader-elect in the U.S. House of Representatives also claims to be very concerned about the deficit,2 He has a project called "YouCut" in which he invites citizens to tell him what to cut.3 On one page, Congressman Adrian Smith (R-Nebraska) reviews spending at the National Science Foundation (NSF). He identifies two projects he regards as questionable and invites citizens to search the NSF database and find others. As Dan Vergano points out, both of the projects Smith singles out for criticism are studying important problems: understanding how remote teams of scientists form to study complex problems and developing sophisticated computational methods. Smith's illustrates a fundamental misunderstanding of how funding is allocated at research agencies.

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This page is an archive of entries from December 2010 listed from newest to oldest.

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