May 2011 Archives

Arseniclife and open science

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WASHINGTON, DC - DECEMBER 02:  Felisa Wolfe-Si...

Image by Getty Images via @daylife

Last December, Science published a paper by Felisa Wolfe-Simon and colleagues claiming to have found A bacterium that can grow by using arsenic instead of phosphorous -- that was the title of their paper. As you probably know, a firestorm erupted when Rosie Redfield posted a detailed critique on her blog concluding that

Basically, [the paper] doesn't present ANY convincing evidence that arsenic has been incorporated into DNA (or any other biological molecule)
There was such an uproar that the paper, which was published online in Science Express, has yet to appear in print. Links to a lot of information about the paper and critiques of it appeared on Twitter with the hashtag #arseniclife.

On Friday, eight technical comments on the original Science Express article and a response to those comments were published -- again in Science Express. The final version of the Wolfe-Simon paper will appear, along with the technical comments, in the 3 June issue of Science. But as Carl Zimmer says in Slate,

For those of us who have been tracking #arseniclife since last Thanksgiving, however, today comes as an anticlimax. There's not much in the letters to Science that we haven't read before. In the past, scientists might have kept their thoughts to themselves, waiting for journals to decide when and how they could debate the merits of a study. But this time, they started talking right away, airing their criticisms on the Internet. In fact, the true significance of the aliens-that-weren't will be how it helped change the way scientists do science. (emphasis added)

World Science Festival

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wsf-2011.png If you're in or near New York City this week, I encourage you to visit the World Science Festival, which is being held there from 1-5 June.

Minds expanded. 5 days. 50 events. Infinite ideas.
Maggie Gyllenhall will play the role of Marie Curie in a reading of Radiance: the passion of Marie Curie at the opening night gala. On Thursday there will be an all-day program exploring the communication of science. The sessions include

  • Science on screen
  • Science storytellers
  • Improvising science (featuring Alan Alda)
  • Telling science stories in print and on the web
And those are just a sample of what's in store. Here's an example of the kind of panel discussion you might see.



I have to say, by the way, that when Mario Livio talks about how Kepler's observations weren't very accurate, "only within 4 percent", I am reminded of how different the features of the world that physicists study are from those that interest me.

Two recent papers

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For the small number of you who might care, here are titles and links to a couple of recent papers that have just appeared.1 The paper in Theoretical Population Biology is heavy going, but if you use microsatellites and score them according to the number of repeat units, you may find something useful in it.2 The New Phytologist paper picks up where an earlier one in American Journal of Botany left off.

Genetic diversity of microsatellite loci in hierarchically structured populations.
Seongho Song, Dipak K. Dey and Kent E. Holsinger. Theoretical Population Biology doi:10.1016/j.tpb.2011.04.004

Extreme environments select for reproductive assurance: evidence from evening primroses (Oenothera)
Margaret E. K. Evans, David J. Hearn, Kathryn E. Theiss, Karen Cranston, Kent E. Holsinger, Michael J. Donoghue. New Phytologist doi:10.1111/j.1469-8137.2011.03697.x

Is this a good idea?

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I don't think we ready to get rid of paper textbooks. Am I just getting to be an old curmudgeon,1 or should I get comfortable with this idea too?

Senior officials at Edinburgh University believe it is unfair to expect undergraduates to resort to pens and paper during critical assessments when most of their coursework is done using a keyboard. (source)
I see the point, and I have some sympathy for it. On a good day, my handwriting is legible. On a bad day, it's godawful. It's never attractive. And I can type much more quickly than I can write longhand, even if I'm writing illegibly.

In nearly everything we ask our students to do other than taking exams, we ask them to give us printed copies,2 and many of them sit in our classes taking notes with laptops.3 Writing out sentences and paragraphs with pen and paper seems anachronistic, and it would be much easier to read the answers if they came in printed form produced on a computer.

[T]he university said safeguards would have to be built into the system to prevent cheating, such as software that prevents access to other networks during exams.
There would have to be more safeguards than that, unless exams were intended to be open book. There would have to be a way of preventing students from gaining access to anything other than the document (or web page) that contained the exam. It is technically possible,4 but doing it on a scale that would allow it to be done for all exams might be prohibitively expensive. And somehow it just seems wrong, but maybe it's because when I was growing up I had to walk eight miles to school in three feet of snow uphill both ways.


Top 10 species for 2011

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ASU_top10newspecies_composite_1_0.jpgEvery year the International Institute for Species Exploration at Arizona State University release a "Top 10" list for species discovered in the preceding year. The list for 2011 has just been released. It includes a cricket that pollinates orchids (my favorite), a fruit-eating lizard, and a bioluminescent fungus among other things.

The BBC had a report on the orchid-pollinating cricket (click here to read the story and see the video), and Arizona State University has a press release announcing the list. Head over there for more information about this year's Top 10 list.

Image from ASU. Click on the image for a larger version.

Colbert's science catfight

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This appeared over a year ago (6 April 2010), but I only learned about it a few days ago.1 Colbert does a fairly decent job of explaining the difference between climate and weather, using the difference between climatologists and meteorologists as the springboard. "It's just like astronomers vs. astrologers."


The Colbert ReportMon - Thurs 11:30pm / 10:30c
Science Catfight - Joe Bastardi vs. Brenda Ekwurzel
www.colbertnation.com
Colbert Report Full EpisodesPolitical Humor & Satire BlogVideo Archive
Or I should say Colbert does a fairly decent job of explaining why so many meteorologists get it wrong if you read his "defense" of meteorologists as a satirical takedown. I see him as making fun of them, filling in for the sportscasters when they're out of town, standing out in hurricanes getting bowled over by the wind. He hardly lets Brenda Ekwurzel get a word in edgewise, and the way in which he "defends" meteorologists doesn't make them look particularly smart.

We can't afford to wait 15 years to show Joe Bastardi he's wrong, but if I forget to remind him of what he said when April, 2025 rolls around, I hope someone reading this will do it for me.

Joe Bastardi (meteorologist for AccuWeather): "In 15 years the earth will be back to 1970s temperatures."

This is a bad idea

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You know that I'm very fond of my Kindle and that I adore my iPad, but even I think this is a bad idea.

The proposal (SB 2120) requires Florida public schools to adopt digital-only textbooks by the 2015-16 school year, and spend at least 50 percent of their textbook budget on digital materials by that time. (source)
Encourage e-books as an enhancement to paper textbooks -- great. Encourage them as an alternative to paper books -- fine. But don't ban paper books. It's just not as easy to flip through the pages of an e-book as it is with a paper book, and it's impossible to look at two or three pages separately to compare illustrations or tables.

Here's Nicholas Carr's take. I think he says it pretty well.

I reported last week on a new study indicating that e-textbooks, despite some real advantages, aren't very good at supporting the variety of "learning styles" that students actually employ in their studies, particularly when compared to printed editions. That research won't be the last word on the subject, but it does show that we're still a long way from understanding exactly what's gained and lost when you shift from printed books to digital ones.
Don't get me wrong. We will see a day when digital textbooks completely replace paper ones, but I'll be astonished if that day has arrived in four years.1

Becoming a strangler fig

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The rap guide to evolution

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Just found this in my inbox:

Baba Brinkman - the award-winning Canadian-born performer - is to launch a campaign, supported by the UK's largest charity the Wellcome Trust, to aide the teaching of evolution in schools - using his acclaimed show The Rap Guide to Evolution and a resource-packed website to assist.

The first step in the campaign is the launch of The Rap Guide to Evolution website later this month (www.rapguidetoevolution.co.uk) which will host a series of 12 specially produced music videos based on the show, as well as supporting materials that will assist teachers in utilising the videos in their work.

I rather like "Survival of the fittest".

Comparing R with other stats packages

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Rlogo.jpgI use R for all of my statistical analyses, unless I need to write a special-purpose Bayesian analysis. Then I'll use WinBUGS, OpenBUGS, or JAGS -- all basically the same thing -- and R2WinBUGS or R2jags to drive them from R. It fits the way I work very well, and more and more faculty and students in my department are using R.

If you're not using R, and you'd like a quick comparison of R and some other statistical/mathematical packages (including SAS, SPSS, and Stata) Brendan O'Connor has put together a brief comparison that's worth looking at.

Extraordinary

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What else can I say?


Peak gasoline

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Container of Gasoline

Image via Wikipedia

You've heard of peak oil, right? "Peak oil is the point in time when the maximum rate of global petroleum extraction is reached, after which the rate of production enters terminal decline." (Wikipedia) I'm not going to take a position on whether or not we've reached peak oil, or when we might reach it. But John Quiggin points out something I hadn't realized.

US gasoline consumption peaked in 2006 and was about 8 per cent below the peak in 2010. Consumption per person has fallen more than 10 per cent.
In other words, the U.S. may have hit "peak gasoline." And it doesn't appear to be just a result of the global financial crisis. Quiggin points out that the 10 per cent drop in consumption is roughly what you'd expect from a short-term price elasticity of -0.25 and an increase in prices of about 40 per cent.

Furthermore, he argues that the short-term elasticity of -0.25 understates the impact on demand, "since in the long run people can change their driving habits, reduce their stock of cars, and choose more fuel-efficient cars". The long-term reduction in gasoline demand could be as much as 40 per cent or even more.1

It all started with the Big Bang

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Since you're reading this, you're not among those taken up in the Rapture, and I thought you might like to know where it all started.


International Day for Biodiversity

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Friday was Endangered Species Day in the United States. Today is the International Day for Biodiversity. The focus this year is on forest biodiversity.


Field notes

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jelly.jpgI envy people who are able not only to write legible field notes, but also to make informative (and beautiful) drawings of their subjects. I'm lucky if I can transcribe my notes into Excel, which tells you something about how boring they are. They're not even lousy prose. They're rows and columns of numbers (typically with plant-ID as the row and column headers like SLA, area, length, width, dry weight, fresh weight).1

I try off an on to make sketches of things, but the results are barely recognizable as objects and only occasionally bear a faint resemblance to the objects they are supposed to resemble.

A new book from Harvard University press edited by Michael R. Canfield celebrates field notes -- Field Notes on Science & Nature.

Covering disciplines as diverse as ornithology, entomology, ecology, paleontology, anthropology, botany, and animal behavior, Field Notes on Science and Nature allows readers to peer over the shoulders and into the notebooks of a dozen eminent field workers, to study firsthand their observational methods, materials, and fleeting impressions.
The scientists included are:

  • George B. Schaller
  • Bernd Heinrich
  • Kenn Kaufman
  • Roger Kitching
  • Anna K. Behrensmeyer
  • Karen L. Kramer
  • Jonathan Kingdon
  • Jenny Keller
  • James L. Reveal
  • Piotr Naskrecki
  • John D. Perrine and James L. Patton
  • Erick Greene
And I'd be remiss in my duties as a faculty member of this department not to point out that there's an alum in that list. Piotr Nascrecki received his Ph.D. in this department working with Rob Colwell as his major advisor.

Endangered species day

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endangered-species-day.jpg
I was just reminded that today is Endangered Species Day.

Endangered Species Day is an opportunity for people young and old to learn about the importance of protecting endangered species and everyday actions that people can take to help protect our nation's disappearing wildlife and last remaining open space. Protecting America's wildlife and plants today is a legacy we leave to our children and grandchildren, so that all Americans can experience the rich variety of native species that help to define our nation. (source)

In 2010, Sen. Sheldon Whitehouse (D-RI) introduced a resolution designating May 21, 2010 as Endangered Species Day with 10 co-sponsors.1 It was agreed to by unanimous consent.

Whereas in the United States and around the world, more than 1,000 species are officially designated as at risk of extinction and thousands more also face a heightened risk of extinction;

Whereas the actual and potential benefits that may be derived from many species have not yet been fully discovered and would be permanently lost if not for conservation efforts;

Whereas recovery efforts for species such as the whooping crane, Kirtland's warbler, the peregrine falcon, the gray wolf, the gray whale, the grizzly bear, and others have resulted in great improvements in the viability of such species;

Whereas saving a species requires a combination of sound research, careful coordination, and intensive management of conservation efforts, along with increased public awareness and education;

Whereas 2/3 of endangered or threatened species reside on private lands;

Whereas voluntary cooperative conservation programs have proven to be critical to habitat restoration and species recovery; and

Whereas education and increasing public awareness are the first steps in effectively informing the public about endangered species and species restoration efforts: Now, therefore, be it

  Resolved, That the Senate--

     (1) designates May 21, 2010, as `Endangered Species Day';

     (2) encourages schools to spend at least 30 minutes on Endangered Species Day teaching and informing students about--

       (A) threats to endangered species around the world; and

       (B) efforts to restore endangered species, including the essential role of private landowners and private stewardship in the protection and recovery of species;

     (3) encourages organizations, businesses, private landowners, and agencies with a shared interest in conserving endangered species to collaborate in developing educational information for use in schools; and

     (4) encourages the people of the United States--

       (A) to become educated about, and aware of, threats to species, success stories in species recovery, and opportunities to promote species conservation worldwide; and

       (B) to observe the day with appropriate ceremonies and activities.

A graphic view of the Mississippi floods

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From New Scientist. Roll over the dots to see how river levels compare at different times.


America's climate choices

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One way to deal with a problem is to pretend it doesn't exist. This approach has the virtue of relieving you from having to come up with a solution, spend money or make tough choices. The downside, of course, is that leaky faucets and other problems rarely solve themselves and, in fact, usually get worse if ignored.
So writes the edtiorial board of U.S.A. Today in an editorial that appeared on the 16th. And what is the problem to which they refer?

Such is the case with climate change, a threat that too many members of Congress, most of them Republicans, have decided to manage by denying the science. That head-in-the-sand approach avoids messy discussions of higher energy prices, but it just got harder to justify.
The editorial board is referring to the National Academy of Sciences report, America's Climate Choices. It was released on the 12th, and it "reiterate[s] the pressing need for substantial action to limit the magnitude of climate change and to prepare to adapt to its impacts" (source).

But here's the kicker. The editors don't just argue that those who oppose finding ways to deal with climate change are "denying the science". They compare the deniers to "birthers".

Taken together, these developments ought to leave the deniers in the same position as the "birthers," who continue to challenge President Obama's American citizenship -- a vocal minority that refuses to accept overwhelming evidence.
Ouch! That has to hurt.


I'm a climate scientist

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Well, that's not true. I'm an evolutionary biologist. But the folks behind this video are climate scientists. (Warning: Like rap, some of the language may not be appropriate for your office.)



Hat tip: The Daily Climate (and an e-mail from a colleague who reminded me that I should bring this to your attention)


For any stat geeks out there

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John Cook now has a Twitter feed promising a new tip for using R every day. Head over to RLangTip to follow it. Here's the first one:

RLangTip.pnghttp://rseek.org

Is college worth it?

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On Sunday, the Pew Research Center released a new report, Is college worth it? The report is based on two surveys, one of a representative sample of adults 18 and older, the other of college and university presidents.1 Here are a few key findings:

  • Most Americans (57%) say colleges fail to provide good value for the money, and even more (75%) say it is too expensive for most Americans.
  • Both those who have a college degree and those who don't think that college graduates are making $20,000 more per year because of the degree.
  • Nearly half of the public (47%) thinks the purpose of a college education is to provide work-related skills and knowledge. Fewer (39%) say the purpose is to help students grow personally and intellectually. The rest say both are important.
  • 74% of college graduates say that their college education helped them to grow intellectually, 69% say it helped them grow and mature as a person, and 55% say it was very useful in helping them prepare for a job or career.
  • A substantial minority of college presidents (38%) say that the U.S. higher education system is headed in the wrong direction.
  • Fewer than 1 in 5 now believe that the U.S. system of higher education is the best in the world now, and fewer than 1 in 10 (7%) think it will be best in the world a decade from now.
  • "Presidents are evenly divided about the main role colleges play in students' lives: Half say it is to help them mature and grow intellectually, while 48% say it is to provide skills, knowledge and training to help them succeed in the working world. Most heads of four-year colleges and universities emphasize the former; most heads of two-year and for-profit schools emphasize the latter."
  • "Only a quarter (24%) of presidents say that, if given a choice, they would prefer that most faculty at their institution be tenured. About seven-in-ten say they would prefer that faculty be employed on annual or long term contracts."
I have to think more about these findings before I can comment intelligently.2

Beyond red vs. blue

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Pew-energy-priorities.pngA couple of weeks ago the Pew Research Center for People and the Press released a very interesting new study, Beyond Red vs. Blue. In addition to a quiz where you can find out where you'd be classified according to Pew's political typology,1 if you browse through the report, you find the remarkable graphic at the left.2 Just stare at that for awhile and think about it.

The first thing that may pop out at you is that 63% of those participating in the survey think it's more important to develop alternative energy sources than to expand oil, coal, and natural gas. That's a much larger fraction favoring alternative energy development than I would have guessed from the chatter I hear on TV or radio or from what I read in newspapers and magazines.

But as Ruy Teixera points out, an even more remarkable thing about those results is that of the 8 different groups Pew identified, only staunch conservatives have a strong preference for expanding production of oil, coal, and natural gas. Libertarians are about equally split. Every other constituency, including, Main Street Republicans are solidly in favor of developing alternative energy sources. Pew points out that the stark divide on energy policy isn't a partisan issue. It's an issue within the Republican Party.

The divide within the Republican base is stark on this issue: fully 66% of Main Street Republicans say alternative energy development should be the focus of America's energy policy, while just 26% would focus on expanding oil, coal and natural gas exploration. In this view, Main Street Republicans agree with the predominantly Democratic groups.
I'll leave it to political scientists to speculate about what appears to be a disconnect between the preferences of a solid majority of Americans and the obstacles that face federal support of alternative energy development, but in the face of strong support across a wide range of the political spectrum, it is no longer plausible to claim that a lack of federal action on developing alternative energy sources is the result of public apathy or oppositioin.

 

10 billion people -- maybe not

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A world map showing countries by fertility rat...

Image via Wikipedia

I am not a demographer, so when the Population Division of the United Nations Department of Social and Economic Affairs tells me that there best guess is (a) that the human population will not reach a peak of 9 billion in the middle of this century, but keep growing instead and (b) that the human population will reach more than 10 billion people by the end of this century, I take them at their word. I know it's a projection, and I know that any projection is fraught with uncertainty, but I also figure that they know what they're doing and that it's reasonable for us to plan for a future with even more people than we were expecting.

Now I'm not so sure.

In this week's Nature, Fred Pearce takes the projections to task. He points out that the change in projections appears to be due largely to an upward revision of fertility rates in the future.1 In 2003, the Population Division started using a figure of 1.85 children per woman as the fertility rate that would be achieved when fertility of women in developing countries converged with that of women in rich countries. In its latest report, the Population Division returned to its pre-2003 estimate of 2.1 children per woman as the fertility rate at which convergence will be achieved, and it's that change that is primarily responsible for the difference in projections.

I'm not in a position to judge whether the Population Divisions number is better than the lower one that Pearce seems to prefer, and I'm not sure whether it makes a whole lot of difference who's right, at least with respect to environmental protection. It's hard for me to imagine that the difference between 9.1 and 9.3 billion people on the planet will have a significant impact on the environmental policies we adopt, and Pearce doesn't seem to be disputing that number.

Since the projections don't diverge until after 2050, it may not make much of a difference to policy makers in any context. Even long-term projections for social insurance programs like Medicare and Medicaid in the U.S. don't go out beyond 2050. By the time we need accurate projections for 2100, we'll be a lot closer to it, and small differences in fertility rates will have far less of an impact on those projections.

Connecticut's budget

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Earlier this week, Governor Daniel Malloy started issuing pink slips to state employees (including 285 at the University of Connecticut). The layoffs were part of his plan to close a gap left in the budget approved earlier this month. Fortunately, the governor and representatives of state employee unions reached an agreement yesterday that will avoid layoffs of any unionized state employees for four years. It saves $1.6 billion over two years.

[T]here would be a hard wage freeze for two years for all unionized employees. It would include all forms of payments, including wages, longevity pay, increments and lump sums. Newly hired state employees would no longer be eligible for longevity pay, which are twice-yearly payments on top of their normal pay. (source)
Details are not being released until union members have seen the details, and the agreement must be approved by members of the unions, but I hope that we have avoided the terrible consequences that would come from nearly 10 per cent of state employees losing their jobs.


The center of the country

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In 1790, the population center of the United States was Kent County, Maryland. By 2000, it was in Phelps County, Missouri, more than 1000 miles to the west. Now,1 it's moved a little farther west and south -- 23.4 miles to Texas County, Missouri.

How do I know this? Because the U.S. Census Bureau told me so. You can go to their website for more information, or simply enjoy the interactive graphic below.

Walter Fitch -- Obituary in Science

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I mentioned a couple of months ago that Walter Fitch died on the 10th of March. Bill Atchley wrote an obituary that appears in today's issue of Science. Here are a couple of paragraphs.

Throughout his career, Walter made substantial contributions to the theory underlying molecular evolutionary change. In the 1960s and 1970s, he developed computer algorithms to infer evolutionary relationships among organisms based on molecular data (protein and DNA sequences), as demonstrated in his classic studies on evolutionary divergence in cytochrome c. His seminal work on molecular homology and estimation of ancestral protein sequences greatly facilitated analytical procedures for describing evolutionary change. He pioneered methods to generate branching diagrams or "phylogenetic trees" to reflect the relationships among species based upon similarities and differences in their physical and/or genetic characteristics. Fitch's work had a major impact on not only biologists but also mathematicians and computer scientists. More recently, he published important contributions to understanding the molecular evolution of influenza virus and HIV.

Walter was the cofounder of the Society for Molecular Biology and Evolution and its journal Molecular Biology and Evolution. He was the society's first president and editor-in-chief of the journal for 10 years. The "Walter M. Fitch Award" given by the society to the most deserving young scientists is a continuing reminder of his legacy.


The higher education market

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Matt Yglesias contends that competition among colleges and universities for students and faculty doesn't lead to a healthy market the way it (often) does for other goods and services. Instead, "simply serves to drive up the overall cost structure of the entire system without doing anything to improve quality of instruction." I'll have to think more about his argument before -- if -- I respond. In the meantime, here's how an economist, Brad DeLong,1 concluded his comments:

I do observe that education and medical care are the two large sectors in which the private market did not have a strong presence a century ago and are also the two large sectors where market competition does not seem to produce lower prices. And I feel that there must be some connection. 

Open access to museum collections

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Yale University is making objects from its libraries and museums available in its Digital Commons. Many universities, herbaria, and museums have done the same, but what makes Yale's effort unique1 is that from one search box

search-box.png
a query will return results from six different collections at Yale: the Peabody Museum, the Center for British Art, the University Art Gallery, the University Library Map Collection, the Lewis Walpole Library Prints and Drawings, and the Office of Digital Dissemination. So for example, a simple query on Prunus maritima not only returns 547 records2 from the Peabody Museum, as I expected, but also 7 from the University Art Gallery and 1 from the Center for British Art.

"High costs of reproduction rights have traditionally limited the ability of scholars, especially ones early in their careers, to publish richly illustrated books and articles in the history of art, architecture, and material and visual culture," according to Mariet Westermann, vice president of the Andrew W. Mellon Foundation. "Yale's new policy provides an important model to follow." (source)
I agree. Thank you Yale.3

Please Steve, say it ain't so

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Behold the iPad in All Its Glory.

Image via Wikipedia

I broke down and bought an iPad last August, and as I've mentioned before, I really like it. The tipping point for me was when I learned that there's a Kindle app for iPad, so that I can read my e-books on it as well as on my (old, first generation) Kindle. Now I'm getting worried.

Some interesting news from the world of e-reading apps in the land of iOS: BeamItDown is shuttering its iFlow Reader app on May 31, saying "Apple has decided that it wants all of the e-book business in iOS for itself and it has has made mid-game rule changes that make it impossible for anyone but Apple to sell e-books at a profit on iOS." (source)
I'm not familiar with BeamItDown, but that last sentence caught my eye. By June 30th all e-readers, including Nook and Kindle, will have to (a) use an in app purchasing scheme rather than re-direction to an external website and (b) share 30% of the take with Apple. So far there's no comment from Amazon.com or Barnes & Noble. I sure hope that they reach an agreement. Having Apple make me buy my e-books through their bookstore is no better than having Microsoft or Google force me to use their products.

Steve, I know you don't care what I think, but if you follow through with this threat and make it impossible for me to buy books directly from Amazon.com or Barnes & Noble if I want to, you're on the "evil" side of my ledger.


AquaNotes

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AquaNotes.pngI have a couple of "Rite in the Rain" All-Weather Journals for taking notes in the field, but here's an idea that I would never have thought of.

AquaNotes provides a notepad that not only has waterproof paper, but also has suction cups that allow you to stick it to the wall of your shower. Never again do you have to lose that brilliant idea you had in the shower. Now all you have to do is write it down!

I quite frequently get ideas in the shower,1 and almost as frequently I forget them before I write them down.2 An AquaNote notepad in the shower might be just what I need -- except for one thing. There's no pencil holder! Where am I supposed to store my pencil?

Budget trouble in Connecticut

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The budget recently passed by the Legislature of the State of Connecticut and signed by Governor Dan Malloy includes $1.4 billion in new taxes for the fiscal year starting this July and another $1.2 billion in new taxes for the following year. It also reduces spending by $3 billion over the next two years, but included in those savings are $2 billion in savings from state employees1 that have not been achieved.

Folks from Governor Malloy's office and from unions representing state employees have been meeting almost since the Governor announced his budget in February to find the savings on which the Governor's budget, now approved, depends. In the event that an agreement isn't reached, layoffs of state employees and further cuts to budgets will follow.

Today, Governor Malloy announced that he has "directed OPM to begin issuing layoff notices in an orderly fashion to the first 4,742 state employees." Included in that total are 285 employees of the University of Connecticut. I am very hopeful that Governor Malloy and union representatives will find a solution that does not involve layoffs. The University has already had to deal reduce expenditures by $45 million in each of the next two years to avoid a deficit. Losing 285 colleagues in addition will lower the quality of service we are able to offer our students.


Scholarly publishing

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Scholarly publishing is a weird business. Academics work at colleges or universities; make discoveries, develop new synthetic understandings, or construct new interpretations of results in their field of research; describe those results in a scholarly article or book;1 send it off to a journal publisher who may, after due consideration, decide to publish it. That "due consideration" typically includes review of the contribution by other academics, and all of this review costs money, even though peer reviewers (except for peer reviewers of books) typically aren't paid for their efforts. Then university libraries buy copies of journals containing those articles.2

For many years, the system worked pretty well. Journal publishers, which were often non-profit scholarly societies, charged reasonable prices for their journals, and libraries could afford to buy them without crowding out purchases of books or other library materials. Ferdinand von Prondzynski, who is now Principal and Vice-Chancellor of Robert Gordon University, identifies this as "a key problem of academic life":

Lecturers must publish, and not just anywhere. The journals that are accepted as good places in which to be seen know this very well, and they abuse the market. They are far too expensive, and as a result really only libraries can afford them. And as library budgets get cut everywhere, they too are now having to be choosy.

In fact, whether we are talking about books or journals, academic publishers present us with really major problems. There are not many of them, and they are not customer-focused. It is time to leave all that behind us. The academy should develop and manage online journals where academics can place their work and where this will be appropriately peer-reviewed. It is time to break away from a publishing sector that has some of the most restrictive practices of the modern business world. It is time to open up publishing opportunities for academics and to make it easy for others to access what has been published.

I'd add only one thing: Some journals are still published by non-profit, scholarly societies and still provide libraries with good value. Libraries should support such journals, while developing new methods of disseminating research that is too frequently hidden behind exorbitant price barriers.

Open science and the private sector

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The drive to make scientific data more openly accessible is growing, and I endorse it. Kristin Shrader-Frechette and Naomi Oreskes point out that efforts to make scientific data accessible have focused on data produced as a result of publicly funded research. But publicly funded research isn't the only research that the public (and other scientists) have an interest in seeing. Privately funded research may be just as relevant to our understanding of public health or the environment as research funded by the National Institutes of Health, the National Science Foundation, the Environmental Protection Agency, or the Department of Agriculture. As Shrader-Frechette and Oreskes argue,

[P]rivately funded science used for public or regulatory purposes should be subject to the same transparency requirements as publicly funded science, and industry requests to protect data, under claims of confidential business interests, should be granted only when public health and safety are demonstrably not at stake.

Universities, public or private, should go even further. They should ensure that the products of any sponsored research, whether funded from public or private resources, are made widely accessible.

The hidden beauty of pollination

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The images from Louie Schwartzberg's movie Wings of Life are extraordinary. Please take a few minutes to sit back and enjoy them because, as Schwartzberg puts it, "We will protect what we fall in love with."

Related articles

You know you're a nerd when...

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il_fullxfull.234232382.jpg
You drool over a collection of 10 plushies that illustrate different statistical distributions. A footnote on the Etsy page describing them even says this:

I use the open-source program R to create the patterns.
What could be better than that?
In the collection you'll find

  • Light Green Standard Normal Distribution
  • Baby Blue t Distribution
  • Light Yellow Chi-Square Distribution
  • Light Pink Log Normal Distribution
  • Lilac Continuous Uniform Distribution
  • Tan Weibull Distribution
  • Olive Green Cauchy Distribution
  • Slate Blue Poisson Distribution
  • Maroon Gumbel Distribution
  • Gray Erlang Distribution
Any guesses on how many degrees of freedom that t distribution plushy has?


Why not to focus on temperature

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Changes in radiative forcings between 1750 and...

Image via Wikipedia

It's been almost 14 years since the Kyoto Protocol was signed. Since the early 1990s, when the UN Framework Convention on Climate Change (UNFCC) was adopted, the focus of global climate negotiations has been on setting targets for emission of greenhouse gases that " [stabilize] greenhouse gas concentrations in the atmosphere at a level that would prevent dangerous anthropogenic interference with the climate system." Although the United States never ratified the Kyoto Protocol, we did ratify the UNFCC, and it entered into force on 21 March 1994. But I think even those who do not believe that action to reduce greenhouse gas emissions is necessary would have to admit that greenhouse gas emissions now are greater in most countries than they were in 1992 when most nations of the world signed the UNFCC.1 Writing in this week's Nature, Tim Lenton suggests that the focus on limiting the rise in global mean temperature to 2°C is a bad idea. Why?

Global average warming is not the only kind of climate change that is dangerous, and long-lived greenhouse gases are not the only cause of dangerous climate change. Target setters need to take into account all the factors that threaten to tip elements of Earth's climate system into a different state, causing events such as irreversible loss of major ice sheets, reorganizations of oceanic or atmospheric circulation patterns and abrupt shifts in critical ecosystems.
So what does he suggest as an alternative? "[R]estricting anthropogenic radiative forcing to limit the rate and gradients of climate change, before limiting its eventual magnitude."

There are good scientific reasons for focusing on radiative forcing rather than temperature. Global average temperature takes a long time to respond, and what it responds to is radiative forcing. It's like the difference between the temperature in the kettle you just put on the stove and the burner that the pot is sitting on. Turn down the burner and the water won't get as hot. And because there are different sources of radiative forcing and those sources vary from region to region, a focus on radiative forcing might help policy makers find ways to accomplish the goal -- preventing dangerous anthropogeneic climate change.

Part of the challenge will be to get the public to understand "radiative forcing". We need a better phrase, and we probably need a better analogy than my kettle and stove. Suggestions encouraged.

Even less dead than I thought

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Not only is Swintec still making typewriters, frabotta points out in a comment that Brother is still making them too. Smith Corona still sells typewriter ribbons and wheels, but I don't see any typewriters on their site. I did, however, find an Olivetti MS 25 Plus manual typewriter on Amazon.com.


10 billion people

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20110503_POPULATION_graphic-popup-v2.jpg

Graphic from the New York Times

For a long time demographers have projected that the world's population would stabilize at about 9 billion in the middle of this century. We crossed the 6 billion mark in 1999, and we are projected to cross 7 billion in late October.

Yesterday the Population Division of the United Nations Department of Social and Economic Affairs released its newest projections. There was a small upward revision of the projected population in 2050 (to 9.3 billion), but the headline news is that the U.N. now projects that population growth will continue to the end of this century, reaching 10.1 billion.

Just like the IPCC, however, the U.N. Population Division considers different scenarios. The high projection variant, which assumes fertility is only half a child greater than in the medium variant just quoted would result in a world population of 10.6 billion in 2050 and 15.8 billion in 2100.

High fertility countries are found mostly in Africa, which is also where the most alarming projections of future population sizes are concentrated,1 but there are 9 in Asia, 6 in Oceania, and 4 in Latin America. Interestingly, China's population is projected to peak in a couple of decades and decline to less then a billion by the end of the century.

There were only about 3 billion people in the world when I was born. We've already added one world to the one I was born in. What will it be like when we add another?


Looking at ecolabels

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As individuals, one of the most important things we can do to protect biodiversity is to consume less. That means living close to where you work,1 using mass transit rather than a personal car,2, limiting purchases of non-essentials, and purchasing products that are produced sustainably. There are many different certifications by many different organizations. Renee Cho has identified a few of those that she thinks are the best. Hop over and take a look.


Typewriters live on -- sort of

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It turns out that Godrej and Boyce isn't the last company in the world making typewriters. Swintec still has factories making them, but it looks as if all of Swintec's models are elctronic. I couldn't find any manual typewriters on its product pages. Maybe Godrej and Boyce is -- was -- the last company making manual typewriters.

The future of biodiversity in the Northeast

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ccb-logo.pngThe Future of Biodiversity in the Northeast: Building on Les Mehrhoff's Legacy
27 May 2011
University of Connecticut

The Center for Conservation and Biodiversity will host a one-day meeting to honor the life of our late colleague Les Mehrhoff. The day will be broken into sessions focused on four areas of interest to Les: New England botany, invasive species, rare and endangered species, and the future of biodiversity in the Northeast. Each session will include a set of three or four invited talks. In addition, the program will include a brief sketch of Mehrhoff's life, tours of UConn's state-of-the art biological collections and greenhouse facilities, and an open mike session at the end of the meeting. There will be an optional evening gathering at a nearby restaurant, where attendees will be able to gather and reminisce.

For more information and a registration form, visit the Center's website.


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