February 2012 Archives

I knew about eye leeches in Madagascar, the kind that squirm behind your eye and start feeding.

Most unsettling is when a leech gets into your eye. A herpetologist who has had the pleasure three times told me about the first time it happened, in a remote rainforest in the middle of the night. "It went round to the back and started feeding," he said. "Oddly enough, I couldn't tell if it was feeding on the eyeball or on the eye socket." He ran to the nearest village, where an old woman, making sense of the meaning behind his frantic gestures, poured a mixture of salt and water into his eye, forcing the leech out. "That," he told me with the ghost of a smile on his lips, "would make most people a little bit twitchy, don't you think?" (source)

But I didn't know about flukes inside the eye, until I saw this.



Those are eye flukes (Tylodelphys) moving inside eye of the fish Gobiomorphus cotidianus (filmed by Isa Blasco-Costa). According to Tommy Leung (citing colleagues from the University of Otago), all of the specimens of this fish collected from Central Otago Lake have this little beauty inside their eyes. As one of Leung's commenters said, these flukes aren't a fluke.

As of 9:00am EST on Monday, nearly 7500 scholars had pledged to refrain from publishing in Elsevier journals, refereeing for Elsevier journals, doing editorial work for Elsevier journals or all three. The protest was spawned, in part, by Elsevier's support of the Research Works Act (RWA).

On 27 February, Elsevier announced that it was withdrawing its support of (RWA). That makes me feel a little less guilty about my paper that will appear in Theoretical Population Biology later this year. But they haven't backed off on their opposition to government mandates for free public access, so I will not send any new papers to an Elsevier journal, nor will I referee or edit for one.

While we continue to oppose government mandates in this area, Elsevier is withdrawing support for the Research Work Act itself. We hope this will address some of the concerns expressed and help create a less heated and more productive climate for our ongoing discussions with research funders. (source)

Fresh snow and five people. Sonja Hinrichsen's snow drawings. Play it full screen.

Snow Circles from Beauregard, Steamboat Aerials on Vimeo.

Hat tip: Ed Yong (@edyong209)

If you know anything about California, Bakersfield is probably one of the last places you'd imagine finding much sympathy for endangered species. Los Angeles? Maybe. Hollywood? Yes. San Francisco? Absolutely. But Bakersfield? Well, yes. At least if you're a San Joaquin kit fox.

Or maybe I should say "Yes and no." The cat-sized San Joaquin kit fox is one of the most endangered animals in California. It's only about 20 inches long, and weighs only 5 pounds (source). Fewer than 7000 are left. And some of them live in Bakersfield, where they're causing problems for the Panama-Buena Vista Union School District.

Michael Brouse, the district's business manager, said nobody can recall "a student-kit fox encounter," but the animals can pose a problem. They leave copious droppings. They get tangled in soccer nets. And, to the chagrin of administrators, they love schools, with their wide-open campuses, brown-bag lunches, and strict adherence to environmental regulations. (source)

Seems that they like it in town, because there aren't as many coyotes -- and many residents are setting out food for them.

"Bakersfield in the past hasn't necessarily been the most endangered-species-sympathetic area," Cypher said, "but many people enjoy having the foxes around."

For 10 years, Linda DeRose, a 71-year-old retired teacher, has watched foxes skitter around the portable classrooms at Stockdale Elementary School across from her house. "Everybody who sees them really likes them. They're really cute, they run real fast, they have big ears. It's amazing they're able to exist in such proximity to people."

Occasionally, it seems that we humans are able to help out an endangered species without even trying (much).

Michael Mann has been the object of merciless attacks from those who refuse to believe that human beings are changing the world's climate. In 1999, he was the lead author on a paper (link; subscription required) that included the infamous "hockey stick" showing that temperatures in the northern hemisphere have increased dramatically since the start of the 20th century.

His book, The Hockey Stick and the Climate Wars, will be released on March 6.¹ It tells the story of how climate science has been undermined by well funded interests determined to prevent adoption of any government policies that would reduce or restrict burning of fossil fuels. That effort has become a war on climate science. As an example, just take a look at a couple of stories about the recently leaked documents from the Heartland Institute (New York Times, Guardian). It's one thing to argue about what kind of response the projected impacts of climate change require. There are many uncertainties about the degree of impacts, the location of impacts, the actions that might be taken to mitigate impacts, and the policies that might reduce the impacts. But one thing about which there is no longer any uncertainty (any more than there's uncertainty that an apple dropped from a tree will fall to the ground) is that our burning of fossil fuels is causing global average surface temperatures to rise.

I mention all of this because, there's a nice profile of Mann at Wired Science. It's short and nicely done. I encourage you to click through and read it. In the meantime, enjoy this video, which accompanies the piece.

But there are good reasons to like LaTeX better than Word, even if you're not doing much mathematics. Look at the difference between this, set in Word
and this, set in LaTexBoth use Hoefler Text at 48pt. Don't see the difference? Look again at the letters in red and notice how the "f" and the "i" collide in fire, the "f" and the "l" in flower, and the "f" and the "j" in fjord (as they do in this text). That's because those letter pairs are set automatically as a single ligature in LaTeX. Word doesn't do that.

I know it's a small thing -- even smaller than comma splices or the Oxford comma, but it makes documents set in LaTeX look a lot nicer than those set in Word.

I suppose I shouldn't care that much, because very little of what I write using either LaTeX or Word is distributed for others to see in that form. It's mostly typeset by journals who (mostly) use systems that take advantage of ligatures and other typographic niceties. But I can't help it if I am mildly obsessive about typography (the way I am about fountain pens).

If you think I'm bad, Dario Taraborelli is probably worse. Those examples are taken from a page on his site where he illustrates at length the beauty of LaTeX.

Reflections from his colleagues and friends can best illustrate how James Crow will be remembered. Harvard geneticist Matthew Meselson has described him as, "One of the greats. Jim brought a rare clarity to all his work." Jan Klein, formerly of the Max-Planck-Institut für Biologie in Tübingen, Germany, has said that, "Jim will remain as perhaps the last of a generation of gentleman-scientists--'gentleman' in the sense of a courteous, gracious man with a strong sense of honor and a strong respect for the past." And University of Wisconsin colleagues Rayla Temin and Don Waller have said that, "He made you happy just to be in the aura he cast" and that no colleague was "warmer or more encouraging, nor respected more." Indeed, Jim Crow will be immortalized in the histories related by those who knew him as a scholar, citizen, and friend. (emphasis added)

That is the final paragraph in another wonderful piece remembering the life and work of James F. Crow. If you haven't yet read the piece by William F. Dove and Millard Susman in today's Science, please head over there and read it now.

Botanists are used to hybridization. It plays a large role in plant evolution. One consequence is what's sometimes called "chloroplast capture." Chloroplasts in most angiosperms are transmitted only through the seed parent. If species A and species B hybridize with species A as seed parent and the hybrid backcrosses repeatedly to species B, the chloroplast from species A will end up in a nuclear background that is (almost) entirely from species B. Species B will have "captured" a chloroplast from species A.

That's pretty easy to understand, and it accounts for most cases where there seems to be horizontal transmission of chloroplasts. But in some cases, this straightforward scenario doesn't seem compatible with other evidence.

Sandra Stegemann and colleagues provide evidence that another mechanism is possible. They grafted cuttings of cultivated tobacco (Nicotiana tabacum) onto stocks of tree tobacco (N. glauca) and another tobacco species (N. benthamiana) and vice versa. The tobacco plants had been engineered with a gene conferring resistance to the antibiotic spectinomycin on their chloroplast genome, and the others with a gene conferring resistance to kanamycin in their nuclear genome. After the grafts fused, they removed tissue from the graft sites and exposed it to selection for resistance to both antibiotics. The tissue could survive only if it included the tobacco chloroplast genome and the other species nuclear genome -- the cellular equivalent of chloroplast capture -- and they found examples.

Then they grew whole plants from these tissues, and the morphology of the plants suggested that genetic transfer in grafts is restricted to chloroplasts. Furthermore, transfer in either direction appears to be equally likely. It doesn't appear that "host" and "captured" chloroplast genomes recombine in any way. There's wholesale replacement of one by the other. Interestingly, mitochondria seem not to be transferred.

There's a long way to go from this experimental demonstration that grafting can lead to horizontal gene transfer and concluding that it's an important mechanism in the wild, but it raises a new and intriguing possibility that we'll have to consider.

A circular economy

The original Powers of ten by Charles and Ray Eames.



And an updated version by Cary and Michael Huang

http://images.4channel.org/f/src/589217_scale_of_universe_enhanced.swf

Unfortunately, the new version starts with an ad and it depends on Flash. That means you won't see anything on your iPad.

Hat tip: Ben Goldacre

What Vincent van Gogh might have done were he alive now.

Starry Night (interactive animation) from Petros Vrellis on Vimeo.

Hat tip: John Maeda (@johnmaeda)

That's the screenshot of my reply to a review request from Theoretical Population Biology. It was a little uncomfortable for me to make that reply because (a) my co-author and I sent off revisions for an invited paper that will appear in a special issue¹ of TPB and (b) one of the editors was my major professor at Stanford and I shared an office with another of the editors for a year or two as a post-doc.

But as you can see, I shook off my discomfort and made a statement.

Nearly 5000 scientists have now signed the pledge.

Writing in the Boston Globe, Gareth Cook summarizes things this way:

Elsevier has settled on a business strategy of exploitation, aligning itself against the interests of the scientific community. Most of the intellectual work that goes into Elsevier's journals is provided for free, by scientists whose salaries are largely paid for by taxpayers. Then Elsevier charges exorbitant rates for its journals, with many titles running in the thousands of dollars a year. This sharply curtails the sharing of results - the fuel of scientific discovery - and makes it prohibitively expensive for the public to read what appears in its pages. Yet for Elsevier, this looks like success: In 2010 Elsevier reported revenues of about $3.2 billion, of which a whopping 36 percent were profit.

I pointed out the Strunk & White rap video in late December. I remember reading E.B. White's essay about his teacher when I was in high school. And I still remember how excited I was when I found a paperback copy of Strunk & White in my college bookstore.

A couple of days ago I added a new Strunk & White book to my collection. I don't have the illustrated edition, and I don't have the most recent addition, although I do have a hardcover copy of the 3rd edition as well as my old paperback from college. My new Strunk & White isn't an edition of Strunk & White, it's a Kindle book about Strunk & White.

The book is Stylized: A Slightly Obsessive History of Strunk & White's Elements of Style. I haven't started reading it yet, but given my peculiar obsession with commas and style, I am looking forward to it.

"I hate the guts of English grammar," E. B White once famously proclaimed. Yet Strunk & White's The Elements of Style is among the most important and timeless books on writing. With its enduring legacy and cultish following, it has inspired countless derivatives and homages, from a magnificent edition illustrated by Maira Kalman to a rap. The book has become a legend in its own right, its story part of our modern creative mythology -- but, like a good fairy tale, it brims with more curious, unlikely, even whimsical details than a mere plot summary might suggest. Those are exactly what Mark Garvey, a 20-year publishing veteran and self-professed extreme Elements of Style enthusiast, explores in Stylized: A Slightly Obsessive History of Strunk & White's The Elements of Style. (Maria Popova)

Michael Eisen:

I want to challenge the key assumption - made by nearly everyone - that choosing not to publish your work in the highest impact factor journal you can convince to accept it is tantamount to career suicide. It is ubiquitously repeated by everyone from the most successful senior scientists to first year graduate students. And, judging by their publishing practices, most of them must believe it to be true. But I don't think it is.

If that seems like heresy, it's because it is heretical. Michael put it more strongly than I would have but I mostly agree.

Since I mostly agree, there's no point in repeating his arguments in favor of that heretical position. I'll focus on a shade of emphasis where we disagree.

In my new position am part of the team that reviews cases for promotion, tenure, and reappointment across all schools and colleges at the University of Connecticut (other than those at the Health Center). A few years ago, I served on the Faculty Review Board, a group of faculty that provides advice to the Provost on promotion, tenure, and reappointment cases where there might be a negative decision.

In those contexts, I've had to judge the credentials of economists, poets, political scientists, artists, sociologists, and philosophers, not to mention the credentials of those in natural science fields well beyond biology. I can't pretend to judge the scholarly qualifications of candidates based on direct reading of publications (for fields where publication is relevant), except in a few fields close to my own research, or the creative contributions of those involved in literature, the visual arts, or performance. I can only judge based on the assessments of experts in those fields and some sense of the quality of the venues in which a  work has appeared.

I know, for example, that it is much more significant for a musician to have presented a solo performance with the New York Philharmonic in its regular concert season than for a musician to have performed the same work with the high school orchestra in my hometown. And it is a much more significant achievement for an evolutionary biologist when she publishes her work in Evolution than when it appears in the Journal of Northeastern Connecticut Evolutionary Biologists.¹

So how have I used that kind of assessment of journal quality in judging promotion and tenure cases? By seeing whether the quality of scholarship suggested by the venues in which it appears is consistent with the evaluations of external evaluators who are expert in the field. It's not, "Oh, this gal has a paper in Evolution. She gets tenure." It's "Oh, this gal has a paper in Evolution. That's a demanding journal, getting a paper or two in there suggests that she is doing very good work, and that's consistent with the high praise that external reviewers are heaping on her. She's someone we want to keep around."²

So on that, Michael and I agree. Choosing not to publish your work in the highest impact factor journal you can convince to accept it is not tantamount to career suicide.

The shade of emphasis on which we disagree is this: You do want to publish your work in high quality journals.³

I've emphasized here the purely practical impact that will have on your prospects for promotion and tenure, but there's an even more basic reason. Your work isn't done until it's communicated. And it's much easier to reach a wide audience of receptive readers when your work appears in high-quality journals than when it appears in obscure journals -- even, I'm afraid, if those obscure journals are open access.⁴

By Tom Spears, The Ottawa Citizen. You owe it to yourself to read the whole thing.

Ernest Small's research colleagues at Agriculture Canada had a mystery. Peering at the cellular innards of a clover plant, they wondered why nothing was behaving the way clover should.

They asked Small, a veteran scientist at the Central Experimental Farm, for help.

It didn't take him long to pinpoint the problem. Their clover was an alfalfa.

Read more: http://www.ottawacitizen.com/technology/Taxing+times+taxonomy/6028252/story.html#ixzz1lFjvqWTF


Hat tip: Sandra Knapp (@SandyKnapp)

Just three South East Asian countries support more than 70 percent of the planet's biological diversity.  A substantial part of the region's human population (and often the poorest part of the population) depends directly on these biodiversity resources to provide food, medicine, shelter, clothing and other needs.  Already in the Philippines we are seeing the impact of poor environmental management on coral reefs - threatening the livelihoods of fishermen and undermining the potential for tourism development. (source)

You're probably thinking to yourself, "Yet another pronouncement by yet another environmentalist about how important biodiversity is." Of course, if you read this blog regularly, that's probably not what you're thinking. You know me well enough to know that if it were just another pronouncement by just another environmentalist, I wouldn't bother to highlight the quote so prominently. Instead, you're wondering "What's his angle here? Who said it this time?"

Stephen Lillie, the British Ambassador to the Philippines.

He wrote that in the context of reporting on a recent meeting involving senior officials from the Philippines, Brunei, Indonesia, and Malaysia "organised by the British Embassy and the ASEAN Center for Biodiversity or ACB (which is based in Los Banos near Manila), the meeting was intended to highlight the importance of correctly valuing biodiversity in a country's economic planning, and how failing to account for the value of ecosystems and biodiversity loss risks wrong choices and decisions."

It is gratifying to see senior government officials take the economic value of biodiversity seriously. As Robert Kennedy put it more than 40 years ago, our

Gross National Product counts air pollution and cigarette advertising, and ambulances to clear our highways of carnage.  It counts special locks for our doors and the jails for the people who break them.  It counts the destruction of the redwood and the loss of our natural wonder in chaotic sprawl.  It counts napalm and counts nuclear warheads and armored cars for the police to fight the riots in our cities.  It counts Whitman's rifle and Speck's knife, and the television programs which glorify violence in order to sell toys to our children.  Yet the gross national product does not allow for the health of our children, the quality of their education or the joy of their play.  It does not include the beauty of our poetry or the strength of our marriages, the intelligence of our public debate or the integrity of our public officials.  It measures neither our wit nor our courage, neither our wisdom nor our learning, neither our compassion nor our devotion to our country, it measures everything in short, except that which makes life worthwhile.  And it can tell us everything about America except why we are proud that we are Americans.

USDA Hardiness Zone Map. Click on the image for an interactive version.

Last week the U.S. Department of Agriculture unveiled a new plant hardiness map. The last one was released over two decades ago -- in 1990. Some of the changes reflect new methods for interpolating data between weather stations. But

Compared to the 1990 version, zone boundaries in this edition of the map have shifted in many areas. The new map is generally one 5-degree Fahrenheit half-zone warmer than the previous map throughout much of the United States. This is mostly a result of using temperature data from a longer and more recent time period; the new map uses data measured at weather stations during the 30-year period 1976-2005. In contrast, the 1990 map was based on temperature data from only a 13-year period of 1974-1986. (from the USDA announcement)

Plants know that the climate is changing. Minimum winter temperatures over most of the U.S. are 5 degrees warmer now than they were two decades ago. The earth is getting warmer, and this is just a little more evidence of that.