Uncommon Ground

What tuna are you eating?

2009-11-20T11:00:00Z

The latest meeting of the international commission created to manage harvests of tunas and other wide-ranging fish species in the Atlantic Ocean ended by setting 2010 quotas for bluefin tuna that conservation groups and United States fisheries officials said were -- while lowered -- still far too high to allow the imperiled fish to recover. (from DotEarth)

The government of Monaco proposed a ban on international trade of bluefin tuna, and was initially supported by the European Union and the U.S. It won't be hard for people who know the fish to recognize bluefin if whole fish are being shipped, but what if they've already been processed into steaks or filets? What then?

A little over a year ago a couple of high school students from Manhattan pointed the way. They used DNA fingerprinting to identify samples of sushi at New York restaurants and found that 25% were misidentified.

Jacob Lowenstein and his colleagues develop a more sophisticated DNA barcode based on cytochrome C oxidase subunit I to distinguish among all tuna species in the genus Thunnus (the genus to which bluefin belongs). They sampled tuna sushi from 31 restaurants in Manhattan and Denver. Among the 68 samples they tested they found some that were from endangered tuna species, some that weren't what they said, and some that were a health hazard.

Five out of nine samples sold as a variant of "white tuna" were not albacore (T. alalunga), but escolar (Lepidocybium flavorunneum), a gempylid species banned for sale in Italy and Japan due to health concerns. Nineteen samples were northern bluefin tuna (T. thynnus) or the critically endangered southern bluefin tuna (T. maccoyii), though nine restaurants that sold these species did not state these species on their menus.

The take home message? I see two. First, Lowenstein and colleagues demonstrate yet again that DNA barcoding can be a useful tool in identifying commercially sold fish (and other products). Second, think twice next time you order a piece of maguro at your favorite sushi bar and ask yourself how confident you are that it's not bluefin (and that the folks who run your sushi bar would know the difference or care).
]]> López Herráez, D., Bauchet, M., Tang, K., Theunert, C., Pugach, I., Li, J., Nandineni, M., Gross, A., Scholz, M., & Stoneking, M. (2009). Genetic Variation and Recent Positive Selection in Worldwide Human Populations: Evidence from Nearly 1 Million SNPs PLoS ONE, 4 (11) DOI: 10.1371/journal.pone.0007888

Carbon offsets

2009-11-19T11:00:00Z

Purchasing offsets for carbon dioxide is an appealing idea. Sometimes we have to travel to meetings or we have to travel for research.¹ Often that travel involves plane flights, and planes emit a lot of carbon dioxide. By purchasing a carbon offset, I invest a small amount of money in a project that removes carbon dioxide from the atmosphere equivalent to what my flight added.² In other words, my flight didn't contribute to global warming.

Responsible Travel was one of the first companies to offer such offsets to travelers.

But last month Responsible Travel canceled the program, saying that while it might help travelers feel virtuous, it was not helping to reduce global emissions. In fact, company officials said, it might even encourage some people to travel or consume more. (source)

Andy Revkin doesn't buy carbon offsets when he travels. I plan to continue buying them, because I'm buying them for travel I would have taken anyway. I'm not traveling more because the offsets are available. And I'll try to travel less, do more with conference calls, and I'll use Skype and web conferencing more often. I'll encourage groups I'm part of to do the same.

Buying offsets in that context has to help at least a little, doesn't it?³
]]> ¹I'll be in South Africa for much of January for work on white proteas (Protea Section Exsertae).
²Or at least I hope that's what's happening. It is very difficulty for an individual consumer to know whether it really works that way. I buy my offsets from Terrapass, which seems to be pretty good. It's not the best, according to Carbon Catalog, but it's the most convenient for me.
³At least so long as the offset projects are real.

Armen Takhtajan (1910-2009)

2009-11-18T15:00:00Z

Armen Leonovich Takhtajan or Takhtajian (Russian: Армен Леонович Тахтаджян; surname also transliterated Takhtadjan or Takhtadzhian) (June 10, 1910 - November 13, 2009), was a Soviet-Armenian botanist, one of the most important figures in 20th century plant evolution and systematics and biogeography. His other interests included morphology of flowering plants, paleobotany, and the flora of the Caucasus. (Wikipedia entry)

I had the privilege of meeting Professor Takhtajan once. He was kind, generous, and extraordinarily knowledgeable. His phylogenetic system has been largely superseded by work of the Angiosperm Phylogeny Group, but his influence will never be forgotten. He died on 13 November, and he will be buried in the Armenian part of the Smolensk cemetery in St. Petersburg tomorrow after a civil funeral at the Komarov Botanical Institute.

Making the interstates green(er)

2009-11-18T13:00:00Z

Interstate 90 heading West through Southern Minnesota. (from Chad Johnson, Creative Commons License)

Interstates aren't green, but Karrie Jacobs has an idea: use interstates as corridors for high-speed rail and transport of energy.

It's been a long time since we've been able to see beyond the traffic and the exhaust fumes. But if we expand the highway system's uses in anticipation of a time when we are no longer dependent on the internal combustion engine, we may also appreciate the beauty in its graceful overpasses, lofty bridges and complex cloverleaf interchanges.

I don't know about "appreciating the beauty of graceful overpasses", but multiple use of existing interstate corridors just makes sense. Gulliver argues that it won't be simple:

First, America's interstates don't always cut through empty prairie--in many places, there won't be enough clearance on either side to build the "adjacent rail lines" Ms Jacobs is so psyched about. And where the interstates do cut through virgin prairie, infrastructure advocates will have the opposite problem: convincing environmentalists and locals that a landscape already sliced in half by I-Whatever should be further defiled.

The clearance problem is real, though in many places there's a wide median that could be used instead of using corridors on one side or the other. And using the median, which in my experience is often very wide in areas where I-Whatever cuts through "virgin" landscapes, won't add to the damage that's already been done.

I'm not prepared to go as far as Gulliver and conclude

Ms Jacobs' broad point is generally correct--infrastructure advocates and environmentalists should see America's highways as an opportunity for better, greener development--not an obstacle.

We have interstates because we have cars. And the American response to traffic congestion is always to add lanes rather than beefing up mass transit. Roads are a problem, but that doesn't mean we can't use them more wisely.

Multitasking doesn't work

2009-11-17T19:00:00Z

Attention, multitaskers (if you can pay attention, that is): Your brain may be in trouble.

People who are regularly bombarded with several streams of electronic information do not pay attention, control their memory or switch from one job to another as well as those who prefer to complete one task at a time, a group of Stanford researchers has found. (source)

Interesting, the study, which was published last August in Proceedings of the National Academy of Sciences, found that habitual media multitaskers "are more susceptible to interference from irrelevant environmental stimuli and from irrelevant representations in memory." It's not clear whether habitual multitasking causes people to be more susceptible to irrelevant information or whether those who are more susceptible to irrelevant information are more prone to be media multitaskers, but it is clear that the minds of multitaskers work differently from the minds of those who aren't.

Perhaps the most intriguing finding of all is that multitaskers are worse at switching tasks than non-multitaskers.

]]>

Stanford's press release about the study
WebWorkerDaily's analysis

Hat tip: OrganizeIT

Monday Pen

2009-11-16T11:00:00Z

The pens at the left are from the Aurora Afrika series. My Aurora Afrika fountain pen is one of my favorites. It's one of my evening pens. (You've met the Pelikans, the 400 and the Niagara Falls. This completes my set of evening pens.) The ballpoint has the same striking design, but when I use a ballpoint, I use a simple, inexpensive Bic or something like that. I don't see the point of investing as much as you have to invest in a pen like an Aurora Afrika simply to have a ballpoint. Having a fine fountain pen is the whole point, so far as I am concerned.¹

The beautiful colors in the resin body speak for themselves, but one of the things I most enjoy about my Afrika is its nib. It took me 6-9 months to get it broken in. It was scratchy until either it adjusted to me, I adjusted to it, or both, but now it leaves a beautiful, wide line. And what makes it even more interesting is that my Afrika has a medium italic nib. Even though my penmanship is far from beautiful, when I write with my Afrika, the line has delightful variations in width and tone. It gives a dull, pedestrian (though legible) line a little spark and verve.

Here's the Fahrney's blurb.

Aurora presents Afrika - the first in a limited, numbered series celebrating the continents of the world. Aurora has captured the life, color and emotion of this adventurous land in the Afrika design. The resin barrel and cap in warm earthtones are hand-turned by a master craftsman and adorned with a matte gold clip and trim. The barrel ring depicts six African tribal shields. The black crown has a semi-precious agate stone set on the top as a symbol of harmony and peace.

Fahrney's no longer mentions the availability of the medium italic nib. I wonder if that means it's no longer available.
]]> ¹I'll concede that it might be worth investing this much in a rollerball, because like a fountain pen, they tend to have a very smooth line that's strong. Ballpoints leave a feeble line unworthy of a fine pen. I don't own a good rollerball, but I'll admit to having been tempted.

An inspirational story

2009-11-15T16:00:00Z

On rare occasions you read a story that reminds you how reslient, how resourceful, and how amazing some people are. This morning was one of those occasions. I read Nicholas Kristof's column in the New York Times about Tererai Trent who recently defended her Ph.D. dissertation at Western Michigan University and will receive her degree next month.

What's so remarkable about her? I can't do her story justice. You'll have to read Kristof's column. I will give you a taste of what's in store for you when you do.

Any time anyone tells you that a dream is impossible, any time you're discouraged by impossible challenges, just mutter this mantra: Tererai Trent.

Don't be such a scientist -- the webinar

2009-11-13T14:00:00Z

I've mentioned Randy Olson's book, Don't be such a scientist, repeatedly over the last several months,¹ and yesterday I received an e-mail from Island Press, Randy's publisher, with the following news:

In a webinar on November 19 at 1PM EST, Olson will draw on his own hilarious-and at times humiliating-evolution from science professor to Hollywood filmmaker and offer his perspective on communicating science at a time when information and facts are more important to the discussion than ever.

Here's a link to the page where you can sign up. It's a GoToMeeting sign up page, and signing up is free and easy.
]]> ¹If you haven't yet bought your copy, hie thee forth and buy yourself a copy -- now!

Awards for science journalism

2009-11-11T15:00:00Z

A radio broadcast on probability told through a tale about a drifting balloon, a newspaper series on the impact of a devastating genetic disease on a family in rural Montana, and a group of gracefully written stories about genetics and evolution are among the winners of the 2009 AAAS Kavli Science Journalism Awards.

Read more at AAAS.org. I was especially pleased to see that Carl Zimmer was recognized "for a trio of articles he wrote for The New York Times on aspects of genetics and evolution."

An announcement from AIBS

2009-11-11T11:00:00Z

AIBS Publishes Darwin Articles Open Access

To celebrate the 150th anniversary this month of the publication of On the Origin of Species, the American Institute of Biological Sciences (AIBS) is publishing open access two peer-reviewed articles about Charles Darwin and his historic insights into evolution.

The two articles are by Kevin Padian of the University of California, Berkeley, and James T. Costa of Western Carolina University. Padian's article, "Ten Myths About Charles Darwin," appeared in the October issue of the AIBS journal BioScience and can be read at http://caliber.ucpress.net/doi/full/10.1525/bio.2009.59.9.10. Costa's article, "The Darwinian Revelation: Tracing the Origin and Evolution of an Idea" is published in the November issue of BioScience and can be read at http://caliber.ucpress.net/doi/full/10.1525/bio.2009.59.10.10. Padian explores some common inaccuracies and untruths about Darwin and his life's work, painting in the process a clear portrait of the man and his struggles to develop a theory to explain the diversity of nature. Costa draws on Darwin's letters and notebooks and other sources to trace the origins of Darwin's key insights, which came to him over many years. Costa suggests that biology teachers can use Darwin's reasoning as a superb example of creative scientific thinking.

In defense of Windows (sort of)

2009-11-10T11:00:00Z

I switched to a Mac a little over a year ago. The evangelism of Mac advocates can be offputting, but Macs are nice. I"m running VMWare Fusion on my MacBook, so I even have Windows (for a few specialized programs that are only available under Windows and don't play well with Wine) and Ubuntu sitting close by whenever I need them. I've never thought Windows was great, but I never thought it was horrible.

Charlie Brooker has a different take.

I know Windows is awful. Everyone knows Windows is awful. Windows is like the faint smell of piss in a subway: it's there, and there's nothing you can do about it. It's grim, it's slow, everything's badly designed and nothing works properly: using Windows is like living in a communist bloc nation circa 1981. And I wouldn't change it for the world, because I'm an abject bloody idiot and I hate myself, and this is what I deserve: to be sentenced to Windows for life.

]]> John Quiggin

Monday Pen

2009-11-09T11:00:00Z

I have a couple of pens that I can't find online images for. I've mentioned the silver Levenger pen that a student of mine gave me almost 15 years ago. I haven't mentioned a Stipula with a partially transparent barrel showing the ink reservoir. I'll keep looking for images of them, and if I can't find ones on-line, I'll eventually pull out my camera and take my own photos.

In the meantime, here's a more recent addition to my collection. In fact, it's the one I'll be writing with tonight -- a Pelikan Niagara Falls. I've only had it for 3-4 years, so it's less familiar than my Pelikan 400, which I've had almost as long as that silver Levenger.

The pelican clip and the striped body mark this pen immediately as a Pelikan, but its body is metal rather than resin. That "heft" gives it a nice hand feel. Unfortunately, the ink doesn't flow as smoothly as it does in my 400. Whether that's because I'm still breaking it in¹ or because there's something different about the nib or the feed, I don't know. But the difference is clear enough that if I had to make a choice and carry only one of my Pelikans with me, the choice would be easy. It would be the 400.

Here's some of what Fahrney's has to say about it:

For its new Wonders of Nature special edition series, Pelikan has created a writing instrument as beautiful as one of the planet's most awesome spectacles - Niagara Falls. Created at the end of the last ice age, this natural wonder borders the U.S. and Canada and is the most powerful waterfall in North America. The falling water is artfully portrayed on the pen using palladium-plated metal that is elaborately inlaid with cobalt blue resin. The result is stunning, set off by the silver clip and rings which sparkle like sunlit drops of water. The Niagara Falls plunger-fill fountain pen has Pelikan's 18K gold and rhodium nib, formed and polished by a master's hand.

]]> ¹As I recall, it took a couple of years of daily writing before my Pelikan 400 became as smooth as it now is.

An update on the Coburn amendment

2009-11-08T13:56:05Z

Last month I noted that Tom Coburn (R-OK) introduced a resolution that would have eliminated funding for political science research at the National Science Foundation. I was delighted to discover this morning that ScienceInsider reported last week that the Coburn amendment was soundly defeated: 36 to 62. I am disappointed that 36 senators voted for the amendment. It's important to note that five Democrats joined 31 Republicans in voting for the amendment.

[I]t wasn't strictly a party-line vote. Five moderate Democrats--Senators Max Baucus of Montana, Evan Bayh of Indiana, Claire McCaskill of Missouri, Ben Nelson of Nebraska, and Jim Webb of Virginia--apparently agree with Coburn's argument that NSF, with a budget of $6.9 billion, is "wasting" federal dollars by spending $9 million a year to support research in the field.

You can find how your Senator voted by clicking here.

Science and advocacy

2009-11-08T11:00:00Z

From Rob McDonald at Cool Green Science:

It is not the job of scientists to produce papers that reinforce a preconceived advocacy position. Rather, it is the job of scientists to lay the facts on the table, so those facts can inform advocacy. (emphasis in the original)

If that sounds familiar, it may be because I wrote this about a month ago:

[T]here's one thing we all must do: be true to the science. We have to be honest about what the data say, even if the data tell us things about the policy we'd prefer to adopt that we'd rather not hear.

Go read all of Rob McDonald's post. It's well worth your time.

Hook -- a restaurant review

2009-11-08T02:00:00Z

I've never reviewed a restaurant here before, but I wrote about Hook a couple of months ago, and my partner and I are in DC this weekend. I made reservations over a month ago to make sure we got a good table, because I really wanted to try it -- and I'm very glad I did. If you live in DC or you visit and you're looking for an excellent seafood restaurant, Hook is much more interesting and creative than Legal Sea Foods or McCormick & Schmick, the fish comes from sustainable sources, and the produce comes from local sources. It costs a little more, but it's worth it.

It starts with the decor, clean and modern. The downstairs bar is busy and loud. If you want something quieter, be sure to make a reservation and ask for a quiet table. They'll probably seat you upstairs where the colors are warmer and there's a lot less noise.¹

A meal consists of three courses, portioned so that you leave feeling satisfied but not stuffed.

The crudo is bite-size portions of raw or house smoked fish with three accompaniments. My partner started with the king salmon. I had the house smoked selection (salmon, mackerel, and bluefish). I had always thought of mackerel as a cheap fish. No more. Prepared well, as it was here, it has a pleasant salty tang and is a perfect way to prepare for the main part of the meal.

For the second course we both had the beet salad with goat cheese, crushed pistachio, and pickled watermelon. The yellow beets had a wonderful mild flavor that perfectly complimented the pistachio. Pickled watermelon was new and delightful. The dressing was red beet puree with olive oil. The menu changes according to what is available in the market, but our very knowledgeable server told us that the beet salad has been on the menu since Hook opened. I highly recommend it.

My partner had dorade (wood-grilled, served whole, bone in) over roasted yukon gold potatoes with grilled sun-dried tomatoes and kalamata olives. He let me taste it. The dorade had a wonderful delicate flavor enhanced by fresh thyme and slices of lemon stuffed inside during grilling. The potatoes had a nice crunch and rich flavor that played off the powerful sweetness of grilled sun-dried tomatoes. I had striped bass, simply grilled on a bed of pureed butternut squash with sweet potatoes and yukon golds. The bass was firm and moist with oil, more body and flavor than the dorade, but it was the tiny sage pgnoli tarts that I will remember longest. Just a pastry shell filled with pignoli, sprinkled with fresh chopped sage and baked until the crust was flaky and the pignoli were golden. Wonderful.

We finished with decaffeinated coffee.

There's only one thing they could do to improve Hook. Open it in a new location closer to a Metro stop. It's in Georgetown a very long walk from the nearest Metro (either Foggy Bottom or Farragut West). We took a taxi from our hotel on Dupont Circle only about $8 each way, but I prefer public transit when it's available.
]]> ¹It was quiet when we arrived around 6:30. By the time we left a little after 8:00 it was noisy, but not annoying and it was still easy to talk and enjoy the excellent decaffeinated coffee (the espresso machine was broken) from a French press.