Sweet home Chicago

June 21, 2011 • 10:33 pm

by Greg Mayer

Jerry will be returning later today (note– the time stamp on these posts is Pacific time, so it’s already Wednesday here in the vicinity of Chicago) to resume full WEIT duties, and I’m sure he will regale us with paeans to, and pictures of, the plethora of pleasures of the palate of which he partook on the plains. But till then, I want to show you what he was missing.

My wife and I recently went on a walking tour of the culinary hotspots of the Gold Coast,  Old Town, and Lincoln Park neighborhoods organized by Chicago Food Planet. Our guide was a moonlighting graduate student, and teaching undergraduates is probably good preparation for handling hungry tourists. We began at Ashkenaz, a Jewish (but not Kosher) deli in the Gold Coast, where we had patsrami reubens, garnished with Ashkenaz’s own store-made dressing.

Our next stop was Tea Gschwendner, a shop we already frequented, which sells loose teas and brewing accessories. The ground up tea-dust that goes into bag tea was compared (unfavorably) to loose tea, while we sampled an unsweetened, fresh-brewed, iced tea.

We moved on to the Spice House, with a huge selection of spices and herbs, especially pre-made mixtures. The dozens (?hundreds) of varieties on the shelves were accompanied by taster-shakers– we could shake a sample on to our hands, and then taste it. You had to lick especially hard between varieties, to cleanse the palate (or hand).

Next up was Old Town Oil, featuring olive oils and balsamic vinegars, all stored in large metal canisters, with tasting cups to allow shoppers to sample the wares. When purchasing, the oil or vinegar is decanted from the canisters into bottles, which are then sealed.

After the savory oils and vinegars, it was a big switch to the sweets at the Fudge Pot.

Here, we got to go back behind the counter, where the candies are actually made.

Delightful Pastries, a European (especially Polish) style bakery, had both sweet and savory items. We sampled the kolaczski. Here are some sweets: eclairs and cannoli.

Finally, we ended up at Bacino’s in Lincoln Park, for stuffed crust pizza. This was very good (though the lower crust served more to hold the filling in than add to the flavor), but, as a New Yorker, it wasn’t pizza.

In addition to bringing us to the various food emporia, our guide provided a lot of interesting city history and architectural details. The information went both ways– I told her, a Lincoln Park resident, about Steve Goodman and the Lincoln Park Pirates. We walked by, and learned the story of the original Playboy Mansion.

We also walked by the side door of the Near North Side home that served as the entrance to the restaurant where, in 1986, Ferris Bueller usurped the luncheon reservation of Abe Froman, the sausage king of Chicago.

There’s no shopping during the tour (it would slow things down too much), but we did make purchases that same day of tea, oil, vinegar, spices, and knishes at various of the places we visited. All provided discount coupons to tour participants. While on the tour, my favorites were the reuben at Ashkenaz, and the pizza at Bacino’s, but that’s probably because those were the two most lunch-like elements of the middle-of-the-day walk. Jerry has said that, as a real Chicagoan, he’ll let me know what he thinks of the places we went. Chicago Food Planet also does tours of Chinatown and Bucktown/Wicker Park–I think we’ll try these on another trip down.

Caracal kittens FTW

June 21, 2011 • 7:51 pm

Since I’ve been out of town, we won’t have a kitteh contest entry this week, but don’t be alarmed: there are many more in the queue and posting will resume next week. In the meantime, reader Michael has sent me this new video of three caracal kittens born at the Oregon Zoo on June 8.  They’re only two weeks old, and oy, are they cute!

We haven’t featured caracals before (Caracal caracal, a scientific name easy to remember); they’re gorgeous, tawny cats with huge tassled ears. They range over the Arabian peninsula, around the southern Mediterranean, and in subsaharan Africa.  They’re relatively large, and can weigh up to 40 pounds. But of course you want to see the kittens:

And here’s an amazing video of a caracal taking down a guinea fowl.  These cats can apparently jump 10 feet into the air (go here to see more leaping).  Watch the whole video, for there are two impressive leaps.

Also note the awkward flight of the African widowbird male (2:10-2:20): sexual selection has given him such long tail feathers that he can barely fly. This shows that natural selection can actually reduce an animal’s viability (that male is an easy meal for predators), so long as its net fitness (total reproductive output) increases. In the case of widowbirds, experiments show that longer-tailed males are much more attractive to females. Sexual selection, then has driven the males to have longer tails because they get more mates, even if their survivorship is reduced.

The seven ages of the scientist

June 21, 2011 • 7:23 pm

At the beginning of my talk the other day, I showed a slide that I’ve often used throughout my career: the “seven ages of the scientist”: that is, the various activities we engage in as our career progresses from our Ph.D. to our dotage. I usually put an arrow next to the stage I’m at when I give the talk (I’m currently at stage 7).

I’m often asked for copies of that slide (in fact, a commenter requested one here), so I reproduce the latest version of the text.  Steal it and alter it if you want!

This melancholy career path is drawn, of course, from Shakespeare’s “All the world’s a stage” speech spoken by Jaques in As You Like It (if you haven’t read it, click the link: it’s wonderful).

The Seven Ages of the Scientist

  1. As student, listens to advisor give talk on student’s own work
  2. As postdoc, gives talks about his/her own work
  3. As professor, gives talks about his/her students’ work
  4. Talks and writes about “the state of the field”
  5. Talks and writes about “the state of the field” eccentrically and incorrectly—always in a self-aggrandizing way.
  6. Gives after-dinner speeches and writes about society and the history of the field
  7. Writes articles about science and religion

Right before my talk, my friend David Hillis (a systematist) noted that there should be a stage 8: “blogs about science and religion.” But of course that doesn’t apply to me since I do not “blog.”

Extinct frog rediscovered– sort of

June 21, 2011 • 12:25 pm

by Greg Mayer

Since I first read about them when I was about 12 years old, I’ve been intrigued by the somewhat mysterious Vegas Valley leopard frogs. Known from a handful of springs, all in what is now more or less metropolitan Las Vegas, they had disappeared before the middle of the 20th century, and had been poorly known before apparently slipping out of existence. But now they’re back– sort of.

Chiricahua leopard frog from Coconino National Forest, Arizona, by Jim Rorabaugh/USFWS.

Evon Hekkala of Fordham University and her colleagues have a paper in press in Conservation Genetics in which, using DNA extracted from specimens of Vegas Valley frogs in the collection of the California Academy of Sciences, they find that Vegas frogs are closely related to the Chiricahua leopard frog of Arizona and nearby areas. In fact, the Vegas frogs are nested within the many samples of Chiricahua frogs they studied. From this they conclude that the Vegas frog is conspecific with the Chiricahua frog, and thus the Vegas Valley leopard frog is not extinct.

That the Vegas frogs (Rana fisheri) are conspecific with the Chiricahua frogs (Rana chiricahuensis) is a not unreasonable inference. North American leopard frogs, once thought to be a single widespread species, have proven to be a complex of several biological species, and although the situation is modestly clear in the eastern United States, there is much work yet to be done in the southwestern US and especially Mexico to figure out what’s going on. The Vegas frogs are not genetically identical to the Chiricahua frogs (contrary to some media reports), and, with only about 1200 base pairs examined at three loci, more differences are sure to be found.

So is the Vegas frog not extinct anymore? This isn’t just a biological species vs. amount-of-difference species concept question. One could accept, under various species concepts (and we know which one is right!), that the Vegas and Chiricahua frogs are conspecific, but still ask, is the Vegas Valley frog still extant because similar, but not identical, frogs continue to exist 100’s of kms away? I’m not sure. The US Endangered Species Act recognizes that population segments, even if they lack nomenclatural recognition or distinction, can be endangered, and be worthy of protection. And if a segment can be endangered, it can, of course, go extinct. So, while I’m glad we’ve learned who the Vegas Valley frogs’ closest relatives are, and that they’re quite similar, and that, due to the rules of nomenclature they will bear the name fisheri, I’m afraid the Vegas Valley frogs are still extinct.

The great herpetologists Albert & Anna Wright and Robert Stebbins summarized most of what will ever be known about the Vegas Valley frogs, and wrote, movingly yet scientifically, of their unsuccessful searches in the Vegas area in the 1940’s (they were last collected in January 1942, and last reported seen in the summer of ’42).  The Wrights concluded:

Our R. fisheri may go with the old springs gone, the creek a mess.

______________________________________________________________

Fisher, J., N. Simon, and J. Vincent. 1969. Wildlife in Danger. Viking, New York

Hekkala, E.R., R.A. Saumure, J.R. Jaeger, H.-W. Herrmann, M.J. Sredl, D.F. Bradford, D. Drabeck, and M.J. Blum. 2011. Resurrecting an extinct species: archival DNA, taxonomy, and conservation of the Vegas Valley leopard frog. Conservation Genetics in press. pdf

Moore, J.A. 1944. Geographic variation in Rana pipiens Schreber in eastern North America. Bulletin of the American Museum of Natural History 82:345-370. pdf

Pace, A.E. 1974. Systematic and biological studies of the leopard frogs (Rana pipiens complex) of the United States. Miscellaneous Publications, Museum of Zoology, University of Michigan 148, pp. 140. pdf

Stebbins, R.C. 1951. Amphibians of Western North America. University of California Press, Berkeley.

Wright, A.H. & A.A. Wright. 1949. Handbook of Frogs and Toads of the United Sates and Canada. Comstock, Ithaca, New York.

David Hillis of the University of Texas (who Jerry just mentioned) has done much of the work that has more recently both clarified, and pointed out the lacunae in, our understanding of leopard frogs. Many of his papers (on leopard frogs and many other subjects) are available here.

Update. David Hillis has kindly commented below, and quotes one of his papers (Hillis and Wilcox, 2005); here’s a link to the pdf of that paper.

Snake oil in the New York Times

June 21, 2011 • 8:03 am

by Greg Mayer

Perhaps just by coincidence, today’s New York Times features two articles concerning snake oil: one about an exhibit at the Philadelphia Museum of Art of posters promoting dubious remedies, and the other about the relationship between Senator Snake Oil, Orrin Hatch of Utah, and the “nutritional supplement” industry.

William H. Helfand Collection/Philadelphia Museum of Art

The exhibit at the Philadelphia Museum of Art features a selection of striking and colorful posters from the William H. Helfand Collection that advertise a variety of patent medicines and mostly questionable nostrums (a number of them are shown on the Times and Museum websites). Sen. Hatch is infamous as the primary sponsor of the “Snake Oil Salesman’s Relief Act of 1994”, which exempted “nutritional supplements” from the requirements of safety and efficacy of the pure food and drug laws. As the Times‘ story details, he has been well remunerated by the industry for his continuing support. Supplement manufacturers are not supposed to claim that supplements cure disease, but they try to skate the line (and sometimes cross over it, as shown in the article) by making vague claims of improving function or energy, and adding very small print disclaimers that say the FDA has not checked any of their claims. Orac at Respectful Insolence follows the supplement industry’s shenanigans fairly regularly.

ASN presidential talk: Ricklefs disses the neutral theory of ecology

June 21, 2011 • 5:55 am

Bob Ricklefs, president of the American Society of Naturalists, spoke last night at the Evolution 2011 meetings. Although his talk was called “My life as a naturalist,” there was little biography or, indeed, natural history, though his theme was that natural history is essential to informing ecological theory.

I won’t go into all the details of Ricklefs’ talk, but wanted to point out that much of it was a critique of an ecological theory that has caused a lot of stir in the last decade: Steve Hubbell’s “neutral theory of biodiversity and biogeography.” This theory was made famous by his book:


(Ricklefs is an evolutionary ecologist at the University of Missouri at St. Louis, while Hubbell, also an ecologist, is now at UCLA.)

I’d like to make this post short, for the “neutral theory” is complicated and, in truth, I don’t understand all the mathematics.  It’s based largely on Hubbell’s famous work on tropical trees on Barro Colorado Island, in Panama, where he spent decades mapping distributions of the many individual trees (and the many species) that inhabit even a small patch of neotropical forest.

From his work, Hubbell proposed that in many communities (not just trees), species are ecologically equivalent to one another, and thus individuals in a group of related species can be regarded as simply selectively identical (i.e., “neutral”) entities whose abundance and identity drift around randomly over ecological and evolutionary time. (There’s an obvious parallel with the “neutral theory” of evolution, in which different alleles of a gene are selectively equivalent and are affected only by random processes.)  According to Hubbell’s theory, it doesn’t matter whether a few square meters of forest is occupied by an individual of species X or Y: the ecological dynamics will be the same.

Any “patterning” of ecological communities,then, is simply an artifact of individuals reproducing and competing with each other as full ecological equivalents.

This flies in the face of years of ecological theory (supported by data) maintaining that species are not ecologically equivalent, but compete with each other based on differential use of resources.  In his book, however, Hubbell claimed that assuming ecological equivalence of all species in a group (e.g., trees) could explain certain patterns of ecology, like species abundance curves showing that some species are very common and many others are quite rate.  It turns out that, with certain assumptions, the neutral theory predicts abundance curves very similar to those seen in nature. The conclusion: since the “neutral” predictions match the data, related species must really be ecologically equivalent.

This theory always puzzled me. I’m not an ecologist, but I knew that there is plenty of evidence from nature that different but related species do use different resources and, though they compete, they are not ecologically identical.  So how could a theory based on palpably false assumptions make accurate predictions about species distributions? My view was that this was simply a coincidence, but I stress again that I am not a trained ecologist and have watched the controversy as an outsider.

But Ricklefs is not an outsider: he’s deeply conversant with both theoretical ecology and natural history (he’s done a ton of field work), and so when he criticized the neutral theory in his talk last night, that was srs bzns.

He leveled several criticisms at the theory:

1. We know that species aren’t ecological equivalents.  As I said, there are plenty of data showing that, for example, plant species inhibit each other’s growth in different ways: if you surround a member of species X with plants of species Y, the inhibition of growth is different from what you see when you surround it with members of its own species, X.  Therefore the fundamental assumption that species are ecologically equivalent is empirically false. Ricklefs also cited a lot of work on birds showing ecological differences between species (Robert MacArthur’s warblers are a famous example) and differential competition.

2.  The nice fit of Hubbell’s predictions to empirical data relies on making untested assumptions about the size of parameters.  One of these is the rate at which new species arise.  If you use other values of this parameter, which is of course unknown, the fit between real data and Hubbell’s predictions isn’t so good.

3.  Species distributions change in regular ways along environmental gradients.  Ricklefs showed distributions of tropical tree species across the Isthmus of Panama (Barro Colorado Island sits in the middle of a lake in the Isthmus).  The array of tree species on the western (wet) side is very—and predictably—different from that on the eastern (dry) side. This is not expected if different tree species are ecological equivalents that respond identically to environmental differences.

4.  Over huge ranges of space in similar environments, the distribution of species in sub-areas remains similar.  If you look at patches of rain forest in similar environments thousands of kilometers apart, the distributions of tree species are pretty much the same. The neutral theory does not predict this: the great distances between those patches means that they should be attaining equilibrium more or less independently, and so shouldn’t show identical distribution of species’ abundance if all species are ecologically equivalent.

5.  Attaining ecological/evolutionary “equilibrium” under the neutral theory requires billions or millions of years.  Ricklefs said that the neutral theory predicts that distributions of species attain Hubbell’s equilibrium values only on times of the order of millions or even billions of years.  Since no area of earth, including the tropics, has been undisturbed for anywhere near that long, the distributions of species we see cannot be those predicted by the neutral theory. There must be some other non-“neutral” explanation for species abundance curves.

Ricklef’s talk included other stuff, but I was most intrigued by these criticisms of a popular and fashionable ecological theory.  I tend to agree with Ricklefs, though I’m not as qualified as he to judge these matters.  He predicted that the “neutral theory of biodiversity and biogeography” will be dead and gone in a decade.  I suspect he’s right.  And I guess I find that judgment congenial, for it leaves species with an individuality that we’ve long appreciated as evolutionary biologists.

My big speech

June 21, 2011 • 4:10 am

My ex-student Mohamed Noor (now a professor at Duke), made a video of my presidential address to the Society for the Study of Evolution on Sunday evening.  He apologizes for the quality of both audio and video, for he filmed the whole thing on his iPhone.  There are five parts, and it’s about an hour long in toto.

I was introduced by another of my ex-students, Allen Orr, a professor at the University of Rochester and my predecessor as SSE president.  If you have the patience, and want to know what our lab has been up to for the past eight or nine years, here it is. I’ll post the first part and links to the four others.

Note that Allen, Mohamed, and I all went to The College of William & Mary, where we got a superb undergraduate education in biology (Bruce Grant mentored all of us).

Part 2

Part 3

Part 4

Part 5


			


	



			
				
		


	

		
Miss USA is pro-evolution!

	June 20, 2011 • 3:21 pm

			


	

		
Remember when I posted about how distressed the Miss USA contestants were about having to answer this question: “Should evolution be taught in public school science classes?”  I predicted much consternation, waffling, and equivocation.


Well, that all happened.  BUT, amazingly enough, the winner of the contest, Alyssa Campanella, gave a strongly pro-evolution answer.


But first watch the diverse answers from the other contestants—there are more waffles here than at IHOP!  It’s hilarious.


After lots of equivocators, Alyssa Campanella, who describes herself as a “huge science geek,” appears as a breath of fresh air at 1:55, followed by other pro-evolution ladies: Katie Hanson of Delaware, Allyn Rose of Maryland, Alida d’Angona of Massachusetts, Brittany Toll of New Mexico, and Lauren Carter from Vermont. I’m not sure why some sources, including P.Z., are reporting that only two contestants were pro-evolution.


Good going, ladies, for showing the courage of your convictions!




What’s your favorite waffle?