Methodology – Page 32 – artdiamondblog.com

“Sometimes It Pays to Read the Old Literature”

(p. A1) Researchers in New York believe they have solved one of the great mysteries of the flu: Why does the infection spread primarily in the winter months?

The answer, they say, has to do with the virus itself. It is more stable and stays in the air longer when air is cold and dry, the exact conditions for much of the flu season.

. . .

(p. A22) To his surprise, Dr. Palese stumbled upon a solution that appeared to be a good second best.

Reading a paper published in 1919 in the Journal of the American Medical Association on the flu epidemic at Camp Cody in New Mexico, he came upon a key passage: “It is interesting to note that very soon after the epidemic of influenza reached this camp, our laboratory guinea pigs began to die.” At first, the study’s authors wrote, they thought the animals had died from food poisoning. But, they continued, “a necropsy on a dead pig revealed unmistakable signs of pneumonia.”

Dr. Palese bought some guinea pigs and exposed them to the flu virus. Just as the paper suggested, they got the flu and spread it among themselves. So Dr. Palese and his colleagues began their experiments.

. . .

As for Dr. Palese, he was glad he spotted the journal article that mentioned guinea pigs.

“Sometimes it pays to read the old literature,” he said.

For the full story, see:

GINA KOLATA. “Study Shows Why the Flu Likes Winter.” The New York Times (Weds., December 5, 2007): A1 & A22.

(Note: ellipses added.)

Government Biologists Spend Big Bucks Protecting Wrong Fish

“Without DNA tests, the rare greenback cutthroat trout, left, and the Colorado River cutthroat fish are difficult to tell apart.” Source of caption and photo: online version of the NYT article quoted and cited below.

(p. 26) DENVER, Oct. 13 (AP) — State and federal biologists, who are smarting from research showing that they may have been protecting the wrong fish the past 20 years, are regrouping in their efforts to restore the rare greenback cutthroat trout to Colorado waters.

Tom Nesler, the state biologist, had hoped to see the fish removed from the endangered species list during his career. He concedes that might not happen if it turns out some of the greenback populations biologists thought they were saving are actually the similar but more common Colorado River cutthroat trout.

A three-year study led by University of Colorado researchers and published in August found that out of nine fish populations believed to be descendants of original greenbacks, five were actually Colorado River cutthroat trout.

The recovery effort was thought to be near its goal of establishing 20 self-sustaining greenback populations.

“Hey, science happens,” said Mr. Nesler with a shrug as he discussed the findings.

. . .

The Colorado Division of Wildlife has spent an average of $320,000 annually for the past five years to restore the greenback. Most of the money has come from state lottery revenue; no state tax dollars have been used.

. . .

“Science is not about proof and certainty,” he said, “it’s about testable hypotheses.”

For the full story, see:

THE ASSOCIATED PRESS. “After Possible ‘Oops,’ a Trout Rescue Project Regroups.” The New York Times, First Section (Sun., October 14, 2007): 26.

(Note: ellipses added.)

Private Money Supports Quest for Dinosaur DNA

Source of graphic: the online version of the WSJ article quoted and cited below.

(p. A1) JORDAN, Mont. — Prospecting in Montana’s badlands, rock ax in hand, paleontologist Jack Horner picks up a piece of the jawbone of a dinosaur. He examines the splinter, then puts it back and moves on. It isn’t the kind of bone he is looking for.

Prof. Horner is searching for something that many scientists believe no longer exists: dinosaur bones that harbor blood cells, protein and, perhaps, even DNA.

"Most people looking for dinosaurs are looking for beautiful skeletons," he says. "We are looking for information."

. . .

Prof. Horner, a curator at the Museum of the Rockies in Bozeman, is among the world’s most influential and offbeat paleontologists. He pioneered studies of dinosaur parent-(p. A12)ing behavior, species variation and bone cells. He is dyslexic, a former Special Forces operative of the Vietnam War era, a MacArthur Foundation "genius" fellow, and a chaired professor of Montana State University who never finished a formal college degree.

"The lenses that people normally use to look at stuff are broken in Jack," says Mary Schweitzer, an assistant professor of paleontology at North Carolina State University, who has worked with him for years. "That’s what makes Jack such a good scientist. Every now and then, every field should get a renegade weirdo in it who challenges assumptions."

. . .

"The chances of finding any [dinosaur] DNA are pretty low," Prof. Horner acknowledges. "I am still hopeful."

In a field mostly outside the mainstream of federal research funding, Prof. Horner has a knack for attracting private grants. Star Wars producer George Lucas, Qualcomm co-founder Klein Gilhousen and Wade Dokken, a developer of Montana real estate, have contributed toward his research, the university says. Nathan Myhrvold, formerly chief technology officer at Microsoft Corp. and co-founder of Intellectual Ventures LLC, is helping to underwrite this season’s fieldwork.

This summer, in Montana’s Hell Creek Formation, Prof. Horner is searching the last landscape inhabited by dinosaurs. More than 65 million years ago, this plain was a wetland where herds of horned Triceratops watered. Today, it is an arid outwash of boulders, cactus and sage. The red and gray soil is littered with white shards of petrified wood that ring like bone china when tapped together and countless crumbs of dinosaur bone.

. . .

"As long as you are not bound by preconceived ideas of what you can find," Prof. Horner says, "there are an awful lot of things you can discover."

For the full story, see:

ROBERT LEE HOTZ. "Dinosaur Hunter Seeks More Than Just Bare Bones; Prof. Horner Searches For Traces of Blood, DNA; Lucky Break From T. Rex." The Wall Street Journal (Fri., August 24, 2007): A1 & A12.

(Note: ellipses added.)

At top, Prof. Horner; at bottom: "Sarah Keenan, 21, an undergraduate at the University of St. Andrews in Scotland who is working this summer for Prof. Horner, covers the fossilized triceratops frill in a protective jacket of plaster." Source of caption and photos: the online version of the WSJ article quoted and cited above.

Marconi Matters

Source of book image: http://palmaddict.typepad.com/photos/uncategorized/big_larsonthunderstruckdrm_1.jpg

Larson’s book plays off a murder mystery against Marconi as the innovator who brought us communication through the air.

I’m most enthused about hte Marconi part. It shows how he proceeded against the theorists of the day, whose theories told them that what he was trying to do was impossible. He was more entrepreneur, than scientist. And it turned out that it was a good thing that the theoretical scientists did not rule, as they might if all decisions about technology were made by the government.

What happened here is an example of what Taleb would call a Black Swan.

Source:

Larson, Erik. Thunderstruck. New York: Crown, 2006.

Let the Evidence Decide if the Mapinguary is Myth or Real

A statue of the mapinguary in Rio Branco, Brazil. Source of the photo: online version of the NYT article quoted and cited below.

RIO BRANCO, Brazil — Perhaps it is nothing more than a legend, as skeptics say. Or maybe it is real, as those who claim to have seen it avow. But the mere mention of the mapinguary, the giant slothlike monster of the Amazon, is enough to send shivers down the spines of almost all who dwell in the world’s largest rain forest.

The folklore here is full of tales of encounters with the creature, and nearly every Indian tribe in the Amazon, including those that have had no contact with one another, have a word for the mapinguary (pronounced ma-ping-wahr-EE). The name is usually translated as “the roaring animal” or “the fetid beast.”

. . .

The giant ground sloth, Megatherium, was once one of the largest mammals to walk the earth, bigger than a modern elephant. Fossil evidence is abundant and widespread, found as far south as Chile and as far north as Florida. But the trail stops cold thousands of years ago.

“When you travel in the Amazon, you are constantly hearing about this animal, especially when you are in contact with indigenous peoples,” said Peter Toledo, an expert on sloths at the Goeldi Institute. “But convincing scientific proof, in the form of even vestiges of bones, blood or excrement, is always lacking.”

Glenn Shepard Jr., an American ethnobiologist and anthropologist based in Manaus, said he was among the skeptics until 1997, when he was doing research about local wildlife among the Machiguenga people of the far western Amazon, in Peru. Tribal members all mentioned a fearsome slothlike creature that inhabited a hilly, forested area in their territory.

Dr. Shepard said “the clincher that really blew me away” came when a member of the tribe remarked matter of factly that he had also seen a mapinguary at the natural history museum in Lima. Dr. Shepard checked; the museum has a diorama with a model of the giant prehistoric ground sloth.

“At the very least, what we have here is an ancient remembrance of a giant sloth, like those found in Chile recently, that humans have come into contact with,” he said. “Let me put it this way: Just because we know that mermaids and sirens are myths doesn’t mean that manatees don’t exist.”

Even so, the mystery of the mapinguary is likely to continue, as is the search.

“There’s still an awful lot of room out there for a large sloth to be roaming around,” Dr. Shepard said.

For the full story, see:

LARRY ROHTER. "A Huge Amazon Monster Is Only a Myth. Or Is It?" The New York Times, Section 1 (Sun., July 8, 2007): 3.

(Note: ellipsis added.)

Some scientists believe that the mapinguary may be based on actual sightings of a real creature related to the Megarium, two of whom are depicted above. Source of the photo: online version of the NYT article cited above.

Source of the map: online version of the NYT article cited above.

Academic Entrepreneurs in a Toxic Wasteland

The Berkeley Pit was once a copper mine, and now holds a lake of toxic waste. Source of photo: online version of the NYT article quoted and cited below.

Here are a few paragraphs from a fascinating story about a couple of people who seem to be practicing what Taleb is preaching in The Black Swan:

BUTTE, Mont. — Death sits on the east side of this city, a 40-billion-gallon pit filled with corrosive water the color of a scab. On the opposite side sits the small laboratory of Don and Andrea Stierle, whose stacks of plastic Petri dishes are smeared with organisms pulled from the pit. Early tests indicate that some of those organisms may help produce the next generation of cancer drugs.

From death’s soup, the Stierles hope to coax life.

“I love the idea of looking at toxic waste and finding something of value,” said Ms. Stierle, 52, a chemistry researcher at Montana Tech of the University of Montana.

For decades, scientists assumed that nothing could live in the Berkeley Pit, a hole 1,780 feet deep and a mile and a half wide that was one of the world’s largest copper mines until 1982, when the Atlantic Richfield Company suspended work there. The pit filled with water that turned as acidic as vinegar, laced with high concentrations of arsenic, aluminum, cadmium and zinc.

. . .

Mr. Stierle is a tenured professor at Montana Tech, but his wife gets paid only for teaching an occasional class or if there is a grant to finance her research. From 1996 to 2001 they applied for dozens of grants, but received only rejection letters. So they financed their own research, using personal savings and $12,000 in annual patent royalty payments. In 2001, they won a six-year, $800,000 grant from the United States Geological Survey.

“Their work is considered a very high-risk approach,” said Matthew D. Kane, a program director at the National Science Foundation. “It takes a long time to get funding, and some luck to find active compounds.”

Unlike scientists at large research universities, who commonly teach only one class a year and employ graduate students to run their laboratories, Mr. Stierle teaches four classes each semester at a college with 2,000 undergraduates and no major research presence.

. . .

The couple said they were negotiating privately with a pharmaceutical company to test some of the compounds they have discovered and possibly turn them into drugs. As they wait, they open another Mason jar filled with murky pit water, draw a sample and return to work.

“The pit very easily could have been a complete waste of time,” Mr. Stierle said. “We just had luck and worked our butts off. We take that first walk into the dark.”

For the full story, see:

CHRISTOPHER MAAG. "In the Battle Against Cancer, Researchers Find Hope in a Toxic Wasteland." The New York Times (Tues., October 9, 2007): A21.

(Note: ellipses added.)

In the photo immediately above, Don and Andrea Steirle work in their lab. The map to the left shows the location of the Berkeley Pit. Source of the photo and map: online version of the NYT article quoted and cited above.

Thales of Miletus Lives

Source of book image: http://store.43folders.com/books-3-1400063515-The_Black_Swan_The_Impact_of_the_Highly_Improbable

This is part entertaining rant and part serious epistemology. I’ve finished 9 of 19 chapters so far–almost all of my reading time spent smiling.

Historians of Greek philosophy used to tell the story of one of the first philosophers, Thales of Miletus, that he once was watching the stars, and fell into a well. The citizens of Miletus made fun of him being an impractical philosopher. To prove them wrong, he used his knowledge to corner the market in something, and made a fortune.

Not a very plausible story, but appealing to us philosophers. (Like Thales, we like to think we could all be rich, if we didn’t have higher goals.)

Well apparently Taleb is the real Thales. He wanted to be a philosopher, got rich on Wall Street using his epistemological insights, and is now using his wealth to finance his musings on whatever he cares to muse on.

Beautiful!

Here’s an amusing sentence that broadened my grin. (It was even more amusing, and profound, in context, but I don’t have time to type in the context for you.)

(p. 87) If you are a researcher, you will have to publish inconsequential articles in "prestigious" publications so that others say hello to you once in a while when you run into them at conferences.

Reference for the book:

Taleb, Nassim Nicholas. The Black Swan: The Impact of the Highly Improbable. New York: Random House, 2007.

Sherwin Rosen Approves a Positive Review of Rosenberg’s Book

Another of Sherwin Rosen’s minor acts of methodological delinquency, this time in his role as co-editor of the Journal of Political Economy, was his asking me to review Alexander Rosenberg’s criticism of the economics profession for drifting further and further into irrelevant mathematical puzzle-solving. My review was basically favorable to Rosenberg, and my memory is that Rosen was quite content with my review.

The reference to my review is:

"Review of: Alexander Rosenberg’s Economics–Mathematical Politics or Science of Diminishing Returns?." Journal of Political Economy 104, no. 3 (June 1996): 655-659.

When Sherwin Rosen Stunned the Fifth World Congress of the Econometric Society

I remember hearing Sherwin Rosen speak to a good-sized auditorium of technical economists at a plenary session of the Fifth World Congress of the Econometric Society in 1985.[i] Rosen was proceeding in his typically bemused style, when he suggested to the stunned audience that they might benefit from re-reading Alfred Marshall. I remember him saying that there are some things in Marshall that we don’t talk about any more, but that we should still talk about. I specifically remember him mentioning that Marshall had said that the success of the institution of contract depended on the correct expectation of a certain level of ethical behavior among the participants in the economy. I wish I could remember the specifics better, but Rosen’s auditors were visibly dismayed, and I supposed that they were thinking something like: ‘read Marshall?, here was the sad sight of a once proud theoretician, going soft and senile.’

[i]I remember a large auditorium-like venue for the session, but could not remember any other session details, so I dug out a copy of the program for the meetings. The only plenary session participation listed for Rosen, was his serving as a discussant for Oliver Hart and Bengt Holmstrom’s “Theory of Contracts” paper, which was delivered on August 19, 1985 (see: “Program . . .,” 1986, p. 471). In searching through Rosen’s publications, I cannot find any evidence that his comment was ever published. In an email response (email dated Nov. 19, 2006) to my inquiry, Bengt Holmstrom has replied: “I know that his comment was not published.”

"Program of the Fifth World Congress of the Econometric Society.” Econometrica 54, no. 2 (March 1986): 459-505.

James Buchanan Convinced Harry Johnson to Over-Rule the Referees

James Buchanan (center) flanked by economics graduate students at the the closing dinner of the 2007 Summer Institute for the Preservation of the History of Economics, held at George Mason University. (Source of photo: me.)

On the evening of Thursday, June 7, 2007, Nobel-prize-winner James Buchanan joined participants for their final dinner-gathering at George Mason’s Summer Institute for the Preservation of the History of Economics.

As a young economist, you are advised that it is never productive to dispute the decisions of journal editors.

But Buchanan, in conversation during the dinner, mentioned that he had only once disputed a journal rejection–of an article submitted to the JPE during Harry Johnson’s editorship. Buchanan said that he wrote Johnson a letter explaining that the referees had totally misunderstood his paper; Johnson read the paper himself, agreed with Buchanan, and published it.

This tells us something about Buchanan, but also something about Johnson. I never took a class from Johnson, but had a conversation with him at a party or reception once, in the last year or two before his death. All I remember about the conversation was that he was polite and respectful to an unknown graduate student, and that somehow we got onto the topic of car advertising.

I remember hearing that sometimes Harry Johnson whittled on wood carving projects during committee meetings. Someone asked him why he did that, and he is reputed to have responded that at the end of the meeting he liked to feel as though something at been accomplished.

Astronauts (and the Rest of Us) Would Benefit from More Unscripted Time

Noctilucent clouds. Source of photo: http://apod.nasa.gov/apod/image/9907/noctilucent_pp.jpg

The excerpt below is from a WSJ summary of an article from the June 2007 issue of Seed.

Many other scientific discoveries have come from astronauts puzzling over strange sights around them. Most of what is known about so-called noctilucent clouds — thin, beautiful wisps that hover at the edge of the Earth’s atmosphere — comes from 30 years of astronauts sketching and trying to photograph them in their spare time. The strength of a certain type of cosmic ray was first recognized in 1969 when Buzz Aldrin asked fellow astronauts if they, like him, were seeing occasional streaks of light when their eyes were closed.

Such discoveries off the beaten path of the National Aeronautic and Space Administration’s research agenda prompt the question attributed to an Apollo program geologist: "If human beings can do much better science than robots, why does NASA make its astronauts do science like robots?"

For the full summary, see:

"Informed Reader; SCIENCE; Why Astronauts Need Down Time in Space." The Wall Street Journal (Weds., May 9, 2007): B15.