Category: Science

Finding the Neanderthal in Us

VindijaCaveCroatiaNeanderthalBones2010-05-19.jpg“The Vindija cave in Croatia where three small Neanderthal bones were found.” Source of caption and photo: online version of the NYT article cited below.

(p. A3) The burly Ice Age hunters known as Neanderthals, a long-extinct species, survive today in the genes of almost everyone outside Africa, according to an international research team who offer the first molecular evidence that early humans mated and produced children in liaisons with Neanderthals.

In a significant advance, the researchers mapped most of the Neanderthal genome–the first time that the heredity of such an ancient human species has been reliably reconstructed. The researchers, able for the first time to compare the relatively complete genetic coding of modern and prehistoric human species, found the Neanderthal legacy accounts for up to 4% of the human genome among people in much of the world today.
By comparing the Neanderthal genetic information to the modern human genome, the scientists were able to home in on hints of subtle differences between the ancient and modern DNA affecting skin, stature, fertility and brain power that may have given Homo sapiens an edge over their predecessors.
“It is tantalizing to think that the Neanderthal is not totally extinct,” said geneticist Svante Pääbo at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, who pioneered the $3.8 million research project. “A bit of them lives on in us today.”
. . .
For their analysis, Dr. Pääbo and his colleagues extracted DNA mostly from the fossil remains of three Neanderthal women who lived and died in Croatia between 38,000 and 45,000 years ago. From thimblefuls of powdered bone, the researchers pieced together about three billion base pairs of DNA, covering about two-thirds of the Neanderthal genome. The researchers checked those samples against fragments of genetic code extracted from three other Neanderthal specimens.
“It is a tour de force to get a genome’s worth,” said genetic database expert Ewan Birney at the European Bioinformatics Institute in Cambridge, England.
In research published Thursday in Science, the researchers compared the Neanderthal DNA to the genomes drawn from five people from around the world: a San tribesman from South Africa; a Yoruba from West Africa; a Han Chinese; a West European; and a Pacific islander from Papua, New Guinea. They also checked it against the recently published genome of bio-entrepreneur Craig Venter. Traces of Neanderthal heredity turned up in all but the two African representatives.

For the full story, see:
ROBERT LEE HOTZ. “Most People Carry Neanderthal Genes; Team Finds up to 4% of Human Genome Comes From Extinct Species, the First Evidence It Mated With Homo Sapiens.” The Wall Street Journal (Fri., MAY 7, 2010): A3.
(Note: ellipsis added.)
(Note: the online version of the review is dated MAY 6, 2010.)

A related article, the online version of which is the source for the caption and photo above, is:
NICHOLAS WADE. “Analysis of Neanderthal Genome Points to Interbreeding with Modern Humans.” The New York Times (Fri., May 7, 2010): A9.
(Note: the online version of the review is dated May 6, 2010 and has the title “Signs of Neanderthals Mating With Humans.”)

VindijaCaveBone2010-05-19.jpg“A close-up of the bone Vindija 33.16 from Vindija cave, Croatia.” Source of caption and photo: online version of the WSJ article quoted and cited above.

Genetically Modified Crops Provide Benefits, Scientists Say

GeneticallyModifiedCornSeed2010-04-19.jpg“A Missouri corn and soybean farmer with a sample of BioTech seed corn.” Source of caption and photo: online version of the NYT article quoted and cited below.

(p. B3) The report is described as the first comprehensive assessment of the impact of genetically modified crops on American farmers, who have rapidly adopted them since their introduction in 1996. The study was issued by the National Research Council, which is affiliated with the National Academy of Sciences and provides advice to the nation under a Congressional charter.

The report found that the crops allowed farmers to either reduce chemical spraying or to use less harmful chemicals. The crops also had lower production costs, higher output or extra convenience, benefits that generally outweighed the higher costs of the engineered seeds.
“That’s a long and impressive list of benefits these crops can provide, and have provided to adopting farmers,” David E. Ervin, the chairman of the committee that wrote the report, said on Tuesday during a webcast news conference from Washington.

For the full story, see:

ANDREW POLLACK. “Study Finds Benefits of Genetically Modified Crops But Warns of Overuse.” The New York Times (Thurs., April 14, 2010): B3.
(Note: the online version of the article was dated April 13, 2010 and has the very different title “Study Says Overuse Threatens Gains From Modified Crops.”)

Highly Reputed Academic Science Journal Found Similar Error Rates in Britannica and Wikipedia

(p. 208) Wikipedia was already highly regarded, anecdotally, but it got a glowing evaluation from the prestigious Nature magazine in December 2005, when it concluded that Wikipedia “comes close” to Britannica in the quality of its science articles. “Our reviewers identified an average of four errors in each Wikipedia article, and three in each Britannica article.”

The news came as a bit of a surprise. Many folks felt Wikipedia did better than they’d have thought, and Britannica did, well, worse than they expected. The result of the study was hotly debated between Nature and Britannica, but to most Wikipedians it was a vindication. They knew that Wikipedia was a minefield of errors, but to be in such close proximity in quality to a traditionally edited encyclopedia, while using such a grassroots process, was the external validation they had been waiting for.
Britannica wasn’t pleased with the methodology, and posted a rebuttal with this criticism: “Almost everything about the journal’s investigation, from the criteria for identifying inaccuracies to the discrepancy between the article text and its headline, was wrong and misleading.” Nature and Britannica exchanged barbs and rebuttals, but in the end, the overall result seemed clear.
“The Nature (sic) article showed that we are on the right track with our current methods. We just need better ways to prevent the display of obvious vandalism at any time,” wrote longtime Wikipedian Daniel Mayer on the mailing list.

Source:
Lih, Andrew. The Wikipedia Revolution: How a Bunch of Nobodies Created the World’s Greatest Encyclopedia. New York: Hyperion, 2009.
(Note: italics in original.)

“Expert Scholarship” Versus “People of Dubious Background”

(p. 71) The acknowledgment, by name, of volunteers in the preface sections of the OED is akin to Wikipedia’s edit history, where one can inspect who contributed to each article. Some Oxford contributors were professors, some royalty, but most were ordinary folks who answered the call. Winchester, in The Professor and the Madman: A Tale of Murder, Insanity, and the Making of the Oxford English Dictionary, tells the story of the “madman” William Chester Minor, a U.S. Civil War survivor whose “strange and erratic behavior” resulted in him shooting an “innocent working man” to death in the street in Lambeth. He was sent to Broadmoor asylum for criminal lunatics. He discovered the OED as a project around 1881, when he saw the “Appeal for Readers” in the library, and worked for the next twenty-one years contributing to the project, receiving notoriety as a contributor “second only to the contributions of Dr. Fitzedward Hall in enhancing our illustration of the literary history of individual words, phrases and constructions.” Minor did something unusual in not just sending submissions, but having his own cataloging system such that the dictionary editors could send a postcard and “out the details flowed, in abundance and always with unerring accuracy.” Until Minor and Murray met in January 1891, no one working with (p. 72) the OED knew their prolific contributor was a madman and murderer housed at Broadmoor.

As we will see in later chapters, a common question of the wiki method is whether one can trust information created by strangers and people of dubious background. But the example of the OED shows that using contributors rather than original expert scholarship is not a new phenomenon, and that projects built as a compendium of primary sources are well suited for harnessing the power of distributed volunteers.

Source:
Lih, Andrew. The Wikipedia Revolution: How a Bunch of Nobodies Created the World’s Greatest Encyclopedia. New York: Hyperion, 2009.
(Note: italics in original.)

Briffa’s Tree Ring Evidence Undermines “Hockey Stick” Global Warming Graph

(p. A12) The problem: Using Mr. Briffa’s tree-ring techniques, researchers in the ’90s built charts suggesting temperatures in the late 20th century were the highest in a millennium. The charts were dubbed “hockey sticks” because they showed temperatures relatively flat for centuries, then angling higher recently.

But Mr. Briffa fretted about a potential issue. Thermometers show temperatures have risen since the ’60s, but tree-ring data don’t move in tandem, and sometimes show the opposite. (Average annual temperatures reached the highest on record in 2005, according to U.S. government data. They fell the next three years, and rose in 2009. All those years remain among the warmest on record.)
In his same 1999 email, Mr. Briffa said tree-ring data overall did show “unusually warm” conditions in recent decades. But, he added, “I believe that the recent warmth was probably matched about 1,000 years ago.”
In other words, maybe the chart shouldn’t resemble a hockey stick.
The data were the subject of heated back-and-forth before the IPCC’s 2001 report. John Christy, one of the section’s lead authors, said at the time that he tried in vain to make sure the report reflected the uncertainty.
Mr. Christy said in an interview that some of the pressure to downplay the uncertainty came from Michael Mann, a fellow lead author of that chapter, a scientist at Pennsylvania State University, and a developer of the original hockey-stick chart.
The “very prominent” use of the hockey-stick chart “overrules what tentativeness some of us actually intended,” Mr. Christy wrote to the National Research Council in the U.S. a month after the report was published. Mr. Christy, a climate scientist at the University of Alabama in Huntsville, provided that email.
“I was suspicious of the hockey stick,” Mr. Christy said in an interview. Had Mr. Briffa’s concerns been more widely known, “The story coming out of the [report] may have been different in tone and confidence.”

For the full story, see:

JEFFREY BALL And KEITH JOHNSON. “Push to Oversimplify at Climate Panel.” The Wall Street Journal (Fri., February 26, 2010): A1 & A12.

GlobalWarmingOversimplifiedGraph2010-02-28.gif

Hockey stick graph is on top; more accurate, but much less publicized graph, is on bottom. Source of graphs: online version of the WSJ article quoted and cited above.

Doubts on Sainthood for U.N.’s Global Warming Nobel Prize Winning Pachauri

GorePachauriNobelPrizes2010-02-28.jpg “Rajendra K. Pachauri, right, the United Nations climate panel’s leader, at a Nobel Peace Prize ceremony with Al Gore in 2007.” Source of caption and photo: online version of the NYT article quoted and cited below.

(p. A1) Just over two years ago, Rajendra K. Pachauri seemed destined for a scientist’s version of sainthood: A vegetarian economist-engineer who leads the United Nations’ climate change panel, he accepted the 2007 Nobel Peace Prize on behalf of the panel, sharing the honor with former Vice President Al Gore.

Critics, writing in Britain’s Sunday Telegraph and elsewhere, have accused Dr. Pachauri of profiting from his work as an adviser to businesses, including Deutsche Bank and Pegasus Capital Advisors, a New York investment firm — a claim he denies.
They have also unearthed and publicized problems with the intergovernmental panel’s landmark 2007 report on climate change, which concluded that the planet was warming and that humans were likely to blame.
The report, they contend, misrepresents the state of scientific knowledge about diverse topics — including the rate of melting of Himalayan glaciers and the rise in severe storms — in a way that exaggerates the evidence for climate change.
But Dr. Pachauri and the Intergovernmental Panel on Climate Change are now under intense scrutiny, facing accusations of scientific sloppiness and potential financial conflicts of interest from climate skeptics, right-leaning politicians and even some mainstream scientists. Senator John Barrasso, a Wyoming Republican, called for Dr. Pachauri’s resignation last week.
Critics, writing in Britain’s Sunday Telegraph and elsewhere, have accused Dr. Pachauri of profiting from his work as an adviser to businesses, including Deutsche Bank and Pegasus Capital Advisors, a New York investment firm — a claim he denies.
They have also unearthed and publicized problems with the intergovernmental panel’s landmark 2007 report on climate change, which concluded that the planet was warming and that humans were likely to blame.
The report, they contend, misrepresents the state of scientific knowledge about diverse topics — including the rate of melting of Himalayan glaciers and the rise in severe storms — in a way that exaggerates the evidence for climate change.

For the full story, see:
ELISABETH ROSENTHAL. “U.N. Climate Panel and Its Chief Face a Siege on Their Credibility.” The New York Times (Tues., February 9, 2010): A1 & A9.
(Note: ellipses added.)
(Note: The online version of the article is dated February 8, 2010, and has the title “Skeptics Find Fault With U.N. Climate Panel.”)

Scientist Helped Kroc Learn Secret of McDonald’s French Fries

One recurring puzzle is the role, if any, for science in innovative entrepreneurship. The episode chronicled below provides one piece of evidence:

(p. 71) I had explained to Ed MacLuckie with great (p. 72) pride the McDonald’s secret for making french fries. I showed him how to peel the potatoes, leaving just a bit of the skin to add flavor. Then I cut them into shoestring strips and dumped them into a sink of cold water. The ritual captivated me. I rolled my sleeves to the elbows and, after scrubbing down in proper hospital fashion, I immersed my arms and gently stirred the potatoes until the water went white with starch. Then I rinsed them thoroughly and put them into a basket for deep frying in fresh oil. The result was a perfectly fine looking, golden brown potato that snuggled up against the palate with a taste like . . . well, like mush. I was aghast. What the hell could I have done wrong? I went back over the steps in my mind, trying to determine whether I had left something out. I hadn’t. I had memorized the procedure when I watched the McDonald’s operation in San Bernardino, and I had done it exactly the same way. I went through the whole thing once more. The result was the same–bland, mushy french fries. They were as good, actually, as the french fries you could buy at other places. But that was not what I wanted. They were not the wonderful french fries I had discovered in California. I got on the telephone and talked it over with the McDonald brothers. They couldn’t figure it out either.

This was a tremendously frustrating situation. My whole idea depended on carrying out the McDonald’s standard of taste and quality in hundreds of stores, and here I couldn’t even do it in the first one!
I contacted the experts at the Potato & Onion Association and explained my problem to them. They were baffled too, at first, but then one of their laboratory men asked me to describe the McDonald’s San Bernardino procedure step-by-step from the time they bought the potatoes from the grower up in Idaho. I detailed it all, and when I got to the point where they stored them in the shaded chicken-wire bins, he said, “That’s it!” He went on to explain that when potatoes are dug, they are mostly water. They improve in taste as they dry out and the sugars change to starch. The McDonald brothers had, without knowing it, a natural curing process in their open bins, which allowed the desert breeze to blow over the potatoes.
With the help of the potato people, I devised a curing system of my own.

Source:
Kroc, Ray. Grinding It Out: The Making of McDonald’s. Chicago: Henry Regnary Company, 1977.
(Note: ellipsis in original.)

Global Warming “Consensus” Achieved by Suppressing Skeptical Research

(p. A25) When scientists make putative compendia of that literature, such as is done by the U.N. climate change panel every six years, the writers assume that the peer-reviewed literature is a true and unbiased sample of the state of climate science.

That can no longer be the case. The alliance of scientists at East Anglia, Penn State and the University Corporation for Atmospheric Research (in Boulder, Colo.) has done its best to bias it.
A refereed journal, Climate Research, published two particular papers that offended Michael Mann of Penn State and Tom Wigley of the University Corporation for Atmospheric Research. One of the papers, published in 2003 by Willie Soon and Sallie Baliunas (of the Harvard-Smithsonian Center for Astrophysics), was a meta-analysis of dozens of “paleoclimate” studies that extended back 1,000 years. They concluded that 20th-century temperatures could not confidently be considered to be warmer than those indicated at the beginning of the last millennium.
In fact, that period, known as the “Medieval Warm Period” (MWP), was generally considered warmer than the 20th century in climate textbooks and climate compendia, including those in the 1990s from the IPCC.
Then, in 1999, Mr. Mann published his famous “hockey stick” article in Geophysical Research Letters (GRL), which, through the magic of multivariate statistics and questionable data weighting, wiped out both the Medieval Warm Period and the subsequent “Little Ice Age” (a cold period from the late 16th century to the mid-19th century), leaving only the 20th-century warming as an anomaly of note.
Messrs. Mann and Wigley also didn’t like a paper I published in Climate Research in 2002. It said human activity was warming surface temperatures, and that this was consistent with the mathematical form (but not the size) of projections from computer models. Why? The magnitude of the warming in CRU’s own data was not as great as in the models, so therefore the models merely were a bit enthusiastic about the effects of atmospheric carbon dioxide.
Mr. Mann called upon his colleagues to try and put Climate Research out of business. “Perhaps we should encourage our colleagues in the climate research community to no longer submit to, or cite papers in, this journal,” he wrote in one of the emails. “We would also need to consider what we tell or request of our more reasonable colleagues who currently sit on the editorial board.”
After Messrs. Jones and Mann threatened a boycott of publications and reviews, half the editorial board of Climate Research resigned. People who didn’t toe Messrs. Wigley, Mann and Jones’s line began to experience increasing difficulty in publishing their results.

For the full commentary, see:
PATRICK J. MICHAELS. “OPINION; How to Manufacture a Climate Consensus; The East Anglia emails are just the tip of the iceberg.” The Wall Street Journal (Fri., DECEMBER 18, 2009): A25.
(Note: the online version of the article is dated DECEMBER 17, 2009.)

Establishments Assume New Methods Are Unsound Methods

(p. 188) For the next two years, Conway coordinated her efforts under Sutherland at PARC with Mead’s ongoing work at Caltech. But she was frustrated with the pace of progress. There was no shortage of innovative design ideas; computerized design tools had advanced dramatically since Mead’s first efforts several years before. Yet the industry as a whole continued in the old rut. As Conway put it later, the problem was “How can you take methods that are new, methods that are not in common use and therefore perhaps considered unsound methods, and turn them into sound methods?” [Conway’s italics].

She saw the challenge in the terms described in Thomas Kuhn’s popular book The Structure of Scientific Revolutions. it was the problem that took Boltzmann to his grave. It was the problem of innovation depicted by economist Joseph Schumpeter in his essays on entrepreneurship: new systems lay waste to the systems of the past. Creativity is a solution for the creator and the new ventures he launches. But it wreaks dissolution–“creative destruction,” in Schumpeter’s words– for the defenders of old methods. In fact, no matter how persuasive the advocates of change, it is very rare that an entrenched establishment will reform its ways. Establishments die or retire or fall in revolution; they only rarely transform themselves.

Source:

Gilder, George. Microcosm: The Quantum Revolution in Economics and Technology. Paperback ed. New York: Touchstone, 1990.
(Note: italics in original.)

For 30 Years “Poincaré’s Elegant Math Prevailed Over Boltzmann’s Practical Findings”

(p. 182) . . . , Poincaré’s elegant math prevailed over Boltzrnann’s practical findings. For some thirty years, Boltzmann struggled to get his ideas across. But he failed. He had the word, but he could not find a way to gain its acceptance in the world. For long decades, the establishment held firm.

So in the year 1906, Poincaré became president of the French (p. 183) Académie des Sciences and Boltzmann committed suicide. As Mead debatably puts it, “Boltzmann died because of Poincaré.” At least, as Boltzmann’s friends attest, this pioneer of the modem era killed himself in an apparent fit of despair, deepened by the widespread official resistance to his views.
He died, however, at the very historic moment when all over Europe physicists were preparing to vindicate the Boltzmann vision. He died just before the findings of Max Planck, largely derived from Boltzmann’s probability concepts, finally gained widespread acceptance. He died several months after an obscure twenty-one-year-old student in Geneva named Albert Einstein used his theories in proving the existence of the atom and demonstrating the particle nature of light. In retrospect, Boltzmann can be seen as a near-tragic protagonist in the greatest intellectual drama of the twentieth century: the overthrow of matter.

Source:

Gilder, George. Microcosm: The Quantum Revolution in Economics and Technology. Paperback ed. New York: Touchstone, 1990.
(Note: ellipsis added.)

NSF Study Shows Many Himalayan Glaciers Growing Larger

HimalayasWesternIce2010-01-07.jpg“This photo taken from the International Space Station in 2004 shows the abundance of ice in the Himalayas, upon which much of the continent of Asia relies for water.” Source of caption and photo: online version of the Omaha World-Herald article quoted and cited below.

(p. 1A) Two UNO professors have discovered that some glaciers in Pakistan are growing in size — a discovery that could toss them into the center of a climate-change controversy.

. . .

(p. 2A) News of the research is beginning to leak into science publications. “Science” magazine, for instance, mentioned the as-yet unpublished University of Nebraska at Omaha research in a November story about the debate over Himalayan glaciers.
The UNO research team will attract more attention Friday, when Shroder and Bishop give their presentation at the American Geophysical Union’s annual conference.
What they’ll present is decades in the making: Shroder first received federal funding to study Afghanistan’s geography and geology in 1977, and he has taken 20 research trips to Pakistan since then.
Using a grant from the U.S. National Science Foundation, Shroder and Bishop and a team of graduate students trekked to a group of glaciers clustered around K2, the second-highest mountain in the world, in 2005.
What they found was startling: Their on-the-ground research and satellite images show that many of the glaciers are growing in the rugged, mostly uninhabited region on the Pakistani-Chinese border.
. . .

Shroder achieved brief fame in intelligence circles when he snuck from Kabul to the Salang Pass in northern Afghanistan in the 1980s. There, he took photos of North Korean troops who had crossed the border to support the Red Army — knowledge that American intelligence agencies didn’t have until Shroder handed over the photos.
Now the veteran professor is bracing himself for a potential backlash when the UNO team’s research paper comes out in the next few weeks.

For the full story, see:
Matthew Hansen. “UNO Scientists Pinpoint Global Warming Oddity in Himalayas.” Omaha World-Herald (Thurs., December 17, 2009): 1A-2A.
(Note: ellipses added.)
(Note: the online version of the article had the title “These glaciers are growing.”)

ShroderJack2010-01-07.jpg

Regents Professor Jack Shroder. Source of photo: http://www.unomaha.edu/glims/img/Portraits/Jack%20shroder-visa.jpg