Science – Page 37 – artdiamondblog.com

“It Isn’t What You Know that Counts–It Is How Efficiently You Can Refresh”

Source of book image: online version of the WSJ review quoted and cited below.

(p. A17) Knowledge, then, is less a canon than a consensus in a state of constant disruption. Part of the disruption has to do with error and its correction, but another part with simple newness–outright discoveries or new modes of classification and analysis, often enabled by technology.
. . .
In some cases, the facts themselves are variable. . . .
. . .
More commonly, however, changes in scientific facts reflect the way that science is done. Mr. Arbesman describes the “Decline Effect”–the tendency of an original scientific publication to present results that seem far more compelling than those of later studies. Such a tendency has been documented in the medical literature over the past decade by John Ioannidis, a researcher at Stanford, in areas as diverse as HIV therapy, angioplasty and stroke treatment. The cause of the decline may well be a potent combination of random chance (generating an excessively impressive result) and publication bias (leading positive results to get preferentially published).
If shaky claims enter the realm of science too quickly, firmer ones often meet resistance. As Mr. Arbesman notes, scientists struggle to let go of long-held beliefs, something that Daniel Kahneman has described as “theory-induced blindness.” Had the Austrian medical community in the 1840s accepted the controversial conclusions of Dr. Ignaz Semmelweis that physicians were responsible for the spread of childbed fever–and heeded his hand-washing recommendations–a devastating outbreak of the disease might have been averted.
Science, Mr. Arbesman observes, is a “terribly human endeavor.” Knowledge grows but carries with it uncertainty and error; today’s scientific doctrine may become tomorrow’s cautionary tale. What is to be done? The right response, according to Mr. Arbesman, is to embrace change rather than fight it. “Far better than learning facts is learning how to adapt to changing facts,” he says. “Stop memorizing things . . . memories can be outsourced to the cloud.” In other words: In a world of information flux, it isn’t what you know that counts–it is how efficiently you can refresh.

For the full review, see:
DAVID A. SHAYWITZ. “BOOKSHELF; The Scientific Blind Spot.” The Wall Street Journal (Mon., November 19, 2012): A17.
(Note: ellipses added, except for the one internal to the last paragraph, which was in the original.)
(Note: the online version of the article was dated November 18, 2012.)

The book under review, is:
Arbesman, Samuel. The Half-Life of Facts: Why Everything We Know Has an Expiration Date. New York: Current, 2012.

Reality Is Not Always “Elegant”

Source of book image: http://images.betterworldbooks.com/067/Ordinary-Geniuses-Segre-Gino-9780670022762.jpg

(p. C9) In the summer of 1953, while visiting Berkeley, Gamow was shown a copy of the article in Nature where Watson and Crick spelled out some of the genetic implications of their discovery that DNA is structured as a double helix. He immediately realized what was missing. Each helix is a linear sequence of four molecules known as bases. The sequence contains all the information that guides the manufacture of the proteins from which living things are made. Proteins are assembled from 20 different amino acids. What is the code that takes you from the string of bases to the amino acids? Gamow seems to have been the first to look at the problem in quite this way.

But he made a physicist’s mistake: He thought that the code would be “elegant”–that each amino acid would be specified by only one string of bases. (These strings were dubbed “codons.”) He produced a wonderfully clever code in which each codon consisted of three bases. That was the only part that was right. In the actual code sometimes three different codons correspond to the same amino acid, while some codons do not code for an amino acid at all. These irregularities are the results of evolutionary stops and starts, and no amount of cleverness could predict them.

For the full review, see:
JEREMY BERNSTEIN. “The Inelegant Universe.” The Wall Street Journal (Sat., August 13, 2011): C9.

The book under review is:
Segrè, Gino. Ordinary Geniuses: Max Delbruck, George Gamow, and the Origins of Genomics and Big Bang Cosmology. New York: Viking, 2011.

Much Innovation Has “Nothing to Do with Science–It’s Just Creative Mankind Chipping Away at Things”

(p. 122) VANE and MULHEARN: The prize rewards specific discoveries, achievements, or breakthroughs in economic science. Your pioneering contributions have opened up a rich seam of research for others to mine. Does academic knowledge largely progress through the lead taken by a small number of creative innovators?
PHELPS: That’s such a good question. It resonates with a subject in the area of innovation theory. The old guys like Arthur Spiethoff thought that progress was due to the great discoveries of the scientists and navigators. Schumpeter (1934) (p. 123) didn’t depart altogether from that, he simply said, well, that’s right but you’ve got to have some entrepreneur to actually implement it. But don’t think there’s much creativity there–everybody knows what’s in the air. And it’s very rare that anything new really gets created in the course of this development work. But now we don’t think about innovation in that way so much. We recognize that once in a while there is a big leap which creates the ground for a surge of innovations to follow. Nowadays we realize that an awful lot of innovation just comes from business people operating at the grass roots having ideas on the basis of what they see around them. Nothing to do with science–it’s just creative mankind chipping away at things. I know that the Sens and the Mundells and the Lucases are towering figures, but they couldn’t have become so if they hadn’t read a lot of papers by, well, pretty average people who are just doing a good job of exploring a question and giving inspiration. I guess the towering figures are people with just a little more drive, a little more imagination, just a little cleverer in putting some things together. In other words, I don’t know the answer to the question [laughter].

For the full interview, from which the above is quoted, see:
Vane, Howard R., and Chris Mulhearn, interviewers. “Interview with Edmund S. Phelps.” Journal of Economic Perspectives 23, no. 3 (Summer 2009): 109-24.

“Extinct” Snail Found Alive

“The oblong rocksnail in Alabama, 12 years after it was declared extinct.” Source of caption and photo: online version of the NYT article quoted and cited below.

(p. D3) A freshwater snail has been rediscovered on the Cahaba River in Alabama, 12 years after it was declared extinct.

Nathan Whelan, a graduate student in biology at the University of Alabama, spotted the snail — called the oblong rocksnail, or Leptoxis compacta — on a small stretch of the river.

For the full story, see:
SINDYA N. BHANOO. “OBSERVATORY; Snails Appear Reborn, or Were Overlooked.” The New York Times (Tues., August 14, 2012): D3.
(Note: the online version of the article has the date August 13, 2012.)

Whelan and co-authors report their findings in:
Whelan NV, Johnson PD, Harris PM (2012) Rediscovery of Leptoxis compacta (Anthony, 1854) (Gastropoda: Cerithioidea: Pleuroceridae). PLoS ONE 7(8): e42499. doi:10.1371/journal.pone.0042499

Big Science Done Privately at Great Risk

Source of book image: http://t0.gstatic.com/images?q=tbn:ANd9GcQPLdrVlC1FT3ojxyxWJLq55AeAs87pw_Bw6ks1ugFnkcI_DBa_1w&t=1

(p. 23) Next time you find yourself grousing when the passenger in front reclines his seat a smidge too far, consider the astronomers of the Enlightenment. In 1761 and 1769, dozens and dozens of stargazers traveled thousands of miserable miles to observe a rare and awesome celestial phenomenon. They went by sailing ship and open dinghy, by carriage, by sledge and on foot. They endured discomfort that in our own flabby century would generate years of litigation. And they did it all for science: the men in powdered wigs and knee britches were determined to measure the transit of Venus.
. . .
The British astronomer Edmond Halley had realized that precise measurement of a transit might give astronomers armed with a clock and a telescope the data they needed to calculate how far Earth is from the Sun. With that distance in hand, they could work out the actual size of the solar system, the great astronomical problem of the era. The catch was that it would take multiple measurements from carefully chosen locations all over the Northern and Southern Hemispheres. But that was somebody else’s problem. Halley knew he wouldn’t live to see the transit of 1761.
That challenge fell to the French astronomer Joseph-Nicolas Delisle, who managed to energize and rally his colleagues in the years leading up to the transit, then coordinate the enormous effort that would ultimately involve scientists and adventurers from France, Britain, Russia, Germany, the Netherlands, Italy, Sweden and the American colonies. When you think about how hard it is to arrange a simple dinner with a few friends who live in the same city and use the same language when e-mailing, it’s enough to take your breath away.
. . .
Sea travel was so risky in 1761 that observers took separate ships to the same destination to increase the chances some of them would make it alive. The Seven Years’ War was on, and getting caught in the cross-fire was a constant concern. One French scientist carried a passport arranged by the Royal Society in London advising the British military “not to molest his person or Effects upon any account.” Others were shelled by the French or caught in border troubles with the Russians. An observer en route to Tobolsk, in Siberia, found himself floating in ice up to his waist when his carriage fell through the frozen river they were traveling in lieu of a road. He made it to his destination. Another, heading toward eastern Finland via the iced-over Gulf of Bothnia, was repeatedly catapulted out of his sledge as the runners caught on the crests of frozen waves. He made it too.

For the full review, see:
JoANN C. GUTIN. “Masters of the Universe.” The New York Times Book Review (Sun., May 20, 2012): 19.
(Note: ellipses added.)
(Note: the online version of the review has the date May 18, 2012.)

The full reference for the book under review, is:
Wulf, Andrea. Chasing Venus: The Race to Measure the Heavens. New York: Alfred A. Knopf, 2012.

Source of image: online version of the NYT article quoted and cited above.

Global Warming Expands Range of Brown Argus Butterfly

“The brown argus butterfly has expanded its range in England.” Source of caption and photo: online version of the NYT article quoted and cited below.

(p. D3) A butterfly species in England is expanding its range, thanks to climate change.

In the current issue of Science, researchers at the University of York report that the brown argus butterfly has spread its reach in England northward by about 50 miles over 20 years as a warmer climate allows its caterpillars to feed off wild geranium plants, which are widespread in the countryside.

For the full story, see:
SINDYA N. BHANOO. “OBSERVATORY; A Butterfly Takes Wing on Climate Change.” The New York Times (Tues., May 29, 2012): D3.
(Note: the online version of the article has the date May 24, 2012.)

The results summarized above are reported to the scientific community in:
Chen, Ching, Jane K. Hill, Ralf Ohlemüller, David B. Roy, and Chris D. Thomas. “Report; Rapid Range Shifts of Species Associated with High Levels of Climate Warming.” Science 333, no. 6045 (August 19, 2011): 1024-1026.

How a Group of “Natural Philosophers” Created Science in a London “Full of Thieves, Murderers and Human Waste”

Source of book image: http://www.edwarddolnick.net/images/clockworkuniverse-cover.jpg

(p. 19) London before the mid-1600s was a general calamity. The streets were full of thieves, murderers and human waste. Death was everywhere: doctors were hapless, adults lived to about age 30, children died like flies. In 1665, plague moved into the city, killing sometimes 6,000 people a week. In 1666, an unstoppable fire burned the city to the ground; the bells of St. Paul’s melted. Londoners thought that the terrible voice of God was “roaring in the City,” one witness wrote, and they would do best to accept the horror, calculate their sins, pray for guidance and await retribution.

In the midst of it all, a group of men whose names we still learn in school formed the Royal Society of London for the Improvement of Natural Knowledge. They thought that God, while an unforgiving judge, was also a mathematician. As such, he had organized the universe according to discernible, mathematical law, which, if they tried, they could figure out. They called themselves “natural philosophers,” and their motto was “Nullius in verba”: roughly, take no one’s word for anything. You have an idea? Demonstrate it, do an experiment, prove it. The ideas behind the Royal Society would flower into the Enlightenment, the political, cultural, scientific and educational revolution that gave rise to the modern West.
This little history begins Edward Dolnick’s “Clockwork Universe,” so the reader might think the book is about the Royal Society and its effects. But the Royal Society is dispatched in the first third of the book, and thereafter, the subject is how the attempt to find the mathematics governing the universe played out in the life of Isaac Newton.
. . .
To go from sinful “curiositas” to productive “curiosity,” from blind acceptance to open-eyed inquiry, from asking, “Why?” to answering, “How?” — this change, of all the world’s revolutions, must surely be the most remarkable.

For the full review, see:
ANN FINKBEINER. “Masters of the Universe.” The New York Times Book Review (Sun., March 27, 2011): 19.
(Note: the online version of the review has the date March 25, 2011, and had the title “What Newton Gave Us.”)

The full reference for the book under review, is:
Dolnick, Edward. The Clockwork Universe: Isaac Newton, the Royal Society, and the Birth of the Modern World. New York: HarperCollins Publishers, 2011.

The Mockingjay as Symbol and Reality

A burning Mockingjay symbol appears on this movie poster for “The Hunger Games.” Source of poster: online version of the NYT article quoted and cited below.

(p. D4) “They’re funny birds and something of a slap in the face to the Capitol,” Katniss explains in the first book. And the nature of that slap in face is a new twist on the great fear about genetic engineering, that modified organisms or their genes will escape into the wild and wreak havoc. The mockingjay is just such an unintended consequence, resulting from a failed creation of the government, what Katniss means when she refers to “the Capitol.” But rather than being a disaster, the bird is a much-loved reminder of the limits of totalitarian control.
. . .
I asked Joan Slonczewski, a microbiologist and science fiction writer at Kenyon College in Ohio, about her take on the mockingjay. Dr. Slonczewski, whose recent books include a text and a novel, “The Highest Frontier,” teaches a course called “Biology in Science Fiction.” The tools needed to modify organisms are already widely dispersed in industry and beyond. “Now anybody can do a start-up,” she said.
That’s no exaggeration. Do-it-yourself biology is growing. The technology to copy pieces of DNA can be bought on eBay for a few hundred dollars, as Carl Zimmer reported in The New York Times in March. As to where D.I.Y. biology may lead, Freeman Dyson, a thinker at the Institute for Advanced Study known for his provocative ideas, presented one view in 2007 in The New York Review of Books. He envisioned the tools of biotechnology spreading to everyone, including pet breeders and children, and leading to “an explosion of diversity of new living creatures.”
Eventually, he wrote, the mixing of genes by humans will initiate a new stage in evolution. Along the way, if he is right, the world may have more than its share of do-it-yourself mockingjays.

For the full story, see:
JAMES GORMAN. “SIDE EFFECTS; D.I.Y. Biology, on the Wings of the Mockingjay.” The New York Times (Tues., May 15, 2012): D4.
(Note: ellipsis added.)
(Note: the online version of the article has the date May 10, 2012.)

“Science Is Weakest in the Lands of Islam”

Source of book image: http://photo.goodreads.com/books/1327925578l/10379376.jpg

(p. 18) The upshot was, while the Greek works in particular were disappearing in Europe, they were being preserved in Arabic to be retranslated later into Latin for a rebirth of “lost” knowledge. This is one half of the point the author makes frequently in the text and, in boldface, as the book’s subtitle.

The other half is that contrary to some doubters, the Arab interest in learning extended well beyond translations: thinkers working alone or in observatories and houses of wisdom were conducting original research during “the world’s most impressive period of scholarship and learning since ancient Greece.” Accordingly, al-Khalili writes that al-Mamun stands as “the greatest patron of science in the cavalcade of Islamic rulers.”
Sometimes al-Khalili, like a lawyer who suspects a jury of unyielding skepticism, strains to give stature to the leading lights of Arabic science in the Middle Ages. But modern historians of science agree that more attention should be given to the Arab contribution to the preservation and expansion of knowledge at this critical period, and the author has done so in considerable detail and with rising passion.
But that was then, and al-Khalili is obligated to end on an inescapable but deflating note: science today is in a chronic state of neglect in the Arab world and the broader Islamic culture of more than one billion people. Al-Khalili spreads the blame widely, citing inadequate financing for research and education, sclerotic bureaucracies, religious conservatism, even an ingrained fear of science. The Pakistani physicist Abdus Salam, perhaps the greatest Muslim scientist of the last century, won a Nobel Prize in 1979 and did what he could to promote a scientific renaissance among his people, without success. “Of all civilizations on this planet, science is weakest in the lands of Islam,” Salam said in despair. “The dangers of this weakness cannot be overemphasized since the honorable survival of a society depends directly on its science and technology in the condition of the present age.”
By recounting Arabic science’s luminous past, al-Khalili says, he hopes to instill a sense of pride that will “propel the importance of scientific enquiry back to where it belongs: at the very heart of what defines a civilized and enlightened society.”

For the full review, see:
JOHN NOBLE WILFORD. “The Muslim Art of Science.” The New York Times Book Review (Sun., May 22, 2011): 18.
(Note: the online version of the review has the date May 20, 2011.)

The full reference for the book under review, is:
al-Khalili, Jim. The House of Wisdom: How Arabic Science Saved Ancient Knowledge and Gave Us the Renaissance. New York: The Penguin Press, 2010.

Models Often “Ignore the Messiness of Reality”

Source of book image: http://www.namingandtreating.com/wp-content/uploads/2011/04/SuperCooperators_small.png

(p. 18) Nowak is one of the most exciting modelers working in the field of mathematical biology today. But a model, of course, is only as good as its assumptions, and biology is much messier than physics or chemistry. Nowak tells a joke about a man who approaches a shepherd and asks, ”If I tell you how many sheep you have, can I have one?” The shepherd agrees and is astonished when the stranger answers, ”Eighty-three.” As he turns to leave, the shepherd retorts: ”If I guess your profession, can I have the animal back?” The stranger agrees. ”You must be a mathematical biologist.” How did he know? ”Because you picked up my dog.”

. . .
Near the end of the book, Nowak describes Gustav Mahler’s efforts, in his grandiloquent Third Symphony, to create an all-encompassing structure in which ”nature in its totality may ring and resound,” adding, ”In my own way, I would like to think I have helped to give nature her voice too.” But there remains a telling gap between the precision of the models and the generality of the advice Nowak offers for turning us all into supercooperators. We humans really are infinitely more complex than falling apples, metastasizing colons, even ant colonies. Idealized accounts of the world often need to ignore the messiness of reality. Mahler understood this. In 1896 he invited Bruno Walter to Lake Attersee to glimpse the score of the Third. As they walked beneath the mountains, Walter admonished Mahler to look at the vista, to which he replied, ”No use staring up there — I’ve already composed it all away into my symphony!”

For the full review, see:
OREN HARMAN. “A Little Help from Your Friends.” The New York Times Book Review (Sun., April 10, 2011): 18.
(Note: ellipsis added.)
(Note: the online version of the review has the date April 8, 2011, and has the title “How Evolution Explains Altruism.”)

The full reference for the book under review, is:
Nowak, Martin A., and Roger Highfield. Supercooperators: Altruism, Evolution, and Why We Need Each Other to Succeed. New York: Free Press, 2011.

Where Credit Is Due

“EVIDENCE; A lab notebook belonging to Albert Schatz, left, with his supervisor, Selman A. Waksman, and discovered at Rutgers helps puts to rest a 70-year argument over credit for the Nobel-winning discovery of streptomycin.” Source of caption and photo: online version of the NYT article quoted and cited below.

(p. D3) NEW BRUNSWICK, N.J. — For as long as archivists at Rutgers University could remember, a small cardboard box marked with the letter W in black ink had sat unopened in a dusty corner of the special collections of the Alexander Library. Next to it were 60 sturdy archive boxes of papers, a legacy of the university’s most famous scientist: Selman A. Waksman, who won a Nobel Prize in 1952 for the discovery of streptomycin, the first antibiotic to cure tuberculosis.

The 60 boxes contained details of how streptomycin was found — and also of the murky story behind it, a vicious legal battle between Dr. Waksman and his graduate student Albert Schatz over who deserved credit.
Dr. Waksman died in 1973; after Dr. Schatz’s death in 2005, the papers were much in demand by researchers trying to piece together what really happened between the professor and his student. But nobody looked in the small cardboard box.
. . .
Thomas J. Frusciano, the head archivist of the Alexander Library special collections, recalled that the Waksman papers had been acquired in 1983, 10 years after the professor’s death, and had even included a vial of streptomycin. He asked a member of his team, Erika Gorder, to search the stacks.
She remembered seeing the small box next to Dr. Waksman’s papers. “I must have passed by it a million times,” she said, “but I always thought it must contain miscellaneous material from the Waksman papers when they were cataloged.”
When she pulled down the box and carefully opened it, however, there, loosely piled inside, were five clothbound notebooks — just like Dr. Waksman’s, but marked “Albert Schatz.”
In the notebook for 1943, on Page 32, Dr. Schatz had started Experiment 11. In meticulous cursive, he had written the date, Aug. 23, and the title, “Exp. 11 Antagonistic Actinomycetes,” a reference to the strange threadlike microbes found in the soil that produce antibiotics. Underneath the title he recorded where he had found the microbes in “leaf compost, straw compost and stable manure” on the Rutgers College farm, outside his laboratory.
The following pages detailed his experiments and his discovery of two strains of a gray-green actinomycete named Streptomyces griseus, Latin for gray. Each strain produced an antibiotic that destroyed germs of E. coli in a petri dish — and, he was to find out later, also destroyed the TB germ. The notebook shows that the moment of discovery belongs to Dr. Schatz.
One of the pages in Experiment 11 had indeed been cut out, but the page was toward the end of the experiment, after Dr. Schatz had made his discovery. There was no evidence of a break in the experiment to suggest that Dr. Schatz might have removed the page to conceal something he didn’t want the rest of the world to know.
And in Dr. Waksman’s own papers — in the 60 boxes — there was confirmation that the professor knew the missing page was not a real issue. His legal advisers had told him bluntly that it was a distraction. As one lawyer wrote, the missing page was “insignificant.”
As for the professor’s story that Dr. Schatz’s uncle had carried off the key 1943 notebook, Dr. Waksman’s own documents make clear it could not have been true. At the time the key notebook was not at Rutgers; it was with university-appointed agents who were preparing the streptomycin patent application. Here, indeed, was evidence that Dr. Waksman had deliberately spread doubt and confusion about Dr. Schatz’s Experiment 11 in a campaign to belittle the work of his student.

For the full story, see:
PETER PRINGLE. “Notebooks Shed Light on an Antibiotic’s Contested Discovery.” The New York Times (Tues., June 12, 2012): D3.
(Note: ellipsis added.)
(Note: the online version of the story has the date June 11, 2012.)

The issues treated above are discussed in more detail in Pringle’s book:
Pringle, Peter. Experiment Eleven: Dark Secrets Behind the Discovery of a Wonder Drug. New York: Walker & Company, 2012.