Science – Page 46 – artdiamondblog.com

Rapid Mutation of RNA-Based Flu Virus Allows Rapid Adaptation to Immune System Response

I found the passage quoted below to be especially illuminating on how rapid mutation helps explain why the flu virus is so successful and dangerous. (An additional important factor is that the virus can survive in birds, without killing them.)
It occurs to me that something akin to rapid mutation (e.g., rapid experimentation) has also been advocated as a way to quickly advance science (Karl Popper), or enterprise (George Gilder).

(p. 105) Whenever an organism reproduces, its genes try to make exact copies of themselves. But sometimes mistakes–mutations–occur in this process.

This is true whether the genes belong to people, plants, or viruses. The more advanced the organism, however, the more mechanisms exist to prevent mutations. A person mutates at a much slower rate than bacteria, bacteria mutates at a much slower rate than a virus–and a DNA virus mutates at a much slower rate than an RNA virus.
DNA has a kind of built-in proofreading mechanism to cut down on copying mistakes. RNA has no proofreading mechanism whatsoever, no way to protect against mutation. So viruses that use RNA to carry their genetic information mutate much faster–from 10,000 to 1 million times faster–than any DNA virus.
Different RNA viruses mutate at different rates as well. A few mutate so rapidly that virologists consider them not so much a population of copies of the same virus as what they call a “quasi species” or a “mutant swarm.”
These mutant swarms contain trillions and trillions of closely related but different viruses. Even the viruses produced from a single cell will include many different versions of themselves, and the swarm as a whole will routinely contain almost every possible permutation of its genetic code.
Most of these mutations interfere with the functioning of the virus and will either destroy the virus outright or destroy its ability to infect. But other mutations, sometimes in a single base, a single letter, in its genetic code will allow the virus to adapt rapidly to a new situation. It is this adaptability that explains why these quasi species, these mutant swarms, can move rapidly back and forth between different environments and also develop extraordinarily rapid drug resistance. As one investigator has observed, the rapid mutation “confers a certain randomness to the disease processes that accompany RNA [viral] infections.”
Influenza is an RNA virus. So is HIV and the coronavirus. And of all RNA viruses, influenza and HIV are among those that mutate the fastest. The influenza virus mutates so fast that 99 percent of the 100,000 to 1 million new viruses that burst out of a cell in the reproduction process (p. 106) are too defective to infect another cell and reproduce again. But that still leaves between 1,000 and 10,000 viruses that can infect another cell.
Both influenza and HIV fit the concept of a quasi species, of a mutant swarm. In both, a drug-resistant mutation can emerge within days. And the influenza virus reproduces rapidly–far faster than HIV. Therefore it adapts rapidly as well, often too rapidly for the immune system to respond.

Source:
Barry, John M. The Great Influenza: The Story of the Deadliest Pandemic in History. Revised ed. New York: Penguin Books, 2005.
(Note: italics in original.)

Small Evidence Kills Big Theory

Big Tyrannosaurus rex and much smaller Raptorex kriegsteini. Source of image: http://scienceblogs.com/notrocketscience/upload/2009/09/raptorex_tiny_king_of_thieves_shows_how_tyrannosaurus_body_p/Raptorex_Trex.jpg

(p. A5) Paleontologists said Thursday that they had discovered what amounted to a miniature prototype of Tyrannosaurus rex, complete with the oversize head, powerful jaws, long legs — and, as every schoolchild knows, puny arms — that were hallmarks of the king of the dinosaurs.

But this scaled-down version, which was about nine feet long and weighed only 150 pounds, lived 125 million years ago, about 35 million years before giant Tyrannosaurs roamed the earth. So the discovery calls into question theories about the evolution of T. rex, which was about five times longer and almost 100 times heavier.
“The thought was these signature Tyrannosaur features evolved as a consequence of large body size,” Stephen L. Brusatte of the American Museum of National History, an author of a paper describing the dinosaur published online by the journal Science, said at a news conference. “They needed to modify their entire skeleton so they could function as a predator at such colossal size.”
The new dinosaur, named Raptorex kriegsteini, “really throws a wrench into this observed pattern,” Mr. Brusatte said.

For the full story, see:
HENRY FOUNTAIN. “Fossil Discovery Challenges Theories on T. Rex Evolution.” The New York Times (Fri., September 18, 2009): A5.
(Note: the online version is dated Sept. 17th and has the slightly different title: “Fossil Find Challenges Theories on T. Rex” but the body of the article seems the same as the print version.)

Scientist Huxley: “The Great End of Life is Not Knowledge But Action”

John Barry calls our attention to the views of Thomas Huxley who gave the keynote address at the founding of the Johns Hopkins University:

(p. 13) A brilliant scientist, later president of the Royal Society, he advised investigators, “Sit down before a fact as a little child, be prepared to give up every preconceived notion. Follow humbly wherever and to whatever abysses nature leads, or you shall learn nothing.” He also believed that learning had purpose, stating, “The great end of life is not knowledge but action.”

Source:
Barry, John M. The Great Influenza: The Story of the Deadliest Pandemic in History. Revised ed. New York: Penguin Books, 2005.
(Note: from the context in Barry, I am not certain whether the Huxley quotes are from the keynote address, or from elsewhere in Huxley’s writings.)

“Recent Temperature Plateau” May Undermine Case for Global Warming

Source of graph: online version of the NYT article quoted and cited below.

(p. A10) The world leaders who met at the United Nations to discuss climate change on Tuesday are faced with an intricate challenge: building momentum for an international climate treaty at a time when global temperatures have been relatively stable for a decade and may even drop in the next few years.

The plateau in temperatures has been seized upon by skeptics as evidence that the threat of global warming is overblown. And some climate experts worry that it could hamper treaty negotiations and slow the progress of legislation to curb carbon dioxide emissions in the United States.
. . .

Underscoring just how little clarity there is on short-term temperature fluctuations, researchers from Britain’s climate change office, in a paper published in August, projected “an end to this period of relative stability,” with half the years between now and 2015 exceeding the record-setting global temperatures of 1998.
Whatever the next decade may hold, critics of global warming have lost no time in using the current temperature plateau to build their case.
“I think it supports the arguments of those who’ve said, ‘What’s the rush for policy on this issue?’ ” said Patrick J. Michaels, a climatologist affiliated with George Mason University and the Cato Institute, a group opposing most regulatory solutions to environmental problems.
. . .

A clearer view of whether the recent temperature plateau undermines arguments for dangerous climate change in the long run should come in a few years, as the predictions made by the British climate researchers are tested. Their paper appeared in a supplement to an August issue of The Bulletin of the American Meteorological Society.
While the authors concluded that there was a 1 in 8 chance of having a decade-long pause in warming like the current plateau, even with rising concentrations of greenhouse gases, the odds of a 15-year pause, they wrote, are only 5 in 100. As a result, the next few years of observations could tip the balance toward further concern or greater optimism.
Meanwhile, social scientists who study the way people understand and respond to environmental problems say it is not surprising that the current temperature stability has created confusion and apathy.

For the full story, see:
ANDREW C. REVKIN. “Plateau in Temperatures Adds Difficulty to Task of Reaching a Solution.” The New York Times (Weds., Sept. 23, 2009): A10.
(Note: the online version lists a date of September 21 and has the title as “Momentum on Climate Pact Is Elusive”, but the body of the article seems to be the same as the print version.)
(Note: ellipses added.)

Scientists Believe Life Emerged from a Process of “Creative Destruction” and Global Warming

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

(p. A9) In a paradox of creation, new evidence suggests that devastating avalanches of cosmic debris may have fostered life on Earth, not annihilated it. If so, life on our planet may be older than scientists previously thought — and more persistent.

Astronomers world-wide have been transfixed by a roiling gash the size of Earth in the atmosphere of Jupiter, caused by an errant comet or asteroid that smashed into the gas giant last month. The lingering turbulence is an echo of a cataclysmic bombardment that shaped the origin of life here 3.9 billion years ago, when millions of asteroids, comets and meteors pummeled our planet.
. . .
But in their super-heated plunge through the atmosphere, these asteroids and meteors may have helped create conditions ideal for emerging life. “Everyone focuses on the meteor that hits the ground,” says geochemist Richard Court at London’s Imperial College. “No one thinks about the products of its journey that get pumped into the atmosphere.”
As they vented, they collectively could have imported billions of tons of life-sustaining water into the air every year, Dr. Court and his colleague Mark Sephton recently determined. They calculated that these showers of volatile rocks delivered 10 times the daily outflow of the Mississippi River every year for 20 million years. By analyzing the fumes emitted under such extreme heat, they discovered these rocks also could have injected billions of tons of carbon dioxide into the air every year.
Combined with so much water vapor, the carbon dioxide could have induced a global greenhouse effect. That could have kept any life emerging on Earth safely in a planetary incubator at a time when the planet might easily have frozen because the Sun radiated 25% less energy than today. “The amount of CO2 that was produced is about the same we produce today through fossil fuel use and we know that is a climate-changing volume,” says Dr. Court.
. . .
“It is literally a revolution in our ideas about how our solar system evolved,” says asteroid expert William Bottke at the Southwest Research Institute. “It could be that our form of life today — every living thing that we see today — is due to this bombardment that happened 3.9 billion years ago.”

For the full commentary, see:
ROBERT LEE HOTZ. “SCIENCE JOURNAL; Some Creative Destruction on a Cosmic Scale; Scientists Say Asteroid Blasts, Once Thought Apocalyptic, Fostered Life on Earth by Carrying Water and Protective Greenhouse Gas.” The Wall Street Journal (Fri., AUGUST 14, 2009): A9.
(Note: ellipses added.)

Global Warming Allows Humans to “Skip” Next Ice Age

“Researchers use a floating platform to take sediment cores from Sunday Lake in southwestern Alaska.” Source of photo and caption: online version of the NYT article quoted and cited below.

(p. A17) The human-driven buildup of heat-trapping greenhouse gases in the atmosphere appears to have ended a slide, many millenniums in the making, toward cooler summer temperatures in the Arctic, the authors of a new study report.

Scientists familiar with the work, to be published Friday in the journal Science, said it provided fresh evidence that human activity is not only warming the globe, particularly the Arctic, but could also even fend off what had been presumed to be an inevitable descent into a new ice age over the next few dozen millenniums.
. . .
In the very long term, the ability to artificially warm the climate, particularly the Arctic, could be seen as a boon as the planet’s shifting orientation to the Sun enters a phase that could initiate the next ice age.
As a result of such periodic shifts, 17 ice ages are thought to have come and gone in two million years. The last ice age ended 11,000 years ago and the next one, according to recent research, could be 20,000 or 30,000 years off discounting any influence by humans. The last ice age buried much of the Northern Hemisphere under a mile or more of ice.
With humans’ clear and growing ability to alter the climate, Dr. Overpeck said, “we could easily skip the next opportunity altogether.”

For the full story, see:

ANDREW C. REVKIN. “Global Warming Is Delaying Ice Age, Study Finds.” The New York Times (Fri., September 4, 2009): A17.
(Note: the online version of the article has the title “Global Warming Could Forestall Ice Age.”)
(Note: ellipsis added.)

The reference to the full scientific presentation of the research is:
Kaufman, Darrell S., David P. Schneider, Nicholas P. McKay, Caspar M. Ammann, Raymond S. Bradley, Keith R. Briffa, Gifford H. Miller, Bette L. Otto-Bliesner, Jonathan T. Overpeck, Bo M. Vinther, and Members Arctic Lakes 2k Project. “Recent Warming Reverses Long-Term Arctic Cooling.” Science 325, no. 5945 (2009): 1236-39.

“The Evidence of His Eyes Overturned 2,000 Years of Accepted Wisdom”

“. . ., the Italian astronomer shows the satellites of Jupiter to Venetian senators in this 1882 illustration.” Source of illustration and caption: online version of the WSJ article quoted and cited below.

(p. A9) A mathematician and experimental physicist, Galileo, however, immediately recognized that what he could see of Venus, Jupiter and the moon through his telescope offered crucial evidence that the sun, not Earth, was the center of our solar system. The evidence of his eyes overturned 2,000 years of accepted wisdom about cosmology in which philosophers had conceived the night sky as a system of crystalline spheres.

Moreover, Galileo quickly shared his observations with scientists throughout Europe by openly publishing his data.
“He wrought a change so fundamental for science and for humanity,” says Munich astronomer Pedro Russo, who is global coordinator of the International Year of Astronomy. “For the first time, we realized we were not the center of the universe.”
But his insistence on contradicting traditional cosmology led to his arrest and trial by the Roman Catholic Church. He was forced to recant his views and imprisoned for life. The Vatican did not formally admit that Galileo was correct until 1992. Now Vatican authorities are planning a statue in his honor.
During his life, Galileo is known to have built at least 100 telescopes, mostly as ornate presentation gifts for his patrons — the powerful Medici family of Florence. Only one is known to survive with its optics intact — the humble device now on show at the Franklin Institute.
“We assume it was personally used by Galileo,” says Paolo Galluzzi, director of the science museum in Florence, which loaned the telescope for the exhibit. “Only this one was found among his property at his death. We believe that this is one of the major tools of his work.”
. . .
“Science is fundamentally about establishing truth for yourself,” says Dr. Pompea in Arizona. “People can make observations, take data and establish for themselves the nature of the universe. They don’t have to take it from someone else or read it in a book.”
Like Galileo, “they can see it.”

For the full story, see:
ROBERT LEE HOTZ. “Galileo’s Discoveries, 400 Years Later, Still Open Eyes
Astronomer’s Telescope, on View Outside Italy for the First Time, Helped Expand Perceptions of the Universe.” The Wall Street Journal (Fri., APRIL 10, 2009): A9.
(Note: ellipsis added.)

“Galileo Galilei.” Source of image and caption: online version of the WSJ article quoted and cited above.

“Established Experts Flee in Horror to All Available Caves and Cages”

(p. 96) While science and enterprise open vast new panoramas of opportunity, our established experts flee in horror to all available caves and cages, like so many primitives, terrified by freedom and change.

Source:
Gilder, George. Recapturing the Spirit of Enterprise: Updated for the 1990s. updated ed. New York: ICS Press, 1992.

The Conflict Between Science and Faith

Professor Krauss is a physicist at Arizona State University.

(p. A15) My practice as a scientist is atheistic. That is to say, when I set up an experiment I assume that no god, angel or devil is going to interfere with its course; and this assumption has been justified by such success as I have achieved in my professional career. I should therefore be intellectually dishonest if I were not also atheistic in the affairs of the world.

— J.B.S. Haldane

J.B.S. Haldane, an evolutionary biologist and a founder of population genetics, understood that science is by necessity an atheistic discipline. As Haldane so aptly described it, one cannot proceed with the process of scientific discovery if one assumes a “god, angel, or devil” will interfere with one’s experiments. God is, of necessity, irrelevant in science.
Faced with the remarkable success of science to explain the workings of the physical world, many, indeed probably most, scientists understandably react as Haldane did. Namely, they extrapolate the atheism of science to a more general atheism.
While such a leap may not be unimpeachable it is certainly rational, as Mr. McGinn pointed out at the World Science Festival. Though the scientific process may be compatible with the vague idea of some relaxed deity who merely established the universe and let it proceed from there, it is in fact rationally incompatible with the detailed tenets of most of the world’s organized religions. As Sam Harris recently wrote in a letter responding to the Nature editorial that called him an “atheist absolutist,” a “reconciliation between science and Christianity would mean squaring physics, chemistry, biology, and a basic understanding of probabilistic reasoning with a raft of patently ridiculous, Iron Age convictions.”

For the full commentary, see:

LAWRENCE M. KRAUSS. “OPINION: God and Science Don’t Mix; A scientist can be a believer. But professionally, at least, he can’t act like one.” The Wall Street Journal (Fri., JUNE 26, 2009): A15.
(Note: italics in original.)

Individual Independent “Biohackers” Hope to Advance Science

“Katherine’s Aull’s closet laboratory in her apartment.” Source of photo and caption: online version of the WSJ article quoted and cited below.

The individual independent scientist used to play an important role in the advance of science, but over time mainly disappeared as the academic scientist, supported by large institutions, became dominant. The dominance of funding from incumbent institutions may constrain major innovations, and so I have speculated that it might be beneficial to find ways for it again to be possible for independent individual scholars to play important roles in science.
Astronomy is one area in which this still happens. The article quoted below points to another domain in which individual scholars might be able to make contributions.

(p. A1) In Massachusetts, a young woman makes genetically modified E. coli in a closet she converted into a home lab. A part-time DJ in Berkeley, Calif., works in his attic to cultivate viruses extracted from sewage. In Seattle, a grad-school dropout wants to breed algae in a personal biology lab.

These hobbyists represent a growing strain of geekdom known as biohacking, in which do-it-yourselfers tinker with the building blocks of life in the comfort of their own homes. Some of them buy DNA online, then fiddle with it in hopes of curing diseases or finding new biofuels.
. . .
Ms. Aull, 23 years old, is designing a customized E. coli in the closet of her Cambridge, Mass., apartment, hoping to help with cancer research.
She’s got a DNA “thermocycler” bought on eBay for $59, and an incubator made by combining a styrofoam box with a heating device meant for an iguana cage. A few months ago, she talked about her hobby on DIY Bio, a Web site frequented by biohackers, and her work was noted in New Scientist magazine.
. . .
(p. A14) Phil Holtzman, a college student and part-time DJ at dance parties in Berkeley, Calif., is growing viruses in his attic that he thinks could be useful in medicine someday. Using pipettes and other equipment borrowed from his community college, he extracts viruses called bacteriophage from sewage and grows them in petri dishes. Mr. Holtzman’s goal: Breed them to survive the high temperatures of the human body, where he thinks they might be useful in killing bad bacteria.
He collects partly treated sewage water from a network of underground tunnels in the Berkeley area, jumping a chain-link fence to get to the source. But Mr. Holtzman says his roommates are “really uncomfortable” with him working with sewage water, so he’s trying to find another source of bacteriophage.

For the full story, see:
JEANNE WHALEN. “In Attics and Closets, ‘Biohackers’ Discover Their Inner Frankenstein; Using Mail-Order DNA and Iguana Heaters, Hobbyists Brew New Life Forms; Is It Risky?” Wall Street Journal (Tues., May 12, 2009): A1 & A14.
(Note: ellipses added.)

Our “Patently Absurd” Patent System

(p. A15) The Founders might have used quill pens, but they would roll their eyes at how, in this supposedly technology-minded era, we’re undermining their intention to encourage innovation. The U.S. is stumbling in the transition from their Industrial Age to our Information Age, despite the charge in the Constitution that Congress “promote the Progress of Science and useful Arts, by securing for limited Times to Authors and Inventors the exclusive Right to their respective Writings and Discoveries.”
. . .

Both sides may be right. New empirical research by Boston University law professors James Bessen and Michael Meurer, reported in their book, “Patent Failure,” found that the value of pharmaceutical patents outweighed the costs of pharmaceutical-patent litigation. But for all other industries combined, they estimate that since the mid-1990s, the cost of U.S. patent litigation to alleged infringers ($12 billion in legal and business costs in 1999) is greater than the global profits that companies earn from patents (less than $4 billion in 1999). Since the 1980s, patent litigation has tripled and the probability that a particular patent is litigated within four years has more than doubled. Small inventors feel the brunt of the uncertainty costs, since bigger companies only pay for rights they think the system will protect.
These are shocking findings, but they point to the solution. New drugs require great specificity to earn a patent, whereas patents are often granted to broad, thus vague, innovations in software, communications and other technologies. Ironically, the aggregate value of these technology patents is then wiped out through litigation costs.
Our patent system for most innovations has become patently absurd. It’s a disincentive at a time when we expect software and other technology companies to be the growth engine of the economy. Imagine how much more productive our information-driven economy would be if the patent system lived up to the intention of the Founders, by encouraging progress instead of suppressing it.

For the full commentary, see:
L. GORDON CROVITZ. “OPINION: INFORMATION AGE; Patent Gridlock Suppresses Innovation.” Wall Street Journal (Mon., JULY 14, 2008): A15.
(Note: ellipsis added.)