Sharon Begley's "Science Journal"

Re: Sharon Begley's "Science Journal"

Postby admin » Tue Oct 29, 2019 2:23 am

Very Old Eggs Reveal A Fast, Changing Path Through Evolution
by Sharon Begley
August 5, 2005; Page B1

Biologists studying how species change over the eons have always been hampered by the little problem of previous generations of a species being, well, dead. Sure, you can infer something about what a creature was like from fossils, but fossils generally fail to preserve much except bone. As a result, some of an animal's most interesting features vanish into the dust of time.

But these days, not even death is forever. A few years ago, biologist W. Charles Kerfoot was examining "cores" -- basically, muck deposited decades earlier -- in a Michigan lake. Lo and behold, he and his colleagues discovered eggs, and not just any eggs. They had been laid long ago by tiny creatures (mostly insects and crustaceans) that no longer lived in the lake. Even better, there was still life in the eggs. Under the right conditions, they would hatch.

"We knew right away that we were founding a whole new field," says Prof. Kerfoot of Michigan Technological University, Houghton. "I call it 'resurrection ecology.' " By hatching the eggs one muddy layer at a time, he realized, he could compare one generation with another to investigate evolutionary change.

It has always struck me as odd that evolutionary biology is caricatured by opponents as being static, a tower of unchanging (and unchangeable) dogma dating from Darwin. In fact, it is full of competing ideas, new discoveries and bickering scientists.

In his resurrection work, Prof. Kerfoot focuses on eggs of a tiny water flea, Daphnia retrocurva, from Portage Lake. He sieves them out of the deep muck, pops them into an incubator, and is a proud papa a few days later. "We've resurrected eggs from 300 years ago," he says. "That's 3,000 generations, equivalent to 120,000 years of evolution for humans."

And evolve is just what the little guys did. Daphnia share Portage Lake with creatures great and small, including predators, such as the shrimplike Leptodora. Prof. Kerfoot wondered whether the daphnia were doing something that biologists had hypothesized, but had struggled to prove -- namely, that the Red Queen in "Alice in Wonderland" was describing evolution when she told Alice, "It takes all the running you can do, to keep in the same place."

In evolutionary biology, the Red Queen Hypothesis means predators and prey must evolve like heck just to keep from falling behind (and to remain able to hunt or elude capture).

Sure enough, daphnia eggs taken from muck with a high population of predators hatched into veritable warriors: They had long spikes on their tails and an impressive helmet, the better to make themselves too prickly to eat. "But as predators became less abundant, spine length and helmets became smaller," says Prof. Kerfoot. "Evidence for the Red Queen is very strong here. It looks like these populations really are changing just to stay in place."

He isn't the only scientist tinkering with classic Darwinism. The reigning theory of the molecular basis of evolution is that whether a mutation takes hold depends solely on natural selection: beneficial mutations last, detrimental ones disappear. But something else may be at work.

If a slew of mutations show up at once, more of them endure, scientists led by Bruce Lahn of the University of Chicago report in the July issue of Trends in Genetics. In my world, that's like an editor flooding you with dozens of suggestions for changes in your column. You're unable to fend them off, so more survive than if the requests come one-by-one over time.

Thousands of scientific papers presume that the fraction of retained mutations depends solely on how beneficial they are. "This theory has been the workhorse of molecular evolution," says Prof. Lahn. His discovery that a gene accepts more mutations when many hit at once is counterintuitive and controversial; a handful of journals actually rejected his paper. But if he is right, the molecular underpinning of evolutionary biology is itself in need of mutation.

Another pillar of evolution is that natural selection sculpts species toward some ideal fitness. In fact, what's "fit" is a matter of opinion. Consider the males of a little reptile called the side-blotched lizard, which come in three kinds. Orange-throated giants beat up on their diminutive blue-throated rivals, which in turn lord it over tiny yellow-throated guys. You'd think the yellows would eventually die out.

But natural selection is more forgiving than that. The yellows are so beneath the contempt of the oranges that they are able to steal assignations with females attracted to the oranges' territory. As a result, the yellows reproduce and survive.

Just as the game rock-paper-scissors has no single winning strategy -- it depends what your opponents choose -- so in lizard-dom there is more than one route to evolutionary fitness.

Critics contend that evolutionary biology is a haughty club that forces members "to circle the wagons against any and all would-be challengers, and to achieve consensus on the most contentious issues," Michael Shermer, director of the Skeptics Society, has written. "This conclusion is so wrong that it cannot have been made by anyone who has ever attended a scientific conference," or dipped so much as a toe into the roiling waters of evolutionary research.
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Re: Sharon Begley's "Science Journal"

Postby admin » Tue Oct 29, 2019 2:23 am

Water-Flea Case Shows That Ability to Adapt Is What's Really Innate
by Sharon Begley
April 22, 2005

HELLS ANGELS have nothing on some water fleas. While these tiny crustaceans are best known for their uncanny ability to skim atop the water's surface, some also boast a "helmet" that makes them tough for a predator to swallow. But other fleas with the same DNA -- clones of the helmeted ones -- have no such armor. And the reason is shaking up the world of genetics.

The helmeted fleas live in a lab aquarium to which scientists added the chemical scent of fish, fleas' main predator. The fleas without helmets come from an aquarium with no fish in sight (or smell). The difference between genetic duplicates reflects the power of environment: It can elicit markedly different traits from the same DNA.

I have written in the past about how environment -- ranging from experiences to diet -- can alter DNA, putting the molecular version of a "not in service" sign on our genes so they remain silent and, as geneticists say, unexpressed. The water flea and other examples of "developmental plasticity" show that a given genotype can develop in any of several ways depending on what environment it's in. And that makes the notion of "innate" look more and more inane.

"If you have a gene with some purported effect, that effect depends on the environment in which it's expressed," says Eric Turkheimer of the University of Virginia. "Anything that looks genetic, because people with that gene always turn out a certain way, might not really be a genetic effect but an artifact of how few environments people with that gene have been exposed to. Once a new environment comes along it can change everything, so what you thought was a fixed effect of a gene isn't."

OAK-TREE caterpillars that hatch in the spring, for instance, eat oak blossoms and grow up to look a bit like flowers. Caterpillars with the same genome, but which hatch in the summer, eat leaves and grow up to look like twigs. The different composition of blossoms and leaves affects what traits the caterpillars' genes produce. If you had never seen spring caterpillars, you would think their genome produces only twiggy caterpillars. But the twiggy look is, as Prof. Turkheimer says, only an artifact of how few environments those caterpillars have been exposed to, not genetic determinism.

In the past few years, scientists have found the first examples of such an effect in people, discovering how life experiences can alter gene-based traits once thought to be innate.

A certain form of a gene called MAOA, for instance, was so closely linked to aggression and criminality that it became known as a "violence gene." In a 2002 study, however, an international team of researchers followed 442 male New Zealanders who carried either of two versions of the MAOA gene. One version produces small amounts of MAOA, an enzyme active in the brain; a dearth of MAOA had been linked to criminality. The other produces high amounts of MAOA, as in a normal brain.

But the study found that men with the low-activity ("violent") form of the gene were no more likely to grow up to be antisocial or violent -- unless they had also been neglected or abused as children. In that case, they were about twice as likely to engage in persistent fighting, bullying, theft and vandalism. If they had the "violence gene" but were raised in a loving and nonabusive family, they turned out fine. A 2004 study by different scientists confirmed this.

IN A 2003 study, geneticists examined claims that one form of a gene called 5-HTT is associated with depression and suicide. Instead, they found that people who carry this form are no more likely to suffer from depression than people with the "healthy" variant -- unless they also experience deeply stressful events. Two papers in 2004 confirmed this.

"These genes were not connected with aggression or depression, respectively, in the absence of exposure to environmental risk," says behavioral geneticist Terrie Moffitt of the University of Wisconsin, Madison, and King's College London. "That different environments can produce different [traits] from the same genotype is now emerging in many fields of health research."

For example, she says, studies show that "the effect of a gene on cholesterol levels depends on environmental risk -- high or low dietary fat. The effect of a gene on gum disease depends on whether you smoke or not."

Exactly how life experiences affect DNA has been most precisely worked out in lab animals. Last summer, Michael Meaney of McGill University, Montreal, and colleagues reported that a gene that shapes how fearful, jumpy and neurotic a rat is can be altered by how regularly its mother licks and grooms it. Maternal care changes the chemistry of a "neuroticism gene," and the rat grows up to be mellow and curious. The genetic trait of neuroticism -- deemed innate because scientists had found a gene "for" it -- is reversible by environment.

"The whole subject of what counts as innate has just exploded," says science historian and physicist Evelyn Fox Keller of the Massachusetts Institute of Technology. "Historically, nature/nurture divided what was fixed from what could be changed. But what our biology really gives us is our plasticity, our ability to respond to our experiences. That's what's innate."
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Re: Sharon Begley's "Science Journal"

Postby admin » Tue Oct 29, 2019 2:24 am

Why Just Detecting Hidden Explosives May Not Cut Deaths
by Sharon Begley
July 8, 2005; Page B1

The explosions that ripped through three subways and a bus in central London yesterday underlined the urgency of determining what measures can reduce casualties from terrorist attacks. Although researchers have made strides in developing technologies to detect explosives at a distance, there is grave concern that such progress still falls short of protecting the public.

New research suggests that even perfect detection may not substantially lower the death toll from bombs set off in urban areas. And in some cases, terrorism experts now recognize a counterintuitive possibility: Warnings may lead to more fatalities.

Americans have an abiding belief in technological fixes, and that faith is now finding expression in the war on terror. The Pentagon's Defense Advanced Research Projects Agency recently commissioned the National Research Council to examine technologies able to detect suicide bombers before they reach their target. In its 2004 report, the NRC concluded that a number of sophisticated sensors, from millimeter-wave imagers to vapor-plume detectors, can detect hidden explosives more than 90 feet away, although none is perfectly specific (no false hits) or perfectly sensitive (no misses).

If, for example, a suicide bomber walked into a crowded plaza, "standoff" bomb detectors might well pick up an unambiguous signal. A terahertz imaging system could spy the telltale wires and explosives in 30 milliseconds, and ultraviolet-visible spectroscopy now in development could sniff out the trace vapors emitted by the ethylene glycol dinitrate in the plastique. Let's say the sensors alerted a security guard, who spotted the terrorist and yelled to the crowd, "Run, it's a bomb!"

In this scenario, the explosives-detection technology worked perfectly. An alarm sounded before a detonation. People were able to run or throw themselves to the ground. But when the bomber exploded, the casualty toll might not have been any less than if the sensors weren't deployed. Even worse, in some situations the intervention -- "Run!" or "Get down!" -- could lead to more casualties, conclude Edward Kaplan of the Yale University School of Management, New Haven, Conn., and Moshe Kress of the Naval Postgraduate School, Monterey, Calif., in a new study.

Even under the best-case assumption of sensors that are perfect, covert and cheap enough to deploy at every city intersection or throughout plazas, early detection unambiguously lowers the casualty count only if the bomber fails to detonate. Ensuring that outcome probably requires ubiquitous deployment of perfect sharpshooters, says Prof. Kress.

Early detection can backfire because of the grisly fact that human beings act as human shields. "There is a trade-off between crowd size and crowd blocking," says Prof. Kaplan. A large, dense crowd puts more people in harm's way, but "the probability of being exposed to a bomb fragment declines exponentially with the size of the crowd." As a crowd flees, there are fewer people near the bomber to absorb the fragments (as when a soldier falls on a grenade) and more people, unshielded, farther away. Simple geometry shows that you can hit more people at a radius 20 feet from a bomber than you can five feet from him.

"If the first ring of unshielded people is at a greater radius, there are more of them, and more will be hit," says Prof. Kaplan.

The same effect occurs if people throw themselves to the ground. That minimizes each person's exposed area, but also at the expense of decreasing human shielding. For bombs with 500 or more fragments (in Israel, 1,000 is typical), "hit the deck" can raise rather than cut casualties. If scores of people fall from an average height of five feet eight inches to 1.5 feet, the scientists calculate, casualties could rise as high as 50 from 37.

"We are not suggesting that standoff detection has no use, but having the ability to detect explosives doesn't automatically make you safe," says Prof. Kaplan. Since the conclusions reflect a best-case scenario -- perfect sensors do not yet exist -- casualty reduction with real-world devices would be even less than the researchers calculate in their study, published online this week in Proceedings of the National Academy of Sciences.

The limits of technology are becoming apparent to those leading the war on terrorism. "Response [to detection of a suicide bomber] is a very difficult problem," says Todd Brethauer, science adviser to the U.S. Interagency Technical Support Working Group. "While there are tremendous efforts under way, don't expect a miracle near term."

Instead, pre-empting bombers before they reach their target and destroying explosives labs is likely to bring a greater payoff. Israel suffered 26 suicide attacks in 2003 and 15 in 2004, a decline it attributes in part to earlier interdictions.

Fathoming who suicide bombers are, what motivates them, and what can stop them has become particularly urgent now that such attacks in Iraq have reached unprecedented levels, with more than 200 this year. That has prompted concern that a generation of terrorists is learning skills it can bring to the U.S. and Europe. Science and experience show that last-minute defense is the wrong way to play this lethal game.
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Re: Sharon Begley's "Science Journal"

Postby admin » Tue Oct 29, 2019 2:25 am

Why George Gershwin May Have Called It 'Rhapsody in Blue'
by Sharon Begley
Wall Street Journal, Science Journal
June, 2002

Like many artists, Carol Steen paints what she sees. But judging by the canvases that fill her loft in Manhattan's NoHo neighborhood, her vision is, well, unusual.

This series of canvases, she explains one afternoon, depicts the shapes and colors that appeared to her -- usually in her mind's eye but sometimes suspended before her -- when she underwent acupuncture treatments. In one, a luminous blue orb weeps emerald crescents. Nearby hang paintings whose images she saw while listening to music: flowing shapes in green, teal, gold and violent.

Ms. Steen is a synesthete, someone whose brain is "cross-activated" so that one sensory experience (feeling or hearing, for instance) triggers a wholly different one (seeing). The result is "a world in multimedia," she says. "Synesthesia is a gift."

Brain researchers couldn't agree more. Because the condition promises to shed light on puzzles ranging from the roots of creativity to the origins of language, says V.S. Ramachandran of the University of California, San Diego, "synesthesia is a gold mine for neuroscience."

He estimates that as many as one person in 200 has synesthesia, which can take as many forms as there are sensory pairings. Novelist Vladimir Nabokov wrote that the sound of a long A in English "has for me the tint of weathered wood, but a French A evokes polished ebony." George Gershwin saw notes in color (ever wonder about "Rhapsody in Blue"?), as did Franz Liszt, requesting of musicians, "Gentleman, a little bluer if you please." For Ms. Steen, the radio creates a kaleidoscope so riveting she prefers to turn off the music when she parks her car. In a rare form, tastes have shapes. One synesthete says a roast chicken in citrus sauce is done to a turn when it is "pointed."

In its most common form, synesthesia makes you always see a particular letter or digit in a particular color. To author Patricia Lynne Duffy, P is invariably pale yellow, R is orange, 5 is purple. "When I think of the alphabet, it's like a sloping scale of brightly colored letters," says Ms. Duffy, whose book "Blue Cats and Chartreuse Kittens" describes her world. One medical professor tells psychologist Thomas Palmeri of Vanderbilt University that although color letters slow down his reading, they help his memory: He breezed through anatomy because the distinct colors of the terms acted as mnemonics.

For decades neurologists figured people like the professor were crazy or lying. Finally, though, brain imaging is establishing the reality of synesthesia. In April, scientists at Goldsmiths College in London reported on MRI scans of synesthetes who hear spoken words in color. The brain area that processes color when you or I stare at a cerulean sky or an emerald fairway is, in these synesthetes, also activated by the spoken word.

Synesthesia probably strikes when the brain takes E.M. Forster's maxim "only connect" to extremes. Everyone is born with extra connections, or synapses. Most get pruned away in childhood. In synesthetes, the extra synapses seem to remain, producing a rich web of circuitry that connects the cortex's color processor to the numeral area next door, or links touch regions to vision regions. Since synesthesia runs in families, defective pruning might reflect a genetic mutation.

While researchers have fun studying people who see Middle C, they're after bigger game. "We hope that synesthesia can give us a window into processes that occur in everyone's brain," says Edward Hubbard of the University of California, San Diego.

Chief among them: creativity (which, after all, is seeing connections that no one before you has) and metaphor (linking seemingly unrelated concepts, as in "Juliet is the sun"). Scientists suspect that crossed wires in the brain's angular gyrus, where information from different senses converges, underlies synesthesia. Not coincidentally, perhaps, when this structure is damaged, your brain can't understand metaphor.

Synesthesia may even explain one of the great mysteries of science -- how language originated. Try this: Draw one spiky shape and one rounded, amoeba-like one. Pretend that, in a lost language, one is a "kiki" and one a "shoosha." Which is which?

Almost everyone says the spiky shape is the kiki. "The spikes mimic the sharp sound of "kiki," says Dr. Ramachandran. If appearances and sounds are really linked in a non-arbitrary way in regular folks just as they are in synesthetes, then early humans could have used sound to represent objects and actions in a way the guy in the next cave would understand. In that case synesthesia, far from being a mere curiosity, offers a window onto the most human of human traits.
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Re: Sharon Begley's "Science Journal"

Postby admin » Tue Oct 29, 2019 2:25 am

Yes, Evolution Still Has Unanswered Questions; That's How Science Is
by Sharon Begley
June 3, 2005; Page B1

Compared with fields like genetics and neuroscience and cosmology, botany comes up a bit short in the charisma department. But when scientists announced last week that they had figured out how plants grow, one had to take note, not only because of the cleverness required to crack a puzzle that dates to 1885, but because of what it says about controversy and certainty in science -- and about the evolution debate.

In 1885, scientists discovered a plant-growth hormone and called it auxin. Ever since, its mechanism of action had been a black box, with scientists divided into warring camps about precisely how the hormone works. Then last week, in a study in Nature, biologist Mark Estelle of Indiana University, Bloomington, and colleagues reported that auxin links up with a plant protein called TIR1, and together the pair binds to a third protein that silences growth-promoting genes. The auxin acts like a homing beacon for enzymes that munch on the silencer. Result: The enzymes devour the silencer, allowing growth genes to turn on.

Yet biology classes don't mention the Auxin Wars. Again and again, impressionable young people are told that auxin promotes plant growth, when the reality is more complex and there has been raging controversy over how it does so.

Which brings us to evolution. Advocates of teaching creationism (or its twin, intelligent design) have adopted the slogan, "Teach the controversy." That sounds eminently sensible. But it is disingenuous. For as the auxin saga shows, virtually no area of science is free of doubt or debate or gaps in understanding.

"Every scientific theory is constantly under scrutiny and has unknowns at its edges," says physicist Lawrence Krauss of Case Western Reserve University, Cleveland. "Singling out evolution makes it appear that evolution is suspect, which it isn't."

For instance, you can start a bar fight if you ask astronomers what the dark matter that pervades the universe is. But up-to-date textbooks rightly note that dark matter exists, even though its composition remains an enigma.

Physicists have been known to sputter in rage over the interpretation of quantum mechanics, which underlies all of modern electronics and often is called the most successful theory in the history of science (physicists aren't known for low self-esteem). Yet quantum mechanics also says the subatomic realm is inherently uncertain. It is impossible, even in principle, to predict when, say, a radioactive atom will decay. All you know is the probability, perhaps 50-50, that it will decay in the next hour. What has happened to the atom after an hour?

One camp holds that it exists in a fuzzy, indeterminate state until you peek at it, arguing that no phenomenon is a phenomenon until it is observed. Another holds that the atom decays in this world but remains intact in a new, parallel world. Controversy galore, but not enough to make anyone seriously doubt quantum theory.

Even some basics of physics are disputed if you dig deep enough. Introductory courses teach that mass is conserved, for instance. "But that couldn't be more wrong," says Frank Wilczek of Massachusetts Institute of Technology, who shared the 2004 Nobel Prize in physics. "Massive particles such as protons are built of quarks and gluons, which have zero mass [unless they are moving]. Mass is far from conserved."

The law that "for every action there is an equal and opposite reaction" isn't universally true either. "It fails for magnetic forces between charged particles," Prof. Wilczek says.

Teach the controversy? Then try the one over water. After the assertion that water's formula is H2O, add an asterisk: There is (controversial) evidence that it is sometimes H1.5O.

The funny thing about demands to "teach the controversy" in evolution is that creationists are focusing on the wrong things. They argue that evolution is wrong because there are no transitional fossils showing how one species evolved into another, for instance. But paleontologists have found fossils that are transitional between whales and their terrestrial ancestors, and between finned creatures and limbed ones.

Creationists also claim that evolution can't explain how small genetic changes could produce new species (rather than the same species with new traits, such as bacteria resistant to antibiotics). But the new field of "evo-devo" shows how minor genetic changes can lead to major structural ones, such as the presence or absence of wings or legs, notes biologist Sean Carroll of the University of Wisconsin, Madison.

Gaps in knowledge? Of course. Every ongoing field of science has them. Physicists can't explain why elementary particles have the masses and other traits they do, but that doesn't invalidate the basic theory of matter. It just means scientists have to keep trying. Say "God did it" if you like, but that isn't science.

Evolution is as well-established by empirical observation as other sciences. There is no serious debate that evolution happens, only deeper questions (left to college and graduate school), such as whether it proceeds gradually or in spasms. "It's dishonest to single out evolution," Prof. Carroll says, "when the very nature of science is to have unresolved questions."
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