Science for science writers

Database analysis of plagiarism shows copycat science is not uncommon
Skip Garner began his accidental journey into scientific misconduct investigation after he developed a computer program that could, as he put it, “help a physicist understand medicine.” Typical searches of Medline, a database of medical and other scientific research papers, rely on typed-in keywords, but his program instantly compares blocks of text, essentially performing a 200-word keyword search. “This is a poor man’s hypothesis generator,” says Garner, of the University of Texas Southwestern Medical Center at Dallas. However, his software revealed hundreds of papers where scientists apparently plagiarized from their colleagues, or themselves. (See Science News blog on plagiarism in science.)

So far, more than 50 articles have been retracted — though the abstracts remain on PubMed, the website portal for searching the Medline database. That number will likely increase: Garner’s laboratory is about halfway through scouring the entire Medline database, which collects about 600,000 new entries each year. The number of “duplicate papers with different authors” appears to be on the rise, he says, which may be a function of shrinking research budgets. (The program is available to use for free at www.etblast.org; the site also contains a link to the DejaVu database — an archive of highly similar papers.) The National Institutes of Health is now using Garner’s technology to check the integrity and novelty of grant submissions. —Laura Beil

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Rapid evolution suggest that mutations can explain historical events
Got milk tolerance? Your ability to digest lactose as an adult is relatively new in the human species. And, said John Hawks of the University of Wisconsin-Madison, provides evidence of rapid evolution over the past 10,000 years.

Evolution doesn’t necessarily take millions of years, Hawks said. Humans have been picking up the pace since they left their nomadic lifestyle behind and decided to take up farming. New environments and new lifestyles applied selective pressures.

“10,000 years ago, no one on Earth had blue eyes,” Haws said. “And brains have been shrinking.” Other evidence of recent activity includes immunity to malaria, changes in genes that affect skin pigmentation and changes in hearing-related genes.

Genome-wide, work suggests that 3,000 mutations — or changes in individual letters that make up a person’s genetic information — are being selected for. There are only 40,000 differences between chimps and humans; 12,000 or so have been selected for.

“That is like 3 million years of evolution packed into the past 20,000 years,” Hawks said.

How is that possible? Hawks points to a dramatic increase in population size. As population grows, mutations become more likely to occur. Therefore it is more likely that a mutation that confers an advantage will pop up.

“If you are waiting for these weird things, you have to have a lot of animals because these variations occur rarely,” he said.

As for the most recent trend in evolution, that is harder to know. Selection does need some time to reveal where it’s putting its pressure. —Elizabeth Quill

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Quantifying consciousness on the way to making cyborgs
Virgil Griffith’s life goal is “to create a machine who feels.” Griffith, a doctoral student in computation and neural systems at Caltech, isn’t the only one. During his talk October 18 he revealed that turning people into cyborgs is the secret passion of many of his Caltech peers. (They contend that they are working on implant devices for the injured bodies of people like Vietnam vets, says Griffith, but if you get them drunk they’ll confess that the real aim is to make cyborgs of us all.)

If the speed with which Griffith spoke is any indication of how fast his neurons are firing, his brain is ablaze. These days much of his neural attention is focused on consciousness (which can be labeled mathematically as the Greek letter phi). Griffith sees consciousness as a continuum, with amoebas on the barely conscious end and humans at the other. Conscious beings have both information and synergy — the sum is greater than the parts — and Griffith is trying to create such beings in a land called Polyworld. His virtual creatures do evolve — they can move to find the equivalent of food, mate and flee an attacker. But they certainly won’t be taking over the world anytime soon. Even with his mile-a-minute presentation, there wasn’t time to hear about his other pet projects, which include data mining, cracking security codes and the development of the Wikiscanner, which identifies who makes (the sometimes fraudulent) edits on Wikipedia.

We still do not have a really good theory of consciousness, says Griffith. He believes the most reasonable scientific approach to a theory is built on two pillars: information and integration. For example, a diode looking at a black screen only knows two states: black screen and not black screen. Conscious beings, on the other hand, have a very large number of states: black screen, green screen, red screen and the zillion other not-black screens out there. That’s a lot of information. As for integration, something like a camera (an array of photodiodes) may seem like it is integrated, says Griffith. But you can slice it up without destroying the information. It is not a single entity; it is a collection of “n” independent parts. A brain on the other hand, you cannot slice up (and have it still work). —Rachel Ehrenberg

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Aging studies in yeast show longer lives without starving
“‘Sweet are the uses of adversity,’” University of Montana microbial geneticist Frank Rosenzweig, quoting Shakespeare, reminded science writers assembled for his talk on studies of yeast and aging. That is, after all, how he and many other biologists explain how limiting nutrient intake works to extend life span.

But now, Rosenzweig said, he has been able to increase life span in yeast without any adversity in diet. The long-lived, well-fed yeast he studies, though, are under some duress: They are suspended with algae-derived beads in a column called the immobilized cell reactor. For the yeast, it might be something like living inside a grape.

“Yeast behave differently immobilized than when they’re planktonic” as they usually are when grown in liquid lab cultures, he said. Physiologically, there were clear differences, and Rosenzweig was pretty sure there would be differences in gene expression.

Caloric restriction has been shown to increase longevity in organisms as diverse as yeast, fruit flies, the roundworm C. elegans, mice, and, for the first time this summer, in monkeys. Many explain the life span effect of a less-than-satisfying diet as the body’s active response to a persistent, if slight stressor, Rosenzweig said, citing David Sinclair’s 2005 “unified theory” of caloric restriction. In Sinclair’s view caloric restriction delays development and reduces metabolic rate, which then somehow weaken the body’s glucocorticoid stress hormone response.

A number of genes have been implicated in aging through these “starving yeast” studies, including one called RIM 15. Rosenzweig also thinks that RIM 15 is active in the immobilized yeast and probably is important for the longevity effect. “RIM 15 clearly plays a role in aging,” he said. But in his yeast, RIM 15 seems to be getting turned on inappropriately, he said.

Rosenzweig compared the immobilized, well-fed yeast with calorie-restricted, planktonic yeast. He found many differences in activity of genes involved in cell cycle regulation, nutrient breakdown and storage, the forming of spores (as yeast do during asexual reproduction) and cell wall remodeling (also believed to be involved in spore-forming).

Another tantalizer: Yeast are reproductively flexible. They can do simple asexual division (simple mitotic budding) or the fancier sexual kind (involving recombining genes in the process of meiosis) with others. Sexual reproduction is restricted to when times are tough, when yeast do like other fungal relatives and turn themselves into tough little spores. The activity Rosenzweig saw in the genes involved in sporulation and cell wall remodeling, hints that perhaps spore-forming could go on even when times are not all bad. “If we can show that immobilizers could sporulate in the presence of an excess of nutrients — that would be a big deal,” he said.

Of course, it could be that living in the equivalent of a grape isn’t all it’s cracked up to be. —Eva Emerson

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In election controversies, statistics should count
When you go to the polls in November and make your choices, the votes will be counted and winners will be announced. But will your vote really count? Sometimes not.

Arlene Ash, a Boston University medical statistician who has devoted lots of time to studying errors in the voting process, says things can, and do, routinely go wrong. Ballots are often discounted and problems with hardware and software frequently occur. When electronic voting machinery does jam, it may not leave a paper trail. Poorly designed ballots may also alter the outcome of an election, says Ash, pointing to the hotly contested 2006 election for the U.S. House of Representatives seat in Florida’s 13th Congressional district, where more than 18,000 votes are estimated to have been lost. In some cases, such a loss of votes will not affect the outcome, but in other cases, as with this one, it does. Ash says some simple statistical methods can be used to distinguish cases where such a loss of votes really matters and when it doesn’t.

Ash is leading an effort with the American Statistical Association to help states figure out how to develop better vote auditing procedures. Her group will meet at the organization’s meeting this fall to draft a statement suggesting ways to use statistical analysis to improve election outcomes. —Susan Gaidos

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Mapping emissions may help scientists find missing carbon
The good news: Only a third of the carbon humans send into the atmosphere actually gets caught there. The bad news: Nobody knows where the rest of it is hiding. And if it comes out, things could get much worse.

Kevin Gurney of Purdue University introduced his talk as “How to be more depressing than Al Gore in less than 45 minutes,” and he delivered. The back story is familiar: thanks to human activity, an extra 9 billion metric tons of carbon goes into the global system every year.

But only 3 billion tons ends up in the atmosphere. About 3 billion tons dissolves in the oceans, and the rest is absorbed on land. “That’s very lucky,” Gurney says. “We’re being helped along by the oceans and the biosphere.”

The carbon that ends up in the ocean is fairly well accounted for. But the biosphere is much more complicated. Scientists don’t know exactly where the carbon is going, whether it’s in trees or the soil or what. Climate scientists call it “the missing sink.”

That uncertainty is worrisome. “If that helpful missing sink were to saturate, emissions would look twice as bad as they are now,” Gurney said.

To try to find the missing sink, Gurney and his colleagues made a map of all the fossil fuel emissions in the United States. The map accounts for industry, motor vehicles (“anything that moves”), buildings and power plants. Another map zooms in to find carbon sources at the street level. The whole thing is on Google Earth (you can play with it here), and in a YouTube animation showing daily variations in carbon emissions all over the country. The team hopes to use the maps to sniff out the missing sink by “taking the endpoint and inferring what happened upstream,” Gurney says. —Lisa Grossman

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Droughts gave early humans survival skills for later travels
Humankind may have survived after leaving Africa thanks to seasonal droughts — not because they created a time of scarcity, but because they produced a time of plenty.

University of Texas at Austin anthropologist John Kappelman presented this counterintuitive idea in a talk titled “Blue Highways,” which followed his fossil digs along the Blue Nile tributaries in Ethiopia. Early humans are thought to have taken one of two routes out of Africa: along the Red Sea, or along the Nile Valley and out across Eurasia.

But “there’s been very little testing on the ground, recovering fossils and sites that actually permit us to evaluate either one of those two hypothetical migration events,” Kappelman said.

Most fossils found to date come from the rift valley on the eastern side of the continent, where dry, flat, exposed land makes for good fossil hunting. In the late 1990s, Kappelman started exploring the tributaries on the western side of the Nile, where no one had looked for fossils before. The last record of western exploration there was from British naturalist Sir Samuel Baker in the 1860s.

“This area that was a blank slate for Africa is finally starting to fill in,” Kappelman said.

Samuel Barker noticed something key: The rivers are dry for most of the year, but every summer the water rushes back “like freight cars,” Kappelman said. The torrent of water gouged out deep holes that retained water even during the dry season, leaving a necklace of isolated pools.

And the pools were full of fish. “The fish were literally in a bucket,” Kappelman says. If early humans stayed near these water holes, they could feast all through the dry season without working too hard.

“We think of dry seasons as a time of adversity. We’re proposing that these were the easy times,” Kappelman says.

Kappelman and his team found double-edged blades that were probably used as arrow heads and evidence of hearth fires in several sites around the Nile. He thinks using these water holes could have taught early humans crucial skills, like fishing with nets or bow and arrow, that helped them survive seasonal and climate changes after migration to other parts of the world.

“It honed the behavioral foraging habits of early humans, and taught them to exploit a wide range of food,” Kappelman said. —Lisa Grossman

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Stuff tells snoops what you’re all about
If you have a burning interest in getting to know someone better, maybe you should snoop. You won’t have to look too hard. University of Texas at Austin psychologist Sam Gosling says the books, photos, music playlists, calendars and sports equipment that litter people’s home, offices and even their websites all contribute to the bigger picture of who they really are.

Gosling and his students are researching the way people reveal who they are through their intimate surrounding and their stuff. In their quest, the researchers search bedrooms, bathrooms and office desks looking for three basic types of clues to the occupant’s personality. The first group of clues is what Gosling calls “identity claims,” and consists of posters, photos and other times that make a symbolic statement or are meant to project a specific image. Sometimes these items provide insight into a person’s interests, but other times they say more about what people want others to think of them as opposed to what they’re actually like, Gosling said.

Other items, such as music, books and DVDs, are often used as “feeling regulators” to help people mange their emotions and thoughts These feeling regulators can provide important clues to what a person is really like. Even the traces left behind as a result of everyday actions can reveal who you are. Gosling points to piles of garbage, food wrappers and notebooks, calling this “behavioral residue.” Together, these types of clues reveal a person’s pattern of thinking, feeling and behaving, and are consistent over time.

Gosling and his crew use this information to rate people on five personality traits: openness, conscientiousness, extraversion, agreeableness and neuroticism. Architects are using the information to help design homes where people can re-create a feeling of comfort and well being.

So where would Gosling look if limited to only one place? That would be a person’s website. People will tell you explicitly what they’re like, and there are so few restrictions to what can be put online, he said.
“If you live in a tiny apartment in New York, you can’t display your love of hang gliding, but you can do that on a website.” —Susan Gaidos

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Discovery of Higgs at Large Hadron Collider might not make all physicists happy
Soon physicists at the world’s most powerful particle accelerator will exhale — when beams of protons there finally begin to collide, even though those collisions will not at first be as violent as originally planned. Physicists at the Large Hadron Collider outside Geneva remain confident, though, that the collisions will eventually attain sufficient energy to produce the Higgs boson, says Nobel laureate Steven Weinberg of the University of Texas at Austin.

As Weinberg recounted to science writers attending the Council for the Advancement of Science Writing’s annual symposium, the Higgs would be the crowning achievement of the standard model of particle physics, the equations that precisely describe the known particles of matter and three of nature’s fundamental forces: the strong and weak nuclear forces and electromagnetism. In the most basic version of the standard model, elementary particles such as electrons and quarks have no reason to possess any mass. But clearly they do, a fact explained most conveniently if a currently unknown particle, the Higgs, secretly inhabits the particle zoo.

“It’s not a sure thing that the Higgs will be found, but it’s highly likely,” Weinberg said. “If the Congress had not had the imbecility to cancel the Superconducting Super Collider [in 1993], it would have been discovered long ago here in Texas.”

Discovery of the Higgs at the LHC would not necessarily be a cause for unrestrained celebration, though. “Many of us are terrified that the LHC will discover a Higgs particle and nothing more,” Weinberg said. That would just confirm the standard model, which everybody believes already. It would not point the way to further progress in solving a deeper problem that physics faces — how to add gravity to the unified theory of the other forces.

A clue to solving that mystery might be provided if the LHC’s collisions generate new particles governed by a mathematical constitution known as supersymmetry, or SUSY for short. SUSY math embodies a deep connection between particles that seem unrelated (in physics lingo, their spins differ). Roughly speaking, for each known particle that transmits a force, a partner matterlike particle would exist; each matter particle would have a forcelike partner. These partner particles must be much heavier than those already known to have escaped detection in previous experiments.

If SUSY describes nature correctly, one of the partner particles would very likely be the constituent of dark matter, the unseen mass in the cosmos inferred from observations of gravitational effects not attributable to visible matter. Dark matter cannot be made of ordinary quarks or electrons, Weinberg pointed out; otherwise the recipe of chemical elements cooked up in the early universe would be much different from that now measured. Cosmic observations indicate that about five-sixths of the matter in the universe is made from some form of exotic particle, possibly one predicted by SUSY.

“I can’t imagine anything more exciting and more gratifying than for the Large Hadron Collider to discover particles, artificially created, which in their natural state form the great bulk of the mass of the universe,” said Weinberg. “That would be some headline.” 

SUSY’s discovery might also offer a clue to that grander problem of merging gravity into the family of forces. Many physicists believe that the most promising approach to solving that problem involves the hypothetical ultratiny entities known as superstrings. If all nature’s particles are just various vibration modes of these tiny strings, gravity and the other forces fit together nicely. But despite a quarter century of intense effort, superstring theory has not produced a cohesive and clear guide to testing its fit with all the observable features of physical existence.

“It has developed mathematically, but not to the point where there is any one theory, or to the point where if we had one theory, we would know how to do calculations to predict things like the mass of the electron or the masses of the quarks,” Weinberg said. “I would say that although there has been theoretical progress, I find it disappointing. “

It may be that a SUSY discovery at the LHC will help, but Weinberg’s hopes are not high, as any LHC-SUSY clue would be very indirect.

“It’s a pity that superstring theory hasn’t developed better,” he said. “I still think it’s the best hope we have. I don’t know of anything else. My own work very recently has been trying to develop an alternative to superstring theory as a way of making sense out of quantum gravity at very high energies, but even though I’m working on this I still find superstring theory more attractive. But not attractive enough.” —Tom Siegfried