Arquivo da tag: Teleologia

Há um limite para avanços tecnológicos? (OESP)

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16 Maio 2016 | 03h 00

Está se tornando popular entre políticos e governos a ideia que a estagnação da economia mundial se deve ao fato de que o “século de ouro” da inovação científica e tecnológica acabou. Este “século de ouro” é usualmente definido como o período de 1870 a 1970, no qual os fundamentos da era tecnológica em que vivemos foram estabelecidos.

De fato, nesse período se verificaram grandes avanços no nosso conhecimento, que vão desde a Teoria da Evolução, de Darwin, até a descoberta das leis do eletromagnetismo, que levou à produção de eletricidade em larga escala, e telecomunicações, incluindo rádio e televisão, com os benefícios resultantes para o bem-estar das populações. Outros avanços, na área de medicina, como vacinas e antibióticos, estenderam a vida média dos seres humanos. A descoberta e o uso do petróleo e do gás natural estão dentro desse período.

São muitos os que argumentam que em nenhum outro período de um século – ao longo dos 10 mil anos da História da humanidade – tantos progressos foram alcançados. Essa visão da História, porém, pode e tem sido questionada. No século anterior, de 1770 a 1870, por exemplo, houve também grandes progressos, decorrentes do desenvolvimento dos motores que usavam o carvão como combustível, os quais permitiram construir locomotivas e deram início à Revolução Industrial.

Apesar disso, os saudosistas acreditam que o “período dourado” de inovações se tenha esgotado e, em decorrência, os governos adotam hoje medidas de caráter puramente econômico para fazer reviver o “progresso”: subsídios a setores específicos, redução de impostos e políticas sociais para reduzir as desigualdades, entre outras, negligenciando o apoio à ciência e tecnologia.

Algumas dessas políticas poderiam ajudar, mas não tocam no aspecto fundamental do problema, que é tentar manter vivo o avanço da ciência e da tecnologia, que resolveu problemas no passado e poderá ajudar a resolver problemas no futuro.

Para analisar melhor a questão é preciso lembrar que não é o número de novas descobertas que garante a sua relevância. O avanço da tecnologia lembra um pouco o que acontece às vezes com a seleção natural dos seres vivos: algumas espécies são tão bem adaptadas ao meio ambiente em que vivem que deixam de “evoluir”: esse é o caso dos besouros que existiam na época do apogeu do Egito, 5 mil anos atrás, e continuam lá até hoje; ou de espécies “fósseis” de peixes que evoluíram pouco em milhões de anos.

Outros exemplos são produtos da tecnologia moderna, como os magníficos aviões DC-3, produzidos há mais de 50 anos e que ainda representam uma parte importante do tráfego aéreo mundial.

Mesmo em áreas mais sofisticadas, como a informática, isso parece estar ocorrendo. A base dos avanços nessa área foi a “miniaturização” dos chips eletrônicos, onde estão os transistores. Em 1971 os chips produzidos pela Intel (empresa líder na área) tinham 2.300 transistores numa placa de 12 milímetros quadrados. Os chips de hoje são pouco maiores, mas têm 5 bilhões de transistores. Foi isso que permitiu a produção de computadores personalizados, telefones celulares e inúmeros outros produtos. E é por essa razão que a telefonia fixa está sendo abandonada e a comunicação via Skype é praticamente gratuita e revolucionou o mundo das comunicações.

Há agora indicações que essa miniaturização atingiu seus limites, o que causa uma certa depressão entre os “sacerdotes” desse setor. Essa é uma visão equivocada. O nível de sucesso foi tal que mais progressos nessa direção são realmente desnecessários, que é o que aconteceu com inúmeros seres vivos no passado.

O que parece ser a solução dos problemas do crescimento econômico no longo prazo é o avanço da tecnologia em outras áreas que não têm recebido a atenção necessária: novos materiais, inteligência artificial, robôs industriais, engenharia genética, prevenção de doenças e, mais do que tudo, entender o cérebro humano, o produto mais sofisticado da evolução da vida na Terra.

Entender como uma combinação de átomos e moléculas pode gerar um órgão tão criativo como o cérebro, capaz de possuir uma consciência e criatividade para compor sinfonias como as de Beethoven – e ao mesmo tempo promover o extermínio de milhões de seres humanos –, será provavelmente o avanço mais extraordinário que o Homo sapiens poderá atingir.

Avanços nessas áreas poderiam criar uma vaga de inovações e progresso material superior em quantidade e qualidade ao que se produziu no “século de ouro”. Mais ainda enfrentamos hoje um problema global, novo aqui, que é a degradação ambiental, resultante em parte do sucesso dos avanços da tecnologia do século 20. Apenas a tarefa de reduzir as emissões de gases que provocam o aquecimento global (resultante da queima de combustíveis fósseis) será uma tarefa hercúlea.

Antes disso, e num plano muito mais pedestre, os avanços que estão sendo feitos na melhoria da eficiência no uso de recursos naturais é extraordinário e não tem tido o crédito e o reconhecimento que merecem.

Só para dar um exemplo, em 1950 os americanos gastavam, em média, 30% da sua renda em alimentos. No ano de 2013 essa porcentagem havia caído para 10%. Os gastos com energia também caíram, graças à melhoria da eficiência dos automóveis e outros fins, como iluminação e aquecimento, o que, aliás, explica por que o preço do barril de petróleo caiu de US$ 150 para menos de US$ 30. É que simplesmente existe petróleo demais no mundo, como também existe capacidade ociosa de aço e cimento.

Um exemplo de um país que está seguindo esse caminho é o Japão, cuja economia não está crescendo muito, mas sua população tem um nível de vida elevado e continua a beneficiar-se gradualmente dos avanços da tecnologia moderna.

*José Goldemberg é professor emérito da Universidade de São Paulo (USP) e é presidente da Fundação de Amparo à Pesquisa do Estado de São Paulo (Fapesp)

Flap Over Study Linking Poverty to Biology Exposes Gulfs Among Disciplines (Chronicle of Higher Education)

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February 1, 2013

Flap Over Study Linking Poverty to Biology Exposes Gulfs Among Disciplines 1

 Photo: iStock.

A study by two economists that used genetic diversity as a proxy for ethnic and cultural diversity has drawn fierce rebuttals from anthropologists and geneticists.

By Paul Voosen

Oded Galor and Quamrul Ashraf once thought their research into the causes of societal wealth would be seen as a celebration of diversity. However it has been described, though, it has certainly not been celebrated. Instead, it has sparked a dispute among scholars in several disciplines, many of whom are dubious of any work linking societal behavior to genetics. In the latest installment of the debate, 18 Harvard University scientists have called their work “seriously flawed on both factual and methodological grounds.”

Mr. Galor and Mr. Ashraf, economists at Brown University and Williams College, respectively, have long been fascinated by the historical roots of poverty. Six years ago, they began to wonder if a society’s diversity, in any way, could explain its wealth. They probed tracts of interdisciplinary data and decided they could use records of genetic diversity as a proxy for ethnic and cultural diversity. And after doing so, they found that, yes, a bit of genetic diversity did seem to help a society’s economic growth.

Since last fall, when the pair’s work began to filter out into the broader scientific world, their study has exposed deep rifts in how economists, anthropologists, and geneticists talk—and think. It has provoked calls for caution in how economists use genetic data, and calls of persecution in response. And all of this happened before the study was finally published, in the American Economic Review this month.

“Through this analysis, we’re getting a better understanding of how the world operates in order to alleviate poverty,” Mr. Ashraf said. Any other characterization, he added, is a “gross misunderstanding.”

‘Ethical Quagmires’

A barrage of criticism has been aimed at the study since last fall by a team of anthropologists and geneticists at Harvard. The critique began with a short, stern letter, followed by a rejoinder from the economists; now an expanded version of the Harvard critique will appear in February inCurrent Anthropology.

Fundamentally, the dispute comes down to issues of data selection and statistical power. The paper is a case of “garbage in, garbage out,” the Harvard group says. The indicators of genetic diversity that the economists use stem from only four or five independent points. All the regression analysis in the world can’t change that, said Nick Patterson, a computational biologist at Harvard and MIT’s Broad Institute.

“The data just won’t stand for what you’re claiming,” Mr. Patterson said. “Technical statistical analysis can only do so much for you. … I will bet you that they can’t find a single geneticist in the world who will tell them what they did was right.”

In some respects, the study has become an exemplar for how the nascent field of “genoeconomics,” a discipline that seeks to twin the power of gene sequencing and economics, can go awry. Connections between behavior and genetics rightly need to clear high bars of evidence, said Daniel Benjamin, an economist at Cornell University and a leader in the field who has frequently called for improved rigor.

“It’s an area that’s fraught with an unfortunate history and ethical quagmires,” he said. Mr. Galor and Mr. Ashraf had a creative idea, he added, even if all their analysis doesn’t pass muster.

“I’d like to see more data before I’m convinced that their [theory] is true,” said Mr. Benjamin, who was not affiliated with the study or the critique. The Harvard critics make all sorts of complaints, many of which are valid, he said. “But fundamentally the issue is that there’s just not that much independent data.”

Claims of ‘Outsiders’

The dispute also exposes issues inside anthropology, added Carl Lipo, an anthropologist at California State University at Long Beach who is known for his study of Easter Island. “Anthropologists have long tried to walk the line whereby we argue that there are biological origins to much of what makes us human, without putting much weight that any particular attribute has its origins in genetics [or] biology,” he said.

The debate often erupts in lower-profile ways and ends with a flurry of anthropologists’ putting down claims by “outsiders,” Mr. Lipo said. (Mr. Ashraf and Mr. Galor are “out on a limb” with their conclusions, he added.) The angry reaction speaks to the limits of anthropology, which has been unable to delineate how genetics reaches up through the idiosyncratic circumstances of culture and history to influence human behavior, he said.

Certainly, that reaction has been painful for the newest pair of outsiders.

Mr. Galor is well known for studying the connections between history and economic development. And like much scientific work, his recent research began in reaction to claims made by Jared Diamond, the famed geographer at the University of California at Los Angeles, that the development of agriculture gave some societies a head start. What other factors could help explain that distribution of wealth? Mr. Galor wondered.

Since records of ethnic or cultural diversity do not exist for the distant past, they chose to use genetic diversity as a proxy. (There is little evidence that it can, or can’t, serve as such a proxy, however.) Teasing out the connection to economics was difficult—diversity could follow growth, or vice versa—but they gave it a shot, Mr. Galor said.

“We had to find some root causes of the [economic] diversity we see across the globe,” he said.

They were acquainted with the “Out of Africa” hypothesis, which explains how modern human beings migrated from Africa in several waves to Asia and, eventually, the Americas. Due to simple genetic laws, those serial waves meant that people in Africa have a higher genetic diversity than those in the Americas. It’s an idea that found support in genetic sequencing of native populations, if only at the continental scale.

Combining the genetics with population-density estimates—data the Harvard group says are outdated—along with deep statistical analysis, the economists found that the low and high diversity found among Native Americans and Africans, respectively, was detrimental to development. Meanwhile, they found a sweet spot of diversity in Europe and Asia. And they stated the link in sometimes strong, causal language, prompting another bitter discussion with the Harvard group over correlation and causation.

An ‘Artifact’ of the Data?

The list of flaws found by the Harvard group is long, but it boils down to the fact that no one has ever made a solid connection between genes and poverty before, even if genetics are used only as a proxy, said Jade d’Alpoim Guedes, a graduate student in anthropology at Harvard and the critique’s lead author.

“If my research comes up with findings that change everything we know,” Ms. d’Alpoim Guedes said, “I’d really check all of my input sources. … Can I honestly say that this pattern that I see is true and not an artifact of the input data?”

Mr. Ashraf and Mr. Galor found the response to their study, which they had previewed many times over the years to other economists, to be puzzling and emotionally charged. Their critics refused to engage, they said. They would have loved to present their work to a lecture hall full of anthropologists at Harvard. (Mr. Ashraf, who’s married to an anthropologist, is a visiting scholar this year at Harvard’s Kennedy School.) Their gestures were spurned, they said.

“We really felt like it was an inquisition,” Mr. Galor said. “The tone and level of these arguments were really so unscientific.”

Mr. Patterson, the computational biologist, doesn’t quite agree. The conflict has many roots but derives in large part from differing standards for publication. Submit the same paper to a leading genetics journal, he said, and it would not have even reached review.

“They’d laugh at you,” Mr. Patterson said. “This doesn’t even remotely meet the cut.”

In the end, it’s unfortunate the economists chose genetic diversity as their proxy for ethnic diversity, added Mr. Benjamin, the Cornell economist. They’re trying to get at an interesting point. “The genetics is really secondary, and not really that important,” he said. “It’s just something that they’re using as a measure of the amount of ethnic diversity.”

Mr. Benjamin also wishes they had used more care in their language and presentation.

“It’s not enough to be careful in the way we use genetic data,” he said. “We need to bend over backwards being careful in the way we talk about what the data means; how we interpret findings that relate to genetic data; and how we communicate those findings to readers and the public.”

Mr. Ashraf and Mr. Galor have not decided whether to respond to the Harvard critique. They say they can, point by point, but that ultimately, the American Economic Review’s decision to publish the paper as its lead study validates their work. They want to push forward on their research. They’ve just released a draft study that probes deeper into the connections between genetic diversity and cultural fragmentation, Mr. Ashraf said.

“There is much more to learn from this data,” he said. “It is certainly not the final word.”

Human hands evolved for punching (Discovery News)

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Analysis by Jennifer Viegas

Wed Dec 19, 2012 06:16 PM ET

Fist

Credit: iStockPhoto

Human hands evolved so that men could make fists and fight, and not just for manual dexterity, new research finds.

The study, published in the Journal of Experimental Biology, adds to a growing body of evidence that humans are among the most aggressive and violent animals on the planet.

“With the notable exception of bonobos, great apes are a relatively aggressive group of mammals,” lead author David Carrier told Discovery News. “Although some primatologists may argue that chimpanzees are the most aggressive apes, I think the evidence suggests that humans are substantially more violent.”

Carrier points out that while chimpanzees physically batter each other more frequently than humans, rape appears to be less common in chimpanzees, and torture and group-against-group forms of violence, such as slavery, are not documented in the animals.

“Chimpanzees are also known to engage in raiding welfare in which one group largely eliminates a neighboring group, but this is not comparable in scope to the genocide that has characterized human history,” added Carrier, a University of Utah biology professor.

For this latest study, he and co-author Michael Morgan, a medical student, conducted three experiments. First, they analyzed what happened when men, aged from 22 to 50, hit a punching bag as hard as they could. The peak stress delivered to the bag — the force per area — was 1.7 to 3 times greater with a fist strike compared with a slap.

“Because you have higher pressure when hitting with a fist, you are more likely to cause injury to tissue, bones, teeth, eyes and the jaw,” Carrier said.

The second and third experiments determined that buttressing provided by the human fist increases the stiffness of the knuckle joint fourfold. It also doubles the ability of the fingers to transmit punching force, mainly due to the force transferred from the fingers to the thumb when the fist is clenched.

In terms of the size and shape of hand anatomy, the scientists point out that humans could have evolved manual dexterity with longer thumbs, but without the fingers and palms getting shorter.

Gorilla hands are closer in proportion to human hands than are other apes’ hands, but they and no other ape — aside from us — hits with a clenched fist.

The researchers additionally point out that humans use fists during threat displays. There is also a difference in body size between males and females, particularly evident with hands and arms. This, Carrier said, is “consistent with the hand being a weapon.”

Human males tend to be more physically violent than women, with men being ten times more likely to commit homicide than females in the U.S., Carrier said. But the research, nonetheless, applies to women as well.

“The bottom line is that women need to fight and defend themselves too,” Morgan told Discovery News. “Women need to fight off attackers and defend themselves from rape.”

Defending children may even help to explain human hand anatomy, since both men and women are often driven to protect their offspring, in addition to fighting with others over territory, resources and for other reasons.

“It can be argued that modern man exists in a world devoid of the evolutionary and selective pressures to which aggression was a beneficial trait,” Morgan said. “Our aggressive behavior remains, but no longer serves an evolutionary purpose.”

Far from random, evolution follows a predictable genetic pattern, Princeton researchers find (Princeton)

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Posted October 25, 2012; 12:00 p.m.

by Morgan Kelly, Office of Communications

Evolution, often perceived as a series of random changes, might in fact be driven by a simple and repeated genetic solution to an environmental pressure that a broad range of species happen to share, according to new research.

Princeton University research published in the journal Science suggests that knowledge of a species’ genes — and how certain external conditions affect the proteins encoded by those genes — could be used to determine a predictable evolutionary pattern driven by outside factors. Scientists could then pinpoint how the diversity of adaptations seen in the natural world developed even in distantly related animals.

Andolfatto bug

The Princeton researchers sequenced the expression of a poison-resistant protein in insect species that feed on plants such as milkweed and dogbane that produce a class of steroid-like cardiotoxins called cardenolides as a natural defense. The insects surveyed spanned three orders: butterflies and moths (Lepidoptera); beetles and weevils (Coleoptera); and aphids, bed bugs, milkweed bugs and other sucking insects (Hemiptera). Above: Dogbane beetle(Photo courtesy of Peter Andolfatto)

“Is evolution predictable? To a surprising extent the answer is yes,” said senior researcher Peter Andolfatto, an assistant professor in Princeton’s Department of Ecology and Evolutionary Biology and the Lewis-Sigler Institute for Integrative Genomics. He worked with lead author and postdoctoral research associate Ying Zhen, and graduate students Matthew Aardema and Molly Schumer, all from Princeton’s ecology and evolutionary biology department, as well as Edgar Medina, a biological sciences graduate student at the University of the Andes in Colombia.

The researchers carried out a survey of DNA sequences from 29 distantly related insect species, the largest sample of organisms yet examined for a single evolutionary trait. Fourteen of these species have evolved a nearly identical characteristic due to one external influence — they feed on plants that produce cardenolides, a class of steroid-like cardiotoxins that are a natural defense for plants such as milkweed and dogbane.

Though separated by 300 million years of evolution, these diverse insects — which include beetles, butterflies and aphids — experienced changes to a key protein called sodium-potassium adenosine triphosphatase, or the sodium-potassium pump, which regulates a cell’s crucial sodium-to-potassium ratio. The protein in these insects eventually evolved a resistance to cardenolides, which usually cripple the protein’s ability to “pump” potassium into cells and excess sodium out.

Andolfatto lab

Lead author Ying Zhen (foreground), Andolfatto (far left), fourth author and graduate student Molly Schumer (near left), and their co-authors sequenced and assembled all the expressed genes in 29 distantly related insect species, the largest sample of organisms yet examined for a single evolutionary trait. They used these sequences to predict how a certain protein would be encoded in the genes of 14 distantly related species that evolved a similar resistance to toxic plants. Similar techniques could be used to trace protein changes in a species’ DNA to understand how many diverse organisms evolved as a result of environmental factors. At right is research assistant Ilona Ruhl, who was not involved in the research. (Photo by Denise Applewhite)

Andolfatto and his co-authors first sequenced and assembled all the expressed genes in the studied species. They used these sequences to predict how the sodium-potassium pump would be encoded in each of the species’ genes based on cardenolide exposure.

Scientists using similar techniques could trace protein changes in a species’ DNA to understand how many diverse organisms evolved as a result of environmental factors, Andolfatto said. “To apply this approach more generally a scientist would have to know something about the genetic underpinnings of a trait and investigate how that trait evolves in large groups of species facing a common evolutionary problem,” Andolfatto said.

“For instance, the sodium-potassium pump also is a candidate gene location related to salinity tolerance,” he said. “Looking at changes to this protein in the right organisms could reveal how organisms have or may respond to the increasing salinization of oceans and freshwater habitats.”

Andolfatto bug

Milkweed tussock moth (Photo courtesy of Peter Andolfatto)

Jianzhi Zhang, a University of Michigan professor of ecology and evolutionary biology, said that the Princeton-based study shows that certain traits have a limited number of molecular mechanisms, and that numerous, distinct species can share the few mechanisms there are. As a result, it is likely that a cross-section of certain organisms can provide insight into the development of other creatures, he said.

“The finding of parallel evolution in not two, but numerous herbivorous insects increases the significance of the study because such frequent parallelism is extremely unlikely to have happened simply by chance,” said Zhang, who is familiar with the study but had no role in it.

“It shows that a common molecular mechanism is used by many different insects to defend themselves against the toxins in their food, suggesting that perhaps the number of potential mechanisms for achieving this goal is very limited,” he said. “That many different insects independently evolved the same molecular tricks to defend themselves against the same toxin suggests that studying a small number of well-chosen model organisms can teach us a lot about other species. Yes, evolution is predictable to a certain degree.”

Andolfatto and his co-authors examined the sodium-potassium pump protein because of its well-known sensitivity to cardenolides. In order to function properly in a wide variety of physiological contexts, cells must be able to control levels of potassium and sodium. Situated on the cell membrane, the protein generates a desired potassium to sodium ratio by “pumping” three sodium atoms out of the cell for every two potassium atoms it brings in.

Cardenolides disrupt the exchange of potassium and sodium, essentially shutting down the protein, Andolfatto said. The human genome contains four copies of the pump protein, and it is a candidate gene for a number of human genetic disorders, including salt-sensitive hypertension and migraines. In addition, humans have long used low doses of cardenolides medicinally for purposes such as controlling heart arrhythmia and congestive heart failure.

Andolfatto bug

Large milkweed bugs (Photo courtesy of Peter Andolfatto)

The Princeton researchers used the DNA microarray facility in the University’s Lewis-Sigler Institute for Integrative Genomics to sequence the expression of the sodium-potassium pump protein in insect species spanning three orders: butterflies and moths (Lepidoptera); beetles and weevils (Coleoptera); and aphids, bed bugs, milkweed bugs and other sucking insects (Hemiptera).

The researchers found that the genes of cardenolide-resistant insects incorporated various mutations that allowed it to resist the toxin. During the evolutionary timeframe examined, the sodium-potassium pump of insects feeding on dogbane and milkweed underwent 33 mutations at sites known to affect sensitivity to cardenolides. These mutations often involved similar or identical amino-acid changes that reduced susceptibility to the toxin. On the other hand, the sodium-potassium pump mutated just once in insects that do not feed on these plants.

Significantly, the researchers found that multiple gene duplications occurred in the ancestors of several of the resistant species. These insects essentially wound up with one conventional sodium-potassium pump protein and one “experimental” version, Andolfatto said. In these insects, the newer, hardier versions of the sodium-potassium pump are mostly expressed in gut tissue where they are likely needed most.

“These gene duplications are an elegant solution to the problem of adapting to environmental changes,” Andolfatto said. “In species with these duplicates, the organism is free to experiment with one copy while keeping the other constant, avoiding the risk that the new version of the protein will not perform its primary job as well.”

The researchers’ findings unify the generally separate ideas of what predominately drives genetic evolution: protein evolution, the evolution of the elements that control protein expression or gene duplication. This study shows that all three mechanisms can be used to solve the same evolutionary problem, Andolfatto said.

Central to the work is the breadth of species the researchers were able to examine using modern gene sequencing equipment, Andolfatto said.

“Historically, studying genetic evolution at this level has been conducted on just a handful of ‘model’ organisms such as fruit flies,” Andolfatto said. “Modern sequencing methods allowed us to approach evolutionary questions in a different way and come up with more comprehensive answers than had we examined one trait in any one organism.

“The power of what we’ve done is to survey diverse organisms facing a similar problem and find striking evidence for a limited number of possible solutions,” he said. “The fact that many of these solutions are used over and over again by completely unrelated species suggests that the evolutionary path is repeatable and predictable.”

The paper, “Parallel Molecular Evolution in an Herbivore Community,” was published Sept. 28 by Science. The research was supported by grants from the Centre for Genetic Engineering and Biotechnology, the National Science Foundation and the National Institutes of Health.

Language is shaped by brain’s desire for clarity and ease (University of Rochester)

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Public release date: 15-Oct-2012
By Susan Hagen
University of Rochester

 VIDEO: Translation: “Referee statue pick up. ” Above is one of the 80 animated video clips used to teach an artificial language to study participants. Cognitive scientists are just beginning to use…

Cognitive scientists have good news for linguistic purists terrified about the corruption of their mother tongue.

Using an artificial language in a carefully controlled laboratory experiment, a team from the University of Rochester and Georgetown University has found that many changes to language are simply the brain’s way of ensuring that communication is as precise and concise as possible.

“Our research shows that humans choose to reshape language when the structure is either overly redundant or confusing,” says T. Florian Jaeger, the Wilmot Assistant Professor of the Sciences at Rochester and co-author of a study published in the Proceedings of the National Academy of SciencesOct. 15. “This study suggests that we prefer languages that on average convey information efficiently, striking a balance between effort and clarity.”

The brain’s tendency toward efficient communication may also be an underlying reason that many human languages are structurally similar, says lead author Maryia Fedzechkina, a doctoral candidate at Rochester. Over and over, linguists have identified nearly identical grammatical conventions in seemingly unrelated languages scattered throughout the globe. For decades, linguists have debated the meaning of such similarities: are recurrent structures artifacts of distant common origins, are they simply random accidents, or do they reflect fundamental aspects of human cognition?

This study supports the latter, says co-author Elissa L. Newport, professor of neurology and director of the Center for Brain Plasticity and Recovery at Georgetown, and the former George Eastman Professor of Brain and Cognitive Sciences at Rochester. “The bias language learners have toward efficiency and clarity acts as a filter as languages are transmitted from one generation of learners to another,” she says. Alterations to language are introduced through many avenues, including the influence of other languages and changes in accents or pronunciation. “But this research finds that learners shift the language in ways that make it better – easier to use and more suitable for communication,” says Newport. That process also leads to the recurrent patterns across languages.

To observe the language acquisition process, the team created two miniature artificial languages that use suffixes on nouns to indicate subject or object. These “case markers” are common to Spanish, Russian, and other languages, but not English. In two experiments, 40 undergraduates, whose only language was English, learned the eight verbs, 15 nouns, and grammatical structure of the artificial languages. The training was spaced over four 45-minute sessions and consisted of computer images, short animated clips, and audio recordings. Then participants were asked to describe a novel action clip using their newly learned language.

 VIDEO: Translation: “Singer hunter chop. ” Unlike English, the artificial languages used in the study have free word order. When the subject and object could be easily confused, participants chose to reshape…

When faced with sentence constructions that could be confusing or ambiguous, the language learners in both experiments chose to alter the rules of the language they were taught in order to make their meaning clearer. They used case markers more often when the meaning of the subject and object might otherwise have caused unintended interpretations. So for example, a sentence like “Man hits wall,” is typical because the subject is a person and the object is a thing. But the sentence “Wall hits man,” as when a wall falls on top of a man, is atypical and confusing since the subject is a thing and the object is a person.

The results, write the authors, provide evidence that humans seek a balance between clarity and ease. Participants could have chosen to be maximally clear by always providing the case markers. Alternatively, they could have chosen to be maximally succinct by never providing the case markers. They did neither. Instead, they provided case-markers more often for those sentences that would otherwise have been more likely to be confused.

The findings also support the idea that language learners introduce common patterns, also known as linguistic universals, conclude the authors. The optional case marking that participants introduced in this experiment closely mirrors naturally occurring patterns in Japanese and Korean—when animate objects and inanimate subjects are more likely to receive case markings.

The history of English itself might reflect these deep principles of how we learn language, says Jaeger. Old English had cases and relatively free word order, as is still true for German. But at some point pronunciation changes began to obscure the case endings, creating ambiguity. In contemporary English, word order has become the primary signal by which speakers could decode the meaning, he says.

“Language acquisition can repair changes in languages to insure they don’t undermine communication,” says Fedzechkina. In light of these findings, new generations can perhaps be seen as renewing language, rather than corrupting it, she adds.

By the same token, says Jaeger, many elements of informal speech can be interpreted as rising from the brain’s bias toward efficiency. “When people turn ‘automobile’ into ‘auto,’ use informal contractions, swallow syllables, or take other linguistic shortcuts, the same principles are at work,” he says. Recent research has shown that these types of shortcuts appear only when their meaning is easily inferable from the context, he adds.

Bits of Mystery DNA, Far From ‘Junk,’ Play Crucial Role (N.Y.Times)

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By GINA KOLATA

Published: September 5, 2012

Among the many mysteries of human biology is why complex diseases like diabetes, high blood pressure and psychiatric disorders are so difficult to predict and, often, to treat. An equally perplexing puzzle is why one individual gets a disease like cancer or depression, while an identical twin remains perfectly healthy.

Béatrice de Géa for The New York Times. “It is like opening a wiring closet and seeing a hairball of wires,” Mark Gerstein of Yale University said of the DNA intricacies.

Now scientists have discovered a vital clue to unraveling these riddles. The human genome is packed with at least four million gene switches that reside in bits of DNA that once were dismissed as “junk” but that turn out to play critical roles in controlling how cells, organs and other tissues behave. The discovery, considered a major medical and scientific breakthrough, has enormous implications for human health because many complex diseases appear to be caused by tiny changes in hundreds of gene switches.

The findings, which are the fruit of an immense federal project involving 440 scientists from 32 laboratories around the world, will have immediate applications for understanding how alterations in the non-gene parts of DNA contribute to human diseases, which may in turn lead to new drugs. They can also help explain how the environment can affect disease risk. In the case of identical twins, small changes in environmental exposure can slightly alter gene switches, with the result that one twin gets a disease and the other does not.

As scientists delved into the “junk” — parts of the DNA that are not actual genes containing instructions for proteins — they discovered a complex system that controls genes. At least 80 percent of this DNA is active and needed. The result of the work is an annotated road map of much of this DNA, noting what it is doing and how. It includes the system of switches that, acting like dimmer switches for lights, control which genes are used in a cell and when they are used, and determine, for instance, whether a cell becomes a liver cell or a neuron.

“It’s Google Maps,” said Eric Lander, president of the Broad Institute, a joint research endeavor of Harvard and the Massachusetts Institute of Technology. In contrast, the project’s predecessor, the Human Genome Project, which determined the entire sequence of human DNA, “was like getting a picture of Earth from space,” he said. “It doesn’t tell you where the roads are, it doesn’t tell you what traffic is like at what time of the day, it doesn’t tell you where the good restaurants are, or the hospitals or the cities or the rivers.”

The new result “is a stunning resource,” said Dr. Lander, who was not involved in the research that produced it but was a leader in the Human Genome Project. “My head explodes at the amount of data.”

The discoveries were published on Wednesday in six papers in the journal Nature and in 24 papers in Genome Research and Genome Biology. In addition, The Journal of Biological Chemistry is publishing six review articles, and Science is publishing yet another article.

Human DNA is “a lot more active than we expected, and there are a lot more things happening than we expected,” said Ewan Birney of the European Molecular Biology Laboratory-European Bioinformatics Institute, a lead researcher on the project.

In one of the Nature papers, researchers link the gene switches to a range of human diseases — multiple sclerosis, lupus, rheumatoid arthritis, Crohn’s disease, celiac disease — and even to traits like height. In large studies over the past decade, scientists found that minor changes in human DNA sequences increase the risk that a person will get those diseases. But those changes were in the junk, now often referred to as the dark matter — they were not changes in genes — and their significance was not clear. The new analysis reveals that a great many of those changes alter gene switches and are highly significant.

“Most of the changes that affect disease don’t lie in the genes themselves; they lie in the switches,” said Michael Snyder, a Stanford University researcher for the project, called Encode, for Encyclopedia of DNA Elements.

And that, said Dr. Bradley Bernstein, an Encode researcher at Massachusetts General Hospital, “is a really big deal.” He added, “I don’t think anyone predicted that would be the case.”

The discoveries also can reveal which genetic changes are important in cancer, and why. As they began determining the DNA sequences of cancer cells, researchers realized that most of the thousands of DNA changes in cancer cells were not in genes; they were in the dark matter. The challenge is to figure out which of those changes are driving the cancer’s growth.

“These papers are very significant,” said Dr. Mark A. Rubin, a prostate cancer genomics researcher at Weill Cornell Medical College. Dr. Rubin, who was not part of the Encode project, added, “They will definitely have an impact on our medical research on cancer.”

In prostate cancer, for example, his group found mutations in important genes that are not readily attacked by drugs. But Encode, by showing which regions of the dark matter control those genes, gives another way to attack them: target those controlling switches.

Dr. Rubin, who also used the Google Maps analogy, explained: “Now you can follow the roads and see the traffic circulation. That’s exactly the same way we will use these data in cancer research.” Encode provides a road map with traffic patterns for alternate ways to go after cancer genes, he said.

Dr. Bernstein said, “This is a resource, like the human genome, that will drive science forward.”

The system, though, is stunningly complex, with many redundancies. Just the idea of so many switches was almost incomprehensible, Dr. Bernstein said.

There also is a sort of DNA wiring system that is almost inconceivably intricate.

“It is like opening a wiring closet and seeing a hairball of wires,” said Mark Gerstein, an Encode researcher from Yale. “We tried to unravel this hairball and make it interpretable.”

There is another sort of hairball as well: the complex three-dimensional structure of DNA. Human DNA is such a long strand — about 10 feet of DNA stuffed into a microscopic nucleus of a cell — that it fits only because it is tightly wound and coiled around itself. When they looked at the three-dimensional structure — the hairball — Encode researchers discovered that small segments of dark-matter DNA are often quite close to genes they control. In the past, when they analyzed only the uncoiled length of DNA, those controlling regions appeared to be far from the genes they affect.

The project began in 2003, as researchers began to appreciate how little they knew about human DNA. In recent years, some began to find switches in the 99 percent of human DNA that is not genes, but they could not fully characterize or explain what a vast majority of it was doing.

The thought before the start of the project, said Thomas Gingeras, an Encode researcher from Cold Spring Harbor Laboratory, was that only 5 to 10 percent of the DNA in a human being was actually being used.

The big surprise was not only that almost all of the DNA is used but also that a large proportion of it is gene switches. Before Encode, said Dr. John Stamatoyannopoulos, a University of Washington scientist who was part of the project, “if you had said half of the genome and probably more has instructions for turning genes on and off, I don’t think people would have believed you.”

By the time the National Human Genome Research Institute, part of the National Institutes of Health, embarked on Encode, major advances in DNA sequencing and computational biology had made it conceivable to try to understand the dark matter of human DNA. Even so, the analysis was daunting — the researchers generated 15 trillion bytes of raw data. Analyzing the data required the equivalent of more than 300 years of computer time.

Just organizing the researchers and coordinating the work was a huge undertaking. Dr. Gerstein, one of the project’s leaders, has produced a diagram of the authors with their connections to one another. It looks nearly as complicated as the wiring diagram for the human DNA switches. Now that part of the work is done, and the hundreds of authors have written their papers.

“There is literally a flotilla of papers,” Dr. Gerstein said. But, he added, more work has yet to be done — there are still parts of the genome that have not been figured out.

That, though, is for the next stage of Encode.

*   *   *

Published: September 5, 2012

Rethinking ‘Junk’ DNA

A large group of scientists has found that so-called junk DNA, which makes up most of the human genome, does much more than previously thought.

GENES: Each human cell contains about 10 feet of DNA, coiled into a dense tangle. But only a very small percentage of DNA encodes genes, which control inherited traits like eye color, blood type and so on.

JUNK DNA: Stretches of DNA around and between genes seemed to do nothing, and were called junk DNA. But now researchers think that the junk DNA contains a large number of tiny genetic switches, controlling how genes function within the cell.

REGULATION: The many genetic regulators seem to be arranged in a complex and redundant hierarchy. Scientists are only beginning to map and understand this network, which regulates how cells, organs and tissues behave.

DISEASE: Errors or mutations in genetic switches can disrupt the network and lead to a range of diseases. The new findings will spur further research and may lead to new drugs and treatments.

 

Evolution could explain the placebo effect (New Scientist)

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06 September 2012 by Colin Barras

Magazine issue 2881

ON THE face of it, the placebo effect makes no sense. Someone suffering from a low-level infection will recover just as nicely whether they take an active drug or a simple sugar pill. This suggests people are able to heal themselves unaided – so why wait for a sugar pill to prompt recovery?

New evidence from a computer model offers a possible evolutionary explanation, and suggests that the immune system has an on-off switch controlled by the mind.

It all starts with the observation that something similar to the placebo effect occurs in many animals, says Peter Trimmer, a biologist at the University of Bristol, UK. For instance, Siberian hamsters do little to fight an infection if the lights above their lab cage mimic the short days and long nights of winter. But changing the lighting pattern to give the impression of summer causes them to mount a full immune response.

Likewise, those people who think they are taking a drug but are really receiving a placebo can have a response which is twice that of those who receive no pills (Annals of Family Medicine, doi.org/cckm8b). In Siberian hamsters and people, intervention creates a mental cue that kick-starts the immune response.

There is a simple explanation, says Trimmer: the immune system is costly to run – so costly that a strong and sustained response could dangerously drain an animal’s energy reserves. In other words, as long as the infection is not lethal, it pays to wait for a sign that fighting it will not endanger the animal in other ways.

Nicholas Humphrey, a retired psychologist formerly at the London School of Economics, first proposed this idea a decade ago, but only now has evidence to support it emerged from a computer model designed by Trimmer and his colleagues.

According to Humphrey’s picture, the Siberian hamster subconsciously acts on a cue that it is summer because food supplies to sustain an immune response are plentiful at that time of year. We subconsciously respond to treatment – even a sham one – because it comes with assurances that it will weaken the infection, allowing our immune response to succeed rapidly without straining the body’s resources.

Trimmer’s simulation is built on this assumption – that animals need to spend vital resources on fighting low-level infections. The model revealed that, in challenging environments, animals lived longer and sired more offspring if they endured infections without mounting an immune response. In more favourable environments, it was best for animals to mount an immune response and return to health as quickly as possible (Evolution and Human Behavior, doi.org/h8p). The results show a clear evolutionary benefit to switching the immune system on and off depending on environmental conditions.

“I’m pleased to see that my theory stands up to computational modelling,” says Humphrey. If the idea is right, he adds, it means we have misunderstood the nature of placebos. Farming and other innovations in the past 10,000 years mean that many people have a stable food supply and can safely mount a full immune response at any time – but our subconscious switch has not yet adapted to this. A placebo tricks the mind into thinking it is an ideal time to switch on an immune response, says Humphrey.

Paul Enck at the University of Tübingen in Germany says it is an intriguing idea, but points out that there are many different placebo responses, depending on the disease. It is unlikely that a single mechanism explains them all, he says.

Why Do Organisms Build Tissues They Seemingly Never Use? (Science Daily)

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ScienceDaily (Aug. 10, 2012) — Why, after millions of years of evolution, do organisms build structures that seemingly serve no purpose?

A study conducted at Michigan State University and published in the current issue of The American Naturalist investigates the evolutionary reasons why organisms go through developmental stages that appear unnecessary.

“Many animals build tissues and structures they don’t appear to use, and then they disappear,” said Jeff Clune, lead author and former doctoral student at MSU’s BEACON Center of Evolution in Action. “It’s comparable to building a roller coaster, razing it and building a skyscraper on the same ground. Why not just skip ahead to building the skyscraper?”

Why humans and other organisms retain seemingly unnecessary stages in their development has been debated between biologists since 1866. This study explains that organisms jump through these extra hoops to avoid disrupting a developmental process that works. Clune’s team called this concept the “developmental disruption force.” But Clune says it also could be described as “if the shoe fits, don’t change a thing.”

“In a developing embryo, each new structure is built in a delicate environment that consists of everything that has already developed,” said Clune, who is now a postdoctoral fellow at Cornell University. “Mutations that alter that environment, such as by eliminating a structure, can thus disrupt later stages of development. Even if a structure is not actually used, it may set the stage for other functional tissues to grow properly.”

Going back to the roller coaster metaphor, even though the roller coaster gets torn down, the organism needs the parts from that teardown to build the skyscraper, he added.

“An engineer would simply skip the roller coaster step, but evolution is more of a tinkerer and less of an engineer,” Clune said. “It uses whatever parts that are lying around, even if the process that generates those parts is inefficient.”

An interesting consequence is that newly evolved traits tend to get added at the end of development, because there is less risk of disrupting anything important. That, in turn, means that there is a similarity between the order things evolve and the order they develop.

A new technology called computational evolution allowed the team to conduct experiments that would be impossible to reproduce in nature.

Rather than observe embryos grow, the team of computer scientists and biologists used BEACON’s Avida software to perform experiments with evolution inside a computer. The Avidians — self-replicating computer programs — mutate, compete for resources and evolve, mimicking natural selection in real-life organisms. Using this software, Clune’s team observed as Avidians evolved to perform logic tasks. They recorded the order that those tasks evolved in a variety of lineages, and then looked at the order those tasks developed in the final, evolved organism.

They were able to help settle an age-old debate that developmental order does resemble evolutionary order, at least in this computationally evolving system. Because in a computer thousands of generations can happen overnight, the team was able to repeat this experiment many times to document that this similarity repeatedly occurs.

Additional MSU researchers contributing to the study included BEACON colleagues Richard Lenski, Robert Pennock and Charles Ofria. The research was funded by the National Science Foundation.

Programa de computador mimetiza evolução humana (Fapesp)

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Software desenvolvido na USP de São Carlos cria e seleciona programas geradores de Árvores de Decisão, ferramentas capazes de fazer previsões. Pesquisa foi premiada nos Estados Unidos, no maior evento de computação evolutiva (Wikimedia)

16/08/2012

Por Karina Toledo

Agência FAPESP – Árvores de Decisão são ferramentas computacionais que conferem às máquinas a capacidade de fazer previsões com base na análise de dados históricos. A técnica pode, por exemplo, auxiliar o diagnóstico médico ou a análise de risco de aplicações financeiras.

Mas, para ter a melhor previsão, é necessário o melhor programa gerador de Árvores de Decisão. Para alcançar esse objetivo, pesquisadores do Instituto de Ciências Matemáticas e de Computação (ICMC) da Universidade de São Paulo (USP), em São Carlos, se inspiraram na teoria evolucionista de Charles Darwin.

“Desenvolvemos um algoritmo evolutivo, ou seja, que mimetiza o processo de evolução humana para gerar soluções”, disse Rodrigo Coelho Barros, doutorando do Laboratório de Computação Bioinspirada (BioCom) do ICMC e bolsista da FAPESP.

A computação evolutiva, explicou Barros, é uma das várias técnicas bioinspiradas, ou seja, que buscam na natureza soluções para problemas computacionais. “É notável como a natureza encontra soluções para problemas extremamente complicados. Não há dúvidas de que precisamos aprender com ela”, disse Barros.

Segundo Barros, o software desenvolvido em seu doutorado é capaz de criar automaticamente programas geradores de Árvores de Decisão. Para isso, faz cruzamentos aleatórios entre os códigos de programas já existentes gerando “filhos”.

“Esses ‘filhos’ podem eventualmente sofrer mutações e evoluir. Após um tempo, é esperado que os programas de geração de Árvores de Decisão evoluídos sejam cada vez melhores e nosso algoritmo seleciona o melhor de todos”, afirmou Barros.

Mas enquanto o processo de seleção natural na espécie humana leva centenas ou até milhares de anos, na computação dura apenas algumas horas, dependendo do problema a ser resolvido. “Estabelecemos cem gerações como limite do processo evolutivo”, contou Barros.

Inteligência artificial

Em Ciência da Computação, é denominada heurística a capacidade de um sistema fazer inovações e desenvolver técnicas para alcançar um determinado fim.

O software desenvolvido por Barros se insere na área de hiper-heurísticas, tópico recente na área de computação evolutiva que tem como objetivo a geração automática de heurísticas personalizadas para uma determinada aplicação ou conjunto de aplicações.

“É um passo preliminar em direção ao grande objetivo da inteligência artificial: o de criar máquinas capazes de desenvolver soluções para problemas sem que sejam explicitamente programadas para tal”, detalhou Barros.

O trabalho deu origem ao artigo A Hyper-Heuristic Evolutionary Algorithm for Automatically Designing Decision-Tree Algorithms, premiado em três categorias na Genetic and Evolutionary Computation Conference (GECCO), maior evento da área de computação evolutiva do mundo, realizado em julho na Filadélfia, Estados Unidos.

Além de Barros, também são autores do artigo os professores André Carlos Ponce de Leon Ferreira de Carvalho, orientador da pesquisa no ICMC, Márcio Porto Basgalupp, da Universidade Federal de São Paulo (Unifesp), e Alex Freitas, da University of Kent, no Reino Unido, que assumiu a co-orientação.

Os autores foram convidados a submeter o artigo para a revista Evolutionary Computation Journal, publicada pelo Instituto de Tecnologia de Massachusetts (MIT). “O trabalho ainda passará por revisão, mas, como foi submetido a convite, tem grande chance de ser aceito”, disse Barros.

A pesquisa, que deve ser concluída somente em 2013, também deu origem a um artigo publicado a convite no Journal of the Brazilian Computer Society, após ser eleito como melhor trabalho no Encontro Nacional de Inteligência Artificial de 2011.

Outro artigo, apresentado na 11ª International Conference on Intelligent Systems Design and Applications, realizada na Espanha em 2011, rendeu convite para publicação na revistaNeurocomputing.

Detribalising Economics (World Economics Association)

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By Rob Garnett [r.garnett@tcu.edu]
World Economics Association Newsletter 2(2), April.2012, page 4

In “Why Pluralism?” (2011), Stuart Birks calls for “greater discussion, deliberation, and cross-fertilization of ideas” among schools of economic thought as an antidote to each school’s autarkic tendency to “see itself as owning the ‘truth’ for its area.” As a philosophical postscript, I want to underscore the catholic reach of Birks’s remarks — his genial reminder, properly addressed to all economists, of the minimal requirements for academic inquiry.

The case for academic pluralism in economics is motivated by the ubiquity of “myside bias” (Klein 2011). Whether methodological, ideological, paradigmatic, or all of the above, such groupthink fuels intellectual segregation and bigotry. It turns schools into echo chambers, sealed off from the critical feedback loops that check hubris and propel scholarly progress.

Pluralists know that “The causes of faction cannot be removed . . . Relief is only to be sought in the means of containing its effects” (Hamilton, Madison, and Jay [1788] 2001, 45). So even as they celebrate paradigmatic diversity, they insist that scholars observe two liberal precepts:

1. academic discourse is a commons, no ‘area’ of which can be owned by any school; and

2. within these spaces of inquiry, scholars bear certain ethical duties as academic citizens.

Academic pluralism is the duty to practice “methodological awareness and toleration” (Backhouse 2001, 163) and “to constantly [seek] to learn from those who [do] not share [one’s] ideological or methodological perspective” (Boettke 2004, 379). It is “academic” because it coincides with the epistemological and ethical norms of modern academic freedom (American Association of University Professors 1940). It is “pluralist” because it entails a commitment to conduct one’s scholarly business in a non-sectarian manner.

Could a critical mass of economists ever be persuaded to enact these scholarly virtues? Yes! But admirers of these virtues must be prepared to teach by example. When Warren Samuels passed away in last August, he was eulogized as a first-rate scholar who advanced pluralism by enacting it consistently over his long career. As the Austrian economist Peter Boettke recalls:

Prior to meeting Warren, I think it would be accurate to say that I divided the world neatly into those who are stupid, those who are evil, and those who are smart and good enough to agree with me. . . . Warren destroyed that simple intellectual picture of the world. . . . He didn’t overturn my intellectual commitments . . . but he made [me] more selfcritical and less self-satisfied, and hopefully a better scholar [and] teacher (Boettke 2011).

The pluralism Warren Samuels personified can be achieved by most economic scholars, teachers, and students to a reasonable degree. If we want economics to regain its standing as a serious and humane social science, we must find more ways to activate these dormant capabilities.

References

American Association of University Professors (1940) Statement of Principles on Academic Freedom and Tenure. Washington, DC.

Backhouse, R. E. (2001) On the Credentials of Methodological Pluralism. In J. E. Biddle, J. B. Davis, and S. G. Medema (Eds.), Economics Broadly Considered: Essays in Honor of Warren J. Samuels, 161-181. London: Routledge.

Boettke, P. J. (2011) “Warren Samuels (1933-2011)”, http://www.coordinationproblem.org/2011/08/warren-samuels-1933-2011.html Accessed August 18, 2011.

Boettke, P. J. (2004) Obituary: Don Lavoie (1950-2001). Journal of Economic Methodology 11 (3): 377-379.

Birks, S. (2011) “Why Pluralism?” World Economics Association Newsletter, vol. 1, no. 1.

Hamilton, A., Madison, J., and Jay, J. (2001) [1788] The Federalist. Gideon edition. G. W. Carey and J. McClellan (eds.) Indianapolis, IN: Liberty Fund.

Klein, D. B. (2011) “I Was Wrong, and So Are You.” The Atlantic, December.

[Editor’s note: Readers may also be interested in Garnett, R. F. (Ed.). (1999). What do economists know? London: Routledge]