Arquivo da tag: Biologia

They Hunt. They Gather. They’re Very Good at Talking About Smells (N.Y.Times)

The answer might come down partly to culture, suggests a study published Thursday in Current Biology.

To better understand why the Jahai have this knack with naming smells, researchers compared a different group of hunter-gatherers on the peninsula, the Semaq Beri, with neighbors who are not hunter-gatherers. Even though they shared related languages and a home environment, the Semaq Beri had a superior ability at putting words to odors. These results challenge assumptions that smelling just isn’t something people are good at. They also show how important culture is to shaping who we are — and even what we do with our noses.

[READ: Ancestral Climates May Have Shaped Your Nose]

In the rainforests of the Malay Peninsula, the Semaq Beri, like the Jahai, are hunter-gatherers. But the Semelai, a group that lives nearby, cultivate rice and trade collected forest items.

Semaq Beri members clearing undergrowth in the durian fruit season. A neighboring group, the Semelai, share a related language but were less adept at naming odors they smelled. Credit: Nicole Kruspe

To test their color and odor naming abilities, the researchers asked members of each group to identify colors on swatches and odors trapped inside pens. When it came to naming more than a dozen odors including leather, fish and banana, the differences were clear. The Semaq Beri used particular terms to describe odor qualities. But when the Semelai tried to identify the source, they often got it wrong. The difference between the two groups was as pronounced as the gap in the earlier study between the Jahai and English-speaking Americans.

“I thought the differences would be more subtle between the two groups,” said Nicole Kruspe, a linguist at Lund University in Sweden who co-authored the study.

Perhaps the importance a culture places on odor influences how people describe it. And if you depend on the forest’s produce to live, you may want to know more subtle attributes that indicate origin, safety or quality.

“A cultural preoccupation with odor is useful in the forest with limited vision,” said Dr. Kruspe.

The Semaq Beri value odors as food-locating resources but also as important pieces of life that can indicate a person’s identity and guide taboos and rules for behavior. But “that in itself doesn’t explain it,” Dr. Kruspe said.

[READ: The Nose, an Emotional Time Machine.]

Perhaps well-practiced skills preserved odor-detecting genes or primed brains to be better odor-detectors — which suggests that without continuing to use this ability, it could one day be lost.

Asifa Majid, a linguist at the Max Planck Institute for Psycholinguistics in the Netherlands and co-author of the paper, has also studied hunter-gatherers with comparable skills in Mexico and worries that pressures of globalization may disrupt these lifestyles, limit access to odors and threaten a vibrant odor lexicon.

One way to explore that possibility would be to see what happens to the lexicon for odors of descendants of hunter-gatherers who have been removed from that lifestyle.

“Unfortunately,” said Dr. Kruspe, “we will probably be able to test for that in a couple of generations.”

Anúncios

Scientists Seek to Update Evolution (Quanta Magazine)

Recent discoveries have led some researchers to argue that the modern evolutionary synthesis needs to be amended. 

By Carl Zimmer. November 22, 2016

Douglas Futuyma, a biologist at Stony Brook University, defends the “Modern Synthesis” of evolution at the Royal Society earlier this month.  Kevin Laland looked out across the meeting room at a couple hundred people gathered for a conference on the future of evolutionary biology. A colleague sidled up next to him and asked how he thought things were going.

“I think it’s going quite well,” Laland said. “It hasn’t gone to fisticuffs yet.”

Laland is an evolutionary biologist who works at the University of St. Andrews in Scotland. On a chilly gray November day, he came down to London to co-host a meeting at the Royal Society called “New Trends in Evolutionary Biology.” A motley crew of biologists, anthropologists, doctors, computer scientists, and self-appointed visionaries packed the room. The Royal Society is housed in a stately building overlooking St. James’s Park. Today the only thing for Laland to see out of the tall meeting-room windows was scaffolding and gauzy tarps set up for renovation work. Inside, Laland hoped, another kind of renovation would be taking place.

In the mid-1900s, biologists updated Darwin’s theory of evolution with new insights from genetics and other fields. The result is often called the Modern Synthesis, and it has guided evolutionary biology for over 50 years. But in that time, scientists have learned a tremendous amount about how life works. They can sequence entire genomes. They can watch genes turn on and off in developing embryos. They can observe how animals and plants respond to changes in the environment.

As a result, Laland and a like-minded group of biologists argue that the Modern Synthesis needs an overhaul. It has to be recast as a new vision of evolution, which they’ve dubbed the Extended Evolutionary Synthesis. Other biologists have pushed back hard, saying there is little evidence that such a paradigm shift is warranted.

This meeting at the Royal Society was the first public conference where Laland and his colleagues could present their vision. But Laland had no interest in merely preaching to the converted, and so he and his fellow organizers also invited prominent evolutionary biologists who are skeptical about the Extended Evolutionary Synthesis.

Both sides offered their arguments and critiques in a civil way, but sometimes you could sense the tension in the room — the punctuations of tsk-tsks, eye-rolling, and partisan bursts of applause.

But no fisticuffs. At least not yet.

Making Evolution as We Know It

Every science passes through times of revolution and of business as usual. After Galileo and Newton dragged physics out of its ancient errors in the 1600s, it rolled forward from one modest advance to the next until the early 1900s. Then Einstein and other scientists established quantum physics, relativity and other new ways of understanding the universe. None of them claimed that Newton was wrong. But it turns out there’s much more to the universe than matter in motion.

Evolutionary biology has had revolutions of its own. The first, of course, was launched by Charles Darwin in 1859 with his book On the Origin of Species. Darwin wove together evidence from paleontology, embryology and other sciences to show that living things were related to one another by common descent. He also introduced a mechanism to drive that long-term change: natural selection. Each generation of a species was full of variations. Some variations helped organisms survive and reproduce, and those were passed down, thanks to heredity, to the next generation.

Darwin inspired biologists all over the world to study animals and plants in a new way, interpreting their biology as adaptations produced over many generations. But he succeeded in this despite having no idea what a gene was. It wasn’t until the 1930s that geneticists and evolutionary biologists came together and recast evolutionary theory. Heredity became the transmission of genes from generation to generation. Variations were due to mutations, which could be shuffled into new combinations. New species arose when populations built up mutations that made interbreeding impossible.

In 1942, the British biologist Julian Huxley described this emerging framework in a book called Evolution: The Modern Synthesis. Today, scientists still call it by that name. (Sometimes they refer to it instead as neo-Darwinism, although that’s actually a confusing misnomer. The term “neo-Darwinism” was actually coined in the late 1800s, to refer to biologists who were advancing Darwin’s ideas in Darwin’s own lifetime.)

The Modern Synthesis proved to be a powerful tool for asking questions about nature. Scientists used it to make a vast range of discoveries about the history of life, such as why some people are prone to genetic disorders like sickle-cell anemia and why pesticides sooner or later fail to keep farm pests in check. But starting not long after the formation of the Modern Synthesis, various biologists would complain from time to time that it was too rigid. It wasn’t until the past few years, however, that Laland and other researchers got organized and made a concerted effort to formulate an extended synthesis that might take its place.

The researchers don’t argue that the Modern Synthesis is wrong — just that it doesn’t capture the full richness of evolution. Organisms inherit more than just genes, for example: They can inherit other cellular molecules, as well as behaviors they learn and the environments altered by their ancestors. Laland and his colleagues also challenge the pre-eminent place that natural selection gets in explanations for how life got to be the way it is. Other processes can influence the course of evolution, too, from the rules of development to the environments in which organisms have to live.

“It’s not simply bolting more mechanisms on what we already have,” said Laland. “It requires you to think of causation in a different way.”

Adding to Darwin

Eva Jablonka, a biologist at Tel Aviv University, used her talk to explore the evidence for a form of heredity beyond genes.

Our cells use a number of special molecules to control which of their genes make proteins. In a process called methylation, for example, cells put caps on their DNA to keep certain genes shut down. When cells divide, they can reproduce the same caps and other controls on the new DNA. Certain signals from the environment can cause cells to change these so-called “epigenetic” controls, allowing organisms to adjust their behavior to new challenges.

Some studies indicate that — under certain circumstances — an epigenetic change in a parent may get passed down to its offspring. And those children may pass down this altered epigenetic profile to their children. This would be kind of heredity that’s beyond genes.

The evidence for this effect is strongest in plants. In one study, researchers were able to trace down altered methylation patterns for 31 generations in a plant called Arabidopsis. And this sort of inheritance can make a meaningful difference in how an organism works. In another study, researchers found that inherited methylation patterns could change the flowering time of Arabidopsis, as well as the size of its roots. The variation that these patterns created was even bigger than what ordinary mutations caused.

After presenting evidence like this, Jablonka argued that epigenetic differences could determine which organisms survived long enough to reproduce. “Natural selection could work on this system,” she said.

While natural selection is an important force in evolution, the speakers at the meeting presented evidence for how it could be constrained, or biased in a particular direction. Gerd Müller, a University of Vienna biologist, offered an example from his own research on lizards. A number of species of lizards have evolved feet that have lost some toes. Some have only four toes, while others have just one, and some have lost their feet altogether.

The Modern Synthesis, Müller argued, leads scientists to look at these arrangements as simply the product of natural selection, which favors one variant over others because it has a survival advantage. But that approach doesn’t work if you ask what the advantage was for a particular species to lose the first toe and last toe in its foot, instead of some other pair of toes.

“The answer is, there is no real selective advantage,” said Müller.

The key to understanding why lizards lose particular toes is found in the way that lizard embryos develop toes in the first place. A bud sprouts off the side of the body, and then five digits emerge. But the toes always appear in the same sequence. And when lizards lose their toes through evolution, they lose them in the reverse order. Müller suspects this constraint is because mutations can’t create every possible variation. Some combinations of toes are thus off-limits, and natural selection can never select them in the first place.

Development may constrain evolution. On the other hand, it also provides animals and plants with remarkable flexibility. Sonia Sultan, an evolutionary ecologist from Wesleyan University, offered a spectacular case in point during her talk, describing a plant she studies in the genus Polygonum that takes the common name “smartweed.”

The Modern Synthesis, Sultan said, would lead you to look at the adaptations in a smartweed plant as the fine-tuned product of natural selection. If plants grow in low sunlight, then natural selection will favor plants with genetic variants that let them thrive in that environment — for example, by growing broader leaves to catch more photons. Plants that grow in bright sunlight, on the other hand, will evolve adaptations that let them thrive in those different conditions.

“It’s a commitment to that view that we’re here to confront,” Sultan said.

If you raise genetically identical smartweed plants under different conditions, Sultan showed, you’ll end up with plants that may look like they belong to different species.

For one thing, smartweed plants adjust the size of their leaves to the amount of sunlight they get. In bright light, the plants grow narrow, thick leaves, but in low light, the leaves become broad and thin. In dry soil, the plants send roots down deep in search of water, while in flood soil, they grow shallow hairlike roots that that stay near the surface.

Scientists at the meeting argued that this flexibility — known as plasticity — can itself help drive evolution. It allows plants to spread into a range of habitats, for example, where natural selection can then adapt their genes. And in another talk, Susan Antón, a paleoanthropologist at New York University, said that plasticity may play a significant role in human evolution that’s gone underappreciated till now. That’s because the Modern Synthesis has strongly influenced the study of human evolution for the past half century.

Paleoanthropologists tended to treat differences in fossils as the result of genetic differences. That allowed them to draw an evolutionary tree of humans and their extinct relatives. This approach has a lot to show for it, Antón acknowledged. By the 1980s, scientists had figured out that our early ancient relatives were short and small-brained up to about two million years ago. Then one lineage got tall and evolved big brains. That transition marked the origin of our genus, Homo.

But sometimes paleoanthropologists would find variations that were harder to make sense of. Two fossils might look in some ways like they should be in the same species but look too different in other respects. Scientists would usually dismiss those variations as being caused by the environment. “We wanted to get rid of all that stuff and get down to their essence,” Antón said.

But that stuff is now too abundant to ignore. Scientists have found a dizzying variety of humanlike fossils dating back to 1.5 to 2.5 million years ago. Some are tall, and some are short. Some have big brains and some have small ones. They all have some features of Homo in their skeletonbut each has a confusing mix-and-match assortment.

Antón thinks that the Extended Evolutionary Synthesis can help scientists make sense of this profound mystery. In particular, she thinks that her colleagues should take plasticity seriously as an explanation for the weird diversity of early Homo fossils.

To support this idea, Antón pointed out that living humans have their own kinds of plasticity. The quality of food a woman gets while she’s pregnant can influence the size and health of her baby, and those influences can last until adulthood. What’s more, the size of a woman — influenced in part by her own mother’s diet — can influence her own children. Biologists have found that women with longer legs tend to have larger children, for example.

Antón proposed that the weird variations in the fossil record might be even more dramatic examples of plasticity. All these fossils date to when Africa’s climate fell into a period of wild climate swings. Droughts and abundant rains would have changed the food supply in different parts of the world, perhaps causing early Homo to develop differently.

The Extended Evolutionary Synthesis may also help make sense of another chapter in our history: the dawn of agriculture. In Asia, Africa and the Americas, people domesticated crops and livestock. Melinda Zeder, an archaeologist at the Smithsonian Institution, gave a talk at the meeting about the long struggle to understand how this transformation unfolded.

Before people farmed, they foraged for food and hunted wild game. Zeder explained how many scientists treat the behavior of the foragers in a very Modern Synthesis way: as finely tuned by natural selection to deliver the biggest payoff for their effort to find food.

The trouble is that it’s hard to see how such a forager would ever switch to farming. “You don’t get the immediate gratification of grabbing some food and putting it in your mouth,” Zeder told me.

Some researchers suggested that the switch to agriculture might have occurred during a climate shift, when it got harder to find wild plants. But Zeder and other researchers have actually found no evidence of such a crisis when agriculture arose.

Zeder argues that there’s a better way of thinking about this transition. Humans are not passive zombies trying to survive in a fixed environment. They are creative thinkers who can change the environment itself. And in the process, they can steer evolution in a new direction.

Scientists call this process niche construction, and many species do it. The classic case is a beaver. It cuts down trees and makes a dam, creating a pond. In this new environment, some species of plants and animals will do better than others. And they will adapt to their environment in new ways. That’s true not just for the plants and animals that live around a beaver pond, but for the beaver itself.

When Zeder first learned about niche construction, she says, it was a revelation. “Little explosions were going off in my head,” she told me. The archaeological evidence she and others had gathered made sense as a record of how humans changed their own environment.

Early foragers show signs of having moved wild plants away from their native habitats to have them close at hand, for example. As they watered the plants and protected them from herbivores, the plants adapted to their new environment. Weedy species also moved in and became crops of their own. Certain animals adapted to the environment as well, becoming dogs, cats and other domesticated species.

Gradually, the environment changed from sparse patches of wild plants to dense farm fields. That environment didn’t just drive the evolution of the plants. It also began to drive the cultural evolution of the farmers, too. Instead of wandering as nomads, they settled down in villages so that they could work the land around them. Society became more stable because children received an ecological inheritance from their parents. And so civilization began.

Niche construction is just one of many concepts from the Extended Evolutionary Synthesis that can help make sense of domestication, Zeder said. During her talk, she presented slide after slide of predictions it provides, about everything from the movements of early foragers to the pace of plant evolution.

“It felt like an infomercial for the Extended Evolutionary Synthesis,” Zeder told me later with a laugh. “But wait! You can get steak knives!”

The Return of Natural Selection

Among the members of the audience was a biologist named David Shuker. After listening quietly for a day and a half, the University of St Andrews researcher had had enough. At the end of a talk, he shot up his hand.

The talk had been given by Denis Noble, a physiologist with a mop of white hair and a blue blazer. Noble, who has spent most of his career at Oxford, said he started out as a traditional biologist, seeing genes as the ultimate cause of everything in the body. But in recent years he had switched his thinking. He spoke of the genome not as a blueprint for life but as a sensitive organ, detecting stress and rearranging itself to cope with challenges. “I’ve been on a long journey to this view,” Noble said.

To illustrate this new view, Noble discussed an assortment of recent experiments. One of them was published last year by a team at the University of Reading. They did an experiment on bacteria that swim by spinning their long tails.

First, the scientists cut a gene out of the bacteria’s DNA that’s essential for building tails. The researchers then dropped these tailless bacteria into a petri dish with a meager supply of food. Before long, the bacteria ate all the food in their immediate surroundings. If they couldn’t move, they died. In less than four days in these dire conditions, the bacteria were swimming again. On close inspection, the team found they were growing new tails.

“This strategy is to produce rapid evolutionary genome change in response to the unfavorable environment,” Noble declared to the audience. “It’s a self-maintaining system that enables a particular characteristic to occur independent of the DNA.”

That didn’t sound right to Shuker, and he was determined to challenge Noble after the applause died down.

“Could you comment at all on the mechanism underlying that discovery?” Shuker asked.

Noble stammered in reply. “The mechanism in general terms, I can, yes…” he said, and then started talking about networks and regulation and a desperate search for a solution to a crisis. “You’d have to go back to the original paper,” he then said.

While Noble was struggling to respond, Shuker went back to the paper on an iPad. And now he read the abstract in a booming voice.

“‘Our results demonstrate that natural selection can rapidly rewire regulatory networks,’” Shuker said. He put down the iPad. “So it’s a perfect, beautiful example of rapid neo-Darwinian evolution,” he declared.

Shuker distilled the feelings of a lot of skeptics I talked to at the conference. The high-flying rhetoric about a paradigm shift was, for the most part, unwarranted, they said. Nor were these skeptics limited to the peanut gallery. Several of them gave talks of their own.

“I think I’m expected to represent the Jurassic view of evolution,” said Douglas Futuyma when he got up to the podium. Futuyma is a soft-spoken biologist at Stony Brook University in New York and the author of a leading textbook on evolution. In other words, he was the target of many complaints during the meeting that textbooks paid little heed to things like epigenetics and plasticity. In effect, Futuyma had been invited to tell his colleagues why those concepts were ignored.

“We must recognize that the core principles of the Modern Synthesis are strong and well-supported,” Futuyma declared. Not only that, he added, but the kinds of biology being discussed at the Royal Society weren’t actually all that new. The architects of the Modern Synthesis were already talking about them over 50 years ago. And there’s been a lot of research guided by the Modern Synthesis to make sense of them.

Take plasticity. The genetic variations in an animal or a plant govern the range of forms into which organism can develop. Mutations can alter that range. And mathematical models of natural selection show how it can favor some kinds of plasticity over others.

If the Extended Evolutionary Synthesis was so superfluous, then why was it gaining enough attention to warrant a meeting at the Royal Society? Futuyma suggested that its appeal was emotional rather than scientific. It made life an active force rather than the passive vehicle of mutations.

“I think what we find emotionally or aesthetically more appealing is not the basis for science,” Futuyma said.

Still, he went out of his way to say that the kind of research described at the meeting could lead to some interesting insights about evolution. But those insights would only arise with some hard work that leads to hard data. “There have been enough essays and position papers,” he said.

Some members in the audience harangued Futuyma a bit. Other skeptical speakers sometimes got exasperated by arguments they felt didn’t make sense. But the meeting managed to reach its end on the third afternoon without fisticuffs.

“This is likely the first of many, many meetings,” Laland told me. In September, a consortium of scientists in Europe and the United States received $11 million in funding (including $8 million from the John Templeton Foundation) to run 22 studies on the Extended Evolutionary Synthesis.

Many of these studies will test predictions that have emerged from the synthesis in recent years. They will see, for example, if species that build their own environments — spider webs, wasp nests and so on — evolve into more species than ones that don’t. They will look at whether more plasticity allows species to adapt faster to new environments.

“It’s doing the research, which is what our critics are telling us to do,” said Laland. “Go find the evidence.”

Correction: An earlier version of this article misidentified the photograph of Andy Whiten as Gerd Müller.

This article was reprinted on TheAtlantic.com.

O bichinho que desafia Deus (El País)

Organismo marinho mostra por que o ser humano não está no topo da evolução

MANUEL ANSEDE

Barcelona 13 JUN 2016 – 21:07 CEST

Os biólogos Ricard Albalat e Cristian Cañestro, com exemplares do 'Oikopleura'.

Os biólogos Ricard Albalat e Cristian Cañestro, com exemplares do ‘Oikopleura’. JUAN BARBOSA 

“Só o acaso pode ser interpretado como uma mensagem. Aquilo que acontece por necessidade, aquilo que é esperado e que se repete todos os dias, não é senão uma coisa muda. Somente o acaso tem voz”, escreveu Milan Kundera em A Insustentável Leveza do Ser. E tem algo que fala, ou melhor, grita, numa praia de Badalona, perto de Barcelona: a que é dominada pela Ponte do Petróleo. Por esse dique de 250 metros, que penetra no mar Mediterrâneo, eram descarregados produtos petrolíferos até o final do século XX. E a seus pés se levanta desde 1870 a fábrica do Anís del Mono, o licor em cujo rótulo aparece um símio com cara de Charles Darwin em referência à teoria da evolução, que gerava polêmica na época.

Hoje, a Ponte do Petróleo é um belo mirante com uma estátua de bronze dedicada ao macaco com rosto darwinista. E, por um acaso que fala, entre seus frequentadores se encontra uma equipe de biólogos evolutivos do departamento de Genética da Universidade de Barcelona. Os cientistas caminham pela passarela sobre o oceano e lançam um cubo para fisgar um animal marinho, o Oikopleura dioica, de apenas três centímetros, mas que possui boca, ânus, cérebro e coração. Parece insignificante, mas, como Darwin, faz estremecer o discurso das religiões. Coloca o ser humano no lugar que lhe corresponde: com o resto dos animais.

“Temos sido mal influenciados pela religião, pensando que estávamos no topo da evolução. Na verdade, estamos no mesmo nível que o dos outros animais”, diz o biólogo Cristian Cañestro. Ele e o colega Ricard Albalat dirigem um dos únicos três centros científicos do mundo dedicados ao estudo do Oikopleura dioica. Os outros dois estão na Noruega e no Japão. O centro espanhol é uma salinha fria, com centenas de exemplares praticamente invisíveis colocados em recipientes de água, num canto da Faculdade de Biologia da Universidade de Barcelona.

O organismo marinho ‘Oikopleura dioica’ indica que a perda de genes ancestrais, compartilhados com os humanos, seria o motor da evolução

“A visão até agora era que, ao evoluir, ganhávamos em complexidade, adquirindo genes. Era o que se pensava quando os primeiros genomas foram sequenciados: de mosca, de minhoca e do ser humano. Mas vimos que não é assim. A maioria de nossos genes está também nas medusas. Nosso ancestral comum os possuía. Não que tenhamos ganhado genes; eles é que perderam. A complexidade genética é ancestral”, diz Cañestro.

Em 2006, o biólogo pesquisava o papel de um derivado da vitamina A, o ácido retinoico, no desenvolvimento embrionário. Essa substância indica às células de um embrião o que têm que fazer para se transformar num corpo adulto. O ácido retinoico ativa os genes necessários, por exemplo, para formar as extremidades, o coração, os olhos e as orelhas dos animais. Cañestro estudava esse processo no Oikopleura. E ficou de boca aberta.

Uma fêmea de 'Oikopleura dioica' cheia de ovos.

Uma fêmea de ‘Oikopleura dioica’ cheia de ovos. CAÑESTRO & ALBALAT LAB

“Os animais utilizam uma grande quantidade de genes para sintetizar o ácido retinoico. Percebi que no Oikopleura dioica faltava um desses genes. Depois vi que faltavam outros. Não encontramos nenhum”, recorda. Esse animal de três milímetros fabrica seu coração, de maneira inexplicável, sem ácido retinoico. “Se você vê um carro se mover sem rodas, nesse dia sua percepção sobre as rodas muda”, diz Cañestro.

O último ancestral comum entre nós e esse minúsculo habitante do oceano viveu há cerca de 500 milhões de anos. Desde então, o Oikopleura perdeu 30% dos genes que nos uniam. E fez isso com sucesso. Se você entrar em qualquer praia do mundo, ali estará ele rodeando o seu corpo. Na batalha da seleção natural, os Oikopleura ganharam. Sua densidade atinge 20.000 indivíduos por metro cúbico de água em alguns ecossistemas marinhos. São perdedores, mas só de genes.

Nosso último ancestral comum viveu há 500 milhões de anos. Desde então, o ‘Oikopleura’ perdeu 30% dos genes que nos uniam

Albalat e Cañestro acabam de publicar na revista especializada Nature Reviews Genetics um artigo que analisa a perda de genes como motor da evolução. Seu texto despertou interesse mundial. Foi recomendado pela F1000Prime, uma publicação internacional que aponta os melhores artigos sobre biologia e medicina. O trabalho começa com uma frase do imperador romano Marco Aurelio, filósofo estoico: “A perda nada mais é do que mudança, e a mudança é um prazer da natureza”.

Os dois biólogos afirmam que a perda de genes pode inclusive ter sido essencial para a origem da espécie humana. “O chimpanzé e o ser humano compartilham mais de 98% do seu genoma. Talvez tenhamos que procurar as diferenças nos genes que foram perdidos de maneira diferente durante a evolução dos humanos e dos demais primatas. Alguns estudos sugerem que a perda de um gene fez com que a musculatura de nossa mandíbula ficasse menor, o que permitiu aumentar o volume do nosso crânio”, diz Albalat. Talvez, perder genes nos tornou mais inteligentes que o resto dos mortais.

Pesquisadores do laboratório de Cristian Cañestro e Ricard Albalat.Pesquisadores do laboratório de Cristian Cañestro e Ricard Albalat. UB

 Em 2012, um estudo do geneticista norte-americano Daniel MacArthur mostrou que, em média, qualquer pessoa saudável tem 20 genes desativados. E isso aparentemente não importa. Albalat e Cañestro, do Instituto de Pesquisa da Biodiversidade (IRBio) da Universidade de Barcelona, citam dois exemplos muito estudados. Em algumas pessoas, os genes que codificam as proteínas CCR5 e DUFFY foram anulados por mutações. São as proteínas usadas, respectivamente, pelo vírus HIV e o parasita causador da malária para entrar nas células. A perda desses genes torna os humanos resistentes a essas doenças.

No laboratório de Cañestro e Albalat, há um cartaz que imita o do filme Cães de Aluguel (“Reservoir Dogs”, em inglês), de Quentin Tarantino: os cientistas e outros membros de sua equipe aparecem vestidos com camisa branca e gravata preta. A montagem se chama Reservoir Oiks, em alusão ao Oikopleura. Os dois biólogos acreditam que o organismo marinho permitirá formular e responder perguntas novas sobre nosso manual de instruções comum: o genoma.

O ‘Oikopleura’ permite estudar quais genes são essenciais: por que algumas mutações são irrelevantes e outras provocam efeitos devastadores em nossa saúde

O cérebro do Oikopleura tem cerca de 100 neurônios e o dos humanos, 86 bilhões. Mas somos muito mais semelhantes do que à primeira vista. Entre 60% e 80% das famílias de genes humanos têm um claro representante no genoma do Oikopleura. “Esse animal nos permite estudar quais genes humanos são essenciais”, diz Albalat. Em outras palavras: por que algumas mutações são irrelevantes e outras provocam efeitos terríveis em nossa saúde.

Os seres vivos possuem um sistema celular que repara as mutações surgidas no DNA. O Oikopleura doica perdeu 16 dos 83 genes ancestrais que regulam esse processo. Essa incapacidade para a autorreparação poderia explicar sua perda extrema de genes, segundo o artigo da Nature Reviews Genetics.

O olhar de Cañestro se ilumina quando ele fala dessas ausências. Os genes costumam atuar em grupo para levar a cabo uma função. Se de um grupo conhecido de oito genes faltam sete no Oikopleura, pois a função foi perdida, a permanência do oitavo gene pode revelar uma segunda função essencial que teria passado despercebida. Esse gene seria como um cruzamento de estradas. Desmantelada uma rodovia, ele sobrevive porque é fundamental em outra. “Essa segunda função já estava no ancestral comum e pode ser importante nos humanos”, diz Cañestro.

“Não existem animais superiores ou inferiores. Nossas peças de Lego são basicamente as mesmas, embora com elas possamos construir coisas diferentes”, afirma. Pense no seu lugar no mundo da próxima vez que mergulhar no mar. Essa neve branca que flutua na água e pode ser vista contra a luz são os excrementos do Oikopleura.

Why E O Wilson is wrong about how to save the Earth (AEON)

01 March, 2016

Robert Fletcher is an associate professor at the Sociology of Development and Change Group at Wageningen University in the Netherlands. His most recent book is Romancing the Wild: Cultural Dimensions of Ecotourism (2014).

Bram Büscher is a professor and Chair at the Sociology of Development and Change Group at Wageningen University in the Netherlands. His most recent book is Transforming the Frontier: Peace Parks and the Politics of Neoliberal Conservation in Southern Africa (2013).

Edited by Brigid Hains

Opinion sized gettyimages 459113790

A member of the military-style Special Ranger Patrol talks to a suspected rhino poacher on 7 November 2014 at the Kruger National Park, South Africa. Photo by James Oatway/Sunday Times/Getty

Edward O Wilson is one of the world’s most revered, reviled and referenced conservation biologists. In his new book (and Aeon essayHalf-Earth, he comes out with all guns blazing, proclaiming the terrible fate of biodiversity, the need for radical conservation, and humanity’s centrality in both. His basic message is simple: desperate times call for desperate measures, ‘only by setting aside half the planet in reserve, or more, can we save the living part of the environment and achieve the stabilisation required for our own survival’. Asserting that ‘humanity’ behaves like a destructive juggernaut, Wilson is deeply concerned that the current ‘sixth extinction’ is destroying many species before scientists have even been able to identify them.

Turning half of the Earth into a series of nature parks is a grand utopian vision for conservation, perhaps even a hyperbolic one, yet Wilson seems deadly serious about it. Some environmental thinkers have been arguing the exact opposite, namely that conservation should give up its infatuation with parks and focus on ‘mixing’ people and nature in mutually conducive ways. Wilson defends a traditional view that nature needs more protection, and attacks them for being ‘unconcerned with what the consequences will be if their beliefs are played out’. As social scientists who study the impact of international conservation on peoples around the world, we would argue that it is Wilson himself who has fallen into this trap: the world he imagines in Half-Earth would be a profoundly inhumane one if ever his beliefs were ‘played out’.

The ‘nature needs half’ idea is not entirely new – it is an extreme version of a more widespread ‘land sparing’ conservation strategy. This is not about setting aside half the Earth as a whole but expanding the world’s current network of protected areas to create a patchwork grid encompassing at least half the world’s surface (and the ocean) and hence ‘about 85 per cent’ of remaining biodiversity. The plan is staggering in scale: protected areas, according to the International Union for the Conservation of Nature, currently incorporate around 10-15 per cent of the Earth’s terrain, so would need to more than triple in extent.

Wilson identifies a number of causes of the current ecological crisis, but is particularly concerned by overpopulation. ‘Our population,’ he argues, ‘is too large for safety and comfort… Earth’s more than 7 billion people are collectively ravenous consumers of all the planet’s inadequate bounty.’ But can we talk about the whole of humanity in such generalised terms? In reality, the world is riven by dramatic inequality, and different segments of humanity have vastly different impacts on the world’s environments. The blame for our ecological problems therefore cannot be spread across some notion of a generalised ‘humanity’.

Although Wilson is careful to qualify that it is the combination ofpopulation growth and ‘per-capita consumption’ that causes environmental degradation, he is particularly concerned about places he identifies as the remaining high-fertility problem spots – ‘Patagonia, the Middle East, Pakistan, and Afghanistan, plus all of sub-Saharan Africa exclusive of South Africa’. These are countries with some of the world’s lowest incomes. Paradoxically, then, it is those consuming the least that are considered the greatest problem. ‘Overpopulation’, it seems, is the same racialised bogeyman as ever, and the poor the greatest threat to an environmentally-sound future.

Wilson’s Half-Earth vision is offered as an explicit counterpoint to so-called ‘new’ or ‘Anthropocene’ conservationists, who are loosely organised around the controversial Breakthrough Institute. For Wilson, these ‘Anthropocene ideologists’ have given up on nature altogether. In her book, Rambunctious Garden (2011), Emma Marris characteristically argues that there is no wilderness left on the Earth, which is everywhere completely transformed by the human presence. According to Anthropocene thinking, we are in charge of the Earth and must manage it closely whether we like it or not. Wilson disagrees, insisting that ‘areas of wilderness… are real entities’. He contends that an area need not be ‘pristine’ or uninhabited to be wilderness, and ‘[w]ildernesses have often contained sparse populations of people, especially those indigenous for centuries or millennia, without losing their essential character’.

Research across the globe has shown that many protected areas once contained not merely ‘sparse’ inhabitants but often quite dense populations – clearly incompatible with the US Wilderness Act’s classic definition of wilderness as an area ‘where man himself is a visitor who does not remain’. Most existing ‘wilderness’ parks have required the removal or severe restriction of human beings within their bounds. Indeed, one of Wilson’s models for conservation success – Gorongosa National Park in Mozambique – sidelined local people despite their unified opposition. In his book Conservation Refugees (2009), Mark Dowie estimates that 20-50 million people have been displaced by previous waves of protected-area creation. To extend protected areas to half of the Earth’s surface would require a relocation of human populations on a scale that could dwarf all previous conservation refugee crises.

Would these people include Montana cattle ranchers? Or Australian wheat growers? Or Florida retirees? The answer, most likely, is no, for the burden of conservation has never been shared equitably across the world. Those who both take the blame and pay the greatest cost of environmental degradation are, almost always, those who do not have power to influence either their own governments or international politics. It is the hill tribes of Thailand, the pastoralists of Tanzania, and the forest peoples of Indonesia who are invariably expected to relocate, often at gunpoint, as Dowie and many scholars, including Dan Brockington in his book Fortress Conservation (2002), have demonstrated.

How will human society withstand the shock of removing so much land and ocean from food-growing and other uses? Wilson criticises the Anthropocene worldview’s faith that technological innovation can solve environmental problems or find substitutes for depleted resources, but he simultaneously promotes his own techno-fix in a vision of ‘intensified economic evolution’ in which ‘the free market, and the way it is increasingly shaped by high technology’ will solve the problem seemingly automatically. According to Wilson, ‘products that win competition today… are those that cost less to manufacture and advertise, need less frequent repair and replacement, and give highest performance with a minimum amount of energy’. He thus invokes a biological version of Adam Smith’s invisible hand in maintaining that ‘[j]ust as natural selection drives organic evolution by competition among genes to produce more copies of themselves per unit cost in the next generation, raising benefit-to-cost of production drives the evolution of the economy’ and asserting, without any evidence, that ‘[a]lmost all of the competition in a free market, other than in military technology, raises the average quality of life’.

Remarkably, this utopian optimism about technology and the workings of the free market leads Wilson to converge on a position rather like that of the Anthropocene conservationists he so dislikes, advocating a vision of ‘decoupling economic activity from material and environmental throughputs’ in order to create sustainable livelihoods for a population herded into urban areas to free space for self-willed nature. The Breakthrough Institute has recently promoted its own, quite similar, manifesto for land sparing and decoupling to increase terrain for conservation.

In this vision, science and technology can compensate for some of humanity’s status as the world’s ‘most destructive species’. And at the pinnacle of science stands (conservation) biology, according to Wilson. He argues: ‘If people are to live long and healthy lives in the sustainable Eden of our dreams, and our minds are to break free and dwell in the far more interesting universe of reason triumphant over superstition, it will be through advances in biology.’ How exactly humans are to ‘break free’ is not explained and is, in fact, impossible according to Wilson himself, given ‘the Darwinian propensity in our brain’s machinery to favour short-term decisions over long-range planning’. As far as Wilson is concerned, any worldview that does not favour protected-area expansion as the highest goal is by definition an irrational one. In this way, the world’s poor are blamed not only for overpopulating biodiversity hotspots but also for succumbing to the ‘religious belief and inept philosophical thought’ standing in the way of environmental Enlightenment.

Let us finish by making a broader point, drawing on Wilson’s approving quotation of Alexander von Humboldt, the 19th-century German naturalist who claimed that ‘the most dangerous worldview is the worldview of those who have not viewed the world’. In viewing the world, we also construct it, and the world Wilson’s offers us in Half-Earth is a truly bizarre one. For all his zeal, (misplaced) righteousness and passion, his vision is disturbing and dangerous, and would have profoundly negative ‘consequences if played out’. It would entail forcibly herding a drastically reduced human population into increasingly crowded urban areas to be managed in oppressively technocratic ways. How such a global programme of conservation Lebensraum would be accomplished is left to the reader’s imagination. We therefore hope readers will not take Wilson’s proposal seriously. Addressing biodiversity loss and other environmental problems must proceed by confronting the world’s obscene inequality, not by blaming the poor and trusting the ‘free market’ to save them.


Half-Earth (AEON)

29 February, 2016

Half of the Earth’s surface and seas must be dedicated to the conservation of nature, or humanity will have no future

by Edward O Wilson

Header essay nationalgeographic 381719

The Serengeti National Park. Photo by Medford Taylor/National Geographic

Edward O Wilson is a professor emeritus in entomology at Harvard. Half-Earth concludes Wilson’s trilogy begun by The Social Conquest of Earth and The Meaning of Human Existence, a National Book Award finalist. 

Edited by Pam Weintraub

Unstanched haemorrhaging has only one end in all biological systems: death for an organism, extinction for a species. Researchers who study the trajectory of biodiversity loss are alarmed that, within the century, an exponentially rising extinction rate might easily wipe out most of the species still surviving at the present time.

The crucial factor in the life and death of species is the amount of suitable habitat left to them. When, for example, 90 per cent of the area is removed, the number that can persist sustainably will descend to about a half. Such is the actual condition of many of the most species-rich localities around the world, including Madagascar, the Mediterranean perimeter, parts of continental southwestern Asia, Polynesia, and many of the islands of the Philippines and the West Indies. If 10 per cent of the remaining natural habitat were then also removed – a team of lumbermen might do it in a month – most or all of the surviving resident species would disappear.

Today, every sovereign nation in the world has a protected-area system of some kind. All together the reserves number about 161,000 on land and 6,500 over marine waters. According to the World Database on Protected Areas, a joint project of the United Nations Environmental Program and the International Union for Conservation of Nature, they occupied by 2015 a little less than 15 per cent of Earth’s land area and 2.8 per cent of Earth’s ocean area. The coverage is increasing gradually. This trend is encouraging. To have reached the existing level is a tribute to those who have led and participated in the global conservation effort.

But is the level enough to halt the acceleration of species extinction? Unfortunately, it is in fact nowhere close to enough. The declining world of biodiversity cannot be saved by the piecemeal operations in current use alone. The extinction rate our behaviour is now imposing on the rest of life, and seems destined to continue, is more correctly viewed as the equivalent of a Chicxulub-sized asteroid strike played out over several human generations.

The only hope for the species still living is a human effort commensurate with the magnitude of the problem. The ongoing mass extinction of species, and with it the extinction of genes and ecosystems, ranks with pandemics, world war, and climate change as among the deadliest threats that humanity has imposed on itself. To those who feel content to let the Anthropocene evolve toward whatever destiny it mindlessly drifts, I say please take time to reconsider. To those who are steering the growth of reserves worldwide, let me make an earnest request: don’t stop, just aim a lot higher.

see just one way to make this 11th-hour save: committing half of the planet’s surface to nature to save the immensity of life-forms that compose it. Why one-half? Why not one-quarter or one-third? Because large plots, whether they already stand or can be created from corridors connecting smaller plots, harbour many more ecosystems and the species composing them at a sustainable level. As reserves grow in size, the diversity of life surviving within them also grows. As reserves are reduced in area, the diversity within them declines to a mathematically predictable degree swiftly – often immediately and, for a large fraction, forever. A biogeographic scan of Earth’s principal habitats shows that a full representation of its ecosystems and the vast majority of its species can be saved within half the planet’s surface. At one-half and above, life on Earth enters the safe zone. Within half, existing calculations from existing ecosystems indicate that more than 80 per cent of the species would be stabilised.

There is a second, psychological argument for protecting half of Earth. The current conservation movement has not been able to go the distance because it is a process. It targets the most endangered habitats and species and works forward from there. Knowing that the conservation window is closing fast, it strives to add increasing amounts of protected space, faster and faster, saving as much as time and opportunity will allow.

The key is the ecological footprint, defined as the amount of space required to meet the needs of an average person

Half-Earth is different. It is a goal. People understand and prefer goals. They need a victory, not just news that progress is being made. It is human nature to yearn for finality, something achieved by which their anxieties and fears are put to rest.

The Half-Earth solution does not mean dividing the planet into hemispheric halves or any other large pieces the size of continents or nation-states. Nor does it require changing ownership of any of the pieces, but instead only the stipulation that they be allowed to exist unharmed. It does, on the other hand, mean setting aside the largest reserves possible for nature, hence for the millions of other species still alive.

The key to saving one-half of the planet is the ecological footprint, defined as the amount of space required to meet all of the needs of an average person. It comprises the land used for habitation, fresh water, food production and delivery, personal transportation, communication, governance, other public functions, medical support, burial, and entertainment. In the same way the ecological footprint is scattered in pieces around the world, so are Earth’s surviving wildlands on the land and in the sea. The pieces range in size from the major desert and forest wildernesses to pockets of restored habitats as small as a few hectares.

But, you may ask, doesn’t a rising population and per-capita consumption doom the Half-Earth prospect? In this aspect of its biology, humanity appears to have won a throw of the demographic dice. Its population growth has begun to decelerate autonomously, without pressure one way or the other from law or custom. In every country where women have gained some degree of social and financial independence, their average fertility has dropped by a corresponding amount through individual personal choice.

There won’t be an immediate drop in the total world population. An overshoot still exists due to the longevity of the more numerous offspring of earlier, more fertile generations. There also remain high-fertility countries, with an average of more than three surviving children born to each woman, thus higher than the 2.1 children per woman that yields zero population growth. Even as it decelerates toward zero growth, population will reach between 9.6 billion and 12.3 billion, up from the 7.2 billion existing in 2014. That is a heavy burden for an already overpopulated planet to bear, but unless women worldwide switch back from the negative population trend of fewer than 2.1 children per woman, a turn downward in the early 22nd century is inevitable.

And what of per-capita consumption? The footprint will evolve, not to claim more and more space, as you might at first suppose, but less. The reason lies in the evolution of the free market system, and the way it is increasingly shaped by high technology. The products that win are those that cost less to manufacture and advertise, need less frequent repair and replacement, and give highest performance with a minimum amount of energy. Just as natural selection drives organic evolution by competition among genes to produce more copies of themselves per unit cost in the next generation, raising benefit-to-cost of production drives the evolution of the economy. Teleconferencing, online purchase and trade, ebook personal libraries, access on the Internet to all literature and scientific data, online diagnosis and medical practice, food production per hectare sharply raised by indoor vertical gardens with LED lighting, genetically engineered crops and microorganisms, long-distance business conferences and social visits by life-sized images, and not least the best available education in the world free online to anyone, anytime, and anywhere. All of these amenities will yield more and better results with less per-capita material and energy, and thereby will reduce the size of the ecological footprint.

In viewing the future this way, I wish to suggest a means to achieve almost free enjoyment of the world’s best places in the biosphere that I and my fellow naturalists have identified. The cost-benefit ratio would be extremely small. It requires only a thousand or so high-resolution cameras that broadcast live around the clock from sites within reserves. People would still visit any reserve in the world physically, but they could also travel there virtually and in continuing real time with no more than a few keystrokes in their homes, schools, and lecture halls. Perhaps a Serengeti water hole at dawn? Or a teeming Amazon canopy? There would also be available streaming video of summer daytime on the coast in the shallow offshore waters of Antarctica, and cameras that continuously travel through the great coral triangle of Indonesia and New Guinea. With species identifications and brief expert commentaries unobtrusively added, the adventure would be forever changing, and safe.

The spearhead of this intensive economic evolution, with its hope for biodiversity, is contained in the linkage of biology, nanotechnology, and robotics. Two ongoing enterprises within it, the creation of artificial life and artificial minds, seem destined to preoccupy a large part of science and high technology for the rest of the present century.

The creation of artificial life forms is already a reality. On 20 May 2010, a team of researchers at the J Craig Venter Institute in California announced the second genesis of life, this time by human rather than divine command. They had built live cells from the ground up. With simple chemical reagents off the shelf, they assembled the entire genetic code of a bacterial species, Mycoplasma mycoides, a double helix of 1.08 million DNA base pairs. During the process they modified the code sequence slightly, implanting a statement made by the late theoretical physicist Richard Feynman, ‘What I cannot create, I do not understand,’ in order to detect daughters of the altered mother cells in future tests.

If our minds are to break free and dwell in the far more interesting universe of reason triumphant over superstition, it will be through advances in biology

The textbook example of elementary artificial selection of the past 10 millennia is the transformation of teosinte, a species of wild grass with three races in Mexico and Central America, into maize (corn). The food found in the ancestor was a meagre packet of hard kernels. Over centuries of selective breeding it was altered into its modern form. Today maize, after further selection and widespread hybridisation of inbred strains that display ‘hybrid vigour’ is the principal food of hundreds of millions.

The first decade of the present century thus saw the beginning of the next new major phase of genetic modification beyond hybridisation: artificial selection and even direct substitution in single organisms of one gene for another. If we use the trajectory of progress in molecular biology during the previous half century as a historical guide, it appears inevitable that scientists will begin routinely to build cells of wide variety from the ground up, then induce them to multiply into synthetic tissues, organs, and eventually entire independent organisms of considerable complexity.

If people are to live long and healthy lives in the sustainable Eden of our dreams, and our minds are to break free and dwell in the far more interesting universe of reason triumphant over superstition, it will be through advances in biology. The goal is practicable because scientists, being scientists, live with one uncompromising mandate: press discovery to the limit. There has already emerged a term for the manufacture of organisms and parts of organisms: synthetic biology. Its potential benefits, easily visualised as spreading through medicine and agriculture, are limited only by imagination. Synthetic biology will also bring onto centre stage the microbe-based increase of food and energy.

Each passing year sees advances in artificial intelligence and their multitudinous applications – advances that would have been thought distantly futuristic a decade earlier. Robots roll over the surface of Mars. They travel around boulders and up and down slopes while photographing, measuring minutiae of topography, analysing the chemical composition of soil and rocks, and scrutinising everything for signs of life.

In the early period of the digital revolution, innovators relied on machine design of computers without reference to the human brain, much as the earliest aeronautical engineers used mechanical principles and intuition to design aircraft instead of imitating the flight of birds. But with the swift growth of both fields, one-on-one comparisons are multiplying. The alliance of computer technology and brain science has given birth to whole brain emulation as one of the ultimate goals of science.

From the time of the ancient human-destined line of amphibians, then reptiles, then mammals, the neural pathways of every part of the brain were repeatedly altered by natural selection to adapt the organism to the environment in which it lived. Step-by-step, from the Paleozoic amphibians to the Cenozoic primates, the ancient centres were augmented by newer centres, chiefly in the growing cortex, that added to learning ability. All things being equal, the ability of organisms to function through seasons and across different habitats gave them an edge in the constant struggle to survive and reproduce.

Little wonder, then, that neurobiologists have found the human brain to be densely sprinkled with partially independent centres of unconscious operations, along with all of the operators of rational thought. Located through the cortex in what might look at first like random arrays are the headquarters of process variously for numbers, attention, face-recognition, meanings, reading, sounds, fears, values, and error detection. Decisions tend to be made by the brute force of unconscious choice in these centres prior to conscious comprehension.

Next in evolution came consciousness, a function of the human brain that, among other things, reduces an immense stream of sense data to a small set of carefully selected bite-size symbols. The sampled information can then be routed to another processing stage, allowing us to perform what are fully controlled chains of operations, much like a serial computer. This broadcasting function of consciousness is essential. In humans, it is greatly enhanced by language, which lets us distribute our conscious thoughts across the social network.

What has brain science to do with biodiversity? At first, human nature evolved along a zigzag path as a continually changing ensemble of genetic traits while the biosphere continue to evolve on its own. But the explosive growth of digital technology transformed every aspect of our lives and changed our self-perception, bringing the ‘bnr’ industries (biology, nanotechnology, robotics) to the forefront of the modern economy. These three have the potential either to favour biodiversity or to destroy it.

I believe they will favour it, by moving the economy away from fossil fuels to energy sources that are clean and sustainable, by radically improving agriculture with new crop species and ways to grow them, and by reducing the need or even the desire for distant travel. All are primary goals of the digital revolution. Through them the size of the ecological footprint will also be reduced. The average person can expect to enjoy a longer, healthier life of high quality yet with less energy extraction and raw demand put on the land and sea. If we are lucky (and smart), world population will peak at a little more than 10 billion people by the end of the century followed by the ecological footprint soon thereafter. The reason is that we are thinking organisms trying to understand how the world works. We will come awake.

Silicon Valley dreamers of a digitised humanity have failed to give much thought at all to the biosphere

That process is already under way, albeit still far too slowly – with the end in sight in the 23rd century. We and the rest of life with us are in the middle of a bottleneck of rising population, shrinking resources, and disappearing species. As its stewards we need to think of our species as being in a race to save the living environment. The primary goal is to make it through the bottleneck to a better, less perilous existence while carrying through as much of the rest of life as possible. If global biodiversity is given space and security, most of the large fraction of species now endangered will regain sustainability on their own. Furthermore, advances made in synthetic biology, artificial intelligence, whole brain emulation, and other similar, mathematically based disciplines can be imported to create an authentic, predictive science of ecology. In it, the interrelations of species will be explored as fervently as we now search through our own bodies for health and longevity. It is often said that the human brain is the most complex system known to us in the universe. That is incorrect. The most complex is the individual natural ecosystem, and the collectivity of ecosystems comprising Earth’s species-level biodiversity. Each species of plant, animal, fungus, and microorganism is guided by sophisticated decision devices. Each is intricately programmed in its own way to pass with precision through its respective life cycle. It is instructed on when to grow, when to mate, when to disperse, and when to shy away from enemies. Even the single-celled Escherichia coli, living in the bacterial paradise of our intestines, moves toward food and away from toxins by spinning its tail cilium one way, then the other way, in response to chemosensory molecules within its microscopic body.

How minds and decision-making devices evolve, and how they interact with ecosystems is a vast area of biology that remains mostly uncharted – and still even undreamed by those scientists who devote their lives to it. The analytic techniques coming to bear on neuroscience, on Big Data theory, on simulations with robot avatars, and on other comparable enterprises will find applications in biodiversity studies. They are ecology’s sister disciplines.

It is past time to broaden the discussion of the human future and connect it to the rest of life. The Silicon Valley dreamers of a digitised humanity have not done that, not yet. They have failed to give much thought at all to the biosphere. With the human condition changing so swiftly, we are losing or degrading to uselessness ever more quickly the millions of species that have run the world independently of us and free of cost. If humanity continues its suicidal ways to change the global climate, eliminate ecosystems, and exhaust Earth’s natural resources, our species will very soon find itself forced into making a choice, this time engaging the conscious part of our brain. It is as follows: shall we be existential conservatives, keeping our genetically-based human nature while tapering off the activities inimical to ourselves and the rest of the biosphere? Or shall we use our new technology to accommodate the changes important solely to our own species, while letting the rest of life slip away? We have only a short time to decide.

The beautiful world our species inherited took the biosphere 3.8 billion years to build. The intricacy of its species we know only in part, and the way they work together to create a sustainable balance we have only recently begun to grasp. Like it or not, and prepared or not, we are the mind and stewards of the living world. Our own ultimate future depends upon that understanding. We have come a very long way through the barbaric period in which we still live, and now I believe we’ve learned enough to adopt a transcendent moral precept concerning the rest of life.

Reprinted from ‘Half-Earth: Our Planet’s Fight for Life’ by Edward O Wilson. Copyright © 2016 by Edward O Wilson. With permission of the publisher, Liveright Publishing Corporation. All rights reserved.

A single-celled organism capable of learning (Science Daily)

Date:
April 27, 2016
Source:
CNRS
Summary:
For the first time, scientists have demonstrated that an organism devoid of a nervous system is capable of learning. Biologists have succeeded in showing that a single-celled organism, the protist, is capable of a type of learning called habituation. This discovery throws light on the origins of learning ability during evolution, even before the appearance of a nervous system and brain. It may also raise questions as to the learning capacities of other extremely simple organisms such as viruses and bacteria.

The slime mold Physarum polycephalum (diameter: around 10 centimeters), made up of a single cell, was here cultivated in the laboratory on agar gel. Credit: Audrey Dussutour (CNRS)

For the first time, scientists have demonstrated that an organism devoid of a nervous system is capable of learning. A team from the Centre de Recherches sur la Cognition Animale (CNRS/Université Toulouse III — Paul Sabatier) has succeeded in showing that a single-celled organism, the protist Physarum polycephalum, is capable of a type of learning called habituation. This discovery throws light on the origins of learning ability during evolution, even before the appearance of a nervous system and brain. It may also raise questions as to the learning capacities of other extremely simple organisms such as viruses and bacteria. These findings are published in the Proceedings of the Royal Society B on 27 April 2016.

An ability to learn, and memory are key elements in the animal world. Learning from experiences and adapting behavior accordingly are vital for an animal living in a fluctuating and potentially dangerous environment. This faculty is generally considered to be the prerogative of organisms endowed with a brain and nervous system. However, single-celled organisms also need to adapt to change. Do they display an ability to learn? Bacteria certainly show adaptability, but it takes several generations to develop and is more a result of evolution. A team of biologists thus sought to find proof that a single-celled organism could learn. They chose to study the protist, or slime mold, Physarum polycephalum, a giant cell that inhabits shady, cool areas[1] and has proved to be endowed with some astonishing abilities, such as solving a maze, avoiding traps or optimizing its nutrition[2]. But until now very little was known about its ability to learn.

During a nine-day experiment, the scientists thus challenged different groups of this mold with bitter but harmless substances that they needed to pass through in order to reach a food source. Two groups were confronted either by a “bridge” impregnated with quinine, or with caffeine, while the control group only needed to cross a non-impregnated bridge. Initially reluctant to travel through the bitter substances, the molds gradually realized that they were harmless, and crossed them increasingly rapidly — behaving after six days in the same way as the control group. The cell thus learned not to fear a harmless substance after being confronted with it on several occasions, a phenomenon that the scientists refer to as habituation. After two days without contact with the bitter substance, the mold returned to its initial behavior of distrust. Furthermore, a protist habituated to caffeine displayed distrustful behavior towards quinine, and vice versa. Habituation was therefore clearly specific to a given substance.

Habituation is a form of rudimentary learning, which has been characterized in Aplysia (an invertebrate also called sea hare)[3]. This form of learning exists in all animals, but had never previously been observed in a non-neural organism. This discovery in a slime mold, a distant cousin of plants, fungi and animals that appeared on Earth some 500 million years before humans, improves existing understanding of the origins of learning, which markedly preceded those of nervous systems. It also offers an opportunity to study learning types in other very simple organisms, such as viruses or bacteria.

[1] This single cell, which contains thousands of nuclei, can cover an area of around a square meter and moves within its environment at speeds that can reach 5 cm per hour.

[2] See “Even single-celled organisms feed themselves in a ‘smart’ manner.” https://www.sciencedaily.com/releases/2010/02/100210164712.htm

[3] Mild tactile stimulation of the animal’s siphon normally causes the defensive reflex of withdrawing the branchiae. If the harmless tactile stimulation is repeated, this reflex diminishes and finally disappears, thus indicating habituation.


Journal Reference:

  1. Romain P. Boisseau, David Vogel, Audrey Dussutour. Habituation in non-neural organisms: evidence from slime mouldsProceedings of the Royal Society B: Biological Sciences, 2016; 283 (1829): 20160446 DOI: 10.1098/rspb.2016.0446

New appreciation for human micro biome leads to greater understanding of human health (Science Daily)

Date: February 14, 2016

Source: University of Oklahoma

Summary: Anthropologists are studying the ancient and modern human micro biome and the role it plays in human health and disease. By applying genomic and proteomic sequencing technologies to ancient human microbiomes, such as coprolites and dental calculus, as well as to contemporary microbiomes in traditional and industrialized societies, Researchers are advancing the understanding of the evolutionary history of our microbial self and its impact on human health today.


University of Oklahoma anthropologists are studying the ancient and modern human microbiome and the role it plays in human health and disease. By applying genomic and proteomic sequencing technologies to ancient human microbiomes, such as coprolites and dental calculus, as well as to contemporary microbiomes in traditional and industrialized societies, OU researchers are advancing the understanding of the evolutionary history of our microbial self and its impact on human health today.

Christina Warinner, professor in the Department of Anthropology, OU College of Arts and Sciences, will present, “The Evolution and Ecology of Our Microbial Self,” during the American Association for the Advancement of Science panel on Evolutionary Biology Impacts on Medicine and Public Health, at 1:30 pm, Sunday, Feb. 14, 2016 in the Marriott Marshall Ballroom West, Washington, DC. Warinner will discuss how major events, such as the invention of agriculture and the advent of industrialization, have affected the human microbiome.

“We don’t have a complete picture of the microbiome,” Warinner said. “OU research indicates human behavior over the past 2000 years has impacted the gut microbiome. Microbial communities have become disturbed, but before we can improve our health, we have to understand our ancestral microbiome. We cannot make targeted or informed interventions until we know that. Ancient samples allow us to directly measure changes in the human microbiome at specific times and places in the past.”

Warinner and colleague, Cecil M. Lewis, Jr., co-direct OU’s Laboratories of Molecular Anthropology and Microbiome Research and the research focused on reconstructing the ancestral human oral and gut microbiome, addressing questions concerning how the relationship between humans and microbes has changed through time and how our microbiomes influence health and disease in diverse populations, both today and in the past. Warinner and Lewis are leaders in the field of paleogenomics, and the OU laboratories house the largest ancient DNA laboratory in the United States.

Warinner is pioneering the study of ancient human microbiomes, and in 2014 she published the first detailed metagenomics and metaproteomic characterization of the ancient oral microbiome in the journal Nature Genetics. In 2015, she published a study on the identification of milk proteins in ancient dental calculus and the reconstruction of prehistoric European dairying practices. In the same year, she was part of an international team that published the first South American hunter-gatherer gut microbiome and identified Treponema as a key missing ancestral microbe in industrialized societies.

Cells talk to their neighbors before making a move (Science Daily)

Comparing notes boosts cells sensing accuracy

Date: January 21, 2016

Source: Emory Health Sciences

Summary: To decide whether and where to move in the body, cells must read chemical signals in their environment. Individual cells do not act alone during this process, two new studies on mouse mammary tissue show. Instead, the cells make decisions collectively after exchanging information about the chemical messages they are receiving.


Like the telephone game — where a line of people whisper a message to the person next to them — an original message starts to become distorted as it travels down the line between cells, report scientists. (Stock image) Credit: © sakkmesterke / Fotolia

To decide whether and where to move in the body, cells must read chemical signals in their environment. Individual cells do not act alone during this process, two new studies on mouse mammary tissue show. Instead, the cells make decisions collectively after exchanging information about the chemical messages they are receiving.

“Cells talk to nearby cells and compare notes before they make a move,” says Ilya Nemenman, a theoretical biophysicist at Emory University and a co-author of both studies, published by the Proceedings of the National Academy of Sciences (PNAS). The co-authors also include scientists from Johns Hopkins, Yale and Purdue.

The researchers discovered that the cell communication process works similarly to a message relay in the telephone game. “Each cell only talks to its neighbor,” Nemenman explains. “A cell in position one only talks to a cell in position two. So position one needs to communicate with position two in order to get information from the cell in position three.”

And like the telephone game — where a line of people whisper a message to the person next to them — the original message starts to become distorted as it travels down the line.

The researchers found that, for the cells in their experiments, the message begins to get garbled after passing through about four cells, by a factor of about three.

“We built a mathematical model for this linear relay of cellular information and derived a formula for its best possible accuracy,” Nemenman says. “Directed cell migration is important in processes from cancer to the development of organs and tissues. Other researchers can apply our model beyond the mouse mammary gland and analyze similar phenomena in a wide variety of healthy and diseased systems.”

Since at least the 1970s, and pivotal work by Howard Berg and Ed Purcell, scientists have been trying to understand in detail how cells decide to take an action based on chemical cues.

Every cell in a body has the same genome but they can do different things and go in different directions because they measure different chemical signals in their environment. Those chemical signals are made up of molecules that randomly move around.

“Cells can sense not just the precise concentration of a chemical signal, but concentration differences,” Nemenman says. “That’s very important because in order to know which direction to move, a cell has to know in which direction the concentration of the chemical signal is higher. Cells sense this gradient and it gives them a reference for the direction in which to move and grow.”

Berg and Purcell understood the best possible margin of error — the detection limit — for such gradient sensing. During the subsequent 30 years, researchers have established that many different cells, in many different organisms, work at this detection limit. Living cells can sense chemicals better than any humanmade device.

It was not known, however, that cells can sense signals and make movement decisions collectively.

“Previous research has typically focused on cultured cells,” Nemenman says. “And when you culture cells, the first thing to go away is cell-to-cell interaction. The cells are no longer a functioning tissue, but a culture of individual cells, so it’s difficult to study many collective effects.”

The first PNAS paper drew from three-dimensional micro-fluidic techniques from the Yale University lab of Andre Levchenko, a biomedical engineer who studies how cells navigate; research on mouse mammary tissue at the Johns Hopkins lab of Andrew Ewald, a biologist focused on the cellular mechanisms of cancer; and the quantification methods of Nemenman, who studies the physics of biological systems, and Andrew Mugler, a former post-doctoral fellow in Nemenman’s lab at Emory who now has his own research group at Purdue.

The 3D micro fluidics allowed the researchers to experiment with functional organoids, or clumps of cells. The method does not disrupt the interaction of the cells.

The results showed that epidermal growth factor, or EGF, is the signal that these cells track, and that the cells were not making decisions about which way to move as individuals, but collectively.

“The clumps of cells, working collectively, could detect insanely small differences in concentration gradients — such as 498 molecules of EGF versus 502 molecules — on different sides of one cell,” Nemenman says. “That accuracy is way better than the best possible margin of error determined by Berg and Purcell of about plus or minus 20. Even at these small concentration gradients, the organoids start reshaping and moving toward the higher concentration. These cells are not just optimal gradient detectors. They seem super optimal, defying the laws of nature.”

Collective cell communication boosts their detection accuracy, turning a line of about four cells into a single, super-accurate measurement unit.

In the second PNAS paper, Nemenman, Mugler and Levchenko looked at the limits to the cells’ precision of collective gradient sensing not just spatially, but over time.

“We hypothesized that if the cells kept on communicating with one another over hours or days, and kept on accumulating information, that might expand the accuracy further than four cells across,” Nemenman says. “Surprisingly, however, this was not the case. We found that there is always a limit of how far information can travel without being garbled in these cellular systems.”

Together, the two papers offer a detailed model for collective cellular gradient sensing, verified by experiments in mouse mammary organoids. The collective model expands the classic Berg-Purcell results for the best accuracy of an individual cell, which stood for almost forty years. The new formula quantifies the additional advantages and limitations on the accuracy coming from the cells working collectively.

“Our findings are not just intellectually important. They provide new ways to study many normal and abnormal developmental processes,” Nemenman says.


Journal References:

  1. David Ellison, Andrew Mugler, Matthew D. Brennan, Sung Hoon Lee, Robert J. Huebner, Eliah R. Shamir, Laura A. Woo, Joseph Kim, Patrick Amar, Ilya Nemenman, Andrew J. Ewald, and Andre Levchenko. Cell–cell communication enhances the capacity of cell ensembles to sense shallow gradients during morphogenesisPNAS, January 2016 DOI: 10.1073/pnas.1516503113
  2. Andrew Mugler, Andre Levchenko, and Ilya Nemenman. Limits to the precision of gradient sensing with spatial communication and temporal integrationPNAS, January 2016 DOI: 10.1073/pnas.1509597112

Borboletas estão encolhendo por causa das mudanças climáticas (O Globo)

Estudo mostra redução no tamanho de duas espécies na Groenlândia

POR O GLOBO

A Boloria chariclea foi uma das espécies analisadas pelos pesquisadores – Divulgação/Toke T. Hoye

RIO — As mudanças climáticas já provocam impactos sobre a Humanidade, mas também sobre algumas espécies animais. Um estudo publicado ontem na revista científica “Biology Letters” mostra que borboletas na Groenlândia se tornaram menores como resposta ao aumento das temperaturas. Para os pesquisadores, a mudança no tamanho corporal prejudica a mobilidade, que pode causar graves consequências à dinâmica populacional e distribuição geográfica das espécies.

Pesquisadores da Universidade de Aarhus, na Dinamarca, analisaram aproximadamente 4,5 mil borboletas de duas espécies diferentes capturadas entre 1996 e 2013. Os resultados apontaram para uma redução no tamanho das asas, na mesma taxa em ambas as espécies, provocada pelo aumento das temperaturas durante o verão. As espécies estudadas foram a Boloria chariclea e a Colias hecla.

— Nossos estudos mostram que machos e fêmeas seguem o mesmo padrão, que é similar em duas espécies diferentes, o que sugere que o clima exerce um papel importante na determinação do tamanho corporal das borboletas na Groenlândia — explicou Toke T. Hoye, pesquisador da Universidade de Aarhus.Esse é um dos primeiros estudos a acompanhar mudanças no tamanho corporal de uma espécie durante um período de mudanças climáticas, e corrobora pesquisas realizadas em laboratório, mas raramente demonstradas em campo.

A Colias hecla está ficando menor por causa dos verões mais quentes no Ártico – Divulgação/Toke T. Hoye

Experimentos apontam que a mudança no tamanho corporal é uma resposta antecipada às mudanças climáticas, que pode acontecer de duas maneiras. Para algumas espécies, uma temporada maior de alimentação pode resultar no aumento do tamanho, enquanto para outras, alterações metabólicas provocam a perda de energia e consequente redução das dimensões.

— Nós, humanos, usamos mais energia quando está frio, porque precisamos manter a temperatura corporal constante — disse Hoye. — Mas para a larva da borboleta e outros animais de sangue frio, que dependem do ambiente para manter a temperatura, o metabolismo aumenta em temperaturas maiores por causa dos processos bioquímicos que se tornam mais rápidos. Dessa maneira, a larva gasta mais energia do que é capaz de consumir. Nossos resultados indicam que essa mudança é tão significativa que a taxa de crescimento das larvas diminui. E quando as larvas são menores, as borboletas também se tornam menores.

As consequências para as borboletas do Ártico podem ser significativas. Com corpos menores, a mobilidade é reduzida. Como as duas espécies vivem apenas no Norte, a redução no tamanho pode ter graves consequências na dinâmica populacional, e prejudicar a dispersão dos insetos.

— Elas vivem tão ao Norte que não podem se mover para regiões mais frias, e elas provavelmente vão desaparecer da parte mais ao Sul da Groenlândia por causa do aumento da temperatura — disse Hoye. — Além disso, sua capacidade de dispersão está se deteriorando, e corpos menores devem resultar em menor taxa de fecundidade. Então, essas espécies do Ártico devem enfrentar desafios severos causados pela rápida mudança climática.

Leia mais sobre esse assunto em  http://oglobo.globo.com/sociedade/sustentabilidade/borboletas-estao-encolhendo-por-causa-das-mudancas-climaticas-17714284#ixzz3o0Y0gr6z
© 1996 – 2015. Todos direitos reservados a Infoglobo Comunicação e Participações S.A. Este material não pode ser publicado, transmitido por broadcast, reescrito ou redistribuído sem autorização.

‘Não somos ratos de laboratório’, diz diretor da Sangamo Biosciences (O Globo)

Aparelho para sequenciamento genético. Para Lanphier, pesquisas com células-tronco não-reprodutivas são as únicas aceitáveis – David Paul Morris BLOOMBERG

Edward Lanphier comanda entidade ligada à medicina regenerativa e pede um freio nas pesquisas de manipulação do DNA com células reprodutivas

POR FABIO TEIXEIRA

RIO – Edward Lanphier comanda a Sangamo Biosciences, uma das entidades que formam a Aliança para a Medicina Regenerativa (ARM, na sigla em inglês), organização que reúne mais de 200 empresas no mundo da área de biotecnologia e instituições de pesquisa. A Aliança pediu uma moratória de prazo indefinido para pesquisas e prática de manipulação do DNA de células reprodutivas.

O debate sobre o tema, que já dura anos, esquentou com o desenvolvimento de técnicas que permitem que a edição de genes ocorra na prática, o que abre a possibilidade de gerar bebês sob medida.

Lanphier anunciou o pedido de interrupção nas pesquisas em um documento assinado por ele e outros membros da aliança. O texto, publicado na “Nature”, revista científica de renome internacional, declara que este tipo de pesquisa não deve ser levada adiante.

Edward Lanphier, diretor-presidente da Sangamo Biosciences – Divulgação

Enquanto nos Estados Unidos e em países europeus ainda não há uma definição prática sobre se é permitida ou não a manipulação genética de células reprodutivas, no Brasil, estudos deste tipo já foram proibidos. A resolução foi publicada em 2004 pela Comissão Nacional de Ética em Pesquisa (Conep), órgão do Ministério da Saúde. Ela diz: “As pesquisas com intervenção para modificação do genoma humano só poderão ser realizadas em células somáticas (não-reprodutivas).” Agora a questão seria o uso ilícito de técnicas desenvolvidas no exterior.

Em entrevista publicada esta segunda-feira na revista digital O GLOBO a Mais, Lanphier explica por que considera que até mesmo a pesquisa básica deve ser banida.

A moratória é geral?

Sim. O pedido de moratória é para que tenhamos um tempo para que todas as partes discutam o assunto. É um pedido. Mas a premissa da qual partimos é que mesmo com essa discussão existe uma linha que não pode ser ultrapassada.

Qual é o principal risco de editar o genoma de células reprodutivas (espermatozoides e óvulos)?

O grande problema é ético, apesar de haver também riscos de segurança e técnicos, que limitam o uso prático. A questão ética ultrapassa a barreira da legislação e políticas de cada país. Ela é fundamental.

Se é possível alterar o genoma, é possível escolher a cor do cabelo, dos olhos ou até da pele de um bebê?

Vai além disso. O problema é não só poder alterar as características de um indivíduo, mas também de todas as futuras gerações. Não somos ratos de laboratório, muito menos algo como um milho transgênico. Como espécie, nós humanos decidimos que somos únicos. Por décadas, os países desenvolvidos debateram a modificação de genes em células reprodutivas e se posicionaram contra isso.

É possível alterar genes que ditam características como inteligência ou até comportamento?

Essa é a nossa preocupação. Pois o indivíduo alterado passará as mudanças para as gerações futuras. Aberta a oportunidade deste tipo de pesquisa, ela pode ser usada para objetivos que não têm valor terapêutico, de tratamento de doenças. É um caminho sem volta. Nós, como sociedade, precisamos pensar no que nos torna humanos. No passado já nos posicionamos contra ações deste tipo, que podem nos levar a uma sociedade pautada pela eugenia.

O senhor poderia explicar a diferença entre a manipulação de células somáticas (não-reprodutivas) e a de óvulos e espermatozoides?

Existe uma diferença fundamental. É preto e branco. Na manipulação de células somáticas, você busca alterar um gene para criar uma resistência no indivíduo contra uma doença específica. Você não altera os genes de futuras gerações, caso a pessoa tenha filhos. A única coisa que se tenta fazer é curar doenças. Existe, porém, uma linha que não deve ser ultrapassada. E ela é alterar óvulos e espermatozoides, pois eles conferem hereditariedade para as características manipuladas.

Se o senhor muda uma única característica e ela é passada para gerações futuras, não é possível que outras mutações inesperadas aconteçam?

Isso é perfeitamente possível. É uma das questões que levantamos. Atualmente a natureza disto e suas possíveis consequências são completamente desconhecidas. Há muitas questões sem respostas. Precisamos responder a todas antes de sequer considerar a questão maior, que é a ética do processo. Ainda é muito cedo. Por isso, pedimos uma moratória.

Quais limites o senhor sente que é necessário criar a longo prazo?

Propusemos a moratória justamente para discutir o assunto. Não existe justificativa para realizar alterações genéticas em células reprodutivas.

O senhor cita uma possibilidade de rejeição da sociedade contra este tipo de pesquisa. O temor é de que isso atinja também a pesquisa com as demais células?

Seria uma rejeição motivada por falta de conhecimento.

Que linhas de estudo são consideradas promissoras?

As doenças com mais chances de serem curadas por este tipo de pesquisa são aquelas que têm um gene específico associado. É o caso de hemofilia, anemia falciforme e vários tipos de câncer. Essas são as oportunidades mais imediatas que se abrem com a pesquisa. Tecnicamente e teoricamente é possível ainda usar a tecnologia para alterar mais de um gene, para curar doenças relacionadas a múltiplos genes.

Há algum argumento a favor da alteração de genes em óvulos e espermatozoides?

Não. Mesmo em situações onde pais tenham genes com falhas ligadas a doenças hereditárias, não se justifica. Há exames pré-natais e tratamentos de fertilização in vitro para contornar estes problemas. Não há justificativa para editar o genoma humano em células reprodutivas.

Se é possível alterar o genoma humano, não é necessário questionar o que nos torna humanos? Não estaríamos criando uma nova espécie?

A grande questão é que, se mudarmos o DNA, mudamos a espécie.

The Snapchat and The Platypus (Medium)

Scissor-testing A New Branch of the Mobile Evolutionary Tree

Andrew McLaughlin

The British Museum still has the first platypus sent back to Europe from Australia, by Captain John Hunter in 1799. There are scissor marks on its duck-bill.

The first platypus specimen studied by European scientists, at the British Museum.

That’s because George Shaw, the first scientist who studied the astonishing specimen, was pretty sure it was a hoax, sewn together by pranksters or profiteers. With its webbed feet, furry pelt, venomous claw, and ducky beak, it was too freakish to be believed; moreover, London society had lately been thrilled, then crestfallen, by a wave of Franken-mermaids and other concocted exotica hawked by foreign sailors. So Shaw’s first move upon examining the platypus was to reach for his scissors, to uncover what kind of clever stitches bound the amalgamation together.

First published illustrations of a platypus, by George Shaw, “The Duck-Billed Platypus,” Naturalist’s Miscellany, Vol. X (1799).

Finding that the platypus was held together by flesh, not thread, Shaw stopped snipping and starting measuring, and marveling. He published a dutiful summary of his anatomical observations, together with field notes from Australia, in the impossibly well-named Naturalist’s Miscellany. Even with the benefit of several additional, later-arriving specimens, he wrote that it was “impossible not to entertain some doubts as to the genuine nature of the animal, and to surmise that there might have been practised some arts of deception in its structure.”

Which brings me to Snapchat.

When a certain kind of person — OK, an older person, where “old” equals 24— first encounters Snapchat, the reaction is typically some mixture of mystification, disbelief, and annoyance. For people who have gotten used to the dominant evolved anatomies of mobile apps, Snapchat seems like an odd and improbable creature.

A typical sentiment:

Or, as the 32-year-old Will Oremus put it in a brilliant and entertaining screed: “Is Snapchat Really Confusing, Or Am I Just Old?

A quick cruise through the app reveals why people born before the dawn of Clinton Administration react so strongly to it: Snapchat’s UI is really different from what we’re used to. What we’re used to is desktop software and its lineal descendants, with their predictably-located upper-margin drop-down menus, scrollable windows and swappable tabs, and logo-bearing application icons. On our mobile devices, designers have forged comfortingly similar UI elements, ever-so-slightly tweaked to work on smaller screens: scrollable feeds, sliding drawers with logically stacked navigation and option menus, all signaled by a homescreen hamburger icon.

Here are some of the ways Snapchat is different:

  • The app opens in camera mode. You don’t start with a social feed like Facebook, Twitter, LinkedIn, or Instagram, an editorial content feed like Digg, Buzzfeed, or the New York Times, a list of friends like Google Hangouts or Line, or a chronology of recent messages like FaceTime, Skype, or Slack. Instead, you start with whatever your phone’s camera is currently aimed at. Snapchat believes that you (should) want to create something — a photo, a short video— for immediate sharing. Snapchat is designed for you to create first, consume later.
  • There is no options menu. You have to navigate around the app without the crutch of a menu adorned with actual words that spell out what you can do and where you can go. But wait, you cry, there is (sometimes) a hamburger icon right there on the homescreen! Only it doesn’t do what you expect. Tapping the hamburger takes you to Snapchat Stories, a sort of expansive, broadcast-like version of the Snapchat snap. It doesn’t open a sliding drawer with a soothing hierarchical options menu. In Snapchat, navigation is done directly, via left/right/up/down thumb slides, supplemented by a handful of redundant touchable icons. People who are used to tapping well-labeled menu options are often baffled by Snapchat; but conversely, it will feel natural to someone whose first software experiences were on a mobile device, rather than a desktop.
  • Snapchat uses icons that change shape and color to signal different things. For example, a solid arrow is a sent snap (image or video); red if without audio, purple if with audio, and blue if a text chat only. The arrow becomes hollow once a friend has opened it. A solid square is a received snap or chat, with the same variations of color and hollowness. There are other icons that alert you when a friend has replayed or taken a screenshot of your snap. It’s not a complicated system, but it is esoteric and native to Snapchat; nothing about it is self-evident to new users.
  • Snapchat doesn’t pester you to keep connecting to more people.Adding friends in Snapchat is bizarrely cumbersome. If you’re used to traditional social apps, your first move will be tap on “Add Friends” (if you can find it), import your phone’s contacts database, and then squint through the entire list, name by name, to see which ones are on Snapchat and manually add them. It’s a huge pain if you have a lot of contacts. But Snapchat conversely makes it super-easy to add a friend when you are physically together by giving you a personally-encoded, QR-like Ghostface Chillah icon that can be snapped by a friend to add you. Notably, when you first set up Snapchat, you find that you can’t import your social graph from Facebook, Twitter, Google, etc. Snapchat draws solely on your phone’s contacts database. Though to some measure driven by necessity (at some point between the introduction of Pinterest’s “Add All My Facebook Friends” feature and the launch of Snapchat, Facebook started blocking new social services from using its social graph to kickstart theirs) Snapchat’s use of the phone’s contacts database reflects its emphasis on intimate, private, person-to-person communications with people you already know (or just met). It also shows Snapchat’s determination not to be dependent on other companies for core elements of its offerings.

So Snapchat’s user interface really is different, and different in ways that turn off a lot of people habituated to the dominant mobile design vocabulary, descended from desktop applications. And yet, Snapchat’s been getting hugely popular, with somebody.

Like any social or communications application, Snapchat has grown through real-world social pathways: its users tell their friends to get on it. If your friends or colleagues don’t use it, you won’t find much value in it. As a result, social and communications services like Snapchat, WhatsApp, WeChat, KakaoTalk, Viber, Line, Kik, etc., can saturate some discrete user clusters (e.g., U.S. Hispanic teens living in Southern California, Brooklyn-based social media junkies, female Korean professionals, etc.) but be almost unknown in others.

In the U.S., for example, Snapchat’s user cohort is overwhelming young — younger than any scaled social app we’ve seen before.

From Business Insider, July 30, 2014, http://www.businessinsider.com/a-primer-on-snapchat-and-its-demographics-2014-6

But the fact that Snapchat has become hugely popular with a wide swath of 12-to-24 year-old Americans doesn’t answer Will Oremus’s basic question. At the risk of stretching my metaphor past the breaking point, it doesn’t tell you whether Snapchat is a platypus (an isolated and precarious evolutionary adaptation well-suited to a specific subcontinental ecology), a fake mermaid (an apparent evolutionary advance that falls apart upon close inspection), or something more like a killer whale (a seemingly unlikely but wildly successful branch of the mammalian tree that has become an apex predator prowling every ocean and climate).


A few weeks ago, my betaworks partners and I found ourselves arguing about Snapchat, the merits of its app interface, and the trajectory of its future path. To get some practical data, and to understand Snapchat more thoroughly, we decided to commit to it, hard, for a week. And then to do the same for other fast-rising communications apps.

To reach meaningful scale, we enforced a herd migration among betaworkers. Starting two weeks ago, we announced that all intra-betaworks communications had to happen via Snapchat. If you wanted to reach us, you had to use Snapchat.

The result has been a scissor-test of Snapchat. We still ended up with conflicting opinions about whether Snapchat is poorly or brilliantly designed (or both). But we all agreed that the experience is more intimate, more private, and more creativity-sparking than we had previously understood. (And I learned the hard way how Snapchat punishes procrastination: one morning, my partner Sam sent me a couple of questions about a pending deal; I quickly scanned them while out on the sidewalk across town; when I returned to the office and opened the app to compose a response, Sam’s chats had disappeared and I couldn’t remember what the questions were.)

There’s one part of Snapchat, though, that really does seem to be grafted on like a fake duck-bill. Snapchat Discover is a new section of the app where big media companies like CNN, ESPN, People, Cosmopolitan, and the Daily Mail post slickly-produced packages that have as much in common with the casual, rough-hewn, intimate, person-to-person snap as Air Force One has with a homemade kite. Snapchat Discover is broadcast, not interpersonal; professional, not amateur; branded, not hacked. Snapchat’s ability to drive attention may ultimately make its Discover platform a viable (native, mobile, short-form) alternative to TV. But for now, it feels like an amphibian limb sutured onto a mammalian torso.

Looking at Snapchat Discover from the perspective of Digg, as a potential someday distribution platform, I can see why Buzzfeed declined to participate, at least for now.


My conclusion from the scissor-test is that Snapchat really is a new and promising branch of the mobile evolutionary tree, but burdened with at least one surgically dubious addition.

The Snapchat week was so much fun, we’re moving on. Last week, we all dogpiled onto Line. This week, WeChat. Next up, in some order, will be WhatsAppKikViberKakaoTalk, and so on.

More test results to come.

You’re powered by quantum mechanics. No, really… (The Guardian)

For years biologists have been wary of applying the strange world of quantum mechanics, where particles can be in two places at once or connected over huge distances, to their own field. But it can help to explain some amazing natural phenomena we take for granted

and

The Observer, Sunday 26 October 2014

A European robin in flight

According to quantum biology, the European robin has a ‘sixth sense’ in the form of a protein in its eye sensitive to the orientation of the Earth’s magnetic field, allowing it to ‘see’ which way to migrate. Photograph: Helmut Heintges/ Helmut Heintges/Corbis

Every year, around about this time, thousands of European robins escape the oncoming harsh Scandinavian winter and head south to the warmer Mediterranean coasts. How they find their way unerringly on this 2,000-mile journey is one of the true wonders of the natural world. For unlike many other species of migratory birds, marine animals and even insects, they do not rely on landmarks, ocean currents, the position of the sun or a built-in star map. Instead, they are among a select group of animals that use a remarkable navigation sense – remarkable for two reasons. The first is that they are able to detect tiny variations in the direction of the Earth’s magnetic field – astonishing in itself, given that this magnetic field is 100 times weaker than even that of a measly fridge magnet. The second is that robins seem to be able to “see” the Earth’s magnetic field via a process that even Albert Einstein referred to as “spooky”. The birds’ in-built compass appears to make use of one of the strangest features of quantum mechanics.

Over the past few years, the European robin, and its quantum “sixth sense”, has emerged as the pin-up for a new field of research, one that brings together the wonderfully complex and messy living world and the counterintuitive, ethereal but strangely orderly world of atoms and elementary particles in a collision of disciplines that is as astonishing and unexpected as it is exciting. Welcome to the new science of quantum biology.

Most people have probably heard of quantum mechanics, even if they don’t really know what it is about. Certainly, the idea that it is a baffling and difficult scientific theory understood by just a tiny minority of smart physicists and chemists has become part of popular culture. Quantum mechanics describes a reality on the tiniest scales that is, famously, very weird indeed; a world in which particles can exist in two or more places at once, spread themselves out like ghostly waves, tunnel through impenetrable barriers and even possess instantaneous connections that stretch across vast distances.

But despite this bizarre description of the basic building blocks of the universe, quantum mechanics has been part of all our lives for a century. Its mathematical formulation was completed in the mid-1920s and has given us a remarkably complete account of the world of atoms and their even smaller constituents, the fundamental particles that make up our physical reality. For example, the ability of quantum mechanics to describe the way that electrons arrange themselves within atoms underpins the whole of chemistry, material science and electronics; and is at the very heart of most of the technological advances of the past half-century. Without the success of the equations of quantum mechanics in describing how electrons move through materials such as semiconductors we would not have developed the silicon transistor and, later, the microchip and the modern computer.

However, if quantum mechanics can so beautifully and accurately describe the behaviour of atoms with all their accompanying weirdness, then why aren’t all the objects we see around us, including us – which are after all only made up of these atoms – also able to be in two place at once, pass through impenetrable barriers or communicate instantaneously across space? One obvious difference is that the quantum rules apply to single particles or systems consisting of just a handful of atoms, whereas much larger objects consist of trillions of atoms bound together in mindboggling variety and complexity. Somehow, in ways we are only now beginning to understand, most of the quantum weirdness washes away ever more quickly the bigger the system is, until we end up with the everyday objects that obey the familiar rules of what physicists call the “classical world”. In fact, when we want to detect the delicate quantum effects in everyday-size objects we have to go to extraordinary lengths to do so – freezing them to within a whisker of absolute zero and performing experiments in near-perfect vacuums.

Quantum effects were certainly not expected to play any role inside the warm, wet and messy world of living cells, so most biologists have thus far ignored quantum mechanics completely, preferring their traditional ball-and-stick models of the molecular structures of life. Meanwhile, physicists have been reluctant to venture into the messy and complex world of the living cell; why should they when they can test their theories far more cleanly in the controlled environment of the lab where they at least feel they have a chance of understanding what is going on?

Erwin Schrödinger, whose book What is Life? suggested that the macroscopic order of life was based on order at its quantum level.

Erwin Schrödinger, whose book What is Life? suggested that the macroscopic order of life was based on order at its quantum level. Photograph: Bettmann/CORBIS

Yet, 70 years ago, the Austrian Nobel prize-winning physicist and quantum pioneer, Erwin Schrödinger, suggested in his famous book,What is Life?, that, deep down, some aspects of biology must be based on the rules and orderly world of quantum mechanics. His book inspired a generation of scientists, including the discoverers of the double-helix structure of DNA, Francis Crick and James Watson. Schrödinger proposed that there was something unique about life that distinguishes it from the rest of the non-living world. He suggested that, unlike inanimate matter, living organisms can somehow reach down to the quantum domain and utilise its strange properties in order to operate the extraordinary machinery within living cells.

Schrödinger’s argument was based on the paradoxical fact that the laws of classical physics, such as those of Newtonian mechanics and thermodynamics, are ultimately based on disorder. Consider a balloon. It is filled with trillions of molecules of air all moving entirely randomly, bumping into one another and the inside wall of the balloon. Each molecule is governed by orderly quantum laws, but when you add up the random motions of all the molecules and average them out, their individual quantum behaviour washes out and you are left with the gas laws that predict, for example, that the balloon will expand by a precise amount when heated. This is because heat energy makes the air molecules move a little bit faster, so that they bump into the walls of the balloon with a bit more force, pushing the walls outward a little bit further. Schrödinger called this kind of law “order from disorder” to reflect the fact that this apparent macroscopic regularity depends on random motion at the level of individual particles.

But what about life? Schrödinger pointed out that many of life’s properties, such as heredity, depend of molecules made of comparatively few particles – certainly too few to benefit from the order-from-disorder rules of thermodynamics. But life was clearly orderly. Where did this orderliness come from? Schrödinger suggested that life was based on a novel physical principle whereby its macroscopic order is a reflection of quantum-level order, rather than the molecular disorder that characterises the inanimate world. He called this new principle “order from order”. But was he right?

Up until a decade or so ago, most biologists would have said no. But as 21st-century biology probes the dynamics of ever-smaller systems – even individual atoms and molecules inside living cells – the signs of quantum mechanical behaviour in the building blocks of life are becoming increasingly apparent. Recent research indicates that some of life’s most fundamental processes do indeed depend on weirdness welling up from the quantum undercurrent of reality. Here are a few of the most exciting examples.

Enzymes are the workhorses of life. They speed up chemical reactions so that processes that would otherwise take thousands of years proceed in seconds inside living cells. Life would be impossible without them. But how they accelerate chemical reactions by such enormous factors, often more than a trillion-fold, has been an enigma. Experiments over the past few decades, however, have shown that enzymes make use of a remarkable trick called quantum tunnelling to accelerate biochemical reactions. Essentially, the enzyme encourages electrons and protons to vanish from one position in a biomolecule and instantly rematerialise in another, without passing through the gap in between – a kind of quantum teleportation.

And before you throw your hands up in incredulity, it should be stressed that quantum tunnelling is a very familiar process in the subatomic world and is responsible for such processes as radioactive decay of atoms and even the reason the sun shines (by turning hydrogen into helium through the process of nuclear fusion). Enzymes have made every single biomolecule in your cells and every cell of every living creature on the planet, so they are essential ingredients of life. And they dip into the quantum world to help keep us alive.

Another vital process in biology is of course photosynthesis. Indeed, many would argue that it is the most important biochemical reaction on the planet, responsible for turning light, air, water and a few minerals into grass, trees, grain, apples, forests and, ultimately, the rest of us who eat either the plants or the plant-eaters.

The initiating event is the capture of light energy by a chlorophyll molecule and its conversion into chemical energy that is harnessed to fix carbon dioxide and turn it into plant matter. The process whereby this light energy is transported through the cell has long been a puzzle because it can be so efficient – close to 100% and higher than any artificial energy transport process.

Sunlight shines through chestnut tree leaves. Quantum biology can explain why photosynthesis in plants is so efficient.

Sunlight shines through chestnut tree leaves. Quantum biology can explain why photosynthesis in plants is so efficient. Photograph: Getty Images/Visuals Unlimited

The first step in photosynthesis is the capture of a tiny packet of energy from sunlight that then has to hop through a forest of chlorophyll molecules to makes its way to a structure called the reaction centre where its energy is stored. The problem is understanding how the packet of energy appears to so unerringly find the quickest route through the forest. An ingenious experiment, first carried out in 2007 in Berkley, California, probed what was going on by firing short bursts of laser light at photosynthetic complexes. The research revealed that the energy packet was not hopping haphazardly about, but performing a neat quantum trick. Instead of behaving like a localised particle travelling along a single route, it behaves quantum mechanically, like a spread-out wave, and samples all possible routes at once to find the quickest way.

A third example of quantum trickery in biology – the one we introduced in our opening paragraph – is the mechanism by which birds and other animals make use of the Earth’s magnetic field for navigation. Studies of the European robin suggest that it has an internal chemical compass that utilises an astonishing quantum concept called entanglement, which Einstein dismissed as “spooky action at a distance”. This phenomenon describes how two separated particles can remain instantaneously connected via a weird quantum link. The current best guess is that this takes place inside a protein in the bird’s eye, where quantum entanglement makes a pair of electrons highly sensitive to the angle of orientation of the Earth’s magnetic field, allowing the bird to “see” which way it needs to fly.

All these quantum effects have come as a big surprise to most scientists who believed that the quantum laws only applied in the microscopic world. All delicate quantum behaviour was thought to be washed away very quickly in bigger objects, such as living cells, containing the turbulent motion of trillions of randomly moving particles. So how does life manage its quantum trickery? Recent research suggests that rather than avoiding molecular storms, life embraces them, rather like the captain of a ship who harnesses turbulent gusts and squalls to maintain his ship upright and on course.

Just as Schrödinger predicted, life seems to be balanced on the boundary between the sensible everyday world of the large and the weird and wonderful quantum world, a discovery that is opening up an exciting new field of 21st-century science.

Life on the Edge: The Coming of Age of Quantum Biology by Jim Al-Khalili and Johnjoe McFadden will be published by Bantam Press on 6 November.

Epigenetics

Transgenerational effects of prenatal exposure to the 1944–45 Dutch famine – BJOG: An International Journal of Obstetrics & Gynaecology

Volume 120, Issue 5, pages 548–554, April 2013

MVE Veenendaal et al.

DOI: 10.1111/1471-0528.12136

http://onlinelibrary.wiley.com/doi/10.1111/1471-0528.12136/full

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Mothers’ stress during 1998 ice storm shows up in children’s DNA, study says (Fox News)

Mothers' stress during 1998 ice storm shows up in children's DNA: study

File photo of the aftermath of an ice storm. (AP Photo/Matt Rourke)

Just how bad was an epic 1998 ice storm in Canada? You can read all about it in the DNA of kids who were born around that time.

An intriguing study in PLoS One finds that women who were especially stressed during the storm gave birth to kids whose immune cells have telltale signs of their mothers’ trouble, reports Raw Story.

The storm was brutal, leaving people without power for more than a month. Researchers at the time surveyed expectant moms to gauge their “objective” distress, measuring things such as how many days they went without electricity.

Then they tracked down their kids more than a decade later and found that moms who were in the most distress bore children whose DNA had specific markers as a result.

The genes affected are related to immune function and sugar metabolism. Toronto’s Globe and Mail has a nice explanation of what’s going on, with help from Suzanne King of McGill University.

It involves “epigenetics,” as opposed to genetics:

  • “An individual’s genetics are like a musical score, and what’s written comes from the mother and father. … Although nothing can change what’s written on the page, environmental factors act as an orchestral conductor might, amplifying some aspects and tempering others, leaving markings, or methylation of the DNA.”

This isn’t necessarily a bad thing.

A pregnant woman in a famine, for instance, might “amplify” traits that would give her child a better chance of surviving—traits that could then backfire in terms of health if the famine goes away.

It’s not clear what, if any, health effects the Canadian kids will see as a result, explains a post at McGill University. But given the genes affected, they might have a greater risk of developing asthma, diabetes, or obesity.

(You can blame your coffee craving on DNA, too.)

This article originally appeared on Newser: Moms’ Stress in Ice Storm Shows Up in Kids’ DNA

Amputees discern familiar sensations across prosthetic hand (Science Daily)

Date: October 8, 2014

Source: Case Western Reserve University

Summary: Patients connected to a new prosthetic system said they ‘felt’ their hands for the first time since they lost them in accidents. In the ensuing months, they began feeling sensations that were familiar and were able to control their prosthetic hands with more — well — dexterity.

Medical researchers are helping restore the sense of touch in amputees. Credit: Image courtesy of Case Western Reserve University

Even before he lost his right hand to an industrial accident 4 years ago, Igor Spetic had family open his medicine bottles. Cotton balls give him goose bumps.

Now, blindfolded during an experiment, he feels his arm hairs rise when a researcher brushes the back of his prosthetic hand with a cotton ball.

Spetic, of course, can’t feel the ball. But patterns of electric signals are sent by a computer into nerves in his arm and to his brain, which tells him different. “I knew immediately it was cotton,” he said.

That’s one of several types of sensation Spetic, of Madison, Ohio, can feel with the prosthetic system being developed by Case Western Reserve University and the Louis Stokes Cleveland Veterans Affairs Medical Center.

Spetic was excited just to “feel” again, and quickly received an unexpected benefit. The phantom pain he’d suffered, which he’s described as a vice crushing his closed fist, subsided almost completely. A second patient, who had less phantom pain after losing his right hand and much of his forearm in an accident, said his, too, is nearly gone.

Despite having phantom pain, both men said that the first time they were connected to the system and received the electrical stimulation, was the first time they’d felt their hands since their accidents. In the ensuing months, they began feeling sensations that were familiar and were able to control their prosthetic hands with more — well — dexterity.

To watch a video of the research, click here: http://youtu.be/l7jht5vvzR4.

“The sense of touch is one of the ways we interact with objects around us,” said Dustin Tyler, an associate professor of biomedical engineering at Case Western Reserve and director of the research. “Our goal is not just to restore function, but to build a reconnection to the world. This is long-lasting, chronic restoration of sensation over multiple points across the hand.”

“The work reactivates areas of the brain that produce the sense of touch, said Tyler, who is also associate director of the Advanced Platform Technology Center at the Cleveland VA. “When the hand is lost, the inputs that switched on these areas were lost.”

How the system works and the results will be published online in the journal Science Translational Medicine Oct. 8.

“The sense of touch actually gets better,” said Keith Vonderhuevel, of Sidney, Ohio, who lost his hand in 2005 and had the system implanted in January 2013. “They change things on the computer to change the sensation.

“One time,” he said, “it felt like water running across the back of my hand.”

The system, which is limited to the lab at this point, uses electrical stimulation to give the sense of feeling. But there are key differences from other reported efforts.

First, the nerves that used to relay the sense of touch to the brain are stimulated by contact points on cuffs that encircle major nerve bundles in the arm, not by electrodes inserted through the protective nerve membranes.

Surgeons Michael W Keith, MD and J. Robert Anderson, MD, from Case Western Reserve School of Medicine and Cleveland VA, implanted three electrode cuffs in Spetic’s forearm, enabling him to feel 19 distinct points; and two cuffs in Vonderhuevel’s upper arm, enabling him to feel 16 distinct locations.

Second, when they began the study, the sensation Spetic felt when a sensor was touched was a tingle. To provide more natural sensations, the research team has developed algorithms that convert the input from sensors taped to a patient’s hand into varying patterns and intensities of electrical signals. The sensors themselves aren’t sophisticated enough to discern textures, they detect only pressure.

The different signal patterns, passed through the cuffs, are read as different stimuli by the brain. The scientists continue to fine-tune the patterns, and Spetic and Vonderhuevel appear to be becoming more attuned to them.

Third, the system has worked for 2 ½ years in Spetic and 1½ in Vonderhueval. Other research has reported sensation lasting one month and, in some cases, the ability to feel began to fade over weeks.

A blindfolded Vonderhuevel has held grapes or cherries in his prosthetic hand — the signals enabling him to gauge how tightly he’s squeezing — and pulled out the stems.

“When the sensation’s on, it’s not too hard,” he said. “When it’s off, you make a lot of grape juice.”

Different signal patterns interpreted as sandpaper, a smooth surface and a ridged surface enabled a blindfolded Spetic to discern each as they were applied to his hand. And when researchers touched two different locations with two different textures at the same time, he could discern the type and location of each.

Tyler believes that everyone creates a map of sensations from their life history that enables them to correlate an input to a given sensation.

“I don’t presume the stimuli we’re giving is hitting the spots on the map exactly, but they’re familiar enough that the brain identifies what it is,” he said.

Because of Vonderheuval’s and Spetic’s continuing progress, Tyler is hopeful the method can lead to a lifetime of use. He’s optimistic his team can develop a system a patient could use at home, within five years.

In addition to hand prosthetics, Tyler believes the technology can be used to help those using prosthetic legs receive input from the ground and adjust to gravel or uneven surfaces. Beyond that, the neural interfacing and new stimulation techniques may be useful in controlling tremors, deep brain stimulation and more.


Journal Reference:

  1. D. W. Tan, M. A. Schiefer, M. W. Keith, J. R. Anderson, J. Tyler, D. J. Tyler. A neural interface provides long-term stable natural touch perception. Science Translational Medicine, 2014; 6 (257): 257ra138 DOI:10.1126/scitranslmed.3008669

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Mind-controlled prosthetic arms that work in daily life are now a reality (Science Daily)

Date: October 8, 2014

Source: Chalmers University of Technology

Summary: For the first time, robotic prostheses controlled via implanted neuromuscular interfaces have become a clinical reality. A novel osseointegrated (bone-anchored) implant system gives patients new opportunities in their daily life and professional activities.


For the first time, robotic prostheses controlled via implanted neuromuscular interfaces have become a clinical reality. Credit: Image courtesy of Chalmers University of Technology

For the first time, robotic prostheses controlled via implanted neuromuscular interfaces have become a clinical reality. A novel osseointegrated (bone-anchored) implant system gives patients new opportunities in their daily life and professional activities.

In January 2013 a Swedish arm amputee was the first person in the world to receive a prosthesis with a direct connection to bone, nerves and muscles. An article about this achievement and its long-term stability will now be published in the Science Translational Medicine journal.

“Going beyond the lab to allow the patient to face real-world challenges is the main contribution of this work,” says Max Ortiz Catalan, research scientist at Chalmers University of Technology and leading author of the publication.

“We have used osseointegration to create a long-term stable fusion between man and machine, where we have integrated them at different levels. The artificial arm is directly attached to the skeleton, thus providing mechanical stability. Then the human’s biological control system, that is nerves and muscles, is also interfaced to the machine’s control system via neuromuscular electrodes. This creates an intimate union between the body and the machine; between biology and mechatronics.”

The direct skeletal attachment is created by what is known as osseointegration, a technology in limb prostheses pioneered by associate professor Rickard Brånemark and his colleagues at Sahlgrenska University Hospital. Rickard Brånemark led the surgical implantation and collaborated closely with Max Ortiz Catalan and Professor Bo Håkansson at Chalmers University of Technology on this project.

The patient’s arm was amputated over ten years ago. Before the surgery, his prosthesis was controlled via electrodes placed over the skin. Robotic prostheses can be very advanced, but such a control system makes them unreliable and limits their functionality, and patients commonly reject them as a result.

Now, the patient has been given a control system that is directly connected to his own. He has a physically challenging job as a truck driver in northern Sweden, and since the surgery he has experienced that he can cope with all the situations he faces; everything from clamping his trailer load and operating machinery, to unpacking eggs and tying his children’s skates, regardless of the environmental conditions (read more about the benefits of the new technology below).

The patient is also one of the first in the world to take part in an effort to achieve long-term sensation via the prosthesis. Because the implant is a bidirectional interface, it can also be used to send signals in the opposite direction — from the prosthetic arm to the brain. This is the researchers’ next step, to clinically implement their findings on sensory feedback.

“Reliable communication between the prosthesis and the body has been the missing link for the clinical implementation of neural control and sensory feedback, and this is now in place,” says Max Ortiz Catalan. “So far we have shown that the patient has a long-term stable ability to perceive touch in different locations in the missing hand. Intuitive sensory feedback and control are crucial for interacting with the environment, for example to reliably hold an object despite disturbances or uncertainty. Today, no patient walks around with a prosthesis that provides such information, but we are working towards changing that in the very short term.”

The researchers plan to treat more patients with the novel technology later this year.

“We see this technology as an important step towards more natural control of artificial limbs,” says Max Ortiz Catalan. “It is the missing link for allowing sophisticated neural interfaces to control sophisticated prostheses. So far, this has only been possible in short experiments within controlled environments.”

More about: How the technology works

The new technology is based on the OPRA treatment (osseointegrated prosthesis for the rehabilitation of amputees), where a titanium implant is surgically inserted into the bone and becomes fixated to it by a process known as osseointegration (Osseo = bone). A percutaneous component (abutment) is then attached to the titanium implant to serve as a metallic bone extension, where the prosthesis is then fixated. Electrodes are implanted in nerves and muscles as the interfaces to the biological control system. These electrodes record signals which are transmitted via the osseointegrated implant to the prostheses, where the signals are finally decoded and translated into motions.

More about: Benefits of the new technology, compared to socket prostheses

Direct skeletal attachment by osseointegration means:

  • Increased range of motion since there are no physical limitations by the socket — the patient can move the remaining joints freely
  • Elimination of sores and pain caused by the constant pressure from the socket
  • Stable and easy attachment/detachment
  • Increased sensory feedback due to the direct transmission of forces and vibrations to the bone (osseoperception)
  • The prosthesis can be worn all day, every day
  • No socket adjustments required (there is no socket)

Implanting electrodes in nerves and muscles means that:

  • Due to the intimate connection, the patients can control the prosthesis with less effort and more precisely, and can thus handle smaller and more delicate items.
  • The close proximity between source and electrode also prevents activity from other muscles from interfering (cross-talk), so that the patient can move the arm to any position and still maintain control of the prosthesis.
  • More motor signals can be obtained from muscles and nerves, so that more movements can be intuitively controlled in the prosthesis.
  • After the first fitting of the controller, little or no recalibration is required because there is no need to reposition the electrodes on every occasion the prosthesis is worn (as opposed to superficial electrodes).
  • Since the electrodes are implanted rather than placed over the skin, control is not affected by environmental conditions (cold and heat) that change the skin state, or by limb motions that displace the skin over the muscles. The control is also resilient to electromagnetic interference (noise from other electric devices or power lines) as the electrodes are shielded by the body itself.
  • Electrodes in the nerves can be used to send signals to the brain as sensations coming from the prostheses.

Journal Reference:

  1. M. Ortiz-Catalan, B. Hakansson, R. Branemark. An osseointegrated human-machine gateway for long-term sensory feedback and motor control of artificial limbs. Science Translational Medicine, 2014; 6 (257): 257re6 DOI:10.1126/scitranslmed.3008933

Bactéria pode ter sistema imune rudimentar, indica estudo (Fapesp)

03 de outubro de 2014

Por Karina Toledo

Agência FAPESP – Um estudo publicado na revista Nature Communications revelou que a bactéria Salmonella enterica é capaz de produzir uma proteína muito semelhante à alfa-2-macroglobulina humana, que desempenha um papel-chave em nosso sistema imunológico.

A hipótese levantada pelos pesquisadores do Instituto de Biologia Estrutural (IBS) de Grenoble, na França, é de que também nas bactérias as macroglobulinas poderiam fazer parte de um sistema de defesa rudimentar. Se a teoria for confirmada por estudos futuros, essas proteínas podem se tornar alvos para o desenvolvimento de novos antibióticos.

“O mais fascinante é que as macroglobulinas são proteínas imensas, formadas por quase 1.700 resíduos de aminoácidos. Para a bactéria sintetizar uma molécula tão grande é porque ela deve ter um papel muito importante”, afirmou a brasileira Andréa Dessen, pesquisadora do IBS e coordenadora, no Laboratório Nacional de Biociência (LNBio), em Campinas, de um projeto apoiado pela FAPESP por meio do programa São Paulo Excellence Chairs (SPEC).

No organismo humano, a missão da alfa-2-macroglobulina é detectar e neutralizar proteases secretadas por microrganismos invasores, disse a pesquisadora. As proteases são enzimas que quebram as ligações entre os aminoácidos das proteínas.

“A macroglobulina impede, dessa forma, que as proteases dos invasores destruam os tecidos do organismo, o que permitiria a infecção de tecidos mais profundos”, explicou.

Além disso, a alfa-2-macroglobulina também se liga a proteases que participam do processo de coagulação sanguínea, evitando que proteínas importantes sejam destruídas indevidamente.

Em estudos anteriores, nos quais o genoma de diversas espécies de bactérias foi sequenciado, pesquisadores alemães já haviam observado a presença do gene da macroglobulina. No IBS, o grupo liderado por Dessen já havia feito a caracterização bioquímica da proteína produzida pelas espécies Escherichia coli e Pseudomonas aeruginosa.

“Agora, de maneira inédita, estudamos a estrutura tridimensional da macroglobulina secretada pela Salmonella enterica por uma técnica conhecida como cristalografia de raios X, que permite visualizar detalhes em nível atômico. E pudemos confirmar que, de fato, ela é muito parecida com a macroglobulina humana”, contou Dessen.

De acordo com a pesquisadora, a descoberta reforça a hipótese de que a alfa-2-macroglobulina tem o papel de proteger a bactéria das proteases secretadas por outras bactérias ou pelo organismo do hospedeiro que ela tenta infectar.

“Em um modelo de camundongo, pesquisadores canadenses mostraram que cepas da bactéria Pseudomonas aeruginosa que não produzem macroglobulina têm menor capacidade de causar doença, ou seja, são menos virulentas. A proteína parece dar uma vantagem à bactéria na hora de colonizar o hospedeiro, mas ainda não sabemos exatamente por quê”, disse.

Desdobramentos

Em um braço da pesquisa que está sendo conduzido no LNBio, com apoio da FAPESP e orientação de Dessen, a pós-doutoranda francesa Samira Zouhir investiga a estrutura da macroglobulina sintetizada por bactérias da espécie Pseudomonas aeruginosa – causadora de diversos casos de infecção hospitalar.

“Se conseguirmos desvendar a estrutura tridimensional da proteína, isso nos dará pistas sobre sua função no processo infeccioso”, disse Dessen.

Quando o papel das macroglobulinas estiver bem compreendido em diferentes espécies de bactérias, acrescentou, essas proteínas poderão se tornar alvo para o desenvolvimento de novos antibióticos.

“Também há pesquisas interessantes em modelo de camundongo mostrando que a aplicação de alfa-globulina humana pode oferecer proteção contra a sepse. Há várias possibilidades de tratamento a serem exploradas”, avaliou a pesquisadora.

O artigo Structure of a bacterial α2-macroglobulin reveals mimicry of eukaryotic innate immunity (doi: 10.1038/ncomms5917), pode ser lido em www.nature.com/ncomms/2014/140915/ncomms5917/full/ncomms5917.html.

Alternate mechanism of species formation picks up support, thanks to a South American ant (University of Rochester )

21-Aug-2014

 

By Peter Iglinski

A queen ant of the host species Mycocepurus goeldii.

A newly-discovered species of ant supports a controversial theory of species formation. The ant, only found in a single patch of eucalyptus trees on the São Paulo State University campus in Brazil, branched off from its original species while living in the same colony, something thought rare in current models of evolutionary development.

“Most new species come about in geographic isolation,” said Christian Rabeling, assistant professor of biology at the University of Rochester. “We now have evidence that speciation can take place within a single colony.”

The findings by Rabeling and the research team were published today in the journal Current Biology.

In discovering the parasitic Mycocepurus castrator, Rabeling and his colleagues uncovered an example of a still-controversial theory known as sympatric speciation, which occurs when a new species develops while sharing the same geographic area with its parent species, yet reproducing on its own.“While sympatric speciation is more difficult to prove,” said Rabeling, “we believe we are in the process of actually documenting a particular kind of evolution-in-progress.”

New species are formed when its members are no longer able to reproduce with members of the parent species. The commonly-accepted mechanism is called allopatric speciation, in which geographic barriers—such as mountains—separate members of a group, causing them to evolve independently.

“Since Darwin’s Origin of Species, evolutionary biologists have long debated whether two species can evolve from a common ancestor without being geographically isolated from each other,” said Ted Schultz, curator of ants at the Smithsonian’s National Museum of Natural History and co-author of the study. “With this study, we offer a compelling case for sympatric evolution that will open new conversations in the debate about speciation in these ants, social insects and evolutionary biology more generally.”

A queen ant of the parasitic species Mycocepurus castrator.

M. castrator is not simply another ant in the colony; it’s a parasite that lives with—and off of—its host, Mycocepurus goeldii. The host is a fungus-growing ant that cultivates fungus for its nutritional value, both for itself and, indirectly, for its parasite, which does not participate in the work of growing the fungus garden. That led the researchers to study the genetic relationships of all fungus-growing ants in South America, including all five known and six newly discovered species of the genus Mycocepurus, to determine whether the parasite did evolve from its presumed host. They found that the parasitic ants were, indeed, genetically very close to M. goeldii, but not to the other ant species.

They also determined that the parasitic ants were no longer reproductively compatible with the host ants—making them a unique species—and had stopped reproducing with their host a mere 37,000 years ago—a very short period on the evolutionary scale.

A big clue for the research team was found by comparing the ants’ genes, both in the cell’s nucleus as well as in the mitochondria—the energy-producing structures in the cells. Genes are made of units called nucleotides, and Rabeling found that the sequencing of those nucleotides in the mitochondria is beginning to look different from what is found in the host ants, but that the genes in the nucleus still have traces of the relationship between host and parasite, leading him to conclude that M. castrator has begun to evolve away from its host.

Rabeling explained that just comparing some nuclear and mitochondrial genes may not be enough to demonstrate that the parasitic ants are a completely new species. “We are now sequencing the entire mitochondrial and nuclear genomes of these parasitic ants and their host in an effort to confirm speciation and the underlying genetic mechanism.”

The parasitic ants need to exercise discretion because taking advantage of the host species is considered taboo in ant society. Offending ants have been known to be killed by worker mobs. As a result, the parasitic queen of the new species has evolved into a smaller size, making them difficult to distinguish from a host worker.

Host queens and males reproduce in an aerial ceremony, in the wet tropics only during a particular season when it begins to rain. Rabeling found that the parasitic queens and males, needing to be more discreet about their reproductive activities, diverge from the host’s mating pattern. By needing to hide their parasitic identity, M. castrator males and females lost their special adaptations that allowed them to reproduce in flight, and mate inside the host nest, making it impossible for them to sexually interact with their host species.

The research team included Ted Schultz of the Smithsonian Institution’s National Museum of Natural History, Naomi Pierce of Harvard University, and Maurício Bacci, Jr of the Center for the Study of Social Insects (São State University, Rio Claro, Brazil).

Busca de novas metodologias direciona conservação biológica (Fapesp)

Pesquisadores avaliam fatores limitantes atuais na área em livro sobre ecologia aplicada e dimensões humanas na governança da biodiversidade (foto: Wikimedia)
03/07/2014

Por Elton Alisson

Agência FAPESP – A necessidade de ampliação da base conceitual e de inovações metodológicas e tecnológicas, além do aprimoramento da gestão, tem limitado a identificação e a solução de problemas relacionados à conservação biológica no planeta.

A avaliação é feita no livro Applied Ecology and Human Dimensions in Biological Conservation, recém-lançado pela editora Springer. A publicação é resultado de dois workshops internacionais realizados pelo Programa FAPESP de Pesquisas em Caracterização, Conservação, Restauração e Uso Sustentável da Biodiversidade (BIOTA-FAPESP), respectivamente, em 2009 e 2010, e dos avanços propiciados por esses eventos.

No workshop de 2009, o tema tratado foi ecologia aplicada e dimensões humanas na conservação biológica. Em 2010, foram abordados programas de estudos de longa duração em biodiversidade relacionados principalmente a monitoramento de padrões de diversidade biológica.

“Uma das novidades desses dois workshops foi abordar a conservação biológica do ponto de vista dos fatores que a limitam, como a necessidade de ampliação de sua base conceitual”, disse Luciano Martins Verdade, professor do Centro de Energia Nuclear na Agricultura (Cena) da Universidade de São Paulo (USP) e um dos editores do livro, à Agência FAPESP.

“Muitas vezes não se sabe como identificar e solucionar os problemas porque faltam conceitos sobre o tema”, afirmou Verdade, que coordenou os dois workshops e é membro da coordenação do Programa BIOTA-FAPESP.

Segundo Verdade, um conceito que precisa ser aprimorado é o da própria diversidade biológica. Ao tratar as espécies como unidades da diversidade biológica – pressupondo que, quanto mais espécies, maior a diversidade biológica de um determinado grupo –, corre-se o risco de subestimar o valor de linhagens mais antigas em termos evolutivos, mas que foram mais conservativas e tiveram menor especiação do que grupos mais recentes.

“Mesmo tendo originado menos espécies, o patrimônio gênico dessas linhagens mais antigas pode ter um valor maior do ponto de vista evolutivo do que o de grupos mais recentes”, avaliou.

Outro conceito que tem sido revisto, segundo o pesquisador, é o do papel histórico da ação humana na montagem dos padrões de diversidade biológica observados atualmente.

Há uma tendência de achar que biomas, como a Floresta Amazônica e até mesmo a Mata Atlântica, tenham áreas intocadas (prístinas) que reflitam padrões de diversidade biológica não influenciados pelo homem.

Ao estudar a história desses biomas, contudo, é possível observar que neles há registros da presença humana de forma significativa nos últimos milênios.

Mesmo antes da chegada dos europeus, no século XVI, já havia um uso da terra expressivo que pode ter se refletido nos atuais padrões de diversidade biológica de biomas como a Floresta Amazônica, apontou Verdade.

“Há registros de que índios caiapós plantavam pomares na Floresta Amazônica em intervalos mais ou menos regulares, contribuindo para aumentar a diversidade florística e, consequentemente, faunística do bioma, uma vez que animais se aproximavam dos pomares atraídos pelas árvores frutíferas e tornavam-se alvo de caça”, disse.

Dessa forma, o papel do ser humano no passado e no presente na montagem dos padrões de biodiversidade é um fator crucial que não pode ser ignorado, ressaltou Verdade.

“A pressão humana associada à expansão da agricultura hoje é tão forte que provavelmente tem causado mudanças genéticas nas espécies que fazem com que, do ponto de vista do patrimônio gênico, elas sejam diferentes daquelas que existiam no passado”, exemplificou.

Monitoramento da biodiversidade

Segundo Verdade, outro fator limitante para a tomada de decisão em conservação biológica é a falta de uma política de monitoramento que permita a detecção de problemas de mudança na biodiversidade dos biomas em tempo de serem solucionados.

Ainda não há um conjunto de indicadores que permita realizar medições da biodiversidade de modo a indicar se uma determinada espécie está em declínio, se virou uma praga ou se o uso que está sendo feito dela é sustentável ou não, segundo Verdade.

Por isso, os autores do livro defendem a necessidade de se estabelecer uma rede mundial de estações de monitoramento da biodiversidade em longo prazo a fim de contribuir efetivamente para os processos de tomada de decisão em matéria de conservação, uso e controle da biodiversidade do planeta.

“A implementação de uma política de monitoramento da biodiversidade necessita de instituições bem estruturadas, que saibam como, quando e o que deve ser monitorado”, avaliou Verdade. “Além disso, também exige a estruturação de programas de pesquisa de longo prazo, como o BIOTA-FAPESP, para ampliar os conceitos e possibilitar a detecção dos problemas relacionados à conservação da biodiversidade.”

Os pesquisadores também apontam no livro a necessidade de desenvolvimento e aprimoramento de métodos de levantamento populacional e de tecnologias que auxiliem na detecção e identificação de espécies em campo e na avaliação de processos ecológicos e evolutivos, especialmente em ambientes já alterados pela ação humana.

“O uso de marcadores moleculares em fezes de animais que normalmente não são fáceis de serem observados em campo, por exemplo, pode auxiliar a estimar a população da espécie de forma menos invasiva e até mesmo mais acurada e precisa do que a observação direta”, avaliou Verdade.

Divisão por seções

O livro Applied Ecology and Human Dimensions in Biological Conservation tem 14 capítulos, escritos por 38 especialistas do Brasil e do exterior, e é dividido em três seções.

Na primeira seção é enfatizada a importância de uma rede ampla de monitoramento de padrões de biodiversidade e o papel dos processos ecológicos, evolutivos e históricos condicionantes dos padrões atuais de biodiversidade.

Já na segunda seção são apresentadas as inovações metodológicas e tecnológicas que permitem o desenvolvimento da conservação biológica. E a terceira seção apresenta exemplos de governança da biodiversidade.

“Os autores dos capítulos trazem informações de ponta em relação a conceitos, inovação e gestão da conservação biológica do ponto de vista da aplicação da Ciência da Ecologia, que chamamos de Ecologia Aplicada, e das dimensões humanas associadas a ela”, disse Verdade.

Applied Ecology and Human Dimensions in Biological Conservation
Lançamento: 2014
Preço: US$ 189 (impresso) e US$ 149 (e-book)
Páginas: 228
Mais informações: www.springer.com/life+sciences/ecology/book/978-3-642-54750-8 .

Rapid Language Evolution in 19th-century Brazil: Data Mining, Literary Analysis and Evolutionary Biology – A Study of Six Centuries of Portuguese-language Texts (Stanford University)

Reporter: Aviva Lev-Ari, PhD, RN

Stanford collaboration offers new perspectives on evolution of Brazilian language

Using a novel combination of data mining, literary analysis and evolutionary biology to study six centuries of Portuguese-language texts, Stanford scholars discover the literary roots of rapid language evolution in 19th-century Brazil.

L.A. Cicero Stanford biology Professor Marcus Feldman, left, and Cuahtemoc Garcia-Garcia, a graduate student in Iberian and Latin American Cultures, combined forces to investigate the evolution of Portuguese as spoken in Brazil.

Literature and biology may not seem to overlap in their endeavors, but a Stanford project exploring the evolution of written language in Brazil is bringing the two disciplines together.

Over the last 18 months, Iberian and Latin American Cultures graduate student Cuauhtémoc García-García and biology Professor Marcus Feldman have been working together to trace the evolution of the  Brazilian Portuguese language through literature.

By combining Feldman’s expertise in mathematical analysis of cultural evolution with García-García’s knowledge of Latin American culture and computer programming, they have produced quantifiable evidence of rapid historical changes in written Brazilian Portuguese in the 19th and 20th centuries.

Specifically, Feldman and García-García are studying the changing use of words in tens of thousands of texts, with a focus on the personal pronouns that Brazilians used to address one another.

Their digital analysis of linguistics development in literary texts reflects Brazil’s complex colonial history.

The change in the use of personal pronouns, a daily part of social and cultural interaction, formed part of an evolving linguistic identity that was specific to Brazil, and not its Portuguese colonizers.

“We believe that this fast transition in the written language was due primarily to the approximately 300-year prohibition of both the introduction of the printing press and the foundation of universities in Brazil under Portuguese rule,” García-García said.

What Feldman and García-García found was that spoken language did in fact evolve during those 300 years, but little written evidence of that process exists because colonial restrictions on printing and literacy prevented language development in the written form.

A national sentiment of “write as we speak” arose in Brazil after Portuguese rule ended. García-García said their data shows an abrupt introduction in written texts of the spoken pronouns that were developed during the 300-year colonization period.

Drawing on Feldman’s experience with theoretical and statistical evolutionary models, García-García developed computer programs that count certain words to see how often they appear and how their use has changed over hundreds of years.

In Brazilian literary works produced in the post-colonial period, Feldman said, they have “found examples of written linguistic evolution over short time periods, contrary to the longer periods that are typical for changes in language.”

The findings will figure prominently in García-García’s dissertation, which addresses the transmission of written language across time and space.

The project’s source materials include about 70,000 digitized works in Portuguese from the 13th to the 21st century, ranging from literature and newspapers to technical manuals and pamphlets.

García-García, a member of The Digital Humanities Focal Group at Stanford, said their research “shows how written language changed, and through these changes in pronoun use, we now have a better understanding of how Brazilian writing evolved following the introduction of the printing press.”

Feldman, a population geneticist and one of the founders of the quantitative theory of cultural evolution, said he sees their project as a natural approach to linguistic evolution.

“I believe that evolutionary science and the humanities have a lot to offer each other in both theoretical and empirical explorations,” Feldman said.

Language by the numbers

García-García became interested in language evolution while studying Brazilian Portuguese under the instruction of Stanford lecturer Lyris Wiedemann. He approached Feldman, proposing an evolutionary study of Brazilian Portuguese, and Feldman agreed to help him analyze the data. García-García then enlisted Stanford lecturer Agripino Silveira, who provided linguistic expertise.

García-García worked with Stanford Library curators Glen Worthey, Adan Griego and Everardo Rodriguez for more than a year to develop the technical infrastructure and copyright clearance he needed to access Stanford’s entire digitized corpus of Portuguese language texts. After incorporating even more source material from the HathiTrust digital archive, García-García began the time-consuming task of “cleaning” the corpus, so data could be effectively mined from it.

“Sometimes there were duplicates, issues with the digitization, and works with multiple editions that created ‘noise’ in the corpus,” he said.

Following months of preparation, Feldman and García-García were able to begin data mining. Specifically, they counted the incidences of two pronouns, tu and você, which both mean the singular “you,” and how their incidence in literature changed over time.

“After running various searches, I could correlate results and see how and when certain words were used to build up a comprehensive image of this evolution,” he said.

Tu was – and still is – used in Portugal as the typical way to say ‘you.’ But, in Brazil, você is the more normal way to say it, particularly in major cities like Rio de Janeiro and São Paulo where the majority of the population lives,” García-García explained.

However, that was not always the case. When Brazil was a Portuguese colony, and up until the arrival of the printing press in1808, tu was the canonical form in written language.

As part of the run-up to independence in 1822, universities and printing presses were established in Brazil for the first time in 1808, having been prohibited by the Portuguese colonizers in what García-García calls “cultural repression.”

By the late 19th century, você emerged as the way to address people, shedding part of the colonial legacy, and tu quickly became less prominent in written Brazilian Portuguese.

“Our findings quantifiably show how pronoun use developed. We have found that around 1840, vocêwas used about 10-15 percent of the time by authors to say ‘you.’ By the turn of the century, this had increased to about 70 percent,” García-García said.

“Our data suggest that você was rarely used in the late 17th and 18th centuries, but really appears and takes hold in the middle of the 19th century, a few decades after 1808. Thus, the late arrival of the printing press marks a critical point for understanding the evolution of written Portuguese in Brazil, ” he said.

From Romanticism to realism

Their research revealed an intriguing literary coincidence – the period of transition from tu to vocêcorrelated with the broad change in the dominant literary genre in Brazilian literature from European Romanticism to Latin American realism.

Interestingly, the researchers noticed that the rapid change was most evident several decades after Brazil’s independence in the 1820s because it took that long for Brazilian writers to develop their own voice and style.

For centuries Brazilian writers were forced to write in the style of the Portuguese, but as García-García said, “with their new freedom they wanted to write stories that reflected their national identity.”

“Machado de Assis, arguably Brazil’s greatest author, is a fine example. His early novels are archetypally Romanticist, and then his later novels are deeply Realist, and the use of the pronouns shift from one to the other,” García-García said.

Nonetheless, in Machado’s work there is sometimes a purposeful switch back to the tu form if, for example, the author wanted to evoke a certain sentiment or change the narrative voice.

“The data-mining project cannot ascertain subtle uses of words and how, in some works, the pronouns are ‘interchangeable,’” he added.

Computational expertise was no substitute for literary expertise, and García-García used the two disciplines in tandem to get a clearer picture in his data.

“I had to stop using the computer and go back to a close reading of a large sample of books, and the literary genre change reflects this period of post-colonial social and historical change,” he said.

Feldman and García-García hope to use their methodology to explore different languages.

“Next we hope to study the digitized Spanish language corpus, which currently comprises close to a quarter of a million works from the last 900 years,” García-García said.

Tom Winterbottom is a doctoral candidate in Iberian and Latin American Cultures at Stanford. For more news about the humanities at Stanford, visit the Human Experience.

http://news.stanford.edu/news/2014/june/evolution-language-brazil-060414.html

Theory on origin of animals challenged: Some animals need extremely little oxygen (Science Daily)

Date: February 17, 2014

Source: University of Southern Denmark

Summary: One of science’s strongest dogmas is that complex life on Earth could only evolve when oxygen levels in the atmosphere rose to close to modern levels. But now studies of a small sea sponge fished out of a Danish fjord shows that complex life does not need high levels of oxygen in order to live and grow.

Sea sponge Halichondria panicea was used in the experiment at the University of Southern Denmark. Credit: Daniel Mills/SDU

One of science’s strongest dogmas is that complex life on Earth could only evolve when oxygen levels in the atmosphere rose to close to modern levels. But now studies of a small sea sponge fished out of a Danish fjord shows that complex life does not need high levels of oxygen in order to live and grow.

The origin of complex life is one of science’s greatest mysteries. How could the first small primitive cells evolve into the diversity of advanced life forms that exists on Earth today? The explanation in all textbooks is: Oxygen. Complex life evolved because the atmospheric levels of oxygen began to rise app. 630 — 635 million years ago.

However new studies of a common sea sponge from Kerteminde Fjord in Denmark shows that this explanation needs to be reconsidered. The sponge studies show that animals can live and grow even with very limited oxygen supplies.

In fact animals can live and grow when the atmosphere contains only 0.5 per cent of the oxygen levels in today’s atmosphere.

“Our studies suggest that the origin of animals was not prevented by low oxygen levels,” says Daniel Mills, PhD at the Nordic Center for Earth Evolution at the University of Southern Denmark.

Together with Lewis M. Ward from the California Institute of Technology he is the lead author of a research paper about the work in the journal PNAS.

A little over half a billion years ago, the first forms of complex life — animals — evolved on Earth. Billions of years before that life had only consisted of simple single-celled life forms. The emergence of animals coincided with a significant rise in atmospheric oxygen, and therefore it seemed obvious to link the two events and conclude that the increased oxygen levels had led to the evolution of animals.

“But nobody has ever tested how much oxygen animals need — at least not to my knowledge. Therefore we decided to find out,” says Daniel Mills.

The living animals that most closely resemble the first animals on Earth are sea sponges. The species Halichondria panicea lives only a few meters from the University of Southern Denmark’s Marine Biological Research Centre in Kerteminde, and it was here that Daniel Mills fished out individuals for his research.

“When we placed the sponges in our lab, they continued to breathe and grow even when the oxygen levels reached 0.5 per cent of present day atmospheric levels,” says Daniel Mills.

This is lower than the oxygen levels we thought were necessary for animal life.

The big question now is: If low oxygen levels did not prevent animals from evolving — then what did? Why did life consist of only primitive single-celled bacteria and amoebae for billions of years before everything suddenly exploded and complex life arose?

“There must have been other ecological and evolutionary mechanisms at play. Maybe life remained microbial for so long because it took a while to develop the biological machinery required to construct an animal. Perhaps the ancient Earth lacked animals because complex, many-celled bodies are simply hard to evolve,” says Daniel Mills.

His colleagues from the Nordic Center for Earth Evolution have previously shown that oxygen levels have actually risen dramatically at least one time before complex life evolved. Although plenty of oxygen thus became available it did not lead to the development of complex life.

Journal Reference:

  1. Daniel B. Mills, Lewis M. Ward, CarriAyne Jones, Brittany Sweeten, Michael Forth, Alexander H. Treusch and Donald E. Canfield. The oxygen requirements of the earliest animalsPNAS, February 17, 2014

Modelo pode ajudar a prever como espécies da Mata Atlântica responderão às mudanças climáticas (Fapesp)

Pesquisadores do Brasil e dos EUA buscam compreensão dos processos evolutivos, geológicos, climáticos e genéticos por trás do padrão atual da biodiversidade (foto:Samuel Iavelberg)

11/02/2014

Por Karina Toledo

Agência FAPESP – Compreender os processos evolutivos, geológicos, climáticos e genéticos por trás da enorme biodiversidade e do padrão de distribuição de espécies da Mata Atlântica e, com base nesse conhecimento, criar modelos que permitam prever, por exemplo, como essas espécies vão reagir às mudanças no clima e no uso do solo.

Esse é o objetivo central de um projeto que reúne pesquisadores do Brasil e dos Estados Unidos no âmbito de um acordo de cooperação científica entre o Programa de Pesquisas em Caracterização, Conservação, Recuperação e Uso Sustentável da Biodiversidade do Estado de São Paulo (BIOTA-FAPESP) e o programa Dimensions of Biodiversity, da agência federal norte-americana de fomento à pesquisa National Science Foundation (NSF).

“Além de ajudar a prever o que poderá ocorrer no futuro com as espécies, os modelos ajudam a entender como está hoje distribuída a biodiversidade em áreas onde os cientistas não têm acesso. Como fazemos coletas por amostragem, seria impossível mapear todos os microambientes. Os modelos permitem extrapolar essas informações para áreas não amostradas e podem ser aplicados em qualquer tempo”, explicou Ana Carolina Carnaval, professora da The City University of New York, nos Estados Unidos, e coordenadora do projeto de pesquisa ao lado de Cristina Miyaki, do Instituto de Biociências da Universidade de São Paulo (IB-USP).

A proposta, segundo Carnaval, é promover a integração de pesquisadores de diversas áreas – como ecologia, geologia, biogeografia, genética, fisiologia, climatologia, taxonomia, paleologia, geomorfologia – e unir ciência básica e aplicada em benefício da conservação da Mata Atlântica.

O bioma é considerado um dos 34 hotspots mundiais, ou seja, uma das áreas prioritárias para a conservação por causa de sua enorme biodiversidade, do alto grau de endemismo de suas espécies (ocorrência apenas naquele local) e da grande ameaça de extinção resultante da intensa atividade antrópica na região.

A empreitada coordenada por Carnaval e por Miyaki teve início no segundo semestre de 2013. A rede de pesquisadores esteve reunida pela primeira vez para apresentar suas linhas de pesquisa e seus resultados preliminares na segunda-feira (10/02), durante o “Workshop Dimensions US-BIOTA São Paulo – A multidisciplinary framework for biodiversity prediction in the Brazilian Atlantic forest hotspot”.

“Convidamos alguns colaboradores além de pesquisadores envolvidos no projeto, pois queremos críticas e sugestões que permitam aperfeiçoar os trabalhos”, contou Miyaki. “Essa reunião é um marco para conseguirmos efetivar a integração entre as diversas áreas do projeto e criarmos uma linguagem única focada em compreender a Mata Atlântica e os processos que fazem esse bioma ser tão especial”, acrescentou.

Entre os mistérios que os cientistas tentarão desvendar estão a origem da incrível diversidade existente na Mata Atlântica, possivelmente fruto de conexões existentes há milhões de anos com outros biomas, entre eles a Floresta Amazônica. Outra questão fundamental é entender a importância do sistema de transporte de umidade na região hoje e no passado e como ele permite que a Mata Atlântica se comunique com outros sistemas florestais. Também está entre as metas do grupo investigar como a atividade tectônica influenciou o curso de rios e afetou o padrão de distribuição das espécies aquáticas.

Desafios do BIOTA

Durante a abertura do workshop, o presidente da FAPESP, Celso Lafer, realçou a importância de abordagens inovadoras e multidisciplinares voltadas para a proteção da biodiversidade da Mata Atlântica. Ressaltou ainda que a iniciativa está em consonância com os esforços de internacionalização realizados pela FAPESP nos últimos anos.

“Uma das grandes preocupações da FAPESP tem sido o processo de internacionalização, que basicamente está relacionado ao esforço de juntar pesquisadores de diversas áreas para avançar no conhecimento. Este programa de hoje está relacionado a aspirações dessa natureza e tenho certeza de que os resultados serão altamente relevantes”, afirmou Lafer.

Também durante a mesa de abertura, o diretor do IB-USP, Carlos Eduardo Falavigna da Rocha, afirmou que o programa BIOTA-FAPESP tem sido um exemplo para outros estados e outras fundações de apoio à pesquisa em âmbito federal e estadual.

Carlos Alfredo Joly, professor da Universidade Estadual de Campinas (Unicamp) e coordenador do BIOTA-FAPESP, apresentou um histórico das atividades realizadas pelo programa desde 1999, entre elas a elaboração de um mapa de áreas prioritárias para conservação que serviu de base para mais de 20 documentos legais estaduais – entre leis, decretos e resoluções.

Joly também falou sobre os desafios a serem vencidos até 2020, como empreender esforços de restauração e de reintrodução de espécies, ampliar o entendimento sobre ecossistemas terrestres e sobre os mecanismos que mantêm a biodiversidade no Estado e intensificar as atividades voltadas à educação ambiental.

Para 2014, Joly ressaltou dois desafios na área de conservação. “Estamos iniciando uma campanha para o tombamento da Serra da Mantiqueira. Já fizemos alguns artigos de jornais, estamos lançando um website específico e vamos trabalhar para conseguir tombar regiões acima de 800 metros, áreas apontadas como de extrema prioridade para conservação no atlas do BIOTA”, disse.

Outra meta para 2014, segundo Joly, é trabalhar para que o Brasil ratifique o protocolo de Nagoya – tratado internacional que dispõe sobre a repartição de benefícios do uso da biodiversidade – até outubro, quando ocorrerá a 12ª Conferência das Partes da Convenção sobre Diversidade Biológica.

“É fundamental que um país megadiverso, que tem todo o interesse de ter sua biodiversidade protegida por esse protocolo internacional, se torne signatário do protocolo antes dessa reunião”, afirmou Joly.

New application of physics tools used in biology (Science Daily)

Date: 

February 7, 2014

Source: DOE/Lawrence Livermore National Laboratory

Summary: A physicist and his colleagues have found a new application for the tools and mathematics typically used in physics to help solve problems in biology.

This DNA molecule is wrapped twice around a histone octamer, the major structural protein of chromosomes. New studies show they play a role in preserving biological memory when cells divide. Image courtesy of Memorial University of Newfoundland. Credit: Image courtesy of DOE/Lawrence Livermore National Laboratory

A Lawrence Livermore National Laboratory physicist and his colleagues have found a new application for the tools and mathematics typically used in physics to help solve problems in biology.

Specifically, the team used statistical mechanics and mathematical modeling to shed light on something known as epigenetic memory — how an organism can create a biological memory of some variable condition, such as quality of nutrition or temperature.

“The work highlights the interdisciplinary nature of modern molecular biology, in particular, how the tools and models from mathematics and physics can help clarify problems in biology,” said Ken Kim, a LLNL physicist and one of the authors of a paper appearing in the Feb. 7 issue ofPhysical Review Letters.

Not all characteristics of living organisms can be explained by their genes alone. Epigenetic processes react with great sensitivity to genes’ immediate biochemical surroundings — and further, they pass those reactions on to the next generation.

The team’s work on the dynamics of histone protein modification is central to epigenetics. Like genetic changes, epigenetic changes are preserved when a cell divides. Histone proteins were once thought to be static, structural components in chromosomes, but recent studies have shown that histones play an important dynamical role in the machinery responsible for epigenetic regulation.

When histones undergo chemical alterations (histone modification) as a result of some external stimulus, they trigger short-term biological memory of that stimulus within a cell, which can be passed down to its daughter cells. This memory also can be reversed after a few cell division cycles.

Epigenetic modifications are essential in the development and function of cells, but also play a key role in cancer, according to Jianhua Xing, a former LLNL postdoc and current professor at Virginia Tech. “For example, changes in the epigenome can lead to the activation or deactivation of signaling pathways that can lead to tumor formation,” Xing added.

The molecular mechanism underlying epigenetic memory involves complex interactions between histones, DNA and enzymes, which produce modification patterns that are recognized by the cell. To gain insight into such complex systems, the team constructed a mathematical model that captures the essential features of the histone-induced epigenetic memory. The model highlights the “engineering” challenge a cell must constantly face during molecular recognition. It is analogous to restoring a picture with missing parts. The molecular properties of a species have been evolutionarily selected to allow them to “reason” what the missing parts are based on incomplete information pattern inherited from the mother cell.

Story Source:

The above story is based on materials provided by DOE/Lawrence Livermore National Laboratory. The original article was written by Anne M Stark. Note: Materials may be edited for content and length.

Animal Cells Can Communicate by Reaching Out, Touching, Study Shows (Science Daily)

Jan. 2, 2014 — In a finding that directly contradicts the standard biological model of animal cell communication, UCSF scientists have discovered that typical cells in animals have the ability to transmit and receive biological signals by making physical contact with each other, even at long distance.

Stock photo. A major reason that animal cell cytonemes had not been observed or studied previously is because these structures are too fragile to survive traditional laboratory methods of preparing cells for imaging. “During the last decade or so, though, there have been fantastic technical advances, including new techniques in genetic engineering, new microscopes that improve the resolution and sensitivity for imaging living cells and the development of fluorescent marker proteins that we can attach to proteins of interest,” the lead researcher explains. (Credit: © Kurhan / Fotolia)

The mechanism is similar to the way neurons communicate with other cells, and contrasts the standard understanding that non-neuronal cells “basically spit out signaling proteins into extracellular fluid and hope they find the right target,” said senior investigator Thomas B. Kornberg, PhD, a professor of biochemistry with the UCSF Cardiovascular Research Institute.

The paper was published on January 2, 2014 in Science.

Working with living tissue from Drosophila — fruit flies — Kornberg and his team demonstrated that cells send out long, thin tubes of cytoplasm called cytonemes, which Kornberg said “can extend across the length of 50 or 100 cells” before touching the cells they are targeting. The point of contact between a cytoneme and its target cell acts as a communications bridge between the two cells.

“It’s long been known that neurons communicate in a similar way — by transferring signals at points of contact called synapses, and transmitting the response over long distances in long tubes called axons,” said Kornberg. “However, it’s always been thought that this mode of signaling was unique to neurons. We have now shown that many types of animal cells have the same ability to reach out and synapse with one another in order to communicate, using signaling proteins as units of information instead of the neurotransmitters and electrical impulses that neurons use.”

In fact, said Kornberg, “I would argue that the only strong experimental data that exists today for a mechanism by which these signaling proteins move from one cell to another is at these points of contact and via cytonemes.”

However, he noted, “There are 100 years worth of work and thousands of scientific papers in which it has been simply assumed that these proteins move from one cell to another by moving through extracellular fluid. So this is a fundamentally different way of considering how signaling goes on in tissues.”

Working with cells in the Drosophila wing that produce and send the signaling protein Decapentaplegic (Dpp), Kornberg and his team showed that Dpp transfers between cells at the sites where cytonemes form a connection, and that cytonemes are the conduits that move Dpp from cell to cell.

The scientists discovered that the sites of contact have characteristics of synapses formed by neurons. They demonstrated that in flies that had been genetically engineered to lack synapse-making proteins, cells are unable to form synapses or signal successfully.

“In the mutants, the signals that are normally taken up by target cells are not taken up, and signaling is prevented,” said Kornberg. “This demonstrates that physical contact is required for signal transfer, signal uptake and signaling.”

Kornberg said that a major reason that animal cell cytonemes had not been observed or studied previously is because these structures are too fragile to survive traditional laboratory methods of preparing cells for imaging. “During the last decade or so, though, there have been fantastic technical advances, including new techniques in genetic engineering, new microscopes that improve the resolution and sensitivity for imaging living cells and the development of fluorescent marker proteins that we can attach to proteins of interest.”

Using these new technologies, Kornberg and his team have captured vivid images, and even movies, of fluorescent signaling proteins moving through fluorescently marked cytonemes.

“We are not saying that cells always use cytonemes for signaling,” Kornberg cautioned. “Hormones, for example, are another method of long distance cell signaling. A cell that takes up insulin does not care where that insulin came from — a pancreas or an intravenous injection. But there are signals of a specialized type, such as those that pass between stem cells and the cells around them, or signals that determine tissue growth, patterning and function, where the identity of the communicating cells must be precisely defined. It’s important that these signals are received in the context of the cells that are making them.”

Kornberg noted that other research teams have made observations that suggest that cytoneme-based signaling may also occur “between stem cells and the cells that instruct them on what they are going to do and where they are going to go.” Cancer cells may also use this method to communicate with their neighbors, he said.

The discovery of animal cell cytonemes and the critical role they play in long distance signaling “opens up a wonderful biology of which we have very little understanding at this point,” said Kornberg. “For example, how do these cytonemes find their targets? How do they know when they have found them? These are some of the questions that we are pursuing.”

Journal Reference:

  1. S. Roy, H. Huang, S. Liu, T. B. Kornberg. Cytoneme-Mediated Contact-Dependent Transport of the Drosophila Decapentaplegic Signaling ProteinScience, 2014; DOI: 10.1126/science.1244624

Rapid Evolution of Novel Forms: Environmental Change Triggers Inborn Capacity for Adaptation (Science Daily)

Dec. 12, 2013 — In the classical view of evolution, species experience spontaneous genetic mutations that produce various novel traits — some helpful, some detrimental. Nature then selects for those most beneficial, passing them along to subsequent generations. 

Surface form and cave form of Astyanax mexicanus differ in many morphological traits, the most prominent being the loss of pigmentation and the loss of eyes in the cave forms. (Credit: Courtesy of Nicolas Rohner)

It’s an elegant model. It’s also an extremely time-consuming process likely to fail organisms needing to cope with sudden, potentially life-threatening changes in their environments. Surely some other mechanism could enable more rapid adaptive response. In this week’s edition of the journal Science, a team of researchers from Harvard Medical School and Whitehead Institute report that, at least in the case of one variety of cavefish, that other agent of change is the heat shock protein known as HSP90.

“It’s a very cool story in terms of the speed of evolution,” says Nicolas Rohner, lead author of the Science paper and a postdoctoral researcher in the lab of Harvard Medical School Genetics Professor Clifford Tabin.

Rohner notes that at some point many thousands of years ago, a population of Astyanax mexicanus (a fish indigenous to northeastern Mexico) was swept from its hospitable river home into the unfriendly confines of underwater caves. Facing a dramatically different environment, the fish were forced to adapt. Living in near total darkness, the fish did away with their pigmentation, developed heightened sensory systems to detect changes in water pressure and the presence of prey and, perhaps most strikingly, they lost their eyes. Although seemingly counterintuitive, the loss of eyes is thought to be an “adaptive” or beneficial trait, as the maintenance of a complex but now useless organ would come at a high metabolic cost. Thus, the fish could reallocate their finite physiological resources to biological functions more helpful in the cave setting.

Eye loss in these fish is considered to be a demonstration of an evolutionary concept known as “standing genetic variation,” which argues that pools of genetic mutations — some potentially helpful — exist in a given population but are normally kept silent. The manifestations of these mutations, that is, their impact on observable phenotypes, don’t emerge until the population encounters stressful conditions. But what exactly keeps those mutations at bay?

Enter Whitehead Member Susan Lindquist, whose research has shown that HSP90 silences such genetic variation in a variety of organisms, from fruit flies, to yeast, to plants. Lindquist’s work found that the normally robust cellular reservoir of HSP90 becomes depleted during periods of physiological stress. The loss of HSP90 activity allowed phenotypic changes to emerge quite rapidly. Although some emergent traits found in her lab were not adaptive, some clearly were.

“The delicate balance of protein folding — especially that controlled by HSP90 — holds the key,” says Lindquist, who is also a professor of biology at MIT and an investigator of the Howard Hughes Medical Institute. “Moderate changes in the environment create stresses on protein folding, causing minor changes in the genome to have much larger effects. Because HSP90 governs the folding of the key regulators of growth and development it produces a fulcrum point for evolutionary change.”

Having seen Tabin’s work on the genetics of eye loss in cavefish, she proposed a research collaboration to determine whether HSP90 had been an evolutionary role-player in this vertebrate. The Tabin and Lindquist labs devised a complex set of experiments with cavefish and surface fish of the same species. Surface fish raised in the presence of a drug that blocks HSP90 activity (thereby mimicking a stressful environment) displayed significant variation in eye size — clearly implicating HSP90’s effects on this trait. Conversely, cavefish raised in the same conditions showed no increase in variation in the size of their eye orbits (although the cave fish have no eyes, their skulls retain the orbital cavity where their eyes once were). Intriguingly, however, these fish emerged with small orbits, showing that the genetics governing eye size remains responsive to HSP90.

Although impressive, these findings were chemically induced, leaving open the question of whether such HSP90-related effects would have been seen in nature. To answer this, researchers examined a host of conditions — ranging from pH to oxygen content to temperature — found in the surface and cave waters that are home to these fish. They discovered a considerable difference in conductivity, as measured by salinity, between cave and surface. Because low conductivity, a condition found in the caves, can trigger a heat shock response, they raised surface fish in water whose conductivity equaled that of native caves.

The results were essentially the same: fish raised in conditions of low conductivity showed significant variation in eye size. The scientists had shown that an environmental stressor could have the same effects as the chemical inhibition of HSP90.

“This is the first time that we can see in a natural setting where the stress came from and observe the variation that results,” says Tabin.

Adds Rohner: “This is the first study showing that this HSP90-mediated mechanism can be applied to vertebrates for real morphological adaptive traits.”

For Dan Jarosz, a former postdoctoral researcher in Lindquist’s lab, the study is an important validation of Lindquist’s work on evolution. Jarosz, now Assistant Professor of Chemical and Systems Biology and of Developmental Biology at Stanford University, had been involved in much of Lindquist’s work on HSP90 as a driver of evolution in yeast. He believes this latest work should help quiet those who are skeptical of the impact of this mechanism throughout the plant and animal kingdoms.

“We now have enough evidence to say that large, rapid environmental change can reveal new variation and change the outcomes of real evolution in nature,” he says.

This work is supported by the National Institutes of Health and the Damon Runyon Cancer Research Foundation.

Journal Reference:

  1. N. Rohner, D. F. Jarosz, J. E. Kowalko, M. Yoshizawa, W. R. Jeffery, R. L. Borowsky, S. Lindquist, C. J. Tabin. Cryptic Variation in Morphological Evolution: HSP90 as a Capacitor for Loss of Eyes in CavefishScience, 2013; 342 (6164): 1372 DOI: 10.1126/science.1240276

Unlocking Biology With Math (Science Daily)

Oct. 7, 2013 — Scientists at USC have created a mathematical model that explains and predicts the biological process that creates antibody diversity — the phenomenon that keeps us healthy by generating robust immune systems through hypermutation.

The work is a collaboration between Myron Goodman, professor of biological sciences and chemistry at the USC Dornsife College of Letters, Arts and Sciences; and Chi Mak, professor of chemistry at USC Dornsife.

“To me, it was the holy grail,” Goodman said. “We can now predict the motion of a key enzyme that initiates hypermutations in immunoglobulin (Ig) genes.”

Goodman first described the process that creates antibody diversity two years ago. In short, an enzyme called “activation-induced deoxycytidine deaminase” (or AID) moves up and down single-stranded DNA that encodes the pattern for antibodies and sporadically alters the strand by converting one nitrogen base to another, which is called “deamination.” The change creates DNA with a different pattern — a mutation.

These mutations, which AID creates a million-fold times more often than would otherwise occur, generate antibodies of all different sorts — giving you protection against germs that your body hasn’t even seen yet.

“It’s why when I sneeze, you don’t die,” Goodman said.

In studying the seemingly random motion of AID up and down DNA, Goodman wanted to understand why it moved how it did, and why it deaminated in some places much more than others.

“We looked at the raw data and asked what the enzyme was doing to create that,” Goodman said. He and his team were able to develop statistical models whose probabilities roughly matched the data well, and were even able to trace individual enzymes visually and watch them work. But they were all just approximations, albeit reasonable ones.

Collaborating with Mak, however, offered something better: a rigorous mathematical model that describes the enzyme’s motion and interaction with the DNA and an algorithm for directly reading out AID’s dynamics from the mutation patterns.

At the time, Mak was working on the mathematics of quantum mechanics. Using similar techniques, Mak was able to help generate the model, which has been shown through testing to be accurate.

“Mathematics is the universal language behind physical science, but its central role in interpreting biology is just beginning to be recognized,” Mak said. Goodman and Mak collaborated on the research with Phuong Pham, assistant research professor, and Samir Afif, a graduate student at USC Dornsife. An article on their work, which will appear in print in the Journal of Biological Chemistry on October 11, was selected by the journal as a “paper of the week.”

Next, the team will generalize the mathematical model to study the “real life” action of AID as it initiates mutations during the transcription of Ig variable and constant regions, which is the process needed to generate immunodiversity in human B-cells.

Journal Reference:

  1. C. H. Mak, P. Pham, S. A. Afif, M. F. Goodman. A Mathematical Model for Scanning and Catalysis on Single-stranded DNA, Illustrated with Activation-induced Deoxycytidine DeaminaseJournal of Biological Chemistry, 2013; DOI: 10.1074/jbc.M113.506550

Bacteria Communicate to Help Each Other Resist Antibiotics (Science Daily)

July 4, 2013 — New research from Western University unravels a novel means of communication that allows bacteria such as Burkholderia cenocepacia (B. cenocepacia) to resist antibiotic treatment. B. cenocepacia is an environmental bacterium that causes devastating infections in patients with cystic fibrosis (CF) or with compromised immune systems.

Artist’s 3-D rendering of bacteria (stock image). (Credit: © fotoliaxrender / Fotolia)

Dr. Miguel Valvano and first author Omar El-Halfawy, PhD candidate, show that the more antibiotic resistant cells within a bacterial population produce and share small molecules with less resistant cells, making them more resistant to antibiotic killing. These small molecules, which are derived from modified amino acids (the building blocks used to make proteins), protect not only the more sensitive cells of B. cenocepacia but also other bacteria including a highly prevalent CF pathogen, Pseudomonas aeruginosa, and E. coli. The research is published in PLOS ONE.

“These findings reveal a new mechanism of antimicrobial resistance based on chemical communication among bacterial cells by small molecules that protect against the effect of antibiotics,” says Dr. Valvano, adjunct professor in the Department of Microbiology and Immunology at Western’s Schulich School of Medicine & Dentistry, currently a Professor and Chair at Queen’s University Belfast. “This paves the way to design novel drugs to block the effects of these chemicals, thus effectively reducing the burden of antimicrobial resistance.”

“These small molecules can be utilized and produced by almost all bacteria with limited exceptions, so we can regard these small molecules as a universal language that can be understood by most bacteria,” says El-Halfawy, who called the findings exciting. “The other way that Burkholderia communicates its high level of resistance is by releasing small proteins to mop up, and bind to lethal antibiotics, thus reducing their effectiveness.” The next step is to find ways to inhibit this phenomenon.

The research, conducted at Western, was funded by a grant from Cystic Fibrosis Canada and also through a Marie Curie Career Integration grant.

Journal Reference:

  1. Omar M. El-Halfawy, Miguel A. Valvano. Chemical Communication of Antibiotic Resistance by a Highly Resistant Subpopulation of Bacterial CellsPLoS ONE, 2013; 8 (7): e68874 DOI: 10.1371/journal.pone.0068874