sábado, 16 de julio de 2016

A lab founded by a tech billionaire just unveiled a major leap forward in cracking your brain's code

This is definitely not a scene from "A Clockwork Orange." Allen Brain Observatory
As the mice watched a computer screen, their glowing neurons pulsed through glass windows in their skulls.

Using a device called a two-photon microscope, researchers at the Allen Institute for Brain Science could peer through those windows and record, layer by layer, the workings of their little minds.

The result, announced July 13, is a real-time record of the visual cortex — a brain region shared in similar form across mammalian species — at work. The data set that emerged is so massive and complete that its creators have named it the Allen Brain Observatory.

Bred for the lab, the mice were genetically modified so that specific cells in their brains would fluoresce when they became active. Researchers had installed the brain-windows surgically, slicing away tiny chunks of the rodents' skulls and replacing them with five-millimeter skylights.

Sparkling neurons of the mouse visual cortex shone through the glass as images and short films flashed across the screen. Each point of light the researchers saw translated, with hours of careful processing, into data: 
  • Which cell lit up? 
  • Where in the brain? 
  • How long did it glow? 
  • What was the mouse doing at the time? 
  • What was on the screen?
The researchers imaged the neurons in small groups, building a map of one microscopic layer before moving down to the next. When they were finished, the activities of 18,000 cells from several dozen mice were recorded in their database.

"This is the first data set where we're watching large populations of neurons' activity in real time, at the cellular level," said Saskia de Vries, a scientist who worked on the project, at the private research center launched by Microsoft co-founder Paul Allen.


The problem the Brain Observatory wants to solve is straightforward. Science still does not understand the brain's underlying code very well, and individual studies may turn up odd results that are difficult to interpret in the context of the whole brain.

A decade ago, for example, a widely-reported study appeared to find a single neuron in a human brain that always — and only — winked on when presented with images of Halle Berry. Few scientists suggested that this single cell actually stored the subject's whole knowledge of Berry's face. But without more context about what the cells around it were doing, a more complete explanation remained out of reach.

"When you're listening to a cell with an electrode, all you're hearing is [its activity level] spiking," said Shawn Olsen, another researcher on the project. "And you don't know where exactly that cell is, you don't know its precise location, you don't know its shape, you don't know who it connects to."

Imagine trying to assemble a complete understanding of a computer given only facts like under certain circumstances, clicking the mouse makes lights on the printer blink.

To get beyond that kind of feeling around in the dark, the Allen Institute has taken what Olsen calls an "industrial" approach to mapping out the brain's activity.

"Our goal is to systematically march through the different cortical layers, and the different cell types, and the different areas of the cortex to produce a systematic, mostly comprehensive survey of the activity," Olsen explained. "It doesn't just describe how one cell type is responding or one particular area, but characterizes as much as we can a complete population of cells that will allow us to draw inferences that you couldn't describe if you were just looking at one cell at a time."

In other words, this project makes its impact through the grinding power of time and effort.

A visualization of cells examined in the project. Allen Brain Observatory
Researchers showed the mice moving horizontal or vertical lines, light and dark dots on a surface, natural scenes, and even clips from Hollywood movies.

The more abstract displays target how the mind sees and interprets light and dark, lines, and motion, building on existing neuroscience. Researchers have known for decades that particular cells appear to correspond to particular kinds of motion or shape, or positions in the visual field. This research helps them place the activity of those cells in context.

One of the most obvious results was that the brain is noisy, messy, and confusing.

"Even though we showed the same image, we could get dramatically different responses from the same cell. On one trial it may have a strong response, on another it may have a weak response," Olsen said.

All that noise in their data is one of the things that differentiates it from a typical study, de Vries said.

"If you're inserting an electrode you're going to keep advancing until you find a cell that kind of responds the way you want it to," he said. "By doing a survey like this we're going to see a lot of cells that don't respond to the stimuli in the way that we think they should. We're realizing that the cartoon model that we have of the cortex isn't completely accurate."

Olsen said they suspect a lot of that noise emerges from whatever the mouse is thinking about or doing that has nothing to do with what's on screen. They recorded videos of the mice during data collection to help researchers combing their data learn more about those effects.

The best evidence for this suspicion? When they showed the mice more interesting visuals, like pictures of animals or clips from the film "Touch of Evil," the neurons behaved much more consistently.

"We would present each [clip] ten different times," de Vries said. "And we can see from trial to trial many cells at certain times almost always respond — reliable, repeatable, robust responses."

In other words, it appears the mice were paying attention.

Allen Brain Observatory
The Brain Observatory was turned loose on the internet Wednesday, with its data available for researchers and the public to comb through, explore, and maybe critique.

But the project isn't over.

In the next year-and-a-half, the researchers intend to add more types of cells and more regions of the visual cortex to their observatory. And their long-term ambitions are even grander.

"Ultimately," Olson said,"we want to understand how this visual information in the mouse's brain gets used to guide behavior and memory and cognition."

Right now, the mice just watch screens. But by training them to perform tasks based on what they see, he said they hope to crack the mysteries of memory, decision-making, and problem-solving. Another parallel observatory created using electrode arrays instead of light through windows will add new levels of richness to their data.

So the underlying code of mouse — and human — brains remains largely a mystery, but the map that we'll need to unlock it grows richer by the day.

ORIGINAL: Tech Insider
Jul. 13, 2016

Shocking New Role Found for the Immune System: Controlling Social Interactions

In a startling discovery that raises fundamental questions about human behavior, researchers at the University of Virginia School of Medicine have determined that the immune system directly affects – and even controls – creatures’ social behavior, such as their desire to interact with others.

So could immune system problems contribute to an inability to have normal social interactions? The answer appears to be yes, and that finding could have significant implications for neurological diseases such as autism-spectrum disorders and schizophrenia.

The brain and the adaptive immune system were thought to be isolated from each other, and any immune activity in the brain was perceived as sign of a pathology. And now, not only are we showing that they are closely interacting, but some of our behavior traits might have evolved because of our immune response to pathogens,” explained Jonathan Kipnis, chair of UVA’s Department of Neuroscience. “It’s crazy, but maybe we are just multicellular battlefields for two ancient forces: pathogens and the immune system. Part of our personality may actually be dictated by the immune system.


Evolutionary Forces at Work
It was only last year that Kipnis, the director of UVA’s Center for Brain Immunology and Glia, and his team discovered that meningeal vessels directly link the brain with the lymphatic system. That overturned decades of textbook teaching that the brain was “immune privileged,” lacking a direct connection to the immune system. The discovery opened the door for entirely new ways of thinking about how the brain and the immune system interact.
Normal brain activity, left, and a hyper-connected brain. (Images by Anita Impagliazzo, UVA Health System)
The follow-up finding is equally illuminating, shedding light on both the workings of the brain and on evolution itself. The relationship between people and pathogens, the researchers suggest, could have directly affected the development of our social behavior, allowing us to engage in the social interactions necessary for the survival of the species while developing ways for our immune systems to protect us from the diseases that accompany those interactions. Social behavior is, of course, in the interest of pathogens, as it allows them to spread.

The UVA researchers have shown that a specific immune molecule, interferon gamma, seems to be critical for social behavior and that a variety of creatures, such as flies, zebrafish, mice and rats, activate interferon gamma responses when they are social. Normally, this molecule is produced by the immune system in response to bacteria, viruses or parasites. Blocking the molecule in mice using genetic modification made regions of the brain hyperactive, causing the mice to become less social. Restoring the molecule restored the brain connectivity and behavior to normal. In a paper outlining their findings, the researchers note the immune molecule plays a “profound role in maintaining proper social function.

It’s extremely critical for an organism to be social for the survival of the species. It’s important for foraging, sexual reproduction, gathering, hunting,” said Anthony J. Filiano, Hartwell postdoctoral fellow in the Kipnis lab and lead author of the study. “So the hypothesis is that when organisms come together, you have a higher propensity to spread infection. So you need to be social, but [in doing so] you have a higher chance of spreading pathogens. The idea is that interferon gamma, in evolution, has been used as a more efficient way to both boost social behavior while boosting an anti-pathogen response.

Understanding the Implications
The researchers note that a malfunctioning immune system may be responsible for “social deficits in numerous neurological and psychiatric disorders.” But exactly what this might mean for autism and other specific conditions requires further investigation. It is unlikely that any one molecule will be responsible for disease or the key to a cure. The researchers believe that the causes are likely to be much more complex. But the discovery that the immune system – and possibly germs, by extension – can control our interactions raises many exciting avenues for scientists to explore, both in terms of battling neurological disorders and understanding human behavior.

Postdoctoral researcher Anthony J. Filiano, left, and Jonathan Kipnis, chairman of UVA’s Department of Neuroscience. (Photo by Sanjay Suchak, University Communications)
Immune molecules are actually defining how the brain is functioning. So, what is the overall impact of the immune system on our brain development and function?” Kipnis said. “I think the philosophical aspects of this work are very interesting, but it also has potentially very important clinical implications.

Findings Published
Kipnis and his team worked closely with UVA’s Department of Pharmacology and with Vladimir Litvak’s research group at the University of Massachusetts Medical School. Litvak’s team developed a computational approach to investigate the complex dialogue between immune signaling and brain function in health and disease.

Using this approach we predicted a role for interferon gamma, an important cytokine secreted by T lymphocytes, in promoting social brain functions,” Litvak said. “Our findings contribute to a deeper understanding of social dysfunction in neurological disorders, such as autism and schizophrenia, and may open new avenues for therapeutic approaches.

The findings have been published online by the prestigious journal Nature. The article was written by Filiano, Yang Xu, Nicholas J. Tustison, Rachel L. Marsh, Wendy Baker, Igor Smirnov, Christopher C. Overall, Sachin P. Gadani, Stephen D. Turner, Zhiping Weng, Sayeda Najamussahar Peerzade, Hao Chen, Kevin S. Lee, Michael M. Scott, Mark P. Beenhakker, Litvak and Kipnis.

This work was supported by the National Institutes of Health (grants No. AG034113, NS081026 and T32-AI007496) and the Hartwell Foundation.

ORIGINAL: News UVA
Josh Barneyjdb9a@virginia.edu
July 13, 2016 

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The discovery was made possible by the work of Antoine Louveau, a postdoctoral fellow in Kipnis’ lab. The vessels were detected after Louveau developed a method to mount a mouse’s meninges — the membranes covering the brain — on a single slide so that they could be examined as a whole. After noticing vessel-like patterns in the distribution of immune cells on his slides, he tested for lymphatic vessels and there they were. The impossible existed. “Live imaging of these vessels was crucial to demonstrate their function, and it would not be possible without collaboration with Tajie Harris,” Kipnis noted. Harris is an assistant professor of neuroscience and a member of the Center for Brain Immunology and Glia. Kipnis also saluted the “phenomenal” surgical skills of Igor Smirnov, a research associate in the Kipnis lab whose work was critical to the imaging success of the study.

martes, 12 de julio de 2016

Monkeys In Brazil Entered The Stone Age 700 Years Ago

A CAPUCHIN WIELDING A HAMMER AGAINST A NUT RESTING ON AN ANVIL. UNIVERSITY OF OXFORD
Humanity is no longer the only species on Earth that has entered the Stone Age. It’s been known for some time now that various other primates use stone tools, including chimpanzees, capuchins, and macaques. Just recently, a study revealed that there was enough archaeological evidence to prove that macaques in Thailand have been crafting geological tools for at least half a century.

Now, it seems that capuchins have them beat. Tools in Brazil, undoubtedly made by capuchin hands, have been dated to be at least 700 years old. This means that just as the Renaissance was beginning in Italy, capuchins were crafting little chisels and hammers out of various stones in South America – although, in all likelihood, they had entered the Stone Age long before this.

As the study in the journal Current Biology notes, the field of primate archaeology is relatively nascent. Michael Haslam, the lead author of this research and the head of the Primate Archaeology (Primarch) project at the University of Oxford, is a pioneer in the field. He’s previously uncovered evidence of stone tool use in Thailand by macaques, but this new discovery is far more of a game-changer.

Until now, the only archaeological record of pre-modern, non-human animal tool use comes from a study of three chimpanzee sites in Cote d'Ivoire in Africa, where tools were dated to between 4,300 and 1,300 years old,” Haslam said in a statement. “Here, we have new evidence that suggests monkeys and other primates out of Africa were also using tools for hundreds, possibly thousands of years.

Brazilian capuchins entered the Stone Age at least 700 years ago. University of Oxford

Capuchins are indubitably clever monkeys. Researchers have long observed them using stones as hand-held hammers and anvils to break open hard, shelled food like cashews and seeds, while younglings watch their elders hammer away and learn from observation.

Their geological knowledge was found to be quite astute anvils were four times heavier than the hammers, and the hammers were four times heavier than the average stones nearby. The anvils tended to be made of layered, flat sandstones, whereas the hammers were forged from pointed, angular quartzite.

Whenever a capuchin is full of delicious nuts, it tends to leave its stone tools by a cache of discarded shells, which over time gets buried by sand and soil. After waiting for the capuchins to scuttle off, the researchers sauntered over to these sites and dug into the ground to see if they could find any older tools.

Using distinctive identifying marks on the tools made by the grinding, slamming, hammering action of long-gone capuchins, 69 tools were successfully excavated from a depth of up to 0.7 meters (2.3 feet), and radiocarbon dated using small pieces of charcoal. The oldest tools were 600 to 700 years of age, which means that 100 generations of capuchins – at least – have been using stone tools. 

They think it’s only a matter of time until older tools are found.
There is an even more tantalizing prospect to this discovery. The European invasion didn’t occur until the year 1500, so the capuchin Stone Age predates this by around 200 years. The indigenous populations of Brazil, therefore, may have come across capuchins breaking open cashew nuts native to this particular area.

It is possible,” Haslam notes, “that the that the first humans to arrive here learned about this unknown food through watching the monkeys and their primate cashew-processing industry.” So instead of monkeys or apes mimicking humans, in this case, it may have been the other way around.
Humans living in the Amazon may have educated themselves about certain stone tools from monkeys once upon a time. ANDRE DIB/Shutterstock

ORIGINAL: IFL Science

lunes, 11 de julio de 2016

Meet the First Artificial Animal

Scientists genetically engineered and 3-D-printed a biohybrid being, opening the door further for lifelike robots and artificial intelligence.

CREDIT: Getty Images
If you met this lab-created critter over your beach vacation, you'd swear you saw a baby ray. In fact, the tiny, flexible swimmer is the product of a team of diverse scientists. They have built the most successful artificial animal yet. This disruptive technology opens the door much wider for lifelike robots and artificial intelligence.

Like most disruption, it started with a simple idea. Kit Kevin Parker, PhD, a Harvard professor researching how to build a human heart, saw his daughter entranced by watching stingrays at the New England Aquarium in Boston. He wondered if he could engineer a muscle that could move in the same sinuous, undulating fashion. The quest for a material led to creating an artificial ray with a 3-D-printed rubber body at the School of Engineering and Applied Sciences at Harvard. Scientists from the University of Illinois at Urbana-Champaign, the University of Michigan, and Stanford University's Medical Center joined the team.

They reinforced the soft rubber body with a 3-D-printed gold skeleton so thin it functions like cartilage. Geneticists adapted rat heart cells so they could respond to light by contracting. Then, they were grown in a carefully arranged pattern on the rubber and around the gold skeleton.

The muscular circuitry is one of the most interesting parts of the research, and there's more about it in this video:


The birth of biohybrid beings
The new engineered animal responds to light so well scientists were able to guide it through an obstacle course 15 times its length using strong and weak light pulses.

The study authors write, "Our ray outperformed existing locomotive biohybrid systems in terms of speed, distance traveled, and durability (six days), demonstrating the potential of self-propelled, phototactically activated tissue-engineered robots."

What biohybrid mean for robots and artificial intelligence
Science of this type is fundamental for engineering special-purpose creations such as artificial worms that sniff out and eat cancer. Or bionic body parts for those who have suffered accidents or disease. Imagine having little swimmers in your system that rush to the site of a medical emergency such as a stroke. The promise of sensor-rich soft tissue frees robots to move more easily and yet not be cut off from needed input. Sensitized robot soft tissue could perform without the energy-sucking heaviness of metal or the artificial barrier of hard-plastic exoskeletons.

Thanks to disruptive, cross-disciplinary applied science like this, entrepreneurs in the next few years will be able to play on the border of what life is, what alive means, and what life can be. Expect to see companies use biohybrid beings to commercialize applications that solve some of the largest, and most lucrative, challenges we face today.

ORIGINAL: INC
BY LISA CALHOUN General partner, Valor Ventures@Lisa_Calhoun

sábado, 9 de julio de 2016

Watch This Amazing 3D Bioprinter Make Artificial Bones From Scratch

Image credit: Aether
If 3D printing is already impacting manufacturing today, what breakthroughs could bioprinting — or printing any mix of organic and inorganic materials — achieve tomorrow? In a recent video, a basic prototype of the Aether 1 bioprinter is shown printing two bones connected by a tendon using six materials that include synthetic bone, conductive ink, stem cells and graphene oxide.

While bioprinted organs are still a long way off — this video offers a glimpse into that future.


According to Aether, the printer works with a wide range of materials — organic, non-organic and both — and is flexible about where those materials come from (instead of requiring anything proprietary). It can include 10 different materials in one print (way more than your average bioprinter) and is compatible with other tools like laser cutters and CNC routers. The printer’s universal tool mounts can even be used with pencils and paintbrushes—or whatever else — for making designs on canvas or other materials.

Such a range of possibilities begins to shift the limitations from the hardware to the imagination of the user. What really stands out in this video is the final product — fabricated bones seeded with two kinds of stem cells hooked together with tendons, transistors, and conductive wires. And this is only a test. What else will researchers and makers come up with?

Of course, if it’s not already obvious, their creation isn’t ready for implantation in anyone, though it does show off the machine’s versatility in an eye-catching way. And beyond versatility, the real selling point may be its price. Aether hopes to offer their printer for around $9,000 — while other bioprinters can cost up to $200,000. 

For such bold claims — can they deliver? The announcement and video is only the first in a series which, according to Aether, will show off even greater functionality. Similar price reductions in 3D printers (that don’t bioprint) have met challenges commercially. But falling prices are a key trend to keep track of in any digitally driven technology like 3D printing.

And it should be noted, there are other companies wading into bioprinting too.

An early player, Organovo is currently working with researchers to use 3D printed tissues to test drug toxicity, and last year, they announced a partnership with cosmetics giant L’Oréal to test beauty products on3D printed skin samples (and hopefully lessen reliance on animal testing). Meanwhile, BioBots is making a bioprinter about the same size and cost as Aether’s but with more focused use cases, like 3D printing tissues for research purposes.

We’ll have to wait for more substantial news to see just how all this fits together. This summer will see the first wave of Aether machines donated to universities and researchers while presale beta units are distributed to customers. By fall 2016, they hope to launch retail sales.

What would you use it for?


ORIGINAL: Singularity Hub

jueves, 30 de junio de 2016

More than 100 Nobel laureates are calling on Greenpeace to end its anti-GMO campaign

Rice field in the Philippines. No Golden Rice here (yet).(Shutterstock)
This week, 109 Nobel laureates signed onto a sharply worded letter to Greenpeace urging the environmental group to rethink its longstanding opposition to genetically modified organisms (GMOs). The writers argue that the anti-GMO campaign is scientifically baseless and potentially harmful to poor people in the developing world.

Joel Achenbach broke the news in the Washington Post, and you can read the full letter here. The signatories include past winners of the Nobel Prize in medicine, chemistry, physics, and economics.

Nobel laureates to Greenpeace: Your anti-GMO campaign has to end
The letter notes that scientific assessments have repeatedly found GM foods are just as safe to eat as conventional foods and don’t pose an inherent risk to the environment (though, like any technology, they can be misused). Greenpeace, it argues, is on the wrong side here:
We urge Greenpeace and its supporters to re-examine the experience of farmers and consumers worldwide with crops and foods improved through biotechnology, recognize the findings of authoritative scientific bodies and regulatory agencies, and abandon their campaign against "GMOs" in general and Golden Rice in particular.

Scientific and regulatory agencies around the world have repeatedly and consistently found crops and foods improved through biotechnology to be as safe as, if not safer than those derived from any other method of production. There has never been a single confirmed case of a negative health outcome for humans or animals from their consumption. Their environmental impacts have been shown repeatedly to be less damaging to the environment, and a boon to global biodiversity.
The laureates also take Greenpeace to task for seeking to block Golden Rice, a strain of not-yet-approved rice that has been genetically enhanced to produce beta carotene — which, its creators hope, might one day alleviate the Vitamin A deficiency that’s causing widespread death and blindness in the developing world:
Greenpeace has spearheaded opposition to Golden Rice, which has the potential to reduce or eliminate much of the death and disease caused by a vitamin A deficiency (VAD), which has the greatest impact on the poorest people in Africa and Southeast Asia. ...

WE CALL UPON GREENPEACE to cease and desist in its campaign against Golden Rice specifically, and crops and foods improved through biotechnology in general;

Now, Greenpeace is far from the only reason Golden Rice has struggled to get regulatory approval — the crop also faces very serious technical challenges. Greenpeace isn’t even the only group seeking to block it. But they’re certainly a high-profile face of GMO opposition, so the laureates are focusing on them.

In a posted response, Greenpeace denied that they were the main reason Golden Rice has failed to come to market, but still showed no sign of ending their broader anti-GMO campaign. We'll get to that, but I do want to elaborate on a few issues the letter raises.

Greenpeace accepts climate science. So why do they dismiss GMO science?
(MICHAEL KAPPELER/AFP/Getty Images)A picture taken on May 3, 2005, shows Greenpeace activists flying a kite displaying a giant corn cob on a field in Seelow, Eastern Germany, to protest against the cultivation of genetically modified maize.

Let’s start off by noting that GMOs will never be a purely scientific issue. Like every policy matter on the planet, the question of how best to incorporate biotechnology into agriculture involves value judgments about what an ideal food system might look like, how to weigh the risks against the benefits, and so on.

But those positions can at least be informed by scientific understanding. To take a different example, on climate change, Greenpeace tends to take very seriously what scientists are telling them. Their website refers frequently to the scientific consensus that the world is getting warmer and humans are the cause.

By contrast, Greenpeace’s public statements on GMOs tend to be startlingly unscientific. On their website, they refer to transgenic crops as "genetic pollution." This is absurd. When scientists create transgenic crops, they frequently use Agrobacterium to transfer genes from one plant or organism to another. But nature does this too: Scientists recently discovered that on two separate occasions in history, Agrobacterium transferred bacterial DNA into the sweet potatoes we now eat. Are sweet potatoes also "polluted"? Because it's the same thing.

In fact, many crop scientists tend to see GMOs as sitting along a continuumHumans have long used all sorts of tools to alter plant DNA and get crops with the traits we desire — this is a big reason farms can feed 7 billion people every year. For thousands of years, farmers interbred crops to alter their genes. Like so:
(James Kennedy)

In the 20th century, plant breeders began exposing crops to radiation or mutagenic chemicals to scramble their DNA and get new traits. Today, scientists use advanced techniques (like transferring genes or CRISPR) that allow even more precision. But it’s the same basic idea. Under the circumstances, it’s no surprise that GMOs don't appear to pose a special health risk. They’re just not fundamentally different.

Now, the vast majority of the public is unaware of this fact. Most people don’t spend much time thinking about how our food is created. (One of the lovely things about the modern age is that we don’t have to.) So, in the abstract, people tend to fall back on their intuitions: Tampering with the DNA of food seems inherently unnatural. Anything "unnatural" triggers disgust. Therefore, GMOs are bad.

Those intuitions are understandable. But they're unsupported by scientific evidence. And rather than seeking to correct those misapprehensions, as they do on climate change, Greenpeace has long sought to inflame those fears. Take this line from their website: "When we force life forms and our world's food supply to conform to human economic models rather than their natural ones, we do so at our own peril." (Never mind that we’ve been doing this since the dawn of civilization.)

The Nobel laureates are, in essence, telling them to knock it off.

Ultimately, the world will face staggering challenges around food and agriculture in the 21st century. The global population is expected to soar past 9 billion, and we’ll need to figure out how to feed everyone without razing too many forests for farmland. Farmers will have to handle the droughts and heat waves that will come with global warming. There are tricky issues around antibiotic overuse, nitrogen pollution, food distribution, and much more.

Genetic engineering certainly won’t solve all those problems. (It might not even solve most of them.) But it ispotentially a valuable tool for, say, breeding plants with higher drought tolerance or engineering foods that are more nutritious. See, for example, this important work on vitamin-fortified bananas in Africa. We should be thinking seriously about how to use these tools as a larger strategy for improving our food system — not sowing fears about "genetic pollution."

Greenpeace’s campaign against Golden Rice is incoherent — though the crop faces other serious challenges

(David Greedy/Getty Images)Plant Biotechnologist Dr. Swapan Datta inspects a genetically modified "Golden Rice" plant at the International Rice Research Institute (IRRI), November 27, 2003.
The Nobel laureate letter particularly criticizes Greenpeace’s opposition to Golden Rice — rice that’s being modified in an attempt to alleviate Vitamin A deficiency — and here it’s worth expanding a bit.

Last year in Slate, Will Saletan wrote a damning piece on how incoherent Greenpeace’s campaign against Golden Rice was. As research advanced, the group kept shifting its position. A sample:
In 2001, Benedikt Haerlin, Greenpeace’s anti-GMO coordinator, appeared with Potrykus at a press conference in France. Haerlin conceded that Golden Rice served "a good purpose" and posed "a moral challenge to our position." Greenpeace couldn’t dismiss the rice as poison. So it opposed the project on technical grounds: Golden Rice didn’t produce enough beta carotene. …

While critics tried to block the project, Potrykus and his colleagues worked to improve the rice. By 2003 they had developed plants with eight times as much beta carotene as the original version. In 2005 they unveiled a line that had 20 times as much beta carotene as the original. GMO critics could no longer dismiss Golden Rice as inadequate. So they reversed course. Now that the rice produced plenty of beta carotene, anti-GMO activists claimed that beta carotene and vitamin A were dangerous. …

In the Philippines, where Greenpeace was fighting to block field trials of Golden Rice, its hypocrisy was egregious. "It is irresponsible to impose GE 'Golden' rice on people if it goes against their religious beliefs, cultural heritage and sense of identity, or simply because they do not want it," Greenpeace declared. But just below that pronouncement, Greenpeace recommended "vitamin A supplementation and vitamin fortification of foods as successfully implemented in the Philippines.

Under Philippine law, beta carotene and vitamin A had to be added to sugar, flour, and cooking oil prior to distribution. The government administered capsules to preschoolers twice a year, and to some pregnant women for 28 consecutive days. If Greenpeace seriously believed that retinoids caused birth defects and should be a matter of personal choice, it would never have endorsed these programs.
It goes on and on like this. Greenpeace has simply dismissed scientific reviews showing that Golden Rice does not pose a threat to human health or the environment. Instead, it continues to file petitions to block all field trials and feeding studies in places like the Philippines.

Now, to repeat what I said above: Greenpeace and other anti-GMO groups aren’t the only obstacle to getting Golden Rice into farmers’ fields. It is fundamentally hard to create a high-yielding strain of rice that consistently produces higher levels of beta carotene. Even after 24 years of testing, researchers still haven’t been able to get Golden Rice to work perfectly in field trials. And they might be struggling even if Greenpeace had given them a pass all along.

In a reply to the Nobel laureates' letter, Greenpeace insisted as much: "Accusations that anyone is blocking genetically engineered ‘Golden’ rice are false," said Wilhelmina Pelegrina, Campaigner at Greenpeace Southeast Asia "‘Golden’ rice has failed as a solution and isn’t currently available for sale, even after more than 20 years of research."

True. But rather irrelevant. It is also fundamentally hard to create a Zika vaccine. It would nonetheless be misguided for me to wage a campaign against researchers working on the project or file a petition to stop trials without any good evidence that it was a risk — even if my protests weren’t the main hold-up.

On a final note, I do think Greenpeace does enormously vital work around the world. They played a crucial role in pressuring soy and beef companies in Brazil to reduce deforestation of the Amazon. Their efforts in China to pare back unnecessary coal-burning plants are one of the most consequential climate campaigns going.

But on GMOs, they are very much in the wrong. Let's hope this letter prods them to reflect and reconsider.
Go deeper:

ORIGINAL: Vox
June 30, 2016

domingo, 26 de junio de 2016

New Life Found That Lives Off Electricity

Scientists have figured out how microbes can suck energy from rocks. Such life-forms might be more widespread than anyone anticipated.

Yamini Jangir and Moh El-Naggar 

Scientists use carbon-fiber electrodes (gray) to lure electricity-eating microbes (orange). These microbes grow incredibly slowly, so attracting them can take time. Researchers left this electrode underground for five months.

Last year, biophysicist Moh El-Naggar and his graduate student Yamini Jangir plunged beneath South Dakota’s Black Hills into an old gold mine that is now more famous as a home to a dark matter detector. Unlike most scientists who make pilgrimages to the Black Hills these days, El-Naggar and Jangir weren’t there to hunt for subatomic particles. They came in search of life.

In the darkness found a mile underground, the pair traversed the mine’s network of passages in search of a rusty metal pipe. They siphoned some of the pipe’s ancient water, directed it into a vessel, and inserted a variety of electrodes. They hoped the current would lure their prey, a little-studied microbe that can live off pure electricity.

The electricity-eating microbes that the researchers were hunting for belong to a larger class of organisms that scientists are only beginning to understand. They inhabit largely uncharted worlds: 
  • the bubbling cauldrons of deep sea vents; 
  • mineral-rich veins deep beneath the planet’s surface; 
  • ocean sediments just a few inches below the deep seafloor. 
The microbes represent a segment of life that has been largely ignored, in part because their strange habitats make them incredibly difficult to grow in the lab.

Yet early surveys suggest a potential microbial bounty. A recent sampling of microbes collected from the seafloor near Catalina Island, off the coast of Southern California, uncovered a surprising variety of microbes that consume or shed electrons by eating or breathing minerals or metals. El-Naggar’s team is still analyzing their gold mine data, but he says that their initial results echo the Catalina findings. Thus far, whenever scientists search for these electron eaters in the right locations — places that have lots of minerals but not a lot of oxygen — they find them.

As the tally of electron eaters grows, scientists are beginning to figure out just how they work. How does a microbe consume electrons out of a piece of metal, or deposit them back into the environment when it is finished with them? A study published last year revealed the way that one of these microbes catches and consumes its electrical prey. And not-yet-published work suggests that some metal eaters transport electrons directly across their membranes — a feat once thought impossible.

The Rock Eaters
Though eating electricity seems bizarre, the flow of current is central to life. All organisms require a source of electrons to make and store energy. They must also be able to shed electrons once their job is done. In describing this bare-bones view of life, Nobel Prize-winning physiologist Albert Szent-Györgyi once said, “Life is nothing but an electron looking for a place to rest.

Humans and many other organisms get electrons from food and expel them with our breath. The microbes that El-Naggar and others are trying to grow belong to a group called lithoautotrophs, or rock eaters, which harvest energy from inorganic substances such as iron, sulfur or manganese. Under the right conditions, they can survive solely on electricity.

The microbes’ apparent ability to ingest electrons — known as direct electron transfer — is particularly intriguing because it seems to defy the basic rules of biophysics. The fatty membranes that enclose cells act as an insulator, creating an electrically neutral zone once thought impossible for an electron to cross. “No one wanted to believe that a bacterium would take an electron from inside of the cell and move it to the outside,” said Kenneth Nealson, a geobiologist at the University of Southern California, in a lecture to the Society for Applied Microbiology in London last year.

Lucy Reading-Ikkanda for Quanta Magazine
In the 1980s, Nealson and others discovered a surprising group of bacteria that can expel electrons directly onto solid minerals. It took until 2006 to discover the molecular mechanism behind this feat: A trio of specialized proteins sits in the cell membrane, forming a conductive bridge that transfers electrons to the outside of cell. (Scientists still debate whether the electrons traverse the entire distance of the membrane unescorted.)

Inspired by the electron-donators, scientists began to wonder whether microbes could also do the reverse and directly ingest electrons as a source of energy. Researchers focused their search on a group of microbes called methanogens, which are known for making methane. Most methanogens aren’t strict metal eaters. But in 2009, Bruce Logan, an environmental engineer at Pennsylvania State University, and collaborators showed for the first time that a methanogen could survive using only energy from an electrode. The researchers proposed that the microbes were directly sucking up electrons, perhaps via a molecular bridge similar to the ones the electron-producers use to shuttle electrons across the cell wall. But they lacked direct proof.

Then last year, Alfred Spormann, a microbiologist at Stanford University, and collaborators poked a hole in Logan’s theory. They uncovered a way that these organisms can survive on electrodes without eating naked electrons.

The microbe Spormann studied, Methanococcus maripaludis, excretes an enzyme that sits on the electrode’s surface. The enzyme pairs an electron from the electrode with a proton from water to create a hydrogen atom, which is a well-established food source among methanogens. “Rather than having a conductive pathway, they use an enzyme,” said Daniel Bond, a microbiologist at the University of Minnesota Twin Cities. “They don’t need to build a bridge out of conductive materials.

Though the microbes aren’t eating naked electrons, the results are surprising in their own right. Most enzymes work best inside the cell and rapidly degrade outside. “What’s unique is how stable the enzymes are when they [gather on] the surface of the electrode,” Spormann said. Past experiments suggest these enzymes are active outside the cell for only a few hours, “but we showed they are active for six weeks.

Spormann and others still believe that methanogens and other microbes can directly suck up electricity, however. “This is an alternative mechanism to direct electron transfer, it doesn’t mean direct electron transfer can’t exist,” said Largus Angenent, an environmental engineer at Cornell University, and president of the International Society for Microbial Electrochemistry and Technology. Spormann said his team has already found a microbe capable of taking in naked electrons. But they haven’t yet published the details.

Microbes on Mars
Only a tiny fraction — perhaps 2 percent — of all the planet’s microorganisms can be grown in the lab. Scientists hope that these new approaches — growing microbes on electrodes rather than in traditional culture systems — will provide a way to study many of the microbes that have been so far impossible to cultivate.

Using electrodes as proxies for minerals has helped us open and expand this field,” said Annette Rowe, a postdoctoral researcher at USC working with El-Naggar. “Now we have a way to grow the bacteria and monitor their respiration and really have a look at their physiology.”

Rowe has already had some success.
In 2013, she went on a microbe prospecting trip to the iron-rich sediments that surround California’s Catalina Island. She identified at least 30 new varieties of electric microbes in a study published last year.They are from very diverse groups of microbes that are quite common in marine systems,” Rowe said. Before her experiment, no one knew these microbes could take up electrons from an inorganic substrate, she said. “That’s something we weren’t expecting.

Just as fishermen use different lures to attract different fish, Rowe set the electrodes to different voltages to draw out a rich diversity of microbes. She knew when she had a catch because the current changed — metal eaters generate a negative current, as the microbes suck electrons from the negative electrode.
Connie A. Walter and Matt Kapust
Yamini Jangir, then a graduate student in Moh El-Naggar’s lab at the University of Southern California, collects water from a pipe at the Sanford Underground Research Facility nearly a mile underground.

The different varieties of bacteria that Rowe collected thrive under different electrical conditions, suggesting they employ different strategies for eating electrons. “Each bacteria had a different energy level where electron uptake would happen,” Rowe said. “We think that is indicative of different pathways.”

Rowe is now searching new environments for additional microbes, focusing on fluids from a deep spring with low acidity. She’s also helping with El-Naggar’s gold mine expedition. “We are trying to understand how life works under these conditions,” said El-Naggar. “We now know that life goes far deeper than we thought, and there’s a lot more than we thought, but we don’t have a good idea for how they are surviving.

El-Naggar emphasizes that the field is still in its infancy, likening the current state to the early days of neuroscience, when researchers poked at frogs with electrodes to make their muscles twitch. “It took a long time for the basic mechanistic stuff to come out,” he said. “It’s only been 30 years since we discovered that microbes can interact with solid surfaces.

Given the bounty from these early experiments, it seems that scientists have only scratched the surface of the microbial diversity that thrives beneath the planet’s shallow exterior. The results could give clues to the origins of life on Earth and beyond. One theory for the emergence of life suggests it originated on mineral surfaces, which could have concentrated biological molecules and catalyzed reactions. New research could fill in one of the theory’s gaps — a mechanism for transporting electrons from mineral surfaces into cells.

Moreover, subsurface metal eaters may provide a blueprint for life on other worlds, where alien microbes might be hidden beneath the planet’s shallow exterior. “For me, one of the most exciting possibilities is finding life-forms that might survive in extreme environments like Mars,” said El-Naggar, whose gold mine experiment is funded by NASA’s Astrobiology Institute. Mars, for example, is iron-rich and has water flowing beneath its surface. “If you have a system that can pick up electrons from iron and have some water, then you have all the ingredients for a conceivable metabolism,” said El-Naggar. Perhaps a former mine a mile underneath South Dakota won’t be the most surprising place that researchers find electron-eating life.

ORIGINAL: Quanta Magazine
June 21, 2016