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EMBO 2012 - International workshop on Evolution in the Time of Genomics

EMBO 2012 - International workshop on Evolution in the Time of Genomics | Amazing Science |

Molecular evolution was born fifty years before the planned Conference, with a seminal paper by Zuckerkandl and Pauling (1962) which demonstrated that aminoacid changes in the globins followed a molecular clock and could provide information on the phylogeny of vertebrates and on the timing of their appearance on earth.

Principal themes and objectives of the event From changes in aminoacids to changes in nucleotides, the molecular level has provided an essential input into evolutionary investigations for the past decades. More recently, the molecular level has moved from the genes to the genome, so far mainly in the case of vertebrates (in which the coding sequences only represent about 2% of the total). The availability of full genome sequences has provided new possibilities for investigators in the field and major problems can now be tackled in a very precise way using bioinformatic tools. Indeed, an example of this approach has been the recent solution (Bernardi, 2007)of a twenty-year-old debate, that between neutralists and selectionists.

One of the major current debates concerns adaptive vs. non-adaptive evolution. Random events in evolution were originally raised as a fundamental problem by Jacques Monod in his famous book "Chance and necessity". The problem has now been shifted to the genome level. A preliminary discussion took place in October 2010 in a Meeting "Chance and Necessity in Evolution" (Ravello, Italy; papers are in press in a special issue of Genome Biology and Evolution). The proposed meeting should go deeper into such a basic issue. While this will be one of the main subject of the meeting in which different views will confront each other (with Bernardi, Jarosz, Koonin, Ohta, Ptashne), other basic topics in Genome Evolution will be addressed. Werner Arber, Hamilton Smith (two Nobel Laureates) and George Church will discuss in depth the results obtained so far "directing" evolution in microbial systems, their interpretation and even the ethical issues raised. Davidson, Gehring and Gojobori will deal with the evolution of developmental processes; Martin, Saccone and Wallace with the evolution of mitochondrial genomes; Okada and Shapiro with the impact of mobile elements on genome evolution; Jeffreys and Saitou with recombination and biased gene conversion; Bustamante, Felsenfeld, Hartl and Haussler with regulation of gene expression and copy number variation in the human genome. Last but not least, Emile Zuckerkandl will recollect the beginning of Molecular Evolution.

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20,000+ FREE Online Science and Technology Lectures from Top Universities

20,000+ FREE Online Science and Technology Lectures from Top Universities | Amazing Science |

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Optogenetics captures synaptic transmission in live mammalian brain for the first time

Optogenetics captures synaptic transmission in live mammalian brain for the first time | Amazing Science |

EPFL scientists Aurélie Pala and Carl Petersen have observed and measured synaptic transmission in a live animal for the first time, using optogenetics* to stimulate single neurons in the mouse barrel cortex (which processes sensory information from the mouse’s whiskers). They shined blue light on the neurons containing a gene-based light-sensitive protein, activating the neurons to fire. Then using microelectrodes, they measured resulting electrical signals in neighboring interneuron cells.

They also used an advanced imaging technique (two-photon microscopy) that allowed them to look deep into the brain of the live mouse and identify the type of each interneuron they were studying.

The data showed that the neuronal transmissions from the light-sensitive neurons differed depending on the type of interneuron on the receiving end. Only a few studies have directly investigated synaptic transmission between specific neocortical neurons in vivo, presumably due to the technical difficulties in obtaining intracellular recordings from connected pairs of neurons in vivo, the authors say in their (open-access) paper in Neuron.

The research overcomes a limitation of in vitro (lab) studies, where associated biomolecules are different from those in a live animal, and where cutting neural tissue for lab work also introduces artifacts, the researchers suggest. “This is a proof-of-concept study,” says Pala, who received her PhD for this work. “Nonetheless, we think that we can use optogenetics to put together a larger picture of connectivity between other types of neurons in other areas of the brain.”

The scientists are now aiming to explore other neuronal connections in the mouse barrel cortex. They also want to try this technique on awake mice, to see how switching neuronal activity on and off with a light can affect higher brain functions.

* Optogenetics works by inserting the gene of an light-sensitive protein into live neurons, from a single cell to an entire family of them. The genetically modified neurons then produce the light-sensitive protein, which sits on their outside, the membrane. There, it acts as an electrical channel – something like a gate. When light is shone on the neuron, the channel opens up and allows electrical ions to flow into the cell; a bit like a battery being charged by a solar cell. The addition of electrical ions changes the voltage balance of the neuron, and if the optogenetic stimulus is sufficiently strong it generates an explosive electrical signal in the neuron

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Computer programs 'mutate' to outlast viruses

Computer programs 'mutate' to outlast viruses | Amazing Science |

The KISS concept—keep it simple, stupid—may work in many situations. However, when it comes to evolution, complexity appears to be the best strategy for longterm survival. Researchers pitted self-replicating computer programs against computer viruses in the domain of the Avida platform for digital evolution. The co-evolution of host and virus ultimately led to organisms with capabilities superior to those of organisms that evolved without battling the viruses, says Luis Zaman of Michigan State University’s BEACON Center for the Study of Evolution in Action.

“The organisms faced off against some pretty nasty viruses, ones that quickly overcame the easy ways of becoming resistant,” says Zaman, who’s now a postdoctoral researcher at the University of Washington.

“This left only more and more complex options for co-evolving hosts. We thought to ourselves, maybe the organisms that were more readily adaptable than the others, more evolvable, would be the ones left standing at the end of the experiments.” The team of scientists showed that the long-lasting hosts were indeed more evolvable. The results are detailed in a study published in PLOS Biology.

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Did Microbes Shape the Human Life Span?

Did Microbes Shape the Human Life Span? | Amazing Science |
The human microbiome may have evolved to selectively target older humans, thereby enabling an extended childhood in our earliest human ancestors.

The age structure of human populations is exceptional among animal species. Unlike with most species, human juvenility is extremely extended, and death is not coincident with the end of the reproductive period. If we examine the age structure of early humans with models that reveal an extraordinary balance of human fertility and mortality. A research team now hypothesizes that the age structure of early humans was maintained by mechanisms incorporating the programmed death of senescent individuals, including by means of interactions with their indigenous microorganisms.

First, before and during reproductive life, there was selection for microbes that preserve host function through regulation of energy homeostasis, promotion of fecundity, and defense against competing high-grade pathogens. Second, the scientists hypothesized that after reproductive life, there was selection for organisms that contribute to host demise. While deleterious to the individual, the presence of such interplay may be salutary for the overall host population in terms of resource utilization, resistance to periodic diminutions in the food supply, and epidemics due to high-grade pathogens. In their work, the team provides deterministic mathematical models based on age-structured populations that illustrate the dynamics of such relationships and explores the relevant parameter values within which population viability is maintained. They argue that the age structure of early humans was robust in its balance of the juvenile, reproductive-age, and senescent classes.

These concepts are relevant to issues in modern human longevity, including inflammation-induced neoplasia and degenerative diseases of the elderly, which are a legacy of human evolution.

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Finding faster-than-light particles by weighing them

Finding faster-than-light particles by weighing them | Amazing Science |

In a new paper accepted by the journal Astroparticle PhysicsRobert Ehrlich, a recently retired physicist from George Mason University, claims that the neutrino is very likely a tachyon or faster-than-light particle. There have been many such claims, the last being in 2011 when the "OPERA" experiment measured the speed of neutrinos and claimed they travelled a tiny amount faster than light. However, when their speed was measured again the original result was found to be in error – the result of a loose cable no less.

Ehrlich's new claim of faster-than-light neutrinos is based on a much more sensitive method than measuring their speed, namely by finding their mass. The result relies on tachyons having an imaginary mass, or a negative mass squared. Imaginary mass particles have the weird property that they speed up as they lose energy – the value of their imaginary mass being defined by the rate at which this occurs. According to Ehrlich, the magnitude of the neutrino's imaginary mass is 0.33 electronvolts, or 2/3 of a millionth that of an electron. He deduces this value by showing that six different observations from cosmic rays, cosmology, and particle physics all yield this same value within their margin of error. One observation, for example, involves the tiny variations in cosmic background radiation left over from the big bang, while another involves the shape of the cosmic ray spectrum.

Skeptics of tachyons often cite conflicts with relativity theory. In fact, the idea of faster-than light tachyons was first suggested in a 1962 article by George Sudarshan and colleagues Bilaniuk and Deshpande as a kind of loophole in relativity. Einstein had shown that it is impossible for particles (or space ships) to be accelerated up to or beyond the speed of light because of the infinite energy required. Sudarshan and his colleagues suggested, however, that if particles were created initially with faster-than-light speed in particle collisions no acceleration or infinite energy would be necessary – something not possible for space ships unfortunately!

Several decades after tachyons were first proposed, and after many fruitless searches for them, three theorists Chodos, Hauser, and Kostelecky suggested in 1985 that they might be hiding in plain sight – specifically that neutrinos are tachyons. This idea led them to propose that protons should beta decay when they travel at sufficiently high speed towards us. Normally, this process is forbidden because it could not conserve energy, but that changes if neutrinos are tachyons, energy can be negative in certain reference frames – in effect negative energy tachyons travel backwards in time. The Chodos-Hauser-Kostelecky proposal is what first led Ehrlich to take up the hunt in 1999 when he claimed support for neutrinos being tachyons based on several cosmic ray studies. His new result, however, relies on data from four other areas besides cosmic rays, and is therefore more robust.

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New record: Ethereal deep-sea fish lives 5 miles underwater

New record: Ethereal deep-sea fish lives 5 miles underwater | Amazing Science |

Scientists have discovered a new species of fish that glides gently through the water on white, translucent wings 5 miles beneath the ocean surface. The newly discovered species is now the world’s deepest known fish recorded at 8,143 m depth. The fish has a novel body form that has not been seen before. It stunned scientists because in other trenches, there is only one fish species at this depth--a snailfish; this fish is really different from any other deep-sea fish that scientists have ever seen.

"We were just blown away when we saw it," said Paul Yancey, a biology professor at Whitman College, Washington who studies how animals adapt to life in the deep sea. "Someone on the ship said it looks like a cross between a puppy, an angel and an eel." The fish was first spotted in November during an international research cruise to the Mariana Trench -- the deepest place on Earth.

The new fish, which has not yet been named, was discovered by accident. In the video above you can see it swimming around a series of tubes that were part of an instrument collecting mud samples from the sea floor.  The camera was supposed to be filming the core collecting, when suddenly this ghostly fish swam into view. It is about 10 inches in length, and almost entirely transparent. The dense white part you can see is actually its skull, visible through its skin, Yancey said. It's lengthy, mostly see-through tail is probably made of gelatin.

"It's moving very slowly so it's not clear how well it can swim," he said. "But there has to be some muscle in there somewhere." The Mariana Trench is located in the Western Pacific, just off the coast of Guam. It starts about 3 miles beneath the ocean surface and stretches to an ultimate depth of 6.8 miles. Humans couldn't survive even at the top rim of the trench. At that depth, the proteins and cells in our membranes would collapse. And at the bottom of the trench, the pressure is so immense it would be like having 100 elephants standing on your head.

One way deep sea animals survive even under the weight of all that water is with a molecule called trimethylamine N-oxide (TMAO) that protects their proteins from being crushed. "It's the molecule that makes marine animals like fish and shrimp smell 'fishy,' " said Yancey, "and in deep sea animals there is a lot more of it."

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Global warming blamed for Pacific coral bleaching

Global warming blamed for Pacific coral bleaching | Amazing Science |

The Marshall Islands is experiencing its worst-ever coral bleaching as global warming threatens reefs across the entire northern Pacific, scientists found in a recent study.

Marine researchers said an El Nino weather pattern had been developing in recent months, raising ocean temperatures and stressing delicate coral reefs. "The worst coral bleaching event ever recorded for the Marshall Islands has been occurring since mid-September," Karl Fellenius, a Majuro-based marine scientist with the University of Hawaii told AFP.

C. Mark Eakin, manager of the US National Oceanic and Atmospheric Administration's Coral Reef Watch programme, said recent observations showed the problem was widespread across the vast waters of the northern Pacific. "Major bleaching was seen in Guam and the Commonwealth of the Northern Marianas Islands, the northwestern Hawaiian Islands (NWHI), the Marshall Islands, and Kiribati," he said.

"Thermal stress levels set new record highs in CNMI and the NWHI and we saw the first widespread bleaching event in the main Hawaiian Islands." Fellenius said coral bleaching was a naturally occurring phenomenon but not on the scale currently being seen. "While bleaching can occur on very hot days in pools of water with little circulation (such as) very low tides on reef flats, it has become a global problem due to greenhouse gas emissions causing elevated temperatures under climate change."

He said sea surface temperatures had been on average half to a full degree Celsius higher than normal for months, adding: "This does not seem like a lot but it makes a big difference to corals." Fellenius said the last major bleaching event was in 1997, when an exceptionally strong El Nino system affected about a quarter of the world's coral reefs.

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SyAm-Ps - a new class of synthetic molecules mimics antibodies to fight cancer

SyAm-Ps - a new class of synthetic molecules mimics antibodies to fight cancer | Amazing Science |

A Yale University lab has crafted the first synthetic molecules that have both the targeting and response functions of antibodies. The new molecules — synthetic antibody mimics (SyAMs) — attach themselves simultaneously to disease cells and disease-fighting cells. The result is a highly targeted immune response, similar to the action of natural human antibodies.

“Unlike antibodies, however, our molecules are synthetic organic compounds that are approximately one-twentieth the size of antibodies,” said David A. Spiegel, a professor of chemistry at Yale whose lab developed the molecules. “They are unlikely to cause unwanted immune reactions due to their structure, are thermally stable, and have the potential to be administered orally, just like traditional, small-molecule drugs.”

Spiegel and his team describe the research in a paper published online Dec. 16 by the Journal of the American Chemical Society. The paper looks specifically at SyAM molecules used to attack prostate cancer. Called SyAM-Ps, they work first by recognizing cancer cells and binding with a specific protein on their surface. Next, they also bind with a receptor on an immune cell. This induces a targeted response that leads to the destruction of the cancer cell.

Spiegel said the process of synthesizing and optimizing the structure of the molecules required considerable time and effort. “We now know that synthetic molecules of intermediate size possess perhaps the most important functional properties of antibodies — targeting and stimulation of immune cells,” he said.

“It’s also noteworthy that molecules of such a small size can bring together two objects as enormous as cells, and trigger a specific functional response, entirely as a result of specific receptor interactions,” Spiegel added. Beyond their potential for treating prostate cancer, SyAMs may have applications for treating other forms of cancer, HIV and various bacterial diseases.

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Computer-based "deep neural network" as good as primates at visual object recognition

Computer-based "deep neural network" as good as primates at visual object recognition | Amazing Science |

Computers aren't best suited to visual object recognition. Our brains are hardwired to quickly see and match patterns in everything, with great leaps of intuition, while the processing center of a computer is more akin to a very powerful calculator. But that hasn't stopped neuroscientists and computer scientists from trying over the past 40 years to design computer networks that mimic our visual skills. Recent advances in computing power and deep learning algorithms have accelerated that process to the point where a group of MIT neuroscientists has found a network design that compares favorably to the brain of our primate cousins.

This is important beyond the needs of automated digital information processing like Google's image search. Computer-based neural networks that work like the human brain will further our understanding of how the brain works, and any attempts to create them will test that understanding. Essentially, the fact that these networks work to a level comparable to primates suggests that neuroscientists now have a solid grasp of how object recognition works in the brain.

To see how current networks hold up, the MIT scientists started by testing primates. They implanted arrays of electrodes in the inferior temporal (IT) cortex and area V4 (a part of the visual system that feeds into the IT cortex) of the primates' brains. This allowed them to see how neurons related to object recognition responded when the animals looked at various objects in 1,960 images. The viewing time per image was a mere 100 milliseconds, which is long enough for humans to recognize an object.

They then compared these results with those of the latest deep neural networks. These networks produce arrays of numbers when fed an image – different numbers for different images. If it groups similar objects into similar clusters in this number matrix representation, it's deemed accurate. "Through each of these computational transformations, through each of these layers of networks, certain objects or images get closer together, while others get further apart," explains lead author Charles Cadieu.

The best network, developed by researchers at New York University, classified objects as well as the macaque - a medium-sized Old World monkey - brain. That's the good news. The bad is that they don't know why. Neural networks are learning from massive datasets containing millions or billions of images, churning through the information with help from the high-performance graphical processing units that power the latest video games. But nobody knows quite what is going on in there as the networks refine their own algorithms.

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The importance of three-way atom interactions in maintaining coherence

The importance of three-way atom interactions in maintaining coherence | Amazing Science |
Quantum computers will someday perform calculations impossible for conventional digital computers. But for that to happen, the core quantum information must be preserved against contamination from the environment. In other words, decoherence of qubits must be forestalled. Coherence, the ability of a system to retain quantum integrity—-meaning that one part of the system can be used to predict the behavior of other parts—-is an important consideration.

Over the past dozen years, remarkable experiments have shown how the coherence of a Bose condensate loaded into optical lattices can collapse and later return. New theoretical work by JQI scientists provides a detailed explanation for this quantum revival. The heart of their theory are interactions involving three atoms simultaneously.

In Bose Einstein condensates (BECs) typically a million atoms are chilled until their respective waves overlap. In effect, they become a single coherent object. If furthermore the BEC is lined up into a series of zones in space using the powerful electric fields of crisscrossing laser beams—-a configuration called an optical lattice—-then the BEC atoms become a sort of crystal.

The effect of the optical lattice is to encase the atoms in stacks of egg-carton-like confinements. Typically about 100x100x100 (one million) egg-carton slots are filled by a BEC cloud. For a million-BEC atom BEC this corresponds to about one atom per lattice site. The atoms in this artificial crystal are spaced much farther apart than the atoms in a natural crystal but still close enough for them to interact in interesting ways.

If suddenly the strength of the lasers is increased, the depth of the well becomes deeper, and the atoms are less likely to tunnel from one compartment to another, and consequently more likely to interact with its partners within that well. What happens to the coherence of the BEC ensemble when atoms are encouraged to interact with each other at close range in the lattice sites? This is what scientists at the Max Planck Institute for Quantum Physics in Garching, Germany set out to explore in an experiment conducted a dozen years ago.

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Mathematicians Make a Major Discovery About Prime Numbers

Mathematicians Make a Major Discovery About Prime Numbers | Amazing Science |

In May 2013, the mathematician Yitang Zhang launched what has proven to be a banner year and a half for the study of prime numbers, those numbers that aren’t divisible by any smaller number except 1. Zhang, of the University of New Hampshire, showed for the first time that even though primes get increasingly rare as you go further out along the number line, you will never stop finding pairs of primes that are a bounded distance apart — within 70 million, he proved. Dozens ofmathematicians then put their heads together to improve on Zhang’s 70 million bound, bringing it down to 246 — within striking range of the celebrated twin primes conjecture, which posits that there are infinitely many pairs of primes that differ by only 2.

Now, mathematicians have made the first substantial progress in 76 years on the reverse question: How far apart can consecutive primes be? The average spacing between primes approaches infinity as you travel up the number line, but in any finite list of numbers, the biggest prime gap could be much larger than the average. No one has been able to establish how large these gaps can be. This past August, two different groups of mathematicians released papers proving a long-standing conjecture by the mathematician Paul Erdős about how large prime gaps can get. The two teams have joined forces to strengthen their result on the spacing of primes still further, and expect to release a new paper later this month.

Many mathematicians believe that the true size of large prime gaps is probably considerably larger — more on the order of (log X)2, an idea first put forth by the Swedish mathematician Harald Cramér in 1936. Gaps of size (log X)are what would occur if the prime numbers behaved like a collection of random numbers, which in many respects they appear to do. But no one can come close to proving Cramér’s conjecture, Tao said. “We just don’t understand prime numbers very well.” Erdős made a more modest conjecture: It should be possible, he said, to replace the 1/3 in Rankin’s formula by as large a number as you like, provided you go out far enough along the number line. That would mean that prime gaps can get much larger than in Rankin’s formula, though still smaller than in Cramér’s.

The two new proofs of Erdős’ conjecture are both based on a simple way to construct large prime gaps. A large prime gap is the same thing as a long list of non-prime, or “composite,” numbers between two prime numbers. Here’s one easy way to construct a list of, say, 100 composite numbers in a row: Start with the numbers 2, 3, 4, … , 101, and add to each of these the number 101 factorial (the product of the first 101 numbers, written 101!). The list then becomes 101! + 2, 101! + 3, 101! + 4, … , 101! + 101. Since 101! is divisible by all the numbers from 2 to 101, each of the numbers in the new list is composite: 101! + 2 is divisible by 2, 101! + 3 is divisible by 3, and so on. “All the proofs about large prime gaps use only slight variations on this high school construction,” said James Maynard of Oxford, who wrote the second of the two papers.

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Scientists locate ‘homing signal’ in the brain, explaining why some people are better navigators

Scientists locate ‘homing signal’ in the brain, explaining why some people are better navigators | Amazing Science |

The part of the brain that tells us the direction to travel when we navigate has been identified by UCL scientists, and the strength of its signal predicts how well people can navigate.

It has long been known that some people are better at navigating than others, but until now it has been unclear why. The latest study, funded by the Wellcome Trust and published in Current Biology, shows that the strength and reliability of ‘homing signals’ in the human brain vary among people and can predict navigational ability.

In order to successfully navigate to a destination, you need to know which direction you are currently facing and which direction to travel in. For example, ‘I am facing north and want to head east’. It is already known that mammals have brain cells that signal the direction that they are currently facing, a discovery that formed part of the 2014 Nobel Prize in Physiology or Medicine to UCL Professor John O’Keefe.

The latest research reveals that the part of the brain that signals which direction you are facing, called the entorhinal region, is also used to signal the direction in which you need to travel to reach your destination. This part of the brain tells you not only which direction you are currently facing, but also which direction you should be facing in the future. In other words, the researchers have found where our ‘sense of direction’ comes from in the brain and worked out a way to measure it using functional magnetic resonance imaging (fMRI).

In the study, 16 healthy volunteers were asked to navigate a simple square environment simulated on a computer. Each wall had a picture of a different landscape, and each corner contained a different object. Participants were placed in a corner of the environment, facing a certain direction and asked how to navigate to an object in another corner.

Dr Martin Chadwick (UCL Experimental Psychology), lead author of the study, said: “Our results provide evidence to support the idea that your internal ‘compass’ readjusts as you move through the environment. For example, if you turn left then your entorhinal region should process this to shift your facing direction and goal direction accordingly. If you get lost after taking too many turns, this may be because your brain could not keep up and failed to adjust your facing and goal directions.”

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Unification of wave–particle duality and Heisenberg's uncertainty principle

Unification of wave–particle duality and Heisenberg's uncertainty principle | Amazing Science |

Interferometers capture a basic mystery of quantum mechanics: a single particle can exhibit wave behaviour, yet that wave behaviour disappears when one tries to determine the particle’s path inside the interferometer. This idea has been formulated quantitatively as an inequality, for example, by Englert and Jaeger, Shimony and Vaidman, which upper bounds the sum of the interference visibility and the path distinguishability. Such wave–particle duality relations (WPDRs) are often thought to be conceptually inequivalent to Heisenberg’s uncertainty principle, although this has been debated in the past. A group of physicists now shows that WPDRs correspond precisely to a modern formulation of the uncertainty principle in terms of entropies, namely, the min- and max-entropies. This observation unifies two fundamental concepts in quantum mechanics. Furthermore, it leads to a robust framework for deriving novel WPDRs by applying entropic uncertainty relations to interferometric models.

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Stanford engineers invent high-tech mirror to beam heat away from buildings into space

Stanford engineers invent high-tech mirror to beam heat away from buildings into space | Amazing Science |

Stanford engineers have invented a revolutionary coating material that can help cool buildings, even on sunny days, by radiating heat away from the buildings and sending it directly into space. A team led by electrical engineering ProfessorShanhui Fan and research associate Aaswath Raman reported this energy-saving breakthrough in the journal Nature.

The heart of the invention is an ultrathin, multilayered material that deals with light, both invisible and visible, in a new way. Invisible light in the form of infrared radiation is one of the ways that all objects and living things throw off heat. When we stand in front of a closed oven without touching it, the heat we feel is infrared light. This invisible, heat-bearing light is what the Stanford invention shunts away from buildings and sends into space.

Of course, sunshine also warms buildings. The new material, in addition dealing with infrared light, is also a stunningly efficient mirror that reflects virtually all of the incoming sunlight that strikes it. The result is what the Stanford team calls photonic radiative cooling – a one-two punch that offloads infrared heat from within a building while also reflecting the sunlight that would otherwise warm it up. The result is cooler buildings that require less air conditioning.

"This is very novel and an extraordinarily simple idea," said Eli Yablonovitch, a professor of engineering at the University of California, Berkeley, and a pioneer of photonics who directs the Center for Energy Efficient Electronics Science. "As a result of professor Fan's work, we can now [use radiative cooling], not only at night but counter-intuitively in the daytime as well."

The researchers say they designed the material to be cost-effective for large-scale deployment on building rooftops. Though still a young technology, they believe it could one day reduce demand for electricity. As much as 15 percent of the energy used in buildings in the United States is spent powering air conditioning systems.

In practice the researchers think the coating might be sprayed on a more solid material to make it suitable for withstanding the elements.

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Explainer: What is 4D printing?

Explainer: What is 4D printing? | Amazing Science |

Additive manufacturing — or 3D printing — is 30 years old this year. Today, it’s found not just in industry but in households, as the price of 3D printers has fallen below US$1,000. Knowing you can print almost anything, not just marks on paper, opens up unlimited opportunities for us to manufacture toys, household appliances and tools in our living rooms.

But there’s more that can be done with 3D printed materials to make them more flexible and more useful: structures that can transform in a pre-programmed way in response to a stimulus. Recently given the popular science name of “4D printing,” perhaps a better way to think about it is that the object transforms over time.

These sorts of structural deformations are not new — researchers have already demonstrated “memory” and “smart material” properties. One of the most popular technologies is known as shape memory alloy, where a change of temperature triggers a shape change. Other successful approaches use electroactive polymers, pressurised fluids or gasses, chemical stimulus and even in response to light.

In a paper published in Nature Scientific Reports, we looked at the design of complex self-deformations in objects that have been printed from multiple materials as a means to customize the object into specific forms.

Unlike many others who have demonstrated how to bend simple paper-like shapes, we constructed a two-dimensional grid structure that deforms itself by stretching or shrinking across a complex three-dimensional surface.

Imagine dropping a flat stretchable cloth onto a randomly shaped object, where the cloth molds over the shape beneath it. In geometrical terms, as the curvature of the cloth changes to fit the object, the distances and areas alter. We took this into account by providing a solution that copes with bending and also expansion in size, and came up with several designs that demonstrated that this is possible.

Head of the MIT’s Self-Assembly Laboratory, Skylar Tibbits, started this line of research a few years ago with expanding materials and simple deformations. The collaboration of researchers from MIT’s Camera Culture group and Self-Assembly Laboratory and the companies Stratasys and Autodesk Inc took this further.

Our approach was to print 3D structures using materials with different properties: one that remained rigid and another that expanded up to 200% of its original volume. The expanding materials were placed strategically on the main structure to produce joints that stretched and folded like a bendy straw when activated by water, forming a broad range of shapes. For example, a 3D-printed shape that resembled the initials “MIT” was shown to evolve into another formation that looks like the initials “SAL.”

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New frontiers: Drones deliver a raft of surprises in 2014

New frontiers: Drones deliver a raft of surprises in 2014 | Amazing Science |
2014 wasn’t the year that drones first entered the consumer lexicon, but it did see the notion of using these unmanned vehicles to our advantage become much more palatable. Package deliveries and carrying out conventional robotic tasks are some concepts that have defined the progress of drones in the past 12 months, but, as is typical of emerging technologies, the more their potential is realized the more they find uses in unexpected new applications. Let’s have a look over some of the year’s more surprising, yet significant, drone projects that promise to shake things up in exciting new ways.
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DNA nanomachine designed to detect viruses such as Ebola has won the Grand Prize

DNA nanomachine designed to detect viruses such as Ebola has won the Grand Prize | Amazing Science |

A DNA nanomachine designed to detect viruses such as Ebola has won the Grand Prize for a team that includes three UNSW students in Harvard University’s Biomod Championships – a biomolecular design competition for undergraduates from around the world. Team EchiDNA – the first Australian team ever to enter the Ivy League university’s annual competition – beat 33 other teams with their ultra-sensitive biosensor which was inspired by the cooperative behavior evident in the natural world. The six students, who were supervised by Dr Lawrence Lee of the Victor Chang Cardiac Research Institute, also won the YouTube video prize at the competition.

The DNA-based nanomachine they developed works like a light switch, turning on and glowing like a beacon when it comes into contact with a specific strand of DNA from a bacterium or virus. “Our concept is inspired by the way biology works and could provide a quicker and cheaper method of alerting scientists and doctors to the presence of disease,” says Dr Lee. “Further down the track we would like to have a sensor that is so sophisticated you can test for bacteria or viruses by plugging a blood sample into your mobile phone.” The DNA that is detected by the biosensor could come from a range of sources, including a mutation associated with cancer or a gene that causes antibiotic resistance, as well as from bacteria and viruses.

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Modern genetics experiments confirm ancient relationship between fins and hands

Modern genetics experiments confirm ancient relationship between fins and hands | Amazing Science |

Paleontologists have documented the evolutionary adaptations necessary for ancient lobe-finned fish to transform pectoral fins used underwater into strong, bony structures, such as those of Tiktaalik roseae. This enabled these emerging tetrapods, animals with limbs, to crawl in shallow water or on land. But evolutionary biologists have wondered why the modern structure called the autopod—comprising wrists and fingers or ankles and toes—has no obvious morphological counterpart in the fins of living fishes.

In the Dec. 22, 2014, issue of the Proceedings of the National Academy of Sciences, researchers argue previous efforts to connect fin and fingers fell short because they focused on the wrong fish. Instead, they found the rudimentary genetic machinery for mammalian autopod assembly in a non-model fish, the spotted gar, whose genome was recently sequenced.

"Fossils show that the wrist and digits clearly have an aquatic origin," said Neil Shubin, PhD, the Robert R. Bensley Professor of organismal biology and anatomy at the University of Chicago and a leader of the team that discovered Tiktaalik in 2004. "But fins and limbs have different purposes. They have evolved in different directions since they diverged. We wanted to explore, and better understand, their connections by adding genetic and molecular data to what we already know from the fossil record."

Initial attempts to confirm the link based on shape comparisons of fin and limb bones were unsuccessful. The autopod differs from most fins. The wrist is composed of a series of small nodular bones, followed by longer thin bones that make up the digits. The bones of living fish fins look much different, with a set of longer bones ending in small circular bones called radials. The primary genes that shape the bones, known as the HoxD and HoxA clusters, also differ. The researchers first tested the ability of genetic "switches" that control HoxD and HoxA genes from teleosts—bony, ray-finned fish—to shape the limbs of developing transgenic mice. The fish control switches, however, did not trigger any activity in the autopod.

When the research team compared Hox gene switches from the spotted gar with tetrapods, they found "an unprecedented and previously undescribed level of deep conservation of the vertebrate autopod regulatory apparatus." This suggests, they note, a high degree of similarity between "distal radials of bony fish and the autopod of tetrapods."

They tested this by inserting gar gene switches related to fin development into developing mice. This evoked patterns of activity that were "nearly indistinguishable," the authors note, from those driven by the mouse genome. "Overall," the researchers conclude, "our results provide regulatory support for an ancient origin of the 'late' phase of Hox expression that is responsible for building the autopod."

♥ princess leia ♥'s curator insight, December 28, 12:00 PM

I knew I was a MERMAID 

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Plans to put cyanobacteria on Mars to generate oxygen

Plans to put cyanobacteria on Mars to generate oxygen | Amazing Science |

Mars is a very harsh and hostile environment for future human explorers and like any other known planet it has no breathable air. That could change someday, and it may be soon enough for our generation to witness it, as the student team from Germany has a bold vision to make a first step to terraform the Red Planet, turning it more Earth-like. The plan is to send cyanobacteria to Mars to generate oxygen out of carbon dioxide which is the main component of Martian atmosphere (nearly 96%). "Cyanobacteria do live in conditions on Earth where no life would be expected. You find them everywhere on our planet!" team leader Robert P. Schröder told "It is the first step on Mars to test microorganisms." The project is participating in the Mars One University Competition and if it wins, it will be send as a payload to Mars, onboard the Dutch company's mission to the Red Planet. Now everyone can vote to help make it happen by visiting the webpage.

The team behind the initiative is composed of a voluntary and interdisciplinary group of students and scientists, from the University of Applied Science and Technical University, both located in Darmstadt, Germany. Cyanobacteria will deliver oxygen made of their photosynthesis, reducing carbon dioxide and produce an environment for living organisms. Furthermore, they can supply food and important vitamins for a healthy nutrition. The team is already testing cyanobacteria with different environmental conditions in quarantined photobioreactors and monitoring their activities to determine the best working solution on Mars.

Schröder reveals that the idea was born in August this year. But why cyanobacteria? "Initial ideas were of a technical nature, but that was too boring for me. In school I liked biotechnology and that have not changed very much. Once I heard of cyanobacteria and how they can survive in harsh conditions on earth and at this special night I had a flashback which grabbed me and convinced me completely," he explains.

So what amount of this bacteria will be needed to fully terraform Mars? "As for now we don't know that really, because we need to find out the best habitable conditions for each strain to cultivate them and then we have references and can calculate it," Schröder says. "We need to test Mars-like conditions and analyze how much energy we have to put into the photobioreactor. So it's a lot work to do."

Mars One will take one project to Mars along with its unmanned lander mission in 2018. Voting submission will be accepted until Dec. 31, 2014. The winning university payload will be announced on Jan. 5, 2015.

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In fossilized fish eye, rods and cones are preserved for 300 million years

In fossilized fish eye, rods and cones are preserved for 300 million years | Amazing Science |
Scientists have discovered a fossilized fish so well preserved that the rods and cones in its 300-million-year-old eyeballs are still visible under a scanning electron microscope.

It is the first time that fossilized photoreceptors from a vertebrate eye have ever been found, according to a paper published Tuesday in Nature Communications. The researchers say the discovery also suggests that fish have been seeing the world in color for at least 300 million years. Rods and cones are cells that line the retina in our eyes. Rods are long and thin, and more sensitive to light than cones. However, cones, which are triangular, allow us to see in color. Both these cells rely on pigments to absorb light. Using chemical analysis, the scientists found evidence of one of these pigments -- melanin -- in the fossilized eye as well.

The fish pictured above is about 10 centimeters long. It was found in the Hamilton Quarry in Kansas, which was once a shallow lagoon. Fossils from this area are remarkably well preserved because they were buried very quickly in sediments in the lagoon, said Gengo Tanaka of Kumamoto University in Japan, the lead author of the paper.  In the case of this fish, an extinct species called Acanthodes bridgei, the preservation process probably also got some help from bacterial activity that left a thin film of phosphate over the eyes before it was buried.  Tanaka said that gills and pigments on other parts of the fish were also preserved. However, he had not looked to see whether organs and nerves were intact as well.

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Deep-learning AI algorithm shines new light on mutations in once obscure areas of the genome

Deep-learning AI algorithm shines new light on mutations in once obscure areas of the genome | Amazing Science |

The so-called “streetlight effect” has often fettered scientists who study complex hereditary diseases. The term refers to an old joke about a drunk searching for his lost keys under a streetlight. A cop asks, "Are you sure this is where you lost them?" The drunk says, "No, I lost them in the park, but the light is better here."

For researchers who study the genetic roots of human diseases, most of the light has shone down on the 2 percent of the human genome that includes protein-coding DNA sequences. “That’s fine. Lots of diseases are caused by mutations there, but those mutations are low-hanging fruit,” says University of Toronto (U.T.) professor Brendan Frey who studies genetic networks. “They’re easy to find because the mutation actually changes one amino acid to another one, and that very much changes the protein.”

The trouble is, many disease-related mutations also happen in noncoding regions of the genome—the parts that do not directly make proteins but that still regulate how genes behave. Scientists have long been aware of how valuable it would be to analyze the other 98 percent but there has not been a practical way to do it.

Now Frey has developed a “deep-learning” machine algorithm that effectively shines a light on the entire genome. A paper appearing December 18 in Science describes how this algorithm can identify patterns of mutation across coding and noncoding DNA alike. The algorithm can also predict how likely each variant is to contribute to a given disease. “Our method works very differently from existing methods,” says Frey, the study’s lead author. “GWAS-, QTL- and ENCODE-type approaches can't figure out causal relationships. They can only correlate. Our system can predict whether or not a mutation will cause a change in RNA splicing that could lead to a disease phenotype.”

RNA splicing is one of the major steps in turning genetic blueprints into living organisms. Splicing determines which bits of DNA code get included in the messenger-RNA strings that build proteins. Different configurations yield different proteins. Misregulated splicing contributes to an estimated 15 to 60 percent of human genetic diseases.

The combination of whole-genome analysis and predictive models for RNA splicing makes Frey’s method a major contribution to the field, according to Stephan Sanders, an assistant professor at the University of California, San Francisco, School of Medicine. “I’m looking forward to using this tool in larger data sets and really getting sense of how important splicing is,” he says. Sanders, who researches the genetic causes of diseases, notes Frey’s approach complements, rather than replaces, other methods of genetic analysis. “I think any genomist [sic] would agree that noncoding [areas of the genome] are hugely important. This method is a really novel way of getting at that,” he says.

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Thinnest-ever imaging platform: Atom-thick CCD could capture images

Thinnest-ever imaging platform: Atom-thick CCD could capture images | Amazing Science |

Synthetic two-dimensional materials based on metal chalcogenide compounds could be the basis for superthin devices, according to Rice researchers. One such material, molybdenum disulfide, is being widely studied for its light-detecting properties, but copper indium selenide (CIS) also shows extraordinary promise.

Sidong Lei, a graduate student in the Rice lab of materials scientist Pulickel Ajayan, synthesized CIS, a single-layer matrix of copper, indium and selenium atoms. Lei also built a prototype—a three-pixel, charge-coupled device (CCD)—to prove the material's ability to capture an image.

The details appear this month in the American Chemical Society journal Nano LettersLei said the optoelectronic memory material could be an important component in two-dimensional electronics that capture images. "Traditional CCDs are thick and rigid, and it would not make sense to combine them with 2-D elements," he said. "CIS-based CCDs would be ultrathin, transparent and flexible, and are the missing piece for things like 2-D imaging devices."

The device traps electrons formed when light hits the material and holds them until released for storage, Lei said. CIS pixels are highly sensitive to light because the trapped electrons dissipate so slowly, said Robert Vajtai, a senior faculty fellow in Rice's Department of Materials Science and NanoEngineering. "There are many two-dimensional materials that can sense light, but none are as efficient as this material," he said. "This material is 10 times more efficient than the best we've seen before."

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Thermoelectric power plants could offer economically competitive renewable energy

Thermoelectric power plants could offer economically competitive renewable energy | Amazing Science |

A new study predicts that large-scale power plants based on thermoelectric effects, such as small temperature differences in ocean water, could generate electricity at a lower cost than photovoltaic power plants.

Liping Liu, Associate Professor at Rutgers University, envisions that thermoelectric power plants would look like giant barges sitting in the tropical ocean, where electricity is generated by heating cold, deep water with warm, shallow water heated by the sun. Liu has published a paper in the New Journal of Physics in which he analyzes the feasibility of such power plants.

"This work is about the new idea of large-scale green power plants that make economic use of the largest accessible and sustainable energy reservoir on the earth," Liu told, speaking of the oceans. This is because the sun heats the surface water to a temperature that, in tropical regions, is about 20 K higher than water 600 m deep. Essentially, the surface water acts as a giant storage tank of solar energy.

As Liu explains, thermoelectric power plants would work by harvesting the energy of ocean waves to pump cold water from a few hundred meters deep up through a long channel. As the cold water nears the surface, it enters a heat exchanger where it is heated by surface water on the outside. The heat exchanger acts as an electric generator, as its tubes are made of thermoelectric materials that can transfer heat through their walls and directly convert temperature differences into electricity.

Large-scale, ocean-based thermoelectric power plants would have many advantages. For one, the "fuel" or temperature differences are free, unlimited, and easily accessible. Also, the plants do not take up space on land. Because they have no moving solid parts, they would have low maintenance costs. In addition, the power output does not depend on the time of day or season. And finally, the method is green, as it does not release emissions.

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How do you test an Ebola vaccine for efficacy?

How do you test an Ebola vaccine for efficacy? | Amazing Science |

As the West African Ebola epidemic enters its second year small batches of experimental vaccines are on the cusp of reaching people in the affected countries. Nature magazine tackles the questions that will determine whether vaccines play a role in ending the current epidemic — and can prevent future flare-ups. Two vaccines are leading contenders to be deployed in West Africa early next year. The furthest along is one co-developed by London-based drug firm GlaxoSmithKline (GSK) and the US National Institute for Allergy and Infectious Disease (NIAID) in Bethesda, Maryland. Their vaccine is made of an inactivated chimpanzee cold-causing adenovirus (called ChAd3) that has been engineered to produce an Ebola protein.

Only efficacy trials — slated for next year in Liberia and Sierra Leone — can determine whether a vaccine can prevent Ebola infection. But researchers are scouring data from safety trials to identify the doses and regimens that offer the best chances of working. Those decisions will be made by mid-January, according to Ballou.

One big question is whether the GSK–NIAID vaccine will need to be accompanied with a booster shot (such as the one manufactured by Bavarian Nordic). Monkeys that were protected from Ebola infection by a similar vaccine had received a booster. But a single-shot regimen would be simpler to administer during the current epidemic in West Africa, as well as future Ebola outbreaks.

Adrian Hill, a vaccine scientist at the University of Oxford, UK, who is leading a safety trial of the GSK–NIAID vaccine in the United Kingdom, is a proponent of a booster. Tests of vaccines against other diseases have shown that boosters can drastically increase the levels of infection-battling antibodies and T cells, a type of white blood cell. On 12 December he told a Washington DC conference on Ebola immunology that Bavarian Nordic's booster worked as expected. Fourteen volunteers who got the booster several weeks after their first shot produced higher levels of antibodies within a week (compared with levels in their blood after the first vaccination) and these responses were similar to those seen in monkeys protected from Ebola.

Hill says that a booster might be the only way to get an Ebola vaccine that prevents infection. Others, such as NIAID director Anthony Fauci, argue that a booster shot is important mostly for prolonging vaccine protection and that higher doses of the first shot should be effective in the short term.

The Liberia trial will probably enrol around 30,000 people living in Monrovia. The plan is for volunteers to be randomly assigned to receive either the GSK–NIAID vaccine, the NewLink–Merck vaccine or a saline-solution injection that will serve as a placebo control. But it is unclear how the suspension of the NewLink–Merck safety trial in Geneva will affect those plans. “If that means it is not going forward rapidly for safety reasons, it would impact on plans for the efficacy trial in Liberia,” Hill says. One possibility is to delay this arm of the trial until additional safety tests are completed.

A phase 3 trial of around 6,000 health-care workers in Sierra Leone is also in the planning stages. The current strategy is for all the volunteers to receive a vaccine (yet to be selected) in a phased roll-out. Researchers will determine whether the vaccine works by comparing infection rates among vaccinated and unvaccinated people.

Officials are also discussing the possibility of a third efficacy trial to test whether a strategy known as ring vaccination can quell the epidemic. In this approach, patients living around a newly diagnosed case are vaccinated, in an attempt to prevent transmission.

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Birds detect approaching storm from almost 600 miles away

Birds detect approaching storm from almost 600 miles away | Amazing Science |

Infrasound may have alerted warblers to the approaching storm, prompting them to fly more than a thousand kilometers to avoid it.

A group of songbirds may have avoided a devastating storm by fleeing their US breeding grounds after detecting telltale infrasound waves.

Researchers noticed the behaviour after analysing trackers attached to the birds to study their migration patterns. They believe it is the first documented case of birds making detours to avoid destructive weather systems on the basis of infrasound.

The golden-winged warblers had just returned from South America to their breeding grounds in the mountains of Tennessee in 2013 when a massive storm was edging closer. Although the birds had just completed a migration of more than 2,500km, they still had the energy to evade the danger.

The storm, which spawned more than 80 tornadoes across the US and killed 35 people, was 900km away when the birds, apparently acting independently of one another, fled south, with one bird embarking on a 1,500km flight to Cuba before making the return trip once the storm had passed.

“We looked at barometric pressure, wind speeds on the ground and at low elevations, and the precipitation, but none of these things that typically trigger birds to move had changed,” said David Andersen at the University of Minnesota“What we’re left with is something that allows them to detect a storm from a long distance, and the one thing that seems to be the most obvious is infrasound from tornadoes, which travels through the ground.”

The scientists cannot be sure that the birds picked up infrasound waves from the storm, but previous work in pigeons has suggested that birds might use infrasound to help them navigate. Infrasound waves range from about 0.5Hz to 18Hz, below the audible range of humans.

The discovery of the evasive action could be good news, said Andersen. “With climate change increasing the frequency and severity of storms, this suggests that birds may have some ability to cope that we hadn’t previously realised. These birds seemed to be capable of making really dramatic movements at short notice, even just after returning on their northwards migration,” he said.

Had the storm arrived a couple of weeks later, the birds may not have taken flight. By that time, they would have been nesting, and females especially may have been less likely to flee. “It’s hard to say what would happen. It may be more advantageous to survive than stay with a nest that is going to be destroyed anyway,” Andersen said.

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Smarter than you think: Crows join humans, apes and monkeys in exhibiting advanced rational thinking

Smarter than you think: Crows join humans, apes and monkeys in exhibiting advanced rational thinking | Amazing Science |
Crows have the brain power to solve higher-order, relational-matching tasks, and they can do so spontaneously, according to new research. That means crows join humans, apes and monkeys in exhibiting advanced relational thinking, according to the research.

Crows have long been heralded for their high intelligence -- they can remember faces, use tools and communicate in sophisticated ways. 

But a newly published study finds crows also have the brain power to solve higher-order, relational-matching tasks, and they can do so spontaneously. That means crows join humans, apes and monkeys in exhibiting advanced relational thinking, according to the research.

Russian researcher Anna Smirnova studies a crow making the correct selection during a relational matching trial.

"What the crows have done is a phenomenal feat," says Ed Wasserman, a psychology professor at the University of Iowa and corresponding author of the study. "That's the marvel of the results. It's been done before with apes and monkeys, but now we're dealing with a bird; but not just any bird, a bird with a brain as special to birds as the brain of an apes is special to mammals."

Here is how it worked: the birds were placed into a wire mesh cage into which a plastic tray containing three small cups was occasionally inserted. The sample cup in the middle was covered with a small card on which was pictured a color, shape or number of items. The other two cups were also covered with cards -- one that matched the sample and one that did not. During this initial training period, the cup with the matching card contained two mealworms; the crows were rewarded with these food items when they chose the matching card, but they received no food when they chose the other card.

Once the crows has been trained on identity matching-to-sample, the researchers moved to the second phase of the experiment. This time, the birds were assessed with relational matching pairs of items.

These relational matching trials were arranged in such a way that neither test pairs precisely matched the sample pair, thereby eliminating control by physical identity. For example, the crows might have to choose two same-sized circles rather than two different-sized circles when the sample card displayed two same-sized squares.

What surprised the researchers was not only that the crows could correctly perform the relational matches, but that they did so spontaneously--without explicit training. "That is the crux of the discovery," Wasserman says. "Honestly, if it was only by brute force that the crows showed this learning, then it would have been an impressive result. But this feat was spontaneous."


Anna Smirnova, Zoya Zorina, Tanya Obozova, Edward Wasserman. Crows Spontaneously Exhibit Analogical ReasoningCurrent Biology, 2014 DOI: 10.1016/j.cub.2014.11.063

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