Category Archives: Science

Gamers Use Foldit to Solve Enzyme Configuration in 3 Weeks That Stumped Scientists for Over a Decade

Gamers have solved the structure of a retrovirus enzyme whose configuration had stumped scientists for more than a decade. The gamers achieved their discovery by playing Foldit, a very cool online game that allows players to collaborate and compete in predicting the structure of protein molecules that I wrote about before: Foldit – the Protein Folding Game. You can download it, play, and help move our understanding forward.

After scientists repeatedly failed to piece together the structure of a protein-cutting enzyme from an AIDS-like virus, they called in the Foldit players. The scientists challenged the gamers to produce an accurate model of the enzyme. They did it in only three weeks.

This class of enzymes, called retroviral proteases, has a critical role in how the AIDS virus matures and proliferates. Intensive research is under way to try to find anti-AIDS drugs that can block these enzymes, but efforts were hampered by not knowing exactly what the retroviral protease molecule looks like.

“We wanted to see if human intuition could succeed where automated methods had failed,” said Dr. Firas Khatib of the University of Washington Department of Biochemistry. Khatib is a researcher in the protein structure lab of Dr. David Baker, professor of biochemistry.

Remarkably, the gamers generated models good enough for the researchers to refine and, within a few days, determine the enzyme’s structure. Equally amazing, surfaces on the molecule stood out as likely targets for drugs to de-active the enzyme.

“These features provide exciting opportunities for the design of retroviral drugs, including AIDS drugs,” wrote the authors of a paper appearing Sept. 18 in Nature Structural & Molecular Biology. The scientists and gamers are listed as co-authors.

This is the first instance that the researchers are aware of in which gamers solved a longstanding scientific problem.

“The focus of the UW Center for Game Sciences,” said director Dr. Zoran Popovic, associate professor of computer science and engineering, “is to solve hard problems in science and education that currently cannot be solved by either people or computers alone.”

The solution of the virus enzyme structure, the researchers said, “indicates the power of online computer games to channel human intuition and three-dimensional pattern matching skills to solve challenging scientific problems.”

With names like Foldit Contenders Group and Foldit Void Crushers Group, the gamer teams were fired up for the task of real-world molecule modeling problems. The online protein folding game captivates thousands of avid players worldwide and engages the general public in scientific discovery.

Direct manipulation tools, as well as assistance from a computer program called Rosetta, encourage participants to configure graphics into a workable protein model. Teams send in their answers, and UW researchers constantly improve the design of the game and its puzzles by analyzing the players’ problem-solving strategies.

Figuring out the shape and misshape of proteins contributes to research on causes of and cures for cancer, Alzheimer’s, immune deficiencies and a host of other disorders, as well as to environmental work on biofuels.

Dr. Seth Cooper, of the UW Department of Computing Science and Engineering, is a co-creator of Foldit and its lead designer and developer. He studies human-computer exploration methods and the co-evolution of games and players.

“People have spatial reasoning skills, something computers are not yet good at,” Cooper said. “Games provide a framework for bringing together the strengths of computers and humans. The results in this week’s paper show that gaming, science and computation can be combined to make advances that were not possible before.”

Games like Foldit are evolving. To piece together the retrovirus enzyme structure, Cooper said, gamers used a new Alignment Tool for the first time to copy parts of know molecules and test their fit in an incomplete model.

According to Popovic, “Foldit shows that a game can turn novices into domain experts capable of producing first-class scientific discoveries. We are currently applying the same approach to change the way math and science are taught in school.”

Amber Pieces Containing Remains from Dinosaurs and Birds Show Feather Evolution

Dinosaur feather evolution trapped in Canadian amber

a study of amber found near Grassy Lake in Alberta – dated from what is known as the Late Cretaceous period – has unearthed a full range of feather structures that demonstrate the progression. “We’re finding two ends of the evolutionary development that had been proposed for feathers trapped in the same amber deposit,” said Ryan McKellar of the University of Alberta, lead author of the report.

The team’s find confirms that the filaments progressed to tufts of filaments from a single origin, called barbs. In later development, some of these barbs can coalesce into a central branch called a rachis. As the structure develops further, further branches of filments form from the rachis.

“We’ve got feathers that look to be little filamentous hair-like feathers, we’ve got the same filaments bound together in clumps, and then we’ve got a series that are for all intents and purposes identical to modern feathers,” Mr McKellar told BBC News.

“We’re catching some that look to be dinosaur feathers and another set that are pretty much dead ringers for modern birds.”
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a picture is emerging that many dinosaurs were not the dull-coloured, reptilian-skinned creatures that they were once thought to be. “If you were to transport yourself back 80 million years to western North America and walk around the forest… so many of the animals would have been feathered,” said Dr Norell.

“We’re getting more and more evidence… that these animals were also brightly coloured, just like birds are today.”

Very cool. Science really is great.

Large Crabs Invading Antarctic as Waters Warm

Giant red king crabs

Large crabs are invading the Antarctic environment and due to their numbers and practices could cause havoc. They look yummy though. And eating them would be doing nature a favor unlike the overfishing of the oceans. Abstract of the open access article, A large population of king crabs in Palmer Deep on the west Antarctic Peninsula shelf and potential invasive impacts:

Lithodid crabs (and other skeleton-crushing predators) may have been excluded from cold Antarctic continental shelf waters for more than 14 Myr [million years]. The west Antarctic Peninsula shelf is warming rapidly and has been hypothesized to be soon invaded by lithodids. A remotely operated vehicle survey in Palmer Deep, a basin 120 km onto the Antarctic shelf, revealed a large, reproductive population of lithodids, providing the first evidence that king crabs have crossed the Antarctic shelf. DNA sequencing and morphology indicate the lithodid is Neolithodes yaldwyni Ahyong & Dawson, previously reported only from Ross Sea waters. We estimate a N. yaldwyni population density of 10 600 kmâˆ’2 and a population size of 1.55 Ã— 106 in Palmer Deep, a density similar to lithodid populations of commercial interest around Alaska and South Georgia. The lithodid occurred at depths of more than 850 m and temperatures of more than 1.4Â°C in Palmer Deep, and was not found in extensive surveys of the colder shelf at depths of 430–725 m. Where N. yaldwyni occurred, crab traces were abundant, megafaunal diversity reduced and echinoderms absent, suggesting that the crabs have major ecological impacts. Antarctic Peninsula shelf waters are warming at approximately 0.01Â°C yrâˆ’1; if N. yaldwyni is currently limited by cold temperatures, it could spread up onto the shelf (400–600 m depths) within 1–2 decades. The Palmer Deep N. yaldwyni population provides an important model for the potential invasive impacts of crushing predators on vulnerable Antarctic shelf ecosystems.

Fun Webcast from WWF: Astonish Me

Made in celebration of the World Wildlife Fund‘s 50th anniversary.

Is Dark Matter an Illusion?

Open access letter asks – Is dark matter an illusion created by the gravitational polarization of the quantum vaccum? by Dragan Slavkov Hajdukovic, CERN

Assuming that a particle and its antiparticle have the gravitational charge of the opposite sign, the physical vacuum may be considered as a fluid of virtual gravitational dipoles. Following this hypothesis, we present the first indications that dark matter may not exist and that the phenomena for which it was invoked might be explained by the gravitational polarization of the quantum vacuum by the known baryonic matter.

Let us start with a major unresolved problem. The measured galaxy rotation curves remain roughly constant at large radii. Faster than expected orbits, require a larger central force, which, in the framework of our theory of gravity, cannot be explained by the existing baryonic matter. The analogous problem persists also at the scale of clusters of galaxies.

The favoured solution is to assume that our current theory of gravity is correct, but every galaxy resides in a halo of dark matter made of unknown non-baryonic particles (for a brief review on dark matter see for instance: Einasto, 2010). A full list of the proposed dark matter particles would be longer than this letter; let us mention only weekly interacting massive particles and axions. In spite of the significant efforts dark particles have never been detected…

The scientific inquiry process continues to be used to try and explain the evidence we gather. Unsettled areas of science show how difficult the discovery process is. Once we have settled on theories it is so easy to explain why basic truths of evolution, geology, chemistry… result in what the evidence shows. But getting to the scientific consensus is a challenging process.

Dark Matter Is an Illusion, New Antigravity Theory Says

Physicist David Evans called the new study a “very interesting theoretical exercise,” but he said he isn’t ready to abandon dark matter just yet. “The evidence for dark matter is now very compelling,” said Evans, of the University of Birmingham, who leads the U.K. team for the ALICE detector at CERN’s Large Hadron Collider.

For example, in 2006 astronomers unveiled a photo of two colliding galaxies known as the Bullet cluster that purportedly showed the separation of matter from dark matter. A similar effect was observed in the Pandora cluster earlier this summer, said Evans, who was not involved in the study.

Hajdukovic said he is currently expanding his theory to account for these observations. His preliminary calculations, he said, suggest that “what is observed in the Bullet cluster and more recently at the Pandora cluster may be understood in the framework of the gravitational polarization of the quantum vacuum.”

CERN physicist Michael Doser agreed that Hajdukovic’s ideas are “unorthodox” but did not immediately dismiss the new theory…
“In a few years,” Doser said, “we should definitely be in a position to confirm or refute [Hajdukovic’s] hypothesis.”

The Politics of Anti-Science

In the 1960’s the USA had an unrealistic view of how much studying and learning about science and engineering could do. Investing is science and engineering is an extremely wise economic (and cultural) endeavor but it isn’t going to solve all the problems that exist. Somehow today we find ourselves with a large number of politically powerful people we take strong anti-science positions. These tactics reduce funding and support for beneficial research and are short sited approaches to public administration. This is an unfortunate turn of events that is damaging the American economy and will have huge damages going forward.

Thankfully other countries have seen how wise investing in science and engineering is and have more than taken up the slack created by the anti-science community. Two favorite tactics of the anti-science leaders is to try and create confusion where there is none and to turn the focus away from serious matters and instead playing silly political games. The silly games will draw donors and voters so if they care about those things more than the country and the future of the country it is a sound tactic. The damage it causes the country however I would hope would limit the use of such tactics however that has not been the case recently.

‘Shrimp On A Treadmill’: The Politics Of ‘Silly’ Studies

Take the case of the “shrimp on a treadmill.” Burnett says the senator’s report linked that work to a half-million-dollar research grant. But that money actually went to a lot of different research that he and his colleagues did on this economically important seafood species.

The treadmills were just a small part of it, a way to measure how shrimp respond to changes in water quality. Burnett says the first treadmill was built by a colleague from scraps and was basically free, and the second was fancier and cost about $1,000. The senator’s report was misleading, says Burnett, “and it suggests that much money was spent on seeing how long a shrimp can run on a treadmill, which was totally out of context.”

John Hart, a Coburn spokesperson, said in an email that “our report never claimed all the money was spent on shrimp on a treadmill. The scientists doth protest too much. Receiving federal funds is a privilege, not a right. If they don’t want their funding scrutinized, don’t ask.”

What the politicians are doing is exactly what this spokesperson suggests – they are withdrawing from the anti-science culture created by some in Washington: they are moving their research to countries that support rather than attack science. That is a very bad thing for the USA. There are a number of very bad economic policies a government can take. Driving scientists and engineers into the arms of other countries is one of the worst.
Continue reading →

New Life Form Found at South African Truck Stop

Man discovers a new life-form at a South African truck stop

An order is one of the big categories of life, a big branch on evolution’s tree. Animal species are named every day, but finding another new order would be equivalent to discovering bats having not previously known they existed. Bats constitute their own order, as do primates, beetles, flies and rodents.
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The Mantophasmatodes look, inescepably, larval (they lack wings, for example, and have no ocelli) and so Picker like others mistook them for immature versions of some known creature, perhaps some weird kind of cricket. When more than three quarters of all species of animals are not yet named, it is hard to know which ones to get excited about finding. Picker went through his collections looking for specimens of Mantophasmatodes. Within weeks, he had found twenty-nine individual Mantophasmatodes. Thirteen living species of Mantophasmatodea have now been named and placed in 10 genera and three different families.

In other words, Zompro has done something more amazing than finding a rare new order of animals. He has discovered a common order of animals that everyone else had missed, a discovery in plain view.

Mantaphasmatodes are not a far away species confined to some remote hunk of rock. They are a whole suite of species, some of which live places as mundane as backyards. They are also a kind of a living extended metaphor for what lurks around us unnoticed all the time.

I was always told as a child that I shouldn’t question so much and just accept what adults have decided. I am sure I was very annoying questioning everything. Especially how amazingly boring they make school. I love learning stuff. In general I did not love school. But questioning that school really should do a better job of making it fun to learn was seen as being a bothersome kid. I should just accept this is how school is and learn. I still think I was right. School is horribly designed to nurture the innate curiosity of people. Rather than seeing the kids that point this out as troublemakers we should see those that perpetuate the current system as troublemakers.

I still remember my sophomore year in high school I was taught by a biology teacher that new very little. They had been a 2nd grade teacher for like 15 years and due to seniority (they didn’t need as many 2nd grade teachers I guess) she bumped the biology teacher from the year before and we were stuck learning from her. In fact, any decently interesting question was more likely to be answered by a student (Peter – who then went to Princeton and then to play for the National Symphony) after the teacher said she didn’t know.

I found biology horrible. And it probably took a decade or more for me to finally notcie how amazingly cool biology. Fantastically cool. The amount of just super interesting biology is so vast that I have huge amounts of great stuff I get to look forward to learning. My teacher made it even worse, but frankly the way it is taught (I would imagine) is pretty bad even if the teacher is good. My high school was populated largely by the kids of Professors and compared to other schools in the USA I was told many times was fantastic (and the data seemed to support that – I believe we have more national merit scholars the year I graduated than all but 1 other public school in the country).

We need to do a much better job of harnessing the native desire to learn people have instead of killing it (which we do far to often). It really is a tragedy. It isn’t noticed because you can get by alright without loving learning. But it reduces the lives people have when they have their love of learning crushed. I didn’t have mine crushed but when I look around at many adults they seem to have done so to a large extent (sometimes it pokes through in a hobby or with their kids). And of course many adults kept a strong love of learning (all those geeks for example – and don’t forget the biologists).

Insightful Problem Solving in an Asian Elephant

Another example of very cool animal behavior. This Asian Elephant, seemed to consider the problem, devise a solution and then go get a stool to reach food that could not be reached without a tool.

Insightful Problem Solving in an Asian Elephant

The “aha” moment or the sudden arrival of the solution to a problem is a common human experience. Spontaneous problem solving without evident trial and error behavior in humans and other animals has been referred to as insight. Surprisingly, elephants, thought to be highly intelligent, have failed to exhibit insightful problem solving in previous cognitive studies. We tested whether three Asian elephants (Elephas maximus) would use sticks or other objects to obtain food items placed out-of-reach and overhead. Without prior trial and error behavior, a 7-year-old male Asian elephant showed spontaneous problem solving by moving a large plastic cube, on which he then stood, to acquire the food. In further testing he showed behavioral flexibility, using this technique to reach other items and retrieving the cube from various locations to use as a tool to acquire food. In the cube’s absence, he generalized this tool utilization technique to other objects and, when given smaller objects, stacked them in an attempt to reach the food. The elephant’s overall behavior was consistent with the definition of insightful problem solving. Previous failures to demonstrate this ability in elephants may have resulted not from a lack of cognitive ability but from the presentation of tasks requiring trunk-held sticks as potential tools, thereby interfering with the trunk’s use as a sensory organ to locate the targeted food.
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Further inspired by KÃ¶hler’s chimpanzee studies, in experiment 4 we conducted 8 additional sessions to investigate whether Kandula would stack items to reach food. For these sessions, the baited branches were hung at a height that could be reached by stacking three butcher block cutting boards or by the use of other objects. In addition, the elephant was given sticks and other enrichment items. Kandula first touched several items and then moved two items, a plastic disk and a block under the suspended branches, placing one front foot on each in an unsuccessful attempt to reach for the branch. He solved the problem in an unexpected novel manner, moving and standing on the object closest in size to the absent cube, a large ball. Standing on unstable platforms such as this had not been previously observed. He repeated this behavior 9 times during this session. During the session’s last minutes, Kandula picked up a block ~2 m from the food and placed it directly on top of a block that he placed under the food in a previous attempt. He stood on the stacked blocks and attempted to reach the food but was unsuccessful. He stacked two blocks again in the second and sixth sessions but each time his trunk was several inches from the food.

This is very cool research. I do wonder why they didn’t provide more videos (and in a more user-friendly format than .mov files). I made them available via YouTube.

It seems like a very interesting area to have more experiments with more elephants (and continuing to work with Kandula: he seems to be very curious elephant, good for him).

Were Remains of a Baby Woolly Mammoth Discovered this Week?

Our blog received a spike in traffic to one of our previous posts (Well Preserved Baby Mammoth Discovered in Permafrost), taking a look at what the cause was I found out is was due to a new baby woolly mammoth possible discovery.

Woolly mammoth calf fossil? No, just a wayward walrus

Authorities in the Yamalo-Nenets region said yesterday morning they were scrambling a helicopter to the location. “If what is said about how it is preserved turns out to be true, this will be another sensation of global significance,” said the leader of the expedition, Natalia Fyodorova.

Disappointment was in store, however. “It turned out to be a walrus skull; apparently a fossilised one,” said Ms Fyordorova, who is the director of the local museum.

All the sites I look at that published the discovery news give no indication that they have learned new info, so I don’t really know what the status of the “discovery” is.

MIT Scientists Find New Drug That Could Cure Nearly Any Viral Infection

New drug could cure nearly any viral infection

The drug works by targeting a type of RNA produced only in cells that have been infected by viruses. “In theory, it should work against all viruses,” says Todd Rider, a senior staff scientist in Lincoln Laboratory‘s Chemical, Biological, and Nanoscale Technologies Group who invented the new technology.
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There are a handful of drugs that combat specific viruses, such as the protease inhibitors used to control HIV infection, but these are relatively few in number and susceptible to viral resistance.

Rider drew inspiration for his therapeutic agents, dubbed DRACOs (Double-stranded RNA Activated Caspase Oligomerizers), from living cells’ own defense systems. When viruses infect a cell, they take over its cellular machinery for their own purpose — that is, creating more copies of the virus. During this process, the viruses create long strings of double-stranded RNA (dsRNA), which is not found in human or other animal cells.

As part of their natural defenses against viral infection, human cells have proteins that latch onto dsRNA, setting off a cascade of reactions that prevents the virus from replicating itself. However, many viruses can outsmart that system by blocking one of the steps further down the cascade.

Rider had the idea to combine a dsRNA-binding protein with another protein that induces cells to undergo apoptosis (programmed cell suicide) — launched, for example, when a cell determines it is en route to becoming cancerous. Therefore, when one end of the DRACO binds to dsRNA, it signals the other end of the DRACO to initiate cell suicide.

Combining those two elements is a “great idea” and a very novel approach, says Karla Kirkegaard, professor of microbiology and immunology at Stanford University. “Viruses are pretty good at developing resistance to things we try against them, but in this case, it’s hard to think of a simple path pathway to drug resistance,” she says.

Each DRACO also includes a “delivery tag,” taken from naturally occurring proteins, that allows it to cross cell membranes and enter any human or animal cell. However, if no dsRNA is present, DRACO leaves the cell unharmed.

Very cool stuff and potentially hugely beneficial. Just a reminder: this works against viruses – not bacteria (just as antibiotics do not work against viruses).