Author Archives: curiouscat

Cat Goes to the Train Station to Meet Its Owner Each Evening

</p> <p><a href="http://video.heraldsun.com.au/2131780176/Feline-trainspotter">Video: Feline trainspotter</a></p> <p>

Graeme, a cat in Melbourne, Australia, walks to the train station with its owner in the morning and then goes off to play (and probably lots of sleep, it is a cat) and then returns in time to meet its owner at the train station after the work day.

The pampered cat cannot get enough of attention, with scores of regulars calling him by name as they stop for a chat and give him a pat on the head. Safety conscious, the sociable moggie is meticulous about using the subway to cross to the city-bound platform, rather than take a dangerous short cut across the tracks.

When the evening peak comes around, Graeme puts on an encore performance, arriving at the opposite platform in time to greet owner Nicole Weinrich as she returns home from work. “He always seems to know which train carriage I am on and will be sitting there behind the yellow line when the doors open, because he is all about safety,” Ms Weinrich said.
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But sometimes Graeme can take his desire to be close to his fans a bit too far – he has been known to jump on the train and get off a station or two later. “He doesn’t do it often, but we do worry about that,” Ms Weinrich said.

She said Graeme, believed to be about 12, had roughed it on the street before being saved from the RSPCA’s “death row” six years ago, so his love of people is tempered by his survival instincts.

Molecule Found in Sharks Kills Many Viruses that are Deadly to People

photo of 3 dogfish sharks
Shark Molecule Kills Human Viruses, Too

“Sharks are remarkably resistant to viruses,” study researcher Michael Zasloff, of the Georgetown University Medical Center, told LiveScience. Zasloff discovered the molecule, squalamine, in 1993 in the dogfish shark, a small- to medium-size shark found in the Atlantic, Pacific, and Indian Oceans.

“It looked like no other compound that had been described in any animal or plant before. It was something completely unique,” Zasloff said. The compound is a potent antibacterial and has shown efficacy in treating human cancers and an eye condition known as macular degeneration, which causes blindness.
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By studying the compound’s structure and how it works in the human body, Zasloff thought it might have some antiviral properties. He saw that the molecule works by sticking to the cell membranes of the liver and blood vessels. While there, it kicks off other proteins, some of which are essential for viruses to enter and survive in the cell.

The researchers decided to test the compound on several different live viruses that infect liver cells, including hepatitis B, dengue virus and yellow fever. They saw high efficacy across the board.
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Zasloff hopes to start human trials in the next few years.
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Marc Maresca, a researcher at Paul CÃ©zanne University in Aix-en-Provence, France, who wasn’t involved in the study, agreed that the concentrations used were quite high, possibly in toxic ranges for some cells, but in an email to LiveScience Meresca also called the study “very exciting.”

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.

Robot Tennis Partners Coming Soon?

The robots in the video, and many more, are being tested at the Flying Machine Arena at the The Institute for Dynamic Systems and Control, Department of Mechanical and Process Engineering, Swiss Federal Institute of Technology – Zurich.

They also usually have a number of challenging projects available. Qualified, motivated students should visit the Theses/Projects page and contact them to learn more. We need more people working on these types of things so I can have my robot basketball team available when I want to play.

Bill Dietrich Gives Carnegie Mellon University $265 Million

Carnegie Mellon is one of the crown jewels of engineering in the USA. While we are busy squandering the economic gains gained through science and engineering investments in the 1950’s, 60’s and 70’s a few universities are continuing to provide huge economic benefit: MIT, Stanford, CalTech, Harvard, University of Wisconsin – Madison… Schools unfortunately seem to be wasting lots of money (on vanity projects and ever increasing administration, and huge pay to overpaid executives), but even so they provide much much more benefit than the costs. Funding from rich, successful businesspeople (Bill Dietrich was a steel executive) is now a huge reason these shiny lights of the American economy continue to shine. On Bill Dietrich’s donation:

This fund, which will become operational upon Dietrich’s passing, will serve as a catalyst for the university’s global initiatives and for its fusion of left-brain and right-brain thinking, such as studies connecting technology and the arts, as well as support future academic initiatives across the university, including undergraduate and graduate programs, scholarship, artistic creation and research.
The gift furthers the university’s ability to educate students in strong interdisciplinary problem-solving and supports the unique recipe for education offered by Carnegie Mellon’s seven schools and colleges, all of which are leaders in their fields.
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Dietrich’s gift, among the 10 largest in the United States, is believed to be the 14th largest gift to higher education worldwide.

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.

Synthetic Biologists Design a Gene that Forces Cancer Cells to Commit Suicide

Killing a cancer cell from the inside out

To create their tumor-killing program, the researchers designed a logic circuit — a system that makes a decision based on multiple inputs. In this case, the circuit is made of genes that detect molecules specific to a type of cervical cancer cell. If the right molecules are present, the genes initiate production of a protein that stimulates apoptosis, or programmed cell death. If not, nothing happens.

Because the genes used to create the circuits can be easily swapped in and out, this approach could also yield new treatments or diagnostics for many other diseases, according to Ron Weiss, an MIT associate professor of biological engineering and one of the leaders of the research team. “This is a general technology for disease-state detection,” he says.
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the researchers created a synthetic gene for a protein, called hBax, that promotes cell death. They designed the gene with two separate safeguards against the killing of healthy, non-HeLa cells: It can be turned off by high levels of microRNAs that are ordinarily low in HeLa, and can also be deactivated by low levels of microRNAs that are normally plentiful in HeLa. A single discrepancy from the target microRNA profile is enough to shut off production of the cell-death protein.

If all microRNA levels match up with the HeLa profile, the protein is produced and the cell dies. In any other cell, the protein never gets made, and the synthetic genes eventually break down.

More very cool research. It is exciting to see how much can be done when we invest in science and engineering research. Of course the path from initial research to implemented solutions is long and complex and often fails to deliver on the initial hopes. But some remarkable breakthroughs achieve spectacular results that we benefit from every day.

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.”