Author Archives: curiouscat

Evidence of Short DNA Segment Self Assembly

Tiny DNA Molecules Show Liquid Crystal Phases, Pointing Up New Scenario For First Life On Earth, University of Colorado:

CU-Boulder physics Professor Noel Clark said the team found that surprisingly short segments of DNA, life’s molecular carrier of genetic information, could assemble into several distinct liquid crystal phases that “self-orient” parallel to one another and stack into columns when placed in a water solution. Life is widely believed to have emerged as segments of DNA- or RNA-like molecules in a prebiotic “soup” solution of ancient organic molecules.
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Such DNA polynucleotides had previously been shown to organize into liquid crystal phases in which the chains spontaneously oriented parallel to each other, he said. Researchers understand the liquid crystal organization to be a result of DNA’s elongated molecular shape, making parallel alignment easier, much like spaghetti thrown in a box and shaken would be prone to line up in parallel, Clark said.

The CU-Boulder and University of Milan team began a series of experiments to see how short the DNA segments could be and still show liquid crystal ordering, said Clark. The team found that even a DNA segment as short as six bases, when paired with a complementary segment that together measured just two nanometers long and two nanometers in diameter, could still assemble itself into the liquid crystal phases, in spite of having almost no elongation in shape.

Structural analysis of the liquid crystal phases showed that they appeared because such short DNA duplex pairs were able to stick together “end-to-end,” forming rod-shaped aggregates that could then behave like much longer segments of DNA. The sticking was a result of small, oily patches found on the ends of the short DNA segments that help them adhere to each other in a reversible way — much like magnetic buttons — as they expelled water in between them, Clark said.
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“In essence, the liquid crystal phase condensation selects the appropriate molecular components, and with the right chemistry would evolve larger molecules tuned to stabilize the liquid crystal phase. If this is correct, the linear polymer shape of DNA itself is a vestige of formation by liquid crystal order.”

Engineering Education Study Debate

Engineering education study draws industry fire by George Leopold, EE Times:

In a radio debate with Salzman on the NPR program “Science Friday,” Intel Corp. Chairman Craig Barrett blasted Salzman’s “backward-looking analysis.” Said Barrett: “The U.S. cannot be successful if we are only ‘average’ ” in math and science. “[S]aying we’re ‘OK’ because we’re average just can’t be right. That’s backward looking. That’s not looking ahead at competition with India, China, Russia and others that are putting heavy emphasis on education.”
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Salzman did, however, conceded one point to his critics, acknowledging that the engineering field in the U.S. isn’t what it used to be. As a profession, “engineering is not a field that has a bright future,” he said. Quoting an engineer interviewed for the Urban Institute study, Salzman said, “It was a great ride, but it’s over.”

Previous posts on the study (The Importance of Science Education – Math and Science Education Assessment). I doubt the engineering ride is over – but everyone is entitled to their opinion. As I have said many times the economic future will be greatly influenced by science and engineering. Those countries that succeed in creating a positive economic climate for science and engineering development will find economic rewards those that fail to do so will suffer. The USA has come through a period where they received great economic benefit from science and engineering supremacy. There is little doubt other centers of excellence will emerge and gain the benefits. But if the USA were to actually fall backward (not just see the relative position decline as other countries gained ground) that will be a serious problem and one I think is unlikely.

New Triceratops Ancestor

Alberta palaeontologists discover new dino genus

Scientists from the Royal Tyrrell Museum and the Canadian Museum of Nature have [discovered]… Eotriceratops xerinsularis (pronounced EE-OH-try-sair-ah-tops ZEER-in-soo-lair-iss)… The dino may be an ancestor of the well-know triceratops, and at the very least, is the group’s earliest known member; researchers say the Eotriceratops lived in southern Alberta 68 million years ago.

It is the largest type of horned dinosaur ever discovered in Alberta, and possibly the world.

According to researchers, Eotriceratops likely reached eight or nine metres from nose to tail. It had a massive skull that featured a solid frill (this alone was three metres in length), and three horns – two above each eye, and another, shorter one, perched on its nose.
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Judging by its teeth, the Eotriceratops was a plant-eater, but one that would have been able to ward off predators.

Programming Ruby

Why I Program In Ruby (And Maybe Why You Shouldn’t):

Harmony and balance make you feel good. American Rubyists frequently take up all the points of Ruby’s power, expressiveness, and efficiency, but they don’t seem to register the point that Ruby was designed to make you feel good. Even Rubyists who want to explain why Ruby makes them feel good often fail to mention that it was expressly designed for that exact purpose.
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Don’t program in Ruby because you want power or efficiency. Don’t program in Ruby because you think you “should”, either. Program in Ruby because you like it. And if you don’t like it, don’t program in it.

Very nice article discussing the importance of joy in work. I enjoy programming in Ruby on Rails.

Who Should Profit from Yellowstone’s Microbes

The Gold in Yellowstone’s Microbes

Year by year, Yellowstone’s hot waters are yielding remarkable new microbial specimens with implications for medicine, agriculture and energy, as well as offering clues to the formation of earliest life on Earth and maybe even on Mars. The potential financial windfalls are enormous, as evidenced by one big jackpot.
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Yellowstone microbes (and those from a few other hot spots on the planet) may also hold great promise for bioremediation — cleaning up chemical pollution, oil slicks and smokestack emissions — as well as the means to accelerate biomass fermentation and develop drought-resistant crops. And there is more to be discovered: Probably less than one percent of Yellowstone’s microscopic life forms have been discovered and studied.
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the National Park Service signed a secretive research-sharing agreement with Diversa Corporation in 1998. Non-profit groups quickly cried “bio-piracy!” when they found out and sued the Service over the arrangement. While a federal court dismissed the case, it ordered the Park Service to address the issue… But the Park Service is still trying to come up with an acceptable, benefits-sharing agreement that might allow bio-prospecting of microbes and disclosure of findings, with a fair return to the Park from any commercial success.

Higgs

The god of small things:

While working on the conundrum, Higgs came up with an elegant mechanism to solve the problem. It showed that at the very beginning of the universe, the smallest building blocks of nature were truly weightless, but became heavy a fraction of a second later, when the fireball of the big bang cooled. His theory was a breakthrough in itself, but something more profound dropped out of his calculations.

Higgs’s theory showed that mass was produced by a new type of field that clings to particles wherever they are, dragging on them and making the heavy. Some particles find the field more sticky than others. Particles of light are oblivious to it. Others have to wade through it like an elephant in tar. So, in theory, particles can weigh nothing, but as soon as they are in the field, they get heavy.

Scientists now know that Higgs’s extraordinary field, or something very similar to it, played a key role in the formation of the universe. Without it, the cosmos would not have exploded into the rich, infinite galaxies we see today. The spinning disc of cosmic dust that collapsed 4.5 billion years ago to form our solar system would never have been. No planets would have formed, nor a sun to warm them. Life would not have stood a chance.

In late summer 1964, two years before he would give his Princeton lecture, Higgs rushed out a succinct letter, packed with mathematical formulae that backed his discovery and sent it to a leading physics journal run from Cern, the European nuclear research organisation in Geneva. The paper was published almost immediately, but went largely unnoticed.

Six Cool Ideas

Six Ideas That Will Change the World

The Pollution Magnet – Eighty-two thousand people die from cancer in Bangladesh every year, many due to arsenic poisoning. But building upon her discovery of a way to get rust nanoparticles to bind to arsenic, Vicki Colvin has invented a new, astonishingly easy way to clean the water supply: SautÃ© a teaspoon of rust in a mixture of oil and lye, which breaks down the rust into nano-sized pieces. Retrieve the rust particles with a household magnet. Then immerse the rust-covered magnet into a pot of contaminated water. Pull out the arsenic. The system is up to a hundred times more efficient than existing methods, and requires no electricity or manufacturing infrastructure, so even the poorest of villagers can use it.

Depending upon government regulations, Colvin’s extraction system should go global in as few as five years. Yet ultimately, Colvin, a professor of chemistry and chemical and biomolecular engineering at Rice University, has bigger plans. She sees her method as just the first step toward developing an easy point-of-use water-purification system that would cover virtually every pollutant. The filter would have a dipstick to tell you what’s in the water and a reader to tell you what you need to add to pull it out — perhaps silver nanoparticles to kill bacteria or a protein to capture pesticides.

Moringa Oleifera: The Miracle Tree

One thing I enjoy brought about by the web is finding interesting tidbits such as – Moringa Oleifera: The Miracle Tree:

For centuries, the natives of northern India and many parts of Africa have known of the many benefits of Moringa oleifera. Its uses are as unique as the names it is known by, such as clarifier tree, horseradish tree and drumstick tree (referring to the large drumstick shaped pods) and in East Africa it is called “mother’s best friend”. Virtually every part of the tree can be used. Native only to the foothills of the Himalayas, it is now widely cultivated in Africa, Central and South America, Sri Lanka, India, Malaysia and the Philippines. This tree, though little known in the Western world, is nutritional dynamite. There are literally hundreds of uses for this tree.

The immature pods are the most valued and widely used of all the tree parts. The pods are extremely nutritious, containing all the essential amino acids along with many vitamins and other nutrients. The immature pod can be eaten raw or prepared like green peas or green beans, while the mature pods are usually fried and possess a peanut-like flavor. The pods also yield 38 – 40% of non-drying, edible oil known as Ben Oil. This oil is clear, sweet and odorless, and never becomes rancid. Overall, its nutritional value most closely resembles olive oil. The thickened root is used as a substitute for horseradish although this is now discouraged as it contains alkaloids, especially moriginine, and a bacteriocide, spirochin, both of which can prove fatal following ingestion. The leaves are eaten as greens, in salads, in vegetable curries, as pickles and for seasoning. They can be pounded up and used for scrubbing utensils and for cleaning walls. Leaves and young branches are relished by livestock. The Bark can be used for tanning and also yields a coarse fiber. The flowers, which must be cooked, are eaten either mixed with other foods or fried in batter and have been shown to be rich in potassium and calcium.

More internet finds: Sarah, aged 3, Learns About Soap – Plumpynut, Miracle Food – The Avocado – More Nutritious Wheat – Cool Mechanical Simulation System – Aerogels – Weird Solids – Awesome Cat Cam

Nigersaurus

photo of the Nigersaurus Jaw Bones

Structural Extremes in a Cretaceous Dinosaur

Nigersaurus taqueti shows extreme adaptations for a dinosaurian herbivore including a skull of extremely light construction, tooth batteries located at the distal end of the jaws, tooth replacement as fast as one per month, an expanded muzzle that faces directly toward the ground, and hollow presacral vertebral centra with more air sac space than bone by volume. A cranial endocast provides the first reasonably complete view of a sauropod brain including its small olfactory bulbs and cerebrum. Skeletal and dental evidence suggests that Nigersaurus was a ground-level herbivore that gathered and sliced relatively soft vegetation, the culmination of a low-browsing feeding strategy first established among diplodocoids during the Jurassic.

This discovery has received a good deal of coverage. Among other things it is great to see this paper is available to everyone who wants to view it because it is published by open access PLoS One. The Nigersaurus was discovered in what is now the Sahara Desert in Niger. When the Nigersaurus was roaming the area, 110 million years ago, the climate was a Mesozoic forest. The dinosaur had a few hundred teeth that were replaced almost monthly (a record). The bones of the head and neck were so minimal and light that the Read more about the Nigersaurus. As the author stated: “One of the stunning things about this animal is how fragile the skull is… Some of the bones are so thin you can shine a light through them.”

Robot Boats Hunt Pirates

Robot Boats Hunt High-Tech Pirates on the High-Speed Seas

The International Maritime Bureau is tracking a 14-percent increase in worldwide pirate attacks this year. And although modern-day pirates enjoy collecting their fare share of booty—they have a soft spot for communications gear—they’re just as likely to ransom an entire ship. In one particularly sobering case, hijackers killed one crew member of a Taiwan-owned vessel each month until their demands were met.

For years now, law enforcement agencies across the high seas have proposed robotic boats, or unmanned surface vessels (USVs), as a way to help deal with 21st-Century techno Black Beards. The Navy has tested at least two small, armed USV demonstrators designed to patrol harbors and defend vessels. And both the Navy and the Coast Guard have expressed interest in the Protector, a 30-ft.-long USV built by BAE Systems, Lockheed Martin and Israeli defense firm RAFAEL.

The Protector, which comes mounted with a 7.62mm machine gun, wasn’t originally intended for anti-piracy operations. But according to BAE Systems spokesperson Stephanie Moncada, the robot could easily fill that role.