Category Archives: Students

Items for students and others, interested in learning about science and engineering and the application of science in our lives. We post many of the general interest items here.

New Approach Builds Better Proteins Inside a Computer

With the aid of more than 150,000 home computer users throughout the world, Howard Hughes Medical Institute (HHMI) researchers have, for the first time, accurately predicted the three-dimensional structure of a small, naturally occurring globular protein using only its amino acid sequence. The accomplishment was achieved with a newly refined computational method for predicting protein structure, which the researchers say can also improve the detail and accuracy of protein structures generated with experimental techniques.

A detailed understanding of a protein’s structure can offer scientists a wealth of information – revealing intricacies about the protein’s biological function and suggesting new ideas for drug design. Researchers often rely on x-ray crystallography to determine a protein’s structure – bombarding the molecule with x-rays and analyzing the resulting diffraction pattern to piece together its structure. But not all proteins are amenable to this time-consuming technique, and those that are do not always yield the atomic-level data researchers would like to have.
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The complex algorithms the researchers developed to carry out these analyses demand a tremendous amount of computing power. More than 150,000 home computer users around the world were an integral part of the project, volunteering their computers to participate in the quest for protein structures through Rosetta@home, a distributed computing project that is based on the Berkeley Open Infrastructure for Network Computing (BOINC) platform.

You can join in via Rosetta@home. Related: Protein Knots – molecular sieve advances protein research – Protein Science Art – Nobel Laureate Discusses Protein Power

Live Long and Prosper

Live Long and Prosper: A Conversation with Cynthia Kenyon:

Cynthia Kenyon, PhD, director of the UCSF’s Larry L. Hillblom Center for the Biology of Aging, smiles a lot these days. And with good reason. She has aging cornered and she knows it. In less than 20 years, her once-crazy idea – that genes regulate aging – has not only gone mainstream, but spawned a huge field of research with giant conclaves and dozens of journal articles published every year.
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One of Kenyon’s lab rotation students – Ramon Tabtiang – in one of his very first experiments, picked a needle out of the haystack that is the C. elegans genome. In short, he found a mutant gene, dubbed daf-2, that made worms live twice as long. C. elegans was — and is — a favorite model for developmental biologists and geneticists because its simple structure and entire three-week life are easily scrutinized under the microscope.

Watching the mutant worms, says Kenyon, was like “witnessing a miracle.” Not only did these worms live longer, they retained good muscle tone, squirmed, sought food and stayed youthful. In comparison, normal, or wild, worms of the same two-week age were flabby, tattered and sedentary. They looked old. The message was clear. The rate of aging was not “fixed in stone,” after all. It could be slowed.

In the years since, Kenyon and her team have made more eye-popping discoveries, including the role of a companion gene, called daf-16, that controls on or off signals in still other genes. Learning more about the insulin pathway in which these genes operate helped her to understand a cascade of signals and responses as they reverberate through individual tissues.

Better yet, by using this information to tweak here and there in the worm genome, Kenyon and her laboratory colleagues have been able to extend a worm’s life up to six times the normal span, with no significant decline in vitality until late in life.

Real-Time Evolution

Real-Time Evolution, Researchers find evidence that a variety of African electric fish may be approaching speciation:

Researchers from Cornell University found that genetically identical fish are sending out two different electric signals, and certain male members of the species ignore some signals emitted by females, responding only to pulses similar to their own. The strict selectivity for specific signals observed in these electric fish may eventually result in different mating groups, leading researchers to surmise that the fish could be on the verge of speciation.

“Evolution is a historical, inferential science—you can’t really see it happening before your eyes,” said Matt Arnegard, a neurobiology and behavior postdoc at Cornell and lead author of the study, which appears in the June issue of The Journal of Experimental Biology. “We think maybe this is an example where we’re really close to seeing it happen before our eyes.”

Packard Faculty Fellowship for Nathaniel Dominy

UC Santa Cruz anthropologist Nathaniel Dominy wins prestigious $625,000 Packard Fellowship

Dominy will receive $125,000 per year for the next five years to support his investigation of the diet and foraging behaviors of hominins, the early human ancestors who lived 2 million years ago. The Packard Foundation awards these fellowships to young scientists and engineers who show exceptional promise and creativity.
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Dominy’s research interests center around the acquisition and consumption of food, which he believes fueled the development of bipedalism and big brains. Two of his recent studies made headlines around the world in recent months: The first added compelling new evidence to the hypothesis that hominins may have eaten starchy, nutrient-rich underground plant structures, including bulbs and tubers, while the second revealed that humans are uniquely equipped to digest starch. The revelation that humans have many more copies of the salivary amylase gene than any of their ape relatives bolsters the idea that starch was a crucial addition to the diet of early humans, and that natural selection favored individuals who could make more starch-digesting protein.

Make the World Better

Three ways to make the world better. First, Kiva is lets you loan money directly to an entrepreneur of your choice. Kiva provides loans through partners (operating in the countries) to the entrepreneurs. Those partners do charge the entrepreneurs interest (to fund the operations of the lending partner). Kiva pays the principle back to you but does not pay interest. And if the entrepreneur defaults then you do not get your capital paid back (in other words you lose the money you loaned). See my post: Helping Capitalism Make the World Better (if you donate to Kiva I have a Curious Cat Kivan – comment to have you link added).

Second, donate using the widget displayed in this post: to William Kamkwamba who built his own windmill in Malawi to get electricity for his home. The donations go to help him with his education and engineering projects. He is a young student and engineer. I have donated $50, I would love to see readers donate – do so and send me a link to your personal blog or personal home page and I will update this post with a link (only to a site obviously associated with you – I reserve the right to link or not link to whoever I want). [the campaign is over so I removed the widget – $943 was raised, the goal was $2,000]. A recent post to his blog: My sisters and cousins with their first books:

Some well-wishers sent many children’s books that are written or take place in countries around Africa in addition to English and American classics such as Where the Wild Things Are. All the children in my neighborhood, most of whom are cousins or sisters share these new books.

Third, create a Kiva like setup for donations that could be used to provide a source for finding remarkable people that have plans for possible donated funds. The potential is huge.

Monarch Butterfly Migration

Monarch Butterfly

Helping track the monarch butterfly migration is a very cool interactive learning projects for students. The Monarch Butterfly Journey North site includes a great wealth of resource with real time reports and answers to science questions.:

A massive migration across Oklahoma, Arkansas, and Kansas this week resulted in the most spectacular sightings of the season. Most miraculous was the mile of clustering monarchs discovered on Sunday in a sunflower field in Kansas. Just think…It’s the first week of October and migrating monarchs are still being spotted across the north.

From the Monarchs in the Classroom website:

Unlike most other insects in temperate climates, monarch butterflies cannot survive a long cold winter. Every fall, North American monarchs fly south to spend the winter at roosting sites. Monarchs are the only butterflies to make such a long, two-way migration, flying up to 3000 miles in the fall to reach their winter destination. Amazingly, they fly in masses to the same winter roosts, often to the exact same trees. Their migration is more the type we expect from birds or whales than insects. However, unlike birds and whales, individuals only make the round-trip once. It is their children’s grandchildren that return south the following fall.

Monarch Travels (2006 post)

To test their ability to reorient themselves, Dr. Taylor has moved butterflies from Kansas to Washington, D.C. If he releases them right away, he said, they take off due south, as they would have where they were. But if he keeps them for a few days in mesh cages so they can see the sun rise and set, “they reset their compass heading,” he said. “The question is: How?”

Proposal to Triple NSF GFRP Awards and the Size of the Awards by 33%

Hillary Clinton’s Innovation Agenda (press release from the campaign):

Triple the number of NSF fellowships and increase the size of each award by 33 percent. At present, the NSF offers approximately 1,000 fellowships per year. This number is not much changed from the 1960s, although the number of college students graduating with science and engineering degrees has grown three fold. The NSF fellowship is the key financial resource for science and engineering graduate students. Hillary will increase the number of fellowships to 3,000 per year. She will also increase each award from $30,000 to $40,000 per year (simultaneously, she will increase the NSF award to each recipient’s school from $10,500 per recipient to $14,000 per recipient to help cover educational costs).

That sounds great to me. I have talked about this before: Increasing American Fellowship Support for Scientists and Engineers. I work for ASEE on the IT systems in support of the NSF Graduate Research Fellowship Operation Center (the ASEE portion of the program) and other engineering fellowship programs). This blog is my own and is not affiliated with ASEE.

The proposed legislation on Graduate Scholar Awards in Science, Technology, Engineering, or Math also has a similar aim and commitment. Here is a post from 2005 on similar proposals. As I mentioned in The Innovation Agenda, 2005 while I agree with this spending I also believe what I said then:

Currently the United States has over $8,000,000,000,000 (that is over $8 trillion – see current count) in debt (increasing by over $400 Billion a year). That brings every person’s share to over $27,000. Given that, it seems reckless to just add spending without either cutting something else or increasing taxes and I don’t see those details in the innovation agenda.

The debt now? Over $9,000,000,000,000 (increasing more than $1.4 billion a day for the last year). More on Washington taxing future generations to pay for what we spend today.

Popular Mechanics 2007 Breakthrough Award: the Windbelt

Shawn Frayne’s Windbelt Wins Popular Mechanics 2007 Breakthrough Award

Frayne’s device consists of a flat, taut membrane that flutters within its housing as air passes through it. At each end of the membrane are magnets that oscillate between metal coils as the band flutters, effectively creating an electric charge. According to the 28-year-old Frayne, prototypes of the Windbelt have generated 40 milliwatts in 10-mph slivers of wind, making his device 10 to 30 times as efficient as the best microturbines.
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Frayne, now based in Mountain View, Calif., gathered a variety of lessons while studying at MIT, especially under the tutelage of Amy Smith (a 2004 MacArthur fellow) in her “D-Lab” class. In this design lab, Frayne learned the politics of delivering technology to poor nations, as well as the technical aspects of mechanical engineering.

I blogged on Amy Smith another blog awhile back: Engineering a Better World (which includes a great web video). Read about 9 more Breakthrough awards.

2007 Solar Decathlon of Homes

Solar Home on National Mall

The National Mall in Washington DC is hosting the 2007 Solar Decathlon of Homes. The link show many photos of homes and interesting information. The event opened to the public today.

The Department of Energy’s Solar Decathlon is a international competition in which 20 university-led teams compete to design, build, and operate the most attractive, effective, and energy-efficient solar-powered house. Every college or university interested in participating wrote a proposal describing how they would organize a team, design and build a house, and raise the funds necessary to have a successful entry. The 20 best proposals were selected and awarded $100,000 dollars from the United States Department of Energy.

The photo shows the Kansas Project Solar House (Kansas State University and University of Kansas) and the Washington Monument in the background.

via: Solar Decathlon Heats Up

New Hearing Mechanism

MIT finds new hearing mechanism

MIT researchers have discovered a hearing mechanism that fundamentally changes the current understanding of inner ear function. This new mechanism could help explain the ear’s remarkable ability to sense and discriminate sounds. Its discovery could eventually lead to improved systems for restoring hearing.
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t has been known for over half a century that inside the cochlea sound waves are translated into up-and-down waves that travel along a structure called the basilar membrane. But the team has now found that a different kind of wave, a traveling wave that moves from side to side, can also carry sound energy. This wave moves along the tectorial membrane, which is situated directly above the sensory hair cells that transmit sounds to the brain. This second wave mechanism is poised to play a crucial role in delivering sound signals to these hair cells.

Related: Solar Powered Hearing Aid