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.

Billions for Science in Stimulus Bill

Science wins big in US economic plan

Democratic leadership in the US House of Representatives unveiled on Thursday an $825 billion economic stimulus bill that includes tens of billions of dollars in new funding for basic research, science infrastructure and clean-energy initiatives.
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House appropriators would pump $3 billion into the National Science Foundation (NSF), $2 billion into the National Institutes of Health (NIH), $1.9 billion into the Department of Energy and $1.5 billion into university research facilities. Much of that money would be directed toward science infrastructure like renovating buildings or laboratories, but the NSF and NIH would receive $2 billion and $1.5 billion respectively that could be used to pay for thousands of basic research grants that have already been approved but for which there was previously not enough money.

It will be interesting to see how this plays out. And short term spikes in funding are problematic for numerous reasons. But I have long argued for the value of investing in science and engineering excellence for long term economic benefit. I am worried the government will fail to provide adequate strategic thought to investments.

Today is Martin Luther King Day in the USA: Watch the entire I Have a Dream Speech.

New Family of Antibacterial Agents Discovered

Bacteria continue to gain resistance to commonly used antibiotics. In this week’s JBC, one potential new antibotic has been found in the tiny freshwater animal Hydra.

The protein identified by Joachim GrÃ¶tzinger, Thomas Bosch and colleagues at the University of Kiel (Germany), hydramacin-1, is unusual (and also clinically valuable) as it shares virtually no similarity with any other known antibacterial proteins except for two antimicrobials found in another ancient animal, the leech.

Hydramacin proved to be extremely effective though; in a series of laboratory experiments, this protein could kill a wide range of both Gram-positive and Gram-negative bacteria, including clinically-isolated drug-resistant strains like Klebsiella oxytoca (a common cause of nosocomial infections). Hydramacin works by sticking to the bacterial surface, promoting the clumping of nearby bacteria, then disrupting the bacterial membrane.

GrÃ¶tzinger and his team also determined the 3-D shape of hydramacin-1, which revealed that it most closely resembled a superfamily of proteins found in scorpion venom; within this large group, they propose that hydramacin and the two leech proteins are members of a newly designated family called the macins.

Source: American Society for Biochemistry and Molecular Biology

Evolution, Methane, Jobs, Food and More

Photo from May 2005 by NASA’s Mars Exploration Rover Spirit as the Sun sank below the rim of Gusev crater on Mars.

Science Friday is a great National Public Radio show. The week was a great show covering Antimicrobial Copper, Top Jobs for Math and Science, Human-Driven Evolution, Methane On Mars, Fish with Mercury and more. This show, in particular did a great job of showing the scientific inquiry process in action.

“Fishing regulations often prescribe the taking of larger fish, and the same often applies to hunting regulations,” said Chris Darimont, one of the authors of the study. “Hunters are instructed not to take smaller animals or those with smaller horns. This is counter to patterns of natural predation, and now we’re seeing the consequences of this management.” Darimont and colleagues found that human predation accelerated the rate of observable trait changes in a species by 300 percent above the pace observed within purely natural systems, and 50 percent above that of systems subject to other human influences, such as pollution

Very interesting stuff, listen for more details. A part of what happens is those individuals that chose to focus on reproducing early (instead of investing in growing larger, to reproduce later) are those that are favored (they gain advantage) by the conditions of human activity. I am amazed how quickly the scientists says the changes in populations are taking place.

And Methane On Mars is another potentially amazing discovery. While it is far from providing proof of live on Mars it is possibly evidence of life on Mars. Which would then be looked back on as one of the most important scientific discoveries ever. And in any even the podcast is a great overview of scientists in action.

This week astronomers reported finding an unexpected gas — methane — in the Martian atmosphere. On Earth, a major source of methane is biological activity. However, planetary scientists aren’t ready to say that life on Mars is to blame for the presence of the gas there, as geochemical processes could also account for the finding. The find is intriguing especially because the researchers say they have detected seasonal variations of methane emissions over specific locations on the planet.

Martian Methane Reveals the Red Planet is not a Dead Planet
The Mars Methane Mystery: Aliens At Last?

Soil Mineral Degrades the Nearly Indestructible Prion

Warped pathogens that lack both DNA and RNA, prions are believed to cause such fatal brain ailments as chronic wasting disease (CWD) in deer and moose, mad cow disease in cattle, scrapie in sheep and Creutzfeldt-Jakob disease in humans. In addition to being perhaps the weirdest infectious agent know to science, the prion is also the most durable. It resists almost every method of destruction from fire and ionizing radiation to chemical disinfectants and autoclaving, which reduce prion infectivity but fail to completely eliminate it.

Other studies have shown that prions can survive in the soil for at least three years, and that soil is a plausible route of transmission for some animals, says Joel Pedersen, a UW-Madison environmental chemist. “We know that environmental contamination occurs in deer and sheep at least,” he notes.

Prion reservoirs in the soil, Pedersen explains, are likely critical links in the chain of infection because the agent does not appear to depend on vectors — intermediate organisms like mosquitoes or ticks — to spread from animal to animal.

That the birnessite family of minerals possessed the capacity to degrade prions was a surprise, Pedersen says. Manganese oxides like birnessite are commonly used in such things as batteries and are among the most potent oxidants occurring naturally in soils, capable of chemically transforming a substance by adding oxygen atoms and stripping away electrons. The mineral is most abundant in soils that are seasonally waterlogged or poorly drained.

full press release

Tiny $10 Microscope

Researchers at Caltech, who developed the revolutionary imaging system, say that the devices could be mass-produced at a cost of $10 each and incorporated into large arrays, enabling high-throughput imaging in biology labs. The device could also broaden access to imaging technology: incorporated into PDA-size devices, for example, the microscopes could enable rural doctors to carry sophisticated imaging systems in their pockets.

The Caltech device uses a system of tiny fluid channels called microfluidics to direct cells and even microscopic animals over a light-sensing chip. The chip, an off-the-shelf sensor identical to those found in digital cameras, is covered with a thin layer of metal that blocks out most of the pixels. A few hundred tiny apertures punched in the metal along the fluid channel let light in. As the sample flows through the microscope, each aperture captures an image. One version of the microscope uses gravity to control the flow of the sample across the apertures. Another version, which allows for much better control, uses an electrical potential to drive the flow of cells.

Data Analysts Captivated by R’s Power

data mining has entered a golden age, whether being used to set ad prices, find new drugs more quickly or fine-tune financial models. Companies as diverse as Google, Pfizer, Merck, Bank of America, the InterContinental Hotels Group and Shell use it.
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Close to 1,600 different packages reside on just one of the many Web sites devoted to R, and the number of packages has grown exponentially. One package, called BiodiversityR, offers a graphical interface aimed at making calculations of environmental trends easier.

Another package, called Emu, analyzes speech patterns, while GenABEL is used to study the human genome. The financial services community has demonstrated a particular affinity for R; dozens of packages exist for derivatives analysis alone. “The great beauty of R is that you can modify it to do all sorts of things,” said Hal Varian, chief economist at Google. “And you have a lot of prepackaged stuff that’s already available, so you’re standing on the shoulders of giants.”

R first appeared in 1996, when the statistics professors Ross Ihaka and Robert Gentleman of the University of Auckland in New Zealand released the code as a free software package. According to them, the notion of devising something like R sprang up during a hallway conversation. They both wanted technology better suited for their statistics students, who needed to analyze data and produce graphical models of the information. Most comparable software had been designed by computer scientists and proved hard to use.

R is another example of great, free, open source software. See R packages for Statistics for Experimenters.

via: R in the news

Yellowstone Youth Conservation Corps

photo of river in Yellowstone National Park by John Hunter

Photo of a river in Yellowstone National Park by John Hunter

Externs.com, another curiouscat.com site, provides links to hundreds of internship opportunities. We highlight some science and engineering internships and plenty of other options too. Visit the internship directory site to find options like the Yellowstone Youth Conservation Corps. The YCC was established to accomplish needed conservation work on public lands and to develop an understanding and appreciation of participating youth in our nation’s natural, historical, and cultural heritage.

The Yellowstone YCC is a program that emphasizes work ethics, environmental awareness and recreational activities. Approximately 30 students are selected each summer from across the country and are expected to complete forty hours of work each week.

In the past, YCC enrollees have been instrumental in building backcountry bridges; trail construction and maintenance; log cabin restoration; painting; and working on a wide variety of resource management, maintenance, and research projects. Many of the projects take place in remote locations within Yellowstone and work crews may be camped out for up to ten days.

Along with the work projects, enrollees spend significant time participating in YCC environmental education and recreation programs. Many of these activities are scheduled in the evenings and on weekends. They include hiking, rafting, fishing, backpacking, ranger led programs, guest speakers, enrollee and staff presentations, and trips throughout the Greater Yellowstone Ecosystem.

To be selected you must be at least 15 and not turn 19 before the term ends in mid August.

via: Send Your Kid to Yellowstone National Park This Summer

So What are Genetic Algorithms?

Genetic Algorithms: Cool Name and Damn Simple is a very nice explanation with python code of genetic algorithms.

What Can Genetic Algorithms Do?
In a word, genetic algorithms optimize. They can find better answers to a question, but not solve new questions. Given the definition of a car, they might create a better car, but they’ll never give you an airplane.
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For each generation we’ll take a portion of the best performing individuals as judged by our fitness function. These high-performers will be the parents of the next generation.

We’ll also randomly select some lesser performing individuals to be parents, because we want to promote genetic diversity. Abandoning the metaphor, one of the dangers of optimization algorithms is getting stuck at a local maximum and consequently being unable to find the real maximum. By including some individuals who are not performing as well, we decrease our likelihood of getting stuck.

Solving the Toughest Problems in Computer Science

Software Breakthroughs: Solving the Toughest Problems in Computer Science, 2004:

Bill Gates’ talk at MIT provided an optimistic view of the next generation of computer science, now that the “rough draft” is done. Gates finds a paradox today in that computer science is poised to transform work and home life, “but people’s excitement level is not as high as it was five years ago during the Internet bubble.” Because most sectors of the computer industry—from microchips to storage, displays to wireless connectivity— continuously improve in performance, Gates predicts a flood of new products and applications. He sported a wristwatch that receives data wirelessly, as well as keeps its user on schedule. Gates describes “rich, new peripherals” such as ultra-wideband digital cameras and he demonstrates software that allows pictures to be archived using a 3D visual interface with a built-in time, date, and keyword database. He says that computer science is merging with and making over such fields as astronomy and biology, by unifying vast, unwieldy data collections into easily navigable libraries. And Gates appears confident that technological breakthroughs will ultimately resolve urgent problems of computer and network security.

Moth Jams Bat Sonar

Superloud moth jams bat sonar

A gray moth with orange highlights called Bertholdia trigona “goes berserk,” making lots of noise above the range of human hearing when a hunting bat approaches, says William Conner of Wake Forest University in Winston-Salem, N.C. Bats rely on their natural sonar to locate flying moths in the dark, but in a lab setup, the bats rarely managed to nab a loud moth.

When researchers disabled the moth’s noisemaking organs, though, bats caught the moths in midair with ease, Conner reported at the annual meeting of the Society for Integrative and Comparative Biology.

Conner says the work is “the first example of any prey item that jams biological sonar.” Conference attendee David Yager of the University of Maryland in College Park says Conner’s experimental paradigm is “very strong, and I do think he has documented jamming by a species of moth.”

Insect-hunting bats and their moth prey have become a classic in the study of evolutionary arms races, Conner says. “This is warfare … The first counter-adaptation is that the insects developed ears.”
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Jamming isn’t the only possible explanation for moth noises, he said. An explosive clicking sound coming back out of the night might startle a bat just a split-second long enough for the moth to get away.