Archive for August, 2009

From the Pamir Mountains: Can you hear me now?

Monday, August 31st, 2009
Researchers from the University of Idaho study ice core samples 17,000 feet above sea level on the other side of the world.

Researchers from the University of Idaho study ice core samples 17,000 feet above sea level on the other side of the world.

I believe I mentioned earlier this month the possibility of having several faculty members blogging from the field this semester while conducting their research. One such possibility - Vladimir Aizen’s research in the Pamir Mountains - really excited me.

Aizen currently is leading a research team to the tops of a 51-mile-long glacier elevated more than 17,000 feet above sea level. There, he is taking deep ice core samples between 700- and 1000-feet long. The team is hoping these cores will prove the value of returning to take a 3,000-foot sample.

The last time he journeyed to the “Roof of the World,” Aizen took some amazing photos and had wonderful stories to tell. I was excited for those to be posted in real time here.

But his cell phone doesn’t work.

Here is the text from a recent email:

HelloKen,

I am in Pamir high mountains now with my international team but I have very limited Internet communication through the satellite phone. The Iridium satellite Communication Company promise to have connection at any place of the World but in fact the signal is very weak and always interrupted. I will prepare some story for our university while I am in filed but I will be able to send it when I will have steady Internet.

With regards from 16,000 fit and -15C cold environmental,

Vladimir Aizen

Are you kidding me?!?! One of the best stories of the world and the promised satellite internet communication doesn’t work! That’s just great!

Anyways, I’ll just have to wait for his return to get the story out. In the mean time, check out the original press release about his last visit to learn more about what he’s doing.

Tuesday Science Times: 8/25

Tuesday, August 25th, 2009

Today’s lead story in the New York Science Times details one oceanographer’s decades-long search for the world’s oldest fossil on the floors of the ocean more than 2 miles beneath the surface.

Peter Rona began his career working for Standard Oil searching for promising new sites in the American Southwest. But he fell in love with the deepest depths of the ocean while visiting family in Manhattan and stumbling upon groups of oceanographers and research ships.

A decade later, Rona had a Ph.D. in marine geology and geophysics from Yale and was investigating the ocean floors.

In 1976 he found a small, hexagonal imprint with hundreds of tiny holes. Perplexed, he asked oceanographers around the world what the imprint might be. His inquiries turned up empty until a scientist in Germany suggested it fit perfectly with the fossil P. nodosum, one of the oldest fossils on record.

After several more trips, the evidence piled up, and Rona is now convinced that the imprints belong to the organism believed to have become extinct 50 million years ago.

But the argument is not over. Rona has yet to capture a living specimen, but he’s certainly trying.

Also in this week’s edition:

  • A profile of a scientist and industry seeking to build complex computer models of how thousands of genes and proteins interact in today’s deadliest diseases.
  • A new study shows that children who have a high sense of guilt grow up to be better at controlling their destructive impulses, though a lack of guilt can be overcome.
  • An interesting recount of the 10-year anniversary of the West Nile outbreak in New York phases into a recollection of the very first cases, intentionally given as an experimental cancer treatment, which spawned the debate creating today’s ethical standards on clinical research.
  • It seems many doctors have no clue when they are using off-label prescriptions – using drugs for reasons other than what they are intended.
  • And finally, there is some evidence that certain diets may help ease arthritis.

Clouds confuse lost souls

Monday, August 24th, 2009

I came across this interesting story in Science NOW, an online collection of short but interesting articles regularly published by Science magazine.

You know how movies always depict people who are lost in the wilderness as walking around in circles? Well, a team of researchers from the Max Planck Institute for Biological Cybernetics in Tubingen, Germany decided to find out if this myth is fact or fiction.

To find out, the team blindfolded a group of volunteers, attached a GPS device to them, and asked them to attempt to walk a straight line across a large field. And, believe it or not, most people could not do it. Some seem to eventually make their way in the correct general direction but with many wobbles and wavers. However, some walked in circles as tight as 20 meters in diameter.

It seems that the human navigation system denied access to visual cues contain very minute errors. If these errors all begin to pile up into the same direction, we walk in circles.

But the study didn’t stop there.

The group also asked volunteers to attempt to walk  a straight line through a section of the Sahara Desert and a forest in Germany. They found the sun helps people navigate a straight line, or at least shadows and other visual cues caused by the sun’s light do.

On sunny days, people could easily walk a line for several hours. But on cloudy days, in both environments, participants ended up walking in circles.

Pretty neat, eh?

Cloning science takes a hit

Friday, August 21st, 2009
Gem was the first clone from the equine family.

Gem was the first clone from the equine family.

It’s a sad day in the world of equine cloning.

Former University of Idaho scientist Gordon L. Woods died unexpectedly yesterday morning near his new university home, Colorado State. Woods led a mule-cloning team here in Moscow several years ago and made national headlines.

In 2003, Woods led a team from the University of Idaho and Utah State University that was the first group to successfully clone an animal from the equine family. The baby mule, named Gem, was born on May 4.

Though Professor Woods left Moscow for greener research pastures in Colorado, it’s a sad day for scientists everywhere when one of its leading, brilliant minds winks out of existence.

In a press release issued by the University of Idaho, spokesman Bill Loftus wrote, “We are shocked and saddened by the loss of Dr. Gordon Woods. He was a talented scientist whose accomplishments in equine cloning drew the attention of media worldwide to the University of Idaho. His willingness to challenge conventional beliefs may help medical researchers develop a new understanding of the origins of some important human diseases. His death is a devastating loss to his many friends and colleagues. The faculty and staff College of Agricultural and Life Sciences and the extended University of Idaho community extend their deepest sympathies to Dr. Woods’ family.”

Evolving a solution

Wednesday, August 19th, 2009

The genetic algorithm program basically uses a sophisticated method of trial and error to find an optimum solution. A high number of experiments are required for the process, such as the many test beakers filled with algae pictured here.

The genetic algorithm program basically uses a sophisticated method of trial and error to find an optimum solution. A high number of experiments are required for the process, such as the many test beakers filled with algae pictured here.

Scientists here at the University of Idaho are stealing nature’s greatest problem solving invention - evolution. They’ve created a genetic algorithm that basically uses trial and error to find the best solution to a problem.

Here’s how it works.

Say you wanted to solve a problem like, what is the best environment for bacteria to live in while producing biofuel? There are too many variables - like pH level, temperature, nutrients, other organisms - for scientists to ever fully understand the system.

So instead, researchers let the computer create a bunch of different random solutions and test each one. They put the results into the genetic algorithm, which takes common traits of the best solutions, adds some random

mutations and creates a group of “offspring” solutions.

By doing this a whole bunch of times, they eventually find the best solution to the problem.

One graduate student - Kate Kurcharzyk - is using the genetic algorithm to find the best way to naturally break down and dispose of the environmental toxin ammonium perchlorate. Ammonium perchlorate is a substance found in groundwater across the country. It can come from rocket fuels near military bases, industrial manufacturing plants, fertilizers or simply the natural environment. Perchlorates, in general, are highly soluable, move into groundwater easily and are thought to interfere with the normal function of the human thyroid, wreaking havoc on hormones and early childhood development.

If the project goes well, Kurcharzyk will find the best set of circumstances for bacteria to naturally dispose of this growing problem in affected sites around the world.

Knock-out

Monday, August 17th, 2009

Scientists at the University of Idaho will try to knock-out diabetes by knocking-out genes.

The National Institutes of Health is providing $525,000 over the next three years to the youngest group of researchers – and the only team from Idaho – ever to receive a EUREKA grant. EUREKA stands for Exceptional, Unconventional Research Enabling Knowledge Acceleration, which means the NIH basically believes the research is risky to fund, but way too promising to ignore.

We’re talking about genetic research, specifically gene knock-outs. About a decade ago, scientists mapped out the entire human genome. However, they have no clue where some of the roads go. By shutting down lanes one gene at a time, they can observe what happens.

But it takes a long time to knock-out a gene. Unless, that is, the new technology works.

Patrick Hrdlicka, assistant professor of bioorganic chemistry along with Madhusudhan and Rod Hill, research scientist and associate professor of animal and veterinary science, respectively, have developed a new method to knock-out genes in record time.

Hrdlicka creates a synthetic strand of DNA that is altered just enough that the two strands of the double helix do not want to bind together. However, they DO want to bind to the natural DNA. When that happens, they change the natural DNA’s structure and stop it from functioning.

Though Hrdlicka can analyze his creation in a lab and characterize the artificial nucleic acids in a laboratory setting, he can’t test it in the real world. Luckily, he crossed paths with Papasani and Hill, who will take his technology and test it in live animals on genes believed to affect the creation of insulin.

So if all goes well, not only will Idaho scientists have found a way to find a gene’s function in record time, they potentially will have also found new ways to treat diabetes and obesity.

Not bad for a few 32-year-olds in northern Idaho.

From the Archives: Cracking the Question of Extraterrestrial Life

Wednesday, August 12th, 2009
This image of Europa captured by NASA’s Galileo spacecraft combines images taken in violet, green and near-infrared filters. The colors have been stretched to show the subtle differences in materials that cover the icy surface of Europa. Image Credit: NASA/JPL/University of Arizona

This image of Europa captured by NASA’s Galileo spacecraft combines images taken in violet, green and near-infrared filters. The colors have been stretched to show the subtle differences in materials that cover the icy surface of Europa. Image Credit: NASA/JPL/University of Arizona

Geology doesn’t constrain one to terrestrial questions. It can take you to other planets and even seek out life outside of Earth’s atmosphere.

The surface of Jupiter’s moon Europa is about as alien as they come. Average temperatures usually run about minus 260 degrees Fahrenheit and intricate cracks run along the surface covered entirely by ice. But under that ice, there could be a giant ocean, and maybe even life.

Simon Kattenhorn, professor of geology, studies these cracks in the moon’s icy surface looking for signs of current geological activity. If evidence is found, it could reveal the best spot to launch an attempt to study the underlying ocean. And recent discoveries of forms of life thriving in the depths of Earth’s oceans near cracks in the ocean floor give scientists reason to believe there might be similar forms of life living in the depths of Europa’s 60-mile-deep ocean.

For more information, read the full press release.

Rising stars

Monday, August 10th, 2009

One thing I have noticed about the University of Idaho is the abundance of highly talented young faculty members. Don’t get me wrong, there are plenty of well-established scientists in the prime of their careers here as well, but something about Moscow seems to attract youthful brilliance.

For example, I recently had the pleasure of meeting Hejun Kang, an assistant professor in the geography department. Last April, Kang was awarded the 2009 Ph.D. Dissertation Award in Transportation Geography from the Association of American Geographers. She completed her Ph.D. at McMaster University in Canada, and was the first student from a Canadian school to ever win the award.

So what did she win for? Basically, Kang developed an algorithm to supplement an existing computer program that takes statistical information about the population’s driving habits and predicts traffic patterns of the future.

Driving statistics are gathered from national surveys given to individuals. The thing is, tips in the cars aren’t always solo. People in the same household or in the same office often share rides. However, the computer forecasting model did not take this into account. It’s not that nobody had thought of it, it’s just really hard to implement that idea into the software.

However, Kang devised a way to compare graphs of the trips and look for similarities that allow the assumption to be made that the two were riding together. Better predictions will help cities plan their roads better, improve traffic management and avoid congestion.

In the future, Kang hopes to apply these statistics into a research project exploring the number of rides shared by an individual and their vulnerability to social exclusion leading to questions of quality of life. The theory is that the more rides people share, the more socially connected they are in general, and the happier they are.

So keep an eye out for this rising star in the future.

You can start by checking out classes in computer technology, transportation and displaying 3-D statistics in the geography department.

Alumnus helped Armstrong get to the moon

Friday, August 7th, 2009

If you think your job is pressure packed, try waiting to see if the thrusters you designed will fire, keeping the country’s first moon mission on course and several American heroes alive.

That’s the situation that faced University of Idaho engineering graduate Clay Boyce in 1969. But fire they did, and the Aerojet team led by Boyce - now 79 nearly 40 years after the mission’s success - got the job done.

There’s a nice story about Boyce and his memories of the project published by the Sacramento Bee recently. Here’s one of my favorite quotes.

“Boyce said mixing with top-tier pros from prestigious engineering schools like Purdue University was intimidating, but he was more than game as he led Aerojet’s team.”

Just goes to show, you don’t have to go to the Harvards and MITs of the world to make a name for yourself.

Super Fast, Super Rare, Super $$$

Thursday, August 6th, 2009

If you thought your high school science experiment was difficult and time-consuming, check this project out!

Eric Brauns, a professor in chemistry, was just awarded $710,000 from the National Science Foundation to build what amounts toan extreme microscope. And if you think the price tag is hefty, try the cost in time on for size - more than two years of assembly required!

The instrument is known as a superfast infrared spectrometer and less than 50 exist in the entire world.

But none exist the way Brauns plans to build his.

In general, an ultrafast infrared spectrometer creates high-powered laser pulses one-ten-trillionth of a second long. To put that in perspective, light can only travel the width of a human hair in that tiny time period. The laser pulses zap whatever is being studied, causing the laser to be scattered and diffracted. By analyzing the pattern of diffraction, scientists can piece together an “image” of the sample’s structure.

But the University of Idaho’s instrument won’t stop there. The instrument creates this laser pulse through a series of optical components. Brauns plans to make use of this by designing the machine to stop the process at several different points, which will create several different kinds of laser pulses.

In effect, the instrument will produce ultrafast pulses tunable from ultraviolet wavelengths to the mid-infrared, allowing many different types of experiments to be conducted. In fact, there are already three other chemistry professors at the University of Idaho waiting in the wings to get their hands on the upcoming instrument.

For more information, and maybe even a clearer explanation, view the full press release.