Thomas R. O'Donnell

Archive for the ‘University research’ Category

A zombie tractor and ISU plant research’s new direction

In University research on April 14, 2014 at 6:30 am
The automated phenotyping robot, or as I call it, the zombie garden tractor: RTK-GPS, autosteer system, multiple 3-D digital camera.

The automated phenotyping robot (zombie garden tractor): RTK-GPS, autosteer system, multiple 3-D digital camera. (From a Patrick Schnable presentation)

The zombie garden tractor gets your attention.

The driverless machine can move through rows of sorghum, going for hours with only a GPS navigation brain to guide it. High-tech cameras, meanwhile, take three-dimensional photos of every sorghum plant it passes – a kind of Google Street View for fields.

More importantly, the unmanned machine represents Iowa State University’s push into phenomics, a research frontier that promises to reshape the way we grow the food and substances we count on.

Just as genomics researchers aim to understand a plant’s total genetic makeup – every letter in the long book of its DNA – and how it influences plant development, phenomics aims to understand plant phenotypes in similar depth.

A phenotype is the way an organism grows, appears and performs, given its genetic makeup, the environment it lives in, and how the two interact.

“What’s cool – and this is what makes it most interesting to me – is the interaction between genetics and environment,” said Patrick Schnable, an ISU distinguished professor of genetics.

Schnable leads ISU’s drive into phenomics research. He took over as director of the Plant Sciences Institute (PSI) in February with the charge to bring it (and the university) to international prominence in one or more research areas.

He’s targeting phenomics, knowing the field is ripe for discovery. Read the rest of this entry »

Cold facts: UNI-led effort probes Arctic sustainability

In University research on March 10, 2014 at 10:07 am
UNI Geography Professor Andrey Petrov, in furry hat and gloves, holds a piece of Lake Baikal ice in front of his face  during his most recent Siberian visit.

UNI Professor Andrey Petrov hold a piece of Lake Baikal during his recent Siberian visit. Credit: Andrey Petrov.

When I contacted Andrey Petrov a week ago, he was returning from the Irkutsk region of Siberia.

The University of Northern Iowa geography professor makes frequent visits to Siberia and other similarly remote – and cold – regions, including Canada’s Yukon Territory and northern Russia. This time he was interviewing residents of villages and towns near Lake Baikal about the region’s reindustrialization. In the last century the area had seen an inflow of industry that went bust. Now it’s rising again, thanks to the search for oil.

“Unfortunately, it’s warmer there than here,” Petrov said from Cedar Falls on Monday, when the thermometer was scraping to get above zero Fahrenheit. “It was pretty sunny there and it was probably 20s. … For them it’s warmer than usual.”

The extreme conditions and isolation are some of the reasons Petrov, a native Russian, returns to places like Irkutsk and Yellowknife. “I’m fascinated with the resilience of people living in difficult conditions,” he says, but the challenges facing Arctic communities go beyond the weather and distance.

Those challenges are the subject of a new project Petrov directs. Headquartered at UNI, the five-year program, supported with nearly $750,000 of National Science Foundation money, will knit researchers from multiple institutions around the globe’s northern regions. Their goal: understanding Arctic communities and how they can enhance their development, health and well being while preserving societies and ecosystems.

It’s a big job. Five years won’t be enough, Petrov says. Read the rest of this entry »

Documents hint at rationale for ISU fraud

In University research on January 21, 2014 at 2:11 pm
Graphic of the HIV virus structure

In this schematic of the Human Immunodeficiency Virus (HIV), the glycoproteins gp41 and gp120 are the base and tip, respectively, of the “spikes” protruding from the membrane. Credit: National Institute of Allergy and Infectious Diseases.

The saga of Dong-Pyou Han and his research misconduct continues.

Late last week, Iowa State University responded to my request for a report the university sent to the Office of Research Integrity (ORI) at the U.S. Department of Health and Human Services.

The documents include Han’s signed admission of how he spiked blood samples to make it appear rabbits developed antibodies to HIV, the AIDS virus.

Michael Cho, the project’s lead researcher, reported the suspected misconduct one year ago this week, and after an investigation stretching into August, pegged Han as the likely culprit. He resigned in October.

Han is the only researcher suspected in the fraud.

The Des Moines Register’s Tony Leys also received the documents – including emails concerning the investigation, which I did not request – and wrote a piece Thursday night. Another piece on Friday quotes Arthur Caplan, the go-to source when journalists need a comment on bioethics.

Leys’ initial story covers Han’s grammatically clumsy mea culpa but omits many details – including what appears to be his rationale for the whole fraud.

Read the rest of this entry »

Iowa State vaccine research scandal: an update

In University research on January 6, 2014 at 1:01 pm

Office of Research Integrity logoAt the time I wrote my last entry, about Iowa State University researcher Dong-Pyou Han’s admitted research misconduct, I had an email seeking additional information out to ISU spokesman John McCarroll.

I wasn’t sure how soon McCarroll would get back to me, given the skeleton staff ISU maintains during semester break, so I went ahead with the post, which raised questions about what kind of a deal Han may have reached to settle charges that he tampered with research for an AIDS vaccine.

McCarroll’s response, just before New Year’s Day, sheds some light on those questions – but not much.

Read the rest of this entry »

ISU scandal a science failure? Not so much

In University research on December 31, 2013 at 1:38 pm

In this blog, I usually highlight Iowa science developments that don’t get a lot of attention. If something is splashed across the headlines, I’ll generally let it go or say little about it. I want to concentrate on things most of the press misses.

What happened at Iowa State University just before Christmas, however, is too big and unusual to let pass: A federal agency announced sanctions against a professor for falsifying research.

The nature of the case and what it gained the offender are unusual. Since the offiense was revealed, bloggers and commentators also have cited it to support their views on everything from vaccinations to climate change.

Read the rest of this entry »

Selected shorts: crappy typing pays off, bone regrowth, and babies grasp food and words

In University research on December 5, 2013 at 12:08 pm
Some illegible scribbles from Tom O'Donnell's reporter's notebook.

A typical selection from my reporter’s notebook. Can you make out any of it?

Anyone who’s seen my handwriting would have a hard time mistaking it for someone else’s. The loops and slashes that fill my reporter’s notebooks are unmistakably mine, even if they’re indecipherable to most people. (Fortunately, I can read them… mostly.)

My typing, of course, is easily legible – even though my typing is pretty terrible. I’m able to erase the typos, blank spaces, merged words and other errors.

Now it turns out that my crappy typing is just as recognizable as my crappy handwriting. In fact, we each have a characteristic typing pattern, and some Iowa State University computer researchers are capitalizing on that to strengthen information security.

Read the rest of this entry »

Exoplanets from a somewhat different angle

In University research on October 27, 2013 at 11:15 pm
TILT TILT pinball machine

Photo credit: Dice.com via photopin cc

It’s often how the best scientific discoveries start: When a scientist says, “Well, that’s weird.”

That was pretty much Steve Kawaler’s reaction when he saw data from Kepler-56, one of dozens of stars NASA’s Kepler space telescope flagged as likely to have orbiting planets, known as exoplanets.

Kawaler, an Iowa State University professor of physics and astronomy, is part of a committee overseeing Kepler’s asteroseismic (no, that’s not a typo) research. Asteroseismology is a lot like Earth-bound seismology, Kawaler says. “It’s the same mathematics, the same physics” describing wave propagation and response to conditions like pressure.

But with stars 3,000 light-years away, as Kepler-56 is, scientists can’t plant monitors on the surface to detect and measure waves, like they do here. Instead, astronomers watch for subtle oscillations in light from the star. The frequency and magnitude of those oscillations, combined with readings from instruments like spectrometers, can tell astronomers a lot, including the radius, mass and age of a star and how fast it rotates.

Asteroseismology and other data seemed to tell Kawaler and others in an international team something about Kepler-56 and its planets that they had never seen before.

Read the rest of this entry »

ISU’s big computer on campus – and why it’s not as flashy as you might think

In University research on September 13, 2013 at 3:43 am
Arun Somani with Cyence, Iowa State University's new high-performance computer, at the Durham Center on campus

Arun Somani with Cyence, Iowa State University’s new high-performance computer, at the Durham Center on campus. Photo by Bob Elbert, ISU News Service.

Iowa State University made a splash late last month when it rolled out its latest high-performance computer, Cyence. News releases and stories touted the $2.6 million machine’s speed: just over 183 teraflops (trillion scientific calculations per second). It would take a single human 5 million to 6 million years to do as many calculations as Cyence can do in a second, the press said.

For ISU, it’s a terrific machine – although it’s a shadow of the world-class supercomputers at Department of Energy, Chinese and European laboratories. Cyence definitely will let ISU researchers do cool things, leading to insights that will advance science.

But the releases and the stories aren’t telling the full story. And they may paint a somewhat inaccurate picture of Cyence’s capabilities.

Read the rest of this entry »

Roundup: Van Allen belts give electrons a jolt, a super scanner and a flood study dries up

In Uncategorized, University research on August 26, 2013 at 5:00 am
Van Allen belts with graph of electron acceleration

Recent observations by NASA’s twin Van Allen Probes show that a local kick of energy accelerates particles in the radiation belts surrounding Earth. The readings help explain how these particles reach energies of 99 percent the speed of light. Image Credit: G. Reeves/M. Henderson

I was in knee pants when I first heard about the Van Allen radiation belts, the donut-shaped rings of charged particles circling the Earth. In the movie (and later television series), “Voyage to the Bottom of the Sea” the belts catch fire, threatening the planet with global warming at hyperspeed – an impossible apocalypse.

The belts were new and little explored then, and one of my siblings told me they were named for their discoverer, James Van Allen, a University of Iowa physicist and a born and bred Iowan. In typical chip-on-the-shoulder Iowa fashion (“Hey, we’re more than corn! We have scientists!”), I’ve been proud of that discovery and its name ever since.

Van Allen’s research brought prestige and fame to U of I’s physics department and attracted some top scientists. And almost 60 years after the belts’ discovery, the university’s research still yields new insights.

The latest, published last month, shows the belts act as a potent particle accelerator, pushing electrons to nearly light speed.

Read the rest of this entry »

Roundup: Obsessive mice, strange quasicrystals and the “peckscreen” (with video)

In Uncategorized, University research on June 16, 2013 at 2:19 pm
High-energy X-ray diffraction patterns from a single grain of iodine-gadolinium-cadmium taken at Argonne National Laboratory's powerful X-ray device, the Advanced Photon Source.

High-energy X-ray diffraction patterns from a
single grain of iodine-gadolinium-cadmium taken at Argonne National Laboratory’s powerful X-ray device, the Advanced Photon Source, with the beam parallel to the grain’s five-fold axis. Scientists can tell something about a material’s structure by the way it diffracts X-rays, with more powerful sources providing greater detail.

For this post, here’s a roundup of a few interesting Iowa science items over the last couple weeks, including obsessive-compulsive and obese mice, a new family of quasicrystals and pigeons pecking touchscreens. (In this case, shouldn’t they be called “peckscreens”?)

If you’re not in the fields associated with these projects, you may not have heard of them. As with a lot of other Iowa science, they didn’t get a lot of attention here at home.

Read the rest of this entry »

NASA flood study splashes down in Iowa

In Uncategorized, University research on June 11, 2013 at 1:17 am
NPOL radar south of Waterloo, Iowa, under a large anvil cloud with mammatus clouds.

NASA’s NPOL radar in late May, located south of Waterloo, Iowa, under a large anvil cloud with mammatus clouds. Copyright Brenda Dolan, Colorado State University.

If you want to study rainfall and floods to help improve satellite predictions of both, you couldn’t choose a better place this year than Iowa.

But Witold Krajewski and the researchers at the University of Iowa’s Iowa Flood Center didn’t know that last year, when they planned the project with NASA’S Goddard Space Flight Center.

Krajewski, the flood center’s director, was persuading NASA to base its study in Iowa because the state has no mountains and sea coasts, which sometimes make it difficult for radar to distinguish rainfall from other things. “We do have floods,” Krajewski says he told the NASA collaborators. “I wasn’t wishing for a flood, but I was saying this when we were in a drought.”

NASA took a chance, despite 2012’s dry weather, and it’s paid off with a rush of data that’s expected to improve computer forecast models’ ability to predict flooding. The study’s observational phase wraps up this week, after employing some powerful radar and a small army of rain gauges and soil moisture sensors.

Read the rest of this entry »

Checking the nursery in a baby star boom

In Uncategorized, University research on June 9, 2013 at 1:28 pm
Infrared composite image of NGC 6334, the Cat's Paw Nebula.

In this composite infrared image of NGC 6334, pink shows gas and dust that make up the nebula, illuminated by bright high-mass stars. Many young stars appear yellow to red and most are found buried within the dark clouds extending from the upper left to the lower right. High-mass stars peek into view by carving out bubbles within the dense clouds of gas and dust that formed them. Click on the image for a high-resolution version. Credit: Sarah Willis, Harvard-Smithsonian Center for Astrophysics; NASA/Jet propulsion Laboratory at Caltech/Spitzer Science Center; Cerro-Tololo Inter-American Observatory/National Optical Astronomical Observatory/Association of Universities for Research in Astronomy/National Science Foundation.

Scorpius is one of the few constellations I can regularly pick out in the summer sky. It often sits low on the southern horizon, with two bright stars marking its pincers and the red multiple star Antares highlighting its long body.

Scorpius, I learned last week, also is home to a star nursery. It’s difficult for amateurs to see, but Iowa State University graduate student Sarah Willis says it’s one of the Milky Way’s most active star-forming regions. In a paper delivered last week at the American Astronomical Society meeting in Indianapolis, Willis described this “star burst,” which is generating tens of thousands of new objects. Read the rest of this entry »

Snail episode illustrates science news’ slow crawl

In Uncategorized, University research on April 22, 2013 at 5:36 pm
snail dime

The tiny shells of the New Zealand mud snail. U.S. Geological Survey photo.

Since I posted it about a week ago, more than 2,000 visitors have read my report on the conservative criticism directed at University of Iowa professors Maurine Neiman and John Logsdon. Along with Jeffrey Boore at the University of California, Berkeley, they study the genetic makeup of two genetic lines of a New Zealand snail, one of which reproduces sexually and the other asexually.

Their goal is to elucidate the genetic foundation for sexual reproduction. But conservative websites, bloggers and pundits from Michelle Malkin to Fox News blasted the four-year, National Science Foundation grant as a waste of tax money for studying “snail sex.” The big number of hits (thanks in large part to Logsdon and Neiman spreading the word) indicates how interested people are in the intersection of science, government and politics.

What’s surprising is how big this was on conservative media, but how other press – even Iowa news operations – missed the story. Read the rest of this entry »

U of I professors slimed for their snail research

In University research on April 15, 2013 at 1:00 pm
snails

Potamopyrgus antipodarum, the New Zealand snail under scrutiny. Image © Bart Zijlstra / http://www.bartzijlstra.com via University of Iowa.

At first, it may sound completely ridiculous: a four-year, $876,000 grant from the federal National Science Foundation (NSF) to study “snail sex.”

That’s how a conservative news website branded it – wrongly. And it’s how two University of Iowa researchers and their California colleague found themselves at the center of the latest debate on government’s role in supporting basic science research, a debate that started with a similar attack on duck penis research. Read the rest of this entry »

Pardon me, but there’s a bioplastic in my froyo

In University research on March 5, 2013 at 1:27 pm
medium_4506658849

photo credit: timlewisnm via photopin cc

Not long ago, I took the teenager to an Orange Leaf frozen yogurt shop. It was kind of bizarre, facing off against a bank of machines dispensing flavors like birthday cake and lychee. I think the kid got a bit of every kind. He didn’t finish.

What this has to do with Iowa science is the shovel-like plastic spoon I used. I happened to look at the back of the handle and saw something surprising.

Read the rest of this entry »

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