Category Archives: Science

Remove the Identical Stretches of DNA Found in Mice, Rats, and Humans and What Happens?

A Real Genetic Headscratcher by Derek Lowe:

As you root through genomic sequences – and there are more and more of them to root through these days – you come across some stretches of DNA that hardly seem to vary at all. The hard-core “ultraconserved” parts, first identified in 2004, are absolutely identical between mice, rats, and humans.
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Even important enzyme sequences vary a bit among the three species, so what could these pristine stretches (some of which are hundreds of base pairs long) be used for? The assumption, naturally, has been that whatever it is, it must be mighty important, but if we’re going to be scientists, we can’t just go around assuming that what we think must be right. A team at Lawrence Berkeley and the DOE put things to the test recently by identifying four of the ultraconserved elements that all seem to be located next to critical genes – and deleting them.

The knockout mice turned out to do something very surprising indeed. They were born normally, but then they grew up normally. When they reached adulthood, though, they were completely normal. Exhaustive biochemical and behavioral tests finally uncovered the truth: they’re basically indistinguishable from the wild type. Hey, I told you it was surprising. This must have been the last thing that the researchers expected.

What a great example of scientists at work. It will be interesting to see where this goes.

Math and Science Education Assessment

Science Friday podcast (NPR radio programming) on the urban institute study mentioned a few weeks ago in: The Importance of Science Education.

Conventional wisdom says that U.S. students don’t measure up well against students in many foreign countries when it comes to math and science skills. But is that really true? A team of researchers have re-assessed the results of several common measures of science education success, and they say the true picture may not be as gloomy as some analysts have said.

“When it comes to math and science, American students are no worse, and often score better, than students from many leading countries,” said Harold Salzman, one of the authors of the new Urban Institute report “Into the Eye of the Storm: Assessing the Evidence on Science and Engineering Education, Quality, and Workforce Demand.” The researchers argue that some of the rankings produced by measures such as the Trends in International Mathematics and Science Study (TIMSS) are due to statistically insignificant differences in scoring.

Read the actual report – Into the Eye of the Storm, Assessing the Evidence on Science and Engineering Education, Quality, and Workforce Demand by B. Lindsay Lowell, Harold Salzman.

Scientists Chart Record Rise in Yellowstone Caldera

Scientists chart record rise in Yellowstone caldera

The floor of Yellowstone National Park’s gigantic volcano has been rising at a record rate in recent years, probably due to an underground blob of molten rock more than 14 times the size of Billings, according to a new study. The Yellowstone caldera rose nearly 3 inches a year for the past three years, faster than anyone has ever recorded. “These are rates three times (greater) than previous historic rates,” said University of Utah seismologist Bob Smith, a lead author of the study to be published in the journal Science today.

But that rapid rising isn’t an indication of an imminent volcanic eruption or hydrothermal explosion at Yellowstone, he said. It appears in line with behavior at other volcanic craters that rise and fall for thousands of years without large-scale, catastrophic eruptions. “These things go up and down,” Smith said. “That’s very common for calderas globally.”

The researchers believe the 463-square-mile slab formed from molten rock in the magma chamber beneath Yellowstone, causing the surface of the caldera to rise.

New and Old Ways to Make Flu Vaccines

New and Old Ways to Make Flu Vaccines by Nell Greenfieldboyce, NPR:

Standard Practice
Pros: Millions of Americans receive this [standard] vaccine every year. It’s safe and well tolerated. Its production begins in hens’ eggs — a tried and true technology for 50 years.
Cons: Eggs must be ordered many months in advance, and millions of doses require millions of eggs.

Live-Attenuated Vaccine
Pros: This newer method of production results in a vaccine that has a flu virus that is crippled, so it can’t cause disease. But the virus is not killed, as is the case in the standard vaccine. The vaccine also can be given as a nasal spray.
Cons: More expensive than standard vaccine, and also produced in eggs. Not approved for young children or older people.

Cell-Based Vaccine
Pros: This vaccine can be produced in giant vats of living cells. Such a production method means it can be scaled up much faster than egg-based vaccines, making it more useful in a pandemic. Several versions have been tested successfully in people.
Cons: Won’t be widely available for a few years. Clinical trials are under way, but no flu vaccine made this way is currently approved by the Food and Drug Administration.

Vast Garbage Float in the Pacific Ocean

Feds want to survey, possibly clean up vast garbage pit in Pacific:

Charles Moore, the marine researcher at the Algalita Marina Research Foundation in Long Beach who has been studying and publicizing the patch for the past 10 years, said the debris – which he estimates weighs 3 million tons and covers an area twice the size of Texas – is made up mostly of fine plastic chips and is impossible to skim out of the ocean. “Any attempt to remove that much plastic from the oceans – it boggles the mind,” Moore said from Hawaii, where his crew is docked. “There’s just too much, and the ocean is just too big.”

The trash collects in one area, known as the North Pacific Gyre, due to a clockwise trade wind that circulates along the Pacific Rim. It accumulates the same way bubbles gather at the center of hot tub, Moore said. A two-liter plastic bottle that begins its voyage from a storm drain in San Francisco will get pulled into the gyre and take weeks to reach its place among the other debris in the Garbage Patch. While the bottle floats along, instead of biodegrading, it will “photodegrade,” Moore said – the sun’s UV rays will turn the bottle brittle, much like they would crack the vinyl on a car roof. They will break down the bottle into small pieces and, in some cases, into particles as fine as dust.

Open Access Legislation May Be Included in HHS Budget Bill

Open Access to Research Funded by U.S. Is at Issue by Rick Weiss:

The idea is that consumers should not have to buy expensive scientific journal subscriptions — or be subject to pricey per-page charges for nonsubscribers — to see the results of research they have already paid for with their taxes. Until now, repeated efforts to legislate such a mandate have failed under pressure from the well-heeled journal publishing industry and some nonprofit scientific societies whose educational activities are supported by the profits from journals that they publish.

But proponents — including patient advocates, who want easy access to the latest biomedical findings, and cash-strapped libraries looking for ways to temper escalating subscription costs — have parlayed their consumer-friendly “public access” message into legislative language that has made it into the Senate and House versions of the new HHS bill.

The opponents of open science are lobbying to keep scientific research funded by taxpayers unavailable to the public. As I have said before it is time to stop supporting those who attempt to stop scientific progress. The out of date thinking behind closed access journals should be discouraged and those journals fighting progress should not be supported. This legislation would bring openness to federal research in a similar manner to the steps taken by Howard Hughes Medical Institute announced for research they fund.

The Study of Bee Colony Collapses Continues

The attempts to discover the causes of the die off of bees in the USA continues. This effort provides a good example of the difficulty of learning what really happens around us. Often, once things are worked out, and explained they seem simple and even obvious. But while trying to figure events taking place (like the bee colony collapses), scientists have significant challenges. The hard work and the application of scientific concepts by scientists allow us to learn and adapt. I think the difficulty can paint a valuable picture of what science is about. That search for understanding is wonderful to see and something fundamental to the human experience. Disappearing Bee Mystery Deepens

One year ago, beekeepers across the country began to report that worker bees were inexplicably abandoning their hives and leaving the brood to die. Although firm statistics are hard to come by, so-called colony collapse disorder may have afflicted as many as 25% of U.S. beekeepers and perhaps others around the world. Possible culprits included pesticides, parasites, and chronic stress from poor nutrition and the long-distance truck rides that many commercial hives undergo.
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For that matter, no one has yet shown that IAPV can cause colonies to collapse. “Until you have introduced the virus and caused disease, you’re just postulating,” cautions Bruce Webb, an entomologist at the University of Kentucky in Lexington. “The conclusive data are not in.”

Presidential Early Career Awards for Scientists and Engineers

The Presidential Early Career Awards for Scientists and Engineers, established in 1996, honors the most promising researchers in the Nation within their fields. Nine federal departments and agencies annually nominate scientists and engineers who are at the start of their independent careers and whose work shows exceptional promise for leadership at the frontiers of scientific knowledge. Participating agencies award these talented scientists and engineers with up to five years of funding to further their research in support of critical government missions.

Awards were announced today – links to some of the awardees:

Jelena Vuckovic, Assistant Professor of Electrical Engineering, Stanford University
Matthew Rodell, Physical Scientist, NASA
Katerina Akassoglou, Assistant Professor of Pharmacology, University of California, San Diego
Carlos Rinaldi, Associate Professor of Chemical Engineering University of Puerto Rico at MayagÃ¼ez
Ahna Skop, Assistant Professor of Genetics, University of Wisconsin-Madison
Krystyn J. Van Vliet, Assistant Professor of Materials Science and Engineering, MIT
Odest Chadwicke Jenkins, Assistant Professor, Department of Computer Science, Brown University

The Importance of Science Education

The Science Education Myth by Vivek Wadhwa:

The authors of the report, the Urban Institute’s Hal Salzman and Georgetown University professor Lindsay Lowell, show that math, science, and reading test scores at the primary and secondary level have increased over the past two decades, and U.S. students are now close to the top of international rankings. Perhaps just as surprising, the report finds that our education system actually produces more science and engineering graduates than the market demands.

The study certainly sounds interesting. I can’t find it (update Vivek Wadhwa provided the link – which will work Monday, also see his comment below), but found an article (which wasn’t easy) by the authors of the report: The Real Technology Challenge. The main point of the article, The Real Technology Challenge, seems to be that the USA should focus on globalization (and focus on educating scientists and engineers to work in a global world).

As I have said before I disagree with those that believe the USA is producing more science and engineering graduates than the market demands. Smart leaders know the huge positive impacts of a large, well educated science and engineering workforce.

Countries that succeed in producing more quality graduates while creating the best economic environment to take advantage of technology innovation (follow this link – it is one of the most important posts about what makes silicon valley so powerful a force at doing just that) are going to benefit greatly. My guess is the USA will be one of those countries; not by reducing the focus on science and engineering education but by increasing it. If not, other countries will, and the USA will suffer economically. The USA also needs to continue to push the economic and entrepreneurship advantages – doing that well is very difficult to achieve and the USA maintains a stronger advantage in that realm – but I will be very surprised if other countries don’t continue to make gains in this area. Even so doing so is much more challenging than just improving education (which is difficult itself just not nearly as difficult) and the USA can continue to benefit from this combination with the right policies.

Primary Science Education in California

Lawrence Hall of Science at the University of California, Berkeley Science Survey:

California, including the San Francisco Bay Area, is home to much US innovation in science and technology. Recent national reports have illuminated the importance of science education in the elementary grades and described concerns for US leadership in science,1 the importance of fostering interest in science early in life,2 and issues with promoting high quality science instruction in the elementary grades,3 nationally,4 and in California.5

At the same time, this region produces inadequate achievement results among its students. Results of the 2005 National Assessment of Education Progress 4th grade science test indicate that California ranked 2nd lowest of all states on eighth grade science achievement, only above Mississippi. During spring 2007, results on the 5th grade California Standards Test (CST) in Science indicate that only 37% of California students and approximately 46% of Bay Area students scored proficient or above6. This means that even in the Bay Area, over half the 5th graders are failing to reach proficiency in science.
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Eighty percent (80%) of K–5th grade multiple-subject teachers who are responsible for teaching science in their classrooms reported spending 60 minutes or less per week on science, with 16% of teachers spending no time at all on science.