Category Archives: Science

Tracking Changes in Individual Molecules

Watching a Biological Jigsaw Puzzle Come Together

Scientists have recorded the action involved in assembling telomerase, an enzyme used by cells to protect their genes during the potentially dangerous process of DNA replication. Using a sophisticated technique for tracking structural changes in individual molecules in real time, they have revealed how three of the protein and RNA components of the enzyme come together, altering their shapes along the way to ensure that the next piece will fit.
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In these more complicated systems, it’s much harder to guess what is going on in the assembly process. But by directly watching things as they happen, this sort of powerful approach will give a lot of new insights.

Very cool stuff. It just keeps coming doesn’t it?

Economic Gains from Science

Gaze into future for state’s economy:

For policymakers, that means: Invest in the state’s educational system, especially the University of Wisconsin System, and use tax policy to encourage investors to supply the money to make business ideas grow.
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TomoTherapy, 10 years old, already employs 500 people. Co-founded by two UW-Madison professors, it was financially backed by investment groups in Madison, Milwaukee and California. The next step may be to follow Madison-area high-tech businesses Third Wave and Sonic Foundry into the public stock market.

GenTel, employing 17, started at University Research Park, has moved to Fitchburg and plans to open an office in North Carolina. The company has found additional financing from investors, including groups in Madison and Appleton. Aruna sprouted from brainpower and research at the University of Georgia, but it licenses human em bryonic stem cell technology from the Wisconsin Alumni Research Foundation. Because UW-Madison is a hotbed of stem cell research, moving its jobs and income to Wisconsin would make sense.

Fighting Elephant Poaching With Science

DNA Technology Leads Scientists to Locations of Elephant Poaching:

The illegal trade in elephant ivory continues unabated despite the fact that it was banned by international convention in 1989. In an effort to hunt down poachers who slaughter thousands of elephants a year for the animals’ tusks, scientists have turned to DNA technology to narrow the search.
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But to pinpoint the precise origin of the tusks can tell authorities where elephants are being slaughtered and which routes are being used to transport the illegal tusks. Armed with this information, the enforcement authorities would find it easier to track down poachers.
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Wasser led a group of researchers who performed a DNA analysis on 67 tusks confiscated in the 2002 Singapore seizure. The genetic material was compared to an existing database of elephant DNA. The researchers determined with near “100 percent accuracy” that the poached elephants came from the savanna within a narrow band of Southern Africa — possibly extending from Mozambique to Angola — with Zambia at its center.

Excellent use of science to gain knowledge which can help determine where best to put effort to counteract poaching.

Correlation is Not Causation

Why so much medical research is rot:

People born under the astrological sign of Leo are 15% more likely to be admitted to hospital with gastric bleeding than those born under the other 11 signs. Sagittarians are 38% more likely than others to land up there because of a broken arm. Those are the conclusions that many medical researchers would be forced to make from a set of data presented to the American Association for the Advancement of Science by Peter Austin of the Institute for Clinical Evaluative Sciences in Toronto. At least, they would be forced to draw them if they applied the lax statistical methods of their own work to the records of hospital admissions in Ontario, Canada, used by Dr Austin.

Dr Austin, of course, does not draw those conclusions. His point was to shock medical researchers into using better statistics, because the ones they routinely employ today run the risk of identifying relationships when, in fact, there are none. He also wanted to explain why so many health claims that look important when they are first made are not substantiated in later studies.

As I said in, Seeing Patterns Where None Exists: “Page 8 of Statistics for Experimenters by George Box, William Hunter (my father) and Stu Hunter (no relation) shows a graph of the population (of people) versus the number of storks which shows a high correlation. “Although in this example few would be led to hypothesize that the increase in the number of storks caused the observed increase in population, investigators are sometimes guilty of this kind of mistake in other contexts.'”

Savanna Chimpanzees Hunt with Tools

Savanna Chimpanzees, Pan troglodytes verus, Hunt with Tools by Jill D. Pruetz and Paco Bertolani:

Broken link removed. See updated post: Chimpanzees Use Spears to Hunt Bush Babies

Although tool use is known to occur in species ranging from naked mole rats to owls, chimpanzees are the most accomplished tool users. The modification and use of tools during hunting, however, is still considered to be a uniquely human trait among primates. Here, we report the first account of habitual tool use during vertebrate hunting by nonhumans. At the Fongoli site in Senegal, we observed ten different chimpanzees use tools to hunt prosimian prey in 22 bouts. This includes immature chimpanzees and females, members of age-sex classes not normally characterized by extensive hunting behavior. Chimpanzees made 26 different tools, and we were able to recover and analyze 12 of these.

Scientifically Illiterate

216 Million Americans Are Scientifically Illiterate:

Let’s start by focusing on the positive. In just 17 years, over 50 million people have been added to the rolls of Americans who can understand a newspaper story about science or technology, according to findings presented last weekend at the American Academy for the Advancement of Science’s annual meeting in San Francisco.

Michigan State University political scientist Jon D. Miller, who conducted the study, attributed some of the increase in science literacy to colleges, many of which in recent years have required that students take at least one science course. Miller says people have also added to their understanding through informal learning: reading articles and watching science reports on television.

Okay, now let’s talk (dare I say rant?) about the 200 million Americans out there who cannot read a simple story in, say, Technology Review or the New York Times science section and understand even the basics of DNA or microchips or global warming.

This level of science illiteracy may explain why over 40 percent of Americans do not believe in evolution and about 20 percent, when asked if the earth orbits the sun or vice versa, say it’s the sun that does the orbiting–placing these people in the same camp as the Inquisition that punished Galileo almost 400 years ago.

Antarctic Robo-sub

Robo-sub takes Antarctic plunge

The submersible, which when not at sea is based at the National Oceanography Centre, Southampton, is built to withstand enormous pressure and can dive to depths of 6.5km (four miles). It is equipped with a number of instruments, including cameras, sonars, and sample-collectors that are deployed using its mechanical arms. It is tethered to its “mothership” – on this expedition the RSS James Clark Ross – with a 10km (6 miles) cable.

Scientists manoeuvre the ROV from a control room onboard the ship, and can see the data it produces in real-time. Professor Dowdeswell said: “When you are sat there in the control room, surrounded by monitors, you really feel that you are down at the sea bed with the ROV. You have to pinch yourself to remember that you are not.”
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Professor Tyler, like Professor Dowdeswell, deemed the mission a success: “The wealth and diversity of the fauna in this area was incredible. “We knew it would be diverse, but when you think the area we were looking at is totally ice-covered for about six to nine months of the year, this is extremely interesting.”

Karl Popper Webcast

Webcast discussing Karl Popper’s ideas by Melvyn Bragg with John Worrall, Anthony O’Hear and Nancy Cartwright, BBC (by the way, the BBC does a wonderful job of running web properties – presenting great material and they don’t break web links by removing content).

Karl Popper is one of the most significant philosophers of the 20th Century, whose ideas about science and politics robustly challenged the accepted ideas of the day. He strongly resisted the prevailing empiricist consensus that scientists’ theories could be proved true.

Popper wrote: “The more we learn about the world and the deeper our learning, the more conscious, specific and articulate will be our knowledge of what we do not know, our knowledge of our ignorance”. He believed that even when a scientific principle had been successfully and repeatedly tested, it was not necessarily true. Instead it had simply not proved false, yet! This became known as the theory of falsification.

He called for a clear demarcation between good science, in which theories are constantly challenged, and what he called “pseudo sciences” which couldn’t be tested.

Biomolecules in Motion

Biomolecules in Motion by Kathleen M. Wong:

Proteins are the parts that make living engines run. They supply cells with energy, build muscle and bone, and catalyze countless other reactions that let the spark of life burn bright. To do their jobs, proteins must curl around substrate molecules, stretch to let their substrates go, travel around cells and assemble into work crews.
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Scientists have long believed that when an enzyme is empty, it gapes open like a hungry alligator, and that after it has caught its substrate, it remains closed until the reaction has been completed. Yang’s single-molecule microscopy studies have turned this notion upside-down. “Even when it has substrate, it doesn’t just bind the substrate tightly and stop moving. It’s still flapping,” he says. This constant motion makes perfect sense, considering how fast enzymes operate; some can process a million substrate molecules per minute. “Like a door, it has to be able to swing even without me going in and out.

Seeing Patterns Where None Exists

I call data dredge studies the “Rorschach tests” of epidemiology, because researchers can pull out characteristics about people in almost unlimited combinations to find all sorts of correlations and conclude just about anything they set out to find. Just like the Rorschach test, seeing patterns where none exists, finding connections that are there but not as strongly as believed, and seeing what one expects to see, are common.

Page 8 of Statistics for Experiments by George Box, Willliam Hunter (my father) and Stu Hunter (no relation) shows a graph of the population (of people) versus the number of storks which shows a high correlation. “Although in this example few would be led to hypothesize that the increase in the number of storks caused the observed increase in population, investigators are sometimes guilty of this kind of mistake in other contexts.” And some might make it in this context 🙂