Jeber’s

Holdren to be named Science Adviser

Finally, after eight years of disdain for the scientific community, we could be getting not just a scientific adviser but a scientific adviser who actually understands the issues facing our country.

Harvard physicist John P. Holdren, a leading authority on global warming and a past president of the nation’s largest organization of scientists, will be President-elect Barack Obama’s science adviser.

Holdren, who was an adviser to the Obama campaign, is a professor of environmental policy and director of the Program on Science, Technology, and Public Policy at Harvard’s Kennedy School of Government and also is director of the Woods Hole Research Center in Falmouth, and a past-president of the American Association for the Advancement of Science.

Holdren’s work has focused on climate change, energy technology and policy, and nuclear proliferation.

“I think if he is appointed he will send a signal to the scientific community, which has been disenchanted in the current administration, that science is very important and will be listened to,” said Sheila Jasanoff, a Kennedy School colleague of Holdren’s who has written extensively about the role of scientific advice in a democracy.

In August, Holdren published an opinion piece in the Globe chastising skeptics of global warming. “The extent of unfounded skepticism about the disruption of global climate by human-produced greenhouse gases is not just regrettable, it is dangerous,” he wrote. “It has delayed — and continues to delay — the development of the political consensus that will be needed if society is to embrace remedies commensurate with the challenge.”

That political consensus will be at the heart of the mission of Obama’s science advisor. The president-elect has clearly stated his intentions to take the issue head-on, saying he would vigorously move ahead with efforts to promote alternative energy sources such as wind and solar and reduce carbon emissions that cause global warming.

AAAS Chief Executive Officer Alan I. Leshner called the apparent appointment “enlightened” in a statement. “John Holdren’s expertise spans so many issues of great concern at this point in history — climate change, energy and energy technology, nuclear proliferation,” he said. “He is widely respected in the United States and around the world as a science leader.” (Source-boston.com)

Holdren has an extensive biography.

John P. Holdren is the Teresa and John Heinz Professor of Environmental Policy and Director of the Program on Science, Technology, and Public Policy in the Belfer Center for Science and International Affairs, John F. Kennedy School of Government, Harvard University. He is also Professor of Environmental Science and Public Policy in Harvard’s Department of Earth and Planetary Sciences and Director of the Woods Hole Research Center.

Trained in engineering and plasma physics at MIT and Stanford, Dr. Holdren co-founded in 1973 and co-led for 23 years the interdisciplinary graduate program in energy and resources at the University of California, Berkeley. His work has focused on causes and consequences of global environmental change, options and choices in energy technology and policy, ways to reduce the dangers from nuclear weapons and materials, and the interaction of content and process in science and technology policy.

He is a member of the National Academy of Sciences (NAS), the National Academy of Engineering (NAE), the American Academy of Arts and Sciences, and the Council on Foreign Relations, and Past President of the American Association for the Advancement of Science. From 1993 through 2004 he served as Chair of the NAS Committee on International Security and Arms Control, leading it over the course of multi-year studies on management of excess weapon plutonium, the future of US nuclear weapons policy, technical issues related to the ratification of the Comprehensive Nuclear Test Ban Treaty, and monitoring and verification of nuclear warheads and materials. He was a member of President Clinton’s Committee of Advisors on Science and Technology (PCAST) from 1994 to 2001 and, in this capacity, chaired PCAST studies on nuclear materials protection, federal energy R&D strategy for the challenges of the 21st century, and international cooperation on energy-technology innovation. In December 1995 he delivered the Nobel Peace Prize acceptance lecture on behalf of the Pugwash Conferences on Science and World Affairs, which he served as Chair of the Executive Committee from 1987 to 1997. From 2002 until the present he has been Co-Chair of the foundation-funded, bipartisan National Commission on Energy Policy. (Source-Contribution to farber.net newsletter)

Like angels dancing on the head of a pin

Ever notice that microscopic dimensions are often given in relation to the width of a single human hair? “That fiber there is less than a third the width of a single human hair.” It must be important to mention a “single” hair. Scientists don’t want us thinking they’re talking about our entire head.

Do you know “off the top of your head” how wide one of your hairs is? Upon hearing something like the above, do you immediately reach up, yank out a hair (sorry my bald friends, you can use armpit hair) and stare at it trying to conceptualize a third of it?

They ought to just state the measurement for all the good it’s doing them to try and create a metaphor for something that thin. And use the metric system. We don’t know what that’s all about, either.

And while I’m on the subject of worn-out metaphors, on the other end of the scale, why is everything compared to the length of a football field? Why not say 100 yards? Not everybody’s a fan of U.S. football. There’s also the economy of words to consider.

People need to use clichès and metaphors selectively, carefully. Sometimes they make more mischief than provide clarity.

Scientists find missing evolutionary link using tiny fungus crystal

Creationists like to latch on to minor points to try and make major claims. One of the more popular latch points for them is the transition from single cell, or simple, lifeforms to the more complex, multicellular forms. Since up until now science has not had a ready explanation for that jump, creationists and the ID crowd want to assume that god must have been responsible. It does no good to tell these people that just because we don’t have an answer to the “how” in many of nature’s processes this does not lead logically to a conclusion that “god did it”.

Well, now we are a bit closer to understanding that change from simple to complex life, and there’s still no sign of a god’s involvement.

The crystal structure of a molecule from a primitive fungus has served as a time machine to show researchers more about the evolution of life from the simple to the complex.

By studying the three-dimensional version of the fungus protein bound to an RNA molecule, scientists from Purdue University and the University of Texas at Austin have been able to visualize how life progressed from an early self-replicating molecule that also performed chemical reactions to one in which proteins assumed some of the work.

“Now we can see how RNA progressed to share functions with proteins,” said Alan Lambowitz, director of the University of Texas Institute for Cellular and Molecular Biology. “This was a critical missing step.”

Results of the study were published in Thursday’s (Jan. 3) issue of the journal Nature.

“It’s thought that RNA, or a molecule like it, may have been among the first molecules of life, both carrying genetic code that can be transmitted from generation to generation and folding into structures so these molecules could work inside cells,” said Purdue structural biologist Barbara Golden. “At some point, RNA evolved and became capable of making proteins. At that point, proteins started taking over roles that RNA played previously – acting as catalysts and building structures in cells.”

In order to show this and learn more about the evolution from RNA to more complex life forms, Lambowitz and Paul Paukstelis, lead author and a research scientist at the Texas institute, needed to be able to see how the fungus’ protein worked. That’s where Golden’s team joined the effort and crystallized the molecule at Purdue’s macromolecular crystallization facility.

“Obviously, we can’t see the process of moving from RNA to RNA and proteins and then to DNA, without a time machine,” Golden said. “But by using this fungus protein, we can see this process occurring in modern life.”

Looking at the crystal, the scientists saw two things, Golden said. One was that this protein uses two completely different molecular surfaces to perform its two roles. The second is that the protein seems to perform the same job that RNA performed in other simple organisms.

“The crystal structure provides a snapshot of how, during evolution, protein molecules came to assist RNA molecules in their biological functions and ultimately assumed roles previously played by RNA,” Golden said.

The rest of the article, and a cool animation of the crystal, at: http://news.uns.purdue.edu/x/2008a/080102GoldenEnzyme.html

ID, it deserves to be Expelled

Writing on the ScienceBlogs, pharyngula is someone I read daily. A while ago he posted this video, which he describes better than I ever could, and attempts to correct a few of the glaring misconceptions spouted by O’Reilly and Stein.

Two people vying to out-stupid each other

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Evolution (or as he called it, “Darwinism”) is a weak theory with many gaps that was fit for the 19th century, but not the 21st. This is a ludicrous statement; Darwin would scarcely recognize what we were talking about if he attended an evolutionary biology conference today. We’ve added genetics, population genetics, molecular biology, and developmental biology to the heart of the theory.
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ID is an effort to fill in the gaps, and is a sincere effort to add new knowledge to the theory. That’s false. Look at the books written by IDists: from Darwin’s Black Box to Icons of Evolution to The Edge of Evolution, they are all about complaining about evolution while providing no new useful suggestions for research.
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This is a free speech issue, we just want to be able to express our side of the story. I don’t see anyone rushing to censor Fox News, or shutting down the printing presses that dare to publish Behe’s or Gonzalez’s books. This is not about free speech, and no one’s speech is being restricted. It is about quality education: will we have our kids taught baseless nonsense because some people want to smuggle their idiosyncratic religious beliefs into the classroom? It’s about quality research: shall we fund and support unproductive and scientifically indefensible ideas because a third-rate character actor likes them? It’s about defending what science is: science is not about wishing something were true and inventing excuse for it; it’s about serious self-criticism and substantial work going into testing ideas. ID simply isn’t science.

I think we get a good glimpse of the dogmatic and dishonest tack Expelled is going to take. It’s going to be one solid wall of lies, insisting that we must privilege the hypothesis that “a deity created life” with the same seriousness that we do population genetics or the biochemistry of abiogenesis.

Has anyone who doesn’t buy into the whole Intelligent Design nonsense seen this movie yet? I’d love to read an objective review.

Tied Up in Knots

From ScienceNewsOnline:

Call it Murphy’s Law of knots: If something can get tangled up, it will. “Anything that’s long and flexible seems to somehow end up knotted,” says Andrew Belmonte, an applied mathematician at Pennsylvania State University in University Park. Belmonte has plenty of alarming anecdotal evidence. “It certainly happens in my house, with the cords of the venetian blind.” But the knot scourge is a global one, as anyone who owns a desktop computer can confirm after peeking at the mess of connection cables and power cords behind the desk.

Now, scientists think they may have found out how and why things find their way into knotty arrangements. By tumbling a string of rope inside a box, biophysicists Dorian Raymer and Douglas Smith have discovered that knots—even complex knots—form surprisingly fast and often. The string first coils up, and then its free ends swivel around the other coils, tracing a random path among them. That essentially makes the coils into a braid, producing knots, the scientists say.

The results’ relevance may go well beyond explaining the epidemic of tangled venetian blind cords. That’s because spontaneous knots seem to be prevalent in nature, especially in biological molecules. For example, knottiness may be crucial to the workings of certain proteins (see “Knots in Proteins”). And knots can randomly form in DNA, hampering duplication or gene expression—so much so that living cells deploy special knot-chopping enzymes.

But even if Raymer and Smith’s results don’t prove to be directly relevant to the molecules of life, they are “a very good beginning” for a general study of physical knots, according to Belmonte. “Now we can at least ask these questions: Are there universal laws of knots?”

I find knots fascinating.  Chaotic systems tend to boggle the mind, and having your mind boggled now and then keeps it well exercised.  Another chaotic state that often frustrates scientists is turbulence.

A report from USA Today:

Turbulence does more than toss around luggage on airplanes and spill coffee on traveler’s laps — it confuses the heck out of scientists. A new experiment may suggest why — fluid dynamicists may have been missing something fundamental about turbulence for a good long time.

Renowned physicist Richard Feynman called turbulence the most important unsolved problem of classical physics, the body of engineering knowledge stretching roughly from Archimedes to Einstein. No one really understands precisely how the flow of gas or liquids transitions from smooth flow to choppy turbulence (not even something as simple as the point at which water from your tap goes from a smooth, or laminar, translucence to burbling foam.)

This drives engineers nuts (I can attest to this as a former engineer) because turbulence disrupts and drags air, gas and liquids that flow in and on everything from pipelines to airplane wings to artificial heart valves — all the apparatus of an industrial society — in ways both costly and unpredictable. To take just one example, turbulence costs U.S. airlines an annual $100 million due to injuries and delays, according to the National Center for Atmospheric Research’s estimates.

Naturally, we do know some things about turbulence, observations that pertain to air, gas and liquids alike. “Generally, the motion of fluids is smooth and laminar at low speeds but becomes highly disordered and turbulent as the velocity increases,” notes a paper by a physics team led by Bjorn Hof of the United Kingdom’s University of Manchester in the current Nature. After making the full-fledged transition from smooth to turbulent flow, the paper adds, “it is generally assumed that, under steady conditions, the turbulent state will persist indefinitely.”

Whoops, maybe not. Experiments described by Hof’s team suggests that assumption may be wrong. The finding in fact suggests that turbulence may be reversible, contradicting decades of engineering dogma, and offering unexpected insight into how turbulence works.

The team looked at turbulence in an pipe nearly 100 feet long with an internal diameter of about 0.16 inches, allowing for turbulence observation times about 10 times longer than those undertaken by any other lab facility, the team contends. By injecting water into water flowing down the pipe to create “turbulent puffs,” the team attempted to measure whether turbulence persisted under different flow conditions. Turbulence cuts the speed of the water flowing out of the center of the pipe about 30% while increasing flow speed on the pipe’s walls, so that water flowing smoothly out of the pipe emerges with a differently-shaped jet than turbulent flow, making the measurements easy.

“In contrast to previous findings,” the team found that turbulence in the pipe always returned to smooth flows, if one waited long enough. The finding suggests that rather than turbulence obliterating smooth flow, fluids somehow retain the ability to reorganize themselves back into a regular pattern.

“This is a conceptual shift and a very intriguing one,” says mechanical engineer Charles Meneveau of the Turbulence Research Group at Johns Hopkins University in Baltimore. “There are big implications for control of pipe flow,” he says, cautioning that the results must now be confirmed by other researchers.

Let’s focus on that last sentence for a moment.  This is what separates scientific inquiry from religious belief; postulations in science are either confirmed or dismissed by other scientists conducting their own experiments, and those findings are tested, as are those findings.  Contrary evidence can derail a promising hypothesis.  In religion, evidence is “faith” based and purely personal.  Lack of evidence is dismissed, and nothing is presented that can be verified empirically.

I hope these articles get your new year started with an exercised brain.

2008 National High School Essay Contest

From Alliance for Science:
2008 National High School Essay Contest
For our second annual National High School Essay Contest we invite students to submit essays of not more than 1,000 words on one of two topics — “Climate and Evolution” or “Agriculture and Evolution.”

Submission deadline is February 29, 2008.

Student prizes start with $300 for first place, and includes incentives for sponsoring teachers. Watch those word counts! Several essays among our early submissions have no word count on the registration form, or the word count is over 1,000. Read the Official Rules – essays must be no longer than 1,000 words!

Eligibility:

All students in grade twelve or below in the United States or U.S. territories. Eligible students must be attending a public, private, parochial school, home school or participating in a high school correspondence program. Eligibility of
prospective winners will be verified before the award of any prizes. Alliance for Science members and their families are not eligible. Essay contest judges and their families are also not eligible.

Essay Ideas:

Throughout the ages, the earth has undergone major climate change. Some present-day cities were once covered in sheets of ice and some temperate zones were once lush tropics. These changes had a significant effect on the types of animals that thrived and the species that became extinct. If climate change speeds up, what will happen to the environments where endangered animals now live? How do the latest scientific projections of the rate of climate change compare with the spans of time over which evolution has occurred? Will new species of plants and animals arise with the characteristics needed to adapt to an altered climate, or will many forms of life simply become extinct?
When considering this issue, think about how evolution has shaped the variation in animal characteristics like fur and insulating features like the down feathers of geese that protect against the cold. “Warm blooded” animals such as mammals are generally more able to cope with temperature variation than reptiles. Are changes in global climate pattern likely to affect the distribution of these different animal types? Consider migratory animals – will changes in the weather disrupt the timing or destinations of migratory birds or animal herds?
Even the human body may not be immune to the impact of climate. Will this alter the future evolution of the human species, or will technological factors completely compensate for any potential change in climate?