MIT votes open-access regarding scientific papers

According to Wired, Scientific publishing might have just reached a tipping point, thanks to a new open access policy at MIT. . . [MIT's] faculty voted last week to make all of their papers available for free on the web, the first university-wide policy of its sort. MIT's Hal Abelson argued that this move "changed the power dynamics between scientific publishers and researchers." He pointed out that publishers "have been reluctant to give up control of the informational resources they have." Open access advocates have argued that "the current scientific publishing paradigm is broken because publishers control the scientific record, not academics"

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If you dig a hole straight down, where would you end up?

If you dig a hole straight down, where will you end up? I live in Missouri. I was always told that I would end up in China. Not true. For that to happen, I would need to start digging my hole in Argentina, not in Missouri. How do I know? I used an antipode finder.

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How to weed out junk science when discussing climate change.

George Will's recent journalistic malpractice has inspired much discussion by many people concerned about climate change. It's a critically important issue given that 41% of Americans currently think that the threat of global warming is being exaggerated by the media. The intellectual energy runs even deeper than criticism of George Will, though, leading us to the fundamental issue of how journalists and readers can distinguish legitimate science from sham (or politicized) science. The Washington Post recently agreed to publish a precisely-worded response to Will by Christopher Mooney. Here's Mooney's opener:

A recent controversy over claims about climate science by Post op-ed columnist George F. Will raises a critical question: Can we ever know, on any contentious or politicized topic, how to recognize the real conclusions of science and how to distinguish them from scientific-sounding spin or misinformation?

Mooney methodically takes Will to task on point after point. For instance, weather is not the same thing as the climate. The state of the art in 1970s climate science has been superseded by 2007 climate science. You can't determine long-term trends in Arctic ice by comparing ice thickness only on two strategically picked days. The bottom line is not surprising. If you want to do science well you have to do it with precision, measuring repeatedly, crunching the numbers every which way and then drawing your conclusions self-critically. What is not allowed is cherry picking.

Readers and commentators must learn to share some practices with scientists -- following up on sources, taking scientific knowledge seriously rather than cherry-picking misleading bits of information, and applying critical thinking to the weighing of evidence. That, in the end, is all that good science really is. It's also what good journalism and commentary alike must strive to be -- now more than ever.

Mooney has given considerable thought to these topics. His byline indicates that he is the author of "The Republican War on Science" and co-author of the forthcoming "Unscientific America: How Scientific Illiteracy Threatens Our Future." I would supplement Mooney's well-written points, borrowing from our federal courts. They have long been faced with the struggle to determine what is real science and what is junk science, and they have settled on what is now called the "Daubert" test, (named after the case first applying the test, Daubert v. Merrell Dow Pharmaceuticals, 509 U.S. 579 (1993)). The Daubert analysis is applied many times every day in all federal courts (and many state courts) all across America. The problem facing judges is that the parties to law suits often produce experts who express scientific theories and explanations that are never heard outside of courtrooms. This justifiably makes judges suspicious. Is the witness doing "real" science or his he/she doing sham science to further the interests of the party paying his/her bills? The Daubert test asks the judge to serve as gatekeeper, to make sure that only legitimate science sees the light of day in courtrooms. Here are the relevant factors:
  • Does the method involve empirical testing (is the theory or technique falsifiable, refutable, and testable)?
  • Has the method been subjected to peer review and publication?
  • Do we know the error rate of the method and the existence and maintenance of standards concerning its operation?
  • Is the theory and technique generally accepted by a relevant scientific community?
Positive answers to each of these factors suggests that the witness is doing real science. Astrology would fail this test miserably. Applied to climate science, the Daubert test would require that we listen carefully to what the scientists talk about with each other, in person and in their peer-reviewed journals. Daubert would require that we know enough about the techniques of climate science to know how it makes its measurements and conclusions. Daubert would certainly require that we know the difference between the weather and the climate. Applying Daubert is not simply a matter of listening to the scientists. Quite often, the scientists are bought and paid for (e.g., scientists working for tobacco companies and corrupt pharmaceutical companies). Applying Daubert requires taking the time to understand how the science works to solve real-world questions and problems and then taking the time to see that its methodology is being used with rigor in this application. There are no shortcuts, expecially for outsider non-scientists. No shortcuts. No cherry-picking.

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Diminishing races, growing family

In the January 22, and 2009 edition of Nature (available only to subscribers online), Aravinda Chakravarti explains that our simplistic notions of "population" and "race" will need to be revised as we enter the age of "personal genomics." Chakravarti teaches at the Johns Hopkins University School of Medicine. Traditionally, we've used geological records to trace our family histories. We are now approaching a time where we will be able to use DNA databases. Whereas our traditional human records take us back several hundred years, our genomes will allow us to explore our ancestry for hundreds of thousands of years. Chakravarti argues that we will be entering unknown territory riddled with surprises and stretching the meaning of the word "family." How close knit is our human "family"?

All living humans are related via a set of common ancestors who lived in Africa about 200,000 years ago. Other studies have since shown that the world beyond Africa was settled even more recently. From 100,000 years ago, descendants of our African forebears spread out to populate other continents . . . the striking implication of this is that all living humans are mosaics with ancestry from the many parts of the globe through which our ancestors trekked. In other words, each of us has around 6.7 billion relatives.

Chakravarti points out that our genealogy-based record-keeping is often riddled with error. It fails to indicate our interrelatedness to each and every other human being, for example. Further, evidence shows that at least one out of 20 people do not know the identity of their genetic father. Thanks to the falling cost of examining entire human genomes (Chakravarti indicates that it has fallen 1000- fold or more), we now have abilities we could only have dreamed of a few decades ago. Personal genomics might well destroy our simplistic notion of "race." Human populations are not intact groups. There is no such thing as genetically characterized racial categories. We are all "multiracial, related to each other only to a greater or lesser extent." Detailed surveys are making it clear that there is no such thing as a discrete racial group. Rather, it is clear that there is a "continuity in variation across the globe, not abrupt transitions between population-specific sequence patterns." Personal genomics would allow us to focus on individual human beings, instead of artificially constructed "racial" populations.

Genome-wide studies ... could result in the individual identity and kinship coming to define populations rather than the other way around. We could test once and for all whether genetic race is a credible concept. This would be tremendously exciting. It is bound to stir up our deeply held notions of who we are, where we came from, our history and thus our politics. .. . it may be time for science to reshape the views of society. By dismantling our notions of race and population, we may better appreciate our common shared and recent history and perhaps more importantly our shared future.

I recently posted on the topic of whether science should study race and intelligence. I think this would be a worthy topic of science (just as is every other potential field of study), but I warned that our current definition of "race" is horribly muddled. We need to get clear on this term, if that is even possible. I found Chakravarti's article to be a refreshing reminder that there might not even be a worthy scientific definition of "race." In fact, it might well be that, once we look carefully at the evidence, we will find that there are actually 6.7 billion "races" out there. Or is it more accurate to conclude that there is only one human race?

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Educational Ruins

Anyone who has actually visited and studied ruins knows that they are created from orderly structures by a particular combination of forces. First comes neglect, when people either lose appreciation for the value of the thing and stop maintaining it, or they simply abandon it. Next comes vandalism, when people actively damage the structure to scavenge materials and souvenirs, to leave their own mark, or to intentionally destroy it. The latter is usually for religious reasons, as in purging earlier figureheads like Hatshepsut, Trotsky or the Bamiyan Buddhas. But this post is about an institutional edifice. Education in the United States is falling into ruins. Sure, it still is funded in a nominal sort of way. But people have forgotten its value. They even vote against tax increases necessary to maintain current standards. Schools are closing; one K-12 building in my neighborhood is now condos. My Junior High school was razed for a housing development. Pharyngula points out how the University of Florida is now planning to shut down its geology department as a cost cutting measure. Geology is the science that gave Darwin the leg up to understand how natural selection works before anyone else. Geology and its understanding affects meteorology, biology, sociology, history, exo-planetary studies, and more. Florida is one of the states in which regular attempts are made to insert Creationism into school itineraries. And geology is the biggest stumbling block to accepting a Young Earth. But I hope that is not their underlying reason. It is simple neglect of education in general. But there is a strong vanadlism movement afoot in this country. Anti-science forces are working hard to put non-scientific ideas into science classes. Texas is a recurring battleground as school administrators attempt to keep up education credentials in spite of the onslaught. Recently, a doomed law is running the gauntlet in the Texas legislature to allow unaccreditable private schools to offer advanced degrees. See Hank's A Master’s in Creationism. If that seemed too harsh, try Pharyngula's If you fail an IQ test in Texas, do they automatically put you in the legislature? Hank is Australian. Yet he cares about how this sort of behavior is making the United States seem ever goofier. To let our once-admirable education system crumble is a step backwards for the world.

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