Archive for the ‘Science and Culture’ Category
Wednesday, September 8th, 2010PZ Myers helpfully posted on the decline of shark populations due to oral cartilage pills. Apparently, the pseudoscience idea that cartilage works as a cancer cure, promoted by this book, has created a cottage industry of shark cartilage pills (unsurprisingly led by the author of the aforementioned book), which in turn has led to overfishing of sharks to harvest their cartilage. And for nothing, since all the reputable studies on the matter agree that shark cartilage does not cure cancer.
It’s always nice to see PZ raising awareness on issues like this, but unhappily shark cartilage pills are undoubtedly only part of the problem. Like so many other creatures around the world, sharks appear to have committed the ultimate sin of being tasty to humans, and so were doomed to extinction as well. Shark Savers is an organization dedicated to saving the shark population, and their primary campaign right now is against shark fin soup (for which sharks are apparently caught so that their fins can be removed, and then dumped back into the ocean). Their site gives similar 80% decline figures to the post PZ linked to, which leads me to believe that it’s not clear is primarily causing the decline. It does leave only one pretty obvious solution, though: stop catching sharks.
Obviously, the majority of the people reading this blog don’t have advanced cancer and aren’t regularly confronted with the opportunity to eat shark. So for good measure I’ll just throw in that the same logic more or less applies to other tasty animals we eat more frequently, like bluefin tuna. So next time you’re look over menu choices or in the supermarket, it may be worth considering that in three years we may eradicate their breeding population.
This post brought to you as part of our continuing series on uplifting observations about the environmental impact of humanity.
Today I learned of independent documentary, Orgasm, Inc., which examines the current race by pharmaceutical companies to develop a female sexual enhancement drug. The idea is that with the remarkable financial success of Viagra, there must be a market for a drug to offer women sexual satisfaction, to which end medical researchers have been aggressively promoting the idea of widespread female sexual dysfunction. As explained in Newsweek piece on the film, “The selling of the female orgasm,” Liz Canner, the filmmaker, was approached by Vivus, a company whose suppository for erectile dysfunction lost its market dominance with the advent of Viagra and wanted her help with their female sex research. Another article in the Guardian identifies the drug (which they subsequently gave up on developing) as an “orgasm cream“, which sounds all kinds of disgusting.
Conveniently, I learned of this film but three days after it debuted in NYC at the Film Society of Lincoln Center, so it looks like I won’t be able to watch it for the foreseeable future without coughing up $30 for a DVD. So I figured I’d help other people avoid making the same mistake and encourage anyone interested to find a screening this summer – the filmmaker is showing it on various campuses in hopes of building up to a nationwide theatrical release. It also looks to be coming to Netflix, although it’s not there yet.
He is known to follow a vegan diet, eating no meat or food containing animal products. In the past, he has worked as a computer network specialist and with the operating system LINUX. [He] wears eyeglasses, is skilled at sailing, and has traveled internationally.
“He” is FBI most-wanted criminal Daniel Andreas San Diego. My thought on reading that was, “sounds like half of the Bard kids I know. Crazy how people with similar interests to people you like can be totally nuts.”
In this way I am different from Erik Marcus, who runs Vegan.com, as he seems to have had a related but much less reasonable reaction: he sounds like people I like, so surely he’s not that bad, right?
Light fisking after the jump.
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Over at Cosmic Variance, Sean Carroll addresses the Wired article on the “end of theory.” He makes a similar argument to mine, only he does it much better. For instance, I didn’t have this excellent one-line demolition of the whole argument: “Theory is understanding, and understanding our world is what science is all about.”
Highly recommended for examples involving Brahe, Kepler, Newton and the Large Hadron Collider.
There’s been a lot of talk on the statistics/machine learning/computer science blogs this week about an article in Wired called The End of Theory. Basically, everyone thinks the author, one Chris Anderson, has lost his damn mind. The piece argues that the enormous amounts of data available to modern computers, combined with advances in statistical modeling and analysis techniques, will lead to a time when the old scientific method is no longer used. The argument is that we will give up the practice of building and testing hypotheses in favor of querying huge databases for correlations. I’ll use the same passage as Ed Felten to sum up the article:
[...] The scientific method is built around testable hypotheses. These models, for the most part, are systems visualized in the minds of scientists. The models are then tested, and experiments confirm or falsify theoretical models of how the world works. This is the way science has worked for hundreds of years.
Scientists are trained to recognize that correlation is not causation, that no conclusions should be drawn simply on the basis of correlation between X and Y (it could just be a coincidence). Instead, you must understand the underlying mechanisms that connect the two. Once you have a model, you can connect the data sets with confidence. Data without a model is just noise.
But faced with massive data, this approach to science — hypothesize, model, test — is becoming obsolete. Consider physics: Newtonian models were crude approximations of the truth (wrong at the atomic level, but still useful). A hundred years ago, statistically based quantum mechanics offered a better picture — but quantum mechanics is yet another model, and as such it, too, is flawed, no doubt a caricature of a more complex underlying reality. The reason physics has drifted into theoretical speculation about n-dimensional grand unified models over the past few decades (the “beautiful story” phase of a discipline starved of data) is that we don’t know how to run the experiments that would falsify the hypotheses — the energies are too high, the accelerators too expensive, and so on.
Among the interesting reactions, we’ve got Andrew Gelman, Drew Conway, Fernando Pereira, Cosma Shalizi, and Ed Felten. They have a range of more and less technical reasons for disagreeing, all of which are interesting and seem on-point to me. Dr. Felten’s explanation of his disagreement is the easiest to understand:
To take a simple example, suppose we discover a correlation between eating spinach and having strong muscles. Does this mean that eating spinach will make you stronger? Not necessarily; this will only be true if spinach causes strength. But maybe people in poor health, who tend to have weaker muscles, have an aversion to spinach. Maybe this aversion is a good thing because spinach is actually harmful to people in poor health. If that is true, then telling everybody to eat more spinach would be harmful. Maybe some common syndrome causes both weak muscles and aversion to spinach. In that case, the next step would be to study that syndrome. I could go on, but the point should be clear. Correlations are interesting, but if we want a guide to action — even if all we want to know is what question to ask next — we need models and experimentation. We need the scientific method.
It’s true that correlations are enough if all you want to do is make money selling ads. In that case, as Anderson says, “Who knows why people do what they do? The point is they do it, and we can track and measure it with unprecedented fidelity. With enough data, the numbers speak for themselves.” But scientists interested in human behavior would see this argument as completely backwards. To a scientist, the behavior is not “the point,” but a place to begin. Science is a process of forming an understanding of the world we live in, and the one thing data mining doesn’t produce is understanding. It may produce actionable predictions, but it won’t explain them to you.
For instance, here’s another claim from the article:
The best practical example of this is the shotgun gene sequencing by J. Craig Venter. Enabled by high-speed sequencers and supercomputers that statistically analyze the data they produce, Venter went from sequencing individual organisms to sequencing entire ecosystems. In 2003, he started sequencing much of the ocean, retracing the voyage of Captain Cook. And in 2005 he started sequencing the air. In the process, he discovered thousands of previously unknown species of bacteria and other life-forms.
It’s great that Craig Venter is able to sequence a bunch of genomes. Everyone agrees this is a cool project. But, more than anything else, it’s a starting point. A bunch of DNA sequences on disk may produce interesting correlations, but they don’t advance our biological understanding of global ecosystems until they’ve been used to build testable hypotheses.
A couple of months ago I was hanging around in the lobby before an invited lecture on machine learning, and wandered into a conversation between the speaker and a couple of the CS faculty here at UCI. Since I’m not entirely comfortable quoting professors from memory months after the fact and without asking permission, I won’t say exactly who, but it was one of the people high up on this list. Anyway, the person in question is an expert in the fields of machine learning and data mining. So I came into the conversation late, and just caught someone repeating a clam from elsewhere that soon machine learning would make the scientific method obsolete; it was a claim very much like Anderson’s. And this professor, whose research involves thinking up clever new ways to mine data, said, “I think that’s exactly the wrong way to think about it.” I don’t remember the rest of the quote verbatim, but the gist was: In a perfect world, machine learning and data mining would become unnecessary, because we would have a sufficiently complete understanding not to have to resort to them. They are effectively stop-gap measures, which we rely on to make predictions (and, in a lot of cases, money) when we’re willing to act without having (or understanding) interpretable reasons. But we shouldn’t look forward to a world when we can stop searching for that understanding.
I know this serves no real purpose here, but it’s obligatory for anyone who cares about science: Expelled.
Tonight, I was scanning a paper in a respected medical journal. The paper was a clinical study that tested some claims of alternative medicine. Halfway in, I came on a paragraph that jumped out at me. It went like this:
The test procedures were explained [to test subjects] by 1 of the authors (E.R.), who designed the experiment herself. The first series of tests was conducted when she was 9 years old. The participants were informed that the study would be published as her fourth-grade science-fair project and gave their consent to be tested.
That’s a pretty bad-ass 4th grader, right there. I always thought that the Disgruntled Chemist’s scientific take-down of Dr. Frank’s No-Pain Spray was pretty cool. But TDC is a professional scientist, and an adult, and the results of his No Pain Challenge have never been published in a peer reviewed journal. None of which can be said about the completely awesome Emily Rosa, who at the age of 11 parlayed a 4th-grade science fair experiment into a publication in the Journal of the American Medical Association.
Rosa’s mother was a nurse, and was frustrated by the widespread adoption of “therapeutic touch” — a form of alternative medicine which involves channeling of life energies. Curious herself, Emily designed an experiment to determine whether or not there was any merit to the claim that practitioners of therapeutic touch could detect life energies.
During each test, the practitioners rested their hands, palms up, on a flat
surface, approximately 25 to 30 cm apart. To prevent the experimenter’s hands from being seen, a tall, opaque screen with cutouts at its base was placed over the subject’s arms, and a cloth towel was attached to the screen and draped over them. [...]The experimenter flipped a coin to determine which of the subject’s hands would be the target. The experimenter then hovered her right hand, palm down, 8 to 10 cm above the target and said, “Okay.” The subject then stated which of his or her hands was nearer to the experimenter’s hand.
The subjects identified the correct hand about 44% of the time — a result statistically no different from random guessing. The moral here should be pretty simple: your techniques are in trouble if a nine year-old can design and execute an experiment to debunk them. Unfortunately, therapeutic touch still seems to be moving units on Amazon.com.
The paper is a real hoot; I just want to point out two more bits that I liked. First, details of a previous experiment:
[A University of Alabama at Birmingham] project compared the effects of TT and sham TT on the perception of pain by burn patients. The final report to the funding agency noted statistically significant differences in pain and anxiety in 3 of 7 subjective measurements, but there was no difference in the amount of pain medication requested.
“So, do you feel better?”
“Uh. Yeah. Sure. Can I have my meds now?”
Then, one of the excuses made by a failed test subject:
[The subject argued that the] experimenter should be more proactive, centering herself and/or attempting to transmit energy through her own intentionality. This contradicts the fundamental premise of TT, since the experimenter’s role is analogous to that of a patient. Only the practitioner’s intentionality and preparation (centering) are theoretically necessary. If not so, the early experiments (on relatively uninvolved subjects, such as infants and barley seeds), cited frequently by TT advocates, must also be discounted.
That’s right — our techniques are no good on skeptical little girls, but they work wonders for barley seeds.
For more good skeptical content on the interwebs, see Sean Carroll at Cosmic Variance on how modern physics has ruled out the possibility of telekinesis.
I’m not sure if it was something in my dinner tonight or if Nature is just really funny this week. A few noteworthy picks:
- “We are not recommending you import alligators into California. That would not be a good idea.”
- ‘Doomsday vault‘ opens
- Meat meter measures marbled muscles: “Japanese researchers have developed a device to objectively assess the deliciousness of meat.”
- Overhyped: Gravity lamp
- Animal-rights activists invade Europe
Jorge Cham, the author of PhD Comics, spoke at UCI last year. Ruth and I were really excited, because it happened just days after we arrived, and (being big fans) we thought this was fortuitous. Unfortunately, we weren’t all that impressed by the talk itself. Dr. Cham was almost unrelentingly negative, without it really being clear what was exaggerated for humor and what was genuine enmity. Perhaps this was a shortcoming on our end, an inability to perceive the nuances, and a reluctance to countenance anything which would discourage us during our first week as graduate students.
But, since then, I read a lot of the comics and I wonder if Cham really “gets it,” where “it” is some vague quality of what makes the pursuit of science so important to people. Take, for instance, the most recent PhD comic, about visiting with astrophysicists. It’s the second half of a two-parter, the first of which got a favorable link from Cosmic Variance, and the people there know a lot more about this stuff than me. The “Beautiful all the way down” bit is nice, but check out this corner of the comic:
You don’t have to be an astrophysicist to understand that this kind of agreement between prediction and observation is just ridiculous. To ask “That’s it,” when “it” is so impressive, just seems silly. Contrast Cham’s response with a comic by someone who definitely “gets it.” Randall Munroe is responsible for the consistently fantastic xkcd. I could be wrong about this, buy my impression is that his comic really blew up around the time that people like P.Z. Myers linked to this comic:
This isn’t to say that PhD isn’t still pretty funny. Every lab on my floor has one or two of the comics tacked up on a wall. But I just don’t understand what Cham thinks he’s proving to whom with these (real or feigned) attitudes.
It seems a researcher named Charles Roselli at Oregon Health & Science University has been conducting experiments to understand what makes sheep gay. This already sounds like a good idea. Apparently, it’s drawn a lot of fire from certain circles, notably