Science

This year’s “The Amazing Meeting” (TAM7) was preceded by a Science-Based Medicine conference, organized by Steven Novella and the Science-Based Medicine blog; the speakers were all contributors to that blog. This summary is from my hand-written notes–I’ve tried to quote and summarize accurately, but keep in mind that some of the quotations and bulleted items may not be verbatim. The conference was videotaped and may become available via DVD or online video; keep an eye on the SBM blog for that. Steven Novella has posted a short summary of the SBM conference at the SBM blog. I am in the process of posting a summary of TAM7 itself, which begins here. (I summarized 2008’s TAM6 here.) Novella’s Introduction The SBM conference began with Novella’s presentation, titled “Science-Based Medicine: Science and Pseudoscience in Clinical Decision Making,” which distinguished science-based medicine (SBM) from the recently popular “evidence-based medicine” (EBM) and explained the motivation for promoting the SBM concept. Novella, assistant professor of clinical neurology at Yale University School of Medicine, began with a slide titled “Foundations of Medicine” which described some historical varieties of medicine: Superstition/philosophy-based medicine.Scientific medicine.Evidence-based medicine (EBM).Eastern vs. Western medicine.Complementary and alternative medicine (CAM).He made the point that modern scientific medicine, which arose in the western world, is relatively young, though attempts to put it on a more scientific footing go back much farther. Next, he discussed “What is science,” first observing that “scientifically formulated” is a meaningless marketing label, then noting that there is a battle of memes about science between its defenders, who use it as a label connoting “objective truth, quality, and professionalism,” and its critics, who use it as a label connoting “arrogance, oppression, and elitism.” Marketers also use it “to imply product safety, effectiveness, and overall value." He argued that we should adopt “common sense standards” which require that treatments “reasonably account for all available evidence,” use “valid and internally consistent logic,” have been rigorously and methodically investigated and judged with fair and unbiased criteria, and are conducted by practitioners who adhere to “standards of ethics and professionalism." Evidence-Based Medicine Next, he looked at evidence-based medicine, a term of art in use for the past couple of decades. EBM begins with the premise that “products and practices that work and are safe are better than those that don’t work or are unsafe,” an uncontroversial premise. It promotes scientific investigation as the measure of what works and is safe. But, according to Novella (and later, other speakers), EBM has “too much focus on evidence, and not enough on logic and prior probability, and good science must consider both.” He argued that EBM made sense at the time it was introduced, because practices were being used largely “because they made sense, not because of supporting evidence.” The introduction of EBM effectively “leveled the playing field, but also opened it up to implausible treatments,” with bad timing due to the rise of complementary and alternative medicine (CAM). The standard reference for evidence in the EBM framework is the Cochrane Reviews. The data reported in the Cochrane Reviews includes not only tests of legitimate medical treatments, but of completely implausible research such as chiropractic treatment for migraine. The problem with the framework is that it assumes that everyone is “playing fair,” it does not account sufficiently for fraud or publication bias (such as the “file drawer effect”), it ignores prior probability, and it “doesn’t adequately consider the big picture of the entire literature.” According to Novella, with EBM it is typical to see the quality of studies decline over time, in order to continue to yield positive results for implausible treatments. He then discussed “The Work of John Ioannidis,” who argues that “most published research findings are false.” The reasons are that The majority of highly-cited initial medical research is later refuted.There’s a bias towards publishing positive studies.There’s a bias towards researchers publishing provocative research. And a “low prior probability worsens the effect,” i.e., studies of treatments with low prior probability are more likely to be refuted. Science-Based Medicine By contrast with EBM, Novella identified the following features to distinguish Science-Based Medicine, SBM: It affirms high-quality science as a basis for standard of care in medicine.It acknowledges the consilience of science.It considered scientific medical plausibility of an intervention when weighing evidence.It considers the overall pattern in the literature.In other words, SBM considers prior probability in a Bayesian sense as part of the evaluation, it looks at whether there is other scientific evidence that casts doubt on the plausibility of a suggested treatment (like violating the laws of physics or including unknown entities and mechanisms), in addition to merely looking at the specific results of controlled trials of the particular treatment. CAM, in particular, is loaded with claims that have extremely low and near-zero prior plausibility, as evidenced by the fact that $1.2 billion of U.S. taxpayer funding to the National Center for Complementary and Alternative Medicine since its founding in 1991 (originally as the Office of Alternative Medicine) has so far yielded zero effective treatments for anything. He stated that finding anomalies argues for deeper research, and we can’t have two inconsistent views that both work. Here, I think he overstated his case, since we have had cases in science where there are mutually inconsistent theories that both work, though we also take the inconsistency as grounds that something is wrong and ultimately needs to be reconciled (e.g., light wave/particle duality, quantum field theory vs. general relativity). Even theories that are wrong at some level can still work for solving certain kinds of problems (e.g., Newtonian physics)–and I’d agree with Novella’s claim that scientific medicine is still in its infancy. A point Novella didn’t make that I would like to insert here is that when you have two inconsistent views that doesn’t mean that only one of them must be wrong–they could both be wrong. Novella did go on to mention two cases where things that seemed initially implausible or lacking in mechanism have turned out to be correct, the postulation of dark energy in physics, and, more directly relevant to the topic at hand, the use of botulinum as a treatment for migraine. This treatment seemed to him completely implausible even though the evidence of trials suggested its effectiveness, and now a mechanism has been discovered and is understood. (My Google searching on this subject, however, yielded some recent evidence that it is not a good treatment for migraines and is no better than placebo, so this appears to me to still be somewhat controversial.) Clinical Decision-Making Novella ended his talk by talking about the process of clinical decision-making and pitfalls that arise as a result of human psychology and limitations. While clinical decision-making “individualizes the best available evidence to a specific patient” and “considers risk vs. benefit in both therapeutic and diagnostic intervention,” this evaluation needs to include not acting as an alternative. In some cases, screening for certain diseases causes more harm than not performing the screening test, because conducting the test will yield far more false positives than true positives. (This is an effect discussed in some detail in John Allen Poulos’ book, Innumeracy, and is a reason not to do things like mandatory HIV screening as a condition of a marriage license, drug testing of grade school students, and certain kinds of security screening for terrorists–if your baseline prevalence of what you’re testing for is very low, your false positive results will swamp your true positive results.) He briefly discussed the claim that “surgery kills more people than car accidents,” noting that it doesn’t really compare against the outcomes that would occur without surgery–far more deaths. He then recounted some examples of pitfalls in the clinical context, such as the human capacity for pattern recognition even when the pattern isn’t really there (pareidolia), the tendency to be “unduly influenced by quirky experience” or to “value experience over evidence,” “failure to consider alternatives,” “over-reliance on non-specific signs and symptoms,” and confirmation bias (e.g., the sorts of heuristics and biases discussed in Kahneman and Tversky’s classic Judgment Under Uncertainty). He then listed a few logical fallacies, pointed out the confounding factor of the placebo effect, and a couple of statistical effects–regression to the mean and the fact that most diseases are self-limiting. Q&A In the Q&A session, someone asked what Novella thought of legislation supporting evidence-based medicine, apparently referring to $1.1 billion in the stimulus package for evidence-based medicine research. Novella said that he thought conceptually it was a good idea but wasn’t familiar with the specifics of the legislation. Another question was whether, given the current state of health care and the desire for reform, SBM would be challenged or supported. Novella said that the delivery of healthcare is a separate issue from how we decide what to research or what treatments are appropriate, and that things will either get much better or much worse. If he had also added that things might also stay about the same in overall quality, I’d say he’s certainly correct; without it, merely probably correct. (Part two of my conference summary, on cancer quackery, is here. Part three, on chiropractic, is here. Part four, on evidence-based medicine and homeopathy, is here. Part five, on chronic Lyme disease, is here. Part six, on online health and social media, and the closing Q&A panel, is here.) ...

I’m in the Phoenix airport waiting for my early morning flight to Las Vegas for today’s conference on science-based medicine, followed by The Amazing Meeting 7, at the new South Point Casino and Hotel. I hope to write up a summary like I did for last year’s TAM 6. Ktisophilos (2009-07-10): Science-based medicine? Is there any other kind? Lippard (2009-07-11): Yes--they distinguished science-based medicine from evidence-based medicine and from complementary and alternative medicine, for example. The U.S. government has spent over $1.5 billion on research on complementary and alternative medicine, for example, since the founding of the NIH's National Center for Complementary and Alternative Medicine. Number of new treatments produced as a result of that research: 0. It's recently come out that some of that research money is going to criminals–people with felony fraud convictions. I'll have much more on this when I write up my summary (probably next week). ...

Charles Blow has an op-ed piece in yesterday’s The New York Times commenting on the spate of recent Republican sex scandals which contains this infographic (an aptly named “blowchart”) ranking the states based on divorce rates, teen pregnancy rates, and subscriptions to online porn sites as a percentage of broadband subscribers. Blow suggests that conservatives address this hypocrisy by becoming more concerned about what goes on in their own bedrooms than in everyone else’s. It also highlights the ineffectiveness of abstinence-only sex education. (BTW, the data for the third column comes from the work of Ben Edelman (PDF), who I’ve cited here before for his excellent work on spyware and adware, and on the ineffectiveness of TRUSTe.) UPDATE (June 30, 2009): There’s at least one error in this chart, in that Tennessee should be red, not blue, near the bottom of the broadband porn column. ...

Stanford neuroscientist Robert Sapolsky giving a lecture on the evolution of schizophrenia, and how schizotypal personality and its associated “metamagical thinking” may be adaptive, and a source or driver for religious belief in a community. (Via boingboing.) Historical Comments Brad (2009-06-09): I love this type of discussion. There does seem to be a touch of post-hoc assumptions, but assumptions that have a large volume of rational support compared to any alternative I can think of. ...

As was mentioned last August by commenter Ktisophilos, Ian Plimer has a new book out on climate change, titled Heaven and Earth: Global Warming: The Missing Science, in which he challenges claims of anthropogenic global warming. Plimer is an Australian professor of geology who I criticized for his methods in debate with creationists, as well as for his reliability and accuracy. He responded by criticizing me with more misrepresentation in his book Telling Lies for God, which contained numerous errors, as well as multiple cases of failure to properly quote and cite sources that he used in writing the book. (The Creation Ministries International documentary for which I was interviewed, Facing the Fire, is about Plimer’s 1988 debate with Duane Gish of the Institute for Creation Research.) It now appears that Plimer’s latest work is also extremely sloppy and contains erroneous source attributions. Tim Lambert at the Deltoid ScienceBlog identifies a long list of problems in the book by page number, points out the facts about Plimer’s misleading figure 3, which doesn’t originate from the source Plimer has claimed, and about another misrepresented source and graph. Some Christians who found Plimer to be worthless as a source on creationism as a result of my critique have nonetheless found him to be a worthwhile source on anthropogenic climate change, such as Bill Muehlenberg and some of the commenters at his CultureWatch blog. This strikes me as an inconsistent position–Plimer has demonstrated unreliability in both debates, and shouldn’t be relied upon as a source for either. That doesn’t mean to ignore what he says, or that everything he says is wrong–it’s just that everything he says needs to be thoroughly checked for accuracy. If it checks out, then it’s better to cite the original source, not Plimer. UPDATE (May 26, 2009): Commenter Paul points out a review of Plimer’s book by Barry Brook, which also includes a link to a point-by-point critique of the book by Prof. Ian Enting of the University of Melbourne (PDF). (This link has been updated as of June 1, 2009 to point to a location that will continue to maintain the most recent version of the critique, as per a comment below from Prof. Enting.) UPDATE (May 28, 2009): Bill Muehlenberg still appears to be refusing to publish contrary opinions from me, continuing his past record. I posted the following two comments on his blog, which he has not allowed through moderation: 1. Comment submitted on the evening of May 22, 2009: I am a critic of creationism and skeptic who challenged Ian Plimer’s methods and reliability in his criticisms of creationism (cited by one of your commenters above). I am sorry to say that Plimer’s methods and reliability continue to be unsound in his contribution to the climate change debate. For example, see the following two blog posts that document errors and falsehoods in his new book: http://scienceblogs.com/deltoid/2009/04/the_science_is_missing_from_ia.php http://scienceblogs.com/deltoid/2009/05/ian_plimer_lies_about_source_o.php I think that Plimer is mostly correct about creationism (it’s nonsense) and mostly incorrect about climate change (there are real trends that correlate with human activity), but given his record he shouldn’t be relied upon as a source in either debate without carefully checking up on everything he says.2. Submitted on the morning of May 23, 2009: Bill: I do hope you will let my comments through moderation. Here is another post from the Deltoid ScienceBlog about Ian Plimer misrepresenting one of his own sources: http://scienceblogs.com/deltoid/2009/05/plimer_and_arctic_warming.phpUPDATE (September 2, 2009): Plimer has descended further into irrationality in his exchange with George Monbiot. UPDATE (December 17, 2009): Plimer engaged in a debate, of sorts, with George Monbiot, on Australia’s “Lateline” program. Monbiot offers his overview of how it went. ...

In an op-ed at the New York Times, Charles Blow offers a rebuttal to the claim that most people follow particular religions because they are raised in those religions with the following: Maybe, but a study entitled “Faith in Flux” issued this week by the Pew Forum on Religion and Public Life questioned nearly 3,000 people and found that most children raised unaffiliated with a religion later chose to join one. Indoctrination be damned. By contrast, only 14 percent of those raised Catholic and 13 percent of those raised Protestant later became unaffiliated. ...

Evidence continues to mount that human decision-making occurs in the brain prior to conscious awareness of the decision, which is evidence against the common religious view of a soul, separate from the brain, which is the seat of all of our mental capacities. It’s also at odds with an overly intellectualized view of human beings held by some atheists (as well as all Scientologists, who consider unconscious decision-making by the “reactive mind” or festering “body thetans” to be the cause of human unhappiness), on which we must strive to make all of our decisions based on conscious, deliberative reason. I don’t think this is a very common view among atheists today, who tend to have some familiarity with evolution and cognitive science, but there are still some out there who have an overly idealized view of what a rational human being should be. A view of human beings that focuses solely on the intellectual and reason is not only at odds with the facts about how our cognition works, it gives short shrift to the importance of social bonds and emotion, which are areas that some religions focus on to the exclusion of the intellectual–with great success in expanding their memberships, at least over the short term.

Cambridge University physicist David MacKay’s book, Sustainable Energy: Without the Hot Air, is available for free download or perusal in a variety of forms including HTML, PDF and PostScript, at the website www.withouthotair.com.

Despite the common concern that immigrants to the U.S. take jobs that would otherwise go to American citizens, immigrants actually create jobs and promote innovation. Two recent articles in The Economist look at this topic. In the March 7, 2009 issue, a study by Harvard economist William Kerr and University of Michigan economist William Lincoln looked at how patent production changes in response to changes in the number of H-1B visa holders, immigrants with technical skills. When the number of H-1B visas was increased by 10%, total patenting increased by 2%, caused mostly by patent activity by immigrants. However, rather than reducing the number of patents by the native population, those also increased. In the March 14, 2009 issue’s special report on entrepreneurship, it’s noted that H-1B visas are capped at 85,000/year, and a maximum of 10,000 from any one country, increasing the wait for large countries such as India and China, where the wait time is about six years. There are over one million people waiting. This issue also notes that about half of Silicon Valley’s startups are founded by immigrants, and about 25% of all U.S. science and technology startups have a CEO or CTO who is an immigrant, and these companies employ 450,000 people and generate $52 billion in annual revenue. A quarter of U.S. patent applications in 2006 name foreign nationals as inventors or co-inventors. ...

The March 7th, 2009 issue of The Economist Technical Quarterly has some items of interest: Cool Earth Solar of Livermore, California is using balloons as solar energy collectors. Narasimharao Kondamudi, Susanta Mohapatra, and Manoranjan Misra of the University of Nevada at Reno have found a way to turn coffee grounds into biodiesel. David Whitten of the University of New Mexico and Kirk Schanze of the University of Florida have built “micro-sized ‘roach motels’” for capturing bacteria in hospitals and on the surfaces of ships. Nicholas Kotov and his team at the University of Michigan have come up with a way to coat cotton threads with carbon nanotubes which can be used to carry electricity, and to add an additional material that reacts with human serum albumin, in order to detect bleeding, which might be used by the military in monitoring soldiers.