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RCT Plausibility Scale

RCT Plausibility Scale

After a few intro paragraphs, I want to present a scale of probability to estimate a value of a “prior” to plug into the formula for obtaining a Bayes Factor. The scale can help to estimate a value, but will still rely on an estimate, the non-quantitative element in Bayesian simulations. However, the checklist may at least provide some objective bases on which to hang a value, and that value would actually make a semi-quantitative statement of its own. Although that value would retain some subjective quality, it would at least be backed by known quantities and laws of nature.

Begging your patience again, I became aware of this problem in 1999 when asked to moderate an online (BioMednet.com) debate on “CAM” among 4 physicians. My role soon morphed into participant-debater when I could not get all to agree on what I thought was obvious common ground to proceed with the discussion – that 1) concepts that violate scientific laws do not have to be subjected to clinical trial (RCT) and that trial results had to be interpreted in light of previous knowledge; and 2) clinical trials could not constitute adequate evidence in the absence of plausibility because their results were too varied and inconsistent. The matter was p-recipitated by systematic reviews (SRs) showing efficacy of acupuncture in back pain. I was truly surprised when one of the participants (Dr. Edzard Ernst) assured me that indeed, RCTs were now the gold standard for efficacy. The debate went downhill from there.

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Posted in: Clinical Trials, Science and Medicine

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Science-Based Nutrition

One of the most successful propaganda campaigns within health care in the last few decades has been the re-branding of nutrition as “alternative” or out of the mainstream of scientific medicine. I have marveled at how successful this campaign has been, despite all the historical evidence to the contrary. I suppose this is partly a manifestation of the public’s short-term memory, but it also seems to reflect basic psychology.

Some History

There is evidence that most ancient cultures recognized the importance of diet in health. The Greeks recognized both the benefits of a varied diet and the negative health consequences of obesity, for example. But knowledge of nutrition was limited to these broad observations and was mixed with superstition and cultural beliefs.

The science of nutrition probably dates back to 1614 when scurvy (the disease that results from vitamin C deficiency) was first recognized as a dietary deficiency, one that could be cured by eating fresh fruits and vegetables. In 1747 Lind conducted what might be the first clinical trial – systematically comparing various diets for the treatment of scurvy and finding that citrus fruits were the key to treatment.

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Posted in: Herbs & Supplements, Nutrition, Public Health, Science and Medicine

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Bad scientific arguments in the service of animal rights activism

One of the greatest threats to the preclinical research necessary for science-based medicine today is animal rights activism. The magnitude of the problem came to the forefront again last week with the news that animal rights terrorists tried to enter the home of a researcher at the University of California Santa Cruz (UCSC) whose research uses mice to study breast cancer and neurologic disease while she and her husband were having a birthday party for one of their children and assaulted her husband, who had gone to the front of the house to confront them. Fortunately, the license plate number of the car fleeing the scene was reported to police, leading to a raid on a house by police and the confiscation of computers and other materials. This attack appeared to be the latest crescendo in an increasing campaign of harrassment and intimidation by animal rights “activists” that has also been observed in nearby Berkeley.

This sort of threat to researchers is not a problem just in Santa Cruz and the Bay area, but in particular has been a problem in southern California as well. Just earlier this week, the University of California Los Angeles announced that it was suing several animal rights groups and individuals suspected of attacks on researchers who use animals, including UCLA Primate Freedom Project, the Animal Liberation Front (ALF), and the Animal Liberation Brigade (ALB), as well as several individuals believed to affiliate with these groups. The inciting event for this action was the second attack on the home of Edythe London, Professor of Psychiatry and Bio-behavioral Sciences and of Molecular and Medical Pharmacology at the David Geffen School of Medicine at UCLA, in early February. Her research involves the use of primate models to study nicotine addiction. In this most recent attack, an attempt was made to set her house on fire. This came on the heels of a previous attack in October, in which animal rights activists flooded her house. Prior to that, animal rights terrorists had indeed succeeded in their aim of intimidating a scientist sufficiently that he gave up animal research after a fellow researcher was targeted with a Molotov cocktail meant for her home that was mistakenly placed on the porch of an elderly neighbor. Also, we in the U.S. often forget how much more radical animal rights extremists are in the U.K., where the campaign of intimidation takes the form of death threats, intimidation of personnel of companies that supply researchers, and even in one case digging up the grave of Gladys Hammond, whose family ran a farm that raised Guinea pigs for use in medical research, and stealing her remains.

Readers may make the argument that my introduction to this discussion is unfairly inflammatory, but I have my reasons for starting this way, and I think they are good ones. First, make no mistake, the aim of the most radical of these activists is nothing short of the cessation of the use of all animals in biomedical research. Second, sooner or later, someone will be hurt or killed. As a researcher who on occasion uses mouse models of cancer myself, I state up front that I could be on the firing line just as much as the UCSC researcher or others and am justifiably disturbed when I hear spokesperson for the ALF Dr. Jerry Vlasak, for example, repeatedly advocate violence against researchers who use animals. In this article, I am not going to discuss the moral issues involved in animal research. What I am going to discuss is the seemingly scientific arguments that some opponents of animal research and animal rights activists like to invoke, arguments increasingly used in addition to the moral arguments that extremists use to justify their actions. If the arguments of opponents of animal rights research were indeed good science, then their appropriation by extremists would not allow me to do much other than bemoan the misuse of valid science as a justification for extremism. Unfortunately, such is not the case, and the bad scientific arguments used by opponents of animal research are often piled onto the extreme moral arguments that fuel actions such as those earlier this week at UCSC. Consequently, given the events of the last month or so, I thought I would take this opportunity to look at some of the common scientific indictments of animal research by its opponents.
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Posted in: Basic Science, Clinical Trials, Politics and Regulation, Science and Medicine

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Prior Probability: the Dirty Little Secret of “Evidence-Based Alternative Medicine”—Continued Again

After the previous posting on the Bayesian approach to clinical trial data, several new comments made it clear to me that more needed to be said. This posting addresses those comments and adds a few more observations regarding the unfortunate consequences of EBM’s neglect of prior probability as it applies to “complementary and alternative medicine” (“CAM”).†

The “Galileo Gambit” and the Statistics Gambit

Reader durvit wrote:

A very interesting example, for a number of people, might be estimating the prior probability for Marshall and Warren’s early work on Helicobacter pylori and its impact on gastroduodenal management. I frequently have Marshall quoted to me as a variation on the Galileo gambit, so establishing whether he and Warren would have been helped or hindered by Bayesian techniques would be useful.

This suggestion raises a couple of issues. First, the “Galileo gambit” regarding Marshall and Warren’s discovery is a straw man (as durvit seems to have surmised). (more…)

Posted in: Homeopathy, Medical Academia, Medical Ethics, Politics and Regulation, Science and Medicine

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Antiscience-Based Medicine in South Africa

South Africa’s Health Minister, Manto Tshabalala-Msimang, is fighting to protect the traditional healers of her country from having their methods tested scientifically. She warns that, “We cannot use Western models of protocols for research and development,” and that she does not want the incorporation of traditional healing to get “bogged down in clinical trials.” Her arguments are anti-scientific and represent a health tragedy for South Africa. However, such attitudes are not uncommon within the community of sectarian medicine and represent some of the common rhetoric used to disguise anti-scientific positions.

This is also not the first controversial statement made by South Africa’s health minister. In 2006 she advocated using garlic and beetroot to treat HIV infection, prompting outrage from South Africa’s academic community. In response to criticism about delays and funding cuts in providing anti-retroviral drugs to HIV sufferers in South Africa, the Health Minister said, “Garlic is absolutely critical, we need to do research on it. We cannot just ridicule it.” South Africa’s president, Thabo Mbeki, resisted calls for Ms. Tshabalala-Msimang’s resignation.

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Posted in: Politics and Regulation, Science and Medicine

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When the popularity of new surgical procedures outpaces science

ResearchBlogging.orgIn science- and evidence-based medicine, the evaluation of surgical procedures represents a unique challenge that is truly qualitatively different from the challenges in medical specialties. Perhaps the most daunting of these challenges is that it is often either ethically unacceptable or logistically impossible to do the gold-standard clinical trial, a double-blind, randomized placebo trial for an operation. After all, the “placebo” in a surgical trial involves patients to anaesthesia, making an incision or incisions like the ones used for the operation under study, and then not doing the operation. Clearly, even leaving the ethics aside, it’s impossible to blind the surgeons and operative team involved to which treatment, real surgery or placebo, the patient is receiving without having a different surgeon do the surgery from the one overseeing the postoperative care of the patient, with the operative surgeon barred from communicating to the postoperative surgeon what happened in the operating room and from participating in the postoperative care of the patient upon whom he operated. This sort of restriction, besides being also highly dubious ethically speaking, goes against the grain of surgical culture, in which a surgeon is expected to provide the postoperative care for his patients almost as a matter of surgical honor. A final problem that complicates any surgical trial is that surgeons of differing technical operating skill will necessarily be involved, and surgical skill is indeed very important in determining outcome. Although there have been examples of double-blinded trials with sham surgery as placebo, for example, in injecting dopamine-producing cells into the brain to treat Parkinson’s disease, difficulties doing such studies tend to force us as surgeons in many cases either to rely on retrospective data, prospective non-randomized data, or, when we’re lucky, a prospective randomized (but not double-blinded) trial of one surgical procedure versus another.
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Posted in: Clinical Trials, Medical Ethics, Science and Medicine, Surgical Procedures

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Prior Probability: the Dirty Little Secret of “Evidence-Based Alternative Medicine”—Continued

This is an addendum to my previous entry on Bayesian statistics for clinical research.† After that posting, a few comments made it clear that I needed to add some words about estimating prior probabilities of therapeutic hypotheses. This is a huge topic that I will discuss briefly. In that, happily, I am abetted by my own ignorance. Thus I apologize in advance for simplistic or incomplete explanations. Also, when I mention misconceptions about either Bayesian or “frequentist” statistics, I am not doing so with particular readers in mind, even if certain comments may have triggered my thinking. I am quite willing to give readers credit for more insight into these issues than might be apparent from my own comments, which reflect common, initial difficulties in digesting the differences between the two inferential approaches. Those include my own difficulties, after years of assuming that the “frequentist” approach was both comprehensive and rational—while I had only a cursory understanding of it. That, I imagine, placed me well within two standard deviations of the mean level of statistical knowledge held by physicians in general.

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Posted in: Clinical Trials, Medical Academia, Science and Medicine

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Antibiotics for Sinusitis

You’re a patient. That cold just isn’t getting better and you have purulent drainage from your nose, and your face hurts and your teeth hurt. You probably have sinusitis, right? You go to a doctor to get an antibiotic.

You’re a doctor. Deep down, you know there’s a good chance the patient has a self-resolving condition.  You’d rather not do x-rays on every patient who presents with these symptoms, because x-rays are expensive, expose the patient to harmful radiation, and they are not always accurate.  You could puncture the sinuses and take a sample for bacteriological culture, but that’s expensive, painful, and the patient would NOT appreciate it. The patient may not really need treatment, but you want very much to do something to help. If you can find a reason to give the patient an antibiotic, you can feel that you have done something worthwhile.  Antibiotics don’t work for a viral infection, but you rationalize that you’re not 100% sure it’s not bacterial, and that sometimes a bacterial infection develops superimposed on a viral infection and mild bacterial infections can develop into severe ones with complications, and maybe you could ward that off.  You convince yourself that it really would be prudent to prescribe an antibiotic. Both you and your patient are happy. The patient gets better. You remember this pleasant experience and are reinforced to do the same next time.

Maybe that’s not such a good idea.

A recent study in JAMA showed that antibiotics were not superior to placebo for treating bacterial sinusitis diagnosed by the clinical criteria used by many primary care physicians. There is a growing concern that we have been overtreating sinus infections. Recent research has also shown that we were overtreating ear infections in children, that many of them resolve just as fast without treatment. That doesn’t mean antibiotics should never be used for ear infections. There are now guidelines for using age and clinical presentation to determine which children to treat and which ones can be safely observed without antibiotics. Most of these observed ear infections will resolve but some will eventually require antibiotics too. The situation with sinusitis is similar: most patients may not need antibiotics, and we’re trying to thrash out better criteria for identifying those who will.

Critics point to this kind of thing as a defect of conventional medicine. We use treatments that are not based on good evidence. We do things for years and then find out we were wrong. New studies are constantly contradicting older studies. We keep changing our minds. (more…)

Posted in: Science and Medicine

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Toxic myths about vaccines

Ever since there have been vaccines, there has been an antivaccination movement. It began shortly after Edward Jenner discovered how to use the weaker cowpox virus to induce long-lasting immunity to smallpox, there has been resistance to the concept of vaccination, a resistance that continues to this very day. Reasons for this resistance have ranged from religious, to fear of injecting foreign substances, to simple resistance to the government telling people what to do. Some fear even the infitessimally small risk that vaccines pose for the benefit of resistance to disease far more than they fear the diseases themselves, a result of the very success of modern vaccines. Of course, vaccines, like any other medical intervention, are not without risks, making it easy for them to jump on any hint of harm done by vaccines, whether real or imagined, even though vaccines are among the very safest of treatments.

One of the biggest myths that antivaccinationists believe and like to use to stoke the fear of vaccines is the concept that they are full of “toxins.” The myth that mercury in the thimerosal preservative commonly used in vaccines in the U.S. until early 2002 was a major cause of autism is simply the most recent bogeyman used to try to argue that vaccines do more harm than good, as was the scare campaign engineered in response to Andrew Wakefield’s poor science claiming a link between the MMR vaccine and autism. Now that study after study have failed to find or corroborate a link between thimerosal in vaccines or vaccines in general and autism to the point where even the most zealous of zealots are having a hard time defending the claim that mercury in vaccines cause autism any more, predictably the campaign against vaccines has fallen back on the old “toxins” myth. If you peruse antivaccinationist websites, it won’t take long to find articles claiming that vaccines are full of the most terrifying and nasty toxins. Examples in the media abound as well. For example, Jenny McCarthy, comic actress and former Playboy Playmate who has been doing the talk show and publicity circuit lately to plug her book in which she claims that vaccines caused her son’s autism and that she was able to cure it with “biomedical” interventions and diet, recently gave an interview in which she said:

What I really am is “anti-toxins” in the vaccines. I do believe that there is a correlation between vaccinations and autism. I don’t think it’s the sole cause, but I think they’re triggering–it’s triggering–autism in these kids. A really great example is…is, sometimes obesity can trigger diabetes. I do believe that vaccines can trigger autism…It’s so much more than just mercury. That is one ingredient in the recipe of autism…I’m talking about all of them. I’m calling for cleaning out the toxins. People don’t realize that there is aluminum, ether, antifreeze, still mercury, in the shots…People are afraid of secondhand smoke, but they’re OK with injecting the second worst neurotoxin on the planet in newborns.

Another example of what I sometimes call the “toxin gambit” comes from Deirdre Imus, wife of shock jock Don Imus, with both husband and wife being well-known and reliable media boosters of the claim that vaccines somehow cause autism:

So, where are the evidenced based (conflict free) studies that prove the safety of these “trace” amounts and proof that there are “no biological effects” of any amount of mercury being injected into our children and pregnant moms? Also, where are the evidence based studies proving the safety of vaccines given to pregnant moms and our children that contain other toxins such as aluminum and formaldehyde?

The most recent example of this tactic comes from an organization called Generation Rescue, which just last week ran a full-page ad in USA Today, paid for in part by Jenny McCarthy and her present boyfriend Jim Carrey:

antivaxgradvertisement.jpg

Besides being one of the most egregious examples of a post hoc ergo propter hoc fallacy that I’ve ever seen from an antivaccination site, this Generation Rescue ad demonstrates clearly a new strategy (or, more properly, a resurrection of an old technique) now that science is coming down conclusively against mercury in vaccines as a cause of autism, a strategy of propagating fear by linking vaccines with “toxins.” So what’s the real story? Are there really deadly toxins in vaccines that parents should be worried about?
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Posted in: Public Health, Science and Medicine, Science and the Media, Vaccines

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Prior Probability: The Dirty Little Secret of “Evidence-Based Alternative Medicine”

This is actually the second entry in this series;† the first was Part V of the Homeopathy and Evidence-Based Medicine series, which began the discussion of why Evidence-Based Medicine (EBM) is not up to the task of evaluating highly implausible claims. That discussion made the point that EBM favors equivocal clinical trial data over basic science, even if the latter is both firmly established and refutes the clinical claim. It suggested that this failure in calculus is not an indictment of EBM’s originators, but rather was an understandable lapse on their part: it never occurred to them, even as recently as 1990, that EBM would soon be asked to judge contests pitting low powered, bias-prone clinical investigations and reviews against facts of nature elucidated by voluminous and rigorous experimentation. Thus although EBM correctly recognizes that basic science is an insufficient basis for determining the safety and effectiveness of a new medical treatment, it overlooks its necessary place in that exercise.

This entry develops the argument in a more formal way. In so doing it advocates a solution to the problem that has been offered by several others, but so far without real success: the adoption of Bayesian inference for evaluating clinical trial data.
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Posted in: Basic Science, Clinical Trials, Homeopathy, Science and Medicine

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