Basic Science

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Is there a reproducibility “crisis” in biomedical science? No, but there is a reproducibility problem

NOTE: Anyone who has seen several derogatory articles about me on the web and is curious about what the real story is, please read this and this.

Journal of Irreproducible ResultsMost scientists I know get a chuckle out of the Journal of Irreproducible Results (JIR), a humor journal that often parodies scientific papers. Back in the day, we used to chuckle at articles like “Any Eye for an Eye for an Arm and a Leg: Applied Dysfunctional Measurement” and “A Double Blind Efficacy Trial of Placebos, Extra Strength Placebos and Generic Placebos.” Unfortunately, these days, reporting on science is giving the impression that the JIR is a little too close to the truth, at least when it comes to reproduciblity, so much so that the issue even has its own name and Wikipedia entry: Replication (or reproducibility) crisis. It’s a topic I had been meaning to write about again for a while. Fortunately, A recent survey published in Nature under the somewhat clickbaity title “1,500 scientists lift the lid on reproducibility” finally prodded me to look into this question again. Before I get to the survey itself, though, I can’t help but do my usual pontificating to provide a bit of background.

Posted in: Basic Science, Pharmaceuticals, Politics and Regulation, Science and Medicine

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“Integrative” medicine versus “alternative” medicine

“Integrative” medicine versus “alternative” medicine

I’ve written a lot about the language issue with respect to alternative medicine. As I like to put it (at least in shortened form), first there was quackery. Quacks did not like that name at all, and thus was born alternative medicine. And the quacks did think it good—for a while. There was a problem, however. “Alternative” medicine implied (correctly, of course) that what was being discussed was not real medicine, and the quacks could not abide that. Thus was born “complementary and alternative medicine” (CAM).

And the quacks thought this very good indeed.

Unfortunately, it was not long before the problem with the term CAM became apparent. It had the word “complementary” in it. The implication of that word, of course, is that what they were doing was still somehow not real medicine. It was complementary to real medicine, the icing on the cake, if you will. Real medicine could do without it, and having that implication in the very name that their evolving specialty had taken on was offensive to the quacks.

So they changed it.

Posted in: Basic Science, Critical Thinking, Science and the Media

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Vaginal Seeding. Ew. That’s nuts. Hmmm, interesting.

A breakdown of bacterial species from your skin's microbiome. As a favor to

A breakdown of bacterial species from your skin’s microbiome. As a favor to pregnant women expectant fathers teenage boys on the internet everyone, this is the image I went with. Click to macrolaarggen (Ikean for embiggen).

Sometimes a headline will cause me to run through a series of reactions in rapid sequence. For example “Mothers facing C-sections look to vaginal ‘seeding’ to boost their babies’ health”:

Early studies show that swabbing a mother’s vagina and transferring it to her baby’s mouth, eyes and skin may stimulate microbiome development similarly to babies born naturally – and protect it from health issues later in life

I mean ick.

But take a step back. Not really. I tend to think of people like “Pig Pen” in Charlie Brown, shedding skin and bacteria into the environment. If we were to really think about each other’s microbiome, we might not have intimate contact with our significant other. Or any other animal. I always point out, when someone lets their dog lick them, that they (the dog) had probably just licked its rear, AKA dog-ass seeding. And no, a dog’s mouth is not cleaner than a human’s, unless your dog brushes and flosses with greater frequency than you. (more…)

Posted in: Basic Science, Evolution, Faith Healing & Spirituality, Humor, Nutrition

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Sharks Get Cancer, Mole Rats Don’t: Clues to Understanding Cancer

We think of cancer as caused by mutations. Mutations are necessary, but not sufficient, to cause cancer. New research indicates that it’s the body’s response to mutant cells that determines whether cancer will develop. James S. Welsh, MD, a radiation oncologist and researcher, has written a book on the immunology of cancer, Sharks Get Cancer, Mole Rats Don’t: How Animals Could Hold the Key to Unlocking Cancer Immunity in Humans. In it, he pieces together clues from animals, pregnancy, Ebola virus, infections, organ transplantation, parasites, and human cancer patients, weaving a web of insights that point to a better understanding of cancer biology and treatment.

Sharks do get cancer

Shark with cancer

Shark with cancer

The first book claiming that sharks don’t get cancer came out in 1992. It persuaded so many people to take shark cartilage that the world market exceeded $30 million and shark populations decreased by as much as 80%. Sharks do get cancer, as you can see in this picture.

Ironically, sharks can even get cancer of the cartilage! And of course shark cartilage supplements don’t prevent cancer in humans. Welsh explains how that myth got started. It was magical thinking based on extrapolation from a legitimate scientific study on angiogenesis where tumor growth in lab animals was suppressed by placing rabbit cartilage next to the tumors.

Posted in: Basic Science, Cancer

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NCCIH Strategic Plan 2016-2021, or: Let’s try to do some real science for a change

It’s no secret that we at Science-Based Medicine (SBM) are not particularly fond of the National Center for Complementary and Integrative Health (NCCIH). Formerly known as the National Center for Complementary and Alternative Medicine (NCCAM) and before that the Office of Alternative Medicine, NCCIH has been the foremost government agency funding research into quackery for the last 24 years, and, of course, that’s the reason we at SBM have been harshly critical of NCCIH since SBM’s inception. Basically, NCCIH not only funds studies of dubious “alternative” therapies, but it also promotes quackery by funding “fellowships” at various institutions to teach “integrative medicine,” or, as we like to call it, “integrating” quackery with real medicine.

Indeed, back in 2009, when President Barack Obama first took office, Steve Novella and I both suggested that the time was ripe for NCCIH to be defunded and its functions allowed to revert back to the already existing Institutes and Centers of the National Institutes of Health. We were under no illusions that this would happen, given that NCCIH always had a powerful protector in the man who was arguably more responsible for creating NCCIH and guarding it against all attempts at defunding or, even worse, forcing it to do more rigorous science, woo-loving Senator Tom Harkin (D-IA). Harkin is no longer in the Senate, having retired at the end of 2014, but NCCIH is still with us, and the nature of government makes it very much that, unless someone with power is willing to expend serious political capital to eliminate it, NCCIH will be with us always, no matter how much it tries to change its name to eliminate anything implying pseudoscience.

So those of us who recognize that NCCIH was created to promote the “integration” of “outside of the mainstream” or “unconventional” treatments (the vast majority of which are quackery) into real medicine have to learn to live with NCCIH and, as much as it might gall us, to try make lemonade out of the lemon by prodding it to doing some actual rigorous science on “complementary and alternative medicine” that have at least a modicum of biological plausibility and avoid wasting taxpayer money on fairy dust treatments whose precepts either violate the laws of physics (e.g., reiki, homeopathy, and other “energy” medicine) or depend on nonexistent anatomy or physiology (e.g., reflexology, craniosacral, traditional Chinese medicine tongue diagnosis).

This brings me to something I saw on the NCCIH Director’s Blog late last week, a post by the director Josephine Briggs, Requesting Comments on NCCIH’s Draft Strategic Plan. Patriotic US citizen and advocate of SBM that I am, how could I turn down such a request? Kimball Atwood didn’t shirk from such a request back when Dr. Briggs was asking for comments on the NCCAM 2011-2015 strategic plan, nor did I.

In fact, you, too, can comment as well. The deadline is April 15.

Posted in: Basic Science, Clinical Trials, Politics and Regulation

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The hijacking of evidence-based medicine

One of our heroes at SBM: John Ioannidis.

One of our heroes at SBM: John Ioannidis.

It’s no secret that I’m a fan of John Ioannidis. So, I daresay, are pretty much all of the editors and regular contributors to this blog. (If you don’t believe me, just type Ioannidis’ name into the blog search box and see how many posts you find.) Over the last couple of decades, Ioannidis has arguably done more to reveal the shortcomings of the medical research enterprise that undergirds our treatments, revealing the weaknesses in the evidence base and how easily clinical trials can mislead, than any other researcher. Indeed, after reading what is Ioannidis’ most famous article, “Why Most Published Research Findings Are False“, back in 2005, I was hooked. I even used it for our surgical oncology journal club at the cancer center where I was faculty back then. This was long before I appreciated the difference between science-based medicine (SBM) and evidence-based medicine (EBM). So it was with much interest that I read an article by him published last week and framed as an open letter to David Sackett, the father of evidence-based medicine, entitled “Evidence-based medicine has been hijacked: a report to David Sackett.” Ioannidis is also quoted in a follow-up interview with Retraction Watch.

Before I get to Ioannidis’ latest, I can’t help but point out that, not surprisingly, quacks and proponents of pseudoscientific and unscientific medicine often latch on to Ioannidis’ work to support their quackery and pseudoscience. They’ve been doing it for years. Certainly, they’re already latching on to this article as vindication of their beliefs. After all, their reasoning—if you can call it that—seems to boil down to: If “conventional” medicine is built on such shaky science, then their pseudoscience isn’t wrong after all, given that the same scientific enterprise upon which conventional medicine is based produces the findings that reject their dubious claims and treatments. Of course, whenever I hear this line of argument, I’m reminded of Ben Goldacre’s famous adage, seen in one form on Twitter here:

The adage can be generalized to all EBM and SBM as well. Just because big pharma misbehaves, EBM has flaws, and conventional medicine practitioners don’t always use the most rigorous evidence does not mean that, for example, homeopathy, acupuncture, or energy medicine works.

Still, when Ioannidis publishes an article with a title provocatively declaring that EBM has been “hijacked,” we at SBM take notice. (more…)

Posted in: Basic Science, Clinical Trials, Medical Academia, Pharmaceuticals, Politics and Regulation

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The Essential Role of Regulation In Human Health and In Ecology: The Serengeti Rules


The doubling time for E.coli bacteria is 20 minutes. With uncontrolled growth, it would take a mere two days for the weight of bacteria to equal the weight of the Earth. What rules determine the actual numbers of bacteria? Why is the world green; why don’t insects eat all the leaves? How does the body maintain homeostasis? What determines the uncontrolled growth of cancers? What happens when you remove natural predators from an ecosystem?

You can find the answers in Sean Carroll’s new book The Serengeti Rules: The Quest to Discover How Life Works and Why It Matters.

Everything is regulated: every kind of molecule, cell, and process in the body is maintained in a specific range and governed by a specific substance or set of substances. Diseases are mostly abnormalities of regulation. Too little insulin = diabetes. Uncontrolled cell multiplication = cancer. To intervene in disease, we need to understand the rules of regulation.

Carroll calls them the Serengeti Rules because of the ecological rules that regulate the predator/prey ratios in Africa. But the same rules apply everywhere, at every level of biology. (more…)

Posted in: Basic Science, Book & movie reviews, Cancer

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Zika virus, microcephaly, and calls to bring back DDT


If there’s one thing I’ve learned over the last decade-plus of blogging about medicine and alternative medicine, it’s that any time there is an outbreak or pandemic of infectious disease, there will inevitably follow major conspiracy theories about it. I saw it during the H1N1 pandemic in the 2009-2010 influenza season, the Ebola outbreak in late 2014, and the Disneyland measles outbreak last year, when cranks of many stripes claimed that either the outbreaks themselves were due to conspiracies (usually, but not limited to, conspiracies to promote the “depopulation” vaccination agenda of—who else?—Bill Gates) or that nefarious forces were seizing on the outbreak to take away our freedom. The second thing I’ve learned is that inevitably people will try to impose their ideology on to the disease and try to use outbreaks to push their own ideological agenda. Indeed, the Ebola outbreak, for example, was rapidly seized on by politicians to promote quarantines and to halt immigration from the affected countries. This year, the biggest infectious disease-related story thus far is the Zika virus outbreak in Brazil that has been linked to microcephaly and other birth defects, and it’s a case of the same stuff, different year.

The Zika virus is a mosquito-borne flavivirus related to dengue virus and transmitted primarily by Aedes aegypti mosquitoes. On the surface, this virus would appear to be relatively benign, with 80% of those infected by it remaining asymptomatic, while the other 20% suffer from what is usually a self-limited, relatively mild illness characterized by fever, rash, arthralgias (joint aches), and conjunctivitis. In the grand scheme of things, after decades of being endemic in many tropical areas Zika virus infection probably didn’t seem so bad and didn’t appear to be much of a public health priority in the regions where Aedes aegypti mosquitoes live, mainly tropical regions in South and Central America, Africa, southeast Asia, and the Pacific islands. Then came the evidence that prenatal infection might cause microcephaly, and everything changed. Not surprisingly, conspiracy theories galore arose with social media speed, as did the ideologically motivated overselling of proposed solutions, such as bringing back DDT to combat the mosquito carrying the disease.

Posted in: Basic Science, Epidemiology, History, Politics and Regulation

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When antivaccine pseudoscience isn’t enough, Bill Maher fawns over Charlie Sheen’s HIV quack

Bill Maher (right) expresses admiration for HIV quack Samir Chachoua (right), who claims to be able to cure people of HIV and cancer using milk from arthritic goats.

Bill Maher (right) expresses admiration for HIV quack Samir Chachoua (left), who claims to be able to cure people of HIV and cancer using milk from arthritic goats.

I know I must be getting older because of Friday nights. After a long, hard week (and, during grant season, in anticipation of a long, hard weekend of grant writing), it’s not infrequent that my wife and I order pizza, plant ourselves in front of the TV, and end up asleep before 10 or 11 PM. Usually, a few hours later, between midnight and 3 AM one or both of us will wake up and head upstairs to bed, but not always. Sometimes it’s all Friday night on the couch.

Last Friday was a bit different. It wasn’t different in that I did fall asleep on the couch sometime around 10 PM. However, unlike the usual case, when I woke up around 1:30 or 2 AM to head upstairs I was stone cold wide awake, feeling like Alex in A Clockwork Orange, eyes held wide open. So I did what I do when insomnia strikes. I popped up the computer and checked my e-mail and Facebook. Immediately, I saw messages asking me if I had seen Real Time With Bill Maher that night and, oh boy, I really should watch Maher. Apprehensive but curious, I fired up the DVR and watched.

And, shortly after the monologue, was totally appalled by this;

Funny, how the segment hasn’t yet been posted to Bill Maher’s YouTube page, as many of his interviews are. If he ever does post it, I’ll switch out the video above for the “official” source. Somehow, though, I doubt that the video will ever be posted, the reason being that it contains an embarrassingly fawning 10 minute interview with “Dr.” Samir Chachoua, better known (at least to skeptics) as Charlie Sheen’s HIV quack. Somehow, when Charlie Sheen was on The Dr. Oz Show a couple of weeks ago, other things were going on and I didn’t blog about it. Fortunately, Steve Novella did. Now, with Sheen’s very own quack who failed him being fawned over by Bill Maher, it gives me a chance to take down three birds with one stone: Bill Maher, Dr. Oz, and, of course, Sam Chachoua. Sadly for Bill Maher, America’s Quack Dr. Mehmet Oz comes off looking a lot better than he does, and that’s saying something.

Posted in: Basic Science, Cancer, Health Fraud, Vaccines

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Is “harnessing the power of placebo” worthwhile to treat anything?

We frequently write about placebo effects here on Science-Based Medicine. The reason is simple. They are an important topic in medicine and, at least as importantly, understanding placebo effects is critical to understanding the exaggerated claims of advocates of “complementary and alternative medicine” (CAM), now more frequently called “integrative medicine” (i.e., integrating pseudoscience with science). Over the years, I (and, of course, others) have documented how CAM advocates have consistently moved the goalposts with respect to the efficacy of their pseudoscientific interventions. As larger and better-designed clinical trials have been done demonstrating that various CAM therapies without a basis in science—I’m distinguishing these from science-based modalities that have been co-opted and “rebranded” as CAM, such as exercise and nutrition—have no specific effects detectable above placebo effects, CAM advocates move the goalposts and claim that CAM works through the “power of placebo” and do their best to claim that “harnessing” that “power of placebo” is a justification to use their treatments. It turns out, however, that when placebo effects are examined rigorously there’s just not a lot of there there, so to speak. Results are underwhelming, and trying to “harness the power of placebo” without an intervention that actually impacts the pathophysiology of disease can even be dangerous. That’s not to say that learning to maximize placebo responses (whatever they are) while administering effective medical treatments isn’t important; rather, it’s to point out that, by themselves, placebo effects are not of much value.

Unfortunately, none of this has stopped what Steve Novella refers to as the “placebo narrative” from insinuating itself into lay discussions of medicine. That narrative proclaims in breathless terms (as Steve put it) the “surprising power of the placebo effect” without putting it into reasonable perspective or even really defining what is meant by “placebo effect.” First, as we have tried to explain time and time again here, there is no single “placebo effect.” There are placebo effects. Second, the only really correct reference to “the placebo response” or “placebo effect” is the outcome measured in the placebo arm of a clinical trial. The problem is that, all too often, discussions of placebo responses conflate the placebo effect measured in a clinical trial with all the other various placebo effects that add up to the response that is measured in that trial. Those effects include reporting biases, researcher biases, regression to the mean, conditioning, and many other components that contribute to what is measured in the outcome of a clinical trial. Another common misconception about placebo effects is that they are somehow “mind over matter,” that we can heal ourselves (or at least reduce our symptoms) through the power of will and mind. This is not true. Placebo effects are not the power of positive thinking.

Posted in: Acupuncture, Basic Science, Clinical Trials, Homeopathy, Science and the Media

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