Archive for Basic Science

H. Pylori, Plausibility, and Greek Tragedy: the Quirky Case of Dr. John Lykoudis

Mark Crislip is on vacation, but through an arduous series of shakings and succussions (beating his head against the wall?) we have channeled part of his essence: This post mostly concerns itself with infectious diseases, thanks to several recent posts on SBM that discussed the plausibility of health claims† and that touched on the recent discovery that most peptic ulcer disease (PUD) is caused by a bacterium, Helicobacter pylori. Several comments and statements quoted in those posts reveal recurrent questions regarding both plausibility itself and the history of the H. pylori hypothesis. In this post I’ll attempt to answer some of those questions, but I’ll also insert some new confusion.

Plausibility ≠ Knowing the Mechanism

Let’s first dispense with a simple misunderstanding: We, by which I mean We Supreme Arbiters of Plausibility (We SAPs) here at SBM, do not require knowing the mechanism of some putative effect in order to deem it plausible. This seems so obvious that it ought not be necessary to repeat it over and over again, and yet the topic can’t be broached without some nebbishy South Park do-gooder chanting a litany of “just because you don’t know how it works doesn’t mean it can’t work,” as if that were a compelling or even relevant rebuttal. Let’s get this straight once and for all: IT ISN’T.


Posted in: Basic Science, History, Science and Medicine

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Chronic Fatigue Syndrome and Retroviruses: Jumping the Gun

When I first heard that a retrovirus had been identified as a possible cause of chronic fatigue syndrome, I withheld judgment and awaited further developments. When I heard that two subsequent studies had failed to replicate the findings of the first, I assumed that the first had been a false alarm and would be disregarded. Not so.

 It’s a classic case of wishful thinking outweighing good judgment. One unconfirmed report of an association between the XMRV virus and chronic fatigue syndrome (CFS) resulted in a rush to test for the virus, speculation about possible implications, and even suggestions for treatment. And the subsequent negative studies did little or nothing to reverse the trend. 

XMRV is Xenotropic murine leukemia virus-related virus. In the past, there were reports that this retrovirus was associated with prostate cancer, but then other reports found no link. In 2009 a study was published in Science, “Detection of an Infectious Retrovirus, XMRV, in Blood Cells of Patients with Chronic Fatigue Syndrome” by Lombardi et al., reporting an association with CFS:

we identified DNA from a human gammaretrovirus, xenotropic murine leukemia virus–related virus (XMRV), in 68 of 101 patients (67%) as compared to 8 of 218 (3.7%) healthy controls. (more…)

Posted in: Basic Science, Science and Medicine

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The Microbial Metagenome

First some background.  I was first directed to the Marshall protocol by a reader who wondered about the information the found on the web.  So I went to the web and looked at the available information, much as any patient would, and discussed what I found there.

I have subsequently been lead to believe that none of the information on the website can be considered up to date or accurate.  As as result of,  I have told that my post is chockablock with errors, although, outside of writing doxycycline where I should have put minocycline, I am left in the dark as to exactly what my errors are.  I am told that it is my responsibility to locate the errors in the last post, yet I can find none when compared to the website.

However, to remedy the deficiency of having reviewed inaccurate and out of date material,  I have been sent 6 articles that I am informed represent the state of the art in understanding the science behind the Marshall protocol.  Ah, the peer reviewed medical literature.  An opportunity to carefully read and critique new  ideas.  It is one of the reasons people publish: to see if their ideas can withstand the scrutiny of others.

Several of these papers concern Vitamin D,  the Vitamin D receptor, and olmesartan which I will review, perhaps, another time.  I don’t find them a compelling read, but it not an area about which I have more than a standard medical knowledge. The other papers concern the role of infection in autoimmune diseases, which I will discuss here.  It is easier as an infectious disease doctor  to read this literature as I am, as least as far as the American Board on Internal Medicine is concerned, a specialist in the field.  Alternatively, I am a closed minded tool of the medical industrial complex who only seeks to push his own twisted, narrow agenda at the expense of suffering patients (1).  We can’t all be perfect.

Posted in: Basic Science, Medical Ethics, Science and Medicine

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Functional Medicine II

In searching for just what FM is, one has to in a way read between lines. Claiming to treat the “underlying cause” of a condition raises the usual straw man argument that modern medicine does not, which of course is untrue. It also implies that there are underlying causes known to them and not to straights. FM claims to treat chronic disease which FM claims is inadequately treated by medicine.  FM claims to be a more advanced approach both in conceptual thinking and in practical management. Such claims are on the face doubtful, but hard to disprove. The way to find out would be to analyze cases they manage and critique them.

I tried to see specific examples of treatments but the web page text book links were not working at the time. I understand others have seen the contents and perhaps can add some information.   I sense a difference between “CAM” and FM – at least among the MDs and DOs -  is that FMers tend to use methods and substances with some degree of scientific or biochemical rationale, even if not proved, moreso than many of the CAMers.  Many seem to practice both systems or do not distinguish between the two systems.  In order to get a sense of the degree to which FM is known, I requested from the web page the names of practitioners in a 50 mile radius of my home (near Palo Alto, Calif.). The names ranged from Santa Cruz (40 miles) to Berkeley (50) and San Francosco (40) and Marin County (Sausalito – 50 miles) The population of that area is about 5 million. They sent 46 names:   MD/DO  31 – (including a nephrologist formerly on the staff of my teaching hospital)   PhD 1   DC 8   Lac 3   ND 2   RN 1   Because I had become aware of FM only 1-2 years ago, I thought 46 was a relatively large number.  The Web page lists four text books published in the past few years. A manuscript of the first one is available on line for downloading (not functioning when I tried.) .  21st Century Medicine: A New Model for Medical Education and PracticeMonograph Set – Functional Medicine Clinical Monograph Set – CME Available Textbook of Functional Medicine Clinical Nutrition: A Functional ApproachAs mentioned, I could not activate the links to those books, and did not have time to get to them individually.  No authors were listed.


Posted in: Basic Science, General, Health Fraud, Herbs & Supplements, Nutrition, Science and Medicine

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The clinician-scientist: Wearing two hats

About a week ago, Tim Kreider wrote an excellent post about the differences between medical school training and scientific training. As the only other denizen of Science-Based Medicine who has experienced both worlds, that of a PhD and that of an MD, and as the one who two decades further along the path than Tim (give or take a couple of years), his musings reminded me of similar musings I’ve had over the years, as well as emphasizing yet again something I’ve said time and time again: Most physicians are not scientists. They are not trained like scientists; they are trained to apply scientific knowledge to the care of their patients. That’s what science-based medicine is, after all, applying science to the care of patients. Not dogma. Not tradition. Not knowledge of antiquity. Science.

Leave dogma, tradition, and “ancient knowledge” to practitioners of “alternative medicine.” That’s where they all belong. Whether you want to call it “alternative medicine,” “complementary and alternative medicine” (CAM), or “integrative” medicine (IM), it rarely changes and almost never abandons therapies that science finds to be no better than placebo, whereas scientific medicine is, as it should be, ever changing, ever improving. I’ll grant you that the process is often messy. There are often false starts and blind alleys, and physicians are all too often reluctant to change their practices in response to the latest scientific findings. We sometimes even joke that for some practices, it takes the supplanting of one generation of physicians with a new generation to get rid of some practices. But change does come when the science and evidence are there. Indeed, for example, in response to evidence that a bacterium, H. pylori, causes duodenal ulcers, medical practice changed in a mere decade, which is about as fast as anyone could do the science and clinical trials to show the validity of the new concept. Although CAM practitioners like to hold up the example of Barry Marshall and Robin Warren, the researchers who discovered that H. pylori causes most duodenal ulcers, as an example of how researchers with radical ideas are ostracized, but that story is largely a myth, as our very own Kim Atwood showed.

The application of science to medicine is a difficult thing. It takes basic scientists and clinicians, but the two of them exist in different worlds. Or so it often seems. That’s why some individuals seek to straddle both worlds. Tim is one such person. So am I. Unfortunately, most people don’t understand what we do very well. We wear two hats. In my case, I’m a surgeon, and I’m a scientist. In Tim’s case, he’s a scientist and a physician, but he doesn’t yet know what kind of physician he will end up being. At the risk of sounding somewhat arrogant, I believe that we, and others like us, represent an important element in bridging the gap between basic science and clinical science, in, essentially, building a more science-based medicine.

Posted in: Basic Science, Clinical Trials, Medical Academia

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Functional Medicine (FM) What Is It?

Functional Medicine – What is it?

After extensive searching and examination, my answer is still – only the originators of “FM” know. Or, at least one must assume they know, because so far as I can see, I certainly see nothing that distinguishes “FM” from other descriptions of sectarian and “Complementary/Alternative Medicine” practices. A difference may lie in the advocates’ assumptions to have found some “imbalance” of body chemistry or physiology before applying one or more unproved methods or substances. From what I could determine, the “imbalance” or dysfunction is usually either imaginary or at least presumptive. And the general principles are so poorly defined as to allow practioners vast leeway to apply a host of unproven methods.

I figured there would be several ways to find out. One would be to read FM’s material – mainly what “they” placed on the Internet. Another would be to enter the system and find out as a patient or as a prospective practitioner what it is that “FM” claims to be. The third would be to listen to a practitioner or advocate on tape, disk, radio, etc.

Posted in: Basic Science, Herbs & Supplements, Nutrition, Science and Medicine

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Does popularity lead to unreliability in scientific research?

One of the major themes here on the Science-Based Medicine (SBM) blog has been about one major shortcoming of the more commonly used evidence-based medicine paradigm (EBM) that has been in ascendance as the preferred method of evaluating clinical evidence. Specifically, as Kim Atwood (1, 2, 3, 4, 5, 6, 7, 8) has pointed out before, EBM values clinical studies above all else and devalues plausibility based on well-established basic science as one of the “lower” forms of evidence. While this sounds quite reasonable on the surface (after all, what we as physicians really want to know is whether a treatment works better than a placebo or not), it ignores one very important problem with clinical trials, namely that prior scientific probability matters. Indeed, four years ago, John Ioannidis made a bit of a splash with a paper published in JAMA entitled Contradicted and Initially Stronger Effects in Highly Cited Clinical Research and, more provocatively in PLoS Medicine, Why Most Published Research Findings Are Wrong. In his study, he examined a panel of highly cited clinical trials and determined that the results of many of them were not replicated and validated in subsequent studies. His conclusion was that a significant proportion, perhaps most, of the results of clinical trials turn out not to be true after further replication and that the likelihood of such incorrect results increases with increasing improbability of the hypothesis being tested.

Not surprisingly, CAM advocates piled onto these studies as “evidence” that clinical research is hopelessly flawed and biased, but that is not the correct interpretation. Basically, as Steve Novella and, especially, Alex Tabarrok pointed out, prior probability is critical. What Ioannidis’ research shows is that clinical trials examining highly improbable hypotheses are far more likely to produce false positive results than clinical trials examining hypotheses with a stronger basis in science. Of course, estimating prior probability can be tricky based on science. After all, if we could tell beforehand which modalities would work and which didn’t we wouldn’t need to do clinical trials, but there are modalities for which we can estimate the prior probability as being very close to zero. Not surprisingly (at least to readers of this blog), these modalities tend to be “alternative medicine” modalities. Indeed, the purest test of this phenomenon is homeopathy, which is nothing more than pure placebo, mainly because it is water. Of course, another principle that applies to clinical trials is that smaller, more preliminary studies often yield seemingly positive results that fail to hold up with repetition in larger, more rigorously designed randomized, double-blind clinical trials.

Last week, a paper was published in PLoS ONE Thomas by Thomas Pfeiffer at Harvard University and Robert Hoffmann at MIT that brings up another factor that may affect the reliability of research. Oddly enough, it is somewhat counterintuitive. Specifically, Pfeiffer and Hoffmann’s study was entitled Large-Scale Assessment of the Effect of Popularity on the Reliability of Research. In other words, the hypothesis being tested is whether the reliability of findings published in the scientific literature decreases with the popularity of a research field. Although this phenomenon is hypothesized based on theoretical reasoning, Pfeiffer and Hoffmann claim to present the first empirical evidence to support this hypothesis.

Posted in: Basic Science, Clinical Trials, Science and Medicine

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Could Francis Collins’ Faith Create Conflicts For His Potential Directorship of NIH?

Francis Collins, M.D., Ph.D., is probably best known for his leadership of the Human Genome Project, though his discoveries of the Cystic Fibrosis, Huntington’s, and Neurofibromatosis genes are also extraordinary accomplishments. Dr. Collins is a world-renowned scientist and geneticist, and also a committed Christian. In his recent best-selling book, The Language Of God, Dr. Collins attempts to harmonize his commitment to both science and religion.

Some critics (such as Richard Dawkins) have expressed reservations about Dr. Collins’ faith, wondering if it might cloud his scientific judgment. Since Collins is rumored to be the most likely candidate for directorship of the NIH, and because I wanted to know if Dawkins et al. had any reason for concern, I decided to read The Language Of God.

First of all, Christians are a rather heterogeneous group – with a range of viewpoints on evolution, science, and the interpretation of Biblical texts. On one extreme there are Christians (often referred to as “young earth creationists” or simply “creationists”) who believe in an absolutely literal interpretation of the Genesis story, and see evolution as antithetical to true faith. Dr. Collins suggests that as many as 45% of Christians may actually be in this camp.

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

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Cancer research: Going for the bunt versus swinging for the fences

A couple of weeks ago, our resident skeptical medical student Tim Kreider wrote an excellent article about an op-ed in NEWSWEEK by science correspondent Sharon Begley, in which he pointed out many misconceptions she had regarding basic science versus translational research, journal impact factors, and how journals actually determine what they will publish. Basically, her thesis rested on little more than a few anecdotes by scientists who didn’t get funded or published in journals with as high an impact factor as they thought they deserved, with no data, science, or statistics to tell us whether the scientists featured in her article were in fact representative of the general situation. Begley’s article caught flak from others, including Mike the Mad Biologist and our very own Steve Novella. Naturally, as the resident cancer surgeon and researcher, I had thought of weighing in, but other issues interested me more at the time.

In retrospect, I rather regret it, given that this issue crops up time and time again. In essence, it’s a variant of the lament that pops up in the press periodically, when science journalists look at survival rates for various cancers and ask why, after nearly 40 years, we haven’t yet won the war on cancer. Because of his youth, Tim probably hasn’t seen this issue crop up before, but, trust me, every couple of years or so it does. Begley’s article and the NYT article strike me as simply “Why are we losing the war on cancer?” 2009 edition.

Now the New York Times has given me an excuse both to revisit Begley’s article and discuss yesterday’s front page article in the NYT Grant System Leads Cancer Researchers to Play It Safe. Basically, they are variants of the same complaints I’ve heard time and time again. Now, don’t get me wrong. By no means am I saying that the current system that the NIH uses to determine which scientists get funded. Those who complain that the system is often too conservative have a point. The problem, all too often, however, is that the proposals for how to fix the problem are usually either never spelled out or rest on dubious assumptions about the nature of cancer research themselves.

Posted in: Basic Science, Cancer, Medical Academia, Politics and Regulation

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Applying evolutionary principles to cancer treatment

ResearchBlogging.orgEDITOR’S NOTE: Unfortunately, this weekend, I was forced to get my slides together for the upcoming SBM Conference, plus editing a manuscript for resubmission, plus working on a manuscript that I should have submitted six months ago, plus reading over some grants, plus…well, you get the idea. What this means is that, alas, I didn’t have any time to prepare one of the new, long posts that you’ve come to love (or hate). Fortunately, there are a lot of other things I’ve written out there that can be rapidly adapted to SBM. For instance, what I am about to present now. Since I wrote this, I’ve thought of a couple of things that I should have said the first time (and was kicking myself for not having done so); so publishing an updated version here allows me to rectify those omissions.

A couple of weeks ago, there was a lot of hype about a study that hadn’t been released yet. Indeed, there was a story in Wired entitled To Survive Cancer, Live With It and an editorial by the study’s lead author in Nature entitled A change in strategy in the war on cancer. Not bad for a study that hadn’t been released yet. Intrepid medical and science blogger that I am, I waited until the actual study was published a week ago the June 1 episode of Cancer Research. It’s a clever study, but the hype over it was a bit overblown. For example:

For all the weapons deployed in the war on cancer, from chemicals to radiation to nanotechnology, the underlying strategy has remained the same: Detect and destroy, with no compromise given to the killer. But Robert Gatenby wants to strike a peace.

A mathematical oncologist at the Moffitt Cancer Center, Gatenby is part of a new generation of researchers who conceive of cancer as a dynamic, evolutionary system. According to his models, trying to wipe cancer out altogether actually makes it stronger by helping drug-resistant cells flourish. Rather than fighting cancer by trying to eradicate its every last cell, he suggests doctors might fare better by intentionally keeping tumors in a long-term stalemate.

Maybe I’m being a bit picky, but what annoys me about the news reports on this study is that the concept of turning cancer into a manageable chronic disease like diabetes or hypertension is not by any means a new idea. Remember, one of my major research interests is the inhibition of tumor angiogenesis. Consequently, I know that the late, great Judah Folkman first proposed the concept of using antiangiogenic therapy to turn cancer into a chronic disease at least as early as the mid-1990′s. The only difference is the strategy that he proposed. The idea had also been floating around for quite a while before that, although I honestly do not know who first came up with it.

But let’s see what Dr. Gatenby proposes. What makes it interesting is that his study actually looks at how scientists have applied evolutionary principles to cancer until recently, argues that we’ve been doing it wrong. He then proposes a way to use the evolutionary dynamics of applied ecology. He may well be on to something. First, here’s the problem:

Posted in: Basic Science, Cancer, Science and Medicine

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