John Mattick's seminar at the University of Toronto

I just learned that John Mattick gave a seminar this morning at the Department of Cell & Systems Biology at the University of Toronto. Unfortunately, I was unable to attend.

Most Sandwalk readers will recognize Mattick as one of the few remaining vocal opponents of junk DNA. He is probably best known for his dog-ass plot but this is only one of the ways he misrepresents science.

More genomes, more variation

The "All of Us Research Program" is an American effort to sequence one million genomes. The stated goal is to study human genetic variants and link them to genetic diseases. The study is complimentary to similar studies in Great Britain, Iceland, and Japan but the American team hopes to include more diversity in their study by recruiting people from different ethnic backgrounds.

All of Us published the results from almost 250,000 genome sequences in a recent issue of Nature (All of Us Research Program Investigators, 2024). They found one billion variants of which 275 million had not been seen before.

Recall that the UK study (UK Biobank) emphasized the importance of variation in determining whether a given region of DNA was functional or not. They noted that regions that were constrained (i.e. fewer variants) were likely under purifying selection whereas regions that accumulated variants were likely junk [Identifying functional DNA (and junk) by purifying selection]. Their results indicated that only about 10% of the genome was constrained and that's consistent with the view that 90% of our genome is junk. The American study did not address this issue so we don't know how it related to the junk DNA controversy.

Note that if 90% of our genome is junk then that represents 2.8 billion base pairs and the potential for more than 8 billion variants in the human population.¹ Some of these will be quite frequent in different groups just by chance but most of them will be quite rare. We'll have to wait and see how this all pans out when more genomes are sequenced. The idea of increasing the detection of unusual variants by sequencing more diverse populations is a good one but the real key is just more genome sequences.

One of the things you can do with this data is to cluster the variants according to the self-identified ethnic group of the participants and All of Us didn't hesitate to do this. They even identified the clusters as races, proving once again that there are clear genetic diffences between these groups, just as you would expect. Given the sensitive nature of this fact, you would also expect a lot of criticism on the internet and that's what happened.

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1. I'm defining a "variant" as a difference from the reference genome sequence. I'm aware of the terminology issue but it's not important here. There will also be a large number of variants in the functional regions.

All of Us Research Program Investigators (2024) Genomic data in the All of Us Research Program. Nature 627:340. [doi: 10.1038/s41586-023-06957-x].

About half of all cancers are just bad luck. It's not your fault.

There's been a lot of talk recently about a paper claiming that two thirds of all cancers are due to bad luck [Bad Luck of Random Mutations Plays Predominant Role in Cancer, Study Shows]. The take-home message was that you could get cancer even if you ate "healthy," took lots of vitamins, didn't smoke, and went to the gym every day. That's not what people wanted to hear.

But scientists have known for decades that many cancers are due to random mutations that just happen. These cancers are not hereditary and are not caused by the environment. There's nothing new here.

That didn't stop a number of people from criticizing the article and some of the criticisms were justified. Nevertheless, what the article showed was that cancers tended to occur more often in tissues with lots of cell divisions (and DNA replications). That's exactly what you expect if random mutations due to replication errors are the cause of the cancer mutations.

David Gorski of Science-Based Medicine sorts it all out for us [Is cancer due mostly to “bad luck”?]. Please read his lengthy article if you want to understand the issues. David Gorski concludes ...

It’s understandable that humans crave explanation, particularly when it comes to causes of a group of diseases as frightening, deadly, and devastating as cancer. In fact, both PZ Myers and David Colquhoun have expressed puzzlement over why there is so much resistance is to the concept that random chance plays a major role in cancer development, with Colquhoun going so far as to liken it to ” the attitude of creationists to evolution.” Their puzzlement most likely derives from the fact that they are not clinicians and don’t have to deal with patients, particularly given that, presumably, they do have a pretty good idea why creationists object to attributing evolution to random chance acted on by natural selection and other forces.

Clinicians could easily have predicted that a finding consistent with the conclusion that, as a whole, probably significantly less than half of human cancers are due to environmental causes that can be altered in order to prevent them would not be a popular message. Human beings don’t want to hear that cancer is an unfortunately unavoidable consequence of being made of cells that replicate their DNA imperfectly over the course of our entire lives. There’s an inherent hostility to any results that conclude anything other than that we can prevent most, if not all, cancers if only we understood enough about cancer and tried hard enough. Worse, in the alternative medicine world there’s a concept that we can basically prevent or cure anything through various means (particularly cancer), most recently through the manipulation of epigenetics. Unfortunately, although risk can be reduced for many cancers in which environmental influences can increase the error rate in DNA replication significantly, the risk of cancer can never be completely eliminated. Fortunately, we have actually been making progress against cancer, with cancer death rates having fallen 22% since 1991, due to combined efforts involving smoking cessation (prevention), better detection, and better treatment. Better understanding the contribution of stochastic processes and stem cell biology to carcinogenesis could potentially help us do even better.

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Baldness Is not a Disease. It Does not Need to Be "Cured"

A recent article in New Scientist made me annoyed. The title in the print edition is Cure for Baldness Finally Cuts It. It starts off with ...

We may be a hair's breadth away from a cure for baldness.

Baldness is not a disease so it doesn't need to be cured.¹ Gray hair is also not a disease and neither are the wrinkles that appear on your face as you get older.

You may choose to disguise baldness with hair transplants or paint your white hairs to make it look like you don't have them. You can even inject botox to hide wrinkles. If you do this, the only disease you have is vanity. And stupidity, for letting the cosmetic industry trick you into feeling guilty about a perfectly natural phenomenon.

I'm never going to let my tax money pay for your vanity "cure." Don't even ask if it should be covered by our public health insurance.

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1. Don't quibble. You know that what I'm talking about is the normal kind of baldness in men that develops as you get older.

October 7-14th Is Quackery Week

The week is half over and nobody told me it's Quackery Week. Perhpas that's because it's only Quackery Week in the USA. The US Senate passed a resolution ...

A resolution designating the week of October 7 through October 13, 2013, as “Naturopathic Medicine Week” to recognize the value of naturopathic medicine in providing safe, effective, and affordable health care.

Don't worry. Orac is on to it with: Naturopaths and vaccines.

But let's not forget that the Canadian College of Naturopathic Medicine makes their students take a course in Homeopathic Medicine and another im Asian Medicine and Acupuncture [Naturopathic "Doctors" Graduate from Convocation Hall on the University of Toronto Campus].

This is one more reason why we have to teach critical thinking in high school and in universities.

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Don't Muzzle Our Doctrors

 
Last summer, the Ontario College of Physicians and Surgeons published a draft proposal on Non-Allopathic (Non-Conventional) Therapies in Medical Practice. It was horrible. As I noted at the time, "The document is flawed from the beginning because it gives credence and respectability to "alternative medicine," otherwise known as non-evidence based medicine or quackery" [Non-Allopathic (Non-Conventional) Therapies in Medical Practice].

Many groups took notice of the draft policy and criticized the Ontario College of Physicians Surgeons for their gutless response to a serious crisis in health. One of those groups was the Committee for the Advancement of Scientific Skepticism, a committee of Canada's Centre for Inquiry [Media Advisory: Ontario Doctors Given the Green Light to Promote Quackery]. The members of CASS worked hard to lobby for changes and they co-ordinated their activities with several other groups that are opposed to the weak-kneed position of the College.¹ The College conducted a survey of its members and discovered that 78% of them opposed the draft policy. About one third of the people who filled out the survey were directed to the site by CASS or its allies [Skeptical Activism Sends a Message to CPSO. Very impressive.

Those behind-the-scenes activities had an impact as more and more people voiced their criticism on the FeedBack Site.

All this lobbying convinced the Toronto Star newspaper that something serious was afoot and yesterday, Sunday Nov. 20, 2011, the newspaper published an editorial that sides with science [Don’t muzzle our doctors]. The paper deserves praise for getting it right and giving us hope that science will win in the end..

Patients walk into allergist Dr. David Fischer’s office almost every day expressing interest in trying “natural” therapies. These range from harmless diet changes to the truly bizarre, like applied kinesiology, says the Barrie physician. It’s an experience shared by other doctors. “We’re on the front line of dealing with ideas for which there is often a dearth of scientific evidence.”

Alternative medicine is booming even without much proof it works. A record 20,000 people are expected at Toronto’s Whole Life Expo at the downtown convention centre next weekend. Three-quarters of Canadians regularly use some form of natural health product, opening their wallets to spend at least $4.3 billion yearly. And the herbs and homeopathic tinctures they buy are just one facet of unconventional medicine — a thriving sector encompassing everything from acupuncture to zone therapy (supposedly stimulating the body’s organs through hand or foot massage).

Ontario’s College of Physicians and Surgeons is bending to the trend with a new policy inhibiting doctors’ criticism of unconventional therapies. In doing so it risks encouraging even broader use of dubious and potentially harmful treatments.

Make no mistake — blind trust in alternative cures can be dangerous. An unknown number of Canadians are opting out of science-based medicine to treat even deadly conditions, like cancer, with unproven “natural” approaches.

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The field of allergy medicine, Fischer’s specialty, is especially prone to alternative approaches. Natural practitioners using applied kinesiology, for example, check for allergy by placing a food item in a patient’s mouth or in their hand. Then they pull down on the person’s free arm to assess its strength. If this “muscle testing” shows notable weakness, the patient is deemed to be allergic.

There is no good evidence that this method works, and no sound scientific reason why it should. Yet patients come in with an interest in that, says Fischer. “I’d like to be able to tell them it’s quackery.”

He may not be in a position to say so much longer under a new policy proposed by the college of physicians and surgeons. It states that doctors are obliged to give a patient their best professional opinion on an alternative treatment goal or decision, but physicians “must refrain from expressing personal, non-clinical judgments.”

....

There’s no denying alternative medicine is immensely popular. Patients are more independent than ever before, often researching their illness and trusting their own solutions. And a host of unconventional “natural” healers has risen capitalizing on that trust — offering unproven therapies with little validity and which, in some cases, are a menace.

The college shouldn’t seek to accommodate that trend or retreat to a neutral corner. Rather it should leave doctors free to punch hard against those peddling dubious cures and to challenge people’s comforting, but irrational, beliefs. Science-based medicine serves patients best. If doctors can’t vigorously defend it, who will?

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1. I'm a member of CASS but I had nothing to do with this campaign.

Non-Allopathic (Non-Conventional) Therapies in Medical Practice

The College of Physicians and Surgeons of Ontario has produced a draft policy on Non-Allopathic (Non-Conventional) Therapies in Medical Practice. The document is flawed from the beginning because it gives credence and respectability to "alternative medicine," otherwise known as non-evidence based medicine or quackery.

The policy is designed to provide guidelines for physicians who are: (1) tempted to employ non-evidence based medicine, (2) tempted to condone non-evidence based medicine in situations where it might harm patients. We all recognize that front-line physicians face these issues all the time and they often find themselves in a position where they disagree with the choices their patients are making.

However, most physicians don't hesitate to tell you that you should stop smoking. They seem to enjoy lecturing you on the benefits of diet and exercise even when it's clear that a patient prefers a different lifestyle. Why should it be any different when a patient reveals that they are taking homeopathic concoctions or when they refuse to vaccinate their children. Don't physicians have a professional responsibility to inform their patients that they are making unwise decisions?

The draft policy address these issues but it does so in a way that's far too lenient toward quack medicine. To begin with, it defines allopathic medicine as,

Different operative terms have been adopted that were deemed to be value-neutral: ‘Allopathic medicine’ refers to traditional or conventional medicine (as taught in medical schools) and ‘non-allopathic therapies’ refer to complementary or alternative medicine.

This is idiotic. "Allopathic" medicine is NOT a value-neutral term. It's the term used by homoepathic quacks to describe medicine that uses drugs to treat patients. By adopting this terminology, the College of Physicians and Surgeons is playing right into the hands of the quacks.

Allopathic Medicine: refers to the type of treatment, diagnostic analysis and conceptualization of disease or ailment that is the primary focus of medical school curricula and which is generally provided in hospitals and specialty or primary care practice.

Non-Allopathic Therapies (Non-Conventional Therapies): refers to a broad range of procedures or treatments that are not commonly used in allopathic medicine; this includes those referred to as complementary or alternative. Non-allopathic therapies tend to differ from allopathic medicine in terms of diagnostic techniques, theories of illness and disease, and treatment paradigms. The categorization of specific therapies as non-allopathic is fluid: as clinical evidence regarding efficacy is accumulated, certain non-allopathic therapies may gain broad acceptance and thus be accepted in allopathic medicine.

I work in a medical school. The operative phase is "evidence-based medicine" and I suspect that's a term used in most medical schools in Ontario. That's what is taught in medical schools and hospitals and that's how you describe proper medicine.

The opposite of evidence-based medicine is "non-evidence-based treatment." Those are not "value-neutral" terms. They are something different—it's called "truth," and truth is not neutral. The College of Physicians and Surgeons needs to acquire some gumption and stand up for what's being taught in the medical schools and stand up for science. This draft policy is ridiculous, it announces that the College is abandoning science and evidence in favor of condoning quackery.

Here's how the draft policy would read if we substitute the true definitions.

Respect Patient Autonomy

Patients are entitled to make treatment decisions and to set health care goals that accord with their own wishes, values and beliefs. This includes decisions to pursue or to refuse evidence-based or non-evidence based therapies.

The College expects physicians to respect patients’ treatment goals and decisions, even those which physicians deem to be unfounded or unwise. In doing so, physicians should state their best professional opinion about the goal or decision, but must refrain from expressing non-clinical judgements.

Nothing has been lost by using "evidence-based" instead of "allopathic." Now, let's look at the meaning of this policy statement.

It's classic gobbledygook because it confuses "respect" with "responsibility." Physicians are not obliged to "respect" parents who refuse to give their child a life-saving blood transfusion. They aren't obliged to "respect" parents who deny their children vaccinations. They certainly don't "respect" parents who abuse their children. And I've never encountered a physician who "respects" smokers and drug users, have you?

Lots of patients don't earn respect and don't deserve it.

Read the guideline carefully as I amended it. If they were adhered to, then no physician could possibly recommend non-evidence based therapies since that would conflict with their professional opinion (or, at least it should). But later on we read,

Providing Non-Allopathic Therapies

When providing non-allopathic therapies, physicians are expected to demonstrate the same commitment to clinical excellence and ethical practice, as they would when providing allopathic care.

What the heck is that all about? The policy should read ...

Any physician who provides non-evidence based therapies (especially for a fee) will be subject to charges of professional misconduct and may lose his/her license to practice medicine in Ontario.

That's the only sensible policy that's consistent with what's written elsewhere in the document. You simply can't provide non-evidence-based therapies while maintaining "a commitment to clinical excellence and ethical practice." That's oxymoronic.

The Committee for the Advancement of Scientific Skepticism (CASS) is very interested in this issue. Read what Michael Kruse has to say on his blog Skeptic North: Ontario Doctors Given Green Light to Promote Quackery.

I would not be writing this if I thought we could do nothing to oppose and change the viewpoint of the CPSO. That is why CASS is calling on members of both the public and the medical field to read the policy and comment on it. There is strong representation in the current comments of supporters of alternative medicine and we do not want all of the feedback to be pro-pseudoscience. Please visit the CPSO policy site above and fill out the comment form available at the bottom of the page. The deadline for this consultation is September 1st 2011, so we must move quickly and let the CPSO know the safety of Ontarians depends upon sound medical opinion based on modern scientific evidence.

Please voice your opinion at Feedback: Non-Allopathic Therapies draft policy. Your response has to sent by email to ThirdPartyProcesses@cpso.on.ca. I have no idea how much censorship is applied to the responses they post—I suspect it's considerable so don't expect criticisms to appear on the website.

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HuffPost Heatlh?

 
I don't read the Huffington Post but Orac over at Respectful Insolence does. He notes that it is about to start a new section called HuffPost Health. Here's how it's going to work.

HuffPost Health will be a clear and balanced resource to provide a comprehensive view of the state of health and health news in a given day. It will provide a forum for intelligent discourse and divergent but respectful points of view. HuffPost Health will empower you with state of the art information you can use to make informed and intelligent decisions that affect your life in meaningful ways.

In this spirit, HuffPost Health's articles and videos will include the best of evidence-based allopathic Western medicine (including drugs and surgery), lifestyle and functional medicine (including nutrition, fitness, stress management, supplements, and love and support), mind/body medicine (including mental and emotional health), women's and men's health issues, and integrative medicine (including complementary and alternative medicine).

I bet you can hardly wait! Neither can Orac 'cause "there'll be a lot of new blogging material." More importantly, Orac notes that HuffPost Health might soon become a handy source of all quackery: HuffPost Health: A soon-to-be one-stop shop for quackery. We're going to need something like this once the Oprah Show and Larry King Live go off the air.

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Lies, Damned Lies, and Medical Science

 
Here's an article from the Atlantic that everyone should read: Lies, Damned Lies, and Medical Science. It highlights the efforts of John Ioannidis to discover what's true and what's not true about modern medical research publications and clinical trials. I think this is going to become one of the hottest topics in science within a few years. The fallout will be horrendous when the public realizes that doctors are not as scientific as we thought.

Some interesting quotes from the article should prompt you to follow the link to the Atlantic website.

It didn’t turn out that way. In poring over medical journals, he was struck by how many findings of all types were refuted by later findings. Of course, medical-science “never minds” are hardly secret. And they sometimes make headlines, as when in recent years large studies or growing consensuses of researchers concluded that mammograms, colonoscopies, and PSA tests are far less useful cancer-detection tools than we had been told; or when widely prescribed antidepressants such as Prozac, Zoloft, and Paxil were revealed to be no more effective than a placebo for most cases of depression; or when we learned that staying out of the sun entirely can actually increase cancer risks; or when we were told that the advice to drink lots of water during intense exercise was potentially fatal; or when, last April, we were informed that taking fish oil, exercising, and doing puzzles doesn’t really help fend off Alzheimer’s disease, as long claimed. Peer-reviewed studies have come to opposite conclusions on whether using cell phones can cause brain cancer, whether sleeping more than eight hours a night is healthful or dangerous, whether taking aspirin every day is more likely to save your life or cut it short, and whether routine angioplasty works better than pills to unclog heart arteries.

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Still, Ioannidis anticipated that the community might shrug off his findings: sure, a lot of dubious research makes it into journals, but we researchers and physicians know to ignore it and focus on the good stuff, so what’s the big deal? The other paper headed off that claim. He zoomed in on 49 of the most highly regarded research findings in medicine over the previous 13 years, as judged by the science community’s two standard measures: the papers had appeared in the journals most widely cited in research articles, and the 49 articles themselves were the most widely cited articles in these journals. These were articles that helped lead to the widespread popularity of treatments such as the use of hormone-replacement therapy for menopausal women, vitamin E to reduce the risk of heart disease, coronary stents to ward off heart attacks, and daily low-dose aspirin to control blood pressure and prevent heart attacks and strokes. Ioannidis was putting his contentions to the test not against run-of-the-mill research, or even merely well-accepted research, but against the absolute tip of the research pyramid. Of the 49 articles, 45 claimed to have uncovered effective interventions. Thirty-four of these claims had been retested, and 14 of these, or 41 percent, had been convincingly shown to be wrong or significantly exaggerated. If between a third and a half of the most acclaimed research in medicine was proving untrustworthy, the scope and impact of the problem were undeniable. That article was published in the Journal of the American Medical Association.

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[Hat Tip, again to John Wilkins]

The Most Famous Speech in Medical History

 
Robert Koch and Tuberculosis.

Koch's Famous Lecture

Robert Koch, a German physician and scientist, presented his discovery of Mycobacterium tuberculosis, the bacterium that causes tuberculosis (TB), on the evening of March 24, 1882. He began by reminding the audience of terrifying statistics: "If the importance of a disease for mankind is measured by the number of fatalities it causes, then tuberculosis must be considered much more important than those most feared infectious diseases, plague, cholera and the like. One in seven of all human beings dies from tuberculosis. If one only considers the productive middle-age groups, tuberculosis carries away one-third, and often more."

Koch's lecture, considered by many to be the most important in medical history, was so innovative, inspirational and thorough that it set the stage for the scientific procedures of the twentieth century....

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Is Acupuncture Better than Toothpicks?

 
Orac is at it again. He describes a pretty good study of the possible effects of acupuncture on lower back pain [Another acupuncture study misinterpreted]. The study showed that patients who got a sham procedure using toothpicks instead of needles reported the same "cure" as those who got two different versions of acupuncture.

In other words, acupuncture doesn't work. The scientific evidence is conclusive. Acupuncture is associated with a potent placebo effect but that's all. Patients can't tell the difference between needles and toothpicks. As long as they think they're getting the full-blown acupuncture treatment they'll report an improvement in lower back pain.

Here's the description of the toothpick technique that "cures" back pain.

Simulated acupuncture. We developed a simulated acupuncture technique using a toothpick in a needle guide tube, which was found to be a credible acupuncture treatment by acupuncture-naïve patients with back pain.Simulating insertion involved holding the skin taut around each acupuncture point and placing a standard acupuncture needle guide tube containing a toothpick against the skin. The acupuncturist tapped the toothpick gently, twisting it slightly to simulate an acupuncture needle grabbing the skin, and then quickly withdrew the toothpick and guide tube while keeping his or her fingers against the skin for a few additional seconds to imitate the process of inserting the needle to the proper depth. All acupuncture points were stimulated with toothpicks at 10 minutes (ie, the acupuncturist touched each acupuncture point with the tip of a toothpick without the guide tube and rotated the toothpick clockwise and then counterclockwise less than 30°) and again at 20 minutes just before they were "removed." To simulate withdrawal of the needle, the acupuncturist tightly stretched the skin around each acupuncture point, pressed a cotton ball firmly on the stretched skin, then momentarily touched the skin with a toothpick (without the guide tube) and quickly pulled the toothpick away using the same hand movements as in regular needle withdrawal. The acupuncturists simulated insertion and removal of needles at the 8 acupuncture points used in the standardized treatment.

Just about anyone could be trained to do this. Think of how much unnecessary back pain could be eliminated if spouses and friends would just poke each other with toothpicks!

I think I'll ask Ms. Sandwalk to try it next time my back hurts.

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