Bad science in the British Journal of Psychiatry

Would you believe that “”the largest, most definitive analysis of the mental health risks associated with abortion, synthesizing the results of 22 studies published between 1995 and 2009 involving 877,181 women, of whom 163,831 had abortions” has determined that “abortion harms women’s mental health”? It concludes that “10% of all mental health problems and 34.9% of all suicides in women of reproductive age” are caused by abortion. Here’s the author’s own summary of the results.

Women who had undergone an abortion experienced an 81% increased risk of mental health problems, and nearly 10% of the incidence of mental health problems was shown to be attributable to abortion. The strongest subgroup estimates of increased risk occurred when abortion was compared with term pregnancy and when the outcomes pertained to substance use and suicidal behaviour.

Those numbers are so extravagantly extreme that there ought to be alarm bells going off in your head right now, and the research had better be darned thorough and unimpeachably clean.

As it turns out, it isn’t. The author of the paper, Priscilla Coleman, is an anti-abortion advocate, and 11 of the 22 studies sampled for the meta-analysis are by…Priscilla Coleman. Methinks there might be a hint of publication bias there, something that has been confirmed statistically by Ben Goldacre.

Jim Coyne has carried out a thorough dissection of the paper, exposing the statistical games she played with the data.

If you examine Figures 1 and 2 in Coleman’s review, you can see that she counts each of her own studies multiple times in her calculation of the effects attributable to abortion. This practice was also roundly criticized in the E-letter responses to her article because each study should only be entered once, if the conditions are met for integrating results of studies in a meta-analysis and providing a test of the statistical significance of the resulting effect size. This may sound like a technical point, but it is something quite basic and taught in any Meta-Analysis 101.

Coleman’s calculation of overall effect sizes for the negative mental health effects of abortion involve integrating multiple effects obtained from the same flawed studies into a single effect size that cannot accurately characterize any of the individual effects – anxiety, depression, substance abuse, and suicide – that went into it. Again we are encountering a nonsensical statistic.

And just how good were the papers that Coleman chose to include in her meta-analysis? She claims they were the best, and that others were excluded because of their poor quality, but it seems other investigators hold her work in low esteeem.

…an APA task force report did find that Coleman studies–the ones she included in her meta analysis–had inadequate or inappropriate controls and did not adequately control for women’s mental health prior to the pregnancy and abortion. A similar verdict about Coleman’s work was contained in the draft Royal College of Psychiatrists report that also considered the bulk of her work too weak and biased to be entered into an evaluation of the effects of abortion on mental health.

I did find this comment by Jim Coyne bitterly amusing.

Readers should be to assume that the conclusions of a meta-analysis published in a prestigious journal are valid. After all, the article survived rigorous peer review and probably was strengthened by revisions made in the authors’ response to a likely “revise and resubmit” decision.

Obviously, you can’t assume that. This is a case where the editors and reviewers failed to do their jobs, and that happens way too often…and now this study has been thoroughly politicized and is being touted by the anti-abortion wackaloons to argue that abortion must be banned…for the good of the women. Which is probably one of the few times they’ve given a damn about the women involved.

But if you want a good, straightforward summary of why Coleman’s paper should have been rejected, that last link is it.

(Also on FtB)

Science overwhelmed by self-defeating awe

This video by Alexander Tsiaras is simultaneously lovely and infuriating; it’s a product of technology and science, and the narration is profoundly anti-science.

There are some technical issues that annoy me about the video — it’s a mix of real imagery and computer animation, and it doesn’t draw a line between what is observed and what is fabricated — but it’s visually stunning and otherwise fairly accurate.

But Tsiaras’s running commentary…it’s mystical airy-fairy glop. It takes awe and turns it into a celebration of ignorance.

Even though I am a mathematician, I look at this with marvel of how do these instruction sets not make these mistakes as they build what is us? It’s a mystery, it’s magic, it’s divinity. Then you start to take a look at adult life. Take a look at this little tuft of capillaries. It’s just a tiny sub-substructure, microscopic. But basically by the time you’re nine months and you’re given birth, you have almost 60,000 miles of vessels inside your body. I mean, and only one mile is visible. 59,999 miles that are basically bringing nutrients and taking waste away. The complexity of building that within a single system is, again, beyond any comprehension or any existing mathematics today.

And that instruction set, from the brain to every other part of the body — look at the complexity of the folding. Where does this intelligence of knowing that a fold can actually hold more information, so as you actually watch the baby’s brain grow — and this is one of the things that we’re doing right now. We’re actually doing the launch of two new studies of actually scanning babies’ brains from the moment they’re born. Every six months until they’re six years old — we’re going to be doing actually to about 250 children — watching exactly how the gyri and the sulci of the brains fold to see how this magnificent development actually turns into memories and the marvel that is us.

And it’s not just our own existence, but how does the woman’s body understand to have genetic structure that not only builds her own, but then has the understanding that allows her to become a walking immunological, cardiovascular system that basically is a mobile system that can actually nurture, treat this child with a kind of marvel that is beyond, again, our comprehension — the magic that is existence, that is us?

It’s not magic, and it’s sure as hell not divinity — it’s chemistry. And it certainly does make mistakes: half of all conceptions end in a spontaneous abortion, and about 15% of all pregnancies where the mother knows she is pregnant spontaneously terminate.

I genuinely despise the tactic so widely used by intelligent design creationists, and here by Tsiaris, of reciting really big numbers and babbling about complexity, complexity, complexity. Yes, it’s complicated. But you can build complicated structures with simple rules, and if you look at these systems, what you find are iterative properties and variation induced by local conditions. And if it’s beyond mathematics today, what are all those mathematicians and biologists doing modeling angiogensis?

And then there’s the rampant assignment of agency to everything. “Where does this intelligence of knowing that a fold can actually hold more information” in the brain come from? It doesn’t. The expansion of the cortex is a consequence of selected variation in mitotic regulators for that region of the brain — it expands like bread dough because the cells are replicating to large numbers, and the confines of the skull cause it to buckle and fold. It’s neurogenesis; there aren’t little angels folding pastry in there.

That entire last paragraph beginning from “how does the woman’s body understand to have genetic structure” is total nonsense. The answer is no, the woman’s body does not “understand”. There is no “knowing” there. There are physical/chemical processes guided by a molecular biology that has been shaped by a few billion years of variation and selection to produce a functional outcome. It’s not magic. It’s not guided by intelligence and intent.

THIS. IS. BIOLOGY.

Yet here is this intelligent, accomplished, technically skilled loon painting it with useless, mystical, misleading bullshit.

That kind of delusion has consequences. Right now, that video is getting featured on anti-maternal-life websites all over the internet. Here’s a self-selected sample of responses to Tsiaras’s work:

“For you created my inmost being; you knit me together in my mother’s womb.”

“Pro-choicers vanquished by Science.”

“This truly is amazing.”

“How could anyone get an abortion after watching this?”

“To say that this is a must see or fantastic is an understatement of the truth.”

I am most amused by the claim “Pro-choicers vanquished by Science.” I’ve been familiar with the developmental series shown in that video for about 30 years, and it confirms to me that there is nothing magical or special about human development that demands that we privilege the human embryo as deserving the full rights of an adult, aware, thinking person. It is meat in motion, driven by unthinking processes. Cow embryos go through the same events, and through the first month or so would be indistinguishable from a human embryo; does this somehow compel the anti-woman brigade to shun steaks?

Here, I have a video of zebrafish development. I don’t have all the gadgets and animation tools that Tsiaras has at his disposal, just a microscope, a video camera, and Quicktime software, but still…this truly is amazing. It’s a must see or fantastic.

Wow. How did a fish embryo know how to do that?

The answer is that it doesn’t. We don’t grant human beings a privileged place in our cultural ethics because they develop from embryos, or because they have a heart that beats with many miles of capillaries, or because we don’t understand every minuscule detail of their formation. If that were the case, the anti-choicers would have to be rushing to protect the fruit flies growing on the bananas in their kitchen and be picketing the battery farms producing chicken eggs. Witnessing development shouldn’t turn rational people into irrational knee-jerk defenders of embryos…it should turn them into developmental biologists who are awed at the grandeur of growth and differentiation, who will spend their lives working to figure out how it all works.

Where Tsiaras sees ineffable unapproachable mystery, I see interesting problems to be solved.

(Also on FtB)

Burzynski going ka-boom

First, a nice bit of news: Marc Stephens, the lunatic who stirred up the recent blogospheric buzz with his clumsy thuggery, no longer has a “professional relationship” with the Burzynski clinic, that warehouse of quackery. One thing about charlatans is that they have a fine-tuned sense of who might be hurting their bottom line.

But the damage has already been done. The Burzynski clinic is getting scrutinized.

Josephine Jones is tracking all the commentary.

And this is rich: Jen McCreight digs into the Burzynski publications list. Would you believe it’s a collection of marginal, low-impact journals and unreviewed conference presentations? Yeah, I knew you would.

(Also on FtB)

Burzynski Clinic: the domain of scoundrels and quacks

Billie Bainbridge is four years old, and she has an inoperable brain tumor, and her prognosis is not good. Her family is desperate, and has been frantically trying to raise money from the community to cover the costs of a treatment they’ve been told might cure her. They need £200,000. They are asking the public to contribute.

Unfortunately, the treatment they want to give her is antineoplaston therapy: it’s pure bunk. The clinic that is trying to suck large sums of money away from the family of a dying child is the Burzynski clinic. So in addition to being a quack, Burzynski is now a vampire, exploiting sick children for profit.

Andy Lewis wrote an article about the false hope of the Burzynski clinic. It’s damning — the Burzynski clinic has been exploiting the sick for years with an exorbitantly priced ‘therapy’ that has never passed Phase III trials.

A scientific organization would respond to such an argument, you would think, with a deluge of data and explanations of the scientific basis of their treatment. Not the Burzynski clinic! Instead, they have some angry hack at their establishment who fired off a whole series of threatening letters to Lewis, claiming legal authority with no evidence that the angry clown, Marc Stephens, has any legal credentials at all. There’s certainly no science behind his rants, and there doesn’t seem to be any legal standing, either.

So Stephens threatens Lewis’s family.

Be smart and considerate for your family and new child, and shut the article down..Immediately.

You can guess how the Internet responds to such thuggish, bullying behavior: by blowing up and pointing out even more loudly the deficiencies of the Burzynski clinic.

So Stephens has started sending these threatening letters to other people, including Rhys Morgan. “GOVERN YOURSELF ACCORDINGLY,” he blusters as he promises libel suits.

I think you all know what to do now. Spread the news of the Burzynski clinic’s quackery far and wide; trumpet it loudly everywhere. The media has been fairly passive about this abuse of children and dying adults for some time now, so let’s make it clear to the world exactly how contemptible these phonies are.

GOVERN YOURSELF ACCORDINGLY.

(Also on FtB)

The Quran is bunk, too

I know you kids like the youtube and hate that tl;dr text stuff, so if you couldn’t find the patience to read my post on Islamic embryology, you can now watch the screen instead. The Rationalizer goes through the ‘science’ in the Quran and shows that it’s largely plagiarized from Galen, and that it also steals Galen’s mistakes, so it’s a beautiful example of a plagiarized error of the type biologists use to demonstrate a lineage.

All the straining Muslim apologists use to fit the science to the few lines of poetry in the Quran (I’m looking at you, Hamzas Tzortzis) are futile and really only demonstrate that the founders of Islam borrowed their message, not from a divine source, but from Greco-Roman medicine.

But perhaps Allah is just another name for Galen.

(Also on FtB)

Acupuncture is bunk

Here’s a terrific webcomic exposing the silliness of acupuncture. People are always citing these awful studies at me that they claim support the efficacy of acupuncture, and like the comic says what I see when I read them is that the advocates have gone “anomaly hunting after any statistically relevant result, usually by cherry-picking data or creative interpretation. You’ll never find a conclusive effect with acupuncture studies”.

I’d really like to hook the traditional Chinese medicine freaks with the cannabinoid bozos who’ve lately been doing the same thing: citing weak results to prop up extravagant claims of near miraculous efficacy. A kookfight to the death!

(Also on FtB).

A little dose of hemp will cure everything

Do these claims make you at all suspicious? A few people on Twitter told me I should look into this panacea.

Cures heart disease!

Eases anxiety and depression!

Removes unsightly moles!

Arthritis! Snoring! Diarrhea! Acne! Diabetes! Removes warts! Mighraines! Lose weight! Alcoholism! Glaucoma!

IT CURES CANCER! All forms of cancer!

And all without any detrimental effects whatsoever!

Add to the extravagant medical claims, the additional accusation that you can’t get this treatment because of a conspiracy by BigPharma and greedy, grasping doctors who want people to suffer so they can charge them lots of money to fix them with agonising tortures that don’t work.

Are you suspicious yet?

These are all claims Rick Simpson and a small group of Canadians make for hemp oil in this video.

You may not want to watch it — I’ve already given you the gist of it, and it’s repetitious and very poorly edited (hint: just because your home movie editing software has a lot of exotic transitions, doesn’t mean you have to use them all). It looks like an infomercial, with a parade of Nova Scotians offering wild anecdotal claims of all the stuff a daily dose of hemp oil cures. These testimonials are presented as the evidence that hemp oil is medically efficacious; they aren’t. Quite the opposite, actually — it all says to me that the promoters found some marginally sick people and fed their desire for wish-fulfillment, and got a slew of meaningless accolades and bizarre conspiracy theories that tell me that what’s going on here is psychology, not medicine.

It’s not just religion that kills people. I watched Rick Simpson claim that he had skin cancer, and that rubbing his marijuana extract healed the lesions overnight, and I thought… people may well die from watching and believing this claim. Some forms of skin cancer (melanoma) are extremely aggressive and dangerous — do not delay, do not play games with weird magic topical creams, get a real doctor to check it out.

The information on the video also gives off a bad vibe.

The following presentation of RUN FROM THE CURE: The Rick Simpson Story was made possible by Rick Simpson and video producer Christian Laurette… made for free to teach YOU how to heal yourself of disease and illness using cannabinoids.

Comments will be moderated to protect those who need this information. We are not asking anyone if it works, we are telling you it works; it is not a debate. Too many uneducated people coming to this channel to speak their mind on a life-saving plant they know nothing about and giving bad advice and in many cases making horrible remarks about the people who brought the information out to you.

No argument! If you disagree with him, you’re uneducated…despite the fact that the pro side consists of rural citizens who seem to know nothing about how to interpret evidence, while his opponents are doctors and scientists.

The video also lies, lies, lies. I’ve often heard quacks say this: “FACT: Chemotherapy kills more people than it saves.” It’s not true. People who are on chemotherapy are more likely to die than people who are not on it, because the only reason those people are on chemotherapy in the first place is that they are really, really sick. It makes nonsensical claims: “THC attacks mutated cells while rejuvenating healthy ones”. How do they know? These aren’t scientists making the claims, these are ordinary townspeople — Simpson makes his formula by doing a crude extraction with naptha or isopropyl alcohol in a bucket he stirs with a stick, and boils it down to an oily residue in a rice cooker (there will be an explosion and fire at his house someday, I predict). He has no tools to examine specific cellular responses, so the source of these claims of a mechanism are being taken directly out of his ass.

At least Simpson is giving his cure-all away for free — all he’s doing is feeding his over-inflated ego at the potential cost of a few lives. He’s not quite like the odious Burzynski Clinic, which bilks people for hundreds of thousands of dollars for an extravagantly promoted therapy that has no good evidence for its efficacy. And at least he has not resorted to threats.

But he’s still a dangerous quack and a crank.

One other thing: I’m all in favor of legalizing marijuana and ending the phony drug war that turns harmless folk into criminals, jacks up the cost, and entices violent thugs into what ought to be simple farming. If you look up Rick Simpson, though, you find all these groups advocating legalization also buying into Simpson’s hazardous and dishonest game. That only discredits the legalization movement.

(Also on FtB)

Islamic embryology: overblown balderdash

I have read the entirety of Hamza Andreas Tzortzis’ paper, Embryology in the Qur’an: A scientific-linguistic analysis of chapter 23: With responses to historical, scientific & popular contentions, all 58 pages of it (although, admittedly, it does use very large print). It is quite possibly the most overwrought, absurdly contrived, pretentious expansion of feeble post hoc rationalizations I’ve ever read. As an exercise in agonizing data fitting, it’s a masterpiece.

Here, let me give you the short version…and I do mean short. This is a paper that focuses with obsessive detail on all of two verses from the Quran. You heard me right: the entirety of the embryology in that book, the subject of this lengthy paper, is two goddamned sentences, once translated into English.

We created man from an essence of clay, then We placed him as a drop of fluid in a safe place. Then We made that drop of fluid into a clinging form, and then We made that form into a lump of flesh, and We made that lump into bones, and We clothed those bones with flesh, and later We made him into other forms. Glory be to God the best of creators.

Seriously, that’s it. You have just mastered all of developmental biology, as taught by Mohammed.

Tzortzis bloats this scrap into a long, tedious potboiler by doing a phrase by phrase analysis, and by comparing it to the work of Aristotle and Galen, who got lots of things wrong. How, he wonders many times, could Mohammed have written down only the correct parts of the Greek and Roman embryological tradition, and avoided their errors, if he weren’t divinely inspired? My answer is easy: because Mohammed only made a vague and fleeting reference to the science of the time, boiling down Aristotle’s key concept of an epigenetic transformation into a few non-specific lines of poetry. Aristotle and Galen got a lot wrong because they tried to be specific and wrote whole books on the subject; you can read the entirety of Aristotle’s On the Generation of Animals. Galen was prolific and left us about 20,000 pages on physiology and medicine.

So, yes, you can find lots of examples in their work where they got the biology completely wrong, and it’s harder to do that in the Quran…because the Quran contains negligible embryological content, and what there is is so sketchy and hazy that it allows his defenders to make spectacular leaps of interpretation. Mohammed avoided the trap of being caught in an overt error here by blathering generalized bullshit, and saying next to nothing. This is neither an accomplishment nor a miracle.

I’ll go through his argument piece by piece, but at nowhere near the length. It’s hard to believe anyone is using this feeble fragment to claim proof of divinity, but then, Christians do exactly the same thing.

  1. “essence of clay”. Tzortzis happily announces that clay contains “Oxygen, Carbon, Hydrogen, Nitrogen, Calcium, Phosphorus, Potassium, Sulfur, Chlorine, Sodium, Magnesium and Silicon; all of which are required for human functioning and development”. These are irrelevant factlets. Clay is a fine-grained hydrous aluminum phyllosilicate; carbon, which is the element to consider in organic chemistry, is present as a contaminant, but the primary elements are aluminum and silicon. It’s nothing like the composition of the human body. This part of Tzortzis case is simply a lie.

  2. “drop of fluid”. Tzortzis tells us that the Arabic word here is “nutfah”, which has a number of meanings, but he likes the interpretation that it implies mingled fluids. Then he babbles on about oocytes and spermatazoa and secretions of the oviduct, none of which are mentioned in the Quran and are completely irrelevant. Bottom line: Arabs noticed long ago that sex involves a mingling of fluids. Brilliant. I think most of us could figure that out without divine inspiration.

    He spends a fair amount of time pointing out that both Aristotle and Galen had a male-centric view of procreation, where the man’s contribution was the dynamic agent and the woman was a passive vessel. They were wrong. In order to rescue the Quran, though, Tzortzis has to bring in Ibn Qayyim, a 13th century Islamic scholar, who pointed out that women have to provide a significant contribution to inheritance, since their traits are also present in the children. This, again, is an obvious and observable property, and the Greeks also argued over the relative contributions of male and female. There is nothing in the Quran that is beyond casual observation or non-existent in the scholarly works of the time.

  3. “in a safe place”. Tzortzis quotes modern embryologists and throws around the terms endometrium, syntrophoblast, implantation, uterine mucosa, proteolytic enzymes, etc., etc., etc. I ask you, is any of that in the quoted verse from the Quran? No. Total bullshit from the apologists. That the embryo grows in a “safe place” — the woman’s belly — is another obvious property.

  4. “a clinging form”. It seems that the word used here means just about anything.

    The Qur’an describes the next stage of the developing human embryo with the word `alaqah. This word carries various meanings including: to hang, to be suspended, to be dangled, to stick, to cling, to cleave and to adhere. It can also mean to catch, to get caught, to be affixed or subjoined. Other connotations of the word `alaqah include a leech-like substance, having the resemblance of a worm; or being of a ‘creeping’ disposition inclined to the sucking of blood. Finally, its meaning includes clay that clings to the hand and thick, clotted blood – because of its clinging together.

    I could call the embryo a sticky blob, too, and stretch and twist the words to match it in the vaguest possible way to a technical description, too…but it doesn’t make it a technical description, and it doesn’t make it informative.

    This section concludes by claiming that the “leech” interpretation of ‘alaqah is accurate, because later in development it looks, he claims, like a leech. Only to a blind man. And further, he applies this term “like a leech” to every stage in the first month of development; the accuracy of the comparison seems irrelevant.

  5. “a lump of flesh”. More of the same. Take the Arabic word (“mudghah”), throw out a bunch of definitions for the word, then force-fit them all into the actual science.

    The next stage of human development defined in the Qur’an is mudghah. This term means to chew, mastication, chewing, to be chewed, and a small piece of meat. It also describes the embryo after it passes to another stage and becomes flesh. Other meanings include something that teeth have chewed and left visible marks on; and marks that change in the process of chewing due to the repetitive act.

    No. I refuse. I’m sorry, but this is patently ridiculous. You do not get to quote the Quran talking about a chawed on scrap o’ meat, and then go on with four pages of windy exegesis claiming that corresponds to the 4th week of human development, the pharyngula stage, as if it is an insightful and detailed and specific description of an embryo. It is not. It is the incomprehending grunt of an ignorant philistine.

  6. “into bones”. Yeah. There is a mingling of fluids in sex, and at birth you have a baby with bones. Somewhere in between, bones must have formed. You do not get credit for noting the obvious without any specifics. Furthermore, turning the phrase “into bones” (‘idhaam) into this:

    There are clear parallels between the qur’anic `idhaam stage and the view modern embryology takes i.e. the development of the axial, limb and appendicular skeleton.

    is pure hyperbole and bunkum. But then, that’s all we get from Tzortzis.

  7. “clothed the bones with flesh”. Tzortzis now talks about myoblasts aggretating and migrating distally, formation of dorsal and ventral muscle masses, innervation of the tissue, and specification of muscle groups. Good god, just stop. The Quran says nothing about any of this. And then to complain that This level of detail is not, however, included in Aristotle’s description, is absurd and ironic. It’s not in Mohammed’s description, either.

    It must be noted that the migration of the myoblasts surrounding the bones cannot be seen with the naked eye. This fact creates an impression of the Divine nature of the Qur’an and reiterates its role as a signpost to the transcendent.

    Crap. The Quran doesn’t describe myoblast migration. There isn’t even a hint that Mohammed saw something you need a microscope to see.

  8. “made him into other forms”. Then Allah did all the other stuff that he needed to do to turn a chunk of chewed meat made of bone and flesh into a person. Presto, alakazam, abracadabra. Oooh, I am dazzled with the scrupulous particularity of that scientific description.

There’s absolutely nothing novel or unexplainable in the Quran’s account of development. It is a vague and poetic pair of verses about progressive development, expressed in the most general terms, so nebulous that there is very little opportunity for disproof, and they can be made to fit just about any reasonable observation. They can be entirely derived from Aristotle’s well-known statement about epigenesis, “Why not admit straight away that the semen…is such that out of it blood and flesh can be formed, instead of maintaining that semen is both blood and flesh?”, which is also a very broad statement about the gradual emergence of differentiated tissues from an amorphous fluid.

Only a blinkered fanatic could turn that mush into an overwrought, overextended, overblown, strained comparison with legitimate modern science. Tzortzis’s paper is risible crackpottery.

(Also on FtB)