Debunking Denialism

Defending science against the forces of irrationality.

Genetic Clusters, Racial Medicine and Fishes

Neurologica Blog

Humans are pattern-seeking animals are are thus prone to detect patterns where none exists. We are also very interested in categorizing things, presumably because it is easier to handle cognitively. Imagine the difficulty we would have if we had to mentally treat each leaf as a separate entity and could not consider them “just a bunch of leaves”! But there is a downside to this as well, because we can be mislead and neglect complicated patterns because our categories are easy and psychological influential. These issues and questions often appear in discussions about human genetic diversity. This is enhanced by the fact that complicated genetic and computational analyses feeds us with visually striking graphs that tickle our imagination, while we do not pay equal attention to the underlying methodology.

However, reality is more complicated. Genetic clusters overemphasize differences, largely ignore similarities and is confounded by low sampling density and geographic distance. Thus, a modern analysis of human genetic variation reveals that it is, with a few exceptions, mostly clinal in nature and that notions of discrete genetic races is not an accurate description.

It is often said that ethnicity is useful in medicine, but this is also more complicated due to confounders such as health disparities, bias, discrimination, healthcare seeking behavior and compliance, as well as socioeconomic status. It turns out that ethnic status is at best a crude proxy for the alleles of a person and sequencing individuals will be much more useful. Finally, a focus on racial medicine has led to misdiagnosis of some diseases, such as sickle-cell anemia, thalassemia and cystic fibrosis.

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Harbingers of Doom – Part V: Botching Philosophy of Science

Here Be Dragons

Previously, we have dealt with a broad range of issues such as the intricate details about medieval maps, biological weapons of mass destruction, anti-psychiatry nonsense about psychopharmacology and changes in diagnostics of social anxiety, misunderstandings of heritability and the question of whether repeated selection of embryos can produce massive gains in IQ, the biological basis of the mind, cryogenically freezing your dying body, uploading your consciousness to a computer server, superintelligent AI risk and the futility of atomically precise manufacturing, at least as traditionally conceived.

In this latest installment, we look at everything from ancient science to statistical significance. Was there no science in antiquity and almost all philosophers just sat around and thought about stuff? Does science desperately need induction? What does it mean for evidence to independently converge on the same general conclusion? What about inferences to the best explanation? Is past experience on dawn the only reason why we might suspect that dawn will also occur tomorrow? Does scientific research fail because the observation of a yellow banana allegedly support the hypothesis that all ravens are black? What is falsifiability? Why is the Duhem-Quine thesis not a large threat to science? How do we know that solipsism is incoherent? We also revisit our favorite bad statistical method NHST, which Häggström continues to defend with teeth and claw.

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Crown Prosecutors Appeal Lenient Toddler Meningitis Sentence

Crown appeals Stephans sentencing

In 2012, David and Collet Stephan failed to provide the necessities of life to their toddler Ezekiel, who died of meningitis-induced hypoxia. Instead of calling an ambulance or traveling to a medical doctor, the couple instead gave pseudoscientific alternative products to Ezekiel, such as garlic, hot peppers, horseradish, maple syrup, berry juice, and miscellaneous naturopathic quackery for a period of over two weeks. It was only when Ezekiel stopped breathing that they decided to call an ambulance and take their son to a hospital and real medical help. The trial started in early March of 2016 and they got convicted for failing to provide the necessities of life. The father got four months in prison and the mother got three months house arrest. They both got 240 hours community service and a probation period of 2 years after their punishment is completed. The father was deemed especially guilty, as he showed no remorse and only got more naturopathic substances, whereas the mother actually researched the disease and contacted a nurse.

The parents, and especially David, has not fully accepted responsibility for their crime. Instead, they have offered a variety of excuses and tried to shift the blame to others. David claimed that the only way to discover that their son had meningitis was to have a 24-hour medical supervision, which is simply not true. He also claims that his son did not die of meningitis, but only because the ambulance was not well-stocked enough. One wonders what David thinks is the cause of the life-threatening breathing difficulties experienced by his son Ezekiel. It occurred before the ambulance arrived and a reasonable person would conclude that it was induced by the untreated meningitis. Yet David does not want to realize this, because that would effectively shatter his cognitive dissonance and force him to realize that he and his wife is responsible for the death of their son.

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David Stephan Gets 4 Months in Jail for Naturopathy Meningitis Death

Jail time for David Stephan

Naturopathy is a form of alternative medicine that push overconsumption of vitamins and minerals, herbalism woo, as well as other types of quackery such as homeopathy and acupuncture. In addition, they are decidedly anti-medicine because they generally oppose vaccines and pharmaceuticals.

It often rests on vitalism, which is the debunked notion that the core feature of life is a mysterious life energy, rather than physical, chemical and biological processes. It also has a near fetishistic obsession with everything “from nature” or “natural”, despite the fact that nature can produce and has produced substances that are incredibly dangerous for humans.

In an investigation of naturopathy and other alternative treatments carried out by the Australian government only a single unpublished systematic review was found, and so they concluded “overall quality of evidence was rated as very low”. In their evaluation, they highlighted risk of bias, low precision, and publication bias.

Who are David And Collet Stephan?

David and Collet Stephan are a married couple living in Alberta, Canada. They are also devoted proponents and practitioners of naturopathy and David was at the very least an employee at the controversial alternative medicine company called Truehope that has been discussed several times before on this website.

In early 2012, their son Ezekiel, a 19-month-old toddler, developed meningitis. It is not clear that this case of meningitis was caused by a vaccine-preventable disease, but it is a possibility, and the family opposed vaccines.

How did their actions lead to the death of their son Ezekiel?

Meningitis is a life-threatening condition that requires immediate medical attention. How did Ezekiel’s parents handle it? Did they call an ambulance? Visit an emergency room? No, far from it. They tried to “boost the immune system” of the child with alleged “natural remedies” such as maple syrup, berry juice, apple cider vinegar, garlic and other food items. They also tried the nutritional supplement Empowerplus from the Truehope company discussed above. Most reasonable people understand that these “treatments” do not work, or at the very least has never been shown to work in large-scale scientific studies.

Ezekiel was sick for almost two weeks. It starting with a fever that the parents attributed to teething, but he soon developed labored and wheezy breathing. It has now that the Stephans started with their herbal “treatments” and put in a humidifier. The toddler mostly stopped eating and drinking, so they have to give him fluids through eye drops. His symptoms likely worsened, but the parents belief in the efficacy of their treatments led them to believe that the boy was improving. He then became increasingly lethargic and unresponsive as well as showing some neurological symptoms. A few days later, the parents noticed increased stiffness that eventually became so severe that his back was arched when laying down.

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Special Treatment for Anthroposophic Substances Will Be Removed

anthroposophic substances no longer given special treatment

Anthroposophic substances will no longer be given special treatment in the pharmaceutical legislation in Sweden. Every since 1993, fake treatments made by proponents of anthroposophy could be used without having any evidence of safety or efficacy, and they could even be injected.

Now, the Swedish government has decided to remove this and force anthroposophy proponents to put their substances through the standard approval or registration pipeline. However, the exemption will first be extended for two years, then there will a transition period for three years and only after a total of five years will they be forced to show that their substances are safe and effective (if they want them to be treated like real medication) or just safe (if they want to settle for homeopathy registration and be denied the possibility of making efficacy claims). This is a welcome development and arguably a small victory for science-based medicine, but it could have been done faster. In the end, it is a reluctant compromise.

What is anthroposophy and anthroposophic substances?

Anthroposophy is a weird mix between pseudoscience and mysticism that was founded by Rudolf Steiner in the late 1800s and has since infiltrated medicine, agriculture and education.

Anthroposophic substances are products made by anthroposophy proponents that typically do not have any evidence for efficacy and safety. Often, these involve homeopathic dilutions and due to an exemption in the Swedish law since 1993, these are given a sales permit and can circumvent normal regulations that cover real medication (approval) or fake treatments that have been shown to be pharmacologically harmless (registration). This special treatment will now end and anthroposophy will be treated like other fake treatments and require at the very least evidence of safety.

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Harbingers of Doom – Part IV: Nanobots and Atomic-Scale Manufacturing

Here be dragons?

Will 3D printing make gun regulation impossible because people can print their own metal guns? Will you never shop food again, but merely download a 3D printing plan for sandwiches and cake? Will you be able to put together any arbitrary substance using atomically precise manufacturing? Is it feasible to use mechanical tools to place atom-by-atom onto a growing substance? Or does this ignore the massive number of atoms required just to make a few grams and that the nanoscale is strongly impacted by thermal noise and intermolecular forces? Is chemical reactions as easy as putting two atoms together or does the system require more? Is the ribosome a case of atomically precise manufacturing? Or is it a messy biological enzyme system that does not involve atom-by-atom assembly, contributes to a stunning error rate of perhaps 30% for protein synthesis and folding and is nothing like a machine? Being a cellular organelle, does this limit the capacity and range of the products that ribosomes and ribosome-like structures can produce? Perhaps more importantly, will self-replicating nanobots consume all life on earth?

Previously, we have debunked fanciful stories about dragons on medieval maps, fearmongering about molecular biology, anti-psychiatry attacks on social anxiety and medications, heritability and embryo selection of IQ, radical life extension, the denial of mind-brain physicalism, destructive teleportation, mind uploading, cryonics and wild speculations about technology-induced mass unemployment and superintelligent artificial general intelligence.

In this fourth installment, we take a closer look at the promises and perils of 3D printing, the alleged feasibility of atomically precise manufacturing, the biological details of the ribosome and protein synthesis, as well as the supposed future existence of self-replicating nanobots and whether or not they are likely to kill all life on earth.

Section XXXI: Why bother 3D printing stuff that can more easily gotten in other ways?

Häggström conjures up a wide range of wonders from the emerging technology of 3D printers (p. 128), such as “sandwich, a pair of sneakers or a kitchen table” or even cars. But Häggström ignores issues such as shoe fitting and the social aspects of preparing and consuming food. It is also unclear how e. g. a submarine sandwich would be done in a 3D printer since it contains a wide range of materials that are not easily constructed in the 3D printer paradigm. For instance, how do you 3D print slices of onions or the appropriate texture of chicken? These technical difficulties might very well be solved in the future. However, there has to be an argument for it, not merely a naive appeal to future technology. This way of thinking was criticized by Häggström in the section on geoengineering discussed in the first part of this articles series.

To drive this point come, consider the journalist Helen Ubiñas who managed to buy an AR-15 semiautomatic rifle in Philadelphia (a similar weapon to the one used in the Orlando mass shooting) in a just 7 minutes (Ubiñas, 2016). If you can legally buy a semiautomatic rifle in 7 minutes at the store, why bother spending a ton of money on a 3D printer, materials and printing it at home? Even if we assume a considerable drop in the cost of a 3D printer, the ease at which one can obtain a weapon is startling. This is not the case in other countries, of course, but then if guns can be successfully regulated, then so can 3D printers.

Häggström also seems concerned about intellectual property rights (p. 128), but despite the advances in file sharing and free streaming services, movies and television series are still being produced at a large scale. People use to predict that the VHS player would be the doom of the movie industry since people could just record the movies from the television. Similar sentiments were expressed on the CD, portable media players, illegal file-sharing, online streaming etc. Turns out that none of these fears turned out to be true. So why should we be concerned now?

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Homeopathy Journal Suppressed Due To “Anomalous Citation Patterns”

Homeopathy Journal

Homeopathy is a form of pseudoscientific quackery from the late 1700s that is based on denying basic chemistry. In reality, the more you dilute something, the weaker the substance becomes (think of mixing lemonade). Homeopaths, on the other and, think that a substance gets stronger when diluted. Mind-bogglingly, they think it is even more powerful when it is so diluted that no molecules are likely to be left of the original substance. They also believe that the substance that caused a disease is also the cure, so if you have a deadly snake bite, you should drink extremely diluted snake venom instead of a dose of the appropriate anti-venom.

The most methodologically rigorous studies shows that homeopathy is not clinically significantly better than placebo. This is to be expected, since you are basically drinking water or eating a sugar pill if you take homeopathic remedies.

What exactly is the Elsevier journal “Homeopathy?”

The Homeopathy journal has existed under various names since 1911 and is the official publication of the Faculty of Homeopathy. Since the 1950s, it has a legal status as an educational institution in England and their current tagline is the Orwellian claim that they are “ensuring the highest standards in homeopathic education and practice”.

This journal is published by Elsevier and its 2014 impact factor 0.758 according to Journal Citation Reports, which makes it among the lowest quality category of journals in the world. Other impact factor metrics were even lower, from 0.3 to 0.5 (according to the journal website).

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Alleged Spoon Bender Anastasia Kutt Resigns from University of Alberta

Spoon Bender Anstasia Kutt resigns

According to her blog, Anastasia Kutt describes herself as an “energy healing therapist”, a “registered Reiki Master/Teacher”, a “certified Trilotherapist” and a “Yuen Method practitioner”. Until very recently, she was also a “workshop facilitator” associated with the University of Alberta. She appears to offer both spoon bending and tantric sex workshops, but her major focus appears to be on providing various Reiki courses to people that include topics such as “psychic surgery”, “aura cleansing”, “chakra cleaning”, “removing specific energy blockages” etc. for the cheap price of 350 USD for the first two levels and 500 USD for the final third level so that you can become a full-fledged “Reiki Master Practitioner”. If you do not mind being fooled into giving away more money, there is even a course to become a “Usui Reiki Master Teacher” for another 800 USD, making it a grand total of 1650 USD. In addition, there is a 100 USD deposit to register for the different courses.

Recently, she organized a workshop at the University of Alberta. Not any workshop, but a workshop that involved the promotion of “energy healing therapies” and spoon bending. Yes, you read that correctly. Spoon bending. A great overview of this issue can be found in this article written by Orac on Respectful Insolence. At least two articles have been published by CBC. Now, it seems that this workshop has been cancelled and that she has resigned from her position at the University of Alberta. This article looks at these recent developments.

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Harbingers of Doom – Part III: Luddism and Computational Eschatology

Here be dragons?

Will naive extrapolations of the exponential advancement in hardware development usher in an era of recursively self-improving artificial general intelligence? Does automation lead to mass unemployment or is this merely another manifestation of the Luddite fallacy that so many people with an ignorance of basic economics fall into? Should we trust technological predictions made by alleged experts, when the predictions made by these experts for the past 60 years have been a complete failure? Is there a clear distinction between instrumental and final goals? Will an AI never change its final goal? Will paperclip maximizes turn all humans and all of the universe into paperclips? Or is this a delusional idea that assumes that programmers routinely let algorithms run infinite loops?

Previously, we investigated the historical question of whether medieval maps really had dragons indicating dangerous places, the risk of the development of biological WMD and immunologically induced meat intolerance as a solution to climate change. We also critically examined anti-psychiatry claims about social anxiety, heritability and embryo selection for IQ, radical life extensions, mind uploading to computers, destructive teleportation and cryonics. In this third installment, we take a closer look at Moore’s law and its implication for the development of artificial intelligence, if robots will cause mass unemployment, the failure of AI predictions, artificial selection as a possible method of producing human-level AI, and if programmers really would let programs run an arbitrarily high iterations of important algorithms. Read more of this post

The Triumph of the Peppered Moths and the Failure of Creationism

Peppered Moths

The peppered moth, Biston betularia, is a species of nocturnal moths that can be found across the Northern hemisphere. In Britain, the two most common morphs are called typica (white with dark irregular patches and spots) and carbonaria (dark melanic). There is also an intermediate morph that is known as insularia.

Before the early 1800s, the melanic morph was unknown. About a hundred years later, this morph completely dominated the population. This coincided with the industrial pollution of forests, thereby depriving the white morph of its good camouflage and allowing the melanic morph to better hide in the surroundings, since trees had been darkened by soot and a lot of lichens died due to sulfur dioxide. This became known as industrial melanism. From the 1960s and to the present, this trend has been reversed. As the air and the environment became less polluted, the melanic morph fell in prevalence and the white morph rose again.

Research of the prevalence of different morphs at different places and times can be found in many scientific papers, such as Kettlewell (1956), Grant, Owen and Clark (1996) and Cook and Saccheri (2003).

Why are peppered moths a case of natural selection in the wild?

This is a fantastic example of natural selection in the wild, because there was a shift in the prevalence of the two forms due to selection from the environment and this occurred both during increased and decreased pollution. This has also been observed in many locations in both Europe and North America, further solidifying the case.

Later research showed that the major mechanism behind this change turned out to be bird predation. Before the pollution, white morphs had a good camouflage against light trees. During the strong pollution era, these were easier to spot by birds against the blackened background, whereas now the melanic morphs had a better ability to hide. As the environment improved, the situation was reversed again.

Creationists try to spread misinformation about these mechanistic details and how frequent these moths rests on different parts of the trees, but whatever they claim, their assertions do not disprove the fundamental fact that natural selection caused the shift in the prevalence of different morphs over time.

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