Archive for the 'Science and Medicine' Category

Nov 29 2021

Get Ready for Omicron

Experts knew, and had been warning, that delta was not going to be the last Greek letter to sweep across the world. The World Health Organization (WHO) tracks variants of the SARS-CoV-2 virus which causes COVID-19. They track variants of interest (VOI) which have been identified as potentially problematic, and variants of concern (VOC) which have been demonstrated to have either increased infectivity, increased illness severity, and/or evasion of preventive measures (such as vaccines or masks). These variants are given a Greek letter designation as they are added to the list. What is now called the omicron variant has been added to the list of VOC. Here’s what we know so far.

The virus appears to have originated in South Africa. Fortunately, South Africa has a robust surveillance system and labs that can grow the virus and do a whole-genome sequence. They were therefore able to identify the variant quickly and share their information with the world. This isn’t the first variant to originate in South Africa, which raises the question of why this is the case? Increased surveillance may be part of the answer, but is not able to fully explain why. Some scientists speculate that South Africa’s large population of HIV infected and inadequately treated people provide a fertile breeding ground for new variants.

Variants are caused by mutations in the virus genome, some of which may alter proteins and therefore viral functions. SARS-CoV-2 does not have a particularly high mutation rate, but because we are having a world-wide pandemic there are lots of opportunities for new mutations to occur. It’s possible that when a person has a prolonged infection the viruses in their system are under selective pressure, so any mutation that might partly evade the immune system will be favored. Those with untreated HIV have an impaired immune response. This may be just enough to provide some selective pressure but not enough to fight off the infection, creating a breeding ground for new variants.

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Aug 31 2021

The Origins of COVID

We are approaching two years into this pandemic and we still haven’t proved the origins of the SARS-CoV-2 virus. However, this is not unusual at all, and in itself is not suspicious. It took 13 years to identify the origin of SARS, and we have never identified the origins of some Ebola outbreaks. But what do we know about the origins of SARS-CoV-2? The question has become highly political, which is unfortunate. Let’s review what the actual evidence has to say.

If we go back to the beginning of the pandemic, the early scientific investigation of the virus found that it was 96% identical to a bat coronavirus in the region. Zoonotic spillover is common, and the virus originated in a part of the world with wet markets and close contact with wild animal populations. Direct examination of the virus also did not show any telltale signs of deliberate manipulation. There has been some scientific debate on this topic, but in the end there is general agreement among scientists that there is no smoking gun of genetic manipulation. For these reasons it was concluded early that the most probable origin of COVID was from animals, either directly from bat to human or through an intermediary.

This conclusion was based on examination of the virus itself and the the reservoirs of similar viruses in the region. This was, and by many still is, considered the most likely origin. Researchers have searched for the precise animal origin, and so far have not found it, but that is not in itself unusual or suspicious.

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Aug 20 2021

Masks Work

By coincidence, in November 2019 I did an investigation into the question – does wearing a facemask reduce the risk of transmitting or getting a respiratory infection? I was in Australia at the time and noticed that their large Asian population frequently wore facemasks in public. It seemed odd, and my initial hypothesis was that this was likely a cultural behavior without supporting evidence. I was surprised to find, when I reviewed the primary literature at the time, that I was wrong. In fact, masks do work, in certain circumstances.

The basic concept is simple – when you breath, talk, cough, or sneeze you exhale tiny droplets, and if you have a viral respiratory illness those droplets are crawling with virus. Masks reduce the spread of those droplets, and otherwise you are basically spraying everyone with a shower of viruses. They are less effective at protecting the wearer, but they do reduce the risk of getting sick as well. However, that reduction is only statistically detectable if you are in a high-risk situation to begin with. This includes being in the same room with someone who is sick, or being in a crowd during an epidemic. Out in the general population not during an epidemic the baseline risk of catching a virus is low, and so there is no statistically detectable benefit from wearing a mask.

This conclusion was based on information available before anyone ever heard the word “Covid-19”. Who would have thought at the time that this entirely scientific question would become so political so fast? The efficacy of mask wearing suddenly became a very important question, so now we have much more research, and some specific to SARS-CoV-2. This research has raised our confidence that masks do, in fact, have efficacy (science-speak for “they work”), but has also drilled down to greater detail. Where does the research stand now?

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Jul 27 2021

Treating Brain Cancer with Magnets

Magnets for healing have a bad rap, one they rightfully deserve. Magnetic snake-oil devices with all sorts of bogus medical claims are as old as magnets themselves. It may have something to do with the fact that magnets seem like magic, exerting and invisible force at a distance. So it’s often an easy sell. Also, magnets are real and do produce a real energy field (unlike the non-existent “life energy” fields common in alternative medicine). So it makes any claims for them seem all the more plausible.

Because of this, magnets do have real medical applications. Perhaps most common is MRI scans – magnetic resonance imaging. But also there is a lot of research into TMS, transcranial magnetic stimulation, for a variety of neurological indications. Our bodies are electromagnetic devices, and we can alter cell function with electricity and magnetic fields. The trick is, applying them in such a way that they can be exploited for benefit rather than causing harm or having no real effect.

For the consumer with insufficient scientific or medical background, it can be very challenging to tell the difference between a legitimate magnetic medical device and a scam. One good rule of thumb – if the magnet is fairly weak (refrigerator magnet level) it is probably worthless. Real biologically active magnets tend to be powerful. Another slightly more technical fact is that biologically active magnets tend to have an alternating field, while magnetic quack devices tend to have a static magnetic field (which has little biological effect).

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Jul 20 2021

We’re Losing the Vaccine Race

In February on SBM I wrote about the Race Against Vaccine Hesitancy. At that point in time the pandemic was receding in the US in the face of a rapid vaccination program, but also the first new variants of SARS-CoV-2 were starting to appear. Essentially I argued that we were in a race between achieving herd immunity and the spread of new variants that might be more contagious or even vaccine resistant. Experts believed that we would know the answer by Summer.

Well, Summer is here, and the answer is in. We lost the race. Vaccine hesitancy won.

This doesn’t mean that the vaccination program has not been massively helpful. It has. As of now 48.6% of the US population is fully vaccinated, with 56.1% having received at least one dose. This includes children under 12, however, who are not currently eligible for any vaccine. A total of 68.3% of adults have been vaccinated, close to the 70% goal set by the Biden administration. From a logistical perspective, this is a success. The program peaked at over 3 million doses given per day. The program meant that the limiting factor was not the availability of vaccines or the ability to distribute and administer them. The limiting factor is people willing to get vaccinated.

While we may have come close, we did not achieve sufficient herd immunity. Part of the problem is that the vaccinated are not evenly distributed throughout the population. Vaccine uptake is patchy, which means there are clusters of unvaccinated people where the virus is free to spread. Arkansas, for example, is only at 35% fully vaccinated.

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Jul 01 2021


I know I just wrote about CRISPR, the powerful gene-editing tool that can make targeted specific alterations to genes, but there is another CRISPR news item I wanted to write about. A recent study published in the NEJM reports the results of a treatment trial using a CRISPR-Cas9 treatment injected into the blood. This is an important proof of concept with implications for the clinical impact of CRISPR.

The study itself involved a rare genetic disease called Transthyretin amyloidosis, also called ATTR amyloidosis, which results from the creation of a misfolded protein that causes damage primarily to nerves and heart tissue. From a genetics point of view, this is conceptually straightforward – turn off the gene making the toxic protein and that should fix the problem. CRISPR is really good at that – it can target the specific gene and then makes cuts in that gene to permanently disable it.

While CRISPR technology is extremely powerful, perhaps the bigger challenge is getting the CRISPR-Cas9 into the desired cells. It is easy to do this in vitro (outside the body in a test tube or dish) but harder to get the CRISPR to the correct cells in a living organism. For this we have been relying primarily on viral vectors, viruses which infect cells, delivering the CRISPR.

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Jun 24 2021

EU Report on Glyphosate

Glyphosate is a weed killer widely used by the agricultural industry and also available for consumer use in products like Roundup. Likely because of its widespread use, it has become a political target. It has also become the focus of high profile lawsuits. This means it is essential that we have objective scientific reviews of the evidence on glyphosate safety. People are still free to have varying opinions regarding the use of pesticides in agriculture, but we should be able to agree on the science. But of course we know that often does not happen. People often distort the science to suit their political or legal agenda.

My purpose here is not to cheerlead for weed killers, or defend any corporation, but to have a clear-eyed view of the published science. Fortunately, there is quite a bit of it, and experts have systematically reviewed this evidence with the purpose of distilling it into bottom-line conclusions about the safety of glyphosate. There have been many, but the most recent one, and therefore most up to date, is a thorough review by the European Union (EU). In a June 2021 11,000 page report they conclude that (in their legalese) – “The AGG proposes that classification of glyphosate as for germ cell mutagenicity
genotoxic or mutagenic is not justified.” They make the same determination for glyphosate not being a carcinogen, having reproductive toxicity, or causing organ toxicity. They did retain its classification that it can “cause serious eye damage.” So yeah, don’t get the stuff directly into your eyes. Regarding ecotoxicity, the EU found that glyphosate is generally safe, however they make an exception for aquatic life, concluding that glyphosate is “toxic to aquatic life”. These latter two concerns were already known and present in prior reviews, and so do not represent any change.

Based upon all of this the review recommends glyphosate for approval for use in the EU. Essentially, if used properly, glyphosate is safe for farm workers, consumers, and the environment. Of course the phrase, “If used properly” is doing a lot of heavy lifting there. And this is where a lot of debate can be had. But in that debate it is critical to consider the alternatives to using glyphosate in farming.

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Jun 03 2021

Return of the Bird Flu

Remember the bird flu? Avian influenza (H5N1) was first discovered in birds in 1996, with the first human crossover detected in 1997. Since then it has been discovered in 50 countries and is endemic in six. If you are old enough to remember, there was a bit of a bird flu panic back in the late 90s. Fortunately, so far, those fears have not been realized. But it’s important to remember that the bird flu is still around. Even more important is to remember that there are thousands of potentially pandemic viruses in the world.

Avian influenza adapted to infect birds, and mostly spreads through poultry. Bird to human transmission (zoonotic infection) is rare, and usually occurs in those who work in the poultry industry with long term exposure. The virus is very deadly, with a case fatality rate of about 60%. Worldwide there are 700 reported human cases. However, the virus does not spread easily from human to human. Such transmission is very rare, and is not sustainable. This is why the virus has not caused an outbreak or worse among humans. There are also other strains of flu virus that primarily infect birds, such as H10N5. We now have the first report of an H10N5 infection in a human, in a poultry worker in China. Contact tracing did not reveal any other cases.

For now we have experienced rare bird to human zoonotic transmission of flu strains primarily adapted to birds (colloquially “bird flu”) without any significant or sustainable human to human spread. So what’s the concern? As was originally raised by in the 90s, the concern is that every time a virus jumps from an animal reservoir to a human there is the potential that it will either mutate or will combine with another virus to cause a new strain that is highly contagious to humans. It happens, as we are now experiencing with the SARS-CoV-2 virus. So what do we do about it?

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May 27 2021

Red Flags of a Crank Study

The pandemic has brought into sharp focus the potential danger of misinformation. There are times when we need to act collectively as a society to accomplish certain goals. This is particularly challenging in a society that is organized around a principle of individualism – a principle I endorse and value. Liberty is a precious right to be jealously defended. But it is not the only right, or principle of value. So at times we have to delicately balance various competing interests. I like my freedom, but I also really like not catching a deadly disease, or spreading it to my family.

In a perfect world (one we definitely do not live in) there would be no need for restrictive or draconian measures. All that would be necessary was distributing information – hey, if you want to protect yourself and others, wear a mask, socially distance, wash your hands, and get vaccinated. If you’re really interested, here are the facts, the published studies, the expert analysis, to back up these recommendations. Here are the error bars and level of uncertainty, the risk vs benefit analysis, and comparison to other options.

This approach is necessary, and works to a degree, but it is insufficient. There are two main shortcomings of the information approach. First, people are only semi-rational beings, not Vulcans. We are susceptible to tribalism, motivated reasoning, confirmation bias, and a host of cognitive biases, faulty heuristics, and logical fallacies. Our intuitions about balancing risk and benefit are also flawed, and we have a hard time dealing with very large numbers. Just peruse the comments to any blog post on this site that is even slightly controversial and you will find copious examples of every type of flawed thinking.

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May 17 2021

Regulation of Supplements Lacking

A recent audit of natural products manufacturers in Canada reveals how lacking regulations are in this industry. Scott Gavura does a good review of this over at SBM. I want to amplify some of what he says and add further context.

For background, so that everyone knows where I am coming from, I tend to take a nuanced approach to regulation. I believe in the power of capitalism and a free market to allocate resources in an organic way that will reflect, at least in part, actual merit. But free markets do not exist in a vacuum, they need to be crafted by an agreed upon set of rules. Further, there are always going to be people who try to work the system, bend the rules, and exploit others. Further, the evolutionary forces at work within a free market do not always favor acceptable outcomes. We know from history what happens in unregulated markets (we don’t have to guess) – they lead to fraud, exploitation, and monopoly. People will use wealth and power to rig the system so they gain more wealth and power at the expense of everyone else. The people who do this best will tend to succeed over time. While 1% of the population displays psychopathic traits, the figure is 4-12% among corporate CEOs.

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