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Friday 30 July 2021

The Cost of Liberty..?

This is a very quick and dirty offering for all those who are hesitant about getting vaccinated. 

I get it. There's so much conflicting information that it's hard to know what to do. Who are we supposed to trust?

Here are some easily checkable facts with no punches pulled, so you can trust yourself to make an informed choice. Medical scientists, and scientists generally, will almost always act, but will always speak, from an abundance of caution. In medical terms, the reasoning behind this is stitched in to the very way professionals think; first, do no harm. Of all the sciences, medical science is keenly aware of the potential for unforeseen consequences. When a physicist makes a dimensionality error in his calculations, the consequence is only that the universe in his head disappears up its own arse. When a medical scientist does that, people can die.  

I can be a bit more direct, but I'm not saying anything (barring the odd stray factual error, which is my doing) that any doctor or medical scientist wouldn't say.

First, the vaccines are safe. This doesn't mean they're risk-free, because putting foreign things in your body is never entirely without risk, but it's orders of magnitude safer than allowing a particular foreign thing - the virus - to enter the body without protection. There are, of course, always going to be a number of adverse reactions, but they are statistically tiny. Most adverse reactions are minor and treatable. Incidence of full allergic reaction is mostly clustered around those who have a tendency to allergies. ALL adverse reactions are tracked closely on the VAERS database, and these data are examined for emerging trends, not least because they tell us about possible environmental factors in reactions by how they're clustered.

It's certainly the case, because we're using a new vaccine, we don't have data on safety in the long term, and this is most definitely a valid concern. However, it's not a well-founded concern, for various reasons. I'll hold the major one in abeyance because I'm going to talk about that separately in detail below, but there are some things being said about the vaccines that simply don't reflect reality.

The most important of these is the notion that the vaccine is 'experimental'. This is nonsense, except insofar as ALL medicine is experimental, including the medicine that's already been validated by centuries of success. That's how science - not just medical science - works.

In fact, the vaccines on offer are based on a range of technologies, but the one that's causing the most consternation based anecdatally on what I've seen, is the notion that mRNA vaccines are new, or that they 'rewrite your genes'. Both of these are nonsense. In fact, mRNA vaccine technology has been in development and use for decades. My first encounter with the technology was probably a decade ago, from a discussion with a dear friend, a research oncologist, who was talking about using closely related technology for targeting specific cancers. 

The simple fact is mRNA vaccines have some distinct safety advantages over conventional vaccines. I won't go into that here, because I'm trying to keep this as concise as possible, but see Qualified Immunity, in which I talk at some length about viruses, vaccines and evolution and how it all works.

I'll come back to other concerns about long term safety, because that's going to require comparison.

Moving on, no safety protocols have been missed in development and testing of any of the vaccines offered. To the extent the process has been faster, this is because of a) motivation, b) wealth of knowledge about viruses and evolution and c) governments getting their interminable bureaucracy out  of the way.

Finally, genuine reactions to vaccines wane over time. In the real world, we set time scales for vaccine reactions to cap at about 6 months. That is to say, anything that occurs more than 6 months after receipt of a vaccine will not be considered related to the vaccine, because genuine adverse reactions happen quickly. In fact, this 6 month time frame is considerably longer than necessary, just out of the abundance of caution we mentioned at the beginning. 3 months is more than sufficient. No event after this is likely to be a result of the vaccine. See this wonderfully detailed but very approachable piece by immunologist Andrew Croxford for much, much more on this:

This is where I need to get a bit blunt. One of the things I've been most frustrated by is the amount of equivocation on what follows. Probably nobody has come out and said this straight to you, so here it is.

You are going to attain immunity. That's not up for debate. It's simply in the nature of viruses and infection that, at some point, everybody will have some degree of immunity. This could change if, for example, we manage to develop effective pharmaceutical interventions to treat the illness but, as it stands, immunity is the whole shooting match. 

The options for achieving immunity are as follows:

i) Get vaccinated

ii) Get infected

iii) Die.

This is an exhaustive list. There are no alternative options.

Of course, you might say, we're all going to die anyway. Technically correct, but death isn't the only outcome. In fact, the probability is extremely high we're all going to get infected anyway, at least to a first approximation. It doesn't matter how you acquire immunity, you're definitely going to get infected. It's quite literally inevitable unless you die of something else first or you manage to remain completely isolated until we can contain the spread and push for something like herd immunity. You're certainly incredibly unlikely to have any sort of extended future without getting infected. 

It's important to note that none of these options are mutually exclusive. You can, in fact, have all three of these happen in the exact order they've been listed here. Yes, you read that right. You can get vaccinated, then get infected (this is what's meant by breakthrough infection) and die from the infection. In fact, you can get infected, survive, get vaccinated, get reinfected later and still die. Vaccines are not a panacea. 

Let's look at these options in detail, starting with the second.

ii) Get infected.

This is an option. Many have acquired immunity this way. This is, in fact, what we mean by acquired immunity, as opposed to conferred immunity; immunity conferred via vaccination or inoculation.

This approach has some distinct disadvantages, though, and it's important to be aware of them.

The first is simply the higher probability of iii. You are considerably more likely to die if you're infected than if you're vaccinated. That's a simple statement of fact. That probability in any given case is based on a huge range of variables. Many of the same variables, in fact, that impact overall health generally. General health, underlying conditions, poverty, ethnicity...

One factor seems to be age, and there's evidence emerging now for precisely why that might be, and it's all to do with how your immune system works. There's an update in Qualified Immunity talking about that. It appears that, in the most severe cases, the worst symptoms may be an autoimmune response; your own immune system is attacking you. This 'T cell' response, as it's known, will become important in a moment.

Two more critical facts about short-term to note about this 'acquired' route to immunity:

1. There are clear data now showing that acquired immunity results in significantly more - and significantly more severe - breakthrough infections. It's not entirely clear why this is, but it's probably got a lot to do with how the immune system responds to it. The immune system can find a solution to the virus that works sufficiently well at blocking binding for the replication rate of the virus, but replication rates evolve. In fact, the existence of a weak solution will drive the virus to evolve escape to that solution. Vaccines are much more precise, because they give the immune system the chance to find the right solution in a controlled setting. This is especially true when we start to talk about variants. It also appears that acquired immunity wanes over time.

2. While infections are currently rising quickest among vaccinated people, almost all the people filling up intensive care beds are unvaccinated. Almost all the people dying are unvaccinated.

Now we need to talk about long term effects, particularly what can only be described as a syndrome (a syndrome is a collection of symptoms, in essence, generally associated with some single, underlying cause) known as long COVID. It's quite a large collection, ranging from general fogginess to joint pain, chronic fever, a whole slew of symptoms with varying degrees of debilitation, and lasting for some considerable time. There are data on patients infected right at the beginning of the first wave still suffering symptoms now, some eighteen months later.

In the appendices of the earlier linked post, there's whole list of only the most troubling and severe consequences of long COVID. Some of it is also about what we can expect of long COVID in the future, such as a reasonably good chance that there will be a spike in Parkinson's and other forms of dementia. Some of those consequences are especially concerning for young people, i.e., under 20s. This has been my most pressing concern, because I'm an educator at heart, and developing brains have enough trouble with all the hormones and stuff without an epidemic of long-term cognitive disorders.

So, just the post-it note version of the T-cell response before we talk about the consequences of vaccination. Your immune system is made up of several components, among which are cells known T cells. These are white blood cells involved in some responses to foreign bodies. They can replicate really rapidly and differentiate for different purposes. This is good. What's not so good is when it goes wrong. In particular, there are some situations in which the T-cells can into very rapid replication and differentiation, and get a bit out of control. The result is premature apoptosis. Apoptosis is the normal death a cell undergoes when it's fulfilled its function (as an aside, most cancers are a failure of this process; your cells become immortal). The end result of this is a kind of toxic soup, and the T-cells start attacking everything, you included. This, where the immune system starts attacking you, is what we mean by autoimmune. 

When your immune system encounters a foreign entity, it throws literally everything at it, including any T-cell it can manufacture. Once your immune system finds a working solution, everything else switches off and production is dedicated to the working antibodies. 

This means, of course, that the quicker your immune system finds the solution, the quicker T-cell response switches off. 

SARS-CoV-2 has now been shown to trigger an autoimmune T-cell response, and it looks not terribly improbable that this accounts for most of the more severe symptoms.

i) Get vaccinated.

Let's talk about the clear disadvantages of the vaccine first and get them out of the way. 

Someone has to stick a needle in your arm.

OK, I'm being facetious. No vaccine is really without risk or concern. The long-term responses to the vaccine are not known, but we're not entirely in the dark about them as some suggest. None of the technology is really new. Some of the solutions for getting the messenger RNA into the cell are novel, but they're novel uses of existing and known technology. The basic binding mechanism is a molecule of fat and electrostatic forces. 

None of the vaccines have any impact on your genetic code. That's just nonsense. The vaccines teach your cells to make an exact replica of a specific part of the virus. This is, in fact, considerably safer than conventional vaccines for the simple reason that conventional vaccines are attenuated or weakened versions of the 'live' virus.

The vaccines do NOT stop you from getting infected or transmitting, nor can any vaccine, because of how vaccines work. They can, because they confer a map of the virus and therefore trigger a correct immune response much quicker, mean that you're infectious for a shorter length of time. It is worth noting, however, that delta can reach levels sufficient for a positive PCR test in as little as four days, with peak infectiousness being reached in the two days prior. That means you can already be at peak infectiousness and have a negative PCR for two whole days.

As a simple matter of statistics and evolution, some pepe will still get sick, and some will even die, after having any combination of the above but, and this is the important part, every single outcome is significantly, measurably improved if you're vaccinated, and the vaccines all currently seem to have measurably better success in beating severe breakthrough infections. That may change, because of evolution, but we currently have good reason to think it can work, if...

This is the 'personal responsibility' part.

Evolution is a well-understood science, easily the best evidenced field in all of science. As a science nerd who primarily pontificates about physics, I'd sell my left nut for a tiny shred of the evidence that underpins evolution - and that's speaking as somebody using technology to share my thoughts with you based on the most profoundly shocking principles in all of physics - for any of the things I usually hold forth on.

That said, I know that a lot of people don't get it, or don't like it, or have ideological opposition to it, or simply don't accept it for their own reasons. I get it. I'm also keenly aware of the Venn diagram showing huge overlap in demographic between groups who are vaccine-hesitant and those who reject evolution. I honestly wish I had something I could say t convince them, but here's what's true.

A partially vaccinated population is in some ways more dangerous than an entirely unvaccinated one, because of one of the simplest and most fundamental principles of natural selection, and it's this; where there is an advantage of any sort, evolution accelerates, and it accelerates in the specific direction of that particular advantage. If one variant replicates slightly faster (the beta variant did this) and this allows it to outrun the vaccine a little longer, it will evolve in the direction of faster replication. If another variant develops differences in the binding site - such differences could be minuscule, just enough to make the binding of the antibody to the virus less than perfect - then it has resistance to the vaccine, even if only a little bit. Future generations of the virus will exploit that, because it's what gave them a chance to be here, very nice, thank you very much. In other words, it will evolve faster, and it will evolve in the direction of making that fit between antibody and spike protein worse and worse until the antibody no longer fits at all - full vaccine escape.

At that point, all bets are off, and we could be back to the lockdown races again while we develop new vaccines.

The longer any portion of the population above a very small number (figures for herd immunity being revised all the time, but at least high 80% range) remains unvaccinated, the more inevitable it becomes that we get an escape variant or, worse, a new strain. A new strain is a version of the virus with entirely new function, i.e., behaving in a different way, as opposed to tiny incremental improvements on existing behaviours. This, incidentally, is the correct answer to Rand Paul's illiterate question to Anthony Fauci that so incensed the good doctor, and rightly so. No, it wasn't gain of function research, it was detail of function research, adjusting existing function incrementally to see the nuts and bolts of how the functions work, i.e., science.

Ultimately, it's like this. I want as many of us to live as long and as well as possible. If you've never had a chronic condition, I promise, you don't want one. Of all the gifts I ever had, it's the one I like the least. 

I want you and yours to be well, and safe and happy. I hate giving unsolicited advice, and especially unsolicited medical advice, but this is a different situation. 

For those for whom this is about freedom, I feel you. I absolutely agree that some of the way this entire shitshow has been managed, especially in two countries of note, has been a colossal over-reach. I know that this over-reach only reached such colossal proportions, though, because of dismissal and inaction by the muppets at the top. Laughing this off and handwaving it away were never the answer.

But this is the boat we're in. More importantly, there's something about freedom that often gets overlooked.

None of us is free unless everybody is. Our freedoms end where the freedoms of others begin. 

Nobody likes this situation. Well, there are a few billionaires that have profited quite handsomely, but those aside, none of us delivering the science are profiting from doing so. I certainly don't. I have nothing to gain from telling you any of this other than your continued existence and well-being and the well-being of those around you. 

I'm a physics geek. Yes, I've written fairly extensively about evolution and other scientific topics, but they're not the things I want to be writing about. I want to write about quantum decoherence and the many-worlds interpretation, and the joys of vectors and spinors.

I've paid close attention to this virus from day one, never with any intention of writing about it, only with being as well-informed as possible to keep myself and those around me as safe as possible. I've had some advantages, of course, precisely because of the broad range of topics I've covered here.

Historically, my motivation in writing here has always been aimed at attempting to undermine a prediction made beautifully eloquently by one of the great physicists of the twentieth century, and quite possibly the most gifted science communicator of the modern age; the sci-commer to which all us mere mortals merely aspire, the late, great Carl Sagan. 

Sagan went to book length to deliver his prediction in a polemic on the state of thought and education. When his book, The Demon-Haunted World was written, I don't know if he truly knew how quickly his prediction would be realised to at least a significant degree.

To slightly nutshell Sagan in a very specific way, Sagan warned against a future world in which the general understanding of science in the public at large and, more importantly, in our leaders, was such that decisions would be made that put people in harm's way.

I've hugely paraphrased Sagan here, and I've spun what he said into a very specific context, but I'm not being misleading about the implications of what he said. In fact, he was talking more in the context of weapons of mass destruction, but what he said applies equally here.

My motivation in writing here has always been as something of a disinfectant against such an eventuality, and I know this motivation is shared by many sci-commers with platforms large and small. 

I make nothing from my writing other than the very occasional kind donation from one of my lovely long-time readers. The reason I write is because it's the thing I can do that might make any difference whatever. 

You're my team, and I want my team to perform at its best, and that works best if we all work together and look after each other. This is my way of doing that. Freedom is a team sport. For liberty to truly mean anything, it has to apply to all of us, and it can't apply to some of us at the cost of others. That isn't liberty, that's slavery. Your freedom to swing your arm ends at my nose, and your freedom to remain unvaccinated ends at putting the lives of others at risk. At the moment, the unvaccinated population represent a clear and present danger to society. I'm sorry, but that's how it is. Nobody wants to mandate this. Nobody wants to impinge on your liberty, but liberty comes with responsibility. The society that protects you to exercise your liberty and punishes those who infringe on it is the responsibility of us all to maintain, and that maintenance requires sacrifices, even if those sacrifices are for the benefit of you and those around you as well as the rest of us. 

Your bodily autonomy is important. It's the foundation of all ethical reasoning. Society recognises, and so do almost all within it, including those who resist masks and vaccines in the name of liberty, that there are some actions through which you waive your bodily autonomy. Not only the commission of crimes, either, but also when you put others at risk. Yelling 'fire' in a crowded theatre is the usual example. There are many things for which you can be arrested simply for speaking, where nobody is harmed, but where people are put at risk. Phoning in a bomb threat hoax, for example. 

The risk represented by the virus having free rein in a partially vaccinated population is a threat to society as a whole. This is considerably greater a risk than yelling anything anywhere, and definitely a greater risk than a bomb hoax.

The best thing I can do to protect your bodily autonomy is to tell you why you should definitely go and get vaccinated. The longer you resist, the more inevitable you make it that society will quite rightly make the decision for you. 

The price of freedom is indeed eternal vigilance. One of the things of which we must be most vigilant is that, in seeking liberty, we don't enslave ourselves to mere ideas. What of those who can't be vaccinated yet, and for whom we have no effective way to manage symptoms or treat infection? We have to be careful in our aim to protect liberty over security not to sacrifice our humanity on the way.

Please be well, stay safe, and look after each other. This is not a dress rehearsal. There is no understudy to come on in your place.

More reading:

Testing Times - How PCR testing works, and why people are wrong about what Karey Mullis, the inventor of the PCR, said about it.

Passport to Pimlico - some thoughts on vaccine passports.

Qualified Immunity - everything you ever wanted to know about viruses, vaccines, evolution and immunity, along with a growing resource of emerging evidence, updated as new research comes in with the most critical information.

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