Chemical jigsaw puzzles: how do chemists identify molecules?

Front cover of Great ExplanationsA quick thing before I get into this month’s chemistry ramble: I’m guessing that you, lovely reader, enjoy reading about science stuff. Especially stuff written by an amazing crowd of hard-working science communicators, one of whom is yours truly. So, please consider spreading the word about this awesome book: Great Explanations. Or even better, pledge! There are some fabulous rewards at the different pledge levels. Either way, thank you x

Okay, back to it! Recently, a bit of an argument blew up on Twitter regarding what is, and isn’t, in covid vaccinations. The particular substance du jour being graphene oxide. The @TakeThatChem account pointed out that one of the sources being touted by some as ‘evidence’ for its presence (the article in question was by Robert O Young, remember him? Yes, the one that did actual jail time) didn’t describe the use of any sort of technique that could identify graphene oxide. Which, just to be clear, is absolutely not an ingredient in covid vaccinations.

The debate culminated with questions about how, exactly, scientists do identify substances on the molecular level. @TakeThatChem wondered if one of the users who had become embroiled in the debate even understood how a chemist might work out a molecule’s structure, and then posted an image.

Screenshot of tweet by @TakeThatChem showing an NMR spectrum (link in text)

This tweet illustrated a technique that can be used to identify molecules.

British students of chemistry first meet images like this somewhere around the age of 17–18, so although this is somewhat advanced, it’s still essentially school-level. Which means that for a chemist, it’s one of those things that’s so familiar that, half the time, we probably forget that the rest of the world will have absolutely no idea what it is.

But for those that have never studied A level chemistry or similar: what is it?

The answer is that it’s a proton NMR, or nuclear magnetic resonance, spectrum. Now, NMR is quite tricky. Bear with me, I’m about to try and explain it in a paragraph…

Here goes: you know magnets? And how, if you put one magnet near another magnet, it moves? Now imagine that certain types of atomic nuclei are basically tiny magnets. If you put them in a really powerful magnetic field, they sort of move. If you then alter that magnetic field, they move as the field varies. A computer records and analyses those changes, and spits out a graph that looks like that one back there – which chemists call a spectrum.

Photo of MRI equipment

Medical MRIs use essentially the same technology as the one used to generate the spectrum

Did I nail it? There’s a lot more to this, not surprisingly. In particular, radio waves are involved. My quick and dirty explanation is the equivalent of describing a car as a box on wheels – it’s broadly true from a distance if you squint a bit, but if you said it in the presence of a qualified mechanic they’d wince and start muttering words like ‘head gasket’ and ‘brake discs’ and ‘you do know this is a diesel engine, yes?’

Anyway, it’ll do for now. If you’re studying NMR at a more advanced level, take a look at this episode of Crash Course Organic Chemistry written by… someone called Kat Day. No idea who that is 😉

The same technique, by the way, is used in medicine – but there you know it as MRI, or magnetic resonance imaging. It turns out that if you shove a human (or pretty much anything that contains a lot of carbon-based molecules) into a powerful magnetic field, the atomic nuclei do their thing. You might imagine that having all your atoms do some sort of cha-cha would hurt, but no – as anyone who’s ever had an MRI will attest, it’s mostly just very loud and a bit dull. The end result is an image with different contrast for different types of tissue. Fatty tissue, for example, tends to show up as areas of brightness, while bone tends to look darker – so it’s useful for diagnosing all sorts of problems.

Photo of jigsaw pieces

Interpreting a proton NMR spectrum can be a bit like looking at a jigsaw pieces

But back to chemistry. Chemists, preferring a simpler life (haha), are often working with single substances. Or at least trying to. If we imagine a molecule as a picture, looking at a proton NMR spectrum is a bit like looking at a mixed-up jigsaw puzzle of that picture. Each individual piece – or peak – in the spectrum represents an atom or a group of atoms.

Each piece tells you something and, at the same time, it also tells you about the bits that are joined to it. In the same way that you might look at a jigsaw piece and think, ‘well, this has a sticky-out bit so the piece that goes next to it must have an inny-bit,’ chemists look at a spectrum and say, ‘well, this bit looks like this, so its carbon atom must be attached to group of atoms like that.’

Okay, so what do the pieces in the spectrum @TakeThatChem posted show us? Well, reading spectra takes practice but, like most things, if you do that practice, after a while you get into the habit of spotting things straight away.

For example, it’s fairly obvious to me that whatever-it-is it probably has a carboxylic acid (COOH) group, and it definitely has a benzene ring. I can also see that the benzene ring has things bonded to opposite points, in other words, if you numbered the carbons in the ring from 1 to 6, it has things attached at carbon 1 and carbon 4. There’s a chain of carbons, which is branched, and there’s another CH3 group somewhere. To get more precise I’d have to look more carefully at the integrals (the differently-sized ∫ symbols over the peaks), hunt for a data sheet and study the scale on the horizontal axis along the bottom.

Photo of white pills

The spectrum is of a common drug substance, but which one…

My brain got as far as ‘hm, maybe it’s aspirin, oh no, it can’t be, because…’ before I came across the already-posted answer. I won’t give it away – spoilers, sweetie – but let’s just say it’s a molecule not a million miles different from aspirin.

So yes, chemists do have the means to identify individual molecules, but it requires a fair bit of knowledge and training to both carry out the techniques and to interpret the results. Despite what Hollywood might have us believe, we don’t (yet) have a machine that intones ‘this material is approximately 40% isobutylphenylpropionic acid, captain’ when you plop a sample into it.

The fact that real chemistry (and science in general) is not simple is precisely why pseudoscience peddled by the likes of Robert O Young is so appealing: it’s nice and easy, it follows a sort of ‘common sense’ narrative, it’s not swathed in all sorts of technical language. Anyone can read it and, without any other training, feel as if they understand it perfectly.

None of us knows what we don’t know. If someone comes along with an easy explanation, it’s tempting to believe it – particularly if they go on to play into our anxieties and tell us what we were hoping to hear.

Which brings me to a thread by the lovely Dr Ben Janaway, one tweet of which said, extremely eloquently:

Please do not harass [people protesting covid vaccines]. Please do not blame them. My education is a privilege they have not been afforded. They do not lack intelligence, they lack being taught how to make sense of very complicated things, most of it hidden. What can we do, listen and talk.

Photo of a facemask, syringe and vaccine vials

Please get vaccinated

His point is a good one. All we can do is keep spreading the word as clearly as possible and just hope that, maybe, it will change one mind somewhere. Because maybe that mind will change another, and maybe sense will spread.

Take care, stay safe, and get vaccinated. Get your flu jab, too, if it’s that time of year in your part of the world.


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Confusing chemical names: why do some sound so similiar?

It’s the end of March as I write this and, here in the UK at least, things are starting to feel a little bit hopeful. We’ve passed the spring equinox and the clocks have just gone forward. Arguments about the rights and wrongs of that aside, it does mean daylight late into the day, which means more opportunities to get outside in the evenings. Plus, of course, COVID-19 vaccines are rolling out, with many adults having had at least their first dose.

Some COVID-19 vaccines contain polyethylene glycol (PEG), a safe substance found in toothpaste, laxatives and other products, according to Science magazine and health expertsAh, yes. Speaking of vaccines… a couple of weeks ago I spotted a rather strange item trending on Twitter. The headline was: “Some COVID-19 vaccines contain polyethylene glycol (PEG), a safe substance found in toothpaste, laxatives and other products, according to Science magazine and health experts.”

Apart from being a bit of mouthful, this seemed like the most non-headline ever. And also, isn’t it the kind of thing that might raise suspicions in a certain mind? In a, “yeah, and why do they feel the need to tell us that, huh” sort of way?

Why on earth did it even exist?

A little bit of detective work later (by which I mean me tweeting about it and other people kindly taking the time to enlighten me) and I had my answer. The COVID-19 sceptic Alex Berenson had tweeted that the vaccine(s) contained antifreeze. Several people had immediately responded to say that, no, none of the vaccine formulations contain antifreeze. Antifreeze is ethylene glycol, which is definitely not the same thing as polyethylene glycol.

I’m not going to go much further into the vaccine ingredients thing, because actual toxicologists weighed in on that, and there’s nothing I (not a toxicologist) can really add. But this did get me thinking about chemical names, how chemists name compounds, and why some chemical names seem terrifyingly long while others seem, well, a bit silly.

A lot of the chemical names that have been around for a long time are just… names. That is, given to substances for a mixture of reasons. They do usually have something to do with the chemical makeup of the thing in question, but it might be a bit tangential.

formic acid, HCOOH, was first extracted from ants

For example, formic acid, HCOOH, takes its name from the Latin word for ant, formica, because it was first isolated by, er, distilling ant bodies (sorry, myrmecologists). On the other hand limestone, CaCO3, quicklime, CaO, and limewater, a solution of Ca(OH)2, all get their names from the old English word lim, meaning “a sticky substance,” which is also connected to the Latin limus, from which we get the modern word slime — because lime (mostly CaO) is the sticky stuff used to make building mortar.

The trouble with this sort of system, though, is that it gets out of control. The number of organic compounds listed in the American Chemical Society‘s index is in excess of 30 million. On top of which, chemists have an annoying habit of making new ones. Much as some people might think forcing budding chemists to memorise hundreds of thousands of unrelated names is a jolly good idea, it’s simply not very practical (hehe).

It’s the French chemist, Auguste Laurent, who usually gets most of the credit for deciding that organic chemistry needed a system. He was a remarkable scientist who discovered and synthesised lots of organic compounds for the first time, but it was his proposal that organic molecules be named according to their functional groups that would change things for chemistry students for many generations to come.

Auguste Laurent (image source)

Back in 1760 or so, memorising the names of substances wasn’t that much of a chore. There were half a dozen acids, a mere eleven metallic substances, and about thirty salts which were widely known and studied. There were others, of course, but still, compared to today it was a tiny number. Even if they were all named after something to do with their nature, or the discoverer, or a typical property, it wasn’t that difficult to keep on top of things.

But over the next twenty years, things… exploded. Sometimes literally, since health and safety wasn’t really a thing then, but also figuratively, in terms of the number of compounds being reported. It was horribly confusing, there were lots of synonyms, and the situation really wasn’t satisfactory. How can you replicate another scientist’s experiment if you’re not even completely sure of their starting materials?

In 1787 another French chemist, Guyton de Morveau, suggested the first general nomenclature — mostly for acids, bases and salts — with a few simple principles:

  • each substance should have a unique name, as short and specific as possible
  • the name should reflect what the substance consisted of, that is, describe its “composing parts”
  • unknown substances should be assigned names with no particular meaning, being sure not to suggest something false about the substance (if you know it’s not an acid, for example, don’t name it someinterestingname acid)
  • new names should be based on old languages, such as Latin

His ideas were accepted and adopted by most chemists at the time, although a few did attack them, claiming they were “barbarian, incomprehensible, and without etymology” (reminds me of some of the arguments I’ve had about sulfur). Still, his classification was eventually made official, after he presented it to the Académie des Sciences.

Chemists needed a naming system that would allow them to quickly identify chemical compounds.

However, by the middle of the 1800s, the number of organic compounds — that is, ones containing carbon and hydrogen — was growing very fast, and it was becoming a serious problem. Different methods were proposed to sort through the messy, and somewhat arbitrary, accumulation of names.

Enter Auguste Laurent. His idea was simple: name your substance based on the longest chain of carbon atoms it contains. As he said, “all chemical combinations derive from a hydrocarbon.” There was a bit more to it, and he had proposals for dealing with specific substances such as amines and aldehydes, and of course it was in French, but that was the fundamental idea.

It caused trouble, as good ideas so often do. Most of the other chemists of the time felt that chemical names should derive from the substance’s origins. Indeed, some of the common ones that chemistry professors are clinging onto today still do. For example, the Latin for vinegar is acetum, from which we get acetic acid. But, since organic chemistry was increasingly about making stuff, it didn’t entirely make sense to name compounds after things they might have come from, if they’d come from nature — even when they hadn’t.

So, today, we have a system that’s based on Laurent’s ideas, as well as work by Jean-Baptiste Dumas and, importantly, the concept of homology — which came from Charles Gerhardt.

Homology means putting organic compounds into “families”. For example, the simplest family is the alkanes, and the first few are named like this:

Like human families, chemical families share parts of their names and certain characteristics.

The thing to notice here is that all the family members have the same last name, or rather, their names all end with the same thing: “ane”. That’s what tells us they’re alkanes (they used to be called paraffins, but that’s a name with other meanings — see why we needed a system?).

So the end of the name tells us the family, and the first part of the name tells us about the number of carbons: something with one carbon in it starts with “meth”. Something with five starts with “pent”, and so on. We can go on and on to much bigger numbers, too. It’s a bit like naming your kids by their birth order, not that anyone would do such a thing.

There are lots of chemical families. The alcohols all end in “ol”. Carboxylic acids all end in “oic acid” and ketones end in “one” (as in bone, not the number). These endings tell us about certain groups of atoms the molecules all contain — a bit like everyone in a family having the same colour eyes, or the same shaped nose.

A chemist that’s learned the system can look at a name like this and tell you, just from the words, exactly which atoms are present, how many there are of each, and how they’re joined together. Which, when you think about it, is actually pretty awesome.

Which brings me back to the start and the confusion of glycols. Ah, you may be thinking, so ethylene glycol and polyethylene glycol are part of the same family? Their names end with the same thing, but they start differently?

Well, hah, yes and no. You remember a moment ago when I said that there are still some “common” names in use, that came from origins — for example acetic acid (properly named ethanoic acid)? Well, these substances are a bit like that. The ending “glycol” originates from “glycerine” because the first ones came from, yes, glycerine — which you get when fats are broken down.

Polyethylene glycol (PEG) is a polymer, with very different properties to ethylene glycol (image source)

Things that end in glycol are actually diols, that is, molecules which contain two -OH groups of atoms (“di” meaning two, “ol” indicating alcohol). Ethylene glycol is systematically named ethane-1,2-diol, from which a chemist would deduce that it contains two carbon atoms (“eth”) with alcohol groups (“ol”) on different carbons (1,2).

Polyethylene glycol, on the other hand, is named poly(ethylene oxide) by the International Union of Pure and Applied Chemistry (IUPAC), who get the final say on these things. The “poly” tells us it’s a polymer — that is, a very long molecule made by joining up lots and lots of smaller ones. In theory, the “ethylene oxide” bit tells us what those smaller molecules were, before they all got connected up to make some new stuff.

Okay, fine. So what’s ethylene oxide? Well, you see, that’s not quite a systematic name, either. Ethylene oxide is a triangular-shaped molecule with an oxygen atom in it, systematically named oxirane. Why poly(ethylene oxide), and not poly(oxirane), then? Mainly, as far as I can work out, to avoid confusion with epoxy resins and… look, I think we’ve gone far enough into labyrinth at this point.

The thing is, polyethylene glycol is usually made from ethylene glycol. Since everyone tends to call ethylene glycol that (and rarely, if ever, ethane-1,2-diol), it makes sense to call the polymer polyethylene glycol. Ethylene glycol makes polyethylene glycol. Simple.

Plastic bags are made from polythene, which has very different properties to the ethene that’s used to make it.

Polymers are very different to the molecules they’re made from. Of course they are, otherwise why bother? For example, ethene (also called ethylene, look, I’m sorry) is a colourless, flammable gas at room temperature. Poly(ethylene) — often just called polythene — is used to make umpteen things, including plastic bags. They’re verrrrry different. A flammable gas wouldn’t be much use for keeping the rain off your broccoli and sourdough.

Likewise, ethylene glycol is a colourless, sweet-tasting, thick liquid at room temperature. It’s an ingredient in some antifreeze products, and is, yes, toxic if swallowed — damaging to the heart, kidneys and central nervous system and potentially fatal in high enough doses. Polyethylene glycol, or PEG, on the other hand, is a solid or a liquid (depending on how many smaller molecules were joined together) that’s essentially biologically inert. It passes straight through the body, barely stopping along the way. In fact, it’s even used as a laxative.

So the headlines were accurate: PEG is “a safe substance found in toothpaste, laxatives and other products.” It is non-toxic, and describing it as “antifreeze” is utterly ridiculous.

In summary: different chemicals, in theory, have nice, logical, tell-you-everything about them names. But, a bit like humans, some of them have obscure nicknames that bear little resemblance to their “real” names. They will insist on going by those names, though, so we just need to get on with it.

The one light in this confusingly dark tunnel is the internet. In my day (croak) you had to memorise non-systematic chemical names because, unless you had a copy of the weighty rubber handbook within reach, there was no easy way to look them up. These days you can type a name into Google (apparently other search engines are available) and, in under a second, all the names that chemical has ever been called will be presented to you. And its chemical formula. And multiple other useful bits of information. It’s even possible to search by chemical structure these days. Kids don’t know they’re born, I tell you.

Anyway, don’t be scared of chemical names. They’re just names. Check what things actually are. And never, ever listen to Alex Berenson.

And get your vaccine!


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The Chronicles of the Chronicle Flask: 2017

We’ve made it! Not only to 2018 (which was starting to look doubtful earlier in the year), but also to the Chronicle Flask’s 100th post. Which doesn’t seem that many, really, but since posts on here frequently run to 1500 words, that adds up to a rather more impressive-sounding 150,000 words or so. I mean, that’s like… half a Brandon Sanderson novel. Oh.

Anyway, it’s time for a yearly round-up. Here goes!

Last January I began with a post about acrylamide. We’d all been enjoying lots of lovely crispy food over Christmas; it was time to tell us about the terrible dangers of such reckless indulgence. The newspapers were covered with pictures of delicious-looking chips, toast and roast potatoes alongside scary headlines such as:  “Crunchy toast could give you cancer, FSA warns”. The truth was not quite so dramatic. Acrylamide does form when foods are cooked to crispiness, and it is potentially harmful, but the quantities which form in food are tiny, and very unlikely to cause you any serious harm unless you literally live on nothing but burnt toast. The FSA (Food Standards Agency) hadn’t significantly revised their guidelines, it turned out, but were in fact only suggesting that the food industry should be mindful of acrylamide levels in food and seek to reduce them as much as possible. That wouldn’t have made for quite such a good “your food is going to killllll you!” story though, I suppose.

In February the spikey topic of vaccination came up. Again. Vaccines are awesome. They protect us from deadly diseases. No, I don’t want to hear any nonsense about “Big Pharma“, and I definitely don’t want to hear how “natural immunity” is better. It’s not. At best, it might provide a similar level of protection (but not in every case), but it comes with having to suffer through a horrible, dangerous disease, whereas vaccination doesn’t. It ought to be a no-brainer. Just vaccinate your kids. And yourself.

It was Red Nose Day in the UK in March, which brought some chemistry jokes. Turns out all the best ones aren’t gone, after all. Did you hear about the PhD student who accidentally cooled herself to absolute zero? She’s 0K now.

April brought a post which ought to have been an April Fool’s joke, but wasn’t. Sceptics often point out that homeopathy is just sugar and water, but the trouble is, sometimes, it’s not. There’s virtually no regulation of homeopathy. As far as I’ve been able to establish, no one tests homeopathic products; no one checks the dilutions. Since a lot of the starting materials are dangerously toxic substances such as arsenic, belladona, lead and hemlock, this ought to worry people more than it does. There has been more than one accidental poisoning (perhaps most shockingly, one involving baby teething products). It really is time this stuff was banned, maybe 2018 will be the year.

In May I turned to something which was to become a bit of a theme for 2017: alkaline water. It’s not so much that it doesn’t do anything (although it really doesn’t), more the fact that someone is charging a premium for a product which you could literally make yourself for pennies. It’s only a matter of dissolving a pinch of baking soda (sodium bicarbonate) in some water.

June brought a selection of periodic tables because, well, why not? This is a chemistry blog, after all! And now we’ve finally filled up period seven they do have a rather elegant completness. 2019, by the way, has just been announced as the International Year of the Periodic Table of Chemical Elements, to coincide with IUPAC’s 100th anniversary and the 150th anniversary of Mendeelev’s discovery of periodicity (his presentation, The Dependence Between the Properties of of the Atomic Weights of the Elements, was made on 6th March 1869). Looks like 2019 will be an exciting year for chemists!

In July it was back to the nonsense of alkaline diets again, when Robert O. Young was finally sentenced to 3 years, 8 months in custody for conning vulnerable cancer patients into giving him large sums of money for ineffective and dangerous treatments. Good. Moving on.

August brought me back to a post that I’d actually started earlier in the year when I went to a March for Science event in April. It was all about slime, and August seemed like a good time to finally finish it, with the school holidays in full swing – what could be more fun on a rainy day at home than making slime? Slime was a bit of a 2017 craze, and there have been a few stories featuring children with severely irritated skin. But is this likely to be caused by borax? Not really. Turns out it’s actually very safe. Laundry detergents in general, not so much. In short, if you want to make slime the traditional way with PVA glue and borax, fill your boots. (Not really – your parents will be uninpressed.)

In September it was back to quackery: black salve. A nasty, corrosive concoction which is sold as a cancer cure. It won’t cure your cancer. It will burn a nasty great big hole in your skin. Do not mess with this stuff.

October carried on in a similar vein, literally. This time with a piece about naturopaths recommending hydrogen peroxide IVs as a treatment for lots of things, not least – you guessed it – cancer. Yes, hydrogen peroxide. The stuff you used to bleach hair. Intraveneously. Argh.

The puking pumpkin!

The end of the month featured a far better use for hydrogen peroxide, that of the puking pumpkin. Definitely one to roll out if, for any reason, you ever find yourself having to demonstrate catalysis.

November brought us, somewhat unseasonally, to tomatoes. Where is the best place to store them? Fridge or windowsill? Turns out the answer involves more chemistry than you might have imagined.

And then, finally, December. Looking for a last-minute Christmas gift? Why not buy a case of blk water? I mean, other than it’s an exorbitantly priced bottle of mysterious black stuff which doesn’t do any of the things it claims to do, and might actually get its colour from coal deposits, that is.

And that, dear friends and followers, is it for 2017! Happy New Year! Remember to be sceptical when the inevitable “deadly food” story appears in a few weeks….


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Vaccines are one of humankind’s best achievements, and we should all be shouting about it

science-fiction-1819026_960_720Imagine aliens finally get around to visiting our planet…

“About two hundred years ago,” explains the alien scientific advisor – let’s call him Spuck – “humans developed a way to prevent disease which they call vaccination. It’s really quite fascinating. They use a needle to place a tiny quantity of a fluid into the muscle under the skin of their arm or leg. The substances are then absorbed into their bodies and cause their highly-evolved immune systems to generate an immune response without, and this is really quite ingenious, Captain, their having to contact the actual diseases or suffer the symptoms. This simple procedure has saved millions of lives worldwide, and saved many millions more from having to suffer less fatal, but none the less still deeply unpleasant, consequences of serious illnesses.”

“Sounds great, Spuck,” says the Captain – let’s call him Birk – “is there a downside?”

“Not really, Captain. Side effects are rare and extremely minor compared to the seriousness of the illnesses themselves.”

“Fantastic. Why are you telling me all this? I’ve got some green-skinned action I’d like to get back to, if you know what I mean.”

“Well, it’s interesting that you should mention unusual skin tones, Captain. A leader has recently come to power who, amongst other things, has expressed concerns about vaccination.

“Valid concerns?”

“The scientific evidence suggests not, sir.”

“Sounds like an idiot, Spuck.”

“I couldn’t possibly comment, sir.”

“Huh. Sounds like he could definitely be detrimental to the future of their race, and besides, I’m bored. Let’s go and shoot some stuff in direct contravention of the Cardinal Directive. Set blazers to ki- I mean, stun. Beam me down, Dottie!”

***

Vaccination. It’s a hot topic at the moment, and one which is so important that I think anyone who has anything to do with science communication ought to be talking about it. I’m not a medical doctor, or an immunologist, or even a biochemist (for more qualified input on the subject, I refer you here, here and here), but I AM capable of recognising scientific consensus and of separating good-quality evidence-based information from conspiracy theory dross.

Vaccination is awesome.

Awesome is a word that is somewhat overused. But I mean it literally. As in, inspires awe. We should stop, for a moment, and just look at how bloody amazing vaccination is. Thanks to these simple, near-painless, injections – most of which we receive as young children and therefore don’t even remember – we are largely protected from the horrors of….

  • Poliosymptoms and complications include fever, vomiting, headache, back pain, joint pain and stiffness, permanent muscle weakness, permanent paralysis and death.
  • Mumpssymptoms and complications include fever, headache, meningitis, painful testicular swelling in males and ovarian inflammation in females, both of which can  result in permanent infertility, pancreatic inflammation and, occasionally, hearing loss. Death from mumps is rare, but does occur in about 1 in 10,000 cases.
  • Tuberculosis – symptoms and complications include fever, loss of appetite, severe fatigue, chest pain, coughing up of blood, scarring of the lungs, internal bleeding and death (death is considerably more likely if the patient does not have access to medical care).
  • Measlessymptoms and complications include fever, painful skin rash, diarrhoea, vomiting, ear infection which can result in deafness, eye infection which can result in blindness, laryngitis, pneumonia, bronchitis, liver infection, encephalitis, and increased likelihood of re-contracting diseases previously survived (measles essentially “wipes” your immune system). Oh yes, and death. As many as 1% of measles patients will die from the disease.

… and umpteen other, horrible diseases, the majority of which most people reading this will have never experienced. Because of vaccination.

Measles rash

A child with a measles rash. The disease can cause serious complications, including immune suppression.

The risks of vaccination are tiny. The most common complications are redness and swelling around the injection site and/or slight temperature which is easily treated with an antipyretic such as paracetamol or ibuprofen. Very occasionally people suffer a serious allergic reaction, but this inevitably happens quickly after the injection is given. Since vaccinations are usually administered in a medical setting, any allergic reaction that does occur can be quickly managed. There have been a few other genuine cases of serious, adverse reactions to vaccines, but problems are still very rare (the swine flu-narcolepsy link, for example, affected 1 in 55,000) and specific to particular vaccines, and the vaccine in question has been quickly investigated.

Like Birk, if you’ve had nothing to do with the anti-vaccination community, you may be thinking this all sounds good. Benefits massive, risks tiny. Fab. Let’s go.

However, the anti-vaccination crowd – a real, and not entirely new, thing – will tell you that this is all lies. They will tell you this loudly, and at length, and repeatedly. They believe that vaccinations cause every health problem from acne to zygomycosis, but particularly the neurodevelopmental condition known as autism.

Vaccines do not cause autism. At all. As Spuck said, the scientific evidence is clear. It’s absolutely ice-from-a-moutain-stream-in-the-middle-of-nowhere crystal clear. Just for one example, a meta analysis published in the journal Vaccine in 2014 looked at studies involving over a million children. The data revealed no relationship between vaccination and autism. None. Nada.

Vaccines, you see, do not cause autism. And actually, it’s about time we stopped wasting precious resources proving that over and over and over and over again and instead focused on what does cause autism, because that would be a question worth answering.

Infection rates dropped enormously in the US after the measles vaccination was introduced.

Infection rates dropped enormously in the US after the measles vaccination was introduced.

Anti-vaxxers will often repeatedly talk about mercury in vaccines. There’s mercury in vaccines, they’ll say, and that’s nasty stuff, so even if we haven’t proved it yet, they must be causing something bad. One problem there: there isn’t any mercury in vaccines. There’s a preservative called thimerosal (or thiomersal) in some flu vaccines – which are not the ones usually given to children – but thimerosal is no more mercury than salt is chlorine.

The anti-vax crowd get whackier after this. Some of them will tell you that vaccinations don’t, in fact, protect against against disease at all – despite huge evidence to the contrary (see also here), not to mention the simple fact that many of our grandparents and even parents remember these diseases, and their complications, as horribly commonplace.

Anti-vaxxers often state that deaths from these diseases were dropping before the vaccines were introduced. This is true. Deaths did drop, because medical science was developing rapidly. A measles patient receiving medical care is, indeed, less likely to die than one left to her own devices. If I may say so, duh.

What vaccines did is to massively reduce infection rates. But just to state the obvious: if people don’t catch a disease, they also can’t die from it.

In short, if an anti-vaxxer shows you a graph, it’s smart to check to the axes labels.

After that they get really loony, and some of them will even tell you things such as smallpox wasn’t eradicated, it was just renamed acne. Or polio has been reclassified as Guillain-Barré syndrome. These ideas are so utterly ridiculous they don’t even deserve rebuke.

This has started up again in the last few days, particularly in the UK, because of the nasty deposit of conspiracy crap that is the film Vaxxed. It’s available online, but I shall not be linking to it here.

The film claims to reveal a massive cover-up at the Centre for Disease Control (the CDC) in America, and evidence that vaccines are generally evil and cause all manner of heinous negative health outcomes. Very little of it is true, and where a tiny nugget of true fact has been included it’s been so beaten and manipulated as to have lost all of its original meaning. There’s an excellent piece about it on Skeptical Raptor website, which I recommend reading before you google the term “vaxxed”. Consider it a sort of inoculation against the nonsense, if you like (hoho).

A Guardian article from 2010 reports on Wakefield.

A Guardian article from 2010 (click for link).

The main brain behind the film is Mr Andrew Wakefield, a former British doctor who was struck off the General Medical Council in 2010, when the GMC said he had acted “dishonestly and irresponsibly.” Wakefield was, it turned out, trying to patent his own measles vaccine. In an effort to further his own aims, he set out to discredit the widely-used MMR (measles, mumps and rubella vaccine) by fabricating results and, in particular, suggesting a link between the MMR and autism. He denied all this, of course, but a libel judge disagreed.

Wakefield is still pushing his message. He is not a particularly nice individual. Listen to him in this video clip, for example, where he responds to Bill Gates comment, made in 2015, that he (Gates) fears a pandemic could wipe out humanity in his lifetime. Actually, I’ll save you the trouble:

“Ho Chi Minh City, you may have seen this, an outbreak of [laughs] the plague in Ho Chi Minh City. The outbreak that they were not prepared for, they never prepared for, and that is the number of children with autism in Ho Chi Minh City has increased by nearly one hundred and sixty times over eight years. So, Bill, just for your edification, the plague that you’re talking about, the next plague, the next epidemic, it’s already here. It’s already here.”

Yes, you heard that right, according to Wakefield autism is a “plague”. Anyone reading this with an autism diagnosis? You have the plague. Nice, huh?

Andrew Wakefield describes autism as a "plague".

Andrew Wakefield describes autism as a “plague”.

For the record, the number of autism diagnoses in Ho Chi Minh has increased sharply over recent years, but this is may well be – as often turns out to be the case – largely due to to better diagnosis. Certainly there’s absolutely no suggestion that it’s linked to the introduction of a vaccine or vaccines. There might be an environmental factor – some sort of pollutant perhaps – but no one is certain at the moment. (To repeat myself: perhaps if we stopped wasting time endlessly disproving the link between vaccines and autism, we’d have a better idea.)

By the way, the woman in that video clip is Polly Tommey. She has an autistic son who’s now in his twenties. Back in 2010 she chose to try and raise awareness of autism by posing in a Wonderbra-style advert, and these days she follows the campaign trail with Wakefield, repeating the message that they “will win”. What exactly they’re going to win isn’t entirely clear. Would preventing vaccination, at the cost of many lives, really be a win?

Vaxxed was due to be shown at the Curzon cinema in Soho, London on Valentine’s Day. It was pulled after the cinema realised what the film was – they had merely leased their premises to private individuals and only realised what was going on when a number of science advocates started complaining.

In a statement, a spokesperson for Curzon Cinemas said:

“We do not wish to profit from a film that has demonstrably caused great distress.”

The heyevent.uk page on Vaxxed, explaining that the location will be "annnounced" two hours before the screening.

The heyevent.uk page on Vaxxed explains that the location will be “annnounced” two hours before the screening.

Tommey was predictably unimpressed by this outcome, which she blamed on “our little five trolls in England,” saying “Britain being who they are, being big wussy pussies, just strike it off.”

Unfortunately, the cancellation turned out to be less of a victory than it first appeared. The anti-vaxx crowd then set out to find a new venue. And this time, they kept it quiet. There are many, many places that will rent you a space to screen a film, and I’ll wager that few of them really check the nature of that film. So, the anti-vaxxers correctly reasoned, if we don’t tell people where it is, no one will be able to stop us. People who had previously bought tickets were told it would be in “Central London”, and that the venue would be revealed two hours before the show.

And so, it happened. At Regent’s University London, a private university which was, incidentally, recently identified as the most expensive place to study in the UK.

In hindsight, this might actually have been worse than a screening at an independent cinema. Dodgy film in a cinema – so what? “Official” screening at a university with Q&A sessions afterwards? Hm, sounds important and… academic. The press, naturally, made the most of it, with headlines such as “Disgraced anti‑MMR vaccine doctor Andrew Wakefield gets invitation to university in London.” Sure, the first line of the actual article says the university has been criticised, but who actually reads beyond the headlines these days? Sounds like he’s being taken seriously, doesn’t it?

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Regent’s University’s response on Twitter on February 15th

Regent’s University responded pretty quickly to say that they hadn’t known what the film was, that they didn’t endorse its views, and that they would be revetting all their clients.

This provoked lots of complaints about freedom of speech, because many people seem to be under the misapprehension that freedom of speech means that any and all organisations and venues have a duty to allow them to repeat their nonsense. This is not what freedom of speech means. Freedom of speech means you can’t be chucked in prison for saying a thing (with some exceptions). It does NOT mean that everyone has to listen to you, or that you can say your thing wherever and whenever you like, whether the place renting you the space likes it or not.

More alarming still was the Q&A session at the end of the screening of Vaxxed. I watched some of it (one for the team, you’re welcome). There was much talk of “getting the message out there”, “sowing the seeds”, “people have to hear the message x times before they’ll start to accept it” and so on. In short, if you didn’t know it was all about vaccines it would start to sound an awful lot like…. well, at best a religion, and at worst a cult.

Wakefield was also asked if he would ever get his name cleared. This was his response:

Wakefield speaking at the end of the Vaxxed screening.

Wakefield speaking at the end of the Vaxxed screening.

“Well, cleared by whom? Here’s a… it’s a really important… cleared by whom? Do I want to be part of the medical profession again? [muttering from the audience] Do I want to be exonerated by the General Medical Council? Do I want to pay them an annual retainer fee? To be part of… Do I really? Is that… that takes time and effort. What is more important? Making films like this? Or trying to clear my name? [applause]

Hang on. If he really cared about getting the science right, about doing the right thing by patients, wouldn’t getting his name cleared and being reinstated as a medical doctor be of utmost importance? If he’s right about vaccines, particularly the MMR vaccine, and if he truly wants to prove it for the good of humanity, what better way than to be exonerated?

But as he says, “that takes time and effort.” What he doesn’t add, of course, is that making films like Vaxxed, travelling around the world spreading his message and hobnobbing with Donald Trump, almost certainly makes him a lot more money than being a doctor ever did. And I’ll bet it’s more fun. Why would he go back to the long hours and hard work that being a regular old doctor entails?

Wakefield is playing an extremely unpleasant and disingenuous game. The really worrying thing is that he and other anti-vaccination campaigners might be gaining ground. Robert F. Kennedy Jr. and Robert De Niro recently announced a $100,000 “challenge” to prove the safety of thimerosal vaccines. Thimerosal has already been extensively investigated – no evidence has ever been found that its inclusion in vaccines causes neurological effects, but anyway, it’s only in a few flu vaccines. Of course, the implication is that all vaccines are unsafe and that no one can prove otherwise – and now those headlines are out there, and that seed has been planted, will people really read further into it? Or will they just decide to skip the visit to the doctor?

The consequences of that are potentially serious. A mumps outbreak was reported in Washington State a week ago, and cases of mumps and measles have also just been reported in Salt Lake County. Last autumn the Guardian reported that the proportion of under-twos receiving their first dose of the MMR vaccine had fallen for the third consecutive year, and there were several reports of measles outbreaks in the UK. Flu outbreaks are also a real concern: years of hearing the phrase “mild flu-like symptoms” have created the misconception that influenza itself is a mild disease. It is not. There have been over 100 deaths from flu in Germany this year alone. People in Germany have access to good healthcare. People are still dying.

Outbreaks put everyone at risk: vaccination is effective, but nothing is 100% effective. In the midst of a full outbreak, even the vaccinated are at risk of catching the disease, and of course, those who are too young to receive the vaccine, or who can’t have it because of a genuine allergy, or because they’re immunocompromised, will be in real trouble. Let’s not forget: measles in particular is a disease with a host of horrible complications, not to mention the potential to reduce a person’s previously acquired immunity to other diseases.

Do we really want to see measles and mumps come back? Really? Because that will ultimately be the result of all of this.

And unfortunately, Captain Birk and Mr Spuck aren’t actually there to fix this mess for us. We need to see sense ourselves.


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Elements, compounds and misleading mercury

Elemental mercury isn't the same as mercury in compounds.

Elemental mercury isn’t the same as mercury in compounds.

Today I read an interesting article about some recent research carried out at the University of Illinois where they demonstrated that the best way to convince parents to vaccinate their children might be to show them the results of the diseases the vaccines prevent. (This, by the way, contradicts some research published in 2014 which showed that this tactic didn’t work. For an excellent discussion of the two, see here.)

Then, because I am just one of those people who can’t resist poking at ulcers with my tongue (you know what I mean) I had a quick look at some of the comments regarding that article. Reassuringly, most people were weighing in on the “yeah, vaccinate!” side of the argument. But not surprisingly there was also a small group of people posting the traditional anti-vaccine arguments. And then, this appeared:

mercury ppm

This is thoroughly silly, and I’ll tell you why.

Well, it did make be go “hmmmmm”, but for the reason you might imagine.

No, you see, what I thought was: “hmmmmm, someone else who has, possibly deliberately, failed to understood the difference between elements and compounds, and how chemical bonding changes properties.”

Allow me to start at the beginning. If you went to a school in the UK (and I would hope it’s similar elsewhere in the world) you learned about elements, compounds and mixtures when you were about 13 years old – if not before. You might have forgotten it since, but I can absolutely, categorically guarantee you that lesson happened. In fact, it was probably a few lessons.

iron sulfide experiment

The much-loved reaction between iron and sulfur.

One experiment much beloved of chemistry teachers since year dot is to take a mixture of sulfur (a yellow powder) and some iron filings (grey) and show that they can be separated with a magnet. Then heat the mixture up so that the two react, with a rather beautiful red glow, to form iron sulfide. This is a blackish solid which is in theory not magnetic (but in practice almost always is) and demonstrate that now the two elements cannot be separated.

Thus we have demonstrated that elements (the iron and the sulfur) have different properties to the compound they formed (iron sulfide), and also that mixtures can be separated fairly easily, whereas breaking compounds up into their constituent elements is much harder. Lovely. Job done.

And yet… so many people seem to have been asleep that day. Or perhaps just didn’t grasp it well enough to continue to apply the principle to other things.

pouring mercury

Elemental mercury

For example, mercury. Mercury, the element (the runny, silvery stuff that you used to find in thermometers) is a heavy metal. Like most of its compatriots, such as cadmium, lead and arsenic, it’s toxic. It can be absorbed through the skin and mercury vapour can be inhaled, so containers need to be tightly sealed. The increasing awareness of the toxicity of mercury is why older readers might remember seeing it ‘in the flesh’, so to speak, at school, whereas younger ones will not – these days it’s rarely even used in thermometers for fear of breakages.

That said, it does occur naturally in the environment, particularly as the result of volcanic eruptions – and very low levels aren’t considered harmful. The dose, as they say, makes the poison. It also occurs as the result of industrial processes, particularly coal-fired power plants and gold production, and occupational exposure is a genuine concern. In particular, chronic exposure is known to cause cogitative impairment. It might the source of the ‘mad dentist’ myth. It’s almost certainly the origin of the phrase ‘mad as a hatter‘.

So in summary, don’t mess about with elemental mercury; it’s not good for your health.

However, as I took some pains to establish, elements and compounds are different things. So what about compounds which contain mercury?

The compound thiomersal

The compound thiomersal

This is where vaccines come in. There is a substance that used to be used as a preservative in (some) vaccines called thiomersal (or thimerosal, in the U.S). You may have heard its name; it comes up quite a lot. Incidentally, it hasn’t just been used in vaccines, but also in various other things including skin-test antigens and tattoo inks.

Now, to be clear, thiomersal IS potentially toxic, however it’s quickly metabolised in the body to ethyl mercury (C2H5Hg+) and thiosalicylate and, although ethyl mercury does, clearly, still contain atoms of mercury, it does not bioaccumulate. In other words, your body gets rid of it. At very low doses (such as those in vaccines) there is no good evidence that thiomersal is harmful.

Still, due to continuing public health concerns, thiomersal has been phased out of most U.S. and European vaccines. In the UK, thiomersal is no longer used in any of the vaccines routinely given to babies and young children in the NHS childhood immunisation programme. And at the moment, all routinely recommended vaccines for U.S. infants are available only as thimerosal-free formulations or contain only trace amounts of thimerosal (≤1 than micrograms mercury per dose).

Let me just say that again. The evidence suggests it’s safe, but it’s been removed anyway as a precaution. If you live in the UK, it’s not in your child’s vaccines, and that includes the new nasal-spray vaccine for flu which has been rolled out over the last few years. If you live in the U.S. it’s probably not, and thimerosal (thiomersal) free versions exist. It does turn up most often in flu vaccines (hence the meme image at the start) but thiomersal-free versions of those also exist in the U.S.

So chances are it’s not in your vaccines. Not in there. Got it? Ok.

ethyl vs methyl mercury

methyl mercury (left) is not the same as ethyl mercury (right)

Now, you may have heard about mercury in seafood. It is an issue, particularly for women who are pregnant, trying to become pregnant or breastfeeding, and is the reason such women are advised not to eat shark and swordfish, and to keep their tuna consumption low. But here’s the thing: it’s a different kind of mercury. In this case, it’s methyl mercury (remember, thiomersal breaks down to ethyl mercury, which is not the same).

Methyl mercury is more toxic than ethyl mercury. Methyl mercury binds to parts of amino acids much more readily than its ethyl cousin, and it’s able to pass through the blood brain barrier and into nerve cells where it causes damage. In addition, ethyl mercury is much more quickly eliminated from the body than methyl mercury. Because of all this, methyl mercury does bioaccumulate (build up in the body), and that’s why large top-of-the-food-chain fish like shark and tuna can have significant levels of it, and why certain groups of people should be careful about eating them.

The FDA’s action level (the limit at or above which FDA will take legal action) for methyl mercury in fish is 1000 ppb (1 ppm). But remember, that’s for the much more dangerous methyl mercury, not ethyl mercury. I’ve been unable to find an equivalent figure for the UK, but I’d imagine it’s similar.

So, where does the 200 ppb mercury figure in the image at the top come from? Well the Environmental Protection Agency does indeed set a ‘maximum contaminant level goal’ for inorganic mercury of 0.002 mg/L or 2 ppb in water supplies. Methyl and ethyl mercury are not inorganic mercury; compounds that fall into this category include mercuric chloride, mercuric acetate and mercuric sulfide, which largely get into water as the result of industrial contamination.

In summary, that meme image at the start is basically comparing apples and oranges. The EPA limit isn’t relevant to vaccines, because it’s for inorganic mercury, which the substance in vaccines isn’t. While we’re about it, the levels applied to fish don’t apply either, because that’s methyl mercury, not ethyl mercury. They’re not the same thing. And all that aside, it’s highly unlikely (if you live in the UK, no chance at all) that there are 50,000 ppb of ethyl mercury in your flu vaccine anyway. AND, let’s not forget, there’s no evidence that the tiny quantities of thiomersal used in vaccines are harmful in the first place.

Phew.

You may note that I’ve studiously avoided the word ‘autism’ in this post so far. But yes, that’s the big concern; that exposure to thiomersal in vaccines could cause autism. Despite multiple, huge, studies in several countries looking for possible links between vaccines and autism, none have been found. Vaccines don’t cause autism. It’s time we stopped wasting enormous amounts of time and resources on this non-link and spent it instead on finding out what does cause it. Wouldn’t that be far more useful and interesting?

Now… if you’re hardcore anti-vaccine and you’ve read this far, and you’re about to hit the comment button and tell me that all this research is just Big Pharma covering things up so they can make money from the ‘million(/billion/trillion) dollar vaccine industry’, just wait a moment.

Stop.

Think about this: how much money could the medical industry make from people actually catching measles, mumps, polio, TB, whooping cough and all the others? Just think of all the money they could make selling antivirals and antibiotics, all the money to be made from painkillers, antipyretics, drugs to treat respiratory symptoms of one kind or another, and everything else? Believe me, it would be much, much more than they make from a single 2 ml dose of vaccine. Why ‘cover up’ research that’s, if anything, reducing their profits?

All these diseases are horrible, and some can be fatal or have genuinely life-changing consequences. That’s proven. Please vaccinate your children, and yourself.

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