Rock bottom: can rocks in your dog’s water bowl protect your lawn?

fractal image, featuring the hashtag #272sci

Take a look at the Twitter hashtag #272sci

One quick thing before I dive into this month’s post: if you’re a Twitter user, check out my series of very tiny science tweets under the hashtag #272sci. The aim is to explain a science thing in one tweet – without using a thread – and it’s 272 because that’s the number of characters I have to use after including the hashtag and a space. So far I’ve covered leaf colours, frothy milk, caffeine and poisonous millipedes. There will be more to come!

Now, speaking of Twitter, a couple of weeks ago Prof Mark Lorch tweeted about Dog Rocks. Dog… what? I hear you ask (really quite understandably).

Well, it turns out that Dog Rocks are a product that you can buy, and that you put into your dog’s water bowl. Your dog then drinks the water that has been sloshing over the rocks, and, this is where we start to run into trouble, this is meant to have an effect on your dog’s urine. This, in turn, is supposed to protect any grass your dog might then pee on.

photo of a patch of dead grass

Dog urine damages grass

All right, so let’s start somewhere in the vague vicinity of some science: if you have a dog, or even if you’ve just spent some time with someone who has a dog, you’ve probably noticed that dog urine isn’t very kind to grass. Commonly, you see something like the photo here, that is, patches of yellow, dead grass, surrounded by quite luscious green growth.

Why is this? It’s because dog urine – like the urine of all mammals – contains urea, CO(NH2)2. Urea forms in the body when animals metabolise nitrogen-containing compounds, in particular, proteins. It’s essentially a way for the body to get rid of excess nitrogen.

People sometimes confuse urea with ammonia, for reasons that I’ll come to in a moment. But they’re not the same thing. Urea is odourless, forms a pH neutral solution and, if you extract it from the liquid in which it is dissolved, produces solid crystals at room temperature.

Pure ammonia, NH3, by contrast, is a gas at room temperature (boiling point -33.3 ℃), forms alkaline solutions (with pH values greater than 7) and has that pungent ‘ngggh get it away from me!’ smell with which we’re probably all familiar.

Sample pots full of pale yellow liquid

Fresh urine contains urea, but little ammonia

Although these two substances aren’t the same, they are linked: many living things convert ammonia (which is very toxic) to urea (which is much less so) as part of normal metabolism. And it also goes the other way, in a process called urea hydrolysis. This reaction happens in urine once it’s out of the body, too, which is the main reason why, after a little while, urine starts to smell really, really bad.

Okay, fine, but what has this got to do with grass, exactly? Well urea (and ammonia, for that matter) are excellent sources of nitrogen. Plants need nitrogen to grow, but dog urine contains too much, and too much nitrogen is bad – in the same way that too much of pretty much anything nice is bad for humans. It damages the blades of grass and a yellowish dead spot appears, often ringed by some particularly lush grass that, being slightly outside the immediate target zone, caught a whiff of extra nitrogen without being overwhelmed.

Back to Dog Rocks. Interestingly, the website includes an explanation not unlike the one I’ve just given on their fact sheet. What it doesn’t do is satisfactorily explain how Dog Rocks are supposed to change the nitrogen content of your dog’s urine.

photo of a dog drinking water

Dog Rocks are meant to be placed in your dog’s water bowl

The website says that Dog Rocks are “a coherent rock with a mechanically stable framework”. Okay… so… Dog Rocks won’t dissolve or break up in your dog’s water bowl. A good start. It goes on to say, “the rocks provide a stable matrix and a micro-porous medium in which active components are able to act as a water purifying agent through ion exchange” and “Dog Rocks will help purify the water by removing some nitrates, ammonia and harmful trace elements thereby giving your dog a cleaner source of water and lowering the amount of nitrates found in their diet.”

You’ll note they’re using the word nitrate. Nitrates are specifically compounds containing the NO3 ion, but I think they’re using the term in a more general way, to suggest any nitrogen-containing compound (including urea and ammonia). And by the way, nitrates are different from the similar-sounding nitrites, which contain the NO2 ion. Fresh urine from a healthy dog (or human, for that matter) shouldn’t contain nitrite. In fact, a dipstick test for nitrite in urine is commonly used to check for urinary tract infections, because it suggests bacteria are present.

Anyway, nitrates/nitrites aside, it’s the last bit of that claim which really makes no sense. Your dog is not ingesting anything like a significant quantity of nitrogen-containing compounds from its water bowl. Urea comes from the metabolic breakdown of proteins, and they come from your dog’s food.

Photo of puppies eating food that I totally picked because it's cute ;-)

The nitrogen-containing compounds in your dogs’ urine come from their food, not their water

It’s faintly possible, I suppose, that Dog Rocks might somehow filter out some urea/nitrates from urine. But then your dog would have to pee through the Dog Rocks and, honestly, if you can manage to arrange that, you might as well train your dog not to pee on your grass in the first place.

I suggest that there are three possible explanations for the positive testimonials for this product. 1) Owners who use it are inadvertently encouraging their dogs to drink more water, which could be diluting their urine, leading to less grass damage. 2) It’s all a sort of placebo effect: owners imagine it’s going to work, and they see what they’re expecting to see, or 3) they’re all made up.

You decide, but there is absolutely no scientifically-plausible way that putting any kind of rocks in your dog’s water bowl will do anything to stop dog pee damaging your grass. This is £15 you do not need to spend. But hey, you could avoid the money burning a hole in your pocket (see what I did there?) by buying me a coffee… 😉


Check out the Twitter hashtag #272sci here, and support the Great Explanations book project here!

Do you want something non-sciency to distract you from, well, everything? Why not take a look at my fiction blog: the fiction phial? You can also find me doing various flavours of editor-type-stuff at the horror podcast, PseudoPod.org – so head over there, too!

Like the Chronicle Flask’s Facebook page for regular updates, or follow @chronicleflask on Twitter. Content is © Kat Day 2021. You may share or link to anything here, but you must reference this site if you do. You can support my writing my buying a super-handy Pocket Chemist from Genius Lab Gear using the code FLASK15 at checkout (you’ll get a discount, too!) or by buying me a coffee – just hit this button:
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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.


Support the Great Explanations book here!

Do you want something non-sciency to distract you from, well, everything? Why not take a look at my fiction blog: the fiction phial? You can also find me doing various flavours of editor-type-stuff at the horror podcast, PseudoPod.org – so head over there, too!

Like the Chronicle Flask’s Facebook page for regular updates, or follow @chronicleflask on Twitter. Content is © Kat Day 2021. You may share or link to anything here, but you must reference this site if you do. You can support my writing my buying a super-handy Pocket Chemist from Genius Lab Gear using the code FLASK15 at checkout (you’ll get a discount, too!) or by buying me a coffee – the button is right here…
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Faking Lateral Flow Tests: the problem with pH

Fruit juices can be used to generate a fake positive on COVID-19 LFTs

On Thursday last week, I got a message from Prof Mark Lorch — my sometime collaborator on supercharacter-based ramblings.

“Have you seen the reports of kids fooling the Covid lateral flow tests and getting false +ve results by adding orange juice to the devices?” he wondered.

At this point, I had not – but I quickly got up to speed. Mark had previously made an excellent video explaining how lateral flow test (LFT) devices work, so it was just a case of working out, firstly, whether the false positives were reproducible, and secondly, speculating what, exactly, was causing them.

Thus ensued some interesting discussion which ultimately led to a couple of articles from Mark. One at The Conversation and another, slightly more recently, at BBC Future.

I won’t delve into LFT-related science, because Mark has covered it (really, check the video and those articles), but I am going to talk a little bit about pH – the scale chemists use to measure how acidic or alkaline solutions are – because as soon as news of this started to gain traction people, predictably, started trying it out themselves. And that was when things got really interesting.

Image

The buffer included with LFTs is effective at neutralising the pH of solutions, for example, cola

Now, firstly, and importantly: the test kits come with a small vial of buffer solution. Buffers are substances which resist pH changes. As I’ve written before, our bodies naturally contain buffer systems, because keeping the pH of our blood and other body fluids constant is important. In fact, if blood pH varies even a little, you’re in all sorts of serious trouble (which is how we can be certain that so-called “alkaline” diets are a load of hooey). Anyway, the important message is: don’t mix any liquid you’re testing with the contents of that phial, because that will neutralise it.

If you want to try this for yourself, just drop the liquid you want to test directly into the window marked S on the test.

That out of the way, let’s get back to pH. It’s a scale, usually presented as going from 0–14, often associated with particular colours. The 0 end is usually red, the 7 in the middle is usually green, while the 14 end is usually dark blue.

These colours are so pervasive, in fact, that I’ve met more than one person with the idea that acids are red, and alkalis are blue. This isn’t the case, of course. The red/green/blue idea largely comes from universal indicator (UI), which is a mixture of dyes that change colour at different pH values. There’s also a common indicator called litmus (people sometimes mix up UI and litmus, but they’re not the same) which is also red in acid and blue in alkali.

Some species of hydrangea produce pink flowers in alkaline soil, blue in acid soil.

There are actually lots of pH indicators, with a wide variety of colour changes. Phenolphthalein, for example, is bright pink in alkali, and colourless in acids. Bromocresol purple (they have such easy-to-spell names) is yellow in acids, and violet-purple in alkalis.

Many plants contain natural indicators. Just to really mix things up, some species of hydrangea produce flowers that are blue-purple when they’re grown in acidic soil, and pink-red in alkaline conditions.

Bottom line? Despite the ubiquitous diagrams, pH has nothing to do with colour. What it is to do with is concentration. Specifically, the concentration of hydrogen ions (H+) in the solution. The more H+ ions there are, the more acidic the solution is, and the lower the pH. The fewer there are, the less acidic (and the more alkaline, and higher pH) it is.

In fact, pH is a log scale. When the concentration changes by a factor of 10, the pH changes by one point on the scale.

This means that if you take an acid with pH of 2, and you dilute it 1 part to 10, its pH changes to 3 (i.e. gets one point more alkaline, closer to neutral). Likewise, if you dilute an alkali with a pH of 10 by 1:10, its pH will shift to 9 (again, closer to neutral).

And what this means is that the pH of substances is not a fixed property.

Louder for anyone not paying attention at the back: the pH of substances is not a fixed property!

Yes, we’ve all seen diagrams that show, for example, the pH of lemon juice as 2. This is broadly true for most lemons, give or take, but if you dilute the lemon juice, the pH rises.

Apple juice dropped directly into the test window gives an immediate “positive” result.

I am by no means an expert in commercial, bottled lemon juice, but I reckon a lot of them have water added – which may well explain why @chrismiller_uk was able to get a positive result, while @BrexitClock, using a French bottle of lemon juice, couldn’t.

Mark and I concluded that the pH you need to aim for is probably around 3–4. Go too low, and you don’t get a positive (and you might wipe out the control line, too). Likewise, too high also won’t work.

Myself, I tried apple juice. I couldn’t find the indicator colour key for my indicator paper (I really must clear out the drawers one of these days) but it’s broadly the same as Mark’s cola photo, up above. In other words, the apple juice is about pH 3. And it gives a beautiful positive result, immediately.

One more interesting observation: Mark recorded some time-lapse video comparing orange juice to (sugar-free) cola. It shows the cola test line developing a lot more slowly. We’re not entirely sure why, but it may be pH again: orange juice almost certainly has a lower pH than cola.

For any parents reading this thinking we’re being terribly irresponsible, fear not: as Prof Lorch has made clear in his articles, you can identify a fake by waiting a few minutes and then dropping some of the buffer solution provided in the test window. As I said above, this will neutralise the pH, and the positive test line will disappear. Extra buffer won’t change a genuinely-positive test, because the antibodies bind very tightly (more technical info here). To quote Mark: “you’d need a swimming pool’s worth of buffer to have any chance of washing [the antibodies] off.”

Alternatively, you can just watch your teenager as they do their tests, and make sure they’re not getting up to anything nefarious…

Have you tried to trick an LFT? If you have, share your results! Look us up on Twitter: @chronicleflask and @Mark_Lorch or add a comment below. We’d love to see your photos!


Do you want something non-sciency to distract you from, well, everything? Why not take a look at my fiction blog: the fiction phial? You can also find me doing various flavours of editor-type-stuff at the horror podcast, PseudoPod.org – so head over there, too!

Like the Chronicle Flask’s Facebook page for regular updates, or follow @chronicleflask on Twitter. Content is © Kat Day 2021. You may share or link to anything here, but you must reference this site if you do. You can support my writing my buying a super-handy Pocket Chemist from Genius Lab Gear using the code FLASK15 at checkout (you’ll get a discount, too!) or by buying me a coffee – the button is right here…
Buy Me a Coffee at ko-fi.com

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!


If you’re studying chemistry, have you got your Pocket Chemist yet? Why not grab one? It’s a hugely useful tool, and by buying one you’ll be supporting this site – it’s win-win! If you happen to know a chemist, it would make a brilliant stocking-filler! As would a set of chemistry word magnets!

Like the Chronicle Flask’s Facebook page for regular updates, or follow @chronicleflask on Twitter. Content is © Kat Day 2021. You may share or link to anything here, but you must reference this site if you do. If you enjoy reading my blog, and especially if you’re using information you’ve found here to write a piece for which you will be paid, please consider buying me a coffee through Ko-fi using the button below.
Buy Me a Coffee at ko-fi.com

Want something non-sciency to distract you from, well, everything? Why not check out my fiction blog: the fiction phial.

 

One Flash of Light, One Vision: Carrots, Colour and Chemistry

“White” light is made up of all the colours of the rainbow.

Sometimes you have one of those weeks when the universe seems to be determined to yell at you about a certain thing. That’s happened to me this week, and the shouting has been all about light and vision (earworm, anyone?).

I started the week writing about conjugated molecules and UV spectrometry for one project, was asked a couple of days ago if I’d support a piece of work on indicators for the RSC Twitter Poster Conference that’s happening from 2-3rd March, and then practically fell over a tweet by Dr Adam Rutherford about bacteria that photosynthesise from infrared light in a hydrothermal vent*.

Oh well, who am I to fight the universe?

Light is awesome. The fact that we can detect it is even awesome-er. The fact that we’ve evolved brains clever enough built all sorts of machines to measure other kinds of light that our puny human eyes cannot detect is, frankly, astonishing.

The electromagnetic spectrum covers all the different kinds of light. (Image source)

Let’s start with some basics. You probably met the electromagnetic (EM) spectrum at some point in school. Possibly a particularly enthusiastic physics teacher encouraged you to come up with some sort of mnemonic to help you remember it. Personally I like Rich Men In Vegas Use eXpensive Gadgets, but maybe that’s just me.

The relevant thing here is that the EM spectrum covers all the different wavelengths of light. Visible light, the stuff that’s, well, visible (to our eyes), runs from about 400 to 700 nanometres.

A colour wheel: when light is absorbed, we see the colour opposite the absorbed wavelengths. (Image source)

Now, we need another bit of basic physics (and biology): we see light when it enters our eyes and strikes our retinas. We see colours when only certain wavelengths of light make it into our eyes.

So-called “white” light is made up of all the colours of the rainbow. Take one or more of those colours away, and we see what’s left.

For example, if something looks red, it means that red light made it to our eyes, which in turn means that, somewhere along the way, blue and green were filtered out.

(Before I go any further, there are actually several causes of colour, but I’m about to focus on one in particular. If you really want to know more, there’s this book, although it is a tad expensive…)

Back to chemistry. Certain substances absorb coloured light. We know them as pigments. Carrots are orange, for example, largely because they contain a pigment called beta-carotene (or β-carotene). This stuff appears, to our eyes, as red-orange, and the reason for that is that it absorbs green-blue light, the wavelengths around 400-500 nm.

β-Carotene is a long molecule with lots of C=C double bonds. (Image source.)

Why does it absorb light at all? Well, β-carotene is a really long molecule, with lots of C=C double bonds. These bonds form what’s called a conjugated system. Without getting into the complexities of molecular orbital theory, that means the double bonds alternate along the chain, and they basically overlap and… smoosh into one long thing. (Look, as the saying goes, “all models are wrong, but some are useful,” – it’ll do for now.)

When molecules with conjugated systems are exposed to electromagnetic light, they absorb it. Specifically, they absorb in the ultraviolet region – the wavelengths between about 200 and 400 nanometres. Here’s the thing, though, those wavelengths are right next to the violet end of the visible spectrum – that’s why it’s called ultraviolet after all.

Molecules with really long conjugated systems start to absorb in the coloured light region, as well. And because they’re absorbing violet and blue, possibly a smidge of green, they look… yup! Orangey, drifting into red.

So now you know why carrots are orange. Most brightly coloured fruit, of course, is that way to attract animals and birds to eat it, and thus spread its seeds. As fruit ripens, it usually changes colour, making it stand out better against green foliage and easier to find. This is the link with indicators that I mentioned at the start: many fruits contain anthocyanin pigments, and these often have purple-red colours in neutral-acidic environments, and yellow-green at the more alkaline end. In other words, the colour change is quite literally an indicator of ripeness.

But the bit of the carrot that we usually eat is underground, right? Not particularly easy to spot, and they don’t contain seeds anyway. Why are carrots bright orange?

Modern carrots are mostly orange, but purple and yellow varieties also exist.

Well, they weren’t. The edible roots of wild plants almost certainly started out as white or cream-coloured, as you might expect for something growing underground, but the carrots which were first domesticated and farmed by humans in around 900 CE were, most probably, purple and yellow.

As carrot cultivation became popular, orange roots began to appear in Spain and Germany in the 15th/16th centuries. Very orange carrots, with high levels of β-carotene, appeared from the 16th/17th centuries and were probably first cultivated in the Netherlands. Some have theorised that they were particularly selected for to honour William of Orange, but the evidence for this seems to be a bit slight. Either way, most modern European carrots do descend from a variety that was originally grown in the Dutch town of Hoorn.

In other words, brightly-coloured carrots are a mutation which human plant breeders selected for, probably largely for appearances.

But wait! There was an advantage for humans, too – even if we didn’t realise it straight away. β-carotene (which, by the way, has the E number E160a – many natural substances have E numbers, they’re nothing to be frightened of) is broken up in our intestines to form vitamin A.

Vitamin A is essential for good eye health.

Vitamin A, like most vitamins, is actually a group of compounds, but the important thing is that it’s essential for growth, a healthy immune system and – this is the really clever bit – good vision.

We knew that. Carrots help you see in the dark, right?

Hah. Well. The idea that carrot consumption actually improves eyesight seems to be the result of a World War II propaganda campaign. During the Blitz, the Royal Air Force had (at that time) new, secret radar technology. They didn’t want anyone to know that, of course, so they spread the rumour that British pilots could see exceptionally well in the dark because they ate a lot of carrots, when the truth was that those pilots were actually using radar.

But! It’s not all a lie – there is some truth to it! Our retinas, at the back of our eyes, have two types of light-sensitive cells. Cone cells help us distinguish colours, while rod cells help us detect light in general.

In those rod cells, a molecule called 11-cis-retinal is converted into another molecule called rhodopsin. This is really light-sensitive. When it’s exposed to light it photobleaches (stops being able to fluoresce), but then regenerates. This process takes about thirty minutes, and is a large part of the reason it takes a while for your eyes to “get used to the dark.”

Guess where 11-cis-retinal comes from? Yep! From vitamin A. Which is why one of the symptoms of vitamin A deficiency is night blindness. So although eating loads of carrots won’t give you super-powered night vision, it does help to maintain vision in low light.

Our brain interprets electrical signals as vision.

How do these molecules actually help us to see? Well, when rhodopsin is exposed to light, the molecule changes, which ultimately results in an electrical signal being transmitted along the optic nerve to the brain, which interprets it as vision!

In summary, not only is colour all about molecules, but our whole visual system depends on some clever chemistry. I told you chemistry was cool!

Just gimme fried chicken 😉


*Ah. I sort of ran out of space for the weird hydrothermal bacteria thing. At least one of the relevant molecules seems to be another carotenoid, probably chlorobactene. The really freaking amazing thing is that there seems to be an absorption at 775 nm, which is beyond red visible light and into the infrared region of the EM spectrum. Maybe more on this another day…


If you’re studying chemistry, have you got your Pocket Chemist yet? Why not grab one? It’s a hugely useful tool, and by buying one you’ll be supporting this site – it’s win-win! If you happen to know a chemist, it would make a brilliant stocking-filler! As would a set of chemistry word magnets!

Like the Chronicle Flask’s Facebook page for regular updates, or follow @chronicleflask on Twitter. Content is © Kat Day 2021. You may share or link to anything here, but you must reference this site if you do. If you enjoy reading my blog, and especially if you’re using information you’ve found here to write a piece for which you will be paid, please consider buying me a coffee through Ko-fi using the button below.
Buy Me a Coffee at ko-fi.com

Want something non-sciency to distract you from, well, everything? Why not check out my fiction blog: the fiction phial.

 

Is there NO way to stop COVID-19?

UK trials have begun of a nasal spray that could prevent COVID-19 infections

A few weeks ago, it was announced that UK trials were beginning of a nasal spray proven to kill 99.9% of the coronavirus that causes COVID-19. The idea, broadly, is that you’d use the spray first thing in the morning, during the day after social interactions, and then again in the evening — and it would prevent the virus from taking hold and making you ill.

Awesome, right? Simple, cheap, portable. Sort of like cleaning your teeth regularly: prevention rather than cure. Combined with a vaccine, particularly for anyone at high risk such as those in healthcare settings, it could put a stop to the whole thing — and might also turn out to be effective on other, less deadly but still annoying, viruses.

But, I hear you ask, what is it? Because if I’m going to squirt something up my nose several times a day, I have questions…

Nitric oxide has the chemical formula NO

Fair enough. It’s actually, mostly, nitric oxide, which has the chemical formula NO.

Yes, there are plenty of wordplay options here. The researchers have already jammed the letters NO into their company name, and done the acronym thing, to get SaNOtize Nitric Oxide Nasal Spray (NONS). If the trials are successful, it’s probably only a matter of time before we get: “Say NO to coronavirus!” marketing. (Any ad agencies reading this, I’m claiming copyright.)

But that aside, unless you’re a chemist you might be thinking about some half-remembered chemical names and frowning at this point. Isn’t that… used in rocket fuel? Or… wait… isn’t that… the nasty smoggy stuff that causes lung problems?

Ah, well, there are several nitrogen oxides. Let me summarise:

Nitric oxides in the atmosphere cause photochemical smog.

There are other nitrogen oxides, not to mention ions — but let’s not spend all day on this. Nitrogen forms this confusing hodgepodge of oxides because it has five electrons in its outermost shell (it’s in group 15 of the periodic table) and because there’s not much difference in the electronegativities of oxygen and nitrogen. So essentially, it can share electrons with oxygen to form bonds in a number of different ways to obtain a stable, full outer shell.

For any students reading this, I’m sorry. You… pretty much just have to remember these. Yes, I know. That’s why experienced chemists so often use the shorthand NOx — we just can’t be bothered keeping all the names straight. (Okay, before someone shouts at me, actually NOx is handy because we’re often talking about more than one oxide at a time, and it allows us to easily express that.)

Back to NO. It’s a colourless gas, and it has an unpaired electron, which makes it a free radical. And… here we go again. Aren’t we supposed to eat lots of antioxidant-rich fruit and vegetables to mop up free radicals? They’re bad, aren’t they?

Viagra (Sildenafil) makes use of the nitric oxide pathway which causes blood vessels to dilate…

Yes and no. Free radicals are reactive species which damage cells and can cause illness and ageing. Too much exposure to free radicals causes something oxidative stress, which is definitely bad. But. It turns out that nitrogen oxide is an important signalling molecule, that is, a molecule which is the body uses to send chemical signals from one place to another. In particular, nitrogen oxide “tells” the smooth muscle around blood vessels to relax, causing those blood vessels to dilate, and increasing blood flow. Viagra (aka Sildenafil) uses the nitric oxide pathway, and I think we all know what that does, don’t we? Good.

Nitric oxide has also been shown to reduce blood pressure, which is generally considered a good thing — up to a point, obviously. This is why you can buy lots of so-called nitric oxide supplements, which, since nitrogen oxide is a gas at room temperature, don’t actually contain nitric oxide on its own. Rather, they’re a mixture of amino acids and other things that supposedly help the body to make NO. But it might be cheaper, and healthier, to eat plenty of beetroot or drink beetroot juice, since there’s evidence that does the same sort of thing.

As always, the dose makes the poison. Too much nitric oxide is definitely problematic, but administered in the right way and in appropriate doses, it’s extremely safe.

It’s suggested that the nitric oxide in the SaNOtize nasal spray destroys the virus and also helps to stop viral replication within cells. Plus, it blocks the receptors that the virus uses to enter cells in the first place. Essentially, it locks the doors and rains down fire on the potential intruders — nice work.

You only need to use the spray occasionally, because developing a COVID-19 infection isn’t instant. First the virus gets into your nose, then it attaches to cells, then it replicates, and then it sheds into your lungs. There are timescales involved here — so long as the spray is used every so often it should do the trick.

Another advantage is that this should, theoretically, work on other strains — where the current vaccines may not. So it could provide a very important stopgap when vaccination isn’t immediately available.

This is only in the early stages of clinical trials so, for now, wear your mask.

All sounds fabulous, doesn’t it? It might be, but, we’re in the early stages with this. Clinical trials have now started in the UK, are already in Phase II in Canada and have been approved to start in the USA. Researchers are hopeful, but we need to wait for the evidence.

So in the meantime, wear a mask, wash your hands, and take a vaccine if you’re offered one. Stay safe out there!


If you’re studying chemistry, have you got your Pocket Chemist yet? Why not grab one? It’s a hugely useful tool, and by buying one you’ll be supporting this site – it’s win-win! If you happen to know a chemist, it would make a brilliant stocking-filler! As would a set of chemistry word magnets!

Like the Chronicle Flask’s Facebook page for regular updates, or follow @chronicleflask on Twitter. Content is © Kat Day 2021. You may share or link to anything here, but you must reference this site if you do. If you enjoy reading my blog, and especially if you’re using information you’ve found here to write a piece for which you will be paid, please consider buying me a coffee through Ko-fi using the button below.
Buy Me a Coffee at ko-fi.com

Want something non-sciency to distract you from, well, everything? Why not check out my fiction blog: the fiction phial.

 

 

Colour me! STEM Heroes colouring book

Someone reminded me the other day of a podcast I hosted in January 2020, in which I hoped that 2020 would bring everyone lots of good things.

Well, if nothing else, we’ve proved that I definitely don’t have prophetic abilities, eh?

But 2020 hasn’t been all unpleasantness. There have been some bright spots, and I’m about to tell you about one! Back in November the science historian and writer, Dr Kit Chapman (@ChemistryKit), tweeted:

“If I were to commission a colouring book of scientists as heroes/villains (they get to pick what they want to be shown as – superheroes, princesses, wizards etc), would you be up for being a model? Colouring book would be free for all. Just a charity thing for inspiring kids.”

Now, how cool is that idea? Kit set up a GoFundMe which raised (as I write this) over £300, and also sourced twenty different STEM “heroes” to feature in the colouring book. His goal was to ensure multiple ethnicities, gender identities and body types were represented, as well as members of the LGBTQ+ and disabled communities and scientists with mental health disorders. In other words: science is for everyone.

Kit is a science writer (a really good one, read his book) so, of course, he had to include at least one science writer in the book, luckily for me!
 My colouring page is Discworld-themed, because of course it is. It’s based on the Alchemists’ Guild, which on the Disc is… quite an exciting place. To quote a conversation between dwarf Cheery Littlebottom and Sam Vimes in the 19th Discworld book, Feet of Clay:

‘I was quite good at alchemy.’
‘Guild member?’
‘Not any more, sir.’
‘Oh? How did you leave the guild?’
‘Through the roof, sir. But I’m pretty certain I know what I did wrong.’

Like Cheery, I no longer work in a lab, but I do very much enjoy writing about horrible smells, scary acids and everyday chemistry.

You can download a full-size, high-resolution version of my colouring page from here, and you can download the entire book in one go, too — that should keep everyone busy in these slow days between Christmas and New Year!

If you do colour a page — any of them — please come and share it with me: @chronicleflask on Twitter.

I won’t say Happy New Year because, well, that didn’t work out so well last time. So, instead, let’s go with happy end of 2020!

See you all soon and remember, if you’re setting fire to a pudding, do keep it away from the curtains.


If you’re studying chemistry, have you got your Pocket Chemist yet? Why not grab one? It’s a hugely useful tool, and by buying one you’ll be supporting this site – it’s win-win! If you happen to know a chemist, it would make a brilliant stocking-filler! As would a set of chemistry word magnets!

Like the Chronicle Flask’s Facebook page for regular updates, or follow @chronicleflask on Twitter. Content is © Kat Day 2020. You may share or link to anything here, but you must reference this site if you do. If you enjoy reading my blog, and especially if you’re using information you’ve found here to write a piece for which you will be paid, please consider buying me a coffee through Ko-fi using the button below.
Buy Me a Coffee at ko-fi.com

Want something non-sciency to distract you from, well, everything? Why not check out my fiction blog: the fiction phial.

Chemical connections: dexamethasone, hydroxychloroquine and rheumatoid arthritis

The chemical structure of dexamethasone (image from Wikimedia Commons)

It’s been widely reported today that a “cheap and widely-available” steroid treatment has been shown to be effective in patients suffering the most severe COVID-19 symptoms, significantly reducing the risk of death for both patients on ventilators and those on oxygen treatment.

Most of the reports have understandably focused on the medical aspects, but this is a chemistry blog (mostly) so *cracks chemistry knuckles* what is dexamethasone, exactly?

Its story starts a little over 60 years ago when, in 1958, a paper was published on “clinical observations with 16a-methyl corticosteroid compounds”. Bear with me, I shall explain. Firstly, corticosteroids are hormones which are naturally produced in our bodies. They do all sorts of nifty, useful things like regulate our immune response, reduce inflammation and help us to get energy from carbohydrates. Two of the most familiar names are probably cortisol and cortisone—both of which are released in response to stress.

The discovery of corticosteroids was an important one. So important, in fact, that a few years earlier, in 1950, Tadeusz ReichsteinEdward Calvin Kendall and Philip Showalter Hench had been awarded a Nobel Prize in Physiology and Medicine for “discoveries relating to the hormones of the adrenal cortex”.

The adrenal glands are two small glands found above the kidneys. The outermost part of these glands is called the adrenal cortex (“cortex” from the Latin for (tree) bark and meaning, literally, an outer layer). In the mid-1930s Kendall and Reichstein managed to isolate several hormones produced by these glands. They then made preparations which, with input from Hench, were used in the 1940s to treat a number of conditions, including rheumatoid arthritis.

This was hugely significant at the time, because until this point the treatments for this painful, debilitating condition were pretty limited. Aspirin was known, of course, but wasn’t particularly effective and long-term use had potentially dangerous side effects. Injectable gold compounds (literally chemical compounds containing Au atoms/ions) had also been tried, but those treatments were slow to work, if they worked at all, and were expensive. The anti-malarial drug, hydroxychloroquine (which has also been in the news quite a lot), had been tried as a “remittive agent”—meaning it could occasionally produce remission—but it wasn’t guaranteed.

Rheumatoid arthritis causes warm, swollen, and painful joints (image from Wikimedia Commons)

Corticosteroids were a game-changer. When Hench and Kendall treated patients with what they called, at the time, “compound E” (cortisone) there was a rapid reduction in joint inflammation. It still caused side effects, and it didn’t prevent joint damage, but it did consistently provide relief from painful symptoms.

Fast-forward to the 1958 paper I mentioned earlier, and scientists had discovered that a little bit of fiddling with the molecular structure of steroid molecules caused them to have different effects in the body. The particular chemical path we’re following here started with prednisolone, which had turned out to be a useful treatment for a number of inflammatory conditions. However, placing a methyl group (—CH3) on the 16th carbon—which is, if you have a look at the diagram below, the one on the pentagon-shaped ring, roughly in the middle—changed things.

The steroid “nucleus”: each number represents a carbon atom (image from Wikimedia Commons)

In 1957, four different molecules with methyl groups on that 16th carbon were made available for clinical trial. One of them was 16a-methyl 9a-fluoroprednisolone, more handily known as dexamethasone.

(Quick aside to explain that on the diagram of dexamethasone at the start of this post, the methyl group on the 16th carbon is represented by a dashed wedge-shape. It’s a 2D diagram of a 3D molecule, and the dashed wedge tells us that the methyl group is pointing away from us, through the paper, or rather, screen. This matters because molecules like this have mirror image forms which usually have very different effects in the body—so it’s important to get the right one.)

Dexamethasone is on the WHO Model List of Essential Medicines

It turned out that dexamethasone had a much stronger anti-inflammatory action than plain prednisolone, and it was also more effective the other molecules being tested. It caused a bigger reduction in symptoms, at lower doses. A win all round. It did still have side effects—weight gain, skin problems and digestive issues—but these were no worse than other steroids, and better than some. In fact, salt and water retention were less with dexamethasone, which meant less bloating. It also seemed to have less of an effect on carbohydrate metabolism, making it potentially safer for patients with diabetes.

Skipping forward to 2020, and dexamethasone is routinely used to treat rheumatoid arthritis, as well as skin diseases, asthma, COPD and various other conditions. It is on the WHO Model List of Essential Medicines—a list of drugs thought to be the most important for taking care of the health needs of the population, based on their effectiveness, safety and relative cost.

In the wake of more and more evidence that COVID-19 disease was leading to autoimmune and autoinflammatory diseases, scientists have been looking at anti-inflammatory drugs to see if any of them might help. The Recovery Trial at the University of Oxford was set up to investigate a few different drugs, including hydroxychloroquine (there it is again) and dexamethasone.

It’s not a miracle cure but, in the most severe cases, dexamethasone—a cheap, 60+ year old drug—might just make all the difference.

And that brings us back to today’s news: in the trial, 2104 patients were given dexamethasone once per day for ten days and compared to 4321 patients who were given standard care. The study, led by Professor Peter Horby and Professor Martin Landray, showed that dexamethasone reduced the risk of dying by one-third in ventilated patients and by one fifth in other patients receiving only oxygen.

It’s not a miracle cure by any means: it doesn’t help patients who don’t (yet) need respiratory support, and it doesn’t work for everyone, but, if you find yourself on a ventilator, there’s a chance this 60+ year-old molecule that was first developed to cure rheumatoid arthritis might, just, save your life. And that’s pretty good news.

EDIT 17th June 2020: Chemistry World published an article pointing out that “the trial results have yet to be released leading some to urge caution when interpreting them” and quoting Ayfer Ali, a specialist in drug repurposing, as saying “we have to wait for the full results to be peer reviewed and remember that it is not a cure for all, just one more tool.


If you’re studying from home, have you got your Pocket Chemist yet? Why not grab one? It’s a hugely useful tool, and by buying one you’ll be supporting this site – it’s win-win!

Like the Chronicle Flask’s Facebook page for regular updates, or follow @chronicleflask on Twitter. Content is © Kat Day 2020. You may share or link to anything here, but you must reference this site if you do. If you enjoy reading my blog, and especially if you’re using information you’ve found here to write a piece for which you will be paid, please consider buying me a coffee through Ko-fi using the button below.
Buy Me a Coffee at ko-fi.com

Want something non-sciency to distract you from, well, everything? Why not check out my fiction blog: the fiction phial.

Practical Pyrotechnics (Happy Birthday, Good Omens!)

The novel, Good Omens, was first published on 10th May 1990.

Today (10th May*) is the thirtieth anniversary of the release of the book Good Omens, which is an old favourite of mine, and one I’ve found science-based excuses to write about before. In honour of the day, I’m going to do it again—but this time I’m going to talk about fire.

Fire plays an important role in both the book and the acclaimed television adaptation. Of course, fire is rather easier to do in a novel, since reading words like “fire” and “flames” are generally quite safe. In TV land, however, it’s a bit trickier. In particular (spoiler alert), at the start of episode five, the bookshop owned by the angel Aziraphale is burning when Crowley arrives and walks in. Crowley, after all, is a demon. From Hell. Fire can’t hurt him.

Except, of course, he’s actually the lovely David Tennant, who is a very much not-fireproof human being. Which poses a few questions: did the film crew really set the bookshop set on fire? Did they really make David Tennant walk into a burning building? How is that done safely? And what did they actually burn?

It turns out that they did, in fact, burn down the bookshop set. According to The Nice and Accurate Good Omens TV Companion, director Douglas Mackinnon “wanted a real fire” and “there were thousands of books, tapestries and beautiful grandfather clocks inside the shop that were real.”

Actual books were harmed in the making of Good Omens (photo used with permission).

Which… argh. Actual books. In flames. I might be a bit traumatised. Give me a moment.

Anyway. The thing is, if you’ve ever set fire to paper you’ll know it’s not very controllable. You can’t just burn books and achieve consistent and, more importantly, safe, flames. The Good Omens TV Companion goes on to explain that the set was rigged with gas lines and flame bars. It doesn’t say what the fuel was, but the probable candidate is propane.

This is where we get to the chemistry. Propane is a hydrocarbon—a molecule made of hydrogen and carbon atoms—and the “prop” part of its name tells us that it contains three carbon atoms. The “ane” part tells us it’s an alkane, and from that, handily, we can work out its formula without having to do anything so mundane as look it up, because the formulas of alkanes follow a rule: CnH2n+2. In other words, take the number of carbons, multiply it by two, add two, and you get the number of hydrogen atoms. This gives us three carbons and eight hydrogens: C3H8.

Propane’s boiling point is -42 oC, meaning it’s a gas at room temperature. You may be familiar with propane canisters which slosh when moved, suggesting liquid, and that’s because the propane is under pressure. The only real difference between a gas and a liquid is the amount of space between the individual particles. In a liquid, the particles are mostly touching one another, while in a gas there are large spaces between them. If you take a gas and squash it into a small volume, so that the particles are forced to touch, it becomes a liquid.

Propane is stored in pressurised canisters (photo used with permission)

But once the propane is allowed to escape from the confines of a pressurised container, at room temperature, its molecules spread out once again, into a gas.

The expansion is BIG. Theoretically, at room temperature, one litre of propane liquid (with a density of 493 g/litre) will expand to occupy roughly 270 litres of space. But, of course, the space it’s expanding into also contains air, so the volume of flammable mixture—approximately 5% propane to 95% air—is actually much higher.

Gases burn faster than either liquids or gases. We know this, of course: it only takes a brief spark to light the gas burner on the cooker hob, for example, but you’d struggle to light a liquid fuel with the same spark (unless it was warmed, and therefore starting to vaporise). The reason is those big gaps between molecules: each molecule in a gas is free, none are “buried” in the middle of a volume of liquid (or solid), so they can all mingle freely with oxygen (needed for combustion) and they all “feel” the heat source and become excited more easily.

Propane is a hydrocarbon with three carbon atoms.

Apart from being a gas at room temperature, propane is also chemically very safe in that it’s non-toxic and non-carcinogenic. It’s also colourless and odourless—although small amounts of additives such as the eggy-smelling ethyl mercaptan (ethanethiol) are sometimes added as a safety precaution, to make leaks more noticeable.

Mechanically there are more hazards. There’s a significant temperature drop when a pressurised liquid expands into a gas. The simplest way to think about this is to think of temperature as the energy of all the particles in a substance divided by its volume. If the volume increases while the number of particles stays the same, the energy is spread out a lot more, so the temperature drops. Potentially, a sudden release of too much gas near a person could severely chill their skin, and even cause frostbite. Plus, of course, although propane isn’t toxic, if it displaces oxygen it could cause asphyxiation, and it’s heavier than air, so it tends to accumulate in the bottom part of a room—precisely where people are trying to do pesky things like breathe.

Yellow flames, and smoke, are a sign of incomplete combustion (photo used with permission).

Then there’s the issue of complete combustion. Generally, when hydrocarbons burn they produce carbon dioxide and water as products, neither of which are too much of a problem for nearby humans (up to a point). However, when there’s not enough oxygen—say, because the fire is inside a building—other products form, in particular carbon monoxide, which is very toxic, and carbon particles, which make a terrible, terrible mess.

I mentioned earlier that a flammable mixture is about 95% air to 5% propane, and this is why. In fact, it’s even more precise than that: for propane to burn cleanly it should be 4.2% propane to 95.8% air. In industry terminology, if there’s not enough propane it produces a “lean” burn, where flames lift from the burner and tend to go out. If there’s more propane (and thus not enough oxygen) it’s called a “rich” burn, which produces large, yellow flames, soot, and the dreaded carbon monoxide.

They did burn the bookshop. But it’s OKAY, it was restored again at the end! (Photo used with permission.)

You might, of course, want a certain amount of yellow flame and smoke, to achieve the right look, but the whole thing needs to be carefully controlled to make sure no one is in danger. It’s all manageable with the use of properly checked, monitored and maintained equipment, but you can imagine that a big effect like the bookshop fire needs a very experienced professional to oversee everything.

For Good Omens, that was Danny Hargreaves (of Real SFX), who’s worked on all kinds of projects from War of the Worlds to Doctor Who. As he says in the Good Omens TV Companion, “everything is under control [but] we took it right to [the] limit.” At one point, he says, he turned off gas lines sooner rather than later and, when director Douglas Mackinnon asked why, had to explain that the roof was about to catch fire.

So, yes, they burned the bookshop set. But it’s all right, everyone. It’s all right. Because (another spoiler) thanks to the powers of Adam Young, everything was restored again afterwards. Phew. All the books were saved. Shh.


*Funnily enough, everyone thought the anniversary was 1st of May. Including the whole Good Omens team. So they made a brilliant lockdown video** to mark the occasion and celebrate. And then it turned out it was actually the 10th. Just an ordinary cock-up, as Crowley would say.

**Which proves the bookshop, with all its books, was fully restored, doesn’t it? Told you.


If you’re studying from home, have you got your Pocket Chemist yet? Why not grab one? It’s a hugely useful tool, and by buying one you’ll be supporting this site – it’s win-win!

Want something non-sciency to distract you? Why not check out my fiction blog: the fiction phial. There are loads of short stories, and even (recently) a couple of poems. Enjoy!

Like the Chronicle Flask’s Facebook page for regular updates, or follow @chronicleflask on Twitter. Content is © Kat Day 2020. You may share or link to anything here, but you must reference this site if you do. If you enjoy reading my blog, please consider buying me a coffee through Ko-fi using the button below.
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Cleaning chemistry – the awesome power of soap

Well, times are interesting at the moment, aren’t they? I’m not going to talk (much) about The Virus (there’s gonna be a movie, mark my words), because everyone else is, and I’m not an epidemiologist, virologist or an immunologist or, in fact, in any way remotely qualified. I am personally of the opinion that it’s not even especially helpful to talk about possibly-relevant drugs at the moment, given that we don’t know enough about possible negative interactions, and we don’t have reliable data about the older medicines being touted.

In short, I think it’s best I shut up and leave the medical side to the experts. But! I DO know about something relevant. What’s that, I hear you ask? Well, it’s… soap! But wait, before you start yawning, soap is amazing. It is fascinating. It both literally and figuratively links loads of bits of cool chemistry with loads of other bits of cool chemistry. Stay with me, and I’ll explain.

First up, some history (also not a historian, but that crowd is cool, they’ll forgive me) soap is old. Really, really, old. Archaeological evidence suggests ancient Babylonians were making soap around 4800 years ago – probably not for personal hygiene, but rather, mainly, to clean cooking pots. It was originally made from fats boiled with ashes, and the theory generally goes that the discovery was a happy accident: ashes left from cooking fires made it much easier to clean pots and, some experimenting later, we arrived at something we might cautiously recognise today as soap.

Soap was first used to clean pots.

The reason this works is that ashes are alkaline. In fact, the very word “alkali” is derived from the Arabic al qalīy, meaning calcined ashes. This is because plants, and especially wood, aren’t just made up of carbon and hydrogen. Potassium and calcium play important roles in tree and plant metabolism, and as a result both are found in moderately significant quantities in wood. When that wood is burnt at high temperatures, alkaline compounds of potassium and calcium form. If the temperature gets high enough, calcium oxide (lime) forms, which is even more alkaline.

You may, in fact, have heard the term potash. This usually refers to salts that contain potassium in a water-soluble form. Potash was first made by taking plant ashes and soaking them in water in a pot, hence, “pot ash”. And, guess where we get the word potassium from? Yep. The pure element, being very reactive, wasn’t discovered until 1870, thousands of years after people first discovered how useful its compounds could be. And, AND, why does the element potassium have the symbol K? It comes from kali, the root of the word alkali.

See what I mean about connections?

butyl ethanoate butyl ethanoate

Why is the fact that the ashes are alkaline relevant? Well, to answer that we need to think about fats. Chemically, fats are esters. Esters are chains of hydrogen and carbon that have, somewhere within them, a cheeky pair of oxygen atoms. Like this (oxygen atoms are shown red):

Now, this is a picture of butyl ethanoate (aka butyl acetate – smells of apples, by the way) and is a short-ish example of an ester. Fats generally contain much longer chains, and there are three of those chains, and the oxygen bit is stuck to a glycerol backbone.

Thus, the thick, oily, greasy stuff that you think of as fat is a triglyceride: an ester made up of three fatty acid molecules and glycerol (aka glycerine, yup, same stuff in baking). But it’s the ester bit we want to focus on for now, because esters react with alkalis (and acids, for that matter) in a process called hydrolysis.

Fats are esters. Three fatty acid chains are attached to a glycerol “backbone”.

The clue here is in the name – “hydro” suggesting water – because what happens is that the ester splits where those (red) oxygens are. On one side of that split, the COO group of atoms gains a metal ion (or a hydrogen, if the reaction was carried out under acidic conditions), while the other chunk of the molecule ends up with an OH on the end. We now have a carboxylate salt (or a carboxylic acid) and an alcohol. Effectively, we’ve split the molecule into two pieces and tidied up the ends with atoms from water.

Still with me? This is where it gets clever. Having mixed our fat with alkali and split our fat molecules up, we have two things: fatty acid salts (hydrocarbon chains with, e.g. COONa+ on the end) and glycerol. Glycerol is extremely useful stuff (and, funnily enough, antiviral) but we’ll put that aside for the moment, because it’s the other part that’s really interesting.

What we’ve done here is produce a molecule that has a polar end (the charged bit, e.g. COONa+) and a non-polar end (the long chain of Cs and Hs). Here’s the thing: polar substances tend to only mix with other polar substances, while non-polar substances only mix with other non-polar substances.

You may be thinking this is getting technical, but honestly, it’s not. I guarantee you’ve experienced this: think, for example, what happens if you make a salad dressing with oil and vinegar (which is mostly water). The non-polar oil floats on top of the polar water and the two won’t stay mixed. Even if you give them a really good shake, they separate out after a few minutes.

The dark blue oily layer in this makeup remover doesn’t mix with the watery colourless layer.

There are even toiletries based around this principle. This is an eye and lip makeup remover designed to remove water-resistant mascara and long-stay lipstick. It has an oily layer and a water-based layer. To use it, you give the container a good shake and use it immediately. The oil in the mixture removes any oil-based makeup, while the water part removes anything water-based. If you leave the bottle for a minute or two, it settles back into two layers.

But when we broke up our fat molecules, we formed a molecule which can combine with both types of substance. One end will mix with oily substances, and the other end mixes with water. Imagine it as a sort of bridge, joining two things that otherwise would never be connected (see, literal connections!)

There are a few different names for this type of molecule. When we’re talking about food, we usually use “emulsifier” – a term you’ll have seen on food ingredients lists. The best-known example is probably lecithin, which is found in egg yolks. Lecithin is the reason mayonnaise is the way it is – it allows oil and water to combine to give a nice, creamy product that stays mixed, even if it’s left on a shelf for months.

When we’re talking about soaps and detergents, we call these joiny-up molecules “surfactants“. You’re less likely to have seen that exact term on cosmetic ingredients lists, but you will (if you’ve looked) almost certainly have seen one of the most common examples, which is sodium laureth sulfate (or sodium lauryl sulfate), because it turns up everywhere: in liquid soap, bubble bath, shampoo and even toothpaste.

I won’t get into the chemical makeup of sodium laureth sulfate, as it’s a bit different. I’m going to stick to good old soap bars. A common surfactant molecule that you’ll find in those is sodium stearate, which is just like the examples I was talking about earlier: a long hydrocarbon chain with COONa+ stuck on the end. The hydrocarbon end, or “tail”, is hydrophobic (“water-hating”), and only mixes with oily substances. The COONa+ end, or “head”, is hydrophilic (“water loving”) and only mixes with watery substances.

Bars of soap contain sodium stearate.

This is perfect because dirt is usually oily, or is trapped in oil. Soap allows that oil to mix with the water you’re using to wash, so that both the oil, and anything else it might be harbouring, can be washed away.

Which brings us back to the wretched virus. Sars-CoV-2 has a lipid bilayer, that is, a membrane made of two layers of lipid (fatty) molecules. Virus particles stick to our skin and, because of that membrane, water alone does a really bad job of removing them. However, the water-hating tail ends of surfacant molecules are attracted to the virus’s outer fatty surface, while the water-loving head ends are attracted to the water that’s, say, falling out of your tap. Basically, soap causes the virus’s membrane to dissolve, and it falls apart and is destroyed. Victory is ours – hurrah!

Hand sanitisers also destroy viruses. Check out this excellent Compound Interest graphic (click the image for more).

Who knew a nearly-5000 year-old weapon would be effective against such a modern scourge? (Well, yes, virologists, obviously.) The more modern alcohol hand gels do much the same thing, but not quite as effectively – if you have access to soap and water, use them!

Of course, all this only works if you wash your hands thoroughly. I highly recommend watching this video, which uses black ink to demonstrate what needs to happen with the soap. I thought I was washing my hands properly until I watched it, and now I’m actually washing my hands properly.

You may be thinking at this point (if you’ve made it this far), “hang on, if the ancient Babylonians were making soap nearly 5000 years ago, it must be quite easy to make… ooh, could I make soap?!” And yes, yes it is and yes you can. Believe me, if the apocolypse comes I shall be doing just that. People rarely think about soap in disaster movies, which is a problem, because without a bit of basic hygine it won’t be long before the hero is either puking his guts up or dying from a minor wound infection.

Here’s the thing though, it’s potentially dangerous to make soap, because most of the recipes you’ll find (I won’t link to any, but a quick YouTube search will turn up several – try looking for “saponification“) involve lye. Lye is actually a broad term that covers a couple of different chemicals, but most of the time when people say lye these days, they mean pure sodium hydroxide.

Pure sodium hydroxide is usually supplied as pellets.

Pure sodium hydroxide comes in the form of pellets. It’s dangerous for two reasons. Firstly, precisely because it’s so good at breaking down fats and proteins, i.e. the stuff that humans are made of, it’s really, really corrosive and will give you an extremely nasty burn. Remember that scene in the movie Fight Club? Yes, that scene? Well, that. (Follow that link with extreme caution.)

And secondly, when sodium hydroxide pellets are mixed with water, the solution gets really, really hot.

It doesn’t take a lot of imagination to realise that a really hot, highly corrosive, solution is potentially a huge disaster waiting to happen. So, and I cannot stress this enough, DO NOT attempt to make your own soap unless you have done a lot of research AND you have ALL the appropriate safety equipment, especially good eye protection.

And there we are. Soap is ancient and awesome, and full of interesting chemistry. Make sure you appreciate it every time you wash your hands, which ought to be frequently!

Stay safe, everyone. Take care, and look after yourselves.


Want something non-sciency to distract you? Why not check out my fiction blog: the fiction phial. There are loads of short stories, and even (recently) a poem. Enjoy!

If you’re studying from home, have you got your Pocket Chemist yet? Why not grab one? It’s a hugely useful tool, and by buying one you’ll be supporting this site – it’s win-win!

Like the Chronicle Flask’s Facebook page for regular updates, or follow @chronicleflask on Twitter. Content is © Kat Day 2020. You may share or link to anything here, but you must reference this site if you do. If you enjoy reading my blog, please consider buying me a coffee through Ko-fi using the button below.
Buy Me a Coffee at ko-fi.com