Brilliant Bee Chemistry!

20th May is World Bee Day, the aim of which is to raise awareness of the importance of bees and beekeeping. So, hey, let’s do that!

I’m helped this month by my horticulturist* dad who, while working in a public garden recently, discovered this honeybee swarm in a honeysuckle. (Me: “what sort of tree is that?” Dad: “a winter flowering Honeysuckle lonicera. It’s a shrub, not a tree!” Yes, despite his tireless efforts I’m still pretty clueless about plants.)

Now, Dad knows what he’s doing in such situations. He immediately called the professionals. One does not mess around with (or ignore) a swarm of bees – one finds a beekeeper, stat. Obviously bees can sting, but they’re also endangered and they need to be collected to protect them. Should you find yourself in such a situation, you can find someone local via the British Beekeepers Association website.

That out of the way, aren’t they gorgeous? A swarm like this is a natural phenomenon, that happens when new queen bees are born and raised in the colony. Worker bees stop feeding the old queen – because a laying queen is too heavy to fly – and then in time she leaves with a swarm. They cluster somewhere, as you see in the photo, while scout bees go looking for a new location to settle. Bees in swarms only have the honey or nectar in their stomachs to keep them going, so they’ll starve if they don’t find a new home, and nectar, quickly.

This is all fascinating, of course, but what does it have to do with chemistry? Well, quite a bit, because bees are brilliant chemists. Really!

Ethyl oleate is an ester and an important chemical for bees (image source)

Firstly, despite what DreamWorks might have taught us, bees don’t have vocal cords, and they don’t sound like Jerry Seinfeld. A lot of their communication is chemical-based (actually, it turns out this is a topic of hot debate in bee circles, but since this is a chemistry blog, I’m not doing waggle dances. No, not even if you ask nicely).

As you might imagine, there are multiple chemicals involved, and I won’t go into all of them. Many are esters, which are known for their sweet, fruity smells, and which are also (at least, the longer-chain ones) the building blocks of fats.

One such chemical is ethyl oleate which plants produce and which, interestingly, we humans also make in our bodies when we drink alcohol. Forager bees gather ethyl oleate and carry it in their stomachs, and they then feed it to worker bees. It has the effect of keeping those workers in a nurse bee state and prevents them from maturing into forager bees too early. But, as forager bees die off, less ethyl oleate is available, and this “tells” the nurse bees to mature more quickly – so the colony makes more foragers. Clever, eh?

In this situation, ethyl oleate is acting as a pheromone, in other words, a substance that triggers a social response in members of the same species. Another example is Nasonov’s pheromone, which is a mixture of chemicals including geraniol (think fresh, “green” smell), nerolic acid, geranic acid (an isomer of nerolic acid) and citral (smells of lemon).

The white gland at the top of the honeybee’s abdomen releases pheromones which entice the swarm to an empty hive (image source)

An interesting aside: geranic acid has been investigated as an antiseptic material. It can penetrate skin, and has been shown to help the delivery of transdermal antibiotics, which are being investigated partly as a solution to the problem of antibiotic resistance. Nature is, as always, amazing.

Anyway, worker bees (which, again contrary to DreamWorks’ narrative, are female) release Nasonov’s pheromone to orient returning forager bees (also female) back to the colony. They do this by raising up their abdomens and fanning their wings. Beekeepers can use synthetic Nasonov pheromone, sometimes mixed with a “queen bee pheromone” to attract honeybee swarms to an unoccupied hive or swarm-catching box.

As my Dad chatted to the beekeepers (partly on my insistence – I was on the other end of my phone texting questions and demanding photos) one substance they were particularly keen to mention was “the alarm pheromone,” which “smells of bananas.”

Ooh, interesting, I thought. Turns out, this is isoamyl acetate, which is another ester. In fact, depending on your chemistry teacher’s enthusiasm for esters, you might even have made it in school – it forms when acetic acid (the vinegary one) is combined with 3-methylbutan-1-ol (isoamyl alcohol).

Never eat a banana by a bee.

Isoamyl acetate is used to give foods a banana flavour and scent. But, funnily enough, actual bananas you buy in the shops today don’t contain very much of it, the isoamyl acetate-rich ones having been wiped out by a fungal plague in the 1990s. This has lead to the peculiar situation of banana-flavoured foods tasting more like bananas than… well… bananas.

Modern bananas can still be upset bees, though. There are numerous stories of unwary individuals who walked too close to hives while eating a banana and been attacked. So, top tip: if you’re going on a picnic, leave the bananas (and banana-flavoured sweets, milkshakes etc) at home.

The reason is that banana-scented isoamyl acetate is released when honeybees sting. They don’t do this lightly, of course, since they can’t pull out the barbed stinger afterwards, and that means the bee has to leave part of its digestive tract, muscles and nerves embedded in your skin. It’s death for the bee, but the act of stinging releases the pheromone, which signals other bees to attack, attack, attack.

One bee sting might not deter a large predator, but several stings will. Multiple bee stings can trigger a lethal anaphylactic reaction, known allergy or not. So although utilising their stingers causes the death of a few (almost certainly infertile) bees, the rest of the colony (including the fertile individuals) is more likely to survive. From an evolutionary perspective it’s worth it – genes survive to be passed on.

Isoamyl acetate

Isoamyl acetate is an ester that smells of bananas, and is an alarm pheremone for bees (image source)

Moving on, I obviously can’t write a whole blog post about bees and not mention honey! We take it for granted, but it’s amazingly complicated. It contains at least 181 different substances, and nothing human food scientists have been able to synthesise quite compares.

In terms of sugars, it’s mostly glucose and fructose. Now, I’ve written about sugars extensively before, so I won’t explain them yet again, but I will just reiterate my favourite soap-box point: your body ultimately doesn’t distinguish between “processed” sugars in foods and the sugars in honey. In fact, one might legitimately argue that honey is massively processed, just, you know, by bees. So, you want to cut down on your sugar intake for health reasons? Sorry, but honey needs to go, too.

Honey is actually a supersaturated solution. In very simple terms, this means there’s an excess of sugar dissolved in a small amount of water. One substance which bees use to achieve this bit of clever chemistry is the enzyme, invertase, which they produce in their salivary glands. Nectar contains sucrose (“table sugar”) and, after the bees collect nectar, invertase helps to break it down into the smaller molecules of glucose and fructose.

“Set” honey is honey that’s been crystallised in a controlled way.

That’s only the beginning, though. There are lots of other enzymes involved. Amylase breaks down another sugar, amylose, into glucose. And glucose oxidase breaks down glucose and helps to stabilise the honey’s pH. One of the molecules produced in the reaction with glucose oxidase produces is hydrogen peroxide, which yet another enzyme, catalase, further breaks down into water and oxygen.

Bees regurgitate and re-drink nectar (yes, I suggest you don’t overthink it) over a period of time, which both allows the sugar chemistry to happen and also reduces the water content. When it’s about one-fifth water, the honey is deposited in the honeycomb, and the bees fan it with their wings to speed up the evaporation process even further. They stop when it’s down to about one-sixth water.

As I said a moment ago, honey is a supersaturated solution, and that means it’s prone to crystallising. This isn’t necessarily bad, in fact, “set” honey (my personal favourite) is honey which has been crystallised in a controlled way, so as to produce fine crystals and a creamy (rather than grainy) product.

The formation of a new honeycomb.

The potential problem with crystallisation is that once the sugar crystals fall out of solution, the remaining liquid has a higher-than-ideal percentage of water. This can allow microorganisms to grow. In particular, yeasts can take hold, leading to fermentation. Honey left on the comb in the hive tends not to crystallise, but once it’s collected and stored, there’s a greater chance that some particle of something or other will get in there and trigger the process. It helps to store it somewhere above room temperature. And honey is naturally hygroscopic, which means it absorbs water. So store it somewhere dry. In short, never put honey in the fridge.

Speaking of yeast and heat, heating changes honey and makes it darker in colour, thanks to the Maillard reaction. Commercial honey is often pasteurized to kill any yeast, which improves its shelf life and produces a smoother product. Also, because honey is naturally slightly acidic (around pH 4), over time the amino acids within in start to break down and this also leads to a darkening of the colour.

One more important safety concern: honey, even when pasteurized, can contain bacteria that produce toxins in a baby’s intestines and lead to infant botulism. So, never give children under one honey. It’s not a risk for older children (and adults) thanks to their more mature digestive systems.

T

Back to Dad’s bees! They were collected in a transport box by two local experts, Sharon and Ian. The bees march into the box two-by-two, wafting Nazonov’s pheromone to signal that this is home. From there, they were safely transferred to a new, wooden hive.

There’s only one way to finish this post, I think, and that’s with one of my all-time favourite Granny Weatherwax moments:

‘Your bees,’ she went on, ‘is your mead, your wax, your bee gum, your honey. A wonderful thing is your bee. Ruled by a queen, too,’ she added, with a touch of approval.

‘Don’t they sting you?’ said Esk, standing back a little. Bees boiled out of the comb and overflowed the rough wooden sides of the box.

‘Hardly ever,’ said Granny. ‘You wanted magic. Watch.’

Happy World Bee Day, everyone and, as always, GNU Terry Pratchett.


* Dad was unsure about the label “horticulturist” but I pointed out that the definition is an expert in garden cultivation and management, particularly someone’s who’s paid for their work. All of which he is. He replied wryly that, “x is an unknown quantity, and a spurt is a long drip.” Love you, Dad x 😄


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.
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Vibrant Viburnum: the fascinating chemistry of fragrant flowers

There’s a Viburnum carlesii bush (sometimes called Koreanspice) near my front door and, right now, it smells amazing. It only flowers for a relatively short time each year and otherwise isn’t that spectacular – especially in the autumn when it drops its leaves all over the doorstop, and I’m constantly brushing them out of the house.

But it’s all worth it for these few weeks in April, when everyone who has any reason to come anywhere near our door says, ‘ooh, what is that smell? It’s gorgeous!’ We also rear butterflies at this time of year, and they love the flowers once they’ve emerged from their chrysalids. (No, of course this isn’t an excuse to include all my butterfly photos in a post. Painted lady, since you ask.)

But let’s talk chemistry – what is in the Viburnum carlesii’s fragrance? Well, it’s a bit complicated. Fragrances, as you might imagine, often are. We detect smells when volatile (things that vaporise easily) compounds find their way to our noses which are, believe it or not, great chemical detectors.

Well, I say great, many animals have far better smell detection: dogs, of course, are particularly known for it. Their noses have some 300 million scent receptors*, while humans “only” have 5-6 million but, and this is the really fantastic part, by some estimates we’re still able to detect a trillion or so smells. We (and other animals) inhale air that contains odour molecules, and those molecules bind to the receptors in our noses, triggering electrical impulses that our brains interpret as smell.

Most scents aren’t just one molecule, but are actually complex mixtures. Our brains learn to recognise combinations and to associate them with certain, familiar things. It’s not that different from recognising patterns of sound as speech, or patterns of light as images, it’s just that we often don’t think of smell in quite the same way.

Viburnum carlesii flowers have a fragrance often described as sweet and spicy.

So my Viburnum bush – and the flowers I’ve cut and put on my desk – is actually pumping out loads of different molecules right now. After a bit of hunting around, I tracked them down to (brace yourself for a list of chemical names) isoeugenol, eugenol, methyleugenol, 4-allylsyringol, vinyl-guaiacol and methyl nicotinate, plus the old favourites methyl salicylate (this stuff turns up everywhere), methyl benzoate (so does this), indole, cinnamic aldehyde and vanillin, and then some isovaleraldehyde, acetoin, hexanal, (Z)-3-hexen-1-ol and methional.

Phew.

Don’t worry, I’m not going to talk about the chemistry of all of those. But just for a moment consider how wondrous it is that our noses and brains work together to detect all of those molecules, in their relevant quantities, and then send the thought to our conscious mind that oh, hey, the Viburnum is flowering! (It’s also pretty astonishing that, in 2021, I can just plug all those names into a search engine and, with only a couple of exceptions, get all sorts of information about them in seconds – back in the old days when I was studying chemistry, you had to use a book index, and half the time the name you wanted wasn’t there. You kids don’t know how good you’ve got it, I’m telling you.)

Anyway, if you glance at those names, you’ll see eugenol popping up quite a bit, so let’s talk about that. It’s a benzene ring with a few other groups attached, and lots of chemicals like this have distinctive smells. In fact, we refer to molecules with these sorts of ring structures as “aromatic” for this exact, historical reason – when early chemists first isolated them, they noticed their distinctive scents.

Eugenol is an aromatic compound, both in terms of chemistry and fragrance (image source)

In fact there are several groups of molecules in chemistry that we tend to think of as particularly fragrant. There are esters (think nail polish and pear drops), linear terpenes (citrus, floral), cyclic terpenes (minty, woody), amines (fishy, rot) and the aromatics I’ve just mentioned.

But back to eugenol: it’s a yellowish, oily liquid that can be extracted from plants such as nutmeg, cloves, cinnamon, basil and bay leaves. This might give you an idea of its scent, which is usually described as “spicy” and “clove-like”.

Not surprisingly, it turns up in perfumes, and also flavourings, since smell and flavour are closely linked. It’s also a local antiseptic and anaesthetic – you may have used some sort of eugenol-based paste, or perhaps just clove oil, if you’ve ever had a tooth extracted.

Plants, of course, don’t go to the trouble and biological expense of making these chemicals just so that humans can walk past and say, “ooh, that smells nice!” No, the benefit for the plant is in attracting insects, which (hopefully) help with pollination. Which explains why my butterflies like the flowers so much. (Another butterfly pic? Oh well, since you insist.) Eugenol, it turns out, is particularly attractive to various species of orchid bee, which use it to synthesise their own pheromones. Nature’s clever, isn’t she?

By the way, notice I mentioned anaesthetics back there? Eugenol turns out to be too toxic to use for this in large quantities, but the study of it did lead to the development of the widely-used drug propofol which, sadly, is pretty important right now – it’s used to sedate mechanically ventilated patients, such as those with severe COVID-19 symptoms. You may have seen some things in the news earlier this year about anaesthetic supply issues, precisely for this reason.

Isoeugenol has the same “backbone” as eugenol, with just a difference to the position of the C=C bond on the right. (image source)

Back in that list of chemical names, you’ll see “eugenol” forming parts of other names, for example isoeugenol. This points back to a time when chemicals tended to be named based on their origins. Eugenol took its name from the tree from which we get oil of cloves, Eugenia, which was in turn named after Prince Eugene of Savoy – a field marshal in the army of the Holy Roman Empire. And then other molecules with the same “backbone” were given the same name with prefixes and suffixes added on to describe their differences. As I said in my last post, this sort of naming system it was eventually replaced with more consistent rules, but a lot of these older substances have held onto their original names.

Still, regardless of what we call the chemicals, the flowers smell delightful. I’m off to replenish the vase on my desk while I still can. Roll on May, vaccines and (hopefully) lockdown easing!

Take care and stay safe.


*it’s even been suggested dogs’ super-powered sense of smell might be able to detect COVID-19 infections.


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

 

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.
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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.

 

 

Sunshine, skin chemistry, and vitamin D

The UK is on the same latitude as Northern Canada (Image Source: Wiki Commons)

As I write this it’s the last day of September in the U.K., which means we’re well into meteorological autumn and summer is, at least here, a distant memory. The weather is cooler and the days are getting shorter. Soon, the clocks will go back an hour, and we’ll shift from BST (British Summer Time) to GMT (Greenwich Mean Time).

Seasons in the U.K. are particularly marked because of our northerly latitude. British weather tends to be fairly mild (thanks, Gulf Stream), and it’s easy to forget just how far north we are – but a quick look at a globe makes it clear: London is actually further north than most of the major Canadian cities, while the Polar Bear Provincial Park in Ontario is roughly on the same latitude as Scotland’s capital city, Edinburgh.

Yes, I hear you say, but what on Earth (hoho) does this have to do with chemistry?

Well, a clever little piece of chemistry happens in human skin, and, if you live in the U.K., it’s about to stop. At least, until next spring.

Some clever chemistry happens in human skin.

There’s a substance in your skin called 7-dehydrocholesterol (7-DHC). It is, as the name suggests, something to do with cholesterol (which, despite its bad press, is an essential component of animal cell membranes). In fact, 7-DHC is converted to cholesterol in the body, but it’s also converted to something else.

You will have heard of vitamin D. It helps us to absorb calcium and other minerals, and if children, in particular, don’t get enough it can lead to rickets – which leads to weak bones, bowed legs and stunted growth. Vitamin D deficiency has also been linked to lots of other health problems, including increased risk of certain cancers, heart disease, arthritis and even type one diabetes.

More recently, vitamin D has been linked to COVID-19. It’s estimated that around 80-85% of people who contract COVID-19 experience mild or no symptoms, while the rest develop severe symptoms and, even if they recover, may suffer life-altering after-effects for many months. Early data suggest that patients with low vitamin D levels are much more likely to experience those severe symptoms. There’s a plausible mechanism for this: vitamin D helps to regulate the immune system and, in particular, helps to reduce the production of cytokines.

It’s possible that having inadequate levels of vitamin D may increase your chances of a severe response to COVID-19.

Cytokines are small proteins which are important in cell signalling, but if the body starts to produce too many in response to a virus it can cause something called a cytokine storm, which can lead to organ failure and death.

It’s proposed that having the right levels of vitamin D might help to prevent such cytokine storms, and therefore help to prevent a severe COVID-19 response. This is all early stages, because everyone is still learning about COVID-19, and it may turn out to be correlation without causation, but so far it looks promising.

One thing you many not know is that vitamin D is, technically, misnamed. Vitamins are, by definition, substances which are required in small quantities in the diet, because they can’t be synthesised in the body.

But vitamin D, which is actually a group of fat soluble molecules rather than a single substance, can be synthesised in the body, in our skin. The most important two in the group are ergocalciferol (vitamin D2) and cholecalciferol (vitamin D3), sometimes known collectively as calciferol.

Shiitake mushrooms are a good source of vitamin D2.

Vitamin D2 is found in fungi, but it’s cleared more quickly from the body than D3, so needs to be consumed in some form daily. Mushrooms are a good source (especially if they’ve been exposed to UV light), so if you like mushrooms, that’s one way to go. Vitamin D3 is hard to obtain from diet – the only really good source is oily fish, although other foods are fortified – but that’s okay because, most of the time, we don’t need to eat it.

Which brings us back to 7-DHC. It’s found in large quantities in the skin, although exactly how it gets there has been the subject of some debate. It used to be thought it was formed from cholesterol via an enzymatic reaction in the intestine wall and then transported to the skin via the bloodstream. But the trouble with this idea is that the blood would pass through the liver, and 7-DHC would be reconverted to cholesterol, never having a chance to build up in skin. A more robust theory is it’s actually synthesised in the skin in the first place, particularly since higher levels are found in a layer closer to the surface (the stratum spinosum) than in the deeper dermis.

We make vitamin D in our skin when we’re exposed to UVB light from the sun.

Anyway, the important thing is that 7-DHC absorbs UV light, particularly wavelengths between 290 and 320 nm, that is, in the UVB range, sometimes called “intermediate” UV (in contrast with “soft” UVA, and “hard” UVC). When exposed to UVB light, one of the rings in the 7-DHC molecule breaks apart, forming something known pre-D3, that then converts (isomerises) to vitamin D3 in a heat-sensitive process.

In short, we make vitamin D3 in our skin when we’re in the sunshine. Obviously we need to avoid skin damage from UV light, but the process doesn’t take long: 10-15 minutes of midday sunlight three times a week, in the U.K. in the summer, is enough to keep our levels up.

Sun exposure is by far the quickest, and certainly the cheapest, way to get your vitamin D. If you live somewhere where that’s possible.

Here’s the thing, though, if you live in the U.K., for a chunk of the year, it’s just not. I’ve pinched the graph here from my husband, whose work involves solar panels, because it makes a nice visual point.

The amount of sunlight we’re exposed to in the U.K. drops sharply in autumn and winter.

From April – September, there’s plenty of energy available from sunlight. But look at what happens from October – March. The numbers drop drastically. And here’s the thing: it turns out that vitamin D production in human skin only occurs when UV radiation exceeds a certain level. Below this threshold? Well, no photocoversion takes place.

In short: if you live in the U.K. you can’t make vitamin D in your skin for a few months of the year. And those few months are starting… round about now.

The NILU has a web page where you can calculate how much vitamin D you can synthesise in your skin on a given day.

If you want to experiment, there’s a website here, published by the Norwegian Institute for Air Research (NILU), where you can enter various parameters – month, longitude, cloudiness etc – and it will tell you how many hours during a given a day it’s possible to synthesise vitamin D in your skin.

Have a play and you’ll see that, for London, vitamin D synthesis drops off to zero somewhere around the end of November, and doesn’t restart until sometime after the 20th of January. In Edinburgh, the difference is even more marked, running from the first week or so of November to the first week of February.

It’s important to realise that it tails off, too, so during the days either side of these periods there’s only a brief period during midday when you can synthesise vitamin D. And all this assumes a cloudless sky which in this country… is unlikely.

The skin pigment, melanin, absorbs UVB. (Image Source: Wiki Commons)

The situation is worse still if you have darker skin because the skin pigment, melanin, absorbs UVB. On the one hand, this is a good thing, since it protects skin cells from sun-related damage. But it also reduces the ability to synthesise vitamin D. In short, wimpy autumn and winter sunshine just isn’t going to cut it.

Likewise, to state the obvious, anyone who covers their skin (with clothing or sunblock), also won’t be able to synthesise vitamin D in their skin.

Fortunately, there’s a simple answer: supplements. The evidence is fairly solid that vitamin D supplements increase blood serum levels as well as, if not better than, sunshine – which, for the reasons mentioned above, can be difficult to obtain consistently.

Now, as I’ve said many times before, I’m not a medical doctor. However, I’m on fairly safe ground here, because Public Health England do actually recommend everyone take a vitamin D supplement from October to May. That is, from now. Yes, now.

I do need to stress one point here: DO NOT OVERDO IT. There always seems to be someone whose reasoning goes along the lines of, “if one tablet is good, then ten will be even better!” and, no. No. Excessive doses of vitamin D can cause vomiting and digestive problems, and can lead to hypercalcemia which results in weakness, joint pain confusion and other unpleasant symptoms.

If you live in the U.K. you should be taking a vitamin D supplement from October-May.

Public Health England recommend everyone in the U.K. take 10 micrograms per day in autumn and winter. Babies under one year should also be given 8.5–10 micrograms of vitamin D in the form of vitamin drops, unless they’re drinking more than 500 ml of infant formula a day (because that’s already fortified).

Amounts can get a little confusing, because there are different ways to measure vitamin D doses, and in particular you may see IU, or “international units“. However, if you buy a simple D3 supplement, like this one that I picked up at the supermarket, and follow the dose instructions on the label, you won’t go far wrong.

So, should you (and everyone else in your family) be taking a simple vitamin D supplement right around now? If you live in the U.K., or somewhere else very northerly, then yes. Well, unless you’re really keen to eat mushrooms pretty much every day. At worst, it won’t make much difference, and at best, well, there’s a chance it might help you to avoid a really unpleasant time with COVID-19, and that’s got to be a good thing.

But, look, it’s not toilet roll. Don’t go and bulk buy vitamin D, for goodness sake.

Until next time, take care, and stay safe.


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!

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.

Lovely lollipops: the chemistry of sugary things

20th July is National Lollipop Day!

Today, July 20th, is apparently national lollipop day in the United States, and general news is… *waves hands* so it seems like a good excuse to write something with lots of pictures of brightly coloured sweets, right? Plus, sugar!

The idea of putting something sugary on a stick to hold and eat is an ancient one. The very earliest humans probably used sticks to collect honey from beehives. Later, the Chinese, Egyptians and people from the Middle East dipped fruits and nuts in honey and used sticks to make them easier to eat.

In the 17th century, boiled sugar sweets were made in England and, again, sticks inserted to make eating easier. This may be where the name “lollipop” originates, since “lolly” is a dialect word for tongue. Later, in the American Civil War era (early 1860s), some sources say hard candy was put on the tips of pencils for children. In 1931 an American named George Smith started making hard candies on sticks, and trademarked the name lollipop — but he reportedly took the name from a racehorse named “Lolly Pop”.

Table sugar is sucrose

Enough history, let’s get to the chemistry! Lollipops are made of sugar, with added colours and flavours. I’ve talked about sugar before, and it’s always worth remembering that we tend to use the word rather loosely in everyday speech.

There’s more than one type of sugar: in particular, the three that are probably most familiar are glucose, fructose and sucrose. Glucose is a simple sugar, and the one you might remember from photosynthesis and respiration equations. It’s essential for life, and you quickly run into serious trouble if your blood glucose levels drop too low (just ask a diabetic).

Like glucose, fructose is a monosaccharide (the simplest form of sugar), and is often called “fruit sugar” because, guess what, it’s common in fruits. Sucrose is what we know as “table sugar” and is a disaccharide, made up of a unit of glucose joined to a unit of fructose. In the body, sucrose is broken up into glucose and fructose.

Rock candy is made from sucrose but, unlike in most lollipops and hard candy, the sugar is allowed to form large crystals

The primary ingredient in lollipops is usually sucrose, which can be persuaded (more in a minute) to set nicely to produce a hard, shiny surface. However, commercial lollipops often also include corn syrup, or glucose syrup, which contains oligosaccharides: larger sugar molecules made from a number of simple sugar molecules joined together. Typically, as the name “glucose syrup” might suggest, these molecules contain units of glucose.

It’s worth mentioning here that corn syrup/glucose syrup isn’t the same as “high fructose corn syrup” or HFCS, in which the glucose molecules have been converted into fructose. This product is cheap, sweet and commercially easy to use, but it’s also controversial. Excessive consumption has been linked to obesity and non-alcoholic fatty liver disease, although the actual evidence is weak: a systematic review in 2014 concluded that there was little evidence it was worse than other forms of sugar. It’s really a problem of quantity: it’s easy and cheap for food manufacturers to throw HFCS into foods and drinks, and of course it tastes delicious, so as a consequence consumers end up eating too much of the stuff. In short: more water and fruit, less cake and fizzy drinks.

But having done the obligatory “eat healthily” thing, one lollipop isn’t going to hurt, is it? So back to that…

Fudge, perhaps surprisingly, contains the crystalline form of sugar

When it cools, sugar forms two different types of solid: crystalline and glassy amorphous (sometimes described as ‘amorphous solid’). Now, you might imagine that sugar as a crystalline solid is found in hard sweets/candies, but, no — it mostly turns up in soft things like fudge and fondant, which contain lots of very tiny crystals, giving an ever-so slightly granular texture. (An exception is rock candy, where the sugar is encouraged to form large crystals.)

The glassy amorphous form of sugar, on the other hand, can be literally like glass: hard, brittle, and transparent. In fact, “sugar glass” has in the past been used to make windows, bottles and so on for special effects in film and television, because it’s much less likely to cause injury than “real” glass. However, it’s very fragile and hygroscopic (meaning it absorbs water, causing it to soften over time) so these days it’s largely been replaced by synthetic resins.

Honey can be used as an inhibitor, to prevent crystallisation

The glassy amorphous form of sugar is achieved by starting with a 50% sugar solution which also contains an inhibitor, to prevent crystals forming spontaneously. Common inhibitors are the corn syrup I mentioned earlier, or cream of tartar (potassium bitartrate), honey or butter.

Exactly which you use depends on the recipe, but they all do essentially the same thing, namely, get in the way of the glucose molecules and prevent them ordering themselves into a regular (crystalline) structure. The mixture is heated to a high temperature (about 155 oC) until almost all the water evaporates — the final candy will only have about 1-2% water — and then cooled until glass transition occurs.

At the glass transition point, the sugar mixture becomes solid.

This is the clever bit, and only happens if crystallisation is inhibited (else crystals form instead). Glass transition happens around 100-150 oC below the melting point of the pure substance. For example, the melting point of pure sucrose is 186 oC, but it undergoes glass transition at around 60 oC.

Glass transition is a reversible change, which we might (if I didn’t generally dislike the concept) call a physical change. It’s a change of phase, where the sugar mixture changes from liquid to solid, but it’s different from crystallisation, because instead of the molecules becoming more ordered, they simply ‘freeze’ in their random, liquid positions. (It is, for the record, annoyingly difficult to show this in diagram form.)

Amorphous solid structures are sometimes called “supercooled liquids”. This isn’t wrong, but personally I think it’s unhelpful (and can lead to nonsense about glass flowing very slowly over time). Once cooled and set, glass, whether window glass or sugar glass, is absolutely not a liquid; it’s a solid.

Of course, to make lollipops, all sorts of colours and flavours are added to the mixture as well, and sometimes more than one mixture is used to create intricate, layered effects. There are even medicinal lollipops which contain, for example, the powerful painkiller fentanyl — the idea being that the patient can administer the dose gradually as needed.

Which brings me to the end. Happy National Lollipop Day! My favourites are Chupa Chups — if you’ve enjoyed this, how about popping over to Ko-fi so I can stock up? And if you’ve been eating sweets, do remember to clean your teeth!


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.

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.


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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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Easy Indicators

Indicator rainbow, reproduced with kind permission of Isobel Everest, @CrocodileChemi1

Recently on Twitter CrocodileChemist (aka Isobel Everest), a senior school science technician (shout out to science technicians, you’re all amazing) shared a fabulous video and photo of a “pH rainbow”.

The effect was achieved by combining various substances with different pH indicators, that is, substances that change colour when mixed with acids or alkalis.

Now, this is completely awesome, but, not something most people could easily reproduce at home, on account of their not having methyl orange or bromothymol blue, or a few other things (that said, if you did want to try, Isobel’s full method, and other indicator art, can be found here).

But fear not, I’ve got this. Well, I’ve got a really, really simple version. Well, actually, I’ve got more of an experiment, but you could make it into more of a rainbow if you wanted. Anyway…

This is what you need:

  • some red cabbage (one leaf is enough)
  • boiling water
  • mug
  • white plate, or laminated piece of white card, or white paper in a punched pocket
  • cling film/clear plastic wrap (if you’re using a plate)
  • mixture of household substances (see below)
  • board marker (optional) or pen
  • plastic pipettes (optional, but do make it easier – easily bought online)

First, make the indicator. There are recipes online, but some of them are over-complicated. All you really need to do is finely chop the red cabbage leaf, put it in a mug, and pour boiling water over it. Leave it to steep and cool down. Don’t accidentally drink it thinking it’s your coffee. Pour off the liquid. Done.

If you use a plate, cover it with cling film

Next, if you’re using a plate, cover it with cling film. There are two reasons for this: firstly, cling film is more hydrophobic (water-repelling) than most well-washed ceramic plates, so you’ll get better droplets. Secondly, if you write on a china plate with a board marker it doesn’t always wash off. Ask me how I know.

Next step: hunt down some household chemicals. I managed to track down oven cleaner, plughole sanitiser, washing up liquid, lemon juice, vinegar, limescale remover and toilet cleaner (note: not bleach – don’t confuse these two substances, one is acid, one is alkali, and they must never be mixed).

Label your plate/laminated card/paper in punched pocket with the names of the household substances.

Place a drop of cabbage indicator by each label. Keep them well spaced so they don’t run into each other. Also, at this stage, keep them fairly small. Leave one alone as a ‘control’. On my plate, it’s in the middle.

Add a drop of each of your household substances and observe the colours!

Red cabbage indicator with various household substances

IMPORTANT SAFETY NOTE: some of these substances are corrosive. The risk is small because you’re only using drops, but if working with children, make sure an adult keeps control of the bottles, and they only have access to a tiny amount. Drip the more caustic substances yourself. Take the opportunity to point out and explain hazard warning labels. Use the same precautions you would use when handling the substance normally, i.e. if you’d usually wear gloves to pick up the bottle, wear gloves. Some of these substances absolutely must not be mixed with each other: keep them all separate.

Here’s a quick summary of what I used:

A useful point to make here is that pH depends on the concentration of hydrogen ions (H+) in the solution. The more hydrogen ions, the more acidic the solution is. In fact, pH is a log scale, which means a change of x10 in hydrogen concentration corresponds to a change of one pH point. In short, the pH of a substance changes with dilution.

Compound Interest’s Cabbage Indicator page (click image for more info)

Which means that if you add enough water to acid, the pH goes up. So, for example, although the pH of pure ethanoic acid is more like 2.4, a dilute vinegar solution is probably closer to 3, or even a bit higher.

Compound Interest, as is usually the case, has a lovely graphic featuring red cabbage indicator. You can see that the colours correspond fairly well, although it does look like my oven cleaner is less alkaline (closer to green) than the plughole sanitiser (closer to yellow).

As the Compound Interest graphic mentions, the colour changes are due to anthocyanin pigments. These are red/blue/purple pigments that occur naturally in plants, and give them a few advantages, one of which is to act as a visual ripeness indicator. For example, the riper a blackberry is, the darker it becomes. That makes it stand out against green foliage, so it’s easier for birds and animals to find it, eat it and go on to spread the seeds. Note that “unripe” colours, yellow-green, are at the alkaline end, which corresponds to bitter flavours. “Ripe” colours, purple-red, are neutral to acidic, corresponding with much more appealing sweet and tart flavours. Isn’t nature clever?

You can make a whole mug full of indicator from a single cabbage leaf (don’t drink it by mistake).

Which brings me to my final point – what if you can’t get red cabbage? Supermarkets are bit… tricky at the moment, after all. Well, try with some other things! Any dark-coloured plant/fruit should work. Blueberries are good (and easy to find frozen). The skins of black grapes or the very dark red bit of a rhubarb stalk are worth a try. Blackberries grow wild in lots of places later in the year. Tomatoes, strawberries and other red fruits will also give colour changes (I’ve talked about strawberries before), although they’re less dramatic.

For those (rightly) concerned about wasting food – you don’t need a lot. I made a whole mug full of cabbage indicator from a single cabbage leaf, and it was the manky brown-around-the-edges one on the outside that was probably destined for compost anyway.

So, off you go, have fun! Stay indoors, learn about indicators, and stay safe.

EDIT: after I posted this, a few people tried some more experiments with fruits, vegetables and plants! Beaulieu Biology posted the amazing grid below, which includes everything from turmeric to radishes:

Image reproduced with kind permission of Beaulieu Biology (click for larger version)

And Compound Interest took some beautiful photos of indicator solutions extracted from a tulip flower, while CrocodileChemist did something similar and used the solutions to make a gorgeous picture of a tree. Check them out!


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.
Buy Me a Coffee at ko-fi.com