Post 150: Choice Chronicles of the Chronicle Flask

From citric to hydrofluoric, acids are an ever-popular topic

I began this blog in 2013, and since then I’ve written at least one post a month. This will be the 150th.

I put love and care into all my posts and, in turn, this blog has been good to me. Although no one’s ever paid me to write it, it has brought me work over the years – many people have asked me to write for them having read things here. But life is busier now than it’s ever been, and it’s time to wind things down. You’ll continue to find my non-fiction here and there, I’ll still be regularly updating my fiction blog, and if you want the latest info, look me up on Twitter. In particular, check out the #272sci hashtag for tiny bits of bite-sized science.

In the meantime, how about a little reminder of some of this blog’s most popular, most important, or just my favourite, posts? Let’s go!

The acid that really does eat through everything (2013)
Turns out, everyone loves acid – this post is one of my all-time most viewed. I guess there’s just something compelling about substances that can dissolve metal, and this one is particular special (and terrifying) for its ability to also dissolve glass and ceramic. (Oh, and sorry about the double spaces after the full stops. It was a long time ago. I know better now.)

Butyric acid, a very smelly molecule (2014)
On the subject of acids, this has been another popular post. I suppose if there’s anything more fun than an acid that eats through the bottle you’re trying to store it in, it’s an acid that smells of Parmesan and vomit. Seriously, it is an interesting one: we’re all familiar with the smell of ethanoic acid (aka acetic acid, found in vinegar), and propanoic acid (propionic acid) merely smells a bit sweaty, but add one more carbon and, hoo boy, you have an utterly revolting stench that some people are so sensitive to they can still detect it weeks, even months, after cleaning.

It’s important to understand what sugar actually is if you want to reduce your intake

Sugar that’s not sugar? (2015)
People talk a lot of nonsense about sugar. A particular pet hate of mine is people calling products sugar-free when they’re nothing of the sort, or implying that the type of sugary ingredient they’ve put in the thing they’re trying to sell you is somehow extra-healthy. If actually reducing your sugar intake is your goal (and it’s not a terrible one), this piece might help.

MMS and CD chemistry – the facts (2016)
This is my simple explainer about MMS (‘miracle’ or ‘master’ mineral solution) and CD (chlorine dioxide). This horrible, nasty fad seems to have faded away in recent years – partly thanks to the fact that even its founder, Jim Humble, admitted it cures nothing – but then again, I have seen CD-MMS linked to pseudoscientific Covid ‘cures’. Let’s hope this post continues to do its job as a useful reference for anyone that needs it.

Absurd alkaline ideas – history, horror and jail time (2017)
Continuing the theme of health, I’ve written several posts about so-called ‘alkaline’ diets, and this isn’t the most popular (that would be Amazing Alkaline Lemons?) but this is the one I wish more people would read. It explains where the whole silly notion came from in the first place. (As does this Twitter thread, slightly more succinctly.)

There really is no need to panic about slime

No need for slime panic: it’s not going to poison anyone (2018)
I’ve yet to meet a child who doesn’t love slime, and every now and then the gooey stuff becomes so popular that we start to see scare stories. So it was in 2018. However, with a few sensible precautions, slime really isn’t dangerous. It’s all explained here.

Let’s speed up the rate at which we recognise our female chemists (2019)
This one was all about the little-known Elizabeth Fulhame. She was the first chemist to describe catalytic reactions – in 1794, when the more famous Berzelius was a mere teenager. Let’s remember her name.

Chemical connections: dexamethasone, hydroxychloroquine and rheumatoid arthritis (2020)
Covid hit us in 2020, and it would prompt more than one post – including this one when dexamethasone had its moment in the spotlight. Probably an unfamiliar drug to most people before this point, dexamethasone was one of the first practical treatments for rheumatoid arthritis in the mid-20th century. Unlike some other much-hyped treatments, we have solid evidence for the effectiveness of this medicine – although it is really only useful for people suffering with very severe symptoms. Still, it’s pretty cool that an old drug turned out to be such a useful tool in a modern pandemic.

There’s chemistry in your skin

Sunshine, skin chemistry, and vitamin D (2020)
To make it a nice, round ten, I’ll sneak in another 2020 post. This one is all about vitamin D. A lot of people are very critical of supplements, and while I understand their position, this particular case is slightly different. If you live in certain parts of the world, you really, really should be considering vitamin D supplementation for at least part of the year, and this post will tell you why.

Brilliant Bee Chemistry! (2021)
This one wasn’t so long ago, but I love it. Bees are fascinating creatures, and if you don’t know what the connection between bees and bananas is, you ought to have a read.


So, this is it, folks – thank you, it’s been fun! Happy New Year!

Content is © Kat Day 2022. You may share or link to anything here, but you must reference this site if you do. You can still 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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The Chronicles of the Chronicle Flask: 2021

In January I wrote about a nasal spray that could prevent COVID-19 infections

It’s Christmas 2021, everyone. Can you believe it? It feels like it’s been 2020 for about five years now, doesn’t it? Anyway, regular followers will know that each year in December I write a ‘Chronicles’ post summing up everything I’ve written about over the year.

But before I get into my time machine and set the dial for January 2021 (the sacrifices I make in the name of science communication, honestly), a quick reminder to check out the #272Sci tag on Twitter for tiny science updates and, for Christmas, #272SciXmas. As I write this, I’ve just done eggnog – yum! Oh, and one more thing, if you’re looking for something to keep the children, and yourself, occupied over the holiday break, why not download some STEM Heroes colouring pages, courtesy of Dr Kit Chapman?

So, without further ado, let’s talk about January! Covid-19 was, and of course is, still very much on everyone’s minds, and this post featured talk of a nasal spray designed to be used regularly to prevent infection. What happened to that, you ask? Well, it hasn’t disappeared! It looks as though some countries are now at the stage of approving sales of the spray, so it may begin to become available sometime in 2022…

February featured light, vision and carrots, which is a less idiosyncratic combination than you might imagine. The Crash Course Organic Chemistry episode that I’d been working on at the time has also just made its way into the world. Check it out!

In March, following some online debate about Covid-19 vaccine ingredients, I took a look at chemical names. Lots of chemicals have similar-sounding names, and there are good reasons for that, but it doesn’t mean they have the same properties. Be wary of anyone trying to imply otherwise…

April was a fragrant tale, with gratuitous butterfly pics

This brings us to April, which is when the Viburnum carlesii bush outside my front door always flowers, bringing its gorgeous scent with it. This was one of my favourite sorts of posts, where chemistry turns out to be a path between umpteen topics – in this case, flowers, butterflies, fragrance molecules, an anaesthetic used to help Covid patients, history, and back to chemical names again. And it gave me an excuse to include lots of butterfly photos, too!

Continuing the nature theme, in May my Dad came across some swarming bees, so it was time to talk about them. Do you know why it might be unwise to eat bananas around bees? You will if you read this!

In June I was a little pushed for time, and so it ended up being a summary of things I’d written recently for The Skeptic, Chemistry World, Crash Course Organic Chemistry and DK Super Science. It’s awesome to see projects out in the wild.

It was back to COVID-19 science in July, as I (along with Mark Lorch) took a look at lateral flow tests, and reports of teenagers finding ways to get fake positive results…

For August I wrote about something I was surprised I hadn’t covered before – neem oil. My orchids are doing rather well, since you ask 😉 One of them is just about to flower again!

Following a little Twitter spat (always a good source of inspiration) September became about how chemists identify molecules, and the skill involved in putting the pieces of these chemical jigsaws together. To mash together a few different quotes: just because you don’t know how it’s done, doesn’t mean someone else is using nefarious magic.

October felt like the time for something light-hearted, so I turned the spotlight on ‘dog rocks’. Can putting rocks in your dog’s water bowl protect your lawn? Short answer: no. But it was fun pulling this one apart. Oh, and as I mentioned at the start, October was also when I started #272Sci – if you’re a Twitter user, check that out!

No, it’s not some sort of weird Guinea pig: it’s ice. But why, and how, does it look like this? Well…

Which brings us to November, back to nature, and what might just be one of my all-time favourites: freezing fungal farts! Have a read – I really enjoyed this one.

And now it’s December! Along with Andy Brunning of Compound Interest I’ve been making daily advent-themed science tweets. As I said in the November post, I intend to wind up the regular monthly blog posts this year. Life has got busy, but it’s all good – I’m excited to see what 2022 will bring. Speaking of which, please do consider supporting the Great Explanations book project here!

But I’m not quite done, because after this I’ll be on post 150, and that seems like a milestone I shouldn’t miss. So, for New Year, I’ll be back with a ‘all time most popular’ post. Watch this space.

In the meantime, I wish you a lovely, and peaceful, Christmas!


Since you’re here, why not take a look at my fiction blog: the fiction phial? And you can also find me doing various flavours of editor-type-stuff at the horror podcast, PseudoPod.org – so head over there, too!

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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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 😄


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A natural remedy that’s full of chemicals?

Blossoms

The summer holidays are here! A time when parents of small children find themselves exploring every park in their local vicinity, quite probably several times (whilst hoping against hope that it doesn’t rain). On just such a quest myself, I recently visited one particular park that was filled with a gorgeous smell.

What was it? A bit of sniffing around quickly identified this tree. Now, I am not a botanist (or even much of a gardener), so I immediately resorted to the rather wonderful Seek app by iNaturalist, which uses some very clever image recognition software to identify plants and animals (disclaimer: accuracy is not guaranteed — don’t eat anything based on this app!)

Seek told me that this was a lime tree, or a linden (genus Tilia). A bit of cross-referencing (thanks Dad!) suggested that it had identified the tree correctly. It’s not an uncommon plant: you’ll probably come across it yourself if you go looking (or smelling).

The name ‘linden’ was more familiar to me. The wood is soft and easily worked, and is used to make musical instruments because it has good acoustic properties. It’s also used to make wooden blinds and other pieces of furniture because it’s lightweight, stable, and holds stains and finishes well.

Linden blossoms can be used to make tea.

But let’s go back to the flowers and their delicious scent. The tree blooms during July and August in the Northern hemisphere. The flowers are sometimes described as mucilaginous — which is a fabulous word meaning, basically, thick and sticky. More specifically: “containing a polysaccharide substance that is extracted as a viscous or gelatinous solution and used in medicines and adhesives.”

Linden flowers are a ‘natural remedy’ with a list of applications in herbal medicine as long as your arm. They contain lots of different substances. One that comes up a lot is farnesol, which is actually a type of alcohol. Of course, it’s nothing like the alcohol we’re familiar with from drinks, which is the much simpler ethanol — but it’s important to remember that ‘alcohol’ actually refers to a class of compounds (which, in simple terms, contain an -OH group like the one in the image here) and not a single substance.

The chemical structure of farnesol

Farnesol turns up in lots of essential oils, such as citronella, rose and lemon grass. It’s used in perfumes to enhance floral scents. But plants don’t make substances just to please humans (well, it’s complicated…). It acts as a pheromone for several insects. Sometimes this doesn’t work out so well for the insects, as it confuses their mating behaviour and effectively acts as a natural pesticide. On the other hand, it actively encourages others: bumblebees release farnesol when they return to the hive to spur other bees into action. It’s the bee equivalent of shouting, ‘oi! Move it you lot, pollen this way!’

Farnesol acts as a pheromone for bumblebees.

Linden flowers also contain one of my all-time favourite chemicals, benzaldehyde. That’s the one that smells of almonds and isn’t a deadly cyanide salt. Its delicious almondy-ness is the reason it’s used as a flavouring and scent, but it’s also a starting material for loads of different chemicals, for example the dye malachite green, which is used to give a green colour to leather, fabric and paper. A form of this dye called ‘brilliant green‘ is mixed with a second, violet, dye to make ‘Bonney’s blue,’ a disinfectant dye used to mark skin for surgeries. Benzaldehyde is also used to make styrene, which is of course used to make the well-known packing material, polystyrene.

And these are just a couple of the substances found in those yummy-smelling flowers. They also contain arabinogalactans, uronic acid, tannins, rutin, hyperoside, quercitrin, isoquercitrin, astragalin and others. In short, a veritable cocktail of different chemicals.

So next time you smell the scent of a lovely flower, just think about all the amazing chemical substances the plant is making. All natural, of course!


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