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:
Buy Me a Coffee at ko-fi.com

 

 

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:
Buy Me a Coffee at ko-fi.com

 

Freezing fungal farts: what is hair ice and why does it form?

Hair ice, in which ice crystals grow in thread-like structures, can be found at northerly latitudes in broadleaf forests [image source]

I’ve written about water before and in particular, if you’ve been paying very close attention, you might remember that November 12th marks the anniversary of the day, in 1783, that Antoine Lavoisier formally declared water to be a compound rather than an element.

Which means that November is always an excellent time to talk about water. But this time, I’m going to focus on its solid state: ice.

A few days ago I stumbled across some beautiful images of hair ice, which prompted me to make a #272sci Twitter post (keep an eye on that hashtag for similar small bits of interesting science). The story behind hair ice is a fascinating one, and not something I could truly cover in 272 characters – so here’s the slightly longer version…

This form of ice is found on dead wood, and it has a few other names, including ice wool or frost beard. Of course, ice naturally forms at 0 ℃ at standard atmospheric pressure, but the form we’re most familiar with looks, to the naked eye at least, rather more random. In fact, it was snowing here just yesterday, which means I have photos!

Ice crystals on a wall in Oxfordshire, UK, in November 2021

As you can (hopefully) see, there’s some regularity to the individual crystals, but they’re sort of growing all over the place. So, how do ice crystals form, and why?

We need to start with the structure of water. Now, you might imagine that a molecule with the formula H2O would have its atoms arranged in a straight line, like this: H–O–H. But it doesn’t, and the reason it doesn’t is that the oxygen atom in the middle has two pairs of electrons which aren’t involved in bonding – which chemists call ‘lone pairs‘.

Imagine, for a moment, that you have a bunch of balloons made up of two sausage-shaped balloons and two round ones, all attached at the neck. What shape would they make, as a whole? Probably, the two long balloons would form a sort of rough V, and the two round ones would stick out, opposite each other.

If you have some balloons to hand, give it a try. It turns out this is actually a pretty good model for water. We end up with a roughly tetrahedral shape, with oxygen in the middle, hydrogen atoms in two of the corners, and the lone pairs in the other two corners.

The H2O atoms in a water molecule adopt a sort of shallow V shape but, if you consider the lone pairs, the molecule actually forms a rough tetrahedron [image source]

This is important because those lone pairs don’t just sit around doing nothing. The element oxygen is very electronegative, which means it likes to attract bonded electrons. Hydrogen, by contrast, is more electropositive, which essentially means it doesn’t.

The result of this is that, although it is very definitely a covalently-bonded molecule (and not made up of ions), the oxygen atom in water has a partially negative charge, while the hydrogens have a partially-positive charge.

Since positive charges attract negative charges, and since molecules don’t exist in isolation. The result is that the hydrogen atoms in one water molecule are attracted to the oxygens in other water molecules. This is called hydrogen bonding.

If your head is spinning as you try to imagine this, take a look at the image below. White is hydrogen, red is oxygen, and the dashed lines represent the attractions between partially-positive hydrogens and partially-negative oxygens.

Do you see the shapes that form? Yes – hexagons!

When water molecules pack together they form hexagonal shapes [image source]

And how many sides does a snowflake have? Yes – six!

It’s not a coincidence: as the temperature drops, molecules that previously had freedom of movement gradually stop moving so much and pack into these hexagonal shapes. Then, water vapour in the air deposits onto this skeleton and, voilà, we end up with six-sided ice crystals.

Now, normally, this happens fairly randomly. Yes, all the snowflakes are hexagonal (and there are images of the different patterns that can form in this graphic from Compound Interest) but, as my photos of ice crystals suggest, they tend to stick out in all directions.

Hair ice is different. The ‘hairs’ appear at what are called wood rays, that is, lines perpendicular to the growth rings of the wood, and it turns out that if a piece of wood forms hair ice once, it will probably keep producing it – which makes things rather easier for the potential photographer!

Each of the hairs is about 0.02 mm thick and, assuming the temperature doesn’t rise above freezing, they can hang around for hours and even days.

Why does hair ice grow in single, curling strands, rather than forming this more typical ‘bushy’ structure?

Which leads to the question: why don’t more ice crystals grow on top of the threads and break up the hair-like structures? After all, if it’s cold enough for ice, it ought to be cold enough for, well, more ice – oughtn’t it?

A quick aside: you’ve probably heard of Alfred Wegener, discoverer of continental drift – an idea that ultimately led to modern tectonic plate theory. These days, those ideas are pretty universally accepted, but when Wegener first proposed continental drift in 1912, he faced a lot of opposition. There was more than one reason for this, but one major one was that Wegener was seen as an outsider to the field of geophysics. His background was in meteorology and polar research. In other words, he spent a lot of time in cold weather conditions.

Which brings me back to the main, ah, thread (sorry). Alfred Wegener described hair ice on wet dead wood in 1918, having observed it the year before, and suggested that mycelium, the thread-like part of a fungal colony, could be involved. He thought this because he could actually see mycelium on the branch surface, which was confirmed by his consultant, Arthur Meyer. Meyer, however, was unable to definitely identify the fungal species at the time.

Some years later, in 1975, scientists named Mühleisen and Lämmle actually managed to grow hair ice on rotten wood in a climate chamber and later still, in 2005, the physicist Gerhart Wagner again suggested that a fungus was involved, although he had no knowledge of Wegener’s observations when he first did so. He went on to carry out experiments with Christian Mätzler in which they were able to reliably grow hair ice on a balcony on nights with freezing conditions.

A photo of hair ice taken in British Columbia, Canada, by Tiarra Friskie

After lots of painstaking (and cold!) observation, they concluded two things: firstly, hair ice forms from water stored in the wood, not atmospheric water – which goes some way to explaining why the structures aren’t more random, as you’d expect if the ice were forming from water vapour in the air.

Secondly, the fungus, as a product of its metabolism, was generating gas pressure, and that was pushing water through the wood rays to the wood surface, where it was fanning out into fine, curling strands.

So, yes, in a way, hair ice is the product of freezing fungal farts. (Yes, yes, very tenuous, but I couldn’t resist ‘freezing fungal farts’, let me have this one.)

There’s a much more scientific explanation in this 2015 paper, the full text of which is freely available online (lots of great photos too!). The culprit turns out to be a fungus called Exidiopsis effusa. Inside the wood, attractions between the water molecules and the wood surface lower the melting point of water slightly, keeping it liquid. Products of wood decomposition left by the fungus also (probably) help to prevent ice forming inside the wood itself.

Once the outside temperature drops, though, the formation of ice crystals on the outer surface of the wood has the effect of drawing out more water, and the result is that the crystals grown in long, thread-like structures – although the fine details of how the fungus does what it does are still a bit of a mystery. Still, it’s nice to find a not-quite-answered science question, isn’t it?

More hair ice in the wild, by Tiarra Friskie

One final thing: just in case you were thinking, oh, come on, is that first picture really real? On the Chronicle Flask Facebook page, a user named Tiarra Friskie commented that they had pictures of this very phenomenon, taken in British Columbia, Canada, and kindly gave me permission to use them. So, here you are: a tiny bit meltier than the picture above, but nevertheless, two guaranteed genuine photographs of hair ice!

If you live somewhere in the vicinity of the latitudes between 45 and 55 °N (which includes most of the UK, by the way), keep an eye out for rotten wood in your local broadleaf forest – if the weather gets cold enough, you might just spot some hair ice yourself.


A little admin note: the chronicle flask blog is now (yikes) almost nine years and 150 posts old. Life is increasingly busy and so, after December 2021, I’m going to stop making monthly updates. But not to worry! You can still follow the Twitter hashtag #272sci for regular tiny pieces of science, and I’ll pop back every now and then. Oh, and please do consider supporting the Great Explanations book project here!

Plus, 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:
Buy Me a Coffee at ko-fi.com

 

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

fractal image, featuring the hashtag #272sci

Take a look at the Twitter hashtag #272sci

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

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

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

photo of a patch of dead grass

Dog urine damages grass

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

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

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

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

Sample pots full of pale yellow liquid

Fresh urine contains urea, but little ammonia

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

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

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

photo of a dog drinking water

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

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

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

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

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

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

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

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

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


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

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

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

 

Chemical jigsaw puzzles: how do chemists identify molecules?

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

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

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

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

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

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

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

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

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

Photo of MRI equipment

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

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

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

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

Photo of jigsaw pieces

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

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

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

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

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

Photo of white pills

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

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

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

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

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

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

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

Photo of a facemask, syringe and vaccine vials

Please get vaccinated

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

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


Support the Great Explanations book here!

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

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

 

 

Neem: nice, nasty or… not sure?

A few days ago it was sunny and slightly breezy outside (yes, it’s August, but I live in the UK – this isn’t as common as you might imagine) and I thought, I should make the most of this and do something about my orchids.

Now, anyone that reads this blog regularly will know that my Dad is a horticulturist. I, however, am not. My fascination with bright colours, interesting smells and complicated naming conventions went down the chemistry route. But I am, oddly, quite good with Phalaenopsis, aka, moth orchids. I don’t really know why, or how, but I seem to have come to some sort of agreement with the ones that live on my kitchen windowsill. It goes along the lines of: I’ll water you once a week, and you make flowers a couple of times a year, and we’ll otherwise leave each other alone, okay?

Scale bugs secrete honeydew, which encourages the growth of sooty moulds

Well, this was fine for years, until we somehow acquired an infestation of scale bugs. These tiny but extremely annoying pests feed by sucking sap from leaves of plants, and they excrete a sticky substance called honeydew. Trust me, it’s not as nice as it sounds. Firstly, it really is sticky, and makes a horrible mess not just of the orchid leaves, but also the area around the plants.

Then it turns out that certain types of mould just love this stuff, so you end up with black spots on the leaves. And, not surprisingly, all this weakens the plant.

So, what’s the answer? Well, there are several. But the one I tend to default to is neem oil.

This stuff is a vegetable oil from the seeds of the Azadirachta indica, or neem, tree. It has a musty, nutty sort of smell, and is fairly easy to buy.

It’s indigenous to the Indian subcontinent and has been historically important in traditional medicine. In fact, The Sanskrit name of this evergreen tree is ‘Arishtha’, which means ‘reliever of sickness’.

So it’s a natural vegetable oil and people have been using it as a remedy for thousands of years – must be totally safe, right? Right?

Well… I’ve said it before, but some of the very best horribly toxic things are entirely natural, and neem is yet another example. Ingestion of significant quantities can cause metabolic acidosis (finally, something that really does have the potential to change blood pH! Er… but not… in a good way), kidney failure, seizures, and brain damage in children. Skin contact can cause contact dermatitis. It’s been shown to work as a contraceptive and, more problematically, it’s a known abortifacient (causes miscarriage).

Neem oil is easy to buy, but it needs to be handled with caution

All this said, as always, the dose make the poison.

One case study in the Journal of The Association of Physicians of India reported on a 36-year-old man who swallowed 30–50 ml (about three tablespoons) of neem oil, in the hope of treating the corns on his feet. As far as I can tell, it didn’t help his corns. It did cause vomiting, drowsiness, a dangerous drop in blood pH and seizures. There’s no specific antidote for neem poisoning, but the hospital managed his symptoms. Luckily, despite the hammering his kidneys undoubtedly took, he didn’t need dialysis, and was discharged from hospital after just over a week.

Now, okay, you’re unlikely to accidentally swallow three tablespoons of any oil, especially not neem which does have quite a strong, not entirely pleasant, smell and (reportedly – I haven’t tried for obvious reasons) a bitter taste. But nevertheless, it’s wise to be cautious, particularly around children who have a smaller body mass and therefore are much more likely to suffer serious effects – up to and including death. In one reported case, a mother gave a 3-month-old child a teaspoon of neem oil in the hope of curing his indigestion – fortunately he survived, but not without some seriously scary symptoms.

Nimbin, a chemical found in neem oil, is reported to have all sorts of beneficial effects [image source]

Okay, so those are the dangers. Let’s talk chemistry. The Pakistani organic chemist Salimuzzaman Siddiqui is thought to be the first scientist to formally investigate the various compounds in neem oil. In 1942 he extracted three compounds, and identified nimbidin as the main antibacterial substance in neem. He was awarded an OBE in 1946 for his discoveries.

I will confess, at this point, to running into a little bit of confusion with the nomenclature. Nimbidin is described, in some places at least, as a mixture of compounds (collectively, tetranortriterpenes) rather than a single molecule. But either way, it has been shown to have anti-inflammatory properties – at least in rats.

Another of the probably-mostly-good substances in neem is nimbin: a triterpenoid which is reported to have a whole range of positive properties, including acting as an anti-inflammatory, an antipyretic, a fungicide, an antiseptic and even as an antihistamine. Interestingly, I went looking for safety data on nimbin, and I couldn’t find much. That could mean it’s safe, or it could mean it just hasn’t been extensively tested.

Azadirachtin, another chemical found in neem, is a known pesticide [image source]

The substance that seems to do most of the pesticide heavy lifting is azadirachtin. This is a limonoid (compounds that are probably best known for their presence in citrus fruits). It’s what’s called an antifeedant – a substance produced by plants to deter predators from munching on them. Well, mostly. Humans have a strange habit of developing a taste for plants that produce such substances. Take, for example, odoriferous garlic, clears-out-your-sinuses horseradish, and of course the daddy of them all: nicotine.

Azadirachtin is known to affect lots of species of insects, both by acting as an antifeedant and as a growth disruptor. Handily, it’s also biodegradable – and breaks down in a few days when exposed to light and water.

That makes it appealing as a potential pesticide, and it’s also generally described as having low toxicity in mammals – its reported LD50 tends to fall into the grams per kilogram range, which makes it “moderately to slightly toxic“. Wikipedia quotes a value (without a source, as I write this) of >3,540 mg/kg in rats.

But… I did find another page quoting 13 mg/kg in mice. That’s quite dramatically different, and would make it extremely/highly toxic. Unfortunately I couldn’t get my hands on the original source, so I haven’t been able to verify it’s not a transposition error.

Let’s assume it isn’t. It would be odd to have such a big difference between mice and rats. Things that poison mice tend to poison rats, too. There might be some confusion over pure azadirachtin vs. “neem extract” – it could be the case that the mixture of chemicals working together in neem create some sort of synergistic (toxic) effect – greater than the sum of all the individual substances. It could be an experimental error, including a contaminated neem sample, or something to do with the way the animals were exposed to the extract.

Neem soap is widely available online, but that may not be a good thing…

It’s difficult to say. Well, it’s difficult for me to say, because I don’t have access to all the primary sources. (Any toxicologists out there, please do feel free to weigh into the comments section!) But either way, as I’ve already mentioned, several case studies have fingered azadirachtin as one of the substances likely to be causing the well-reported nasty side effects.

If you’re asking this chemist? I say be careful with the stuff. If you decide to use it on your plants, keep it out of reach of children, and wear some good-quality disposable gloves while you’re handling it (I put some on after I took that photo back there). If you’re pregnant, or trying to become pregnant, the safest option is to not use it at all.

Which brings me to neem soap.

Yup. It’s sold as a “natural” treatment for skin conditions like acne. I won’t link to a specific brand, but it’s easy to find multiple retailers with a simple Google search. I looked at one selling soap bars for £6.99 a pop, containing 10% (certified organic, because of course) neem oil. Did I mention back there that neem is known to cause contact dermatitis? I’m fairly sure I did. None of the products I saw had obvious safety warnings, and I certainly found nothing about safety (or otherwise) for pregnant women.

Plus – worryingly, not least because children are more likely to get things in their mouth – you can also buy kids and babies versions, again purporting to contain 10% neem oil.

I even found neem toothpaste. Which… given people often swallow toothpaste… yikes.

My moth orchids are looking much healthier now I’ve got rid of all the scale bugs!

Now again, and for the umpteenth time, the dose makes the poison. The case studies I’ve mentioned involved, at a minimum, swallowing a teaspoon of pure neem oil, and you’re not getting that sort of quantity from smears of toothpaste. But, at the same time, when it comes to pregnancy and babies, it’s generally sensible to apply a precautionary principle, especially for things like soap and toothpaste for which alternatives with well-established safety profiles exist.

Bottom line? Would I use these products? I would not.

But I do use neem to treat the scale bugs on my orchids, and they’re doing much better than they were. Fingers crossed for more flowers!


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

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

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

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

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

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

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

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

Image

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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


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

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

The Skeptic, Chemistry World, and Crash Course: where to find me!

Thanks to Andy Brunning for the fab profile pic – do check out Compound Interest‘s Women In Chemistry series!

It’s been a busy month! Actually, a busy few months, and it occurred to me that some people that follow this blog might have missed some of my other projects. Recently, I’ve written for The Skeptic, Chemistry World, and Crash Course Organic Chemistry.

That’s great, I hear you say, where do we find all this amazing content? Allow me to supply a convenient list!

THE SKEPTIC
Dodgy diagrams in ads matter, if we want people to understand the value of chemistry

A little while ago an advert for a Volkswagen service plan turned up on Twitter with the tagline: “We have a formula for good customer service.” It pictured… [read the rest here]

CHEMISTRY WORLD
Are we giving chemicals bad names?
Back in the distant past – that is, early 1990s – I sat in a dusty lecture theatre, listening to an organic chemistry lecturer as he wrote on a blackboard that rotated in an enormous loop…. [read the rest here]

CRASH COURSE ORGANIC CHEMISTRY
• Episode 22: E1 and E2 Reactions
• Episode 23: Determining SN1, SN2, E1, and E2 Reactions
• Episode 26: How to Identify Molecules – Proton NMR
• Episode 27: An Overview of Aldehydes and Ketones
(There are more of these to come, so watch this space.)

I’ve also been writing content for DK: look out for Super Science, available from 5th August (it’s going to be a really beautiful book).


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

Like the Chronicle Flask’s Facebook page for regular updates, or follow @chronicleflask on Twitter. Content is © Kat Day 2021. You may share or link to anything here, but you must reference this site if you do.
Buy Me a Coffee at ko-fi.com

 

 

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.
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.