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!

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

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

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

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

Oh well, who am I to fight the universe?

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Vitamin A is essential for good eye health.

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

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

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

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

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

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

Our brain interprets electrical signals as vision.

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

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

Just gimme fried chicken 😉


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


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