Puzzling pool problems?

We’re half way thorough the Rio 2016 Olypics, and it will have escaped no one’s notice that there have been a few little problems with one of the pools.

Maria Lenk Aquatic Enter, Tuesday, Aug. 9, 2016. (AP Photo/Matt Dunham)

Maria Lenk Aquatic Enter, Tuesday, Aug. 9, 2016. (AP Photo/Matt Dunham)

First, the water turned a mysterious green colour. Then there were reports of a ‘sulfurous’ smell, with German diver Stephan Feck reported as saying it smelled like a “fart”.

The diving pool seemed to be the worst affected, but the water-polo pool next to it also suffered problems, and competitors complained of stinging eyes.

So what on earth was happening? An early suggestion was that copper salts were contaminating the water. It’s not unheard of for copper compounds to get into water supplies, and it would certainly explain the colour; copper chloride solutions in particular are famously greeny-blue. But what about that sulfurous smell? Copper chloride doesn’t smell of sulfur.

Was the strange pool colour due to algae bloom?

Was the strange pool colour due to an algae bloom, like this one in Lake Erie?

The most likely culprit was some sort of algae bloom – in other words rapid algae growth – with the smell probably coming from dimethyl sulfide, or DMS. There’s a singled-celled phytoplankton called Emiliania huxleyi which is particularly famous for producing this smelly compound. In fact, it actually has more than one very important role in nature: the smell is thought to alert marine life that there’s food nearby, but it also seeps into the atmosphere and helps with cloud formation, helping to control our planet’s temperature. Without these reactions, Earth might not be nearly so habitable.

But how did algae manage to grow in the pool? The pool chemicals should have prevented it, so what had happened? An Olympic official then went on to make the comment that “chemistry is not an exact science,” which of course led to much hilarity all around. Chemistry is, after all, incredibly exact. What chemistry student doesn’t remember all those calculations, with answers to three significant figures? The endless balancing of equations? The careful addition of one solution to another, drop by drop? How much more ‘exact’ would you like it to be?

But I had a bit of sympathy with the official, because I suspect that what they actually meant – if not said – was that swimming pool chemistry is not an exact science. And while that, too, is hardly accurate, it is true that swimming pool chemistry is very complicated and things can easily go wrong, particularly when you’re trying to work on an extremely tight schedule. They could hardly, after all, close down all the pools and spend several days carrying out extensive testing in the middle of the sixteen-day-long Olympic Games.

Rio 2016 Olympics Aquatics Stadium (Image: Myrtha Pools)

Rio 2016 Olympics Aquatics Stadium (Image: Myrtha Pools)

When a pool is first built and filled, things are, theoretically, simple. You know exactly how many cubic litres of water there are, and you know exactly how much of each chemical needs to be added to keep the water free of bacteria and other nasties. Those chemicals are added, possibly (particularly in a pool this size) via some kind of automated system, and the pH is carefully monitored to ensure the water is neither too alkaline (basic) nor too acidic.

There’s a certain amount of proprietary variation of swimming pool chemicals, but it essentially all comes down to chlorine, which has been used to make water safe now for over 120 years.

Originally, water was treated to make it alkaline and then chlorine gas itself was added. This produced compounds which killed bacteria, in particular sodium hypochlorite, but the practice was risky. Chlorine gas is extremely nasty stuff – it has, after all, been used as a chemical weapon – and storing it, not to mention actually using it, was a dangerous business.

However, hundreds of people swimming in untreated water is a recipe for catching all kinds of water-borne disease, so it wasn’t long before alternatives were developed.

The Chemistry of Swimming Pools (Image: Compound Interest - click for more info)

The Chemistry of Swimming Pools (Image: Compound Interest – click graphic for more info)

Those alternatives made use of the chemistry that was happening anyway in the water, but  allowed the dangerous bit, with the elemental chlorine, to happen somewhere else. And so hypochlorite salts began to be manufactured to be used in swimming pools.

As the lovely graphic from Compound Interest illustrates, sodium hypochlorite reacts with water to form hypochlorous acid, which in turn goes on to form hypochlorite ions. These two substances sit in an equilibrium, and both are oxidants, which is good because oxidants are good at blasting bacteria. The equilibria in question are affected by pH though, which is one reason why, quite apart from the potential effects on swimmers, it’s so important to manage the pH of pool water.

There are a couple of different chemicals which can be added to adjust pH. Sodium bicarbonate, for example, can be used to nudge the pH up if needed. On the other hand, sodium bisulfate can be used to lower pH if the water becomes too alkaline.

Open-air pools have particular problems

UV light breaks down the chemicals that are used to keep swimming pool water clean.

This can all be managed extremely precisely in an unused, enclosed pool. But once you open that pool up, things become less simple. Open-air pools have a particular problem with UV light. Chlorine compounds are often sensitive to UV – this is why CFCs are such a problem for the ozone layer – and hypochlorite is no exception. In the presence of UV it breaks down in a process called photolysis to form chloride ions and oxygen. This means that outdoor pools require more frequent treatments, or the addition of extra chemicals to stabilise the ‘free available chlorine’ (FAC) levels.

Sadly, I haven’t managed to make it over to Rio, but from what I’ve seen the Aquatic Centre has a roof which opens up, which means that the pool water is indeed being exposed to UV light.

So perhaps the chemical levels simply dropped too low, which allowed algae to proliferate? Possibly aggravated by environmental conditions? Indeed, initially this seemed to be the explanation. FINA, the international governing body of aquatics, issued a statement on Wednesday afternoon which said:

“FINA can confirm that the reason for the unusual water color observed during the Rio diving competitions is that the water tanks ran out of some of the chemicals used in the water treatment process. As a result, the pH level of the water was outside the usual range, causing the discoloration. The FINA Sport Medicine Committee conducted tests on the water quality and concluded that there was no risk to the health and safety of the athletes, and no reason for the competition to be affected.”

This prompted people to wonder how on earth chemical levels were allowed to run out in an event as significant as the Olympics – did someone forget to click send on the order? – but still, it seemed to explain what had happened.

FINA issued a new statement

FINA issued a new statement on Sunday

Until today (Sunday), when more information surfaced as Olympic officials announced that they were going to drain at least one of the swimming pools and refill it. This is no small feat and will involve considerable cost: after all, we’re talking about millions of gallons of water. But it seems to be necessary. As Rio 2016’s director of venue management Gustavo Nascimento said:

“On the day of the Opening Ceremonies of the Games, 80 litres of hydrogen peroxide was put in the water. This creates a reaction to the chlorine which neutralises the ability of the chlorine to kill organics. This is not a problem for the health of anyone.”

Whoops. Yes indeed. Hydrogen peroxide reacts with chlorine to produce oxygen and hydrochloric acid. In fact, hydrogen peroxide is actually used to dechlorinate water which contains levels of chlorine that are too high. It might not be the very worst thing you could add to the water (when you think of all the things that could end up swimming pools) but it’s definitely up there.

Why and how this happened doesn’t, at the moment, appear to be clear. Presumably someone is for the high jump, and not just on the athletics field.

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Are you ok? You look a little flushed.

PrintYesterday was World Toilet Day (yes, really). This is actually an admirable campaign by WaterAid to raise awareness of the fact that one in three people around the world don’t have access to a safe and private toilet. This, of course, leads to unsanitary conditions which results in the spread of infection and disease. You’ve probably never given it a second thought, but loos literally save lives.


Has the TARDIS’ replicator function gone funny?

So, with the topic of toilets in mind, I started thinking about chemical loos. If you live in the UK, the name Portaloo ® will probably spring to mind. This has practically become a generic word for a portable toilet, but it is (like Hoover, Sellotape and others) actually a brand name. I’m told that in America they call them porta-pottys or honey-buckets, which I rather like. In any case, all the chemicals and plastic make them seem like modern inventions, surely?

Actually, not at all. The idea of a self-contained, moveable toilet that you can pick up and take from place to place may be newer, but people have been using chemical toilets for hundreds of years. For example after, ahem, ‘business’ had been completed in an an old-fashioned wooden outhouse – basically a tall box built over a hole in the ground – the user would sprinkle a little lye or lime down the hole to help with the smell.


Don’t get sodium hydroxide on the toilet seat.

Both of these are strongly basic chemicals. Lye is either sodium hydroxide or potassium hydroxide, and lime is calcium oxide. Both mix with water to form extremely corrosive, alkaline solutions and, incidentally, give out a lot of heat in the process. Both are very damaging to skin. These were the days before health and safety; whatever you did, you had to try not to spill it on the seat.

Urea, a key chemical in urine, reacts with strong alkalis in a process known as alkaline hydrolysis. This produces ammonia, which is pretty stinky (if rather tough on the lungs), so if nothing else that helped to cover up other smells. Ammonia also kills some types of bacteria (which is one reason it’s popular in cleaning products). Flies generally don’t like high concentrations of it either, so that’s another plus.

Alkalis also have another effect in that decomposition of human waste is pH dependent; it works better in acidic conditions. Adding lye or lime raises the pH and slows down this decomposition. On top of this (literally) both lime and lye are hygroscopic: they absorb water. This keeps moisture down and allows a solid ‘crust’ to form on the surface of the waste, making it difficult for any volatile, smelly chemicals to escape. Lovely.

Bleach and ammonia could result in a rocket up your...

Bleach and ammonia could result in a rocket up your…

One word of caution: it’s very, very important you don’t try to clean such an outhouse with any kind of bleach. Bleach, which contains sodium hypochlorite, reacts with ammonia to form hydrogen chloride, chlorine gas and chloramine. None of which are good for your health. Even more dramatically (if this is more dramatic than death – you decide) if there’s lots of ammonia you might get liquid hydrazine, which is used in rocket fuels because it’s explosive. Who knew that toilet chemistry could also be rocket science?

But you don’t find buckets of lye in modern chemical toilets (although, apparently, there are still some people out there using it). So what’s in there? At one time, formaldehyde, otherwise known as methanal, was common. You probably recognise it as embalming fluid; the stuff that Damien Hirst floated that shark in. It’s an extremely effective preservative. Firstly, it kills most bacteria and fungi and destroys viruses, and secondly it causes primary amino groups in proteins to cross-link with other nearby nitrogen atoms, denaturing the proteins and preventing them from breaking down.


Don’t worry, this won’t appear in your chemical toilet.

Interestingly, whilst definitely toxic in high concentrations, formaldehyde is a naturally-occuring chemical. It’s found in the bloodstream of animals, including humans, because it’s involved in normal metabolism. It also appears in fruits and vegetables, notably pears, grapes and shiitake mushrooms. The dose, as they say, makes the poison. I mention this because there are certain campaigners out there who insist it must be completely eliminated from everything, something which is entirely unecessary not to mention probably impossible (just for the hell of it, I’m also going to point out here that an average pear contains considerably more formaldehyde than a dose of vaccine).

All that said, because formaldehyde is extremely toxic in high concentrations, and because it can interfere with the breakdown processes in sewage plants (because it destroys bacteria), formaldehyde isn’t used in toilets so much anymore. In fact, many of the mixtures on sale are explicitly labelled “formaldehyde-free”. Modern formulations are enzyme-based and break down waste by biological activity. They are usually still dyed blue (if you work your way though the colour spectrum, it’s probably the least offensive colour), but usually using food-grade dye. As a result, what’s left afterwards is classed as sewage rather than chemical waste, making it easier to deal with.

Toilet twinning So, this has been brief tour around the fascinating world of toilet chemistry. You’d never have guessed there was so much to it, would you? Now, have you considered twinning your toilet?

Words of woo: what does ‘alkalise’ mean?


‘alkaline’ diets usually revolve around eating lots of fruit and vegetables – no bad thing, but it won’t change your body’s pH

If you hang around in the unscientific chunks of the internet for any length of time, as I find myself doing from time to time, you start to come across certain words that get used over and over. They are usually words that sound very sciency, and they’re being used to make things sound legitimate when, if we’re honest, they’re really not.

One such word is ‘alkalise’ (or ‘alkalize’). I’ve met it often ever since I wrote my post ‘Amazing alkaline lemons?‘. So, what does this word mean?

Good question. Google it, and at least the first three pages of links are about diets and how to ‘alkalise your body’ featuring such pithy lines as:

“It’s not really a diet… it’s a way of eating” (is there a difference?)
“Alkalise or live a life of misery” (gosh)
“Alkalise or die” (blimey)
“Alkaline water” (apparently this is a thing)
“Why it’s important to alkalise your water” (using our overpriced products)

In fact, I had to click through several pages of Google links before I even got to something that was simply a definition. (I’m aware that Google personalises its search results, so if you try this yourself you might have a different experience.) Certainly, there are no legitimate chemistry, biochemistry – or anything else like that – articles in sight.

Hunt specifically for a definition and you get turn basic and less acidic; “the solution alkalized”‘ (The Free Dictionary), to make or become alkaline. (Dictionary.com) and, simply, ‘to make alkaline’ (Collins).


pH 7 is neutral, more than 7 is basic

The first of these is interesting, because it refers to ‘basic’. Now, as I’ve explained in another post, bases and alkalis are not quite the same thing. In chemistry a base is, in simple terms, anything that can neutralise an acid. Alkalis, on the other hand, are a small subset of this group of compounds: specifically the soluble, basic, ionic salts of alkali metals or alkaline earth metals.

Since there are only six alkali metals (only five that are stable) and only six alkaline earth metals (the last of which is radium – probably best you steer clear of radium compounds) there are a rather limited number of alkalis, namely: lithium hydroxide, sodium hydroxide, potassium hydroxide, rubidium hydroxide, caesium hydroxide, beryllium hydroxide, magnesium hydroxide, calcium hydroxide, strontium hydroxide, barium hydroxide and radium hydroxide. There you go. That’s it. That’s all of them. (Okay, yes, under the ‘soluble in water’ definition we could also include ammonium hydroxide, formed by dissolving the base, ammonia, in water – that opens up a few more.)

This, you see, is why real chemists tend not to use the term ‘alkalise’ very often. Because, unless the thing you’re starting with does actually form one of these hydroxides (there are some examples, mostly involving construction materials), it’s a little bit lead-into-gold-y, and chemists hate that. The whole not changing one element into another thing (barring nuclear reactions, obviously) is quite fundamental to chemistry. That’s why your chemistry teacher spent hours forcing you to balance equations at school.

No, the relevant chemistry word is ‘basify‘. This is such a little-known word that even my spell checker complains, but it’s just the opposite of the slightly better-known ‘acidify’ – in other words, basify means to raise the pH of something by adding something basic to it. Google ‘basify’ and you get a very different result to that from ‘alkalise’. The first several links are dictionary definitions and grammar references, and after that it quickly gets into proper chemistry (although I did spot one that said ‘how to basify your urine’ – sigh).

What does all this mean? Well, if you see someone using the word “alkalising” it should raise red flags. I’d suggest that unless they’re about to go on to discuss cement (calcium hydroxide is an important ingredient in construction materials) cocoa production or, possibly, certain paint pigments, then you can probably write off the next few things they say as total nonsense. If they’re not discussing one of the above topics, the chances are good that what they actually know about chemistry could safely fit on the back of a postage stamp, with space to spare, so nod, smile and make your escape.

For the record, you absolutely don’t need to alkalise your diet. Or your urine*. Really. You don’t.

And please don’t waste your money on alkaline water.


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There’s no good evidence that drinking lemon juice has a significant impact on urine pH.

* In the event that you actually have problematically acidic urine, perhaps due to some medical condition, there are proven treatments that will neutralise it (i.e. take it to around pH 7, which is the pH urine ought to be, roughly). In particular, sodium citrate powder can be dissolved in water to form a drinkable solution. Of course, if this is due to an infection you should see a doctor: you might need antibiotics – urinary tract infections can turn nasty. Yes, I am aware that the salt of the (citric) acid in lemons is sodium citrate, however there is no good evidence that drinking lemon juice actually raises urine pH by a significant amount. And yes, I’m also aware that dietary intake of citrate is known to inhibit the formation of calcium oxalate and calcium phosphate kidney stones, but that’s a whole other thing. If you have kidney stones there are a number of dietary considerations to make, not least of which might be to cut down on your consumption of certain fruits and vegetables such as strawberries and spinach (and ironically, if you look at some of the – entirely unscientific – lists of acid-forming and alkali-forming foods these are almost always on the alkaline side).

Basic Chemistry


The other end of the pH scale.

When you start writing a blog it’s hard to predict what people will find most interesting. Inevitably, it’s not what you expected. For example, two of The Chronicle Flask’s most-read posts are about rhubarb and lemons. Perhaps people are more interested in fruit than I ever imagined. Or perhaps I’m getting a lot of hits from people mistakenly looking for recipes.

Or maybe it’s because both feature the ever-interesting topic of acids. In which case, I should probably write something else about acids.

So, this is a post about bases.

Just in case this spectacular bit of contrariness isn’t immediately obvious, bases – some of which are called alkalis (I’m coming to that in a minute) – are at the other end of the pH scale to acids. Acids are the things with a pH value of less than 7, and bases have pH values of more than 7. So basically (hoho), they’re the opposites of acids.

whysoblueI’m using the word base deliberately, and not just because of all the brilliant chemistry puns you can make with it. The more familiar word is probably alkali, but while all alkalis are bases, not all bases are alkalis.

Alkalis are often described as soluble bases. More precisely, alkalis are produced from the metals in group 1 (the ‘alkali’ metals) and group 2 (the ‘alkaline earth’ metals) of the periodic table. The more general term, base, applies to anything that can neutralise an acid. Chemists have another definition: a base is a proton (H+ ion) acceptor, while acids are proton donors (actually chemists have yet another definition, but the proton acceptor one is the one that gets trotted out most often).

The distinction between alkalis and bases does matter to chemists and the two types of substance usually look quite different – bases tend to come in solid lumps or powders (baking soda, for example) and alkalis are more likely to arrive as a solution in a bottle – but in terms of chemistry they both get involved in the same type of chemical reaction, which is neutralising acids.

Indigestion tablet advertWe make use of this all the time, whether we realise it or not. For example if you’re suffering from acid indigestion you probably reach for the indigestion tablets. An advertising campaign for a particular brand of these says that they “turn excess acid into water and other natural substances”. Those ‘natural substances’ are salts – presumably it was decided that the word ‘salt’ had too many negative connotations (which is probably true: how many people would pop a pill that promised to turn into salt in their tummy?) The main ingredient in the tablets in question is calcium carbonate; a base that reacts with stomach acid to produce calcium chloride. Which is definitely a salt, if not the one most people think of when they hear the word.

Tangentially, calcium chloride is also a food additive with the E number E509. It falls into the category of anti-caking agents, which is sort of funny when you think about it.

Anyhoo, that’s one place you use a base (rhyming now as well as punning, sorry). You’re actually making one yourself every time you eat, because your liver produces a substance called bile (bloggers love bile) which helpfully neutralises the acid your stomach produces. If it didn’t, your intestines would get damaged by that acid, so it’s important stuff.

Interestingly, in a lot of the older medical traditions (you know, swallow three leeches with meals, turn around three times under a full moon and bury a toad under a horseradish in a mock turtle) the body’s health depended on the balance of four ‘humors’, or vital fluids: blood, phlegm, ‘yellow bile‘ (choler), and ‘black bile‘. If you had too much of the last two, it was supposed to cause aggression and depression, and in fact the Greek names for them are the root of the words cholera and melancholia.

It’s interesting that in the 21st century many people are obsessed with ‘alkalinizing‘ the body (just check out the comments on that lemons post) when for thousands of years people have understood that too much alkali is probably a bad thing. Public understanding of science has really moved on hasn’t it?

soapBile does something else that’s really quite important in the body, it helps you to digest fats. Bases are generally really good at breaking down fats. This is another thing that’s been known for quite a while, ever since soap was first discovered about (sources vary quite considerably on this) six thousand years ago. Soap is made by a process of saponification, in which fats react with a strong base, usually sodium hydroxide (otherwise known as caustic soda, or sometimes lye). This breaks apart the fat molecules to make glycerol and carboxylate salts (they’re the soap bit). Because of this use, sodium hydroxide features in a famous, and rather gruesome scene, in the film Fight Club.


The fire diamond for NaOH

Because bases are so good at breaking down fats they’re actually surprisingly (or not, if you’ve just watched that Fight Club clip)dangerous, especially because they’re also quite good at breaking down proteins. Your skin is mostly fat and protein, so they can do quite a bit of damage. Remember fire diamonds? The one for sodium hydroxide has a 3 in the blue box, which means that short exposure could cause ‘serious temporary’ or ‘moderate residual’ injury – yikes.

Corrosive hazard symbol

Corrosive hazard symbol

The European hazard symbol is even more alarming, featuring a hand with holes being burned through it. Of course, acids have symbols like these too, but people sort of expect acids to do this kind of stuff. Whereas they’re often (unless they’re chemists) strangely unaware of the dangers of alkalis. For example there’s the a famous, and gruesome, story of the serial killer John George Haigh, who famously dissolved the bodies of his victims in oil drums full of concentrated sulfuric acid. It worked quite well, but he was caught eventually when the police searched his workshop and found sludge containing three human gallstones and part of a denture.

Sulfuric acid is a particularly powerful acid, and is undoubtedly incredibly dangerous stuff, but sodium hydroxide is not much safer. It will cause instantaneous and serious burns, and solid sodium hydroxide gets incredibly hot if it’s added to water. In fact, the water will quickly boil if you’re not careful.

In May last year American Carmen Blandin Tarleton was in the news because she had just received a face transplant. She needed it because her estranged husband had doused her with concentrated sodium hydroxide six years previously. She had undergone fifty-five operations before she made the decision to get the transplant. The pictures are really quite horrific. I won’t reproduce one here; you can see the result of the attack if you follow the link above. Tarleton has also written a book about her experiences. She was left blind and horribly disfigured, with burns to 80% of her body. Doctors described it as “the most horrific injury a human being could suffer”. Sodium hydroxide is not nice stuff.

It’s surprisingly, shockingly, easy to buy sodium hydroxide. Because it’s used in soap-making, you can get it quite easily. It’s even available on Amazon. And of course it’s an ingredient in lots of drain cleaners available in supermarkets. When they say you should wear gloves to handle this stuff, it’s definitely not health and safety gone mad. You really should. Even I would (and I’m really bad about wearing gloves).

So spare a thought for bases. They’re just as interesting, and certainly no nicer or safer than their acidic cousins. In fact, they’re so good at breaking down fat and protein that they could arguably be more dangerous. And next time you’re cleaning out your oven, do remember to wear your gloves.