Running Off to Join the Circus


This blog went silent for a little while there, and now returns with big news for this blogger!

I got a last-minute offer to join the Shell Questacon Science Circus/ANU Master of Science Communication (Outreach) programme, and dropped off the air to organise my life for the interstate move this involved.

Click the image above to see the Shell Questacon Science Circus site and check out our tour details for the year.

Note that this is still a personal blog and has no official affiliation with or support from Shell, Questacon, or the Australian National University.

Word of the Day: Aromatic

Here’s an experiment for you: ask a stranger to tell you about something organic and aromatic. Most people will probably look at you strangely and tell you about some beautiful pesticide-free roses, or an expensive boutique wine, If, however, they just say “benzene?”, you’ve probably found yourself a chemist.

Aromatic molecules are a sub-group of organic molecules with at least part of their structure made up of atoms (usually most or all of them being carbon) arranged in a ring with some particular features.

A few different ways of representing the common aromatic molecule, benzene.

A few different ways of representing the common aromatic molecule, benzene.

The hourglass shapes on the representation second along on the bottom row above are p-orbitals, the areas where the electrons that make double bonds are. Note that every atom in the ring has one, and the lobes of the hourglass shapes are perpendicular to the plane of the ring. The number of electrons in p-orbitals around the ring must satisfy Hückel’s Rule; that is, there must be 4n + 2 of them, where n is some positive integer, or zero.

Aromaticity matters because aromatic units are flat, rigid, and extremely stable, which gives them particular, useful chemical properties. Three of the twenty amino acids that form the basic chemistry of living things are aromatic, and so are all the nucleotides in DNA and RNA.

Their flatness, rigidity, and common features with DNA does make some aromatic compounds particularly harmful to living things. You may have heard of polycyclic aromatic hydrocarbons, or PAHs, a byproduct of burning anything from fossil fuels to firewood. Some of these are harmless, but the particular shape of others makes them especially dangerous. Benzo[a]pyrene is one example; it gets inserted into DNA causing mutations which may in turn cause cancer. It is one of the many compounds in cigarette smoke that appears to be involved in the link between smoking and cancers of the respiratory system. (Science 18 October 1996: Vol. 274 no. 5286 pp. 430-432)

Benzo[a]pyrene: it'll really ruin your whole week.

Benzo[a]pyrene: it’ll really ruin your whole week.

Aromatic molecules were probably originally so named because some of the first ones discovered did have strong, distinctive aromas, but most don’t have this feature, and most strongly odorous molecules aren’t organic — they’re far more likely to be terpines or esters… or something else entirely.

One of the handful of aromatics which are aromatic in the other sense: Naphtalene, the smelly component of mothballs.

Thank you to Chris P. for the suggestion, and to the UC Davis ChemWiki and Chris P. for the refresher on the four conditions for aromaticity and Hückel’s Rule.

What colour are electrons?

This isn’t the flippant question it may look like.

“Colour” is a property of subatomic particles, a lot like electrical charge. It has absolutely nothing to do with colour in the normal sense. Just as charge leads to interactions via electromagnetic forces, so colour leads to interactions via so-called strong forces.

Taking that back another step: there are four fundamental forces of nature. The two of them that you are extremely familiar with are the electromagnetic and gravitational forces. These are long-range forces; they act over large distances. The other two, the weak and strong forces, act on the atomic and subatomic scale, so you only encounter their effects in a very indirect way. The strong force is particularly important as it’s the force that sticks the protons and neutrons in the nuclei of atoms together. (You wouldn’t otherwise expect nuclei to stick together; the electromagnetic interactions are between positively charged protons, so they are repulsive, and gravity is far too weak to fight against this. In fact, the strong force gets its name because it needs to be very strong to hold nuclei together.)

Charges come in two types: positive and negative. The charges give rise to electromagnetic fields, which in turn result in electromagnetic forces being exerted on other objects with charge.

Colour is a little different: it comes in three types. This is why the “colour” label is so convenient; our eyes see in combinations of three colours. Colour displays use three colours. So, colour’s equivalent to positive and negative are labelled as red, green, and blue.

This doesn’t mean that a “blue” particle is blue in any visible sense, it’s just a label.

The strong field produced by a particle of some colour gives rise to an attractive force acting on particles of the other two colours, and a repulsive force acting on quarks of the same colour.

Antimatter particles come in slightly different colours. Where the anti-charge is just the charge of the opposite sign, (e.g. an antielectron is the positively charged positron) anti-colour is… well, anti-colour. The anti-particle of something red would be antired, which is different from blue or green. Coloured particles clump together to make bigger particles in a way that makes the bigger particle “white”, by making red-green-blue (or antired-antigreen-antiblue) trios or by pairing a colour and its anticolour.

Not all particles have colour, just as not all particles have charge. Things without colour are called colourless.

Only two groups of particles do have colour: quarks and gluons. Quarks are the fundamental particles which stick together in trios to make things like protons and neutrons, part of a larger group referred to as baryons, and pairs to make things like pions and kaons, part of the larger group called mesons. Gluons belong to a class of particle called the gauge bosons. Basically, though, a gluon is to the strong force what a photon of electomagnetic radiation is to the electromagnetic force.

Electrons belong in none of these categories: they are not baryons, they are not mesons, and they are not gluons. (The class electrons belong in happen to be called leptons.)

Electrons also don’t scatter light to give rise to colour in the usual sense; while a bound electron may absorb and emit coloured light depending on the state it’s sitting in within the atom or material it’s bound up in, that’s indicative of the energy difference between a pair of states and has nothing really to do with a fundamental property of the electron itself.

So to answer the question we started with, electrons are colourless, both in the normal and the quantum mechanical sense.

Word of the Day: Organic

Organic seems to be the word of the decade, it seems. In common usage, it refers to a particular philosophy of food and natural fiber production, involving limiting processing of the product, favouring naturally-derived fertilisers and pesticides, and so on. The concept gives people the warm-and-fuzzies, so it’s also used a fair bit as a marketing device. Anyone with a bit of background in chemistry has probably had a good laugh — or a small fit of rage, either way — at “organic salt” and bottled “organic water”.

What’s the joke?

Well, to a scientist, especially a chemist, “organic” means “contains carbon.”

… okay, there are a small handful of specific exceptions to that: carbon monoxide, carbon dioxide, cyanides, carbides, and carbonate salts behave too differently to other carbon-containing chemicals, so they’re classified as inorganic, but anything else with carbon in its structure that you care to name is organic, from methane to DNA to ethanol to polystyrene.

Salt is sodium chloride — no carbon. Water is an oxygen atom with two hydrogen “mickey mouse ears” bonded to it. Not organic.

On the other hand, all food and fiber is made up of predominantly organic components. Or the interesting parts are, at least. Most food is mostly water, really.

So, if you’re a chemist, regadless of your stance on the organic food and fibre philosophy, the “organic” craze is quite a laugh.

States of Matter: Amorphous Solids

At some point during your science studies, you would have been introduced to the idea of The Three States of Matter: solid, liquid, and gas. As you may have realised when thinking about, for example, the melting of glass, or contemplating the nature of a flame, this three state model doesn’t tell the whole story. Solid, liquid, and gas are more like three categories into which more specific states of matter fit. This series explores some of these states which perhaps don’t seem to fit neatly into the three states model as you may have learned it.

There is a pervasive, persistent, and entirely incorrect idea that glass is an extremely high viscosity liquid. The reason this comes about makes a certain amount of sense: glass has the same chemical composition as crystalline quartz, but has a liquid-like lack of long-range order.

The associated claim that glass does flow over time is incorrect. “Evidence” is given by pointing out that early glass windows tend to be thicker at the bottom. This “evidence” is actually incorrectly attributed: glass panes with anything resembling a truly uniform thickness are a very recent advance. Until the early twentieth century, the only way to make a nearly flat sheet of glass was to start by blowing a globe or cylinder, then squashing it flat while it is still hot, either directly down onto itself or after cutting the shape open. The result is a glass pane with significant thickness variations, including typically one edge being thicker than the rest. Logically, these windows were usually installed with the thicker, heavier edge at the bottom. The idea that the glass of the windows has flowed down over time is completely contradicted by the fact that there are occasional examples of these glass panes being installed with the thick edge at the top or on one of the sides.

Glass does not flow until you heat it up past its glass–liquid transition temperature (almost the same as a melting point, more on that shortly.) Glass has both a fixed volume and a fixed shape. The only thing that glass has in common with a liquid is that disorder of its atoms. Even then, the atoms vibrate around fixed positions, as is typical of a solid, rather than moving relatively freely as they would in a liquid.

Glass is a solid.

It is, however, part of a class of solids that often get neglected. It is a perfect example of an amorphous solid.

Continue reading


After another wave on my facebook feed of shared articles expressing concern, derision, and even outright fear over the diagnostic criteria given in the Diagnostic and Statistical Manual of Mental Disorders (DSM), currently in its fifth edition, I feel the need to write a little something here.

The DSM is essentially not much more than a means of linking a set of pathological traits with a shorthand definition. This can be useful when communicating between different health professionals or to health insurance companies, and when gathering statistics and conducting research on mental illness. It doesn’t generate new diseases, really, just labels to quickly describe observed illnesses.

The DSM itself explains that for something to be a mental illness, well, it has to cause illness — it needs to be “associated with present distress[…]or disability[…]or with a significant increased risk of suffering.”
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Word of the Day: Degenerate

There are many words which take a very different meaning in their scientific context to what they might mean in everyday use.

One that can cause a little bit of shock, then perhaps a giggle, is “degenerate”, used as an adjective.

Usually when you call someone or something degenerate, you are being insulting. It has connotations of stupidity, inferiority, degredation. In science, it can be much more innocent.

If you’re in physics or chemistry class and a pair or set of things get called “degenerate”, all it means is that they have the same amount of energy. So, there’s nothing wrong with a pair of degenerate electrons, they are just two electrons hanging out with the same energy.