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.


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.

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.

Word of the Day: Massive

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

One which always amuses me a little is “massive”.

Normally, when you call something massive, you mean it’s really rather large. You might look at me in bemusement if I call an electron “massive”. You may wonder what on earth an electron is big compared to. (The answer to that is: nothing, really. The electron is generally considered to be a point particle.)

What I actually mean is that the electron has mass. An electron is massive. An atom is You are massive. A photon is massless.

Massive: it doesn’t have to be big, it just has to have a non-zero mass.

Word of the Day: Law

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

Among these is “law”. When we talk about a law of science, we don’t mean “one of the strongest rules of science”. A law is simply a (often mathematical) description of something that happens. The law of conservation of energy (or mass-energy for those who are learning about mass-energy equivalence) is: “energy cannot be created or destroyed, only transformed.” Mathematically you can write that same thing as

ΔE = 0

It doesn’t tell you how the energy is conserved or transformed or anything, just that it is. (You’d need a theory to explain the mechanism!)

Laws can be changed. Laws can break down or fail to apply under particular unforseen circumstances. For example, Newton’s Laws of Motion are incorrect when you start comparing things moving close to the speed of light relative to each other, but they are still laws… they just don’t apply under some circumstances.

Principles serve the same purpose as laws; for example, Archimedes’ Principle, or The Principle of Least Action.

Word of the Day: Theory

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

One such word that causes an awful lot of confusion is “theory”. As in, “theory of plate tectonics” or “theory of quantum electrodynamics“, but also as in “it’s just a theory, but…”

When people talk about having a theory in everyday language, usually they mean a hypothesis with very little evidence to back it up. A hunch, a feeling, a guess, an idea.

In science, a theory actually falls at entirely the other end of the spectrum. A theory is an explanation of the mechanism of how an observed phenomenon comes about which is strongly supported by empirical evidence.

A theory is different from a law not in the strength of it’s evidence, but in what it tells you. A theory deals with the mechanism behind a phenomenon. A law describes a phenomenon without dealing with how it comes about. If you like, a theory is an explanation, a law is a description.

This distinction causes a lot of confusion when it comes to the theory of evolution by natural selection. Evolution as a process is an observed phenomenon, not a theory. It can be seen in the lab. It can be exploited through deliberate selection by humans to create and modify domestic animal breeds. The theory part — the part that describes the mechanism — is “by natural selection.” To talk about the “theory of evolution” is to use a shorthand for the actual theory, compounding the confusion caused by not knowing the different scientific meaning of the word “theory”.