The Story of the Atom

Possibly the earliest scientific question we as a race attempted to answer was ‘what is our world made of’. People reasoned that everything had to be made of something- all the machines and things we build have different components in them that we can identify, so it seemed natural that those materials and components were in turn made of some ‘stuff’ or other. Some reasoned that everything was made up of the most common things present in our earth; the classical ‘elements’ of earth, air, fire and water, but throughout the latter stages of the last millennia the burgeoning science of chemistry began to debunk this idea. People sought for a new theory to answer what everything consisted of, what the building blocks were, and hoped to find in this search an answer to several other questions; why chemicals that reacted together did so in fixed ratios, for example. For a solution to this problem, they returned to an idea almost as old as science itself; that everything consisted of tiny blobs of matter, invisible to the naked eye, that joined to one another in special ways. The way they joined together varied depending on the stuff they made up, hence the different properties of different materials, and the changing of these ‘joinings’ was what was responsible for chemical reactions and their behaviour. The earliest scientists who theorised the existence of these things called them corpuscles; nowadays we call them atoms.

By the turn of the twentieth century, thanks to two hundred years of chemistry using atoms to conveniently explain their observations, it was considered common knowledge among the scientific community that an atom was the basic building block of matter, and it was generally considered to be the smallest piece of matter in the universe; everything was made of atoms, and atoms were fundamental and solid. However, in 1897 JJ Thomson discovered the electron, with a small negative charge, and his evidence suggested that electrons were a constituent part of atoms. But atoms were neutrally charged, so there had to be some positive charge present to balance out; Thomson postulated that the negative electrons ‘floated’ within a sea of positive charge, in what became known as the plum pudding model. Atoms were not fundamental at all; even these components of all matter had components themselves. A later experiment by Ernest Rutherford sought to test the theory of the plum pudding model; he bombarded a thin piece of gold foil with positively charged alpha particles, and found that some were deflected at wild angles but that most passed straight through. This suggested, rather than a large uniform area of positive charge, a small area of very highly concentrated positive charge, such that when the alpha particle came close to it it was repelled violently (just like putting two like poles of a magnet together) but that most of the time it would miss this positive charge completely; most of the atom was empty space. So, he thought the atom must be like the solar system, with the negative electrons acting like planets orbiting a central, positive nucleus.

This made sense in theory, but the maths didn’t check out; it predicted the electrons to either spiral into the nucleus and for the whole of creation to smash itself to pieces, or for it all to break apart. It took Niels Bohr to suggest that the electrons might be confined to discrete orbital energy levels (roughly corresponding to distances from the nucleus) for the model of the atom to be complete; these energy levels (or ‘shells’) were later extrapolated to explain why chemical reactions occur, and the whole of chemistry can basically be boiled down to different atoms swapping electrons between energy levels in accordance with the second law of thermodynamics. Bohr’s explanation drew heavily from Max Planck’s recent explanation of quantum theory, which modelled photons of light as having discrete energy levels, and this suggested that electrons were also quantum particles; this ran contrary to people’s previous understanding of them, since they had been presumed to be solid ‘blobs’ of matter. This was but one step along the principle that defines quantum theory; nothing is actually real, everything is quantum, so don’t even try to imagine how it all works.

However, this still left the problem of the nucleus unsolved; what was this area of such great charge density packed ¬†tightly into the centre of each atom, around which the electrons moved? What was it made of? How big was it? How was it able to account for almost all of a substance’s mass, given how little the electrons weighed?

Subsequent experiments have revealed an atomic nucleus to tiny almost beyond imagining; if your hand were the size of the earth, an atom would be roughly one millimetre in diameter, but if an atom were the size of St. Paul’s Cathedral then its nucleus would be the size of a full stop. Imagining the sheer tinyness of such a thing defies human comprehension. However, this tells us nothing about the nucleus’ structure; it took Ernest Rutherford (the guy who had disproved the plum pudding model) to take the first step along this road when he, in 1918, confirmed that the nucleus of a hydrogen atom comprised just one component (or ‘nucleon’ as we collectively call them today). Since this component had a positive charge, to cancel out the one negative electron of a hydrogen atom, he called it a proton, and then (entirely correctly) postulated that all the other positive charges in larger atomic nuclei were caused by more protons stuck together in the nucleus. However, having multiple positive charges all in one place would normally cause them to repel one another, so Rutherford suggested that there might be some neutrally-charged particles in there as well, acting as a kind of electromagnetic glue. He called these neutrons (since they were neutrally charged), and he has since been proved correct; neutrons and protons are of roughly the same size, collectively constitute around 99.95% of any given atom’s mass, and are found in all atomic nuclei. However, even these weren’t quite fundamental subatomic particles, and as the 20th century drew on, scientists began to delve even deeper inside the atom; and I’ll pick up that story next time.

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Drunken Science

In my last post, I talked about the societal impact of alcohol and its place in our everyday culture; today, however, my inner nerd has taken it upon himself to get stuck into the real meat of the question of alcohol, the chemistry and biology of it all, and how all the science fits together.

To a scientist, the word ‘alcohol’ does not refer to a specific substance at all, but rather to a family of chemical compounds containing an oxygen and hydrogen atom bonded to one another (known as an OH group) on the end of a chain of carbon atoms. Different members of the family (or ‘homologous series’, to give it its proper name) have different numbers of carbon atoms and have slightly different physical properties (such as melting point), and they also react chemically to form slightly different compounds. The stuff we drink is that with two carbon atoms in its chain, and is technically known as ethanol.

There are a few things about ethanol that make it special stuff to us humans, and all of them refer to chemical reactions and biological interactions. The first is the formation of it; there are many different types of sugar found in nature (fructose & sucrose are two common examples; the ‘-ose’ ending is what denotes them as sugars), but one of the most common is glucose, with six carbon atoms. This is the substance our body converts starch and other sugars into in order to use for energy or store as glycogen. As such, many biological systems are so primed to convert other sugars into glucose, and it just so happens that when glucose breaks down in the presence of the right enzymes, it forms carbon dioxide¬†and an alcohol; ethanol, to be precise, in a process known as either glycolosis (to a scientist) or fermentation (to everyone else).

Yeast performs this process in order to respire (ie produce energy) anaerobically (in the absence of oxygen), so leading to the two most common cases where this reaction occurs. The first we know as brewing, in which an anaerobic atmosphere is deliberately produced to make alcohol; the other occurs when baking bread. The yeast we put in the bread causes the sugar (ie glucose) in it to produce carbon dioxide, which is what causes the bread to rise since it has been filled with gas, whilst the ethanol tends to boil off in the heat of the baking process. For industrial purposes, ethanol is made by hydrating (reacting with water) an oil by-product called ethene, but the product isn’t generally something you’d want to drink.

But anyway, back to the booze itself, and this time what happens upon its entry into the body. Exactly why alcohol acts as a depressant and intoxicant (if that’s a proper word) is down to a very complex interaction with various parts and receptors of the brain that I am not nearly intelligent enough to understand, let alone explain. However, what I can explain is what happens when the body gets round to breaking the alcohol down and getting rid of the stuff. This takes place in the liver, an amazing organ that performs hundreds of jobs within the body and contains a vast repetoir of enzymes. One of these is known as alcohol dehydrogenase, which has the task of oxidising the alcohol (not a simple task, and one impossible without enzymes) into something the body can get rid of. However, most ethanol we drink is what is known as a primary alcohol (meaning the OH group is on the end of the carbon chain), and this causes it to oxidise in two stages, only the first of which can be done using alcohol dehydrogenase. This process converts the alcohol into an aldehyde (with an oxygen chemically double-bonded to the carbon where the OH group was), which in the case of ethanol is called acetaldehyde (or ethanal). This molecule cannot be broken down straight away, and instead gets itself lodged in the body’s tissues in such a way (thanks to its shape) to produce mild toxins, activate our immune system and make us feel generally lousy. This is also known as having a hangover, and only ends when the body is able to complete the second stage of the oxidation process and convert the acetaldehyde into acetic acid, which the body can get rid of relatively easily. Acetic acid is commonly known as the active ingredient in vinegar, which is why alcoholics smell so bad and are often said to be ‘pickled’.

This process occurs in the same way when other alcohols enter the body, but ethanol is unique in how harmless (relatively speaking) its aldehyde is. Methanol, for example, can also be oxidised by alcohol dehydrogenase, but the aldehyde it produces (officially called methanal) is commonly known as formaldehyde; a highly toxic substance used in preservation work and as a disinfectant that will quickly poison the body. It is for this reason that methanol is present in the fuel commonly known as ‘meths’- ethanol actually produces more energy per gram and makes up 90% of the fuel by volume, but since it is cheaper than most alcoholic drinks the toxic methanol is put in to prevent it being drunk by severely desperate alcoholics. Not that it stops many of them; methanol poisoning is a leading cause of death among many homeless people.

Homeless people were also responsible for a major discovery in the field of alcohol research, concerning the causes of alcoholism. For many years it was thought that alcoholics were purely addicts mentally rather than biologically, and had just ‘let it get to them’, but some years ago a young student (I believe she was Canadian, but certainty of that fact and her name both escape me) was looking for some fresh cadavers for her PhD research. She went to the police and asked if she could use the bodies of the various dead homeless people who they found on their morning beats, and when she started dissecting them she noticed signs of a compound in them that was known to be linked to heroin addiction. She mentioned to a friend that all these people appeared to be on heroin, but her friend said that these people barely had enough to buy drink, let alone something as expensive as heroin. This young doctor-to-be realised she might be onto something here, and changed the focus of her research onto studying how alcohol was broken down by different bodies, and discovered something quite astonishing. Inside serious alcoholics, ethanol was being broken down into this substance previously only linked to heroin addiction, leading her to believe that for some unlucky people, the behaviour of their bodies made alcohol as addictive to them as heroin was to others. Whilst this research has by no means settled the issue, it did demonstrate two important facts; firstly, that whilst alcoholism certainly has some links to mental issues, it is also fundamentally biological and genetic by nature and cannot be solely put down as the fault of the victim’s brain. Secondly, it ‘sciencified’ (my apologies to grammar nazis everywhere for making that word up) a fact already known by many reformed drinkers; that when a former alcoholic stops drinking, they can never go back. Not even one drink. There can be no ‘just having one’, or drinking socially with friends, because if one more drink hits their body, deprived for so long, there’s a very good chance it could kill them.

Still, that’s not a reason to get totally down about alcohol, for two very good reasons. The first of these comes from some (admittely rather spurious) research suggesting that ‘addictive personalities’, including alcoholics, are far more likely to do well in life, have good jobs and overall succeed; alcoholics are, by nature, present at the top as well as the bottom of our society. The other concerns the one bit of science I haven’t tried to explain here- your body is remarkably good at dealing with alcohol, and we all know it can make us feel better, so if only for your mental health a little drink now and then isn’t an all bad thing after all. And anyway, it makes for some killer YouTube videos…