The Epitome of Nerd-dom

A short while ago, I did a series of posts on computing based on the fact that I had done a lot of related research when studying the installation of Linux. I feel that I should now come clean and point out that between the time of that first post being written and now, I have tried and failed to install Ubuntu on an old laptop six times already, which has served to teach me even more about exactly how it works, and how it differs from is more mainstream competitors. So, since I don’t have any better ideas, I thought I might dedicate this post to Linux itself.

Linux is named after both its founder, Linus Torvalds, a Finnish programmer who finished compiling the Linux kernel in 1992, and Unix, the operating system that could be considered the grandfather of all modern OSs and which Torvalds based his design upon (note- whilst Torvald’s first name has a soft, extended first syllable, the first syllable of the word Linux should be a hard, short, sharp ‘ih’ sound). The system has its roots in the work of Richard Stallman, a lifelong pioneer and champion of the free-to-use, open source movement, who started the GNU project in 1983. His ultimate goal was to produce a free, Unix-like operating system, and in keeping with this he wrote a software license allowing anyone to use and distribute software associated with it so long as they stayed in keeping with the license’s terms (ie nobody can use the free software for personal profit). The software compiled as part of the GNU project was numerous (including a still widely-used compiler) and did eventually come to fruition as an operating system, but it never caught on and the project was, in regards to its achieving of its final aims, a failure (although the GNU General Public License remains the most-used software license of all time).

Torvalds began work on Linux as a hobby whilst a student in April 1991, using another Unix clone MINIX to write his code in and basing it on MINIX’s structure. Initially, he hadn’t been intending to write a complete operating system at all, but rather a type of display interface called a terminal emulator- a system that tries to emulate a graphical terminal, like a monitor, through a more text-based medium (I don’t really get it either- it’s hard to find information a newbie like me can make good sense of). Strictly speaking a terminal emulator is a program, existing independent of an operating system and acting almost like one in its own right, directly within the computer’s architecture. As such, the two are somewhat related and it wasn’t long before Torvalds ‘realised’ he had written a kernel for an operating system and, since the GNU operating system had fallen through and there was no widespread, free-to-use kernel out there, he pushed forward with his project. In August of that same year he published a now-famous post on a kind of early internet forum called Usenet, saying that he was developing an operating system that was “starting to get ready”, and asking for feedback concerning where MINIX was good and where it was lacking, “as my OS resembles it somewhat”. He also, interestingly,  said that his OS “probably never will support anything other than AT-harddisks”. How wrong that statement has proved to be.

When he finally published Linux, he originally did so under his own license- however, he borrowed heavily from GNU software in order to make it run properly (so to have a proper interface and such), and released later versions under the GNU GPL. Torvalds and his associates continue to maintain and update the Linux kernel (Version 3.0 being released last year) and, despite some teething troubles with those who have considered it old-fashioned, those who thought MINIX code was stolen (rather than merely borrowed from), and Microsoft (who have since turned tail and are now one of the largest contributors to the Linux kernel), the system is now regarded as the pinnacle of Stallman’s open-source dream.

One of the keys to its success lies in its constant evolution, and the interactivity of this process. Whilst Linus Torvalds and co. are the main developers, they write very little code themselves- instead, other programmers and members of the Linux community offer up suggestions, patches and additions to either the Linux distributors (more on them later) or as source code to the kernel itself. All the main team have to do is pick and choose the features they want to see included, and continually prune what they get to maximise the efficiency and minimise the vulnerability to viruses of the system- the latter being one of the key features that marks Linux (and OS X) over Windows. Other key advantages Linux holds includes its size and the efficiency with which it allocates CPU usage; whilst Windows may command a quite high percentage of your CPU capacity just to keep itself running, not counting any programs running on it, Linux is designed to use your CPU as efficiently as possible, in an effort to keep it running faster. The kernel’s open source roots mean it is easy to modify if you have the technical know-how, and the community of followers surrounding it mean that any problem you have with a standard distribution is usually only a few button clicks away. Disadvantages include a certain lack of user-friendliness to the uninitiated or not computer-literate user since a lot of programs require an instruction typed into the command bar, far fewer  programs, especially commercial, professional ones, than Windows, an inability to process media as well as OS X (which is the main reason Apple computers appear to exist), and a tendency to go wrong more frequently than commercial operating systems. Nonetheless, many ‘computer people’ consider this a small price to pay and flock to the kernel in their thousands.

However, the Linux kernel alone is not enough to make an operating system- hence the existence of distributions. Different distributions (or ‘distros’ as they’re known) consist of the Linux kernel bundled together with all the other features that make up an OS: software, documentation, window system, window manager, and desktop interface, to name but some. A few of these components, such as the graphical user interface (or GUI, which covers the job of several of the above components), or the package manager (that covers program installation, removal and editing), tend to be fairly ubiquitous (GNOME or KDE are common GUIs, and Synaptic the most typical package manager), but different people like their operating system to run in slightly different ways. Therefore, variations on these other components are bundled together with the kernel to form a distro, a complete package that will run as an operating system in exactly the same fashion as you would encounter with Windows or OS X. Such distros include Ubuntu (the most popular among beginners), Debian (Ubuntu’s older brother), Red Hat, Mandriva and Crunchbang- some of these, such as Ubuntu, are commercially backed enterprises (although how they make their money is a little beyond me), whilst others are entirely community-run, maintained solely thanks to the dedication, obsession and boundless free time of users across the globe.

If you’re not into all this computer-y geekdom, then there is a lot to dislike about Linux, and many an average computer user would rather use something that will get them sneered at by a minority of elitist nerds but that they know and can rely upon. But, for all of our inner geeks, the spirit, community, inventiveness and joyous freedom of the Linux system can be a wonderful breath of fresh air. Thank you, Mr. Torvalds- you have made a lot of people very happy.

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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…