Tuesday 26 February 2008

Amazon Vine to reviewers: Please stop saying things are crap

Amazon recently launched their Vine program in the UK, and I was one of the lucky few thousand or so people to get in on it. For the uninitiated, Vine is a scheme whereby well-regarded reviewers on Amazon can get free stuff, in exchange for reviewing the product within a certain timeframe. I like free stuff, but alas most of it is either crap, obscure, or only available in such a small quantity as to be pointless.

Once upon a time I wrote reviews for a games website, which also meant free stuff, and I rapidly became aware of the problem in deciding how to grade something which I got free of charge, when everyone else would have to shell out for it. A mild irritation to a reviewer (who must of course get all the way through to write the review) might be enough to make someone give up in disgust at the product if they've paid good money for it. Well, this has been on my mind since I wrote my first, and so far only, review. Given the sheer number of reviews that Amazon get back for low-value items (there are only a half-dozen or so freebies to choose from, and you only get the chance once a month) and that there's no requirement that a review be good, the system's already going to skew review averages in a bad way, and completely bury genuine "I went out and had to pay for this" reviews.

And then, Amazon sends me this:

Dear Valued Vine Voices,

Thank you for your commitment to Amazon Vine. The opinions you provide are invaluable to our customers as they make their purchase decisions, and we are grateful for your participation in the process.

We want to remind you that several vendors submit unfinished versions of their products to the Vine programme in hopes that you will write pre-release reviews about them. Please be aware that these samples have not completed the manufacturing process and
should not be held to the same standards as finished products. For example, publishers often submit unfinished works, called galleys, that are likely to include typos, repetitive content, errors in syntax, and may be missing glossaries, indices, table of contents, photos, etc.Please take this into consideration as you craft your reviews. We ask that you focus instead on the potential of the overall product. In the case of books, please write about the overall quality and context of the author's message as opposed to the editorial features of the book. If you have any questions about writing reviews, please contact us at vine-support@amazon.co.uk. Thank you again for your continued support of the programme.

The Amazon Vine Team

It's not just books, either. The Vine forums (they're private) reveal that the copies of The Ferpect Crime and other DVDs are sent out on recordable DVDs with no menus or extras. Pre-release stuff is a perk of the program, of course (and of reviewing in general) but using unfinished pre-release stuff as warm-up reviews for the real thing doesn't strike me as ideally suited to Amazon's Customer Review pile, where the advantage was always that somebody had been playing around with the "real thing" for a while and could pick up on any little quirks or flaws.

I worry that non-members who are not aware of this policy of sending out preview items (that link in the opening paragraph is the only information you get on the program) might be misled by a whole lot of speculative "reviews" on the basis of an incomplete preview product. In any case we're limited to whatever content the publisher decides to send out. Sending out dozens of preview items with the explicit instructions that the reviewers be generous and vague in describing them in the reviews section is verging on astroturfing, in my not-so-humble opinion, and certainly reduces the value of Vine reviews, and Amazon reviews in general.

(The Vine catalogue does not provide any indication what content is pre-release and what is identical to the finished product, so perhaps we're to write all our reviews under the assumption that what we're seeing perhaps isn't the real deal. I might be reading too much into the email though.)

Incidentally, The Elements by Second Person, the album I reviewed and linked to above, comes from Sellaband, a rather novel little indie publisher. Sellaband, it transpires, arranged for "promotion to the 50 most active reviewers on The Vine" as part of its distribution deal with Amazon. I'm not sure what that promotion was (I'm not one of their most active reviewers, by a long shot) but I have to wonder how it's affected the review scores for that album. Anyone want to come forwards?

(It's been suggested to me that it's a marketing misphrase, and that they simply mean 50 albums are sent out to any Vine reviewers, as we're all meant to be amoungst Amazon's most active. That tallies with the number of Vine reviews that have appeared for the album.)

Saturday 23 February 2008

Real spam of genius

One of the fun things about a .ac.uk email address is that you get a subtly different kind of spam. Dodgy "tuition fee funding" emails from half-wits, say:

Tel: 0705-381-2013
Fax: 0705-381-2013


Dear sir/ma,

I am Dr Cheryl Mayfeild; Director ,Student Funding, Westfam Foundation. It has come to my notice that you may want an eligibility in our limited funding for this year as we have a targeted funding of 10,000 students and in which 7,500 have applied.

This may be only the first step in making up your mind whetherto take a free fund of 10,000GBP to augment or cover your tuition fees , living expenses,accomodation,etc. and it is important that you make the right decision for you.

The list of questionaire at the bas e of this letter is your application form which must be filled and emailed back to westfamreg@gmail.com , for official registration.

Further information is also available on our mini-site http://westfamfoundation .blogspot.com
Sincerely yours,
Dr Cheryl Mayfeild.

fill this Application form:

student informmation

Course Name:
College/university Name:
Full Name:
Zip Code
Personal Email:

Drivers License
State Issued:
License Number:

Parent or Guardian Data
Parents Names
Parents Phone
Parents E-mail Address
Father's Employer

Privacy Report:
This is to assure you that none of your information shall released to any third party (except on your permission). we run a private encryption database to keep your information safe and secure.
We store and process your personal information in our database, and we protect it by maintaining physical, electronic and procedural safeguards in compliance with applicable federal and state regulations. We use computer safeguards such as firewalls and data encryptionn to safe-guard your information.
Thanks for your understanding,
Westfam Foundation

I could point out all the missing apostrophes, too, but it's not worth the effort. Maybe they're a legitimate UK operation like their blog (check it out; blogger doesn't want to delete it for some reason) suggests, and they just got confused about what country their prospective benificiaries are in. Or not. Those phone numbers are personal-use call-forwarding by the way. I'd call them up to take the piss, but I suspect they're routing to a premium rate phone scam number. Hey, it looks like teachers can benefit too!

You also get the latest breakthroughs, straight to your inbox:

Definitive Periodic Law is revealed in arrangement of new Periodic Table, repeating sequential numbers of protons discovered in Groups 1 through 18 in the elements of the new ENERGY WAVE of the Periodic Table. The elements in the new ENERGY WAVE of the Periodic Table are given in the ground state, which is one electron for each proton. This arrangement provided a unique opportunity to observe the nucleus of the elements. By incorporating the sequential numbers of protons underlying the Energy Levels K, L, M, N, O, P, & Q in shell blocks s, p, d, and f of the Group elements, it revealed what had been hidden and veiled in the complexity of electron configurations. Sequential numbers of protons are observed to repeat in the Group elements from period to period. This is the true revealed energy force creating the similar physical and chemical properties of Groups 1 through 18 from period to period in the Periodic Table. The ENERGY WAVE of the Periodic Table had revealed Definitive Periodic Law… “Definitive Periodic Law is the number of protons underlying the Energy Levels K, L, M, N, O, P, & Q, in the nucleus of the Elements. These sequential numbers of protons repeat in shell blocks s, p, d, and f, forming groups that have similar physical and chemical properties from period to period.” These sequential numbers of protons are the cornerstones of the nucleus and provide the atomic orbitals of the electrons the foundation for their spatial relationship to the nucleus as described by the azimuthal (angular) and magnetic numbers of quantum chemistry. These sequential numbers of protons are very important, as they reveal new explanation to chemical bond angles and the molecular geometry and structure of molecules.

ISBN-13: 978979623510

Publisher: Energy Spectrum Publishing

Publish Date: November 2007

80 pp 70 Color illustrations

Formatting as in the original. I imagine that if you took a high school chemistry student, kept him up all night before his exams, pumped him full of caffiene, and told him you were going to shoot him if he didn't get an A, that's the sort of thing you'd get on the paper. Either he's restating a lot of what we know about chemistry and nuclear physics in a completely obscure way, or it's word salad. The "periodic law" is the cycle of properties you get when you arrange elements by mass, and it does allow you to get some useful predictions out as a described in that post. Although it's a very good model, it's limited to an approximation of the real, deep quantum mechanical behaviour which gives rise to that cycle. You run into areas where that approximation doesn't hold, so you have to accept that the properties of elements aren't just a function of their mass and that there's something else going on. (One of the nice things about learning chemistry is that you gradually learn more and more complex models, but don't leave the old ones behind. It's like running through the scientific method in time-lapse, and gives you a better feel for how science as a discipline works as a result.)

Anyway, I certainly can't make head nor tail of the email, even with the help of their website. Any takers? I'm tempted to blow the $25 on ordering a copy for entertainment value (I buy Nexus for the same reason, and I'd be doing them a favour), but quack physics has a tendency to be both bizarre and boring. (Okay, maybe real physics has that problem sometimes, but at least it's useful and does cool stuff).

Thursday 21 February 2008

Wii Bowling: Serious Business

It's probably a good time to introduce my particular research area, "computational theoretical chemistry". As I discussed in the last long post, the ability of atoms to stick together comes from electrons' tendency to pair up, and atoms' need to fill up "shells". I'll elaborate on this in more detail, but the important point to take from this is that chemistry (the science of how matter comes together) is all about electrons. They're tiny, tiny little particles. The lightest nucleus, that of hydrogen, is two thousand times heavier than the electron it binds. That tiny mass means that the crazy rules of quantum mechanics dominate.

Now, the maths required to describe quantum mechanics is well known (Einstein was behind one of the seminal papers in at the start of the 20th century, and it got him the Nobel prize), and so we can use this maths to predict what a particular chemical system is like, but it's fairly torturous. It's possible to describe a hydrogen atom with a pen and paper, but as soon as you go above that (the simplest chemical entity, with just one electron to describe) you have to start making simplifications to even be able to solve the problems in principle. These approximations involve lots of repetitive methods. If you can remember trying to do long division, or find square roots by Newton's method, then you've done a similar sort of thing. We say that these methods of solving the problem are numerical rather than analytical.

Fortunately it wasn't too long before electronic computers (and theoreticians like John Pople who knew how to make them dance) came on the scene, so we could feed these long, boring problems into dumb but fast boxes and get the answers. This is computational, theoretical chemistry. These days there are lots of stupendously powerful computers to work with and handle all sorts of complicated problems. We work hand-in-hand with experimentalists, helping to figure out what could be going on in their experiments. In return, the experimentalists give us a way to test how accurate our predictions are.

As it happens, it's still very difficult to perform calculations on big systems. The way around this is to use simpler and simpler methods. Eventually you throw out quantum mechanics altogether and start describing molecules as little lumps (atoms) stuck together with springs (bonds). The springiness of the springs comes from experimental observations of similar bonds (a bond between a carbon atom and a hydrogen atom is always pretty much the same springiness, say). Then you solve the maths for that system, which is fortunately relatively simple. The theories behind weights and springs and so on are called "classical mechanics", and these were pretty well sussed by the end of the 19th century. Applying them to chemistry like this is called "molecular dynamics". It's got some limitations - you can't break the springs, usually, and some subtle effects can be missed - but it's still very powerful. The Folding@Home project uses this sort of method to study how proteins fold up, because they're absolutely huge.

There's no point in having a breath-takingly fast computer if you can't have a bit of fun with it, mind you. The Pittsburgh Supercomputing Centre decided to set up a simulation of a bunch of buckyballs - little spheres of carbon which are distant relations of the graphite in a pencil - and make a scientifically accurate game of microscopic Wii bowling. In fact they've hooked the remote into the spiffy molecular dynamics package NAMD and the spiffy visualisation tool VMD, to create something they've dubbed "WiiMD". Be sure to check out their YouTube videos. Many of these things are very difficult to look at by experiment. (You have to look at things sideways, and pick apart what's going on indirectly. I really do enjoy a good experimental method, mind you. I've kind of missed the detective work of decoding mysterious wiggly lines.)

Apologies for not updating sooner - I've been overrun in the lab (nothing like an upcoming presentation to convince you to get your work into order). I'll do a little video to discuss bonding in more detail, in particular how molecules interact with each other, and also a post about reactions, the changes which molecules go through. Then eventually some more quantum mechanics to put the stuff about valence bond theory into context. See you then!

Monday 18 February 2008

Academic misconduct and getting away with it

The American Chemical Society's C&EN is reporting on a truly spectacular piece of academic misconduct. They've actually got a blog for it, if you wish to comment. Go ahead and read it, I'll be here when you get back.

Pretty blatant, isn't it? If a book or an album were ripped off that way, it'd be pretty easy to spot. Unfortunately the sheer volume of scientific papers published, and the number of journals available, gives fraudulent research a lot of hiding places. For a dodgy paper to survive, it first has to dodge peer review, in which researchers in that field look it over and decide whether the research itself is legitimate and the paper is well put-together, and then escape detection by the journal readers themselves.

Peer review has plenty of problems. It often involves handing over your research to academic rivals, a topic which C&EN raised last week (they've moved this article to a blog as well). Scientific papers are often very specialised, so it must be tempting for a reviewer (who works in that field, but doesn't know the particular specialism very well) to let something through because it "looks good" even though a specialist would immediately see that it's a load of garbage. Likewise, if the reviewer doesn't work in that specialist area, they may not be familiar with the literature and therefore may not notice that a paper is a duplicate. The readership has the same difficulty in uncovering a problem. If a paper's not in their specialism, they may be reluctant to report that it looks like gibberish for fear that they may be wrong. And even a specialist can't be expected to read every paper in his or her field. There are simply too many journals, and dodgy papers tend to get published in the obscure ones, or at the very least, not the journal they're ripping off!

I had this problem when I was marking lab reports recently - the answers a few questions were copy-and-paste jobs from a report I had marked the week before, and only the odd wording and bass-ackwards chemistry in one particular sentence jogged my memory. In the end I had to come up with a ruse for recalling the last week's papers to check them out. A little more effort, and it would've escaped un-noticed, especially if I'd had more than a half-dozen or so papers to mark. (One of the things that really annoys me about plagiarism is that I get suspicious and find myself going back and forth between papers following up spurious similarities, which means it takes longer to grade.)

What can we do? Electronic plagiarism-detection is a start but is useless in the face of many forms of misconduct and may lead to dubious, lazy marking practices. There's a lot of money to be made by selling automagic fixes for complex problems, and software is only as good as its database. Stay vigilant, I suppose. Don't take a paper at face value just because it's outside of your research comfort zone. Scepticism is healthy in science, after all. I'm pretty new at this, but it seems to me that the skills necessary to spot academic misconduct (inquisitiveness about new fields, reading journal articles properly and not just going over the abstract with a highlighter) are the same skills needed to be a good scientist.

Further reading:
Pharyngula on a baffling failure of peer review.
Deja Vu, a duplicate-publication-finder with a very good database.
Wikipedia's article on scientific misconduct is a fun starting point for some lunchtime browsing.

Saturday 16 February 2008

Valency: sticking atoms together

To recap my last Long Post, everything in the world is made up of atoms. These (nearly) indivisible units combine in different ways to make different things. These things are called "compounds". What do they look like? How do they work? That's what I'll try to explain in this post.

Atoms and bonds

It's actually pretty easy to say what elements a compound is composed of, in what proportion. Any volume of water, for example, contains twice as many hydrogen atoms as oxygen atoms. That gives us its chemical formula (or more specifically its empirical formula), H2O. Likewise, big bad carbon dioxide is CO2.

As it happens, the chemical formulas here also describe a single molecule of that substance. Pictures of molecules are pretty commonplace. They usually show a bunch of atoms represented by coloured balls, linked together by sticks which represent "chemical bonds", whatever those are. The number of bonds an atom will form is specific to that atom, and decides what sort of structures it can form. Here's an oxygen atom (red), and some hydrogen atoms (white), and there's only a couple of ways I can stick them together:

So, if we had a cloud of carbon dioxide, and we zoomed in far enough, eventually we'd see individual molecules, and closer still, we'd see that each molecule is made up of a carbon atom and two oxygen atoms stuck together. There's a different way of building things up, though. Salt, for example, has the chemical formula NaCl, usually we don't get a single unit "NaCl" - instead we get a big collection of Na (sodium) and Cl (chlorine) stuck together in a ratio of one-to-one, like Na800Cl800.

What decides how many bonds an atom can make? One of the best pictures for this - which works on many different conceptual levels - is valence bonding.

Valence bonding

There are around 100 different elements to choose from in making molecules. The selection box is called the Periodic Table. Here's the "main group":

They're arranged in order of the weight of individual atoms from the top left to the bottom right. Oddly, we have a cycle in the elements (or "periodicity", hence the name of the table), where if you start at a particular atom and go along eight steps, we have something similar. Dmitri Mendeleev spotted this when he was creating this table, which is why the main group table has eight columns, which we call chemical groups. Mendeleev had to leave gaps and suppose there were missing, unknown elements with properties similar to their neighbours above and below to keep the pattern going. This was a great intuition - although the reason for the cycle wasn't understood at the time - and it worked remarkably well.

Starting from the top right, we have helium, He. This is really chemically inert - an atom of helium doesn't do much, preferring to sit around on its own. Going down one (eight atoms heavier) an atom of Neon (Ne) is also inert, but it's a bit heavier. Then there's Ar, Argon, which is heavier again, and so on. These are called the noble gases, or inert gases. They're the last column, so that's group eight (VIII).

This is interesting, but because these elements don't really do anything, it doesn't give us any insight into chemistry, so let's go along to group four (IV). Here we have carbon, silicon, and germanium. Carbon can form methane, CH4. Silicon can form silane, SiH4. Germanium can form germane, GeH4. We could reasonably suggest that carbon and its relatives can stick to any four other atoms. We would say they all have a valency of four.

This idea, called valence bond theory, was an early breakthrough in chemistry. By comparing different compounds, we can come up with the valencies of the different elements. It increases from a valency of 1, in group I, to a valency of 4 in group IV. Then it declines again, from a valency of 3 in group V to a valency of 0 in group VIII. By satisfying these valencies, we can stick atoms together to make compounds. Oxygen has a valency 2, so you need two of them to satisfy carbon's valency of 4 and make CO2. You may notice that this means there are two bonds going between the carbon and each oxygen. These "double bonds" really exist, and are much stronger than single bonds.

Shared electrons and where valency comes from

If you're an inquisitive sort, you'll be wondering where this valency thing comes from, and why it's associated with this number eight. To think about that, we have to look at the structure of the atom. From a chemist's point of view, there's a tiny little, heavy indestructible lump called a nucleus with a particular positive electrical charge, +1 for example. Around this nucleus in a very big, very loose cloud are light particles called electrons, each of which has a charge of -1. Opposites attract, so the +1 charge of our hypothetical atom can attract and hold 1 electron.

Let's start with some of the oddities of the main group, the first two elements. An atom with a +1 nucleus and 1 electron is called hydrogen. If you want to give the nucleus a bigger charge, you have to stick some more stuff in there, so the next atom, with a +2 nucleus and 2 electrons, is heavier. It's called helium. As it happens, if an atom only has two electrons, they're very happy together and the atom doesn't need to do anything else to be stable. This is a "closed shell"

Atoms want to have closed shells where possible, so a hydrogen atom is on the lookout for one electron. It can get to this by sharing an electron with another hydrogen atom. They then each have two electrons, and the molecule as a whole has a closed shell. Having one electron to share gives hydrogen its valency of 1:

Pairing up valence electrons by sharing like this is called covalent bonding.

Let's go up to lithium, +3 with 3 electrons around it. The first two form an s-shell on their own, leaving one electron to form an s-shell of its own. We call this the "core", and those two electrons are core electrons. We're left with one electron to deal with, giving the molecule a valency of 1. For this reason, we call this electron a "valence" electron.

As it happens, lithium's really bad at holding onto this odd electron. In fact, everything in its group is pretty easy to take an electron from, if another atom really wants it. This is fine, though - by taking that electron away, it gets down to the same closed shell as helium. By giving up this electron, though, lithium winds up only two electrons for its +3 nucleus. That's a +1 charge left. As it has a charge, we call it an ion. Whatever snagged lithium's electron has picked up an extra electron, so it now has a charge of -1 (it is also an ion). Opposite charges attract, so the two ions will stick together:

Reaching a closed shell by giving up electrons like this is an exampe of an ionic bond. Bonds can really be in between the two situations - the shared electrons can be a bit off-centre rather than in the middle (we'd call this a polarised covalent bond) or way off centre (completely ionic). Either way, you can only get one negatively-charged ion with each positively charged ion, so that's valence 1.

So, atoms like to pair up their electrons, and they particularly like to get to a closed shell by doing this. If you get a closed shell, the valence count "resets", at least when we look at going from helium to lithium. This is an interesting diversion, but the original question is: why this cycle every 8 atoms? We're getting there.

Boron is in group III, which is +5 with 5 electrons. The first two electrons form a closed, s-shell core as in lithium. That leaves us with 3 valence electrons. It can then use those to pair The same holds for carbon - group IV, 6 electrons, 2 in the core and 4 valence. So it can share those 4 to form 4 bonds, like we saw earlier.

Now, when you get up to nitrogen, group V (+7, 7 electrons) you might reasonably assume that because it has 5 valence electrons (remember, 2 electrons go into a core) it will be able to form 5 bonds by pairing those up. You'd be wrong, though! Actually, the closed shell for the main-group elements (except hydrogen and helium) has eight electrons, basically a 2-electron s-shell plus an extra 6-electron thing called a p-shell. Nitrogen has 5 valence electrons already, so it only needs 3 more and it's in business. So, it pairs up 3 of its valence electrons with electrons from other atoms. The other 2 electrons pair up on their own:

Nitrogen has 5 valence electrons and only has a valency of 3. So, that explains why the valence starts going back down when we get past carbon. The need to form a closed shell starts to take over, and atoms start pairing their own electrons off with each other. We can see the same thing with oxygen, which has 8 electrons, a valency of 6, and only forms 2 bonds with hydrogen atoms to form water:

Next up is fluorine. It has 9 electrons, of which 7 are valence. Fluorine only needs 1 electron to reach the closed shell, then. That means it's actually pretty tenacious when it comes to grabbing electrons. In fact it's just the sort of thing which will steal an electron from lithium as mentioned before:

Last, but not least, we have neon. It has 10 electrons, of which 8 are valence. That's the closed shell, right? It doesn't have any need for more electrons, so it hardly interacts with other things at all. And once we have a closed shell of 8 electrons, we have to start building up electrons around it again, using everything underneath as a core. So, that's where this cycle of 8 comes from. Elements with a similar number of valence electrons have the same sort of needs with regards to grabbing other atoms' valence electrons.

Summing up

Most of this post has been about satisfying atoms' need to link to other things, without discussing what sort of structures it makes. I've tried to keep it fairly simple, to get across this idea that an atom of a particular element can only stick to a specific number of other atoms, determined by this property we call valency. This comes from the number of electrons on the outside of an atom, and the need to pair those electrons up and/or form a closed shell around the atom. There are two "characters" a bond can have - it can be about sharing electrons (covalent), or transferring them completely (ionic), although often bonds can be found which lie in between.

Next, I'll be writing about how molecules stick together to form larger structures. Eventually, the limitations of valence bond theory will become apparent, but it's a good starting point. Now that I've addressed this, I'll get on to how molecules stick to each other, and I should be in a position to explain what my supervisor's paper is about.

Friday 15 February 2008

What we need more of is (being on the cover of) Science

For my PhD, I'm looking at chemical processes which happen when an electron is put into (or perhaps, taken out of) a system. As it happens my supervisor and his collaborators were finishing up a paper on this when I started work, and it just got published in Science. They even got the cover picture, up top. We're all really pleased about this: it's a neat bit of research on a familiar molecule, coming at it from both the experimental and theoretical sides, and having it published in a high-profile journal should lead to some interesting discussions. (If I'd started my PhD a couple of months earlier, I'd probably be a coauthor on this paper, which would've been great for my first year report. On the other hand, it's good to have an established bit of research to work outwards from.)

In a sense, all chemistry is about electrons - they're the enigmatic little particles whose interactions stick atoms together, to create molecules. That'll be the subject of my long post tomorrow. On Sunday, I'll also write a little about this paper, and the sort of stuff I'm going to be working on for the next few years.

Thursday 7 February 2008

It's usually a good idea to read the bottle

Orac reports on a spa which mistakenly used hydrogen peroxide, instead of water, to give enemas. Their excuse is that they looked the same. Well, when I was doing high school chemistry, we were taught a rhyme on the danger of making that assumpion:

Jenny was a schoolgirl,
Now Jenny is no more
For what she thought was H20
Was H2SO4

(I kept it in my head mostly as a way of remembering the chemical formula for sulphuric acid.)

It's a pretty fundimental rule of working in a chemistry lab that you assume everything is out to get you, and unless labelled otherwise, all clear liquids are deadly poisons which cause cancer on sight, never mind consumption. Likewise colourless solids which resemble nothing so much as table salt or castor sugar or sherbert are assumed to be pure, crystallised death unless the bottle says otherwise. (Yes, even chemistry researchers can paranoid about "chemicals" like everyone else. If there's hydrofluoric acid sitting around the lab, I'd like some warning before I pour it in a glass beaker and start wandering over to the wastes bottle with it.)

I really have to wonder what this person was like in their high school chemistry class. I should be a little grateful- the enema story gives that old rhyme an exciting new context:
Jenny was an enemist
Now Jenny has no backside
For what she thought was H20
Was hydrogen peroxide.

That quote I mentioned yesterday


From one of my (many, many) Gaussian03 log files.

The quantum mechanics of Mario World

NB: The links in this post are to flash video players which may fire up on their own. If you're watching at work or school, don't get yourself in bother.

Two posts in and already I'm going a little off topic, so I'm going to have to come up with some justification here. My own research is in the field of computational chemistry, which is a fancy way of saying I simulate the sorts of things that go on in real laboratories. To simulate something, you need a deep nuts and bolts understanding of it, which in chemistry often means quantum mechanics. Quantum mechanics is punishingly unintuitive, but if you're willing to sit back and accept them without explaination as to their origins, some of the results are fun.

One of these fun ideas is the "many universe" interpretation, the idea that in random events (on a small scale!) every possible scenario plays out somewhere. These different scenarios run along together until some event has to choose one scenario over another. This is brilliantly illustrated in this video, where a very difficult customised level of Mario World has been attempted many dozens of times and the runs overlaid on eachother. Every time Mario runs into an obstacle, he'll either get past it or fail, which gradually whittles things down. For a similar idea in a racing game, see The 1K Project. For a retro shooter version, there's Averaging Gradius.

The Mario video is actually a great lesson in a chemical principle, too. For non-chemists this will become clearer when I do my chat about reactions, but to cut a long story short, in chemistry the same reaction will be going off in a million slightly different ways at once, and usually dozens, or hundreds of different reactions are happening in the same beaker. You invariably have the same reaction going backwards and forwards. What's important is the average effect - even if only a tenth of the Marios make it to the end gate on each run, over time, practically all the Marios are going to make it. There's a great quote about this which I've misplaced, and I'll hopefully add tomorrow. If you've been watching UK TV lately, particularly Channel 4 last Friday, you'll probably see another similarity too, but I don't want to spoil things for anyone who's not seen the show in question.

Sunday 3 February 2008

Elements and reactions

Chemistry doesn't have a great public profile. Biology's pretty straightforward - it's the wet, squishy, science of life, so it's easy to see what it ties into. Everything else is pretty much either physics (big cool space things) or maths (the equation for the perfect cheese sandwich and such). Chemistry only really comes up as "chemicals" of one sort or another, be it drugs or poisons or preservatives or other artificial things that you don't want to spend too much time around. So with this in mind I decided to start off this blog with an explaination of what chemistry is, so that non-scientists could follow what I'm saying. Hopefully. Enjoy!

Chemistry is the science of the structure of matter, and how substances can be changed from one to another. Of course this is a very rough definition. You can change the structure of a Lego house by taking it to bits and reassembling it as a car, or turn a pile of uranium into a pile of plutonium by bombarding it with whooshy Science Particles, but those aren't chemistry. Chemistry deals with figuring out, and messing with, the structure at a particular scale, the scale which makes life work day-to-day.

It was alchemy, which amoungst other things frittered with trying to turn boring old lead into retirement-tastic gold, which gave birth to chemistry. The alchemists were doing what we'd call chemical reactions, in a very controlled setting - they put aqua regia (a nasty brew of scary acids) and some gold into a pot, heat it a little, and see what happens (the gold dissolves). Alas they didn't know that turning metals into one another falls outside of the realm of chemistry, so they were doomed from the outset. The problem lies with the notion of chemical elements.

Elements are a very old idea which is fairly intuitive. Everything in the world is a mixture of elements, the theory says - earth, fire, wind and water for example. The way they combine makes the difference between a cat and a tree and a rock. When you set wood alight, the fire gets out and it turns into ash, say. The elements themselves are basic and universal, like Lego bricks. Alchemy, as with chemistry, broke things down and put them together in order to find out what the real building blocks were (clue: not Lego) and how you could put them together. As it turns out, gold - and most metals, for that matter - are chemical elements. No amount of messing about with ever-hotter fires will break gold down into something else.1

It turns out that matter has the same sort of granularity as Lego, too. Imagine that you've got a big block made from yellow Lego bricks. You can break it down into individual yellow bricks. Likewise, you can chemically break down a lump of gold into individual grains of gold, called atoms.

With this atom theory, everything starts to come together. You can't break atoms down - each atom is an indivisible, particular chemical element, be it gold or carbon or lead or oxygen. Those atoms combine in various ways to give the materials around us. When they come apart from eachother and recombine in a different way, you have a chemical reaction, which turns material into another, and this happens under the sort of conditions you see in the everday world. As an example, your body takes in food, rich in carbon atoms, as well as air, rich in oxygen. You breathe out carbon dioxide gas, which a mixture of the carbon and oxygen.

How, exactly, do these elements combine together to give the substances we know? Why does the body bother changing food and oxygen into a pile of troublesome carbon dioxide gas? I'll discuss those in the next couple of introductory posts, on molecules and energy.

1Actually, you can break down elements and turn them into eachother, but this is very difficult. It wasn't really possible until around the 20th century, and is part of the field of nuclear physics. I'll bring this up when I write about the structure of the atoms themselves next time.