Tag: science

Nov 26 2009

Wonderful Life

You might have noticed I’m happy to go off into areas of science which are not my own with gleeful abandon, applying a physicist’s mind to what I find. This week I’m off to see the biologists, Mrs SomeBeans is a zoologist – so in a sense, I sleep with the enemy. Twitter puts me in touch with so many more of the biological persuasion.

Animals are very well covered in TV documentaries but their view is somewhat partial, favouring the furry and cute, but there’s so much more.

I think my appreciation for the wonders of the tree of life was first stimulated by “Wonderful Life” by Stephen Jay Gould. This book describes the fossils uncovered in the Burgess Shale a collection of fossils, from almost the very earliest life in the record – 500 million years ago. Gould is making two key points in his book, the first is that the so-called Cambrian explosion of species threw up a very diverse range of body plans; his second point is that the ones that survived did so almost by chance, there wasn’t anything obviously superior about them. Richard Dawkin’s book, “The Ancestor’s Tale” is also well worth a read.

I should explain body plan: this is the overall layout of the animal. So for the tetrapods (including mammals, reptiles, amphibians, birds) you get four appendages. Insects: the plan is six legs, three body parts and an exoskeleton. I’m reliably informed that snakes are tetrapods, although I’m struggling with this particularly since one of my advisers previously tried to persuade me that mohair came from mo’s. Basic rule seems to be that you can lose bones, fuse bones but not gain bones.

Once you appreciate this body plan stuff you start to get offended by representations of mythical beasts like angels and centaurs: they are clearly mammalian so angels can either have wings or they can have arms, they can’t have both! Similarly centaurs can either have two pairs of horsey legs and no arms or a pair of horsey legs and a pair of arms, what they can’t have is two pairs of horsey legs and two arms. The only reason I’m letting off the fairies is that I suspect they might be insects.

As a physicist, I really like this approach. Physicists basically have poor memories which shapes their approach to science, they like nice simple rules that encapsulate as much information as possible. You also spot them looking for “the simplest possible” model. So being freed from the requirement to learn lots of animal names by the simple expedient of calling them all ‘tetrapods’ is great. It’s true that the tree of life is more complicated than that but the principle is there. If you want to go into this in more depth, the technical name for this study is phylogenetics… *time passes as I get completely distracted*

At this point I originally made my usual error by referring to other living animals as being further down the tree of life: they’re not, we’re all leaves on the surface of the tree. A good way to wind up a biologist is to refer to another currently living species as ‘primitive’. They don’t like this because, as they point out, they’ve been evolving for just as long as us! So, rather than referring to them as ‘primitive’ here are a couple of distant leaves: Hagfish are the only vertebrates to have a skull, but not a spinal column. They evade capture by covering themselves in slime. And as for tunicates, they start with a notochord (a precursor to a spinal cord) as larva but give it up as adults which indicates a certain bloody-mindedness that I admire. (it’s a tunicate that decorates this post, at the top).

Rather more interesting than yet another furry animal…

Nov 15 2009

The past is a foreign country

I’ve been hanging out with historians recently (both online and in real life), so it got me thinking about how scientists treat history. The 150th anniversary of the publication of “On the Origin of Species” is coming up too, so it seemed like a good time to write this post.

My impression is that historians are about the reading of contemporary material, and drawing conclusions from that material; a realisation I came to writing this is that historians seem to have the same sense of wonder and passion for historical minutiae as I have for nature and science. I remember talking to a historian of science who was working on an original manuscript of some important scientific work, it quickly become clear that this was much more exciting for her than me. To me the exciting thing was the theory presented in it’s modern form, I wasn’t very interested in the original.

In science it isn’t the original presentation that’s important: I haven’t read Newton’s Philosophiæ Naturalis Principia Mathematica, Maxwell’s A Treatise on Electricity and Magnetism, any of Einstein’s four “Annus Mirabilis” papers, Galileo’s Dialogue Concerning the Two Chief World Systems, Darwin’s On the Origin of Species, the list goes on…

And that’s not to mention the real contemporary material: correspondence, notes and labbooks. I have a sequence of about 20 labbooks in the loft from 15 years of research, supplemented by a hoard of files and e-mails stored on my computer, covering the same period. I’m not sure I even want to try to reconstruct what I was thinking over that period – let alone try it on someone else’s records! It’s not that I’m remiss as a scientist, we just don’t read original material.

The original presentation of an idea may not be the clearest, and it may well be that it makes more sense later to present it as part of a larger whole, and to be honest scientists can be a bit hit and miss: Newton’s physics is great but the alchemy was bonkers. Science comes in bits, these days the bits are the size of a journal article and it’s only when you’re doing active research at the cutting edge that you need to keep track of the bits.

Mathematical notation is an issue for original publications. For example, Maxwell’s equations, which describe electromagnetism (radio waves, electricity, light…) are a monster in his original presentation but can be squished down to four short lines in modern notation (actually a notation introduced not long after his original paper). There’s a rule of thumb that each equation in an article halves the number of readers, therefore I link you to Maxwell’s 1865 version on page 2 of this document with the modern version at the bottom of page 6…
impressive, no?

A bit of history is introduced into the teaching of science but it’s either anecdotal such as the apple falling on Newton’s head, Gallileo dropping things off towers, Sadi Carnot and his wacky exercises, or we might give a quick historical recap as we introduce a subject. But to be honest it’s really all window dressing, the function of this history is to provide a little colour and give students the opportunity to do some exercises which are tractible.

Are scientists losing out as a result of this historical blindness? History should certainly inform us of our place in society, and our future place in society (okay – I’m talking about cash here!). I’m less sure that it has something to teach us on the ‘craft’ of science, this is something that comes from professional training – perhaps it would help if we were not presented with such caricatures of our scientific heroes.

So that’s my view, how wrong can I be?

Nov 09 2009

Pretty molecular models

And now I leap off into a topic in which I am not properly trained: molecular biology!

You sometimes get the impression  that scientists lead dull lives because they over-analyse things, they’ve lost their sense of wonder. The thing is: the more you know, the more you wonder.

One step up from atoms, you find molecules – atoms bound together. Starting things simple, here’s caffeine:

As every chemist kno carbon (C) atoms are black, nitrogen(N) atoms are blue, oxygen(O) atoms are red and hydrogen (H) atoms are white. (Not really but those are their traditional colours in molecular models).  Isn’t it beautiful? You can play with an interactive version here. In real life chemistry is more messy than this which is why I’m a physicist rather than a chemist.

The caffeine molecule is about 1 nanometer across, 1 (US) billionth of a meter. To give you a feel for the size of a nanometre: think of a grain of rice – about 1mm across, now imagine a kilometre. Walk your kilometre with the grain of rice, I walk a kilometre in about ten minutes and it takes me past two roundabouts, a gym and a postbox. Now look at you grain of rice again. To a caffeine molecule, a grain of rice is a kilometre wide.

Molecular models of this sort are a representation of reality, the things they miss out are: (1) in real life molecules are not static, they’re jiggling away furiously through the action of thermal energy (2) generally they’re going to be surrounded by solvent molecules (often water, which are also zipping and wiggling around) (3) they’re sort of soft, fuzzy and deformable and different parts of the molecule will be sticky or slippery according to their chemical nature. Ten years ago a good question at any molecular modelling seminar was to ask about the solvent molecules, the usual answer was “there aren’t any” – this usefully puts molecular modellers in their place since we’re rarely interested in molecules without solvent. Perhaps things have moved on since those days.

Life specialises in bigger molecules than caffeine, exquisitely crafted into little machines. And the incredible things is that all of life (humans, mammals, reptiles, birds, snails, bees, tardigrades, sponges, plants, algae, bacteria, fungi, weird bacteria that live in hot underwater vents) share the same 4-letter DNA code, which codes for the same set of 21 amino acids which build all the proteins to make life. Many of the proteins themselves aren’t hugely dissimilar across all the plant and animal kingdoms, particularly those to do with the most basic operations (processing DNA, converting food to energy).

Proteins are strings of amino acids: each different type of protein has a different sequence of amino acids.
Protein molecules typically contain many (a hundred or more) amino acids. The amino acid sequence is known as the primary structure, next up is the secondary structure: alpha-helices and beta-sheets. Different amino acid sequences can produce alpha-helices and beta-sheets that look the same. These structures are represented using “ribbons”:

This is a model of lysozyme, the alpha-helices are shown in red and the beta-sheets are yellow, bits of “random coil” amino acid sequence are shown in green. Lysozyme is about 5 nanometres from one end to the other. You can play with an interactive version here. The amazing thing about proteins is that their 3D structure forms spontaneously and very rapidly when they are synthesised in the cell, this process is known as ‘folding’. Furthermore the folded, or tertiary structure, of the protein is the same every time – it has to be or the protein won’t do it’s job. One of the great challenges in molecular biology is that, despite knowing the amino acid sequence of a protein from the DNA which encodes it, working out the 3D structure is a question of measurement, or comparison with other sequences of known folded structure.

Lysozyme is a physicist’s protein, you can buy it in bottles by the gram. I’ve worked on lysozyme, looking to see how it unfolds on a surface when heated.

You can go see more protein structures on http://proteopedia.org/, the lysozyme model above is 132L. I could play on there for hours…

References
Green, R.J., Hopkinson, I. & Jones, R.A.L. Unfolding and intermolecular association in globular proteins adsorbed at interfaces. Langmuir 15, (1999), 5102-5110.

Oct 03 2009

Schrodinger’s flippin’ cat!

There comes a time in a blogs life when a bit of a rant is called for, here’s mine or at least the first one. To be honest it’s a fairly discrete, civilised rant – because that’s the sort of chap I am. It’s about cliches in science.

Quite some years ago, Stephen Jay Gould wrote an essay entitled “The case of the creeping fox-terrier clone”, published in “Bully for Brontosaurus“. In it he describes how he was writing a piece on evolution using the time-worn example of the horse, and in particular an animal named hyracotherium also known as eohippus or “The Dawn Horse”. The problem for Professor Gould was that he found himself on the point of typing that eohippus was “the size of a fox-terrier”, the thing is he had no idea how big a fox-terrier was! That’s right, Prof Gould (who I think writes very nicely) was about to commit a cliche to paper, and rather admirably he stopped and had a bit of a think instead. Now the reason he was about to write this was that he’d read it many times before, it’s a very standard story in evolution. He wasn’t alone, many writers have written how “eohippus was the size of a fox-terrier”, and doubtless many of them had no idea how big a fox-terrier was. Many readers have, no doubt, read those words, nodded sagely to themselves and said “All is well, I know that eohippus was the size of a fox-terrier”. It’s not really the cliche that’s the problem, the problem is that we’ve gone through the motions of communicating an idea, but sort of failed. Just in case it was bothering you, a fox-terrier is about the same size as eohippus, or roughly 40cm at the shoulder ;-)  I reckon that’s about the same size as a large lamb.

This isn’t an isolated example, science writing (and education) is riddled with cliche, not just cliche in word, but cliche in thought. My own bugbear is Schrödingers cat, of whom surely everyone must have heard. Erwin Schrödinger was one of the fathers of quantum mechanics.

IM IN UR QUANTUM BOX � MAYBE.
 (I have a bit of a weakness for lolcats)

Briefly, Schrödingers “thought experiment” is as follows: take one quantum mechanical system (a radioactively decaying material is common), one cat, one diabolical system to kill the cat based on a random event from the quantum mechanical system and one opaque, cat-proof box. Combine ingredients and wait…now open the box. The argument put is that prior to opening the box the cat is in an uncertain state between dead and alive (which is true of the quantum system, atoms in the radioactive material could be said to be decayed and undecayed simultaneously). 

However, Schrödinger prefaces this thought experiment thusly: “One can even set up quite ridiculous cases.” Schrödinger didn’t think his cat was genuinely in some weird half-way house between dead and alive he was quite clear that it was very definitely one or the other and the problem was that for systems obeying quantum mechanical rules this wasn’t the case. That’s the useful point in this thought experiment: “There’s something weird that goes on between the quantum and the classical and we don’t know what it is”. Yet time after time you see this experiment described without the critical proviso. People go away with the false impression that undead cats exist!

oh dear I can feel my self getting a bit incoherent now… special relativity, I’ve taught special relativity, it’s genuinely a marvelous intellectual leap that solved a couple of serious problems in physics. It has some real world applications (understanding my old friend the synchrotron, GPS satellites, lifetimes for relativistic muons in the atmosphere etc). But the text book examples we give to students are rather worn, nope, “worn” is the wrong word. “flippin’ ridiculous” gets a bit closer. Here’s one:

“You have a 10 meter long ladder, and a 5 meter long shed. How fast must the ladder enter the shed in order for it to appear to fit inside to a stationary observer?”

I can tell you the answer: it’s “really fast” – some large fraction of the the speed of light. To put it another way, a ladder travelling at the requiste speed could travel the length of the equator in something under quarter of a second, that’s probably a little faster than your reaction time and I’m sure you have an intuitive feel for the length of the equator. My point here is that (1) You’re going to struggle to get your ladder going that fast (2) if that ladder’s going past you that fast, the absolute last thing on your mind is going to be “ooo…look, the 10m ladder is fitting into the 5m shed”. If your shed is in a vacuum then you won’t get killed by massive plasma shockwave, but how many sheds have you seen in a vacuum? For part 2 of this experiment one may find some halfwit has placed a concrete block at the back of the shed to check the ladder really is fitting into the shed by bringing the ladder to an instant standstill inside the shed. Once again, when ladder hits concrete whether ladder fits into shed is the least of your worries. Assuming that you were in a vacuum, your ladder/concrete collision is going to release “absolutely loads” of energy – fusion bomb scale. There you go, I’ve lost it completely now. Special relativity teaching is full of everyday objects (trains and rulers are typical) traveling at implausible speeds, and it really winds me up!

Don’t get me started on “Alice and Bob“, the quantum cryptographers and if one more string theorist tells me that all the extra dimensions are “curled up very small”, there’s going to be some hurtin’.

And relax… I feel better now that I’ve written it down.