Dr Administrator

Author's posts

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 25 2009

Wordless Wednesday

Nov 19 2009

Not Waving but Drowning

I thought I’d write a little post about Google Wave, and more generally the uptake of new software.

Wave is a recent innovation from Google, currently in restricted beta. It’s a combination of e-mail, instant messaging and wiki. So if you even feel the need to utilise e-mail, instant messaging and wiki functionality simultaneously then this is the app for you. Actually, that’s a little unfair.

This is what it looks like:

So, broadly it looks like an e-mail client. I won’t describe the details here but you can get a better idea from the very fine Complete Wave Guide.

At the moment the problem with Google Wave is that the a relatively small number of people have been given the equivalent of e-mail addresses and told to randomly e-mail each other. Unsurprisingly they’re spending a lot of time “e-mailing” each other about Wave. However, there is serious potential in Wave, aside from the traditional Waving about Wave I got lucky and managed to have a non-Wave useful discussion on Wave. It started with a thing that looked like an e-mail (I had a bunch of questions), my interlocutor started answering the questions in real time. Wave allows you to launch chat at any point in an e-mail, not only that it always you to see  your colleague typing character-by-character. In earlier forays this had been irritating but for a ‘real’ question it was actually rather useful – I could see my colleague getting the wrong end of the stick and put him right promptly. We managed to usefully flit between several conversations, adding things as they occurred to us and the end result is a nice record of a branching conversation.

As a wiki / document preparation system I’m less convinced. The core formatting available in Google Wave is fairly basic, although it can be extended significantly using gadgets and robots, but I can’t see it being a comfortable way of working together on anything other than quite a short document.

I can see this being a great replacement for interminable e-mail threads between multiple participants, and even a way of writing minutes for a bunch of people sitting in a room with each other. If Google Wave were ubiquitous and people were willing to use it, then it would be a significant improvement over e-mail. Ubiquity may be attained in the future for the domestic user – I could imagine it becoming available as an option in Google Mail. To be honest I see far more applications for the business user and there, for larger organisations, uptake will be much slower.

This leads to another issue, even if they have access will people use such a tool? I’m dubious about this, I work in the research arm of a large commercial organisation. So you’d expect this group to be more tech savvy than average, but uptake of new software is pretty slow, people have taken to instant messaging but not wikis, reference management software, revision control, all things you might expect them to find useful. Once you get past the standard business suite of Word, Excel, PowerPoint and Outlook enthusiasm peters out and arguably mastery of even these applications is limited. This isn’t a criticism of my colleagues, it highlights how difficult it is to gain traction with new software. When it comes down to it remembering how to use software is  hard and unnatural so not surprisingly we don’t do it very well.

Ultimately Google Wave is another tool, in a toolbox that is overflowing.

Nov 18 2009

Wordless Wednesday

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?