Nov 29 2010

Book review: Trilobites! by Richard Fortey

Triarthus_lateral
Triarthrus eatoni from Beechers Trilobite bed

This week I’m reporting on “Trilobite! Eye witness to evolution” by Richard Fortey, which I came to via Attenborough’s “First Life” TV programme and advice from @crafthole. As usual this is intended as part notes for my own edification and part review. I read the Kindle version of this book, I’d recommend getting the paper version since the publishers have made no effort to incorporate any of the illustrations from the book into the electronic edition.

Fortey has a rather literary style which makes for rather pleasing reading: the book starts with a walk along the cliffs beyond Boscastle to a location used by Thomas Hardy in “A pair of blue eyes” where the hero comes face to face with a trilobite embedded in the cliffs. The book covers the discovery of trilobite anatomy; evolution, the drifting continents and what makes a palaeontologist tick.

Trilobites were common in the relatively early history of life on earth, during the Cambrian period, about 500 million years ago and became extinct at the end of the Permian period about 250 million years ago. The book starts with a description of trilobite anatomy – you can see the details on the wikipedia page. The basic fossil remnants are the hard shell of the trilobite, the upper surface shield – the closest living relatives to trilobites are things like woodlice and the horseshoe crab (which Fortey eats in Thailand!). Generally legs and soft parts do not fossilise, so it was some time before these structures were understood.

The first written record of a trilobite was by Dr Lhwyd in a letter to Martin Lister, reported to the Royal Society in 1699. It is a fleeting mention, and he mis-identifies his find as a “skeleton of some flat fish”, noting that they are abundant but his illustration is quite clearly of a trilobite. Dr Lhwyd writes from Wales and much of the early history of the trilobite’s discovery is tied up with Wales, trilobites are characteristic of the Cambrian period, named after Wales.

The image at the top of this post illustrates the discovery of trilobite legs. Most trilobites lost their legs in the fossilisation process, they are flimsy and poorly armoured. However in the case of the Beechers’ trilobite bed special preservation circumstances have fossilised the legs, in this case picked out in ‘fools gold’ or iron pyrite.

I was rather impressed by the chapter on trilobite eyes, as reported in my post on First Life, trilobite eyes are made from calcite – an array of calcite hexagonal prisms in the eye channels light to light receptors. Calcite is birefringent, one of the features of this property is that light only travels along the prisms to the light sensors if it enters them square on. So the relatively large number of calcite prisms in trilobite eyes suggest resolution comes from directional selectivity of the prisms. Some trilobite eyes are more complex than this: the Phacops eye is comprised of fewer prisms but with cunning lenses at the outside faces which work using magnesium concentration gradients to eliminate chromatic aberration – this suggests they channel light to multiple light receptors. Calcite is calcium carbonate, but the calcium can be selectively replaced by magnesium which changes it’s optical properties – in terms of man-made optics this type of thing is feasible but it’s pretty sophisticated. Reading this on the train the temptation to grab fellow commuters and jab my finger at the appropriate paragraph shouting “Have you read this about trilobite eyes, it is flippin’ incredible!!” was almost overwhelming!

Fortey is clearly passionate about his topic, as he says of breaking rocks to find the trilobites therein:

“Hardened criminals used to be required to do the same thing before it was banned as inhumane. I loved it.”

He works as a palaeontologists tasked with identifying trilobites, and if necessary creating new species. I learnt that the Linnean binomial system is slightly more complex than I thought, as well as having a two part name each species is tagged with the name of the person who first described a species this helps the expert in the field trace the original citation for a species. You gain the impression of someone able to identify one trilobite of a myriad potential species from mere fragments, in the manner of those archaeologists who can apparently build a pot, complete with its history, from a tiny shard. As arthropods with tough exoskeletons, trilobites moulted their shells to grow – each animal strewing the landscape with potential fossil fragments: fossil factories, Fortey calls them. He goes into some detail of the inferred life styles of trilobites and their development i.e how juveniles grow into adults. For some of the developmental stuff it would be nice to see the supporting fossils: it sounds ferociously difficult separating juvenile forms from different species of trilobite.

The large variety of trilobites, and their appearance in the early days of fossilising life, makes them a useful tool in the study of how evolution operates. Fortey rebuts the proposal by Stephen Jay Gould in “Wonderful Life” for a Cambrian explosion producing massive diversity of forms, beyond what we see now. Arguing from research by former colleagues that the variation in forms discovered in the Burgess Shale is much smaller than Gould claims. The difference being in the interpretation of how diverse forms are from relatively indistinct fossils. This is perhaps a warning to the casual reader that controversies are easily hidden in the popular science literature.

A second application of trilobites is in the dating of rocks: they are very common, fossilise well and, over a period of time, evolved into many distinctive forms which makes them ideal for the purpose. Finally they can also be used in the reconstruction of ancient continents: identifying common collections of trilobites in disparate parts of the world suggests they were originally found in one place.

As mentioned at the top of page, my Kindle edition of this book was bereft of illustrations but by the power of google, I can give you phacops, famous for it’s fancy eyes, ollenelus – one of the commonest of the early trilobites, calymene blumenbachii pleasingly convex as Fortey says, paradoxides another early species, Ogygiocarella debuchii as discovered by Dr Lhywd.

I found this book most useful as an insight into the mind of a palaeontologist and a taxonomist.

Further reading
An overview of trilobites
A piece by Fortey in American Scientist on trilobites (pdf)

Nov 25 2010

Kindle-ing

kindleAnother in an occasional series of gadget reviews, and more general thoughts on books. This time I look at the Amazon Kindle, my latest gadgety purchase – I have the WiFi only version with added leather carry case. The Kindle is an electronic device onto which books can be downloaded from a range of sources. In a sense the device is a side issue, Kindle software is available for smartphones (I have it on my HTC Desire), and computers. The main action for the Kindle is in the ecosystem: it makes it very easy to spend money on Amazon!

There are quite a few books available in the Kindle Store on Amazon, both free and paid. The paid offerings are a little cheaper than their paper equivalents but not hugely so. In addition PDF files can be read using the device, it will also play MP3 audio files. The Kindle Store also has links out to places where free content can be downloaded. For example, Project Gutenberg holds a wide variety of out of copyright material in a variety of e-book formats.

As long as you’re prepared to compromise a little you’ll not run short of things to read –  I’d like to read the Patrick O’Brian Aubrey-Maturin series but they are not yet available for download. Only three of the top ten Amazon bestsellers are available in Kindle format at the moment. So far I’ve bought “Trilobite!” by Richard Fortey and “22 days in May” by David Laws. I also have “Sustainable Energy – without the hot air” by David Mackay which I got as a free download, and converted to an appropriate format using Calibre e-book Management, this is available as a community conversion of the original HTML files. Books can be transferred to the Kindle by WiFi, or direct cable connection. Buying books is magically easy – press button, wait a minute and you’re done!

Compared to an HTC Desire the Kindle interface feels rather clunky, I kept wanting to change pages by touch! Having said this moving from page to page is ergonomically easy: there are a couple of handy page forward / page backward buttons suited to either handedness. Page changes feel ever so slightly ponderous with a bit of a flash as the page changes. The battery life is very good, the display is e-ink based and so static display takes no power, only switching pages requires power. The display size is about right and it is very nice to read from, when I first opened the device I assumed the picture on the screen was a piece of paper for display purposes. There are a range of options for adjusting text size, spacing and so forth, although I found some glitches with text size control.

The Kindle is ideal for plain text, however for text with diagrams it is a bit hit-and-miss, although the quality of the display is good enough to show quite detailed greyscale images in the case of the Fortey book these have simply not been included by the publisher. The Mackay book includes figures but the placement of the figures in the text has largely been done automatically and is a bit wobbly. I’d really like to try a book with illustrations which have been done properly – any recommendations then please comment.

The benefit of the Kindle with non-fiction is that searching, bookmarking, and highlighting are all relatively straightforward. I have religious objections against making marks in paper books – I think as a result of using the library as a child. It’s also possible to add notes to a book and to see the “favourite” notes of others.

The problem is the Kindle misses the display aspects of book owning and reading; my house is full of books collected over 20 years. They are my extended phenotype; they tell you something about me. If you visit my house you can see my books – you might want to borrow one. The Kindle cuts this away, you can’t see what is on my Kindle, and if even if you could, you couldn’t borrow it. I’ve tried to replicate the bookshelf aspect in my Shelfari account, where you can see what I am reading and what I have read. I’m also missing the pile of books beside my bed. I’m an old-fashioned animal that misses physical objects.

Overall: not at all bad, reading raw text is comfortable, the whole buying new text is frighteningly easy, and a range of formats can be read. I’m looking forward to using the Kindle to avoid my mortal holiday fear – that I might run out of things to read!

Nov 21 2010

A little bit of politics

This is, to put it pretentiously, a meta-politics post rather than a post about particular political tendencies. It arises following a few months of Coalition government and a lot of chat on twitter and elsewhere, it is a personal view.

I joined a political party because I couldn’t be doing with the “plague on all your houses” view of politics. That I joined the Liberal Democrats is perhaps a sign I wasn’t fully committed to the alternative! Commitment to a party is a ticket to complain with confidence, you have a defined ground to defend and a crowd to back you in attacking the opposition. The downside of this is you tend to believe that any other criticism comes from a purely party political standpoint, and you in some ways tied to views that you don’t hold. This does make me somewhat rare: the Liberal Democrats have around 65,000 members, Tories 250,000 and Labour 166,000 (source), so of a voting population of 30,000,000 people less than 2% are members of a political party.

I struggle with mindless opposition, so end up always being mildly pro-government. To me standing on the sidelines and complaining automatically that the government is doing it wrong, whilst not proffering alternative solutions, or even tweaks to proposed solutions, is intellectually barren. I’ve been a party member for 20 years, for most of that time I’ve been an inactivist. Since the election I’ve been much more involved, this is partly due to the internet: online activism is the sort of activism I can cope with but also the fact of being in power brings home what the point is: not just to have policies but to enact them.

The Coalition has also brought to light the various strands of the Liberal Democrats: the old social democrats who left the Labour Party, original Liberals and the Tory equivalent of the social democrats. If you’re interested I’m probably closest to the latter group although I never considered joining the Tories (those Young Conservatives were a bit extreme).

No party really adequately captures an individual’s views – how can it? And further to this, many people find themselves utterly out of tune with the electorate and so destined to be unhappy with whatever government is in power. The benefit of a party out of power (and out of the likelihood of power) is that you can confidently project your desires on them without real fear of contradiction since they are untested in the white-heat of government. The problem with party politics is that it supresses attempts to gain consensus on key, long term issues and it does it’s best to supress free thought amongst parliamentarians.

Funnily enough in many senses the politically committed, by which I mean party members, get on with each other better than they do with the uncommitted. This was visible back in my days as an undergraduate, the members of the political clubs interacted with each other and disagreed quite considerable. Labour and Tory were despicably extreme ;-) but we shared a degree of enthusiasm for the political programme. The politically committed are approximately tied to a point of view, which can be argued with. The uncommitted can drift along in happy opposition to everything.

I have my own personal view of political change, which is that the British are largely non-revolutionary and they vote a government into power not because they offer compelling new ideas but because they believe they will offer broad continuity and that the incumbents have been sufficiently reduced in their eyes by the ordinary attrition of government that it is now time for a change.

Coalition is a novel position for a party to find itself: Britain hasn’t seen coalition since the Second World War. The interesting thing for a Liberal Democrat these days is how to behave in government, particularly in coalition government where the policies of the government differ from those of the party. I think this is worth repeating “In a coalition, the policies of the government are not the same as the policies of the component parties”. The government is still the government and as such there is a low limit to how much rebellion within it’s own ranks it can bear – this is true regardless of whether the government is a single party of a coalition. For the rest of the party things are somewhat easier. Liberal Democrats should argue for the party’s policies – particularly those being enacted by the government. They should be thoughtfully critical where they think the government is going wrong – this is our best opportunity to influence the workings of government across the board.

Nov 16 2010

First Life

Charnia, Image by Leicester Museum

The latest, and perhaps last, David Attenborough TV series is the two episode First Life: about the very earliest life on earth. It ends as the first life emerges from the sea.

David Attenborough is a hero in our household: Mrs SomeBeans and I saw his “Life on Earth” series at an impressionable age; he is our matchmaker, were it not for “Life on Earth” Mrs SomeBeans would not have gone to university to study zoology, which is where she met me – at university, not as a zoology specimen, I hasten to add! The good thing about a David Attenborough nature programme, is that they are rich enough that even someone who had done a degree in zoology will actually learn quite a lot of stuff. Attenborough’s autobiography, Life on Air , is also well worth a read – perhaps the most striking thing is the realisation that someone still alive was involved in creating the TV documentary format.

Returning to “First Life”: the programme starts with Charnia  a fossil identified in Charnwood Forest – close to where Attenborough grew up, it was the first fossil found in Precambrian rocks, dating to at least 580million years ago, which had previously been thought devoid of life. As a time yardstick: the earth is about 4billion years old and the dinosaurs flourished between 230million and 65 million years ago. Charnia looks like a simple frond, it lived in the sea. It is distinct from the later fossils found in the Precambrian and has no modern relatives – in this sense it was a dead-end for life.

Following the Charnwood Forest fossils (examples of which are found around the world) the program turns to two further earlier fossil collections at Mistaken Point in Canada and in the Ediacara Hills in Australia. These data from a slightly later period. The Ediacara fossils were the first such collection of fossils found, whilst those at Mistaken Point are the most diverse. As fossils they are fairly subtle marks in the rocks, the creatures from which they derived were soft-bodied – it’s surprising the range of conclusions the experts come to on such markings: inferring early reproduction and feeding strategies.

The second episode focussed largely on the fossils found in the Burgess Shale, in the Canadian Rockies, I’ve written about them previously. The key point is that the Burgess Shale assemblage dating to about 500million years ago, exhibits an enormous range of forms – more diverse than seen now, many of which have subsequently become extinct. The fossilisation conditions of the Burgess Shale mean that the soft parts, rather than just the hard parts of the animals are preserved. Seeing them on film there are several striking things: the Burgess Shale quarry is tiny, perched half way up a steep scree slope and the fossils are smaller than I had thought most only two or three centimetres long and very subtle – thin film like fossils only visible in the rock from certain angles.

In contrast the fossil trilobites from the Atlas Mountains in Morocco were outright awesome (not a word I use often or lightly). They’re beautifully detailed, and in full 3D including all manner of weird, delicate bristles and appendages Stacks of pictures of the trilobites can be found using the appropriate Google Search. That looks a bit of a dry description, they really are flippin’ fantastic fossils. I’d never realised such fossils existed! The fossil below is from a species which became extinct 400 million years ago – the trilobites became extinct 250 million years ago.

Trilobite: Walliserops Trifurcatus (Image from FossilMall)

Apparently the eyes of the trilobite are made from calcite lenses – unlike any modern animal. This is interesting because calcite is birefringent so the eyes could potentially have given trilobites polarisation sensitive vision. It implies a high degree of control of the crystallisation of the mineral. Along with the trilobites, sizeable sea scorpions (eurypterid) were found – some up to 2.5metres in length (see here) – this is 1950’s b-movie sized arthropod!

First Life is a nice little series about something deeply interesting: how the very first life looked and is nicely executed with location work, expert contributions from real experts and computer graphics visualisations of the living creatures derived from the often badly squashed and indistinct fossils. I wish it had been longer! Thanks to a fellow tweep I have put Richard Fortey’s “Trilobite: Eye Witness to Evolution” on my reading list.

Nov 09 2010

A diversion in my life

In the past my blog was my diary, which was entirely private. I kept a diary on my Psion for a number of years before the feeling that I should make a daily, or at least a regular, entry on the minutiae of my life became oppressive and I gave up. More recently I resumed as a blogger, and rather than writing down minutiae I wrote in a more formal, extended style on things that were happening, or on my mind, for a more public audience. It still provided a record of what I thought when.

This post is difficult in the sense that it is somewhat private: I had a minor operation on the 23rd September and only now am I about to go back to work. My minor operation turned out to be a little more complicated then expected. The aftermath has taken up a significant portion of my time and dominated my thoughts for the last 6 weeks. I hasten to add that at no time has my life (or any part of my body) been at serious risk and I have only occasionally been in minor, localised pain and been a little inconvenienced. This is all a storm in a tiny little teacup, but it is my teacup and I have had some sort interesting experience along the way.

I will be circumspect about the exact nature of my affliction. I started with a visit to a GP, who packed me off to the consultant at my local hospital. This is where I had my “unexpected prostate examination”. *That* wasn’t the affected part! A useful experience really, because at some point later in my life a semi-regular prostate exam will probably be a good idea and to be honest, there’s nothing to it. Warning signs: men, if you are semi-clad and a doctor asks you to roll on your side and pull your knees up to your chest – ask him why first!

I have medical insurance as a taxable benefit of my job. My initial intention was to stick with the NHS – my local hospital is over the road from where I live, whilst the private hospital, I believed, was many miles away. It turned out the private hospital was closer, and the wait was shorter and the consultant clearly thought me mad for not exercising my insurance. My initial private consultation was just 4 days after I raised the issue, on a Saturday morning, with potentially my operation the following Thursday. As it was the operation was delayed a few weeks because I had visitors at work on the Friday coming from Sweden – and it seemed wrong to bounce them and then my surgeon was going on holiday, to Sweden, for a couple of weeks. Compare this with initial consultation wait of 1 month, and operation scheduled for almost three months later on the NHS. I don’t see this as a criticism of the NHS: to provide fast service requires that you have more capacity than you strictly need – we choose not to fund the NHS to that level. I’ve been very happy with my local NHS GP service, and the quality of the medical care they provide – I’m sure that the quality of the medical care I would have received from the local hospital would be similarly excellent.

The nice things about private medicine are: it happens pretty quickly (and conveniently), the surroundings are nice and you’re better separated from your fellow man.  The people who join you in private medical care may or may not be more pleasant than those with whom you are treated with in the NHS but they do not generally share a room with you!

I didn’t sleep the night before my operation: I’d never had a general anaesthetic before and to be honest I was a little bit scared – it didn’t help that I’m passingly familiar with historical pre-anaesthesia tales of operations for bladder stones and a mastectomy: I had a minor fear that I would be fully conscious but unable to communicate. I was also scared I wouldn’t have my operation, because to be honest things were getting a bit difficult. My final fear was that I would wake from my anaesthetic with caffeine withdrawal – I’d been fasting for the previous 18 hours or so.

To start the day of my operation properly a wasp stung me on my toe!

General anaesthesia is extinction: there is consciousness, there is nothing, there is consciousness. Chatting to the anaesthetist as I went under I discovered I was getting propofol. I suspect the porters tasked with returning post-operative patients to their rooms have a collection of the most utter gibberish known to man. For my part I supplied them with the prime factors of my room number: 2 and 13, thank you for asking.

The first week or so after my operation passed easily, I’d expected to be off work for a week and I had some books to read. I even made a new website for the Chester Liberal Democrats. The next week or so it sort of dawned on me that the consultants slightly sweaty brow after the operation and the advice that I would take “a long time to heal” did mean something and I was indeed going to take “a long time to heal”. So here I am 6 weeks later during which I’ve largely been confined to the house.

Somewhat surprisingly I’ve done OK: I’ve read a lot, I’ve fiddled around with various computer programs, blogged a bit, shredded many old bills, re-organised things and not watched daytime TV and not even listened to the radio a great deal.

A visit to the consultant at about week 3 was somewhat surprising – I didn’t things were going too well, he thought they were going great! He has always appeared somewhat disdainful of patients, GP’s and a willingness to prescribe antibiotics for imaginary infection. He said mine was one of the more difficult operations of my type that he’d done. I suspect he wanted the medal I claimed for myself on that one.

The doctor (and consultants) views on the solubility of soluble stitches are quaint – their reported view is that they dissolve in 10-14 days. I started off with 20 stitches, six weeks ago. Number of stitches which have disappeared through dissolution: 3; Number that I’ve helped out: 12. Number remaining: 5. The nurse seemed a bit more clued up and said they “took ages”. I suspect the problem is that patients assume that they shouldn’t tell the doctor they’ve been fiddling with their stitches, so the doctor continues in the happy belief that stitches dissolve.

So that’s the story of my last 6 weeks, the funniest thing in all this is something my dad said; unfortunately it makes it pretty much absolutely clear what my operation was, and so I might leave it to an ephemeral tweet.