Tag: Book Reviews

Dec 30 2010

Book review: Mutants by Armand Marie Leroi

Mutants Armand Marie LeroiChristmas is a time for reading, so in addition to Rolt’s Brunel biography I have also read “Mutants: On the form, varieties & errors of the human body” by Armand Marie Leroi.

This is a story of developmental biology told through the medium of mutants, people for whom development doesn’t go quite to standard plan.

The book runs through a sequence of distinct mutations: Siamese twinning, deformities to arms and legs, skeletal defects, dwarfs and giants, various sexual variations, albinism and hairiness, and finally ageing. His approach does not revel in the freak show aspects of human mutants rather makes a brief reference to the historical recognition of such mutations and uses this as a jumping off point for discussion of modern biological understanding.

Mutations have long been an area for scientific study because it was realised that studying malfunction would provide clues to the mechanisms of normal development.

The marvel of developmental biology is that it is a method of construction completely at odds to the human way of making complex devices. Rather than a complex entity assembling pieces to a plan, biology starts with an instruction set which builds order out of chaos with no external help. It is self-organisation, creation from (nearly) nothing with no supporting infrastructure. There are non-biological self-organising systems and we make use of some of them industrially, but there is nothing that matches the complexity, the heterogeneity that biology can achieve.

The fundamentals of development biology are genes coding for proteins that tell you where you are in the developing embryo and trigger growth or differentiation on that basis i.e. “I find myself in the presence of proteins A, B, and C at these particular concentrations, therefore I must make a leg”. As an example, the proteins noggin and bone morphogenetic protein 4 (BMP4) define the top and bottom of the growing embryo – in simple terms noggin stimulates the growth of the brain. Whimsical naming of a protein may seem like a good idea in the lab but I imagine it makes discussions with parents about the problems of their perhaps-dead child difficult.

An intriguing point is the frequent robustness of developmental mechanisms, often as not molecular biologists have identified a “critical” protein, created a “knock-out” mouse lacking that protein and discovered that the mouse developed relatively well – other developmental systems having compensated for the loss.

The diverse effects of mutations can be surprising, for example there is a condition called Kartagener’s Syndrome whereby the internal organs of the body are flipped left-right – the heart, rather than lying slightly on the left of the body lies on the right and so forth. People with this syndrome have respiratory problems, a diminished sense of smell and sterility. The cause of these apparently disparate problems is a faulty cilia motor, cilia are small hairs on the surface of a cell that move. In the lungs and nose they whip about to move mucus around, in men the cilia motor drives the tail of sperm, and in the developing embryo the whipping of cilia break the left-right symmetry. Hence failure of the cilia motor proteins leads to a diverse set of impacts.

In addition to proteins which induce specific behaviours, there are proteins which have a more overarching impacts, such as those produced in the pituitary gland, malfunctions of which can lead to dwarfism or gigantism.

As usual my butterfly mind has fixed on some less relevant portions of the book. Plato giving voice to Aristophanes in The Symposium posited that sexual desire can be explained because man and woman were once combined: in fact three pairings existed man-man, man-woman and woman-woman. These creatures were physically joined, having four arms and legs, two heads and two “privy members”. However, they were troublesome (cartwheeling on their eight limbs is explicitly mentioned) – so Zeus separated them into the men and women. And now everyone seeks to find their original partner thus explaining homo- and hetero-sexuality. There’s some suggestion that Plato was making a little fun of Greek myth here!

Thanks to this book I have learned that the male scrotum is the homologous structure to the female labia, the two halves have fused to form a handy sack. The development of sexual organs finds the male really as something that has failed to become female.

Leroi finishes with signposts to a couple of open areas in developmental biology, one is race: people have a moderate ability to identify racial groups and tie them to countries but current genetics cannot match this ability often finding much bigger variations within populations. As Leroi highlights, this is a fraught area in social terms but it is interesting that differences obvious to people are not obvious to genetics. Secondly he mentions beauty: does beauty tell us something about genetic fitness?

This book highlights the huge gap between knowing the base pair sequence of DNA and understanding how the organisms arise from that sequence. At times the language gets technical a little too quickly and it could really have done with some explanatory diagrams.

Dec 26 2010

Book review: Isambard Kingdom Brunel by L.T.C. Rolt

800px-Carvedras_ViaductThis week I’ve been reading L.T.C. Rolt’s “Isambard Kingdom Brunel: The definitive biography of the engineer visionary, and Great Briton”. The book was written in 1957, it comes with a substantial foreword highlighting the unrivalled access that Rolt had to the Brunel family papers referring back to Samuel Smiles, an early biographer of the Victorian engineers, as an inspiration. It also contains a couple of provisos as to how current thinking differs from Rolt’s book, slightly in Rolt’s dismissal of one of Brunel’s contemporary critics and more substantially in his accusation that his business partner, John Scott Russell, was largely responsible for the enormous difficulties faced in the construction of the ship SS Great Eastern.

The book is divided into three parts: the first covering Brunel’s early life, marriage and training. The second his role in the Great Western Railway and the third in his ship building activities.

Isambard Kingdom Brunel lived 1806-59; he had a French father, Marc Brunel who had fled France following the Revolution and an English mother, Sophia Kingdom. Marc Brunel was a significant engineer in his own right, responsible for one of the earliest production lines (for sailing “block” manufacture). Before the age of sixteen the young Isambard was apprenticed to Henry Maundslay (in London) an engineer and Abraham-Louis Breguet (in Paris) a maker of chronometers, watches and scientific instruments – both men exceedingly highly regarded in their field.

Isambard’s first engineering job was as the onsite engineer for the Thames Tunnel which his father had designed, at the time Isambard was 20. The tunnelling was enabled by his father’s invention of the tunnelling shield, tunnelling seems a generous description of the process – really it was “building a brick tube slightly beneath (and sometimes not) the floor of the Thames River”. The whole enterprise was highly dangerous, with the Thames breaking through into the tunnel several times – killing a number of the tunnellers. The tunnel was not finished during Isambard’s tenure.

Following this experience Brunel started to put forward plans for engineering jobs around the country; one of his first designs was for the Clifton Suspension Bridge in 1831, at the time this came to nothing in part because of the Bristol Riots which had come about when the House of Lords voted down the Great Reform Act. Meanwhile he was also commissioned to act as engineer for what he called the “Great Western Railway”, linking London to Bristol – having surveyed an initial route. His plan was accepted and much of his initial work was in pushing an act through parliament to enable the building. It’s striking just how mobile Brunel was in his days of supervising the building of the Great Western Railway, in a time before railways and other rapid means of transport he was criss-crossing the 120 miles of the route at a staggering rate. He seems to have this in common with William Smith – maker of the first geological map of Great Britain.

The Great Western Railway ultimately extended into Devon and Cornwall, where Brunel constructed a series of timber viaducts. None of these remain in their original form, they were built at a time when cheap, very durable timber was available from the Baltic, subsequently supplies of timber were not so cheap, or durable and such structures became uneconomic and were replaced with brick or masonry. Also in the West Country Brunel constructed an “atmospheric railway” between Exeter and Newton Abbott. The engineering high points of the Great Western Railway were the Royal Albert Bridge at Saltash, and the Box Tunnel – outside Bath.

The final third of the book covers Brunel’s shipbuilding activities, the SS Great Western – the first purpose built trans-Atlantic steam ship, the SS Great Britain an early iron-hulled and propeller-driven trans-Atlantic passenger ship and finally the SS Great Eastern. The Great Eastern was accurately described as a leviathan – eventually completed in 1858, it was not surpassed in size or weight for 40 years. Its construction: delayed, over-budget, subject to protracted legal and commercial wrangling, accident prone, appears to have contributed to Brunel’s early death. Originally the ship was intended for the England-Australia route, its enormous size meant it should have been able to make the journey without re-fuelling with coal. Ultimately it was most successfully used as a cable-laying ship – laying the first trans-Atlantic telegraph cable, its large size meant it could carry a lot of cable and the combination of paddle and propeller drive meant it was exceedingly manoeuvrable.

One activity I was unaware of was Brunel’s part in designing, building and shipping a temporary hospital to the Crimea, at Renkioi, this task was completed in just five months from start to end.

A couple of things strike me about Brunel: firstly, the work he was doing was at the cutting edge of technology – when he planned the Great Western Railway the first passenger railway in the world had only just been built, the SS Great Britain was amongst the first propeller and iron-hulled ships, similarly the atmospheric railway – yet these were enterprises on a large scale. Secondly, the engineer was much more in the board room and in parliament arguing for enabling acts than is the case now. As a result of a fractious episode of “In our time” I flippantly suggested that Brunel built steam engines for fun, but reading this book – I don’t think he did, there’s little sense of joy, only driving ambition. I am still enormously in awe of Brunel. I am a sort of scientist who sees no great division between science and engineering, men like Brunel had a scientific approach to their work but also left a lasting, tangible mark on Britain not only in the things they physically built but the ideas and methods they introduced. I’ve attended a conference dinner on the SS Great Britain, where we toasted IKB rather than the queen.

As a memorial to Isambard Kingdom Brunel the Institute of Civil Engineers determined to complete the Clifton Suspension Bridge, shortly after his death. I think he would have liked it, both as a memorial and a thing of engineering beauty.

Further Reading: Analysing the paint on the Saltash Bridge (here and here) by Patrick Baty.

Dec 05 2010

27 days to power in May

This is a joint review of the books “22 days in May” by David Laws and “5 days to power” by Rob Wilson on the negotiations to form the Coalition government following the May 2010 General Election. The Laws book is his personal account of those negotiations, and his subsequent brief period in office. The Wilson book is drawn more widely, although he is a Conservative MP. The title of this blog post is a search engine unfriendly mashup of the two titles.

The Liberal Democrats started planning for negotiations in the event of a hung parliament towards the end 2009, this was done secretly by Danny Alexander, David Laws, Chris Huhne and Andrew Stunell on the direction of Nick Clegg. Their consensus, pre-election, was that depending on electoral arithmetic a coalition with Labour or a “confidence and supply” with Tories were the best outcomes for the hung parliament regime where no party had an overall majority. However, Chris Huhne argued that coalition with the Tories was better than “confidence and supply”. Confidence and supply means that the junior party supports the senior for votes of confidence, and for budgetary votes. Huhne argued that under these circumstances LibDems would get all of the blame for difficult government decisions which they supported, without any say over policy. The Tories set up a similar group approximately two weeks before the election comprising William Hague, Ed Llewellyn, George Osborne and Oliver Letwin. Labour apparently did no group planning, their negotiating team comprised Lord’s Mandelson and Adonis (a former LibDem), Ed Balls, Ed Miliband and Harriet Harman. The civil service also seems to have been very well prepared to support negotiations and had a strong preference for coalition over other forms of government. There are strong hints that the civil service were deeply concerned at the prospect of a minority government, or a “confidence and supply” agreement would be bad for confidence in the economy.

The 2010 general election gave the Tories 306 seats, Labour 258, Liberal Democrats 57 and other parties 28 seats (including 8 DUP, 6 SNP, 5 Sinn Fein). This would give a Lib-Lab pact a majority over the Conservatives of 8 seats but with 28 votes with smaller parties so not technically a majority. A Tory-LibDem coalition gives 363 seats, with a majority over Labour of 105. Such a pact can take a rebellion (i.e. MPs of the coalition voting against it) of 35, in theory a Lib-Lab coalition could take no rebellion. In practice the 5 Sinn Fein MPs would likely not vote and the SNP would be unlikely to vote with Tories, except if there was something in it for Scotland.

This electoral maths suggest to me that the only real choice was what form the agreement with the Tories should take: no agreement – likely leading to a new election, “confidence and supply” or full coalition. Coalition with Labour looked really hairy in terms of numbers of seats but there was a lot of enthusiasm in the Liberal Democrats and some enthusiasm in Labour for this. The generation of LibDem MPs who had entered the parliament opposing Tory governments (Paddy Ashdown, Vince Cable, Charles Kennedy, Don Foster etc) were particularly keen. Gordon Brown was keen to form a coalition, and from the Labour team Mandelson and Adonis. Clearly from a negotiating point of view the fact that a coalition with Labour was feasible was a strong card to play.

Steve Richards, in The Independent, prefers to characterise the Coalition agreement between LibDem and Tory as the result of a take over by Orange Book Liberal Democrats, against the will of the party. This seems to misunderstand the internal workings of the party: both the parliamentary party (Commons and Lords) and the federal executive were consulted at the time on how negotiations should progress. They also voted on the outcome, as did the wider membership at a special conference held shortly thereafter. Many of these would be people just like me who would have been nervous of coalition with Tories, and many would have initially preferred coalition with Labour. However, ultimately all of these groups voted emphatically for coalition with the Tories. One striking thing in the whole process was the amount of time the LibDems spent on internal consultation – Labour apparently did none of this, and in the Tory party it was cursory and ad hoc.

Lord Adonis has disputed David Laws assertion that the Labour team were disengaged and unhelpful in the negotiating process, and largely supported the Richards view of an Orange Book take over. Laws has responded to that accusation. Personally I’m happy to accept David Laws view of the Labour stance in negotiations: the external signs from Labour were that there was a substantial lack of will to form coalition in the parliamentary party (Blunkett, Reid, Burnham, Darling apparently all against), and that little or no preparation had been made to try to negotiate a coalition should the opportunity arise. Why was this? Was it an oversight? Did they feel formation of a coalition with the Liberal Democrats was so trivial as not to require any preparation? The accusation that the Labour negotiation team may have been split flies because it is so self-evidently plausible. My view is that the Labour party as a whole were tired of government, could not face coalition with a non-existent majority and could not face the prospect of implementing the cuts required (and promised by them too) to address the deficit. There’s no doubt that for some of them coalition with any other party, except with the most supine partner was anathema.
David Laws book is the one to read for LibDems or those wishing to understand LibDems better, the Wilson book is better for a more rounded view of the formation of the coalition. His tone with regard to his dear leader is somewhat grating but I’m sure others would say the same of the Laws book. A full account of the negotiations from the Labour perspective would be useful.
A vignette that I’ve not seen reported elsewhere: George Osborne offered David Laws a post in the shadow cabinet in 2004 and a cabinet post, were he to defect. Laws refused.

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!