Book review: Mutants

Christmas 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.

Review of the year: 2010

In a heroic attempt to be timely, I am writing a “Review of the [my blogging] year” post - it’s the first full blogging year for me.

A new feature after my first few months of blogging are book reviews: my house is full of books, and although I’ve read (nearly) all of them I can’t remember the contents. I don’t really consider my book posts to be reviews: they are notes on books for my own future edification. I generally only post on non-fiction although I did write more generally about science fiction. You can see all my reading for the year on Shelfari. The focus of my non-fiction reading is very broadly the history of science, I think my favourite of these was “The World of Gerard Mercator”; this is the story of mapmaking from a time when the full extent of the world was just being discovered. I’ve also read a lot about the Royal Society; this is their 350th anniversary year and, in Britain at least, it was at the heart of the scientific revolution. It’s through the Royal Society that I did my first bit of original source reading: “The History of the Royal Society of London by Thomas Sprat”, published in 1667. A strange experience stimulated by the people I have met on twitter.

Every so often I do a bit of hunting out of data; for example “A sceptical look at the economy” pulled together numbers on the deficit, the debt and how they have changed over time - a useful learning experience and something I refer back to. I also quite like “Occupations of MPs”, which shows that MPs are overwhelmingly barristers. News reports often fail to provide context to stories, and these posts are my attempts to find that context. At one point I even combined fiddling with data and the history of science in one post, extracting membership of the Royal Society data and plotting it: “The Royal Society and the Data Monkey”.

As a continuation of the data monkey thoughts, I did some blogging on computer programming which is my modern equivalent of fiddling about with projects in a shed. “That’s nice, dear” is an overview of programming and some pretty maps I made with election data, the title from my wife: it’s her usual response to me excitedly displaying my latest achievement! I also made “A set of blog posts on SQL” about which I kept very quiet. The hunting out of data and programming run together really, several of my data posts have been the result of significant amounts of programming, for example: “Yields from income tax”.

When I started blogging my intention was to blog about science, in a way that people who were generally not so interested in science might read. I’ve enjoyed doing this, my blog post on the periodic table is one of the most frequently accessed, possibly due to students doing their homework! Some of the scientific posts are on work I’ve done, such as “Understanding mayonnaise”, some are on things I simply find interesting: like “Fun with fluids” which features video of dolphins playing with vortex rings and others are about the life of a scientist, such as: “Publication, publication, publication”.

I’ve also done quite a lot of current affairs blogging, some of this is straightforward rant brought on by newspaper articles but some of it is party political. At the beginning of the year you wouldn’t have known I was a Liberal Democrat party member – I think everyone knows now! Amongst other things I did a post election summary here, and more recently I wrote a slightly more philosophical post. Perhaps most entertaining is my doom-laden post election “I was up for Evan Harris”, my most visited post for the year - I think because of graph, showing the inequities of the first-past-the-post electoral system, was linked from the comments in a Guardian “Comment is Free” article.

Personally the year was slightly eventful: alongside the usual holidays (Westendorf for skiing and the Lake District) I had a little operation after which, somewhat surprisingly, I was confined to the house for 6 weeks in September and October. It was an odd time, ultimately I found I got on quite well confined to the house reading and doing little things in programming disturbed only intermittently by the fear that, health-wise, things weren’t going to plan. I still struggle to understand where my blog lies with regard to personal and private, for a while I kept a diary which was like a blog. My diary was never particularly personal: it recorded facts and where I was when, with the odd diversion into slightly longer entries on books I had read.

Somewhat less common this year for me were photography blog posts, aside from the photos for a calendar, the holiday posts above and a solitary walk post, I don’t seem to have done many this year. Mrs SomeBeans aka The Inelegant Gardener has been much more active on the photography front.

This September we installed photovoltaic(PV) solar panels, to go with the thermal solar panels we got a couple of years ago. PV solar is made economic by the feed-in-tariff, which is exceedingly generous, on our East facing roof we generate approximately the same amount of electricity as we use during the late summer. Now, with the panels covered in snow, we generate nothing. This was also the year of Shiny, my new HTC Desire: not really used as a phone but more a laptop replacement for the home and I also got myself a Kindle ebook.

I’ve enjoyed reading through my blog posts; they provide reminders of my mental activities. I like to maintain the facade that blogging is just for me, but in truth I’m pathetically happy to see the viewing stats rising on a post.

Happy New Year to you all!

Book review: Isambard Kingdom Brunel

This 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.

Christmas Calendar 2010

For the past few years I’ve been making my own calendars, as a Christmas present. As best I can I use photos taken in the stated month. This year half of them are taken by Mrs SomeBeans and half by me.

The cover image – A Caiman Lizard, living at Chester Zoo

January – our house in the snow, and the dark – a small amount of white balance fiddling required to reduce the orange cast from the sodium street lights.

February – ski-ing in Westendorf in the Austrian Tyrol

March – A hellebore, Mrs SomeBeans will have taken this one

April – some sandstone from the Sandstone trail, this will be from close to Frodsham.

May – Allium and a bee, bees are difficult to photo because they move around so much

June – The bark of the Strawberry tree

July – A lilac-breasted roller at Chester Zoo, a photograph from a works day out

August – A building at Trentham Gardens – for some reason this makes me think of India

September – Helenium, Mrs SomeBeans making good use of the macro lens she allowed me to buy!

October – A gilded water-buffalo at Biddulph Grange, every garden needs one

November – Witch hazel leaves taking their autumn colour

December – Frost, fog and weak sun by the Shropshire Union Canal

What’s on the end of the stick?

Once again I return to science. Lately I’ve been playing with some calculations of the diffusion of one thing into another. This is for work – can’t say what, it’s top secret ;-) I have to admit I’ve rather enjoyed it.

Diffusion calculations ultimately amount to an accounting exercise: this is true of much of physics. You have a bunch of stuff of some sort, and you want to calculate where your stuff will be at some time in the future. The stuff may be electric fields, magnetic fields, heat, molecules or atoms but the point is that new stuff can only be created or destroyed following simple rules and stuff will only travel from one place to another according to other simple rules. Largely it’s a problem of conservation – the amount of stuff is conserved, if stuff leaves one place it must turn up somewhere else.

For diffusion the stuff is molecules, for the purposes of these particular calculations the stuff is not created or destroyed. In the crudest case diffusion is just driven by different amounts of stuff in different places, this is enough to drive the redistribution of stuff since at the molecular level everything is jiggling around at random. If you start with more stuff in one place than another and jiggle it all around at random ultimately it ends up uniformly distributed.

Things can get a bit more complicated, for example you might be interested in your stuff moving into a different environment where it’s not so happy to be or your stuff might be reactive but this is just a smallish change in the basic rules. You also need to define an appropriate boundary condition – what your stuff was doing at one instant in time. 

The rules and boundary conditions are expressed as a set of equations; these may have an analytical solution – that’s to say you can write down a further equation that specifies where everything is and when (which you can make into a pretty picture for the boss). Or you may have to carry out a numerical solution: divide time and space up into little pieces and apply the rules in small steps – this is an inelegant but frequently necessary method which, if done naively, can bite you on the arse. Or more technically: “exhibit undesirable numerical instability”.

It turns out that the analytical solution for my current problem can be found in Crank’s “Mathematics of Diffusion”, and so the main work was in making a story for those less interested in equations. The fundamental rules for diffusion are elegant and beautiful, the solutions for specific cases can be ugly and a bit hairy. This is where my skill comes in, to be honest I’m not that good at maths so I couldn’t solve the equations myself – but given a bit of time I can work out which equation is the solution to my problem and carry out calculations with it.

My original adventures with diffusion started in the mid-nineties whilst I was a postdoctoral researcher at the physics department in Cambridge – I was funded by Nestle to measure water diffusing into starch. They were interested in this because at the time they were making a KitKat icecream, which involved putting damp icecream next to crispy wafer with the entirely predictable outcome: the wafer went soggy even when the icecream was stored at –20^oC. I spent 18 months or so doing experiments and calculations to demonstrate the very obvious which was if you want to stop your crispy wafer going soggy the best thing to do is coat it in something lardy and therefore water-repellent – chocolate is good! In the meantime I learnt a wide range of things about diffusion and experiments.

Water diffusing into starch turns out to be a more involved case from a modelling point of view because of the whole “going soggy” thing: basically the properties of the starch change with their water content so there’s feedback between how much water there is and how easy it is for more water to arrive. I did experiments to see where the water was in the starch. This was done using stray-field nuclear magnetic resonance imaging (STRAFI), which required the sample to be stuck on the end of a stick and shoved up the bore of a big magnet, hence the title of this post.

This is another illustration of scientific impact: the core results I relied on for my couple of weeks of calculation date back decades or even hundreds of years. The rules for diffusion were first formulated by Fick in 1855, and since then work has been on-going in solving the equations for ever more complex situations. The 18 months I spent 15 years ago meant that when I returned to it rather then spending several months getting acquainted I could drop pretty much straight in and get some useful results within a couple of weeks. It’s difficult to say what the financial impact for my company might be, with any luck it will save some people at the lab bench a bit of time because results that, are on the face of it, a little odd will have a clear explanation or it may turn out that the calculations show they should stop what they’re doing now because it will never work.

References

1. Hopkinson, I., R. A. L. Jones, P. J. McDonald, B. Newling, A. Lecat, and S. Livings. “Water ingress into starch and sucrose : starch systems.” POLYMER 42, no. 11 (May 2001): 4947-4956.
2. Hopkinson, I., R. A. L. Jones, S. Black, D. M. Lane, and P. J. McDonald. “Fickian and Case II diffusion of water into amylose: a stray field NMR study.” CARBOHYDRATE POLYMERS 34, no. 1 (December 5, 1997): 39-47.
3. Crank, J. “The Mathematics of Diffusion” Oxford Science Publications.

Nevil Maskelyne and Maiden-pap

This post is about Nevil Maskelyne and his 1775 measurements of the Scottish mountain, Schiehallion (know locally at the time as Maiden-pap), made in order to determine the mass of the earth. My interest in this was stimulated by the Gotthard Base Tunnel breakthrough, since the precision of drilling seemed pretty impressive (8cm horizontal, 1cm vertical see here). There’s a technical explanation of the surveying here. You may wonder how these two things are related.

It’s all about gravity: gravity is the force exerted by one object on another by virtue of their masses. The force is proportional to the masses of the two objects multiplied together divided by the distance between the centres of the two objects squared. This is Isaac Newton’s great insight, although he only applied it to the orbits of celestial bodies. The mass of an object depends on both its density and its volume.

Maskelyne measured the mass of Schiehallion by looking at the deviation of a plumb line from vertical. The problem for the Gotthard Tunnel is that, if you’re surveying underground, measuring the vertical could be hard because if the density of the rocks around you is different in different directions then a plumb-line will deviate from vertical. Actually it’s probably not a huge problem for the Gotthard Base Tunnel, the deviations Maskelyne measured were equivalent to about 1cm over the 14km length of the Gotthard Base Tunnel sections. Furthermore Maskelyne was looking at an isolated mountain: density of about 2500kgm^-3 surrounded by air: density about 1kgm^-3, under the Alps the variations in density will be far smaller. So we can relax – density variations probably won’t be an important effect. Although it’s interesting to note that the refraction of light by air is significant in the Gotthard Tunnel survey.

Oddly, Newton didn’t consider Maskelyne’s measurements possible, thinking that the force of gravity was insignificant for objects more mundane than worlds. However he demonstrated that for a largish mountain (3 miles high and 6 miles wide) there would be a deviation of the plumb line from vertical of “2 arc minutes”. Angles are measured in degrees (symbol:^o) – there are 360^o in a circle. Conventionally, if we wish to refer to fractions of a degree we talk about “minutes of arc”, there are 60 minutes in a degree; or even “seconds of arc” – there are 60 seconds of arc in 1 minute of arc. 1 second of arc is therefore 1/1,129,600th of a circle. At the time of Newton’s writing (1687) this deviation of 2 minutes of arc would have been measurable.

Why is measuring the mass of a mountain a job for the Astronomer Royal, as Nevil Maskelyne was at the time? Measuring how much a plumb line is deflected from the vertical is not simple because normally when we want to find vertical we use a plumb line (crudely a string with a weight at the end). The route out of this problem is to use the stars as a background against which to measure vertical. Maskelyne’s scheme was as follows:

1. Find a mountain which stands isolated from it’s neighbours, with a ridge line which runs East-West and is relatively narrow in the North-South direction. This layout makes experiments and their analysis as simple as possible.
2. Measure the deviation of a plumb line against a starry background at two points: one to the north of the ridgeline and one to the south (the plumb line will deviate in opposite directions at these two locations).
3. Carefully survey the whole area, including the location of the the two points where you measured the plumb line and the size and shape of the mountain.
4. Calculate the mass of the mountain from the survey of its size and shape (which gives you it’s volume) and the density of the rocks you find on the surface.
5. From the mass of the mountain and the deviation of the plumb line you can work out the density, and therefore mass, of the earth

Measuring the location of stars to the required accuracy is a tricky business since they appear to move as the earth turns and the precision of the required measurement is pretty high. I worked out that using the 3m zenith sector (aka “telescope designed to point straight up”) the difference in pointing direction is about 0.1mm for the two stations – this was measured using a micrometer – essentially a a fine-threaded screw where main turns of the thread only add up to a small amount of progress. The ground survey doesn’t have such stringent requirements, although rather more time was spent on this survey than the stellar measurements.

Reading the 1775 paper that Maskelyne wrote is illuminating: at one point he lists the various gentleman who have visited him at his work! The work was paid for by George III who had provided money to the Royal Society for Maskelyne to measure the “transit of Venus”, some cash was left over from this exercise and the king approved it’s use for weighing the earth.

The value for the density of the earth that Maskelyne measured 235 years ago is about 20% less than the currently accepted value – not bad at all!

 References

1. The wikipedia article is good, including history and physics of the measurements (equations for those that want): http://en.wikipedia.org/wiki/Schiehallion_experiment
2. This presentation to the Royal Philosophical Society in Glasgow in 1990 has a lot of historical background: http://www.sillittopages.co.uk/schie/schie90.html
3. Maskelyne’s initial paper “An account of observations made on the mountain Schehallien for finding its attraction” Phil. Trans., 1775, 65, 500-542 is surprisingly readable, and provides details of the experimental measurements. The final analysis of the data was published later. 
4. Map of Schiehallion on Bing (OS mode): http://bit.ly/g1tufF

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.

This makes me angry

This makes me angry:

Instead nice, gentle Nick Clegg has secured the position of Britain’s most hated man. He has been burnt in effigy by student rioters. Police have told him that he must no longer cycle to work for fear of physical attack. Excrement has been shoved through the letter box of his Sheffield constituency home, from which his family may now have to move for safety reasons.

Peter Oborne in the Telegraph

I can hear the Labour apologists winding themselves up for response already: "Was his family in residence when the shit was pushed through the letter box? Have you got a crime number for that? It's terrible, but you know he betrayed the people who trusted in him. Moving out of the home is just theatrical." The president of the National Union of Students, Aaron Porter, Labour party member, decries the "betrayal", the breaking of a pledge. Anyone like odds on how likely it was that he voted for the Liberal Democrats? Let's face it: he didn't, he didn't vote for the party that he's excoriating for not implementing the policy he didn't vote for, the only party to oppose tuition fees. All those Labour folk, talking of the "betrayal", they didn't vote against tuition fees either. "Satirical" they say of David Mitchell advocating pissing through Nick Clegg's letterbox , it isn't satirical if someone's actually done it.

As the riots progress an army of armchair revolutionaries bemoan the violence of the police, as buildings are smashed up. "The police should simply keep the protesters moving on, so they don't cause any trouble". "The police are stupid", they say, "I could manage a large crowd of protesters, some intent on violence, much better than them. That's why I'm sitting here tweeting about it." "The police van was bait, because every right-thinking person when they see an unattended police van thinks: "Fuck me, I better smash the crap out of that"."

I used to think it was the Tories who felt power was their divine right but now I know it's Labour. Len McCluskey, leader of Unite, a Labour affiliated union calls for demos to topple the government, speaking approvingly of the poll tax riots. John McDonnell, Labour MP, says:

I know the Daily Mail will report me again as inciting riots yet again. Well, maybe that is what we are doing.

Beaten in an election, they use weasel words to get people out on the street smashing stuff up. "These cuts aren't what people voted for, they voted, but they didn't vote for this. They really meant to vote for Labour, the party who repeatedly reneged on promises to introduce fairer voting. The party who said they were going to reduce the deficit by making cuts, but now only have a blank piece of paper; who can magically make the deficit painlessly go away."

For the first time in 60 years Liberal Democrats are in government, they are in government at a time when the country faces the largest budget deficit it has had in many decades, it is a crap time to be in government. They are taking hard decisions that Labour would not have the guts to take. For some this is a "betrayal", they'll happily contribute to an atmosphere that means a family gets shit pushed through the letterbox of their home, and a columnist in a respected paper can applaud it.

But more than ever before I am proud to say "I agree with Nick".

Tuition Fees

Since I am repeatedly in the position of discussing tuition fees on twitter, I thought it helpful to put down my thoughts in one place without the 140 character constraint.

I'm in favour of supporting universities, and students, via general taxation because the benefits of university education are public: they benefit all of us. I, along with many others, benefited directly from a free university education 20 years ago. I, along with other people and companies, currently benefit from university trained lawyers, nurses, doctors, engineers and so forth, regardless of my own education. I believe that the higher education system should be reformed to separate teaching and research, and also that we should consider all post-18 training in the context of any reforms to university education i.e. we should not distinguish between plumbers and physicists - they are equally valuable. As I watched water freely flowing from a burst pipe last winter, I strongly believed the former more valuable than the later.

The Liberal Democrats have been very tied up over tuition fees because they signed a pledge to vote against tuition fees, largely it has been asserted that the pledge on fees indicates that it takes priority over all other manifesto pledges. In retrospect it would have been wise not to make such a pledge which could so easily invite such a distinction. In their defence I think it illustrates that LibDem MPs did not anticipate fully finding themselves in Coalition government, unsurprising given the last 60 years of elections. Nick Clegg did attempt to persuade the party to scrap this pledge towards the end of 2009, which would have been a politically wise move. It's worth noting that the LibDems could fulfil their pledge to the letter if they were in opposition, or in a looser electoral pact, in neither of these cases would they be able to influence the policy of the government so their opposition would be entirely decorative. No doubt many believe that LibDems should have given up Coalition government on this issue, that would have been stupid and pointless.

Politically I believe the appropriate response to not being able to fulfil the pledge is to say that the LibDems are sorry they did not receive a sufficient electoral mandate to enable them to fulfil this pledge and other manifesto pledges in coalition government. I note that more experienced government parties, such as Labour, have found it easy to brazenly ignore their pre-election pledges on tuition fees, twice, without little protest from the Labour dominated National Union of Students.

The discussion on tuition fees is made in a context where, in Liam Byrne's words "there is no money", all of the major Westminster parties proposed to address a large deficit mainly by making cuts to government spending, rather than raising taxation. In light of this, and the Browne report, making a bid for even flat central funding in the higher education sector was always going to be an uphill struggle.

I estimated previously that tuition fees could be replaced by an increase of 2p on basic rate tax, or 8p on higher rate tax and the Greens have proposed 4p on corporation tax to fund higher education. Those are tax increases of 10%, 20% and 15% respectively.  Clearly combinations of these three elements would also work. However, it must be recognised that higher education will always be in competition with other claims on the public purse. If you had £7bn to spend would higher education be your first priority? Or would it be schools, benefits, hospitals or tax cuts?

The scheme proposed by the Coalition does shift paying for university education further from general taxation. However, I believe Vince Cable has done a fair job of adding LibDemery to the Browne report, commissioned by Labour. In particular covering part-time education, capping tuition fees, and attempting to make repayment progressive. The principle difference to a pure graduate tax is that a tuition fee is stated, if not paid up front. A large number of people seem keen to imply that tuition fees will be payable up front, which they are not, and simultaneously claim that poorer students will be put off applying - perhaps because they have been repeatedly told fees will be payable up front.

As for what LibDem MPs should do when presented with the relevant parliamentary bill. It's quite clear that backbench LibDem MPs should abstain, those that vote against are free to do so but should suffer the consequences in terms of party discipline. Government ministers are in a less clear position, the Coalition agreement does allow for them to abstain, however particularly in Vince Cable's case, where he was heavily involved in developing the proposed legislation and feels happy with the results, it seems to me he must vote in favour - anything else just looks strange. There is a logic for all Liberal Democrat government ministers voting for the tuition fee proposals, this would be the case in a simple, one-party majority government.

In a coalition government, the policy of the component parties is not the same thing as the policy of the government. I tentatively believe the LibDems should retain an ambition to fund higher education from general taxation, I struggle to see how this policy will be implemented in the next 10 years but I do not feel this should rule out LibDems holding it as a policy. I believe, in future, the LibDems should avoid, like the plague, making pledges in the form that they made on tuition fees. They should also apply a disclaimer to their manifesto that they will negotiate to implement what they can from the manifesto but only in majority government will they pledge to deliver all policies.