May 26 2016

Book review: Lab Girl by Hope Jahren

labgirlLab Girl by Hope Jahren is an unusual book. It’s an autobiography which mixes in a fair amount of plant science. It is beautiful to read. It is strong on what being a scientist means. The closest comparison I can think of are Richard Feymann’s “Surely you are joking, Mr Feynmann” memoirs which are rather more anecdotal.

Lab Girl is chronological, starting from Jahren’s early memories of visiting the lab in her father’s school after hours but then fast forwarding to her academic career setting up laboratories in Georgia, Baltimore and finally Hawaii. It isn’t encyclopaedic in providing a detailed record of Jahren’s personal and scientific life.

A thread through the whole book is Bill, her trusty research assistant. Bill starts as a keen undergraduate who Jahren takes on when she gets her first academic position. I think in some ways Bill is something of a product of the US academic system, with support staff often funded on short term grants. In the UK such people tend to be employed on a permanent basis by the institution. My Bill was Tom when I was a PhD student, Pete and Roger when I was an assistant director of research. As a lecturer I didn’t have a Bill, and maybe that was my problem.

Several themes intertwine through the book. There is the day to day activity of a lab: labelling things, repetitive sample preparation, measuring things, fighting with equipment to get it to measure things. Wrangling undergraduates and postgraduates. There are trips out into the field. For Jahren, as a biologist, the field is very literally the field (or Irish bog, Canadian tundra etc). There is attending academic conferences. Mixed with this there is the continual struggle for tenure and funding for your research and the fight for resources with grants that don’t go quite far enough.

It’s fair to say Jahren put in an awful lot more hours than I did as a young academic but then I didn’t turn into an successful, older academic. Make of that what you will. It’s difficult to measure your success as an academic, grant applications are so hit and miss that winning them is only a measure of your luck and skill at writing grant applications, papers are relatively sparse and rarely provide much feedback. Sometimes putting in hours seems the only way of measuring your worth.

A second strand is plant biology, mingling basic background and the cutting edge research that Jahren does. I absorbed this in ambient fashion, I now think a little more like a tree. I didn’t realise that willow deliberately drop  whole branches so as to propagate themselves. This explains the success of our willow dome construction which was made by unceremoniously plonking willow sticks into the ground and weaving them together. They then gamely got on and grew. Soil is a recurring theme in the book, the teaching of the taxonomy of soil to undergraduates in particular. I had glimpses of this rich topic whilst doing a Kaggle challenge on tree cover. Finally, there is mass spectroscopy and isotope analysis.   

And finally there is the personal, Jahren’s mental health, her struggles with pregnancy, marriage and a growing son. Some of this is painful and personal reading but its good to hear someone saying what we perhaps find unsayable. Lab Girl says relatively little about the difficulties she particularly faced as a woman, although Jahren has written about it elsewhere.

I observed a while back when reviewing In Defence of History that whilst historians seemed interested in literary style in technical writing, scientists rarely did. Lab Girl is an exception, which makes it well worth a read.

At the end of the book, Jahren asks us all to plant a tree. I pleased to say we’ve achieved this, although perhaps not quite the right sort of trees for American sensibilities, used to larger gardens. In the front garden we have a crab apple tree which, in the right sort of year, flowers on my birthday. There are several apple trees spread through the front garden. In both front and back gardens we have acers and now, at the bottom of the garden we have an amelanchier. I have longed for a Cedar of Lebanon in my front garden but fear I will never own a house large enough for this to be practicable.

May 18 2016

Book review: Mauve by Simon Garfield

mauveMauve: How one man invented a color that changed the world by Simon Garfield is a biography of William Perkin. Who first synthesised the aniline dye, mauve, in 1856 at the age of 18.

Synthetic dyes were to form the catalyst for the modern chemical industry, an area close to my heart since I worked at Unilever on fluorescent and “shader” dyes for the colouring of laundry and teeth. For my undergraduate degree and PhD I was close to organic synthesis labs but didn’t participant with any any enthusiasm (everything gets mixed up and you can poison, burn or explode yourself!).

The book starts with a trip by William Perkin to the United States in 1906, and a series of events to celebrate the fiftieth anniversary of his discovery. It’s very reminiscent of similar celebrations on a visit of Lord Kelvin at around the same time. By the later years of his life he was lauded in his field, if not so much beyond it.

Chemistry as a subject was relatively unformed in the middle years of the 19th century. Lavoisier, Davy, Dalton and others had laid the foundations of the modern subject in the early years of the century but it looked nothing like it does today. Chemical formulae were understood but their structural meaning was still a mystery and certainly not liable to routine elucidation. There were chemical industries of sorts, such as the manufacture of gunpowder, the preparation of dyes and tanning. Coal gas was made from coal, producing a variety of by-products including coal tar.

Perkin was studying at the Royal College of Chemistry as an assistant to August Hofmann who was focused on the idea of synthesising quinine from coal tar. He had been encouraged in his scientific studies by Faraday, and Hoffmann had personally intervened with his father for him to study at the Royal College, who had a career in architecture in mind for him.

There is a superficial similarity in the chemical compositions of aniline, a component of coal tar, and quinine. At the time it seemed plausible to synthesis the one from the other. Quinine was highly valued as an antimalarial drug whose supply was very limited. In the end quinine was not to be synthesised until 1944 by Robert Woodward. The synthesis of useful analogues of natural compounds continues to be one of the driving forces in synthetic chemistry.

In 1856, whilst trying to make quinine, Perkin synthesised an attractive colour (mauve) that dyed silk. Such a discovery was not entirely novel or unknown, the colouring properties of coal tar derivatives had been observed before. However, Perkin saw commercial potential and approached a Scottish dye manufacturer, Robert Pullar for advice. At the time dyes such as madder, indigo and cochineal were derived from animal or vegetable matter and were expensive and unpredictable. The natural growth process meant you were never quite sure of the quality of product you were making, or using.

Colouring something is only half the story with dyes, it is also important that the dye sticks to the target and stays there after washing or exposure to light. The techniques and materials for achieving this depends on whether the target is cotton, silk, wool, paper or whatever. With a new class of dyes, new techniques were required. So alongside the colouring material Perkin also provided technical services to help his customers use the dyes he made.

The business was boosted when mauve became a fashionable colour, worn by Queen Victoria. Perkin grew his factory in Greenford, and ultimately sold it when he was 35 for around £100,000 (which appears to be something around £75million in current value). After this he seems to have focused on further research rather than any other commercial venture. His motivation for selling up seemed to be that German companies had become dominant in the production of dye. It was felt that they had better access to trained technical personnel, and their companies were more willing to spend money on research (a complaint still heard today). Then, as now, it was argued that the British were good at inventing but not exploiting.

From dyes the synthetic chemical industries expanded into new areas. In the first instance dyes were useful in themselves in preferentially staining different microscopic structures. It was then discovered that some of them had biological activity, such as methylene blue. And from the aniline dyes were synthesised the antibiotic sulfa drugs and then other, uncoloured medicines.

The synthetic adventure was to continue with synthetic polymers which, in common with mauve, started as an unpromising black sludge at the bottom of a reaction vessel.

The chemical industry in Britain was resuscitated by World War I. Britain found itself dependent on German companies for dyes for military uniforms and precursors to explosives at the onset of war. The strategy, repeated across many industries, was for government to take direct control with the resulting organisations continuing after the war. For the chemical industry this lead to formation of ICI, Imperial Chemical Industries. The manufacture of bulk chemicals has largely moved to China now and ICI broke up and was sold between the early nineties and 2010.

Mauve is an enjoyable read but lacks depth.

May 10 2016

Book review: Coalition by David Laws

Coalition: The Inside Story of the Conservative-Liberal Democrat Coalition Government by David Laws does exactly what it says on the tin. It is the story of the Coalition running from 2010-15 from the point of view of someone at the heart of the action on the Liberal Democrat side. David Laws was a member of the negotiating team which took the party into the Coalition and a regular attendee at meetings of the Quad (where differences between the Coalition parties were thrashed out). Later he was a secretary of state in Education.

Laws finishes the book by answering three questions which I list below and are a useful way of organising this review.

Did the coalition work as a form of government?

The Coalition lasted the full parliamentary term, contrary to what many people expected. Both parties in the Coalition implemented significant chunks of their manifesto, and there didn’t seem to be many great dramas over votes unexpectedly lost. The members of the coalition seemed to get on OK, there was a dispute resolution system involving the Quad (Nick Clegg, Danny Alexander, David Cameron and George Osborne) and, in extremis, David Cameron and David Clegg alone. Laws appears a rather amiable chap and seemed to get along with many of his Coalition opposite numbers, particularly Oliver Letwin, Ken Clarke, George Osborne, even Michael Gove (whom he also found infuriating).

Laws writes quite a lot about his experiences in the Department for Education, and it becomes increasingly clear to me that the stories you see about chaos in government are typically an “inside job”. In this case Gove and his advisor Dominic Cummings briefing against the free school meals Laws championed. You can see Cummings hand in the briefings against Cameron now they are on opposite sides of the EU referendum debate. It follows from similar internecine struggles during the Blair and Brown years, and you can see it now in Corbyn’s Labour party. It is not absent in the Liberal Democrats, Laws highlights that part of the pain of tuition fees for the party was in the deep division within the party. Regardless of what had been achieved, half the party would remain unconvinced and if the party doesn’t believe then what hope persuading the public? Vince Cable’s frequent, contrary, interventions on the economy had a similar effect. And the polling done by his friend, Matthew Oakshott to undermine Nick Clegg. 

The accusation that senior Tories act very directly and explicitly in their own self-interest and that of their major donors is all the more damning coming from someone who clearly has a lot of time for them. Areas like the response to the Leveson enquiry are muted because of Tory Party enthusiasm for keeping papers on side. The proposed Mansion Tax is quashed to keep Tory party donors onside, it being raised by both Labour and Liberal Democrats is welcomed though. The Tories, particularly George Osborne, were repeatedly looking to cut the welfare bill (except for pensioners) largely because they didn’t see claimants as “their people”.

The “English Votes for English Laws” announcements made on the day of the Scottish referendum victory very much put a dampener on the result, and was done by Cameron for short-term gain.

After the 2015 election we can see that Liberal Democrats had a substantial restraining influence on the Tories in power, the distributional impact of changes for the budget is much more heavily skewed against lower income groups than it was under the Coalition (see here for the 2010-15 figures and here for the 2015-19). Legislation like the parliamentary boundary changes and the “Snooper’s Charter” are now going ahead, previously blocked by Liberal Democrats.  

What were it’s achievements?

The Liberal Democrat achievements in government have been summarised in Mark Pack’s rather fine infographic or the eponymous What the Hell Have the LibDems Done? website.

In summary:

  • Increased personal tax allowance to £10600 from £6475 in 2010;
  • Pupil premium / free school meals;
  • Pensions triple lock;
  • Overseas aid target;
  • Early years education entitlement;
  • Shared parental leave;
  • Pensions and benefit uprating in line with high inflation;
  • Equal marriage;
  • Mental health access standards;

The introduction of equal marriage was a surprise bonus, not in anyone’s manifesto but pushed through by Liberal Democrat Lynne Featherstone with the support of Theresa May despite continually opposition from backbench Tories and surprisingly, initial opposition from Labour and Stonewall.

Constitutional reform was the area where Liberal Democrats fell down, not getting either electoral reform or reform of the House of Lords. Neither of these are areas where the public shows any interest, and nor do they have the support of either Labour of Tory parties so perhaps failure was inevitable. In contrast to the EU referendum and the Scottish referendum there appears to be no call for a second referendum on AV.

What could Liberal Democrats have done better?

It was widely touted in the Liberal Democrats that coalition would be electorally damaging, given the experience of other smaller liberal parties in coalition in Europe and elsewhere. I think we gradually took this to heart as we lost councillors, then MEPs and finally all but eight of our MPs but none of us were really prepared for the final blow. Now following the first local and Scottish parliament elections after the end of the Coalition we are starting to win back seats and grow support.

Much of our loss in votes came pretty much immediately that we formed a coalition with the Tories, so one thing we could have done is not formed a coalition. I don’t support this idea, David Laws doesn’t support this idea, and he cites a whole load of other Liberal Democrats who don’t support this idea. The last 5 years have been the best time to be a Liberal Democrat at least since I joined the party in about 1990, our policies actually got implemented in government – which is the whole point of being a political party!

Inevitably attention will turn to the tuition fees vote, Laws’ first prescription for this is not to have made the promise to scrap tuition fees in the 2010 election. His second prescription, to have vetoed the idea is probably right in retrospect but didn’t happen because we were still trying to work out how to make coalition work and weren’t confident of our actions. As it stands the current tuition fee policy works, in the sense that enrolment in universities and enrolment from lower income groups continues to rise. It is a graduate tax in all but name with the advantage that you don’t avoid it by emigrating and it can be collected from EU students.

The NHS Bill is another idea which Liberal Democrats should have vetoed, largely in my view because it was unhelpful at a time when the NHS was supposed to be making large efficiency savings. It would also have helped the Tories in not damaging their fragile reputation over the NHS. Lansley was sacked as Secretary of State for Health for contaminating the brand of the Tories over the NHS, to be replaced by Jeremy Hunt(!).

From a more technical point of view Laws toys with the idea of going for more senior Secretary of State positions in the government rather than the more junior ministerial positions that were taken, Danny Alexander and Nick Clegg both held quite senior positions but they were someone else’s deputies. Our strength in Cabinet was propertional to our share of seats rather than our share of votes. Other Liberal Democrats such as Vince Cable held top positions but in less important departments.  

The style of the book is crisp, it rattles through around 50 short chapters. The quoted dialogue sounds incredibly wooden, I recommend not buying any fiction Laws’ might write! If you’re interested in politics then I thoroughly recommend this book, if nothing else it gives a clear insight into how coalition government can work in the UK. For Liberal Democrats it is an essential record of what we achieved in government. Whilst there may be more detached, historical reports in the future there is unlikely to be one better from the core of the action.

Apr 08 2016

Book review: An Introduction to Geographical Information Systems by Ian Heywood et al

HeywoodI’ve been doing quite a lot of work around Geographical Information Systems recently. So I thought I should get some background understanding to avoid repeating the mistakes of others. I turned to An Introduction to Geographic Information Systems by Ian Heywood, Sarah Cornelius and Steve Carver, now in its fourth edition.

This is an undergraduate text, the number of editions suggests it to be a good one. The first edition of Introduction was published in 1998 and this shows in the content, much of the material is rooted in that time with excursions into more recent matters. There is mention of CRT displays and Personal Data Assistants (PDA). This edition was published in 2011, obviously quite a lot of new material has been added since the first edition but it clearly forms the core of the book.

I quite deliberately chose a book that didn’t mention the latest shiny technologies I am currently working with (QGIS, Open Layers 3, spatial extensions in MariaDB) since that sort of stuff ages fast and the best, i.e. most up to date, information is on the web.

GIS allows you to store spatially related data with the ability to build maps using layers of different content and combine this spatial data with attributes stored in databases.

Early users were governments both local and national and their agencies, who must manage large amounts of land. These were followed by utility companies who had geographically distributed infrastructure to manage. More recently retail companies have become interested in GIS as a way of optimising store location and marketing. The application of GIS is frequently in the area of “decision support”, along the lines of “where should I site my…?” Although, “how should I get around these locations?” is also a frequent question. And with GPS for route finding arguably all of us carry around a GIS, and they are certainly important to logistics companies.

From the later stages of the book we learn how Geographic Information Systems were born in the mid to late 1960s became of increasing academic interest through the 1970s, started to see wider uptake in the eighties and became a commodity in the nineties. With the advent of Google Maps and navigation apps on mobile phones GIS is now ubiquitous.

I find it striking that the Douglas-Peucker algorithm for line simplification, born in the early seventies, is recently implemented in my favoured spatially enabled database (MariaDB/MySQL). These spatial extensions in SQL appear to have grown out of a 1999 standard from the OGC (Open Geospatial Consortium). Looking at who has implemented the standards is a good way of getting an overview of the GIS market.

The book is UK-centric but not overwhelmingly so, we learn about the Ordnance Survey mapping products and the UK postcode system, and the example of finding a site for a nuclear waste repository in the UK is a recurring theme.  

Issues in GIS have not really changed a great deal, projection and coordinate transforms are still important, and a source of angst (I have experienced this angst personally!). We still see digitisation and other data quality issues in digitized data, although perhaps the source is no longer the process of manual digitization from paper but of inconsistency in labelling and GPS errors.

One of the challenges not discussed in Introduction is the licensing of geographic data, this has recently been in the news with the British government spending £5 million to rebuild an open address database for the UK, having sold off the current one with the Royal Mail in 2013. (£5 million is likely just the start). UN-OCHA faces similar issues in coordinating aid in disaster areas, the UK is fairly open in making details of administrative boundaries within the UK available electronically but this is not the case globally.

I have made some use of conventional GIS software in the form of QGIS which although powerful, flexible and capable I find slow and ugly. I find it really hand for a quick look-see at data in common geospatial formats. For more in-depth analysis and visualisation I use a combination of spatial extensions in SQL, Python and browser technology.

I found the case studies the most useful part of this book, these are from a wide range of authors and describe real life examples of the ideas discussed in the main text. The main text uses the hypothetical ski resort of Happy Valley as a long running example. As befits a proper undergraduate introduction there are lots of references to further reading.

Despite its sometimes dated feel Introduction to Geographic Information Systems does exactly what it says on the tin. 

Mar 22 2016


Picture1A new job has brought me a new mode of transport for my daily commute. No longer do I spend an hour and a half on Merseyrail each day, instead I cycle across Chester (8 miles or 50 minutes a day). This isn’t a novelty to me, we lived in Cambridge for nearly 10 years and everybody cycles there. Although I passed my test many years ago, I don’t drive. So when it came to my new job cycling was the obvious way to work. Some people take the bus but for me that would mean one bus into the centre of town and one bus back out again – it’s quicker to cycle.

I’m a cycling commuter, rather than a dedicated cyclist who dons lycra and takes up a fancy road bike for the cycle to work. I wear a running top and cycling windproof but work shoes and trousers. The greatest innovation since my Cambridge days is the “transformer panniers” which convert from panniers to rucksack, ideal for day trips to London when I cycle to Chester’s main station. I treated myself to a new bike for the commute – a Rayleigh Loxley – cost equivalent to 3 months of Merseyrail travel to Liverpool.

I get wet surprisingly infrequently, I’ve flipped between shorts and rainproof trousers for rainy days. Winter rain on bare legs gives one an expensive-spa tingling sensation. I find waterproof trousers a bit clammy. Snow and ice haven’t been a problem this year. My dad was a life long cycling commuter, and recommended keeping a full change of clothes at to work in case of unexpected rain.

I try to be as visible as possible, my jacket is acid green – slightly short of full high viz, I have a high viz helmet cover, two sets of lights front and back and lights on my spokes. I considered going for the super-blingy spoke lights.

I’m well catered for at work, whilst car drivers are squeezed into a space which seems to be 25% too small, I have a bike shed pretty much to myself except for an occasional motorbike and at most two other bikes. Not only that my bike is guarded through the day by a steady stream of smokers! If I wanted I could have a shower.

Amongst my colleagues I’m viewed as something of a novelty, of the 100 or so people on site I’m the only one who cycles regularly and there are rarely as many as three bikes in the shed. A few people have asked about my ride, their main concern seems to be safety.

I’ve found optimising my route has taken a while. There’s a chunk of cycle route on the way out of Chester towards the Business Park, that bit’s fine. The route expires shortly before I reach my destination which is inconvenient, cycling three sides of the Business Park to get to my office seems excessive and it’s on dual carriageway with poor crossings – there is no cycle route. The piece of the road out of town which gets me fairly directly to my office is a bit narrow, as is the fragment of pavement that I’d need to traverse. A twisty path across the end of the Business Park is clearly not designed to cycle, and is unlit with an awkward gate at the end. A rather lovely looking route along Duke’s Drive is blocked at the Business Park end, this is a pity.

The rest of the route is more a case of finding the quietest roads, cycling through the town centre is not great – it’s cobbled, has a one way system and the pedestrians dodge backward and forward unpredictably. The pavements on the Grosvenor bridge are a bit too narrow, and the roadway is too. So you either menace pedestrians or have large vehicles itching to get past you.

It seems my cycling is more reliable than driving, two or three times in the last few months a large fraction of the people I work with have been held up by up to an hour by traffic.

The only thing I really miss about the train is the lost reading time.

(Click here for an Google Map of my route)

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