Tag: women writers

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.

Dec 17 2015

Book review: The Invention of Nature by Andrea Wulf

inventionofnatureThe Invention of Nature by Andrea Wulf is subtitled The Adventures of Alexander von Humboldt – this is his biography.

Alexander von Humboldt was born in Berlin in 1769, he died in 1859. The year in which On the Origin of Species was published. He was a naturalist of a Romantic tendency, born into an aristocratic family, giving him access to the Prussian court.

He made a four year journey to South America in 1800 which he reported (in part) in his book Personal Narratives, which were highly influential – inspiring Charles Darwin amongst many others. On this South American trip he made a huge number of observations across the natural and social sciences and was sought after by the newly formed US government as the Spanish colonies started to gain independence. Humboldt was a bit of a revolutionary at heart, looking for the liberation of countries, and also of slaves. This was one of his bones of contention with his American friends.

His key scientific insight was to see nature as an interconnected web, a system, rather than a menagerie of animals created somewhat arbitrarily by God. As part of this insight he saw the impact that man made on the environment, and in some ways inspired what was to become the environmentalist movement.

For Humboldt the poetry and art of his observations were as important as the observations themselves. He was a close friend of Goethe who found him a great inspiration, as did Henry David Thoreau. This was at the time when Erasmus Darwin was publishing his “scientific poems”. This is curious to the eye of the modern working scientist, modern science is not seen as a literary exercise. Perhaps a little more effort is spent on the technical method of presentation for visualisations but in large part scientific presentations are not works of beauty.

Humboldt was to go voyaging again in 1829, conducting a whistle-stop 15,000 mile 25 week journey across Russia sponsored by the government. On this trip he built on his earlier observations in South America as well as carrying out some mineral prospecting observations for his employers.

Despite a paid position in the Prussian court in Berlin he much preferred to spend his time in Paris, only pulled back to Berlin as the climate in Paris became less liberal and his paymaster more keen to see value for money.

Personally he seemed to be a mixed bag, he was generous in his support of other scientists but in conversation seems to have been a force of nature, Darwin came away from a meeting with him rather depressed – he had not managed to get a word in edgewise!

I’m increasingly conscious of how the climate of the time influences the way we write about the past. This seems particularly the case  with The Invention of Nature. Humboldt’s work on what we would now call environmentalism and ecology are highly relevant today. He was the first to talk so explicitly about nature as a system, rather than a garden created by God. He pre-figures the study of ecology, and the more radical Gaia Hypothesis of James Lovelock. He was already alert to the damage man could do to the environment, and potentially how he could influence the weather if not the climate. There is a brief discussion of his potential homosexuality which seems to me another theme in keeping with modern times.

The Invention of Nature is sub-subtitled “The Lost Hero of Science”, this type of claim is always a little difficult. Humboldt was not lost, he was famous in his lifetime. His name is captured in the Humboldt Current, the Humboldt Penguin plus many further plants, animals and geographic features. He is not as well-known as he might be for his theories of the interconnectedness of nature, in this area he was eclipsed by Charles Darwin. In the epilogue Wulf suggests that part of his obscurity is due to anti-German sentiment in the aftermath of two World Wars. I suspect the area of the “appropriate renownedness of scientific figures of the past” is ripe for investigation.

The Invention of Nature is very readable. There are seven chapters illustrating Humboldt’s interactions with particular people (Johann Wolfgang von Goethe, Thomas Jefferson, Simon Bolivar, Charles Darwin, Henry David Thoreau, George Perkins Marsh, Ernst Haeckel and John Muir). Marsh was involved in the early environmental movement in the US, Muir in the founding of the Yosemite National Park (and other National Parks). At first I was a little offended by this: I bought a book on Humboldt, not these other chaps! However, then I remembered I actually prefer biographies which drift beyond the core character and this approach is very much in the style of Humboldt himself.

Nov 14 2015

Book Review: Canals: The making of a nation by Liz McIvor

canalsCanals: The making of a Nation by Liz McIvor is a tie-in with a BBC series of the same name, presented by the author. It is about canals in England from the mid-18th century through to the present day although most of the action takes place before the end of the 19th century.

The chapters of the book match the episodes of the series which are thematic, rather than chronological. Each chapter introduces a different topic, loosely tied to a particular canal.

The book starts with a discussion of the growth of London, and the Grand Junction canal linking it to Birmingham. The guild system was a factor in limiting the growth of the capital until the mid-18th century. The “Bubble Act” of 1720, enacted in the aftermath of the South Sea Bubble likely also had an impact. It prevented the formation of any joint stock company without an act of parliament to approve. It was repealed in 1825 before the railways saw their enormous growth. The Grand Junction canal was built as Birmingham became a manufacturing hub and London a great city with many requirements for daily life, and also a showroom to at least the United Kingdom, if not the world.

I was chastened to discover that the Bridgewater canal, one of the earliest of “canal boom” projects of the 18th century is only just up the road from me in Chester. I’d always assumed it was close to the town of a very similar name in Somerset! Bridgewater is named for the Duke of Bridgewater, Francis Egerton, for which the pub just over the road from me is presumably named. The Bridgewater canal was built around 1760, linking the Duke’s coal mines at Worsley to Manchester. With this revelation I realise that the Bridgewater canal and the Liverpool to Manchester railway, the first exclusively steam railway, are sited very close to each other.

Support for manufacture was the theme of canal building in the North of England, and also around Birmingham with canals built to move bulky raw materials to factories placed to benefit from hydraulic power, and benevolent climates for the processing of materials such as cotton. Manufacturers such as Josiah Wedgewood were keen to see their fragile wares safely make the outward journey to the showrooms of London.

The Kennet and Avon canal was built to provide navigable water access from Bristol to London. William Smith, who produced the first geological map of Great Britain is introduced in this chapter. I read more about him in The Map that Changed the World by Simon Winchester. The digging of canal cuts and tunnels reveal the local geology. Nowadays we see canals as bucolic thoroughfares but when they were built they were raw cuts indicating industrialisation.

The Manchester Ship Canal was opened in 1894 to bypass the port of Liverpool, these were the dying days of canal building. 154 died in its construction and 1404 were seriously injured from a workforce of 16,361. For comparison, projects such as the 2012 London Olympics and the close-to-completion Crossrail project are of similar scale yet have casualty numbers hovering around zero although these are best-in-class projects for health and safety. In this chapter McIvor talks more of the Irish “navigators” who built the canals, and something of the early trade union movement.

The families that worked the canals were seen as outsiders, once the long networks were set up they led an itinerant lifestyle with no fixed church or school for their children. The Victorian moralists arguing for improved conditions for the boat families seem to do so from the point of view of pointing out how bloody awful they were!

It’s interesting to see the likes of Thomas Telford and John Rennie cropping up repeatedly in this book. They have the air of rockstar engineers, not a niche found these days. Perhaps this is a result of the work of the Victorian writer, Samuel Smiles, who was very keen on self-improvement and wrote biographies of these men to promote his ideas.

To me the book lacks a little prehistory, the great boom for canal building in the UK was at the end of the 18th century but the very first “pound lock” in England was built in 1566 on the Exeter canal. What went on between these two times? And what was happening elsewhere in the world? Perhaps the answer here is that the canals in Britain never represented a technological revolution, they were always about the social and commercial climate being right.

Canals: The Making of a Nation is an unchallenging read, well-suited to a holiday. If you’re on a canal boat it won’t tell you much about the particular bridges and tunnels you pass over but it will give you a strong feeling for the lives of the people that built and used the canals, and why they were built in the first place.

Oct 31 2015

Book review: Effective Computation in Physics by Anthony Scopatz & Kathryn D. Huff

ecipThis next review, of “Effective Computation in Physics” by Anthony Scopatz & Kathryn D. Huff, arose after a brief discussion on twitter with Mike Croucher after my review of “High Performance Python” by Ian Micha Gorelick and Ian Ozsvald. This in the context of introducing students, primarily in the sciences, to programming and software development.

I use the term “software development” deliberately. Scientists have been taught programming (badly, in my view*) for many years. Typically they are given a short course in the first year of their undergraduate training, where they are taught the crude mechanics of a programming language (typically FORTRAN, C, Matlab or Python). They are then left to it, perhaps taking up projects requiring significant coding as final year projects or in PhDs. The thing they have lacked is the wider skillset around programming – what you might call “software development”. The value of this is two-fold – firstly, it is a good training for a scientist to have for careers in science. Secondly, the wider software industry is full of scientists, providing students with a good grounding in this field is no bad thing for their future employability.

The book covers in at least outline all the things a scientist or engineer needs to know about software development. It is inspired by the Software Carpentry and The Hacker Within programmes.

The restriction to physics in the title seems needless to me. The material presented is mostly applicable to any science, and those working in the digital humanities, undertaking programming work. The examples have a physics basis but not to any great depth, and the decorative historical anecdotes are all physics based. Perhaps the only exception to this is the chapter on HDF5 which is a specialised data storage system, some coverage of SQL databases would make a reasonable substitute for a more general course. The chapter on parallel computing could likewise be dropped for a wider audience.

The book is divided into four broad sections. Including in these are chapters on:

  • Command line operations;
  • Programming in Python;
  • Build systems, version control, debugging and testing;
  • Documentation, publication, collaboration and licensing;

Command line operations are covered in two chunks, firstly in the basic navigation of the file system and files followed by a second chapter on “Regular Expressions” which covers find, grep, sed and awk – at a very basic level.

The introduction to Python is similarly staged with initial chapters covering the fundamentals of the core language, with sufficient detail and explanation that I learnt some new things**. Further chapters introduce core Python libraries for data analysis including NumPy, Pandas and matplotlib.

Beyond these core chapters on Python those on version control, debugging and testing are a welcome addition. Our dearest wish at ScraperWiki, a small software company where I worked until recently, was that new recruits and interns would come with at least some knowledge and habit for using source control (preferably Git). It is also nice to see some wider discussion of GitHub and the culture of Pull Requests and issue tracking. Systematic testing is also a useful skill to have, in fact my experience has been that formal testing is most useful for those most physics-like functions.

The final section covers documentation, publication and licensing. I found the short chapter on licensing rather useful, I’ve been working on some code to analyse LIDAR data and have made it public on GitHub, which helpfully asks which license I would like to use. As it turns out I chose the MIT license and this seems to be the correct one for the application. On publication the authors are Latex evangelists but students can chose to ignore their monomania on this point. Latex has a cult-like following in physics which I’ve never understood. I have written papers in Latex but much prefer Microsoft Word for creating documents, although Google Docs is nice for collaborative work. The view that a source control repository issue tracker might work for collaboration beyond coding is optimistic unless academics have changed radically in the last few years.

I’d say the only thing lacking was any mention of pair programming, although to be fair that is more a teaching method than course material. I found I learnt most when I had a goal of my own to work towards, and I had the opportunity to pair with people with more knowledge than I had. Actually, pairing with someone equally clueless in a particular technology can work pretty well.

There is a degree to which the book, particularly in this section strays into a fantasy of how the authors wish computational physics was undertaken, rather than describing how it is actually undertaken.

To me this is the ideal “Software development for scientists” undergraduate text, it is opinionated in places and I occasionally I found the style grating but nevertheless it covers the right bases.

*I’m happy to say this since I taught programming badly to physics undergraduates some years ago!

**People who know my Python skills will realise this is not an earthshattering claim.

Jun 29 2015

Book review: Gut by Giulia Enders

Gut-by-giulia-endersIt seems a while since I last reviewed a book here. Today I bring you Gut: The Inside Story of our Body’s Most Underrated Organ by Giulia Enders.

The book does exactly what it says on the tin: tell us about the gut. This is divided into three broad sections. Firstly the mechanics of it all, including going to the toilet and how to do it better. Secondly, the nervous system and the gut, and finally the bacterial flora that help the gut do its stuff.

The writing style seems to be directed at the early to mid-teenager which gets a bit grating in places. Sometimes things end up outright surreal, salmonella wear hats and I still don’t quite understand why. The text is illustrated with jaunty little illustrations.

From the mechanical point of view several things were novel to me: the presence of an involuntary internal sphincter shortly before the well-known external one. The internal sphincter allows “sampling” of what is heading for the outside world giving the owner the opportunity to decide what to do with their external sphincter.

The immune tissue in the tonsillar ring was also a new to me, its job is to sample anything heading towards the gut. This is most important in young children before their immune systems are fully trained. Related to the tonsils, the appendix also contain much immune tissue and has a role in repopulating the bacteria in the large intestine with more friendly sorts of bacteria following a bout of diarrhoea.

The second section, on the nervous system of the gut covers things such as vomiting, constipation and the links between the gut and depression.

The section on the bacterial flora of the gut gathers together some of the stories you may have already heard. For example, the work by Marshall on Helicobactor Pylori and its role in formation of stomach ulcers. What I hadn’t realised is that H. Pylori  is not thought to be all bad. Its benefits are in providing some defence against asthma and autoimmune diseases. Also in this section is toxoplasmosis, the cat-born parasite which can effect rats and humans, making them more prone to risk-taking behaviour.

I was delighted to discover the use to which sellotape is put in the detection of threadworms – potential sufferers are asked to collect threadworm eggs from around the anus using sellotape. I can imagine this is an unusual experience which I don’t intend to try without good reason.

There is a small amount of evangelism for breast-feeding and organic food which I found a little bit grating.

As usual with electronic books I hit the references section somewhat sooner than I expected, and here there is a clash with the casual style of the body of the book. Essentially, it is referenced as a scientific paper would be – to papers in the primary literature.

I don’t feel this book has left me with any great and abiding thoughts but on the other hand learning more about the crude mechanics of my body is at least a bit useful.