Tag: review

Feb 14 2011

Book Review: For all the tea in China by Sarah Rose

ForAllTeaChinaBookI’ve been on a bit of a reading spree: next up is “For all the tea in China” by Sarah Rose. This is the story of Robert Fortune and his trips to China in the mid-nineteenth century to obtain tea plants and the secret of tea manufacture for the East India Company to use in India.

Robert Fortune (1812-1880) was a botanist with a modest background. Starting his working life at the Royal Botanic Garden Edinburgh, he later became Curator of the Chelsea Physic Garden. These were relatively poorly paid posts, however there were few such positions to support a professional botanist without their own means of support. He made several substantial visits to the Far East, funded by the Horticultural Society of London and the British East India Company. He died a wealthy man in large part through the wide range of plant introductions he had made, as well as through sales of artefacts he had acquired in the Far East. The list of introductions is well worth a skim through for the modern gardener:

The East India Company had been given a monopoly of trade to the Far East in 1600, through this monopoly they had built a lucrative trade in silk and tea from China, as well as effectively running India. The trades from China were matched with trades into China of opium from India, by the middle of the 19th century addiction to opium was a significant problem in China. The volume of trade it brought made the East India Company a very significant contributor to British government income (of order 10%). Although there are now many global corporations, the East India Company was one of the first and in many ways most powerful. The company was ultimately to lose its dominance following the Indian Mutiny in 1858, and was finally wound up in 1874. The mutiny was likely the cumulation of a long process since the monopoly that the East India Company enjoyed was not popular with free-marketeers who were starting to come to the fore.

At the time of Fortune’s first trip to China in 1845 the English had long been drinking tea imported from China, in exchange for opium grown in India. The English drank both green and black teas, although unlike the Chinese they added milk and sugar (obtained from another British colonial outpost). The Chinese were keen to keep the secret of both the tea plant, and its manufacture into tea leaves for making tea. Whilst the British, in particular the East India Company were keen to get these secrets believing (correctly) that tea would grow well in Himalayan India and would make a good profit. Some tea was already being grown in the Assam district of India but is was derived from inferior Chinese plants. The tea plant is Camellia sinensis a close relative of the decorative camellias of which Fortune also introduced some species.

Before Fortune’s first visit to China it had not even been established that black tea and green tea came from the same plant, but were processed differently. His trips required considerable subterfuge: Westerners had only recently been allowed into anywhere other than a limited number of ports in China, as a result of the first Opium War and Fortune’s activities went considerably beyond what was allowed even under these revised regulations. One of Fortune’s discoveries was that green tea had been coloured by the Chinese for the export market using Prussian Blue (which is toxic) and gypsum. Following a couple of false starts he was eventually able to transport a large number of highest quality tea plant seedlings to Darjeeling in India, as well as providing skilled tea makers and extensive notes on the tea making process.

The key to Fortune’s success in shipping out tea plants from China were Wardian cases, these are essentially sealed glass environments containing soil and some water. Plants, or more importantly, troublesome seeds could be sealed into these containers and as long as they remained sealed, and given some light there would be a good chance of their biological cargo surviving a lengthy sea journey through a range of climates. Prior to this discovery long distance transplantations were tricky. Nowadays we see Kew Gardens as largely a place of leisure, but in the 19th century it was very much at the heart of the Empire in terms of facilitating the movement of plants around the world for commercial reasons. This type of activity was also an early interest of the Royal Society.

It’s difficult not to draw parallels between the state sanctioned opium trade which the United Kingdom used to support, and its current attitude to drug smuggling. Nor between the industrial espionage of the East India Company in the 19th century, and the current issues with the Chinese approach to intellectual property.

I found the sections of the book reporting Fortune’s travels a bit unfulfilling: they seemed to be a sequence of travel anecdotes involving the mischief caused by his Chinese servants – this style does affect other parts of the books. However, more generally the book made me curious to know more about the East India Company, the Opium Wars and so forth and I felt I’d learnt something about the introduction of tea to India.

I’m tempted by Fortune’s book: Three years’ wanderings in the Northern Provinces of China 

Feb 10 2011

Book review: The Immortal Life of Henrietta Lacks by Rebecca Skloot

HenriettaLacksThe Immortal Life of Henrietta Lacks by Rebecca Skloot is an unusual book. It is part cell biology: the story of cell-lines kept alive perpetually in the laboratory; it is part story of Henrietta Lacks and her family from whom the first of these cell-lines (called HeLa) was derived; it is the story of how medical ethics has evolved over the last 60 years and it is part story of the story.

Henrietta Lacks’ cells were taken at the Johns Hopkins Hospital in Baltimore in 1951 and cultured by George Gey during her treatment for an aggressive cervical cancer from which she subsequently died at the age of thirty-one, later that year. Gey, with the help of Lacks’ cells, was the first person to successfully maintain a cell-line. The cells cultured are cancer cells rather than normal cells. Following his work a wide range of other cell-lines were cultured from a variety of organs and species, however it subsequently turned out that many of these were actually the HeLa cell-line which turned out to be particularly pernicious. Researchers would start with a culture of different cells, but they would die to be replaced by HeLa cell “contaminants”.

Once Gey had started the cell-line he gave them away freely to other researchers, however it was not very long before the HeLa cells were being sold commercially. An early application of the HeLa cell-line was in testing the newly developed Salk vaccine for polio, the first of many, many applications. More dubiously Chester Southam injected the cancerous cells into prisoners, and subsequently into many patients. This was with the view to seeing if they developed within the body, the problem was that the patients were not informed that the cells were cancerous. This practice ended when three young Jewish doctors aware of the Nuremburg Code, proposed as a result of post-war trials of Nazi doctors responsible for horrific human experimentation, refused to take part in the experiments.

To my mind the unique part of the book is the in depth coverage of Henrietta Lacks’ family through to the present day. Rebecca Skloot tells in detail the long persistent trail to talk to them, an African-American family who certainly have good reason to be suspicious of white people asking about Henrietta. The Lacks’ were never a model family but then there is no reason for them so to be. Race and medicine have a poor history in the US. The Tuskagee Syphilis experiments perhaps being the lowest point, in which African-Americans were denied effective treatment for the disease so the full course of its symptoms could be observed. Other racism is less direct, as relatively poor Americans the Lacks family have reduced access to the treatments arising from the cells of their ancestor. If she were a white child, Elsie Lacks, Henrietta’s mentally disabled daughter would not have died at the Crownsville State Hospital, certainly not in such terrible circumstances.

In 2011 the cell lines derived from Henrietta Lacks would not have been called HeLa. Possibly her cells would not have been collected at all, requiring full informed consent. Her name would have become known to all including the family. The family would not have learned of the gruesome details of her death at the “hands” of an aggressive cervical cancer via a book whose author had been given Henrietta Lacks medical records.

To my mind the real shortcomings of the scientists were not in what they did in the first instance but how they failed to support the Lacks’ not with money but with information. Until Skloot and Christoph Lengauer showed them and spoke to them, no-one had explained exactly what cells had been taken, what had been done with them, the significance of Henrietta Lacks to science or the specific knowledge of her condition did or did not have to their health in terms which they could understand; giving them a book on cell biology was not enough.

Skloot relates three stories of discoveries arising from a specific persons’ cells: the Lacks story and those of Ted Slavin and John Moore. Slavin was born a haemophiliac and as a result of the blood transfusions that he had to receive as a result of his condition he contracted Hepatitis B, however he did not succumb to this disease, he was immune. His doctor told him that this made him special, and that his blood was valuable and he subsequently profited from this knowledge by selling samples of his blood. John Moore, on the other hand, had hairy-cell leukemia and only discovered his blood was valuable after his doctor had patented his cell-line, he was subsequently involved in lengthy legal action to regain some control of his cells.

As a scientist whose work once touched, peripherally on human tissue culture and who recently had surgery from which such tissue was taken this is a somewhat uncomfortable story. In the project I worked on a postdoc was tasked with organising consent forms for, I think, blood vessels removed during a procedure i.e. they were a by-product. In this instance the specifics of the cells were not important – they were destined for frequently unsuccessful experiments. From our point of view the best possible outcome would been that the materials we had synthesised proved to be a congenial home for blood vessel wall cells. In this case nothing of monetary value is derived directly from the donors cells.

For my own part: I have no problem with researchers using my medical offcuts, I do feel unhappy with the idea that my specific cells might be valuable and that I might not get a proportion of that value.

Dec 30 2010

Book review: Mutants by Armand Marie Leroi

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

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

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

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

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

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

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

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

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

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

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

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

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

Nov 29 2010

Book review: Trilobites! by Richard Fortey

Triarthus_lateral
Triarthrus eatoni from Beechers Trilobite bed

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Aug 03 2010

Bamboo Pen and Touch

This is a tiny technology review. I recently bought a Wacom Bamboo Pen and Touch tablet, I say recently – I picked it up from the post office a little over 2 hours ago!

I used a Wacom tablet extensively as a mouse replacement at work some years back, and rather liked it. I only gave up because I moved into industry from academia and they are a bit more fussy about what I attach to the PC with which I am provided. At home the pen interface didn’t work quite so well because at the time I was quite keen on computer games, first-person shooters in particular, and controlling the little man in such a game using a pen is exceedingly challenging, to say the least.

The big benefit of a pen interface to my mind is that I can hold the pen whilst typing, then when I need to do some “mousing” I don’t have to scrabble around for the mouse. The whole process is just much smoother.

Unlike my original Wacom tablet this model will accept both pen and touch (with your fingers) input – I must admit I’m not really anticipating using the touch input. It appears to support the range of multi-touch gestures that a smartphone will accept. The active area of the tablet is roughly journalists notepad size which makes it small for an artist type tablet.

In terms of software, the installation attempts to guide you into some spoken tutorials which treat you like a moron – praising fulsomely your every successful pen-stroke. None of this is actually necessary since using a pen is largely intuitive and all you really need to learn is what the right-click simulation is (it’s the button on the body of the pen) and what the configurable buttons on the tablet do.

I have the tablet installed on a Windows 7 system, which is “ink” aware – it understands interacting via a pen: A little palette will pop out wherein the miracle of the “handwriting recognition” is performed – being able to read my scrawl is impressive but it’s a bit like a talking dog: it’s very clever but ultimately pointless on a computer with a keyboard. Office 2007 is also ink aware, you can open up a document and scribble on a separate layer – obviously the first thing I did was draw a big circle around something and wrote “bollocks” next to it.

The tablet also comes with some little mini-apps in which you can doodle and play games, you can also download more mini-apps. They don’t look fantastically useful.

All in all I think we’re going to be happy together – holding the pen feels just like old times!