Tag Archive: biology

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.

Apr 05 2014

Book review: Darwin’s Ghosts by Rebecca Stott

darwinsghosts_bookcoverCharles Darwin’s On the Origin of Species was rushed into print after a very long gestation when it became clear that Alfred Russell Wallace was close to publishing the same ideas on evolution. Lacking from the first edition was a historical overview of what went before, pertinent to the ideas of evolution. On the occasion of the publication of the first American edition, Darwin took the opportunity to address the lack. Darwin’s Ghosts: In search of the first evolutionists by Rebecca Stott is a modern look at those influences.

After an introductory, motivating chapter Darwin’s Ghosts works in approximately chronological order.  Each chapter introduces a person, or group of people, who did early work in areas of biology which ultimately related to evolution. The first characters introduced are Aristotle, and then Jahiz, a Persian scholar working around 860AD. Aristotle brought systematic observation to biology, a seemingly basic concept which was not then universal. He wrote The History of Animals in about 350BC. The theme of systematic observation and experimentation continues through the book. Jahiz extended Aristotle’s ideas to include interactions of species, or webs. His work is captured in The Book of Living Beings.

Next up was a curiosity over fossils, and the inklings that things had not always been as they were now. Leonardo Da Vinci (1452-1519) and, some time later, Bernard Palissy (1510-1590) are used to illustrate this idea. Everyone has heard of da Vinci. Palissy was a Hugenot who lived in the second half of the 16th century. He was a renowned potter, and commissioned by Catherine de Medici to build the Tuileries gardens in Paris but in addition he lectured on natural sciences.

I must admit to being a bit puzzled at the introduction of Abraham Trembley (1710-1784), he was the tutor of two sons of a prominent Dutch politician. He worked on hydra, a very simple aquatic organism and his wikipedia page credits him as being one of the first experimental zoologists. He discovered that whole hydra could regenerated from parts of a “parent”.

Conceptually the next developments were in hypothesising a great age for the earth coupled to ideas that species were not immutable, they change over time. Benoît de Maillet (1656-1739) wrote on this but only posthumously. Similarly Robert Chambers (1802-1871) was to write anonymously about evolution in Vestiges of the Natural History of Creation first published in 1844. Note that this publication date is only 15 years before the first publication of the Origin of Species.

The reasons for this reticence on the part of a number of writers is that these ideas of mutability and change collide with major religions, they are “blasphemous”. This becomes a serious issue over the years spanning 1800. Erasmus Darwin, Charles’s grandfather, was something of an evolutionist but wrote relatively cryptically about it for fear of his career as a doctor. I reviewed Desmond King-Hele’s biography of Erasmus Darwin some time ago. At the time when Erasmus wrote evolution was considered a radical idea, both in political and religious senses. This at a time when the British establishment was feeling vulnerable following the Revolution in France and the earlier American revolution.

I have some sympathy with the idea that religion suppressed evolutionary theory, however it really isn’t as simple as that. The part religion plays is as a support to wider cultural and political movements.

The core point of Darwin’s Ghosts is that a scientist working in the first half of the 19th century was standing on the shoulders of giants or at least on top of a pile of people the lowest strata of which date back a couple of millennia. Not only this, they are not on an isolated pinnacle, around them are others also standing. Culturally we are fond of stories of lone geniuses but practically they don’t exist.

In fact the theory of evolution is a nice demonstration of this interdependence – Darwin was forced to publish his theory because Wallace had essentially got the gist of it entirely independently – his story is the final chapter in the book. For Wallace the geographic ranges of species were a key insight into forming the theory. A feature very apparent in the area of southeast Asia where he was working as a freelance specimen collector.

Once again I am caught out by my Kindle – the book proper ends at 66% of the way through, although Darwin’s original essay is included as an appendix taking us to 70%. Darwin’s words are worth reading, if only for his put-down of Richard Owen for attempting to claim credit for evolutionary theory, despite being one of those who had argued against it previously.

I enjoyed this book, much of my reading is scientific mono-biography which misses the ensemble nature of science which this book demonstrates.

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.

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