Tag: biology

Jul 24 2021

Book review: The Code Breaker by Walter Isaacson

code_breakerFor my summer holiday reading I have The Code Breaker by Walter Isaacson, the author was recommended by a friend. It is the story of CRISPR gene editing, and Jennifer Doudna, one of the central characters in the development of this system and winner of the Nobel Prize for Chemistry in 2020 with Emmanuelle Charpentier for this work.

CRISPR is an acronym for "clustered regularly interspaced short palindromic repeats", a name derived from the DNA sequences that prompted its discovery. CRISPR are the basis of a type of immune system for bacteria against viruses. The CRISPR repeats form a fingerprint which matches the viral DNA and the associated system of enzymes allows a bacteria to snip out viral DNA which matches this sequence.

Whilst CRISPR is interesting in itself, it has applications in gene editing as a cure for disease in humans. CRISPR simply requires a short piece of RNA to match the target DNA in a gene to carry out its editing job. Short RNA sequences are easy to synthesise making CRISPR superior to earlier gene editing techniques. In addition there is potential to use CRISPR as a diagnostic tool for identifying infections such as covid and even as a cure for viral diseases. The Code Breaker does a good job of explaining CRISPR to a fair depth.

There is a section of the book on gene editing in humans and the moral issues this raises. Perhaps central to this is the story of He Jiankui, the Chinese scientist who led the work to carry out germ line edits to add a gene protective against HIV. Germ line gene edits mean editing the genes in an early stage embryo which means that all the cells in the child it gives rise to have the edit, including reproductive cells, hence the gene edit will be passed on to descendants. This is considered more radical than somatic cell gene editing where the changes stop with the person treated. I must admit to having some sympathy for He Jianku. Principally Western scientists had made a great show of considering the moral issues in germ line editing eventually deciding that the time was not yet right, but going against a moratorium or regulation in the area. This seems an ambiguous position to me, and the associated comments that Jiankui had done his work for publicity is a bit rich from a group of scientists who have been so competitive in the research over CRISPR. Jiankui conducted his research with the approval of his local ethics board but was subsequently disavowed by the Chinese authorities and then convicted.

Coronavirus is woven through the book because the work on CRISPR is very relevant here from a scientific point of view, and the key characters including the author are involved, as we all are! As far as I can tell Doudna et al have been involved heavily in conventional covid19 testing and have done research on CRISPR-based diagnostic tests which have great potential for the future – essentially they would allow any viral illness to be definitively tested at home (rather than a sample being sent off to do PCR test) – but are not yet used in production. Similarly there is the potential for CRISPR-based vaccines but these are not yet been deployed in anger. The Pfizer and Moderna vaccines are based on RNA but use older technology.

A chunk of the book covers the patent battles over CRISPR principally involving Doudna and her co-workers and Feng Zheng, scientist at the Broad Institute. The core of the patent dispute is how obvious the step from understanding the operation of the CRISPR system (which Doudna’s team demonstrated first) to applying it to human cells (which Zhang did first) is. I think my key learning from this part of the book is that I’m not very interested in patent battles! Tied up with the patent issue is the question of the great science Prizes which similarly give a winner takes all reward to a small group. The Nobel Prizes have a limit of three on the number of winners, so do more recently instituted prizes. Science simply isn’t done this way, and hasn’t been for a long time. There’s a group of at least a dozen scientist at the core of the CRISPR story and probably more, singling out a couple of people for a reward is invidious. It made me wonder whether the big science prizes are really about the prize giver rather than the winner.

The book is written in the more journalistic style that has arisen in scientific biography relatively recently, that’s to say there is a lot of incidental detail about where Isaacson met people and their demeanour than in older scientific biographies. I must admit I find this a bit grating, I’ve tended towards collective biographies recently rather than single person biographies which have a bit of a "great man" feel to them. However, I’m starting to make my peace with this new style – it makes science feel like a more human process, and makes for a more readable book. It’s fair to say that this is in no way a "great man" biography, although Doudna and her life and personality are a recurring theme other people get a similar treatment.

Feb 05 2021

Book review: Entangled Life by Merlin Sheldrake

entangled_lifeEntangled Life by Merlin Sheldrake is a book which came to me via my wife, as she read it she kept providing me intriguing nuggets of information about fungi so I thought I would read it next. For the older reader Sheldrake might be a familiar name, his father Rupert Sheldrake was something of a character perhaps best known for his theory of morphic resonance.

Entangled Life is not a dry, systematic study of fungi but rather a rambling exposition with much biographical detail. Each chapter contains a good description of some facet of fungi, alongside some broader discussion of the people and places Sheldrake visited to write the chapter and musings on the broader meaning of the facet.

The first chapter, entitled "A Lure", is on truffles, looking back this chapter is designed to entice us into reading further by talk of a very financially valuable, and desirable fungi. Sheldrake takes us to the woods of Italy for a truffle hunting trip providing scientific detail alongside the human story.

Next comes "Living Labyrinths", inviting us to change our mindset about how an organism is put together. Fungi are not like plants or animals, they are a network composed of hyphae. Different fungi have different network structures, and the hyphae in a network can be arranged in different large scale structures such as chords and rhizomorphs. The mycelium network can transport substances over distances, and also signals, although it isn’t clear how they do this. Mycelium networks can "solve" maze-like problems, I’ve seen reports of this in the past and I don’t see it as evidence of intelligence – essentially the networks solve a diffusion problem by using diffusion. They are a type of analogue computer.

"The intimacy of strangers" introduces us to lichens – fungi-algae symbionts. The structure of lichens and symbiosis were discovered in the second half of the 19th century. The discovery was something of a revelation, previously there had been organisms and their parasites – none of the cooperation that symbiosis is founded on. It is fair to say we are still learning a lot about lichens, including the fact that the partners in lichens can be quite fluid. Lichens challenge our ideas about what it means to be a species.

"Mycelial Minds" is definitely the most terrifying chapter – it details how ophiocordyceps takes over carpenter ants and has them behaving in very specific ways (climbing to a high point on a stem and waving their legs around) for the furtherance of the fungi. Also discussed in this chapter are LSD and the Psilocybin mushrooms, fungi or their derivatives that are psychoactive in humans.

"Before roots" covers the long standing relationship between plants and fungi – it is proposed that it was fungi that hauled plants out of the waters and onto land, hundreds of millions of years ago. Fungi specialise in accessing minerals locked in rocks, and the remains of lichens would have formed the first soils on land (they still do, when new land from volcanic activity or otherwise is exposed). This would have provided water-borne plants with a mechanism for accessing nutrients on dry land. Fungi still form a critical partnership with plants, extending and enhancing the plant’s own root network in exchange for energy derived from the sun by photosynthesis – fungi cannot photosynthesise themselves.

"Wood wide webs" talks about how forests are knitted together with mycelium networks which link one tree to another, and another. In a small patch of woodland one tree was found to be linked to 47 others via the mycelium network. The mycelium network can transmit some of the plant distress signals as well as moving nutrients from one tree to another. In some ways Sheldrake dislikes the reference to the Wood Wide Web because it sees the trees as the "servers" in network and the fungi reduced to the lowly cables and routers.

"Radical mycology" – the science side of this chapter is the development of fungi for the remediation of pollution and producing recyclable "green" materials. It starts with a discussion on the coal measures laid down in the Carboniferous period – this was a time when the mechanisms for decomposing wood were limited. Since then fungi have evolved which are efficient in degrading lignin – a key component in wood – this is a rare skill. The human side is the longstanding mycology counter culture, fungi have not had a high academic profile but have attracted an enthusiastic amateur following initially interested in psilocybin mushrooms but now more generally involved in research and discovery.

"Making sense of fungi" – the scientific element of this chapter is around fungi particularly their use in making alcohol. I was intrigued to learn of the "drunken monkey" hypothesis of our taste for alcohol – essentially our ape ancestors used alcohol as an indicator to find ripe (or even over-ripe fruit). Humans have a mutation in an enzyme which enables them to process alcohol, otherwise it would be (more) toxic to us – they evolved this ability before they started deliberate fermentation to make alcohol.

One of the recurring themes of this book is how relatively little studied fungi are, they don’t fit into our neat, longstanding picture of the living world consisting of plants and animals, and individuals rather than symbionts being the fundamental unit of biological thought.

I found Entangled Life a fascinating and enjoyable read, and I didn’t even have to buy the book!

Mar 05 2020

Book Review: The Egg & Sperm Race by Matthew Cobb

egg_and_spermI follow quite a few writers on Twitter, and this often leads me to read their books. The Egg & Sperm Race by Matthew Cobb is one such book. It traces the transition in thinking on the reproduction of animals, including humans, which occurred during the second half of the 17th century.

Prior to this we had some pretty odd ideas as to how animals reproduced, much of it carried over from the Ancient Greeks. Ovid and Virgil both claimed that you could make bees by burying a bull with its horns protruding from the ground, waiting and then cutting off the horns to release the bees! This confusion is not surprising, the time between mating and the appearance of young is quite long, and the early stages of the process are hidden by being very small, and deep inside animals.

A random “fact” I cannot help but repeat is that Avicena wrote that “a scorpion will fall dead if confronted with a crab which a piece of sweet basil basil has been tied”. I wonder sometimes with quotes such as these whether they are a result of mistranslation, or a bored scribe. The point really is such ideas were not discounted out of hand at the time. The Egg & Sperm Race starts with a description of da Vinci’s copulating couple which is beautiful but wrong – da Vinci connects the testicles to the brain – these structures do not exist.

The heart of the action in The Egg and Sperm Race is in the Netherlands, in England the Royal Society showed relatively little interest in generation aside from some experiments on the spontaneous generation of cheese mites. The Chinese and Arab scholars who had worked in various fields showed little interest in generation.

The central characters are Jan Swammerdam, Niels Stensen (known as Steno) and Reinier de Graaf, who met in Leiden at the university in the early 1660s when they were in their early twenties. Swammerdam and Steno were a little older than de Graaf and were close friends. Soon after meeting in Leiden they visited Paris where they continued to build contacts in the scientific community.

In understanding generation a first step was to realise that all animals came from other animals of the same species, and that this meant mating between two animals of the same species. Steno went to Italy and worked with Francesco Redi’s whose experiments were key to this, he checked exhaustively that insects did not arise from the putrefaction of material. Swammerdam was also interested in insects, classifying four different types of invertebrate development and showing that in moths traces of the adult form are found in the caterpillar. At the time it was not clear that the larval stage and the adult were the same species.

A second step was to realise that all animals came from eggs of some sort, William Harvey –  of blood circulation fame – did experiments in this area but although he stated this conclusion but it was not well-supported by his experiments. In the period at the beginning of this book, the role of the ovary was not understand. Steno carried out dissections on fish both those that laid eggs, and those that gave birth to live young from this he concluded that the ovaries were the source of eggs and asserted that this was the case for humans as well. This idea rapidly gained acceptance.

The discovery of the human egg, and its origins in the ovary, was the subject of a dispute between de Graaf and Swammerdam on priority. The Royal Society decided in favour of van Horne with whom Swammerdam had worked on the dissection and illustration of female reproductive anatomy. To modern eyes the written record of the dispute, in letters, and publications is surprisingly personal. De Graaf died at the age of 32 just prior to the Royal Society decision. It was a difficult time in the Netherlands with the country at war with England and France with France troops invading parts of the country.

Leeuwenhook cast a spanner into the works with his microscopical studies, he observed spermatozoa but not the female egg and as a result became a “spermist”, believing that life came from the sperm in contrast to the “ovists” who believed life came from the egg. We now know that they are both right. The human egg was not observed until 1826 by von Baer. And I have to mention Spallazani’s experiments on frogs wearing taffeta shorts, demonstrating that male sperm was required to fertilise the female egg.

The final chapter covers events from the end of the 17th century or a little later to present day. Linneaus’s classification work, and Darwin’s theory of evolution follow on from some of the core realisations of this earlier period. Neither Linneaus’ work nor Darwin’s work make much sense if you don’t believe that animals (and plants) grow from eggs/seeds which came from the same species. It wasn’t until von Baer’s work in the early 19th century that the female egg was observed.

Aug 11 2018

Book review: Chrysalis: Maria Sibylla Merian and the Secrets of Metamorphosis by Kim Todd

merianChrysalis: Maria Sibylla Merian and the Secrets of Metamorphosis by Kim Todd has a self-explanatory title, it is about the life of Maria Sibylla Merian a scientific illustrator who lived 1647-1717, and the life cycle of insects – their metamorphosis.

“Scientific illustrator” does not feel like the right term for Merian. She actively collected insects, at all stages in their lifecycles to study how they developed. This involved learning how how to nurture the insects. Her illustrations showed the insects through the stages of their lives alongside the plants on which they lived and fed. This is close to a study of ecology which didn’t really gain recognition as an area of study until the early 19th century. In her fifties she spent a couple of years in Surinam where she continued her study of more exotic creatures.

She was born in Frankfurt where she lived until she married and moved to Nuremburg, also in what is now Germany. Her father, Matthäus Merian was an illustrator, as was her stepfather Jacob Marrel, her husband Johann Andreas Graff, was one of Marrel’s apprentices. In 1685 Merian left her husband to go to a religious community in the Netherlands (the Labadists in Wieuwerd) with her mother and two daughters. She left Wieuwerd in 1691 to live in Amsterdam where she stayed until her death in 1717, aside a two year trip to Surinam.

Surinam had been “visited” by Europeans in the 16th century, and the Dutch had gained control of it from the English in the late 17th century. The English got New Amsterdam, now New York, as a quid pro quo. The colony was under the control of the Dutch West India Company and Labadists had been amongst those that gone out to the colony, their stories returning with them to the community at Wieuwerd. Surinam was not unknown land but it was tropical, and the colonial government were keen to get people out to the country to make a more well-rounded society. Merian went there to study insects in the same way as she had done in Europe but was, to some degree foiled by the conditions: deep jungle, rife with disease. Nevertheless her study there led to the publication of her book: Metamorphosis insectorum Surinamensium. I must admit I’m rather tempted by this facsimile.

Merian received a good deal of encouragement from father and stepfather in pursing art but the guild and business systems of the time made it difficult for her to work professionally as an artist. She seems to have got by by forming relationships with a range of nature enthusiasts for whom she carried out commissions, selling her illustrations individually, and trading in specimens for cabinets of curiosities.

She appears to have been remarkably independent for the period. Caroline Herschel lived somewhat later than her in England but her work in astronomy was tied to her brother, William. Similarly her exact contemporary, Elisabeth Hevelius, who had her own reputation as an astronomer was closely coupled to that of her husband.

Merian lived in a time when the study of nature was evolving. People were still seriously asking whether certain forms of life appeared spontaneously (the Royal Society’s cheese mite experiments). Linneas had not yet created his nomenclature for living things. Gentlemen were populating “cabinets of curiosities” but they were disorganised assemblages of artefacts. She was a contemporary of Jan Swammerdam, Antonie van Leeuwenhoek and Robert Hook.

The past can be difficult to understand, the meanings of words can shift quite dramatically. For example, René Antoine Ferchault de Réaumur said “The crocodile is certainly a fierce insect, but I am not in the least disturbed about calling it one!”.

This is all to say that Merian could quite reasonably be described as working at the cutting edge of biology.

Merian is surprisingly well-documented, this seems to be as a result of a couple of factors. Her family were moderately high-profile and as publishers / illustrators naturally left substantial records. She published several books which were reprinted over the next hundred years or so, her illustrations appeared, sometimes unattributed, in other publications. A chunk of her papers were acquired by Peter the Great and ended up in St Petersburgh where they were re-discovered in the 1970s.

Her work seems to have attracted criticism in the early 19th century, on grounds of inaccuracy understandable, since by this time her books were over 100 years old. This criticism was possibly also driven by the changing character of naturalists, they were starting to professionalise, and no doubt also linked to her gender. Many of her male contemporaries had some funny ideas but this is often glossed over.

I enjoyed Chrysalis it covers Merian’s life in some detail whilst bringing in a good flavour of the times in which she lived and the people she interacted with.

May 06 2017

Book review: Where the Animals Go by James Cheshire and Oliver Uberti

animalsgoIt is becoming a tradition for me to receive a beautiful James Cheshire and Oliver Uberti coffee table book for my birthday. A couple of years ago it was The Information Capital, this year it was Where the Animals Go.

Where the Animals Go is a collection of stories and visualisations all relating to the tracking of animals, each story occupies at most a few pages and is accompanied by a couple of maps which trace the paths of one or more of the species in question across the earth. The maps are beautiful.

The book starts with an introduction which covers the evolution of animal tracking technology. The bulk tracking of the movement of animals on an hourly or faster basis has become easier with the advent of commodity GPS devices since the 1990s. Some of these raw data are now being published on aggregation websites such as Movebank.

Precursors to these GPS tracking systems are old-fashioned bird-ringing – a passive technique which relies on recapture of animals and has been around since the early 19th century. The Argos system relies on data from tags being transmitted to a small constellation of satellites – it has lower temporary and spatial resolution than GPS. There are also radio and acoustic tracking methods which have been around from the sixties.

In the text we discover how ants have been tracked in an artificial nest using tiny bar codes, and Daphnia zooplankton have been tracked with fluorescent nanoparticles in a tiny aquarium. Penguin colonies have been identified, and numbers estimated, from satellite imagery of the guano (posh word for poo) that they stand amidst.

I must admit to being a bit of an enthusiast for tracking myself, particularly when out skiing or walking. I used use GPS to geotag my photographs – parenthood has put a stop to such pursuits. I started using GPS about 10 years ago when the process was a bit clunky both in terms of the hardware and the software to process tracks. Nowadays I can record a GPS track on my watch or a mobile phone. So I can easily see how advances in technology relate to advances in the study of animal movement with GPS sensors becoming feasible for ever smaller animals.

After introducing the technology there are then three parts covering animals on the land, in the water and in the air.

The tracks of troops of baboons seemed most similar to the tracks of my Alpine skiing holidays. In this study a number of baboons from the same troop were tracked, this made it possible to see something of the leadership, or otherwise, behaviour of the baboons but this is actually unusual – in most cases a small number of individuals from a group are tracked.

Most entertaining are the tracks of animals who have been relocated for human convenience, and promptly return to the place from whence they came – pythons and crocodiles are in this group. Sadly, I suspect this type of behaviour does not end well for the animals concerned.

Related to this are those animals who live in close proximity to humans and find their why blocked by major highways, mountain lions in California – for example. Animal tracking can show the degree to which major highways cause a problem, and also show the way to solutions in providing corridors.

Sometimes tracking clears animals of what humans consider to be mis-deeds – the tracking, by acoustic sensors, of sharks in Hawaii falls into this category. More benignly it has been discovered that oilbirds in Venezuela did not simply foray out of their nesting caves at night and return at dawn, thus failing to carry out vital ecosystem services such as dispersing seeds. Instead GPS tracking showed that they spent days out in the forest foraging, and roosting in trees.

Generally the animals portrayed are depicted moving in a plane (mathematically speaking) across the land but sometimes they break out into the third dimension – an example is vultures spiralling upwards on thermals. Hang-gliding friends I know would be interested in this. Also included are the bar-headed geese, who migrate across the Himalayas, it turns out they generally stick to the lowest altitudes they can get away with, however they still exhibit great endurance in high altitude flying.

The accompanying text provides detail on what we see in the maps, and also some human interest in the scientists who collected the data.

Another beautiful book, and the references are sufficient for you to go and find out more about any of the individual stories. There is a dedicated website where you can see excerpts of Where the Animals Go.