Tag: biology

Mar 18 2024

Book review: An Immense World by Ed Yong

My next review is of An Immense World by Ed Yong, subtitled How Animal Senses Reveal the Hidden Realms Around Us. I reviewed Yong’s previous book, I Contain Multitudes a while back. Somewhat foolishly I was slightly reluctant to pick this one up since I felt I was clued up on the “five senses”. I was incredibly wrong about this quick judgement. First of all, “five senses” are a human-centric view promulgated by the ancient Greeks, secondly it turns out we have been learning a lot about animal senses in my lifetime and show no signs of letting up.

The book is divided into 12 reasonably long chapters, treating smells and tastes, light, colour, pain, heat, contact and flow, surface vibrations, sound, echoes, electric fields, and magnetic fields. Finishing with a chapter on how senses work together and one on the pollution of the senses in the natural environment with artificial light and sound. We can see here the traces of the original five senses but some are split (light and colour, sound and echoes), taste and smell are merged; magnetic fields and electric fields are new introductions.

A key concept which is found throughout the book is the idea of “umwelt”, the perceptual world of an organism, which was coined by Jakob von Uexküll in 1909. Touching on the penultimate chapter first, this “umwelt” is almost impossible for us to fully appreciate – we can’t even be sure how the senses we share are experienced by other animals. Let alone how they work together with other senses that we don’t have.

One comfort of this book is that it turns out that human senses are not that bad. Yong cautions though that absolute comparisons across species are often wrong, and don’t account for large variations between individuals. His goal is to talk about diversity rather than ranking. A general theme is that although some animals might exceed us in terms of acuity, often it is the speed at which a response can be made that is the critical factor.

All of the chapters involve Yong talking to scientists, not just about the science but how and where it is done, which is engaging.

For smell the key ability that animals have over humans is better sampling so that scent traces can be followed, snakes do this with their forked tongues whilst dogs do so with subtly designed airways. I was also interested to learn that sea birds are sensitive to dimethyl sulphoxide which is an indicator for a bountiful ocean, and whose concentration likely serves as a large scale map. Taste is covered in just a couple of pages, essentially it is used by animals as a final go/no go decision on eating stuff – smell is a much more subtle sense.

It turns out human vision is pretty good compared to other animals, at least in certain aspects. Only eagles and other raptors have better acuity, certain flies have vision which is up to 10 times faster than ours. Many animals can sense light outside the human visual range, in the ultra-violet and infra-red and use this ability for specific purposes. I think the key takeaway for me was that the human visual system is not a blueprint for all visual systems, mantis shrimps, for example have a ridiculous number of different types visual receptors but they are used in a very different way to ours – almost like a set of special purpose triggers for motion, colour, light direction rather then general receptors whose signals are processed by the brain. It also seems that the colour vision is just not that important for survival – many people get by with impaired colour vision, and although colour vision like ours is not rare amongst certain groups it is in no way necessary for survival.

Yong makes a point about how our own senses guide our view of the mental world of other animals, we see cows as passive because they are not always looking around at their environment, as we do but they have virtually panoramic vision so they don’t need to constantly move their heads to see what is going on around them.

The chapter on pain starts with the naked mole-rat, whose tolerance of very high levels of carbon dioxide in their burrows is enabled by their limited ability to sense the pain induced by acidic substances (carbon dioxide forms carbonic acid). Much of pain research seems to be about belatedly realising that all manner of animals feel pain, and perhaps we shouldn’t inflict it.

Heat is generally detected by the TRP channel proteins, with different variants responsible for for different temperatures including “dangerously hot” and “dangerously cold” the temperature at which they are triggered varies from animal to animal. Melanophila (fire) beetles have incredibly sensitive heat sensing organs that can detect fires by their infra-red emissions from miles away. Similarly snakes are able to detect the direction heat is coming from, with signals processed alongside sight.

It turns out that touch is quite a varied sense, we think in terms of our fingers touching solid surfaces but for many animals the feel of flow in water is more important. The feeling of flow of water helps predators catch their prey, and fish to school together. Related is sensitivity to surface vibrations, which insects and other invertebrates have developed to an incredible degree. The songs of certain insects in surface vibrations are as sophisticated as bird song.

My favourite fact from the chapter on sound is that owls have one ear higher than the other so that they can locate sounds vertical by arrival time. I also learned that zebrafinches have very high sensitivity to the fine structure of their songs but are less sensitive to the notes they sing, it made me think a little of “tone” in guitar playing.

We should see echolocation as touching with sound, it wasn’t until the 1930s that it was appreciated that bats echolocated, and rather later for dolphins. Echolocation can be remarkably sensitive, dolphins can not only identify different materials from echolocations but they can match an object “seen” with echolocation to one “seen” with their eyes. Military interest in echolocation is essentially a result of a recognition that human technology lags biology.

Another novel sense, as far as humans are concerned, is electric. It has long been known that some fish used electricity as a weapon, but only in the 1950s was it recognised that it was also used for sensing. There are two types of electrosensing, one is active – like echolocation but it is omnidirectional and there is no wait for a signal return. The second is passive, some animals can detect the weak electric fields of animals going about their normal business. In common with echolocation the animals that use it have exquisite control over the frequencies, and sequences, of the probe pulses they generate.

Sensitivity to magnetic fields is the most elusive of senses, it has only been recognised relatively recently and we still don’t know for sure exactly how animals are sensitive to magnetic fields – there has been no conclusive identification of the receptor cells.

Astronomers have long been concerned with light pollution but it has only been more recently that biologists have realised it is a significant threat to animals. Similarly with sound, we are sensitive to noise pollution close up but don’t appreciate the significant noise pollution in pristine-looking environments.

I thoroughly enjoyed this book, as I did I Contain Multitudes. The style is engaging, and the subject matter is fascinating.

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.