"How Life Works" by Philip Ball

This book radically transformed my understanding of cellular biology. 

I'm not a biologist but I was a science teacher and I taught that the genome programs cells; that sections of DNA unwind and are used as templates to make strands of messenger RNA which then float out into the cytoplasm and are in turn used as templates for making proteins. That's not false. But, as Ball points out, that doesn't explain how some of my body cells develop into neurons and others, which have exactly the same DNA, into skin cells and others into blood cells and others into heart, lung, liver, spleen ...

By describing recent research on protein synthesis and embryo development, Ball shows that:

• Genes rarely have a unique function. The same gene which does one thing in a fruit fly can do something totally different in a human.
• Many morphologies are the result of combinations of genes.
• Genes can be 'switched' off or on by proteins. 
• Messenger RNA molecules seem to be made up of bits of heterogeneous nuclear RNA fragmented and then stitched together.
• The cells in multicellular life forms operate differently from bacterial cells.  
• Proteins fold because some sections of the protein chain attract water, others repel it. This also means that proteins can embed themselves into a cell wall.
• Changes in gene function can be caused by signals coming from outside the nucleus or even outside the cell itself. These signals can be electrochemical (as in neuron transmission), chemical (eg hormones), or even mechanical (eg when a cell is stretched). 
• Many developments involving proteins are combinatorial. This reduces 'noise' and makes the system more robust. If one enzyme doesn't work, another may be found to do the job. Molecular promiscuity with combinatorial fuzzy logic might be the only way for genetically identical cells to work together in diverse but specialised states. This also means that protein networks can develop new functions without losing old ones, which enables evolution to happen.
• Multicellularity has only happened twice: for plants and for animals (fungi don't count). There were significant changes in the ways that genes developed and communicated after the evolution of mammals and particularly placental mammals.  
• The epigenetic landscape is composed of a variety of bifurcating river valleys down which the cell tends to progress in a process called canalization. This landscape develops as the cells grow producing "a delicate dance of contingency and inevitability” like the growth of a city. (Ch 6) The valleys in the landscape can act as 'attractors' but genetic changes can alter where these attractors are.
• Cells have an awareness of their environment. Perhaps awareness of one’s surroundings is a fundamental feature of life.
• A random mixture of two morphogens, one an activator and one an inhibitor, in which the inhibitor diffused faster than the activator, creates patches in which one or the other morphogen predominates. This is responsible for eg patterned skins, the arrangement of hair follicles or feathers, the fractal branching of lung tissue, and even fingers (and fingerprints). 

This book also explained how a living cell, which appears to flout the second law of thermodynamics which insists that in an equilibrium system randomness tends to increase, can become increasingly organised. It points out that there are systems in physics, such as phase separation and crystallisation, which are inherently organised and that life appears to use these.  

I also learned:

• How tortoise shell cats get their markings and why 2999/3000 are female. 
• Why identical twins can be different from birth.
• Why planarian flatworms are effectively immortal. 
• How a human embryo develops and how an undeveloped embryo can be found inside the brain of itself developed twin. 
• That there is a gene called Sonic hedgehog. 
• How cells can 'request' the blood system to provide them with capillaries.
• Why humans mostly have their liver on the right, and their stomach and spleen on the left.

It was hard work. The information is very condensed and I needed to concentrate and take notes. But in the end I was rewarded in spectacular fashion. This is one of those books that provokes a paradigm shift, a revolution in the way one thinks.

Other brilliant books by Philip Ball that I have read include:

• Critical Mass: How One Thing Leads to Another 
• H2O: A Biography of Water
• The Devil's Doctor: Paracelsus and the World of Renaissance Magic and Science
• The Water Kingdom: A Secret History of China
• Beyond Weird: Why Everything You Thought You Knew About Quantum Physics is Different 

Selected quotes:

• “Looking to the genome for an account of  how life works is rather like ... looking to a dictionary to understand how literature works.” (Prologue)
• “There has never been a machine made by humankind that works as cells do.” (Prologue)
• “Life is a hierarchical process, and each level has its own rules and principles.” (Prologue)
• “The price of metaphor is eternal vigilance.” (Ch 1)
• “Cells commit to fates by noticing and assessing what their neighbours are doing. It's rather like voting with a show of hands: we might sneak a look at how others are voting before deciding.” (235)
• “Life doesn't make systems that can do or construct a single thing, that produces entities ... that embody a wide range of options ... In normal circumstances, the system converges on the outcome(s) favoured by natural selection, while still maintaining enough phenotypic variability to be evolvable. Evolution does not know ... what it is going to need tomorrow - so it must keep its options open.” (Ch 7)
• “Life ... can be considered as a computation that aims to optimise the acquisition, storage, and use of ... meaningful information.” (Ch 9) 

A superb book. August 2024; 460 pages

This review was written by the author of Bally and Bro, Motherdarling  and The Kids of God

"Where do camels belong?" by Ken Thompson

 This brilliant book by an ecologist is a polemic against the division of species in 'native' and 'alien'. He shows that the idea of 'naturalness' is wrong-minded by asking where camels belong: in the middle east or in North America (where they evolved and then went extinct) or in South America (where llamas and alpacas etc represent the greatest species diversity from the camel root) or in Australia (the only country where camels are feral).  He suggests that the myth of nativeness assumes something special about this moment in time, the writer of a key text, “Elton believed firmly that species belong to wherever they happen to be right now, irrespective of length of tenure or of where they had evolved or migrated from. More than that, he believed that belonging confers rights of occupancy, that these rights extend indefinitely into the future, and that natives are morally superior to aliens.” (Ch 2)

He goes on to suggest that the talk of 'invasive' aliens is based on a very few cases where an introduction (normally by humans) caused damage to an ecosystem and that normally the arrival of aliens increases biodiversity, or would do except that “Invasion biologists worry a lot about biodiversity, but only native biodiversity; introduced species are not allowed to contribute to biodiversity. alien species can never add to biodiversity.” (Ch 12). He suggests that most examples of harm are caused because human agency alters ecosystems and this provides an opportunity for new (alien) species to thrive where the established species can't (because their environment has been changed which means that “Blaming an alien for filling the gap left by declining natives looks like shooting the messenger.” (Ch 4)

He provides oodles of evidence and gives a short (and easy-to-read) course in biogeography and ecology. He demonstrates that the evidence for alien harm is often based on dubious science: “I was going to say that ... I debunk the myth that alien species constitute the second largest global threat to biodiversity (after habitat destruction). But on reflection I think that assertion has been debunked so often ... that it no longer deserves the status of a myth, and is best described merely as a straightforward lie.” Ch 2)

He lambastes the ridiculous ideas built upon the idea of nativeness as enshrined in laws which don't take account of the fact that most 'invasions' are done without (conscious) human agency: “Nowadays, for plants with the right kind of seeds, socks are a major dispersal pathway.” (Ch 1)

It's very convincing ... and made even better by an author who can really write well and is often very funny

And, of course, it has huge implications for humanity. Who is 'entitled' to the United States: the post-Columbian immigrants or the Native Americans? And the perjorative language used again 'invasive alien' plants and animals resonate quite strongly with the way some right-wing politicians talk about human immigrants. 

Selected quotes:

• “Conservation is a value-laden activity ... ‘Nativeness’ appears to offer the prospect of unambiguous attributes that make something worth conserving; or, in the case of its absence, worth exterminating, or at least controlling. To question this approach is close to heresy.” (Introduction)
• “Species are born, and then they die. That is, is they evolve by natural selection from earlier species, and eventually they go extinct.” (Ch 1)
• “By definition species evolved in one particular spot, but later they may spread to occupy a much wider range.” (Ch 1)
• “Brown tree ... snakes climb pylons and frequently short out power lines, causing power cuts. In fact somewhere on Guam experiences a snake-related power cut about every other day.” (Ch 3)
• “The modern world is essentially a mosaic of new ‘anthropogenic biomes’” (121) This is why “in the last few thousand years, and especially in recent centuries and decades ... being a rat or a weed has turned out to be the golden ticket in life.” (Ch 7)
• “The Wildlife and Countryside Act Schedule 9 ... lists the species that cannot legally be introduced into the wild ... it now includes several species of Cotoneaster ... spread far and wide by birds, none of which can be persuaded to read Schedule 9.” (Ch 8)
• “The difficulty here is the inevitable collision between the law, which deals in black and white absolutes, and ecology, where a grey fog predominates.” (Ch 8)
• “Assisted migration of endangered species is a small step in the direction of allowing them to compete on a playing field that still slopes uphill, but slightly less steeply than before.” (Ch 10)
• “Sometimes it seems many conservationists would prefer a species to go extinct than to survive somewhere it doesn't ‘belong’.” (Ch 10)

Great fun to read ... and eye-opening.

This review was written by the author of Motherdarling  and The Kids of God January 2022; 223 pages

"Metazoa" by Peter Godfrey-Smith

 Subtitled "Animal Minds and the Birth of Consciousness" this book, by the author of the brilliant Other Minds, asserts that consciousness is a characteristic of most animal thinking. 

His evidence is his extensive and detailed studies of marine life from sponges and corals to shrimps, fishes and octopuses. All living things, he suggests, sense and use what they sense to modify their actions: “Sensing has its raison d’etre in the control of action.” (Ch 3). Thus bacteria can move towards preferred chemicals, plants sense gravity and grow their roots downwards, animals detect food and move towards it etc. 

Most multicellular animals, he tells us can “modulate the interpretation of sensory information by the animal’s registration of what it is presently doing. ... If an animal does do this, it is now sensing the world in a way that tracks the divide between self and other.” (Ch 4) This is also the prime thesis of Andy Clark’s Surfing Uncertainty; that our consciousness is created by a repeated ‘error correction’ between what we expect to happen and what we sense happening; that dreams are experienced as unreal because they are only our uncorrected expectations.

This has led to the concept of self: “Subjectivity involves feelings and seemings; agency is doing and initiating. All living things (or all living things composed of cells) exhibit something like subjectivity and agency, but these features take a different form in the animal case.” (Ch 5)

It can also be very funny, for example in this description of an octopus fight: “Females quite often throw at males who are pestering them. On one occasion, a video shows a female octopus throwing debris repeatedly at one particular male over a period of a few hours. About half of these throws hit him, and others missed only because the male ducked or was belowdecks. Toward the end, the male who had been on the receiving end seemed to be getting used to these assaults; he began to duck quite early as the thrower began loading up, and the final broadsides went (mostly) over his head.” (Ch 6)

Selected quotes

• “A puzzle in front of us seems to resist the usual methods. What we should do in response is build knowledge around it, expecting that as we do this, the puzzle will transform and disappear.” (Ch 1) 
• “A human gut holds our food. In addition, our guts contain countless living bacteria, from which we benefit as long as things stay in balance. This kind of collaboration is extremely common in animals.” (Ch 2) This understanding of an individual human as some sort of ecosystem put me in mind of Turtles All the Way Down by John Green in which the heroine reflects, in chapter one: "Humans are approximately 50 per cent microbial, meaning that about half of the cells that make you up are not you at all. ... If half the cells inside of you are not you, doesn't that challenge the whole notion of me as a singular pronoun, let alone as the author of my fate."
• “This is the arthropod way of evolving: when in doubt, add some legs.” (Ch 4)
• “As evolution proceeded, animals became a new kind of intersection point, or nexus, in the world’s networks of causal pathways. When an animal picks up information of various kinds through the sense, it becomes a point at which lines converge. When it is an initiator of action, it becomes a point from which casual lines diverge.” (Ch 5)
• “An ongoing feature of philosophy is its generation of wildly exaggerated theories. ... This is a pathology of the field.” (Ch 5)
• “A lot of octopus conflict looks like ... a giant pillow fight, between pillows.” (Ch 6)

A thought-provoking book. It is sometimes a little heavy-going but some of the descriptions of marine fauna are wonderful.

December 2021; 281 pages

This review was written by the author of Motherdarling  and The Kids of God

"Other Minds: The Octopus and the Evolution of Intelligent Life" by Peter Godfrey-Smith

This is a beautifully written book about the intelligence of octopi and cuttlefish which are cephalopods. “If we can make contact with cephalopods as sentient beings, it is ... because evolution built minds twice over. This is probably the closest we will come to meeting an intelligent alien.” (p 9) Along the way it becomes an enquiry into what it means to have a consciousness. “For some animals, there's something it feels like to be such an animal. there is a self, of some kind, that experiences what goes on.” (p 10)

It starts tracing the evolution of the nervous system. After all, even bacteria can react to stimuli and therefore may be said to have some version of sentience:

• “The bacterium will swim in a straight line as long as the chemicals it senses seem better now than those it sensed a moment ago. If not, it’s preferable to change course.” (p 17)

The crucial factor is that the bacteria can in some sense detect the actions they themselves take. This feedback loop between sensory input and action and sensory input is the beginning of self awareness. And because one bacterium can detect things that other bacteria do it is the beginning of communication and socialisation. So when cells begin to get together in multicellular organisms we have the rudimentary mechanisms for a nervous system.

• “The receptors on the surfaces of bacterial cells are sensitive to many things, and these include chemicals that bacteria themselves tend to excrete” (p 18)
• “If a chemical is both produced and sensed by a particular kind of bacteria, it can be used by those bacteria to assess how many individuals of the same kind are around.” (p 18)
• “Chemicals that are made because they'll be perceived and responded to by others ... brings us to the threshold of signalling and communication.” (p 19)

At this stage I was getting excited. After all, Andy Clark in Surfing Uncertainty, working in the world of artificial intelligence, suggests that a computationally frugal solution for intelligence involves an organism making an expectation and comparing the sensory data with the expectation so that a simple error reduction algorithm can improve the expectation. This involves a feedback loop and here we see something similar being evolved from the simplest forms of cellular life.

G-S gives an example in technology developed to aid the blind. There is a system that uses a camera to change vision into tactile sensations on the skin of a blind person. The person soon learns to experience “objects located in space” BUT “only when the wearer is able to control the camera.” (p 80)

Of course, multicellular life had to evolve before cell specialisation could start developing proper nervous systems. But this wasn't as difficult as it might at first look. It has evolved independently more than once. “The transition to a multicellular form of life occurred many times, leading once to animals, once to plants, on other occasions to fungi, various seaweeds, and less conspicuous organisms.” (p 20)

And once predation begins (probably in the Cambrian) each organism must be aware of the others which adds further urgency to the evolution of sensory-action feedback loops. “From this point on, the mind evolved in response to other minds.” (p 36)

The only thing that makes animals different is that they have greater capacity to take actions and so need to be even faster at sensing their own actions. “All living things affect their environment by making and transforming chemicals, and also by growing and sometimes by moving, but it is muscle that gives rise to rapid, coherent action on large spatial scales. It makes possible the manipulation of objects, the deliberate and rapid transformation of what is around us.” (p 82) This “interaction between perception and action” is critical. (p 83)

And the next stage for feedback loops is our own thoughts. G-S suggests that the internalization of language, “Vygotsky’s transition ... was also an important evolutionary event.” (p 152) He spends some time on inner speech:

• “When we look inside, most people find a flow of inner speech, a monologue that accompanies much of our conscious life.” (p 138)
• “Ordinary speech functions both as input and output ... We both speak and hear, and we can hear what we say. Even talking to yourself out loud can be a useful way of approaching a problem.” (p 144)
• “In speech, the creation of an efference copy enables you to compare your spoken words to an inner image of them; this can be used to work out whether the sound ‘came out right’.” (p 145)
• This then means that we can “put together sentences that we don't intend to say, sentences and fragments of language that have a purely internal role. ... We can put things in order, bring possibilities together, can list and instruct and exhort.” (p 147) This is particularly useful for Kahneman’s [ref Thinking, Fast and Slow] “System 2” thinking, the “slow, deliberate style of thinking we engage in when we encounter novel situations ... [which] tries to follow proper rules of reasoning, and tries to look at things from more than one side.” (p 147)
• This resonates with the “workspace theory of consciousness” (p 149)
• Inner speech is especially prominent when “we bring attention to bear on our own thought processes, reflect on them, and experience them as our own.” (p 152)
• “When you write something for yourself to read ... it is a communication between your present self and a future self.” (p 155)

There is also an interesting argument about ageing. Why do species age at different rates: trees last hundreds of years, humans perhaps a hundred, cephalopods mostly two? The idea is that “When molecular accidents put mutations into the population ... the late-acting mutations will be cleaned out less efficiently than early-acting ones.” (p 166) “So mutations with good effects early in life and the bad effects later in life will accumulate; natural selection will favour them.” (p 167) Therefore some populations have evolved such that the bad mutations tend to affect them later in life ... and it seems like spontaneous ageing. The life-span is thus partly a matter of evolutionary chance and partly governed by the balance of reproduction and predation. When the octopus lost its hard shell it became much more susceptible to predation which meant that it had to live its life a lot quicker because, sooner or later, a sharp-toothed fish would eat it. Presumably humans are mostly prey to diseases which, sooner or later, will get them, so they are able to evolve genes which allow then to fight the diseases for a while even at the cost of dying later.

Other thoughts from this brilliant book:

• Cuttlefish sometimes deeply ignore visitors to their watery world. “Being ignored so deeply makes you wonder if you are entirely real in their watery world, as if you are one of those ghosts who does not realise they are against.” (p 118)
• “When animals did crawl onto the dry land, they took the sea with them. All the basic activities of life occur in water-filled cells bounded by membranes, tiny containers whose insides are remnants of the sea.” (p 200)

A readable and intensely thought-provoking book. March 2018; 204 pages

The author has now written a sequel: Metazoa: Animal Minds and the Birth of Consciousness

This review was written by the author of Motherdarling  and The Kids of God

"Life on the Edge" by Jim Al-Khalili and Johnjoe McFadden

This book is about Quantum Biology.

The essential thesis of this work is that life is too ordered to have developed by chance from the random fluctuations of thermodynamics. Each living cell requires the coordination of a number of organelles; even the molecules of RNA which might have formed the first replicating molecules are highly complex and ordered. Enzyme processes which are the fundamental processes of life are carefully structured, although the language that this book uses (the enzymes unzip, cut, select etc) tends to prejudice one's thinking towards assigning a purposeness which the enzymes may not possess. Instead of thermodynamics, the authors propose that life requires the more ordered processes of quantum physics.

The two effects they believe are most useful to life are quantum tunnelling and quantum entanglement. Quantum tunnelling makes use of the wave nature of particles; since the particle wave means that the particle is delocalised in space it has a possibility that it is on the far side of an energy barrier so that it can react even when the energetics suggest it won't. The delocalisation also makes possible 'quantum search': instead of randomly trying out one combination after another you can explore all possibilities at the same time.

But the problem with quantum effects is that they are on a very very small scale and that the waviness feature can be disrupted by 'measurement' which in practice means interaction with another particle. Given how busy and crowded and hot the inside of a cell is, it seems surprising that there isn't a permanent state of decoherence. But these authors suggest that the cell uses tricks to ensure coherence for long enough for the necessary actions for life can take place; in one occasion they suggest that this takes place by a synchronising of oscillations within the cell which is the same thing as is suggested by Stephen Strogatz in Sync.

This is a serious scientific book and they provide great evidence for what they are suggesting. But at the end I was unsure how important it all was. There are electrons and protons inside the molecules that make up cells and these very tiny particles inhabit the quantum universe and follow quantum rules. So it is surely inevitable that the chemical reactions that make and are used by enzymes utilise quantum mechanics, after all, chemistry is all about electron transfer. There surely is no dispute about this. I think what they are suggesting is that the fact that quantum physics underpins the chemistry means that the odds on the spontaneous generation of life are much better than they first appear.

OK. It is obviously harder than we first thought to create life. Even the simplest organisms we know have extraordinarily complex internal structures. If it is too difficult to create complex molecules by random reactions then we are left with the possibility that life wasn't generated in the early history of this planet but was either created or arrived from elsewhere (although this still begs the question of how it arose elsewhere). But if quantum effects makes it too easy to create complex molecules than why was life apparently only created once? (These authors seem to suggest that the complex molecules somehow competed and only one life form remained after natural selection had taken place but if it really is that easy to create complex molecules why has this process only happened when the earth was very young?) In the end you have to assume that there is only one type of life that is viable but that it is relatively easy to spontaneously generate this form. After all, astrobiologists tell us that there are very few elements which have the appropriate reactions so that it is almost certain that only carbon-based life forms can exist in this universe.

This was an incredibly well-written book with lots of lovely asides (mostly about the bizarre life histories of the scientists mentioned) and it explains some really difficult stuff superbly well. I am not sure to what extent I was convinced by the thesis but it was great fun reading it.

May 2016; 433 pages

"Deep Time" by Henry Gee

This is a book about palaeontology, the study of fossils. That makes it sound very dry and dusty. By Henry Gee knows how to tell a good story and every chapter is full of reminiscences, such as when he was hunting for human remains with the Leakeys, his student work experience classifying fish fossils in the Natural History Museum or and who went to which pub during the disputes that introduced cladistics to palaeontology.

I also adored his chapter headings which show evidence of a wide range of reading far beyond I would have expected from a fossil hunter. But I guess you need a decent stash of books for the long dark desert nights:

• Chapter 1 is called Nothing Besides Remains, quoting Ozymandias but adding a nice double meaning
• Chapter Two: Hunting Unicorns, refers to a essay by Jorge Luis Borges about Kafka
• Chapter 3: There are More Things, quotes Hamlet's remark to Horatio
• And Chapter 7: Are We Not Men? is from a work by H.G.Wells

Gee's main thrust is to consider palaeontology as a science. He points out that fossils represent a few brief glimpses of bones out of millions of years of evolution. He reminds us that evolution is not purposeful nor is it a progression and that if we try to understand evolution from the point of view of creating adaptations that we see in the modern world we are assuming that the environmental conditions millions of years ago that led to the creation of a species were the same as now. So, for example, feathered birds might have had an evolutionary advantage millions of years ago for reasons we cannot now guess and it might have been entirely an accident that they are also useful skin coverings for an animal that flies.

From Gee's point of view the brilliant thing about cladistics is that it doesn't assume any heritage or ancestral linkages. It simply groups fossils by their features into 'sister-groups' and uses the Principle of Parsimony to derive the best possible tree diagram summarising relationships between the individuals.

Gee makes his arguments thoroughly; sometimes I thought points were repeated more than they needed to be. He also explains cladistics on a very simple level and I would like to have known a little more about these techniques, especially since cladistics can be used to explore the relationships (and thus possibly infer the ancestry) of Chaucerian manuscripts and of languages.

But on the whole this was a thoroughly enjoyable Science book about an area of Science I had not previously believed could be so much fun.