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Wetware: A Computer in Every Living Cell
In the tradition of as Erwin Schrödinger’s What Is Life? and Richard Dawkins’s The Selfish Gene , a distinguished cell biologist explains how living cells perform computations
How does a single-cell creature, such as an amoeba, lead such a sophisticated life? How does it hunt living prey, respond to lights, sounds, and smells, and display complex sequences of movements without the benefit of a nervous system? This book offers a startling and original answer. In clear, jargon-free language, Dennis Bray taps the findings of the new discipline of systems biology to show that the internal chemistry of living cells is a form of computation. Cells are built out of molecular circuits that perform logical operations, as electronic devices do, but with unique properties. Bray argues that the computational juice of cells provides the basis of all the distinctive properties of living systems: it allows organisms to embody in their internal structure an image of the world, and this accounts for their adaptability, responsiveness, and intelligence. In Wetware , Bray offers imaginative, wide-ranging and perceptive critiques of robotics and complexity theory, as well as many entertaining and telling anecdotes. For the general reader, the practicing scientist, and all others with an interest in the nature of life, the book is an exciting portal to some of biology’s latest discoveries and ideas.
How does a single-cell creature, such as an amoeba, lead such a sophisticated life? How does it hunt living prey, respond to lights, sounds, and smells, and display complex sequences of movements without the benefit of a nervous system? This book offers a startling and original answer. In clear, jargon-free language, Dennis Bray taps the findings of the new discipline of systems biology to show that the internal chemistry of living cells is a form of computation. Cells are built out of molecular circuits that perform logical operations, as electronic devices do, but with unique properties. Bray argues that the computational juice of cells provides the basis of all the distinctive properties of living systems: it allows organisms to embody in their internal structure an image of the world, and this accounts for their adaptability, responsiveness, and intelligence. In Wetware , Bray offers imaginative, wide-ranging and perceptive critiques of robotics and complexity theory, as well as many entertaining and telling anecdotes. For the general reader, the practicing scientist, and all others with an interest in the nature of life, the book is an exciting portal to some of biology’s latest discoveries and ideas.
288 pages, Paperback
First published May 26, 2009
88 people are currently reading
857 people want to read
About the author
Dennis Bray
13 books6 followersAn interview of the author.
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Displaying 1 - 30 of 39 reviews
September 17, 2018
The first chapter was fabulous - I wanted to give it an 8 out of 5! Then the second chapter didn't have anything new for me (maybe it would for others). The following chapters only offered a little elaboration on the musings of the first chapter - are single celled entities sentient? Ultimately the book does not provide an answer.
I began to be suspect about the intentions of the book with the references to evolution (being the cause of the intricacies we see). Then or page 141 he claims evolution retained 26 amino acids after 1.5 billion years of evolution. He wasn't there, no one (we know of) was. It is just fanciful speculation on his part. The five rating is down to a 4.
Unfortunately the author then uses the next section as propaganda for evolutionary theory - as much desired reading as Intelligent Design writings - both are two dimensional solutions to a five dimensional problem. At one point he mentions that DNA is the pinnacle of design, with no shame, that design implies intent.
He offers numerous analogies to human designed items (e.g. a comparison to 100 bottles of different Scotch) without realizing he is in essence saying "looks like a duck, swims like a duck, walks like a duck, quacks like a duck," but it is not a duck. He relies on the billions of years of time to produce genetic masterpieces.
Oceans have been washing up sand on beaches for billions of years yet we have no sand sculptures to appreciate. With his logic the beaches should be full of them.
I began to be suspect about the intentions of the book with the references to evolution (being the cause of the intricacies we see). Then or page 141 he claims evolution retained 26 amino acids after 1.5 billion years of evolution. He wasn't there, no one (we know of) was. It is just fanciful speculation on his part. The five rating is down to a 4.
Unfortunately the author then uses the next section as propaganda for evolutionary theory - as much desired reading as Intelligent Design writings - both are two dimensional solutions to a five dimensional problem. At one point he mentions that DNA is the pinnacle of design, with no shame, that design implies intent.
He offers numerous analogies to human designed items (e.g. a comparison to 100 bottles of different Scotch) without realizing he is in essence saying "looks like a duck, swims like a duck, walks like a duck, quacks like a duck," but it is not a duck. He relies on the billions of years of time to produce genetic masterpieces.
Oceans have been washing up sand on beaches for billions of years yet we have no sand sculptures to appreciate. With his logic the beaches should be full of them.
This entire review has been hidden because of spoilers.
January 1, 2012
Wetware: A Computer in Every Living Cell (Dennis Bray, not Rudy Rucker) is a short clearly guided tour on the analogies between biology and computing. Bray walks the reader through the protein-driven algorithms that generate complex behavior even in single-celled organisms without nervous systems, biological sensory mechanisms, cellular communications, and the basics of neurons.
The book raises thought-provoking questions - how much is computing merely a familiar analogy like clockwork in Descartes time, and how much is information processing a fair way to understand what happens in a biological system. How much of a difference does it make that biological life is carbon and liquid-based, and computing is silicate and dry? How much of a difference does it make that bio life is self-powering and self-replicating, unlike robots which depend on extrinsic mining, metallurgy, electric power generation. How much of a difference - seemingly large - between the elegant, simpler, and fragile creations of human engineers - and the convoluted, nuanced and fragile works of evolution?
Wetware is not particularly technical. An interested reader can follow up to find much more about any of the subjects it touches in more detail. One of the things that I liked about the book is how it avoids the occupational hubris that affects some works in the field. Bray calls out Wolfram, of course, but also Stuart Kauffman and Rodney Brooks for overconfidence about the relationship between their simulations and biological life. Bray falls prey to this a little bit in his chapter on neural networks, a field where he has done some professional work. Neural nets are useful algorithms loosely inspired by the biological model, but the intermediate steps in biological circuits which support multiple inputs and connections don't seem that much like the hidden layers of neural nets to me.
Bray does a good job of writing his sentences with subjects, verbs, and connected referents which makes it easier to follow complicated multi-step processes. This may seem elementary but is not as common as it should be. By contrast Nick Lane's book on Mitochondria, which is as far as I can tell brilliant, is harder than it needs to be. Not because it uses some technical terms and walks the reader through live debates and contrasting theories - it's fair to ask the reader to think - but because his sentences don't parse, and the reader needs to read them twice and then guess what "it" and "this" refer to. I need to reread Lane's book to understand it better before I write about it.
The book raises thought-provoking questions - how much is computing merely a familiar analogy like clockwork in Descartes time, and how much is information processing a fair way to understand what happens in a biological system. How much of a difference does it make that biological life is carbon and liquid-based, and computing is silicate and dry? How much of a difference does it make that bio life is self-powering and self-replicating, unlike robots which depend on extrinsic mining, metallurgy, electric power generation. How much of a difference - seemingly large - between the elegant, simpler, and fragile creations of human engineers - and the convoluted, nuanced and fragile works of evolution?
Wetware is not particularly technical. An interested reader can follow up to find much more about any of the subjects it touches in more detail. One of the things that I liked about the book is how it avoids the occupational hubris that affects some works in the field. Bray calls out Wolfram, of course, but also Stuart Kauffman and Rodney Brooks for overconfidence about the relationship between their simulations and biological life. Bray falls prey to this a little bit in his chapter on neural networks, a field where he has done some professional work. Neural nets are useful algorithms loosely inspired by the biological model, but the intermediate steps in biological circuits which support multiple inputs and connections don't seem that much like the hidden layers of neural nets to me.
Bray does a good job of writing his sentences with subjects, verbs, and connected referents which makes it easier to follow complicated multi-step processes. This may seem elementary but is not as common as it should be. By contrast Nick Lane's book on Mitochondria, which is as far as I can tell brilliant, is harder than it needs to be. Not because it uses some technical terms and walks the reader through live debates and contrasting theories - it's fair to ask the reader to think - but because his sentences don't parse, and the reader needs to read them twice and then guess what "it" and "this" refer to. I need to reread Lane's book to understand it better before I write about it.
March 3, 2018
"Wetware: A Computer in Every Living Cell" is a reassuringly reasonable book compared to books I could imagine with the same title. It lives up to the promise of that title, giving a crackling account of the discrete switching networks of proteins reactions causing conformational changes that enable and disable their function. Chapters three and four are particularly strong at this, and the last two chapters have very strong flashes in this regard. This book successfully defends its thesis: the cell really does have the power to implement a kind of concurrent logical computation.
These rousing descriptions are embedded in a more contemplative text, waxing philosophically about computer programs and robots. It comes down on philosophical issues in a scientifically nuanced way, admitting that we have yet not figured out any coherent way to know whether or not cells or other creatures have experiences, but estimating that they don't given their paltry biological endowments, despite their impressive capabilities.
When not in either of these modes, the text is explaining more biological phenomena, that I've read more clearly and diagrammatically elsewhere, though it is unquestionably competent throughout. I might have wished it got more into detail of exactly how more of these computational networks worked, but that might have made it less accessible, and it is very readable throughout. One criticism is that the book doesn't seem to have any grip on the theory of computational complexity, and I think mistakes ordinary complication for complexity.
Overall, this is the book of somebody who's been musing about thoughts for years, and finally decided to put them on paper. Given that the topics are broad ranging and have a philosophical bent, it's nice to see them rendered so soberly and biologically grounded.
These rousing descriptions are embedded in a more contemplative text, waxing philosophically about computer programs and robots. It comes down on philosophical issues in a scientifically nuanced way, admitting that we have yet not figured out any coherent way to know whether or not cells or other creatures have experiences, but estimating that they don't given their paltry biological endowments, despite their impressive capabilities.
When not in either of these modes, the text is explaining more biological phenomena, that I've read more clearly and diagrammatically elsewhere, though it is unquestionably competent throughout. I might have wished it got more into detail of exactly how more of these computational networks worked, but that might have made it less accessible, and it is very readable throughout. One criticism is that the book doesn't seem to have any grip on the theory of computational complexity, and I think mistakes ordinary complication for complexity.
Overall, this is the book of somebody who's been musing about thoughts for years, and finally decided to put them on paper. Given that the topics are broad ranging and have a philosophical bent, it's nice to see them rendered so soberly and biologically grounded.
October 2, 2023
I will be decrepit and in my deathbed with almost everything lost, the faces of my family, my favorite songs, but one thing will remain.
Mitochondria is the powerhouse of the cell.
Wetware is a popular introduction to microbiology, framed by Bray's contention that even the simplest cell is an information processing system. And as even basic observation shows, this must be true. E. coli moves towards nutrients and away from poisons. Amoebas are microscale apex predators, stretching towards lesser protozoans with psuedopods. And higher organisms are delicately orchestrated complexes of organs and tissues, grown from a single zygote that contains every necessary instruction encoded in the four base pairs of DNA.
Information processing is the central metaphor of our era, much as clockwork was that of Newton's. However, as a popular book, Wetware is often frustratingly vague about the details. Methylation turns proteins and genes on and off. The addition or removal of phosphorus groups from proteins provides necessary energy to combat entropy and also serves to time processes. But information as we use it is all symbolic processing, which as the Church-Turing thesis argues is the same thing, no matter the hardware. Binary digital logic is just the easiest to engineer. Wetware processing is something profoundly different, an analog process of protein interaction occurring at the speed of molecular diffusion. A physics simulation of a single cell would be a massive computational endeavor, yet it's unclear of a statistical abstraction would preserve whatever vital processes makes the whole thing work.
Fascinating, especially for someone who last took a bio course in 9th grade, but I wanted something deeper and bolder.
Mitochondria is the powerhouse of the cell.
Wetware is a popular introduction to microbiology, framed by Bray's contention that even the simplest cell is an information processing system. And as even basic observation shows, this must be true. E. coli moves towards nutrients and away from poisons. Amoebas are microscale apex predators, stretching towards lesser protozoans with psuedopods. And higher organisms are delicately orchestrated complexes of organs and tissues, grown from a single zygote that contains every necessary instruction encoded in the four base pairs of DNA.
Information processing is the central metaphor of our era, much as clockwork was that of Newton's. However, as a popular book, Wetware is often frustratingly vague about the details. Methylation turns proteins and genes on and off. The addition or removal of phosphorus groups from proteins provides necessary energy to combat entropy and also serves to time processes. But information as we use it is all symbolic processing, which as the Church-Turing thesis argues is the same thing, no matter the hardware. Binary digital logic is just the easiest to engineer. Wetware processing is something profoundly different, an analog process of protein interaction occurring at the speed of molecular diffusion. A physics simulation of a single cell would be a massive computational endeavor, yet it's unclear of a statistical abstraction would preserve whatever vital processes makes the whole thing work.
Fascinating, especially for someone who last took a bio course in 9th grade, but I wanted something deeper and bolder.
January 12, 2010
From B&N Synopsis:
"In clear, jargon-free language, Dennis Bray taps the findings of the new discipline of systems biology to show that the internal chemistry of living cells is a form of computation. Cells are built out of molecular circuits that perform logical operations, as electronic devices do, but with unique properties. Bray argues that the computational juice of cells provides the basis of all the distinctive properties of living systems: it allows organisms to embody in their internal structure an image of the world, and this accounts for their adaptability, responsiveness, and intelligence."
Biography:
"Dennis Bray is professor emeritus, University of Cambridge, and coauthor of several bestselling and influential texts on molecular and cell biology. In 2007 he was awarded the prestigious European Science Prize in Computational Biology. He lives in Cambridge, UK."
My Take:
Nearly finished reading, trying to keep my mind from entering Professor Bray's world without exploding, can't wait to finish my first read so I can start over. I call this one a nine-time read.
"In clear, jargon-free language, Dennis Bray taps the findings of the new discipline of systems biology to show that the internal chemistry of living cells is a form of computation. Cells are built out of molecular circuits that perform logical operations, as electronic devices do, but with unique properties. Bray argues that the computational juice of cells provides the basis of all the distinctive properties of living systems: it allows organisms to embody in their internal structure an image of the world, and this accounts for their adaptability, responsiveness, and intelligence."
Biography:
"Dennis Bray is professor emeritus, University of Cambridge, and coauthor of several bestselling and influential texts on molecular and cell biology. In 2007 he was awarded the prestigious European Science Prize in Computational Biology. He lives in Cambridge, UK."
My Take:
Nearly finished reading, trying to keep my mind from entering Professor Bray's world without exploding, can't wait to finish my first read so I can start over. I call this one a nine-time read.
September 14, 2024
An absolutely fantastic read for anyone interested in life, free will, biology, intelligence, networks, or anything science related. Fantastic writer!
January 11, 2011
The thesis of this book by Braid is courageous but potentially brilliant: many of the attributes that we associate only to high-level organisms (which, to put them into one, are the capacity of creating an internal image of the external world) are actually present also at single cell level - in this liquid computational processing environment called wetware.
If you can excuse the fact that the style of Braid is boring, I guess partly because of the intrinsically hyper-descriptive character of biological trainings and expositions, then this book ranks as a potential gem. The author's opinion is essentially a corollary of recent developments and evidence of the computational power of chemical networks, particular of protein networks, enshrined and compartimentalized within membranes, that is within cells.
2 main reflections are in order, if the conjecture reveals true: 1) the central nervous system, to which we attribute the origin and control of such supposedly high-level behaviors, is not necessary to them, thus not probably its origin, as well, but more probably a refinement and structuralization of the sets of feedback and logical loops already working at molecular level; 2) mimicking molecular biology (liquid, carbon-based, energy-efficient, resource-efficient yet robust) in the perspective of artificial intelligence or, more simply, enhanced artificial computational power has still a lot to progress to reach evolution's achievements - though they can be back-engineered, eventually.
Recommended to newcomers and to those fascinated with networks in search for biological substrates to investigate.
If you can excuse the fact that the style of Braid is boring, I guess partly because of the intrinsically hyper-descriptive character of biological trainings and expositions, then this book ranks as a potential gem. The author's opinion is essentially a corollary of recent developments and evidence of the computational power of chemical networks, particular of protein networks, enshrined and compartimentalized within membranes, that is within cells.
2 main reflections are in order, if the conjecture reveals true: 1) the central nervous system, to which we attribute the origin and control of such supposedly high-level behaviors, is not necessary to them, thus not probably its origin, as well, but more probably a refinement and structuralization of the sets of feedback and logical loops already working at molecular level; 2) mimicking molecular biology (liquid, carbon-based, energy-efficient, resource-efficient yet robust) in the perspective of artificial intelligence or, more simply, enhanced artificial computational power has still a lot to progress to reach evolution's achievements - though they can be back-engineered, eventually.
Recommended to newcomers and to those fascinated with networks in search for biological substrates to investigate.
May 9, 2012
If I was reviewing this book for its quality as popular science, I would give it two stars. The writing is often too complicated, introducing new terminology for the sake of an example and instead leaving the reader confused as to what a particular scientific experiment is. Furthermore, the majority of the educational material of the book is introduced in the first half, the second half being an overly-long treatment of minute examples of previously-introduced concepts.
That being said, I review books based on what I got out of them. With limited knowledge of what a cell even was, diving into this book was a treat. The idea that cells are essentially computers composed of thousands of lego pieces shaking around randomly in a box is awe-inspiring (my analogy, not the authour's). Though I struggled with the material enough that I make no claim to having really conquered the book (occasionally the jargon would lull me to sleep), my questions about the very basic building blocks of life, and their probably origins, are at least partially answered. If there is anything more I wish I got from this, it would be a deeper treatment of some of the foundational experiments. I am already forgetting some of the reasons we know things are as they are. To have retained the names of the discovers and their methods would have been a great foundation moving forward.
That being said, I review books based on what I got out of them. With limited knowledge of what a cell even was, diving into this book was a treat. The idea that cells are essentially computers composed of thousands of lego pieces shaking around randomly in a box is awe-inspiring (my analogy, not the authour's). Though I struggled with the material enough that I make no claim to having really conquered the book (occasionally the jargon would lull me to sleep), my questions about the very basic building blocks of life, and their probably origins, are at least partially answered. If there is anything more I wish I got from this, it would be a deeper treatment of some of the foundational experiments. I am already forgetting some of the reasons we know things are as they are. To have retained the names of the discovers and their methods would have been a great foundation moving forward.
May 11, 2011
The title and the foreword of the book were promising. The computational capabilities of cells are now under a wide research program, and this book promised to be a good and enhanced state-of-the-art. However, the book is full of old-fashion biology prejudices. For example, the author states in a reiterative fashion that cells are not to be equalled by any "artificial" machine simply because cells have more possible states. Author is not aware of the digital and analogical computers difference, not to talk about the formal basis of computation.
The concept of biological transistor is, however, well presented and much more may had been achieved if the tonic from chapters three and four were followed during the rest of the book.
An interesting metaphor, from my point of view, is the one relating learning in neural networks and metabolic networks. Metabolic networks are the result of adaptation, and as such, they represent what the organism has learnt from its environment.
The concept of biological transistor is, however, well presented and much more may had been achieved if the tonic from chapters three and four were followed during the rest of the book.
An interesting metaphor, from my point of view, is the one relating learning in neural networks and metabolic networks. Metabolic networks are the result of adaptation, and as such, they represent what the organism has learnt from its environment.
January 12, 2014
If you have studied biology sometime in the past and would like to know some of what is happening in the world of academic biochemistry today, this is the book for you. Written for us laypeople, Dennis Bray takes us into the world of single cell animals and bacteria, and later into the multi-cell and even human world. Scientists are learning more about cell chemistry every day -- too much for us to keep up with. Yet the complex mechanisms and their functions are fascinating and the author's rendering illuminating.
Furthermore, for most of us, the mechanisms of evolution are daunting and difficult to fathom. Many of us harbor some misgivings about randomness and complexity. In the depth of our minds is this lingering suspicion that perhaps creationism has some basis in fact after all. No matter where you may be on the spectrum of belief, it is good to delve into the rich facts of cell life.
Read this book; you won't regret it.
Furthermore, for most of us, the mechanisms of evolution are daunting and difficult to fathom. Many of us harbor some misgivings about randomness and complexity. In the depth of our minds is this lingering suspicion that perhaps creationism has some basis in fact after all. No matter where you may be on the spectrum of belief, it is good to delve into the rich facts of cell life.
Read this book; you won't regret it.
Currently reading
April 15, 2013Well, I was expecting a flight of genius, something about bio-mimesis and its difficulties as developers encounter something akin to cellular consciousness. However, I have yet to see it. So far, it's plodding and unhelpful. The question of why synthetic biology might differ from electronic or chemical processes hasn't been addressed as yet.
I don't mean whether a microbe knows whether its name is Joe or Frank. But isn't it possible that bacteria have a sociobiological behavior pattern? Or a sympathetic suicide function in response to resource constraints? These would amount to "moods" which affect the rate of response of protein switches, no?
I hope Bray hits the right button soon. He's losing me.
I don't mean whether a microbe knows whether its name is Joe or Frank. But isn't it possible that bacteria have a sociobiological behavior pattern? Or a sympathetic suicide function in response to resource constraints? These would amount to "moods" which affect the rate of response of protein switches, no?
I hope Bray hits the right button soon. He's losing me.
August 19, 2015
Bray paints a vivid and detailed picture of the biological algorithms and circuitry ingrained in the almost infinite complexity of life. It is here that we see the computational pre-programmed adaptability that James Shapiro refers to as "Natural Genetic Engineering". Although Bray still seems intent on waving that Dariwinian magic wand that I have always found to be at the apex of intellectual laziness, it is still refreshing to see the active logical forward-looking undercurrents of biological evolution taken seriously. These are the ideas that will drive our understanding of biology in the 21st century.
December 20, 2009
A compelling comparison of biological systems and computers focusing on the mechanisms that enable life, communication, and sentience. Dennis Bray does an excellent job at explaining complex concepts in simple, yet vivid language. He has an ability to crystalize thoughts and present arguments clearly and succinctly. His use of metaphor comparing the life of a cell to the programmed computation of a machine is interesting and removes some of the mystery behind how these complex systems behave.
January 19, 2014
I studied biology as an undergrad and continue to do research in the field. This books was awesome. Easy to read and not to scientific but instead asked (and tried to offer insight on) philosophical questions relating to life. It talks how cells are very similar to basic machines but humbly concedes that life is driven by a "force" that we still do not understand; no matter how life-life machines get, they still won't be alive. Highly recommend it as it introduces an emerging and very sophisticated field in biology
November 29, 2016
Didn't make as much contact with theoretical computer science as I was hoping, but still lots of good stuff. The explanation of how protein interaction networks can manifest transistor-equivalent components (as well as basic logic gates) was enlightening. Primary takeaway: single-celled organisms, with their "nervous systems" made of protein interaction networks, already deserve the intentional stance.
June 3, 2014
After seconding the other positive remarks, I will add that the book outlines many fascinating phenomena, for example about protozoans, that are hard to extract from the ponderous tomes we are accustomed to slogging through. Really, you may never think the same way again about single-celled organisms.
October 26, 2016
An excellent book that has let me see cells from an entirely new perspective. It was easy to read, while it also included a lot of depth and details, satisfying my curiosity. I particularly enjoyed learning about hydra - the actual living tiny animals. When I have a good microscope, I will need to find one.
July 19, 2019
This is an excellent introduction to systems biology. No prior knowledge or interest required. Readers will come away understanding what it means to say that "life computes", and terms like "protein nanomachines" will make perfect sense. If you don't think "wow" at least once while reading this, you have absolutely no imagination.
September 17, 2021
I expected this to be way more "out there" given the title, but it turns out it's a pretty solid, measured overview of cellular biology. Bray does a great job imparting the complexities of the world of the cell, a tiny metropolis whirring with constant activity. His main focus is on the role of proteins, which perform an incredible number of actions through allostery and chemical modifications, many of which certainly have a computational character. He describes how protein modification can serve as a kind of memory, both for single-celled organisms and scaling up to complex eukaryotes like us.
Bray's claims for parallels between biological systems and computers are far more modest than the subtitle would indicate: he concedes that neuronal firing can be thought of as a binary switch, but notes that this is an abstraction that elides a whole universe of differences. Neurons have an enormous number of synapses feeding the action potential mechanism, coordinating complicated chemical networks into the off-on of the electrical pulse. Those chemical substrates can change in short- and long-term ways that can make all the difference in the performance of systems, and we're just scratching the surface in understanding those effects. There is an incommensurable gap between the machines we build, no matter how steep we gallop up the curve of Moore's Law, and the multivalent complexity of biology. Bray is agnostic about whether we'll ever learn to harness that type of complexity for our own information processing designs.
While this wasn't as bold of a thesis as I expected, I found it absolutely top-notch in terms of explaining the general features of the cellular level. If nothing else, it really fired my imagination about the activities hidden within and beneath our consciousness. Highly recommended.
Bray's claims for parallels between biological systems and computers are far more modest than the subtitle would indicate: he concedes that neuronal firing can be thought of as a binary switch, but notes that this is an abstraction that elides a whole universe of differences. Neurons have an enormous number of synapses feeding the action potential mechanism, coordinating complicated chemical networks into the off-on of the electrical pulse. Those chemical substrates can change in short- and long-term ways that can make all the difference in the performance of systems, and we're just scratching the surface in understanding those effects. There is an incommensurable gap between the machines we build, no matter how steep we gallop up the curve of Moore's Law, and the multivalent complexity of biology. Bray is agnostic about whether we'll ever learn to harness that type of complexity for our own information processing designs.
While this wasn't as bold of a thesis as I expected, I found it absolutely top-notch in terms of explaining the general features of the cellular level. If nothing else, it really fired my imagination about the activities hidden within and beneath our consciousness. Highly recommended.
September 2, 2022
This book explores the complex world of a single cell and how it resembles man-made computers and robots.
This book centers on the author's research simulating how an E. coli bacterium navigates the world, seeking out food and avoiding toxins. Through this lens, Bray analyzes the mechanics of perception, analysis, decision making, and movement at the level of single molecules and their chemical interactions. He draws fascinating parallels between these processes and the workings of digital circuitry, showing how they are computationally similar, despite their wildly different forms.
This is one of the most novel and eye-opening books I have ever read! The picture Bray paints is vivid, complex, and incredibly fascinating. There's a lot of molecular biology and computer science here, but its been carefully streamlined and simplified to be easy for novices to take in. Although it's not fully demonstrated, I find the central premise of this book compelling and important: the higher consciousness and intelligence of human beings is the product of aggregating and building hierarchical layers of complexity out of the tiny, primitive pseudo-consciousness and pseudo-intelligence of each individual cell.
This book is a great introduction to the beauty, sophistication, and remarkable intelligence of even the simplest of lifeforms. They make electronic computers look primitive, and give valuable insight into how higher forms of intelligence such as our own can emerge through evolution.
This book centers on the author's research simulating how an E. coli bacterium navigates the world, seeking out food and avoiding toxins. Through this lens, Bray analyzes the mechanics of perception, analysis, decision making, and movement at the level of single molecules and their chemical interactions. He draws fascinating parallels between these processes and the workings of digital circuitry, showing how they are computationally similar, despite their wildly different forms.
This is one of the most novel and eye-opening books I have ever read! The picture Bray paints is vivid, complex, and incredibly fascinating. There's a lot of molecular biology and computer science here, but its been carefully streamlined and simplified to be easy for novices to take in. Although it's not fully demonstrated, I find the central premise of this book compelling and important: the higher consciousness and intelligence of human beings is the product of aggregating and building hierarchical layers of complexity out of the tiny, primitive pseudo-consciousness and pseudo-intelligence of each individual cell.
This book is a great introduction to the beauty, sophistication, and remarkable intelligence of even the simplest of lifeforms. They make electronic computers look primitive, and give valuable insight into how higher forms of intelligence such as our own can emerge through evolution.
February 24, 2023
This is a wonderful book on a fascinating topic... how cell biochemistry (biophysics) can produce the complexity necessary to produce the higher functions of complex life (or complex behavior of single-cell organisms). While the book does not fully answer this question, it does take the reader on the tour of existing complexity in our biomolecular machinery. Introduced is the concept of protein-based logic and it enabling extremely complex logic to be "computed" by cells with (possibly greater) efficiency than electronic circuits. I find it interesting that on several occasions the author went out of their way to indicate the lack of necessity for Intelligent Design. Still there was No/None/Zero/Zilch discussion of how the existing complexity of the cell Got There. Take for instance, my favorite, the microtubules in all eukaryotic cells (and I've google to learn also in simpler form in Bacteria (known as “bacterial microtubules” (bMTs))! I'd bet we'd find the same micro-robot-biomachines running down these fibers too; why not reuse code! I'm seriously looking to read further and would love to hear about authors who've taken their academic blinders off!
February 27, 2021
A fascinating mind opening book
As an EE/CS I found these book fascinating as it opened my mind to understand new forms of networks and associated computation. It also provided me with a better understanding of many aspects of biology that I found more obscure until now. Not all the parallels with electronic circuits are correct in the form, but are certainly correct in the significance. What is now really easy for me is to see these biological mechanisms within cells and/or assembly of cells, as control system, which behavior has been studied for more than a century and can be tackled with powerful mathematic and algorithmic tools. I can certainly see how future development in biologic understanding could further benefit bringing in known techniques that have been used in the EE/CS.
As an EE/CS I found these book fascinating as it opened my mind to understand new forms of networks and associated computation. It also provided me with a better understanding of many aspects of biology that I found more obscure until now. Not all the parallels with electronic circuits are correct in the form, but are certainly correct in the significance. What is now really easy for me is to see these biological mechanisms within cells and/or assembly of cells, as control system, which behavior has been studied for more than a century and can be tackled with powerful mathematic and algorithmic tools. I can certainly see how future development in biologic understanding could further benefit bringing in known techniques that have been used in the EE/CS.
November 23, 2022
Great topic - interesting read. My favorite parts were the detailed examples of various biological systems and bacteria behavior.
The main concepts I took away were that biological cells/units are computers (Bray focuses a lot of attention on the computational behavior of protein), and although these biological computers share many features with common hardware computers, there are differences (e.g. hardware computers send electrical signals via wires whereas biological computers signal using biochemical reactions and diffusion.)
I recommend the read for anyone interested in the topic, but the concepts could have been developed more thoroughly and tied together with examples in a more structured manner. The book felt like a compilation of various descriptions of bacteria and cell behavior with the occasional general remark that "X functions like a computer".
The main concepts I took away were that biological cells/units are computers (Bray focuses a lot of attention on the computational behavior of protein), and although these biological computers share many features with common hardware computers, there are differences (e.g. hardware computers send electrical signals via wires whereas biological computers signal using biochemical reactions and diffusion.)
I recommend the read for anyone interested in the topic, but the concepts could have been developed more thoroughly and tied together with examples in a more structured manner. The book felt like a compilation of various descriptions of bacteria and cell behavior with the occasional general remark that "X functions like a computer".
August 25, 2024
"For a mouse, these computations take place in the central nervous system. Once a decision has been made, signals must be sent to the appropriate organs for action. In a mouse, electrical signals travel along nerves to muscles and cause them to contract. I would like you to convince you that systems of protein molecules can perform all of these tasks. They provide a single cell with the equivalent of sensory organs, nerves, and muscles." (72)
"But Skip's [the dog's] muteness would make an essential difference. Not just because it renders him incapable of communicate his internal state to anyone else but also because it would leave that internal state so impoverished. Without language a creature lacks concepts. ... He is unable to share our sense of time: he has no past or future, just the here and now." (133)
"But Skip's [the dog's] muteness would make an essential difference. Not just because it renders him incapable of communicate his internal state to anyone else but also because it would leave that internal state so impoverished. Without language a creature lacks concepts. ... He is unable to share our sense of time: he has no past or future, just the here and now." (133)
April 6, 2021
Some books give new information, and others provide a change in perspective. Biologically speaking, this book did not offer anything new but rephrased known biological processes (metabolic networks, allosteric proteins, phosphorylation...) as information processing—worth reading as an interesting point of view. The most intriguing aspect is that this wetware is neither designed nor trained using gradients (as is done in machine learning). So it is worth exploring evolutionary algorithms to create novel (biological) computing systems.
September 16, 2025
The author is chock full of wonder and enthusiasm, which sweeps you along the book, the authors vision and narrative of cellular biology. Unfortunately it’s not quite enough. Hand wavy explanations, half baked analogies, despite assuming a decent amount from the readership at the same time dumbing things down… I wish he focused on a couple individual examples all the way through instead of briefly touching on many (and having them blend together). Also a bit dated when it comes to robots/deep learning. Still. Dizzying. Cell bio should give any person vertigo.
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September 20, 2021Pascal and Fermat defined the “expected value” of a game, which measured how profitable it would be on average if played repeatedly.
I don’t bet on the table,” he said. “Instead, I bet with people around the table who have prejudices—superstitious ideas about lucky numbers.” Nick knew the casino had the edge, so he made wagers with naive fellow gamblers instead.
I don’t bet on the table,” he said. “Instead, I bet with people around the table who have prejudices—superstitious ideas about lucky numbers.” Nick knew the casino had the edge, so he made wagers with naive fellow gamblers instead.
July 6, 2023
Excellent overall frame: cells create models of and respond to their environments through a protein neural net (which we now call an interactome).
But I wish it had two things: 1) Less philosophical ramblings and 2) Was updated with our knowledge of the last 15 years, placing interactomes into Herbert Simon's model of modular and robust hierarchy (of protein networks).
Close, but not quite there.
But I wish it had two things: 1) Less philosophical ramblings and 2) Was updated with our knowledge of the last 15 years, placing interactomes into Herbert Simon's model of modular and robust hierarchy (of protein networks).
Close, but not quite there.
February 12, 2023
Highly readable and short book. In essence, proteins are “shape computing devices” of life. An enzyme (a type of protein) is essentially a transistor with two states, with output state regulated by another binding molecule (base transistor). Complex things can be understood with powerful analogies from a simpler domain. To understand “deep life” in us and in every cell, this is a great primer.
January 12, 2020
Interesting to get a little insight into how complex cells actually are and how they might store information and so on. The actual technical biological details and various pathways I didn't fully follow but it was still fun.
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