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Arrival of the Fittest: Solving Evolution's Greatest Puzzle
Although Darwin could explain how evolution preserves useful adaptations over time, the mechanisms behind its speed and efficiency eluded him. In this radical rethinking of Darwinian evolution, Wagner offers a solution to that enduring mystery. He draws on 15 years of research using the latest experimental and computational technologies to uncover the principles of innovability that allow the creation of such complicated adaptations as lactose digestion, camouflage and the antifreeze proteins produced by Arctic cod.
304 pages, Hardcover
First published October 2, 2014
About the author
Andreas Wagner
42 books58 followersLibrarian Note: There is more than one author with this name on GR
Andreas Wagner is Professor in the Institute of Evolutionary Biology at the University of Zurich and an award-winning science writer. He received his PhD from Yale and has held research positions at the Institute for Advanced Study in Berlin and the Los Alamos National Laboratory in New Mexico. The author of more than 150 scientific papers published in leading journals including Nature and Science, this is his first book popularizing his new evolutionary systems research. He lives in Zurich.
Andreas Wagner is Professor in the Institute of Evolutionary Biology at the University of Zurich and an award-winning science writer. He received his PhD from Yale and has held research positions at the Institute for Advanced Study in Berlin and the Los Alamos National Laboratory in New Mexico. The author of more than 150 scientific papers published in leading journals including Nature and Science, this is his first book popularizing his new evolutionary systems research. He lives in Zurich.
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Displaying 1 - 30 of 93 reviews
June 1, 2015
It's true that evolutionary development of life depends on random mutations, but it's more complicated than that. Nature's building blocks of life (metabolic systems, protein interactions, and gene regulation networks) are unimaginably complex, yet they are endowed with inherent properties that are both innovatable and robust (i.e. progressive and conservative at the same time).
The author makes the point that there is insufficient time in the universe for random mutations acting alone to create life. The author makes this point with the following quotation:
The author goes on to explain that adaptations are not just driven by chance, but by a set of laws that allow nature to discover new molecules and mechanisms in a fraction of the time that random variation would take. Metabolic systems, protein interactions, and gene regulation networks share a particular kind of robustness such that even drastic changes to the underlying structure leaves their operations unchanged. For example, the complex of chemical reactions that metabolize glucose in E. coli can overlap by as little as 20 percent and still function perfectly well.
At the same time, very small genetic changes can radically alter the phenotype. Some such alterations portend certain death, but a few lead to powerful new innovations: the ability to fly, for example, or the first light-sensitive cells eventually leading to photosynthesis. Searching all the genetic possibilities at random would take forever, but a species — with all the same functions, but widely varying genes — can search millions of genetic options all at once, dramatically increasing evolution’s efficiency.
Robustness itself is a response to environmental complexity. To withstand heat, cold, moisture, and dryness, living things developed a modular toolset of molecules such as amino acids, which combined in complex ways to produce a range of innovations in response to any given problem.
The author clearly suggests that the environment is a key factor in species adaptation. In an elegantly written final paragraph in one of the later book chapters he notes:
Genotype networks are a concept used in systems biology to study sets of genotypes having the same phenotype, and the ability of these to bring forth novel phenotypes. Genotype networks are a key to innovability.
Innovability means ability/capability to innovate.
This book knocked my sock off, that's why I gave it five stars. When I listen or read books about the cutting edge of science I am usually exposing myself to concepts that I've previously been exposed to. I continue to go through books on the subject in order the help the information to soak into my understanding. This book on the other hand has some explanations of the complexity of evolution and life that were new to me.
The author makes the point that there is insufficient time in the universe for random mutations acting alone to create life. The author makes this point with the following quotation:
The first vertebrates to use crystallins in lenses did so more than five hundred million years ago, and the opsins that enable the falcon’s vision are some seven hundred million years old. They originated some three billion years after life first appeared on earth. That sounds like a helpfully long amount of time to come up with these molecular innovations. But each one of those opsin and crystallin proteins is a chain of hundreds of amino acids, highly specific sequences of molecules written in an alphabet of twenty amino acid letters. If only one such sequence could sense light or help form a transparent cameralike lens, how many different hundred-amino-acid-long protein strings would we have to sift through? The first amino acid of such a string could be any one of the twenty kinds of amino acids, and the same holds for the second amino acid. Because 20 x 20 = 400, there are 400 possible strings of two amino acids. Consider also the third amino acid, and you have arrived at 20 x 20 x 20, or 8,000, possibilities. At four amino acids we already have 160,000 possibilities. For a protein with a hundred amino acids (crystallins and opsins are much longer), the numbers multiply to a 1 with more than 130 trailing zeroes, or more than 10^130 possible amino acid strings. To get a sense of this number’s magnitude, consider that most atoms in the universe are hydrogen atoms, and physicists have estimated the number of these atoms as 10^90, or 1,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000. This is “only” a 1 with 90 zeroes. The number of potential proteins is not merely astronomical, it is hyperastronomical, much greater than the number of hydrogen atoms in the universe. To find a specific sequence like that is not just less likely than winning the jackpot in the lottery, it is less likely than winning a jackpot every year since the Big Bang.” In fact, it’s countless billions of times less likely. If a trillion different organisms had tried an amino acid string every second since life began, they might have tried a tiny fraction of the 10^130 potential ones. They would never have found the one opsin string. There are a lot of different ways to arrange molecules. And not nearly enough time.In other words, there's more than simple random mutation needed for life to develop. So what would that be?
The author goes on to explain that adaptations are not just driven by chance, but by a set of laws that allow nature to discover new molecules and mechanisms in a fraction of the time that random variation would take. Metabolic systems, protein interactions, and gene regulation networks share a particular kind of robustness such that even drastic changes to the underlying structure leaves their operations unchanged. For example, the complex of chemical reactions that metabolize glucose in E. coli can overlap by as little as 20 percent and still function perfectly well.
At the same time, very small genetic changes can radically alter the phenotype. Some such alterations portend certain death, but a few lead to powerful new innovations: the ability to fly, for example, or the first light-sensitive cells eventually leading to photosynthesis. Searching all the genetic possibilities at random would take forever, but a species — with all the same functions, but widely varying genes — can search millions of genetic options all at once, dramatically increasing evolution’s efficiency.
Robustness itself is a response to environmental complexity. To withstand heat, cold, moisture, and dryness, living things developed a modular toolset of molecules such as amino acids, which combined in complex ways to produce a range of innovations in response to any given problem.
The author clearly suggests that the environment is a key factor in species adaptation. In an elegantly written final paragraph in one of the later book chapters he notes:
"...Environmental change requires complexity, which begets robustness, which begets genotype networks, which enable innovations, the very kind that allow life to cope with environmental change, increase its complexity, and so on, in an ascending spiral of ever-increasing innovability...is the hidden architecture of life"Two words were used so often in this book that I had to check on their meanings. I've decided to provide their definitions here:
Genotype networks are a concept used in systems biology to study sets of genotypes having the same phenotype, and the ability of these to bring forth novel phenotypes. Genotype networks are a key to innovability.
Innovability means ability/capability to innovate.
This book knocked my sock off, that's why I gave it five stars. When I listen or read books about the cutting edge of science I am usually exposing myself to concepts that I've previously been exposed to. I continue to go through books on the subject in order the help the information to soak into my understanding. This book on the other hand has some explanations of the complexity of evolution and life that were new to me.
May 10, 2016
I really wanted to love this book. I am a scientist. And luckily I am one who happens to love science. And I particularly love the topics this book covers (evolutionary genetics and bioinformatics). It is written with great wit, poise and profound knowledge. Unfortunately for Andreas Wagner, who is clearly a talented author as well as scientist, the topics at hand are difficult to write about without being repetitive and at times, simply rather dull. I just could not love this book, though I tried.
It was a hard slog. Wagner has the sense to realise when the writing is becoming boring. He tries at such moments to inject little anecdotes about the persons conducting the science in order to break the monotony. It is not enough. The library of genetic data existing in multiple dimensions is undoubtedly an effective metaphor for communication, but it does not make reading about it any easier. Wagner makes the topic easy to understand for the lay person. But that does not make reading about it a pleasure.
Because it is not a pleasure to read you must put in extra effort to pay attention to the writing. To understand it fully. If you let your mind wander at all, you'll find yourself having to reread entire chapters, not just the last couple of paragraphs. This was tiresome for me and I'm a scientist! I could not realistically recommend this to a lay person with only an interest in pop-sci books and no good mathematical background.
I am torn in my assessment of this book. It is excellently written, highly informative and can be understood, even by non-scientists, quite readily (if they pay close attention). This makes it a resounding success as a teaching exercise. It would receive 5/5 on that front. If however you wish to read it for pleasure (as it is marketed) the topic is not one that lends itself to narrative structure nor eloquence and it is perhaps not the book for you...
It was a hard slog. Wagner has the sense to realise when the writing is becoming boring. He tries at such moments to inject little anecdotes about the persons conducting the science in order to break the monotony. It is not enough. The library of genetic data existing in multiple dimensions is undoubtedly an effective metaphor for communication, but it does not make reading about it any easier. Wagner makes the topic easy to understand for the lay person. But that does not make reading about it a pleasure.
Because it is not a pleasure to read you must put in extra effort to pay attention to the writing. To understand it fully. If you let your mind wander at all, you'll find yourself having to reread entire chapters, not just the last couple of paragraphs. This was tiresome for me and I'm a scientist! I could not realistically recommend this to a lay person with only an interest in pop-sci books and no good mathematical background.
I am torn in my assessment of this book. It is excellently written, highly informative and can be understood, even by non-scientists, quite readily (if they pay close attention). This makes it a resounding success as a teaching exercise. It would receive 5/5 on that front. If however you wish to read it for pleasure (as it is marketed) the topic is not one that lends itself to narrative structure nor eloquence and it is perhaps not the book for you...
March 7, 2015
Highly conceptual, “Arrival of the Fittest” walks you through the steps, not just of understanding a difficult question, but of learning a new kind of thinking. The creationist argument that since natural selection only preserves innovative traits and never actually creates them—and so the likelihood of anything as complex as a human body coming about through natural selection is about the same as a 747 being built by a tornado tearing through a junkyard—exploits the limitations of our ready-made intuitions. It's hard for us to imagine how it might have happened, so we're ready to throw up our hands and say it must be supernatural, in the same way we leap from our ignorance about how ancient structures were built to the conclusion that they must be the work of extraterrestrials. But, stated another way, this argument boils down to the suggestion that, since it's difficult for our human intelligence to conceive of the evolutionary processes that led to complex life, there must be some sort of human-like intelligence behind it. (And saying that the notional creator’s intelligence is simply superior doesn’t save the argument from absurdity—it merely raises the more difficult question of how this being that’s even more impressive than humans came about.)
Wagner doesn't devote much space to dealing with creationism, but it's hard for anyone to read books about evolution in the US without carrying on a silent argument with the intelligent design folk in the back of our minds. The other old argument that “Arrival of the Fittest” reminds me of is that nature could only be comprehensible to us if it was created for us, by a being at least in some respects like us. Both of these arguments, it becomes clear, drastically overestimate the powers of human intellect and human imagination. Wagner at several points draws an analogy between evolution and technology, and one of his examples is the jet engine. Even the 747 had to come about through an evolutionary process—since no single human mind could have conceived of it ex nihilo. The process of invention took place by steps, and the availability of parts was necessary before design by recombination could take place. So it is with evolution.
Wagner's method relies heavily on a dual mix of abstraction and analogy. And the product is both clear and fascinating. He first asks us to imagine a library housing every possible book that could be written using a single alphabet. Most of the books are gibberish—they aren't viable for reading. But the idea is to help us think about the vast potential of randomly varying letter sequences when every change has a chance of altering a book’s meaning. The letter sequences are, naturally enough, analogs of genetic sequences. Wagner starts with the most basic requirement for a living being, a functioning metabolism. It turns out that metabolisms can consist of any number of possible chemical reactions, and every metabolism that works to give an organism sufficient energy is like a book in the universal library that has some kind of coherent meaning.
“And just as the universal library contains all meaningful books, the library of metabolisms contains all ‘meaningful’ metabolisms—those that allow an organism to survive—and many more, because not all metabolisms are meaningful, just as not all books are. Some metabolisms cannot procure energy, or they fail to manufacture important molecules. These are like the books where some chapters, paragraphs, or sentences are coherent but the book as a whole does not make sense. And many other metabolic texts are gibberish” (71-2).
The next steps are to try to imagine how big the library is and how easy it is to get from one section to another, keeping in mind that you can only take one step at a time in any direction. For simplicity’s sake, we imagine mutations as affecting a single gene at a time. The change has to be viable—resulting in a coherent text or a surviving organism. So you can’t leap from one part of the library to another. However, the library has to have more dimensions than the three we’re accustomed to inhabiting in real libraries. This is because the change can occur in any letter of the book or gene sequence. Each one represents a different direction we may travel through the library. Here’s where our vaunted human intellect reaches its limit; we can’t think in more than three (maybe 4, if you add time) dimensions, so it’s all but impossible for us to appreciate the vast potential of stepwise innovation. Wagner uses the term “hyperastronomical” to describe the number of potential gene combinations.
“Evolving organisms are like visitors to the metabolic library. Gene deletions and gene transfer allow them to walk through the library, to step from one metabolic text to another, often an immediate neighbor. All of a text’s neighbors form a neighborhood in this library, and such neighborhoods are as important for evolution as a city neighborhood is for people’s lives. City neighborhoods are useful because of proximity—everything is reachable within a few easy steps—and neighborhoods in the metabolic library are important for the same reason. Evolution can reach them in a few small steps, minor edits in a genotype. But residents of a city’s neighborhoods can walk in only four cardinal directions—north, south, east, or west—whereas evolution can head in five thousand directions. (Don’t even bother trying to visualize that.) And therefore the neighborhood of a metabolic text may be vastly more interesting, surprising, and diverse.” (92)
This is an abstract way of explaining how you get from photosensitive cells in a simple organism to the unimaginably complex eye of a bird-of-prey—though Wagner does trace this evolution more concretely through a series of actual creatures representing each level of complexity.
Each succeeding chapter in “Arrival of the Fittest” takes on a higher level of organization, from amino acids, to proteins, to regulatory circuits, and then moves onto to the connection between innovation in evolution and innovation in technology. One of the themes Wagner continually revisits is that for us humans to unravel the mysteries of evolution we’ve had to have the proper technology in place. We had to be able to understand the structure of DNA. We had to be able to sequence genes. We had to be able to do calculations with hyperastronomical numbers. All of this left me thinking that a thinking mind could only have come from nature—because no thinking mind, unaided by technology, can even begin to conceive of nature in all of its diversity and complexity. If there were such a thing as a creator, it would be more machine than human—and it would have come into existence through a process resembling evolution.
Wagner doesn't devote much space to dealing with creationism, but it's hard for anyone to read books about evolution in the US without carrying on a silent argument with the intelligent design folk in the back of our minds. The other old argument that “Arrival of the Fittest” reminds me of is that nature could only be comprehensible to us if it was created for us, by a being at least in some respects like us. Both of these arguments, it becomes clear, drastically overestimate the powers of human intellect and human imagination. Wagner at several points draws an analogy between evolution and technology, and one of his examples is the jet engine. Even the 747 had to come about through an evolutionary process—since no single human mind could have conceived of it ex nihilo. The process of invention took place by steps, and the availability of parts was necessary before design by recombination could take place. So it is with evolution.
Wagner's method relies heavily on a dual mix of abstraction and analogy. And the product is both clear and fascinating. He first asks us to imagine a library housing every possible book that could be written using a single alphabet. Most of the books are gibberish—they aren't viable for reading. But the idea is to help us think about the vast potential of randomly varying letter sequences when every change has a chance of altering a book’s meaning. The letter sequences are, naturally enough, analogs of genetic sequences. Wagner starts with the most basic requirement for a living being, a functioning metabolism. It turns out that metabolisms can consist of any number of possible chemical reactions, and every metabolism that works to give an organism sufficient energy is like a book in the universal library that has some kind of coherent meaning.
“And just as the universal library contains all meaningful books, the library of metabolisms contains all ‘meaningful’ metabolisms—those that allow an organism to survive—and many more, because not all metabolisms are meaningful, just as not all books are. Some metabolisms cannot procure energy, or they fail to manufacture important molecules. These are like the books where some chapters, paragraphs, or sentences are coherent but the book as a whole does not make sense. And many other metabolic texts are gibberish” (71-2).
The next steps are to try to imagine how big the library is and how easy it is to get from one section to another, keeping in mind that you can only take one step at a time in any direction. For simplicity’s sake, we imagine mutations as affecting a single gene at a time. The change has to be viable—resulting in a coherent text or a surviving organism. So you can’t leap from one part of the library to another. However, the library has to have more dimensions than the three we’re accustomed to inhabiting in real libraries. This is because the change can occur in any letter of the book or gene sequence. Each one represents a different direction we may travel through the library. Here’s where our vaunted human intellect reaches its limit; we can’t think in more than three (maybe 4, if you add time) dimensions, so it’s all but impossible for us to appreciate the vast potential of stepwise innovation. Wagner uses the term “hyperastronomical” to describe the number of potential gene combinations.
“Evolving organisms are like visitors to the metabolic library. Gene deletions and gene transfer allow them to walk through the library, to step from one metabolic text to another, often an immediate neighbor. All of a text’s neighbors form a neighborhood in this library, and such neighborhoods are as important for evolution as a city neighborhood is for people’s lives. City neighborhoods are useful because of proximity—everything is reachable within a few easy steps—and neighborhoods in the metabolic library are important for the same reason. Evolution can reach them in a few small steps, minor edits in a genotype. But residents of a city’s neighborhoods can walk in only four cardinal directions—north, south, east, or west—whereas evolution can head in five thousand directions. (Don’t even bother trying to visualize that.) And therefore the neighborhood of a metabolic text may be vastly more interesting, surprising, and diverse.” (92)
This is an abstract way of explaining how you get from photosensitive cells in a simple organism to the unimaginably complex eye of a bird-of-prey—though Wagner does trace this evolution more concretely through a series of actual creatures representing each level of complexity.
Each succeeding chapter in “Arrival of the Fittest” takes on a higher level of organization, from amino acids, to proteins, to regulatory circuits, and then moves onto to the connection between innovation in evolution and innovation in technology. One of the themes Wagner continually revisits is that for us humans to unravel the mysteries of evolution we’ve had to have the proper technology in place. We had to be able to understand the structure of DNA. We had to be able to sequence genes. We had to be able to do calculations with hyperastronomical numbers. All of this left me thinking that a thinking mind could only have come from nature—because no thinking mind, unaided by technology, can even begin to conceive of nature in all of its diversity and complexity. If there were such a thing as a creator, it would be more machine than human—and it would have come into existence through a process resembling evolution.
February 1, 2018
The philosopher Henri Bergson once wrote that every philosopher only ever really pursues one single idea, continuously reformulated, in different ways. While Andreas Wagner isn't exactly a philosopher, The Arrival of the Fittest is, if nothing else, a condensation of just what it means to take an idea and run with it to the end, hammering it home from just about every other angle. As for the idea itself, it's actually pretty straightforward: because evolution takes place among entire populations of individuals, and because there can be multiple genetic variations that give rise to same adaptive traits (there are many genetic routes to the same 'trait destination'), evolution can fast-track it's search for adaptive novelties by scouring through entire libraries of genetic change at the same time, with each library containing what amounts to multiple copies of the same book.
While I'm slightly skewing Wagner's own library metaphor (he writes instead of a single, multi-dimensional 'genotype library', in which multiple readers - individuals in a population - work their way through) the idea, I hope, is the same. The question then is why this solves 'evolution's greatest puzzle' - what, exactly, is the puzzle to solve? Well, it's in the first part of the title: the arrival of the fittest. While the mechanism of natural selection nicely explains why some genetic variants make the evolutionary cut while others don't (the survival of the fittest), it doesn't quite explain how all that variation got there in the first place. The usual solution given is that of random genetic drift: through copying errors and so fourth, nature will stumble across the right evolutionary solutions to make birds and mice and everything nice. But, in truth, this isn't quite enough.
The problem is the familiar one of monkeys banging away on a typewriter: after a long enough time, will any monkey produce a work of Shakespeare? Probably not. And so with random genetic change and the production of all the variety and complexity of life we see today. With the discovery of genotype networks however, things become alot easier - the trick is in realizing that unlike Shakespeare, nature didn't just produce 37 plays for monkeys to stumble across, but trillions upon trillions of them: that is, trillions upon trillions of ways to arrive at the same evolutionary solutions. Or, to use the lingo, nature is robust as all hell. Such is the idea that's detailed here, across multiple 'levels' of life, from DNA to metabolic networks, regulatory circuits, and even certain aspects of technology (as with computer chip designers, who, taking a leaf out of nature's page, employ simulated evolution to arrive at the best circuit designs for their silicon).
It's all very cool stuff, though one wonders if it really was worth the book-length treatment of it given here. While Wagner certainly has a flair for striking prose, many of the chapters here did feel rather padded out, as if an idea in search for applications - as many of them as they are. Part of the problem, in fact, is that in Wagner's attempt to make the science as digestible as possible, what might have taken a few paragraphs to get across ends up taking entire chapters. It's not even until about 170 pages in that Wagner actually even names the phenomenon he's discussing - phenotypic robustness, which, depending on my mood, is either an incredibly impressive or incredibly insulting feat. All in all, this is a great introduction to some of the cutting edge of evolutionary theory, even if, at the end of the day, it remains just that - an introduction. 3.5/5
While I'm slightly skewing Wagner's own library metaphor (he writes instead of a single, multi-dimensional 'genotype library', in which multiple readers - individuals in a population - work their way through) the idea, I hope, is the same. The question then is why this solves 'evolution's greatest puzzle' - what, exactly, is the puzzle to solve? Well, it's in the first part of the title: the arrival of the fittest. While the mechanism of natural selection nicely explains why some genetic variants make the evolutionary cut while others don't (the survival of the fittest), it doesn't quite explain how all that variation got there in the first place. The usual solution given is that of random genetic drift: through copying errors and so fourth, nature will stumble across the right evolutionary solutions to make birds and mice and everything nice. But, in truth, this isn't quite enough.
The problem is the familiar one of monkeys banging away on a typewriter: after a long enough time, will any monkey produce a work of Shakespeare? Probably not. And so with random genetic change and the production of all the variety and complexity of life we see today. With the discovery of genotype networks however, things become alot easier - the trick is in realizing that unlike Shakespeare, nature didn't just produce 37 plays for monkeys to stumble across, but trillions upon trillions of them: that is, trillions upon trillions of ways to arrive at the same evolutionary solutions. Or, to use the lingo, nature is robust as all hell. Such is the idea that's detailed here, across multiple 'levels' of life, from DNA to metabolic networks, regulatory circuits, and even certain aspects of technology (as with computer chip designers, who, taking a leaf out of nature's page, employ simulated evolution to arrive at the best circuit designs for their silicon).
It's all very cool stuff, though one wonders if it really was worth the book-length treatment of it given here. While Wagner certainly has a flair for striking prose, many of the chapters here did feel rather padded out, as if an idea in search for applications - as many of them as they are. Part of the problem, in fact, is that in Wagner's attempt to make the science as digestible as possible, what might have taken a few paragraphs to get across ends up taking entire chapters. It's not even until about 170 pages in that Wagner actually even names the phenomenon he's discussing - phenotypic robustness, which, depending on my mood, is either an incredibly impressive or incredibly insulting feat. All in all, this is a great introduction to some of the cutting edge of evolutionary theory, even if, at the end of the day, it remains just that - an introduction. 3.5/5
August 4, 2015
I finished this Thursday night, and I thought about it for a while, and then I listened to the epilogue again Friday morning, and then Friday evening I read a stack of reviews of both the physical book and the audiobook, and I came to a rather disconcerting conclusion. I had no idea what the author was saying. One of the reviews on Audible described this book as "impenetrable for the non-scientist" and another says:
I hate to have to admit that I'm a lay person, but I am. I have a liberal arts degree with an enduring interest for the sciences, specifically biology. I read an okay number of science-y books on an annual basis, and my understanding of them is usually fine. Additionally, I don't usually have any trouble listening to audiobooks. In fact, finding most of them too plodding, I usually listen at somewhere between 1.25x and 1.5x depending on the narrator. So what went wrong here?
I think that Wagner's writing is pretty obtuse, perhaps not deliberately so, but I was mortified when I finished the book and realized that I had no clear idea of what the difference between genotype and phenotype was (college science is nearly two decades back at this point). One minute and two sentences on the internet was all it took to clear that up, and once I read the definitions I realized that Wagner had covered this, and that a good portion of the book was about how genotype does not necessarily equal phenotype, which is one of the mechanism of those problem-solving leaps that organisms can make, but goodness gracious, it went right over my head in the text. The same person I quoted above suggests some prerequisites to reading this, and I might try that and give this a second go. Perhaps a chapter at a time, or maybe the paper book from my local library.
It can be slow going on audio. The author necessarily builds large, complex analogies for explaining molecular interactions. If you become distracted, let your mind wander, or stop and start the audio throughout the day or week, it's relatively easy to lose the author's argument.
I hate to have to admit that I'm a lay person, but I am. I have a liberal arts degree with an enduring interest for the sciences, specifically biology. I read an okay number of science-y books on an annual basis, and my understanding of them is usually fine. Additionally, I don't usually have any trouble listening to audiobooks. In fact, finding most of them too plodding, I usually listen at somewhere between 1.25x and 1.5x depending on the narrator. So what went wrong here?
I think that Wagner's writing is pretty obtuse, perhaps not deliberately so, but I was mortified when I finished the book and realized that I had no clear idea of what the difference between genotype and phenotype was (college science is nearly two decades back at this point). One minute and two sentences on the internet was all it took to clear that up, and once I read the definitions I realized that Wagner had covered this, and that a good portion of the book was about how genotype does not necessarily equal phenotype, which is one of the mechanism of those problem-solving leaps that organisms can make, but goodness gracious, it went right over my head in the text. The same person I quoted above suggests some prerequisites to reading this, and I might try that and give this a second go. Perhaps a chapter at a time, or maybe the paper book from my local library.
August 19, 2016
Um livro muito bom (para mim) que fica em um meio do caminho estranho. O Andreas Wagner é um dos pesquisadores mais inovadores na área de como evoluem sistemas biológicos (a biologia de sistemas). Já li e citei vários artigos dele, é sem dúvida uma das pessoas mais indicadas para falar sobre o assunto. Mas esse livro ficou em uma encruzilhada que considero ruim. Por um lado, fala de uma parte de biologia evolutiva que não é muito acessível ao grande público, com as interações entre genes, proteínas, reguladores, redes metabólicas e afins. Por outro, esse assunto é super importante e interessante para biólogos (a quem recomendo o livro, mas para esse público grande parte do livro é desnecessária, já que recapitula evolução, genética e outras áreas que não acrescentam muito para quem já conhece.
A ideia principal, como sistemas biológicos são organizados de maneira que exploram muito rapidamente a evolução de novas características e ao mesmo tempo são robustos, é na minha opinião uma das descobertas recentes mais importantes. Por isso o livro é interessante. Mas para quem essa informação é acessível uma boa parte do livro é desnecessária (um review seria mais prático) e para quem isso não é acessível, o livro é denso demais. Pode servir a leigos interessados em evolução, mas outros livros como o Quando Éramos Peixes: Uma viagem pelos 3,5 mil milhões de anos de história do corpo humano fazem isso muito melhor. É um conteúdo que contribui mais em um livro sobre ideias mais amplas, como o The Evolution of Everything: How New Ideas Emerge que citou ele, do que como uma obra em si.
A ideia principal, como sistemas biológicos são organizados de maneira que exploram muito rapidamente a evolução de novas características e ao mesmo tempo são robustos, é na minha opinião uma das descobertas recentes mais importantes. Por isso o livro é interessante. Mas para quem essa informação é acessível uma boa parte do livro é desnecessária (um review seria mais prático) e para quem isso não é acessível, o livro é denso demais. Pode servir a leigos interessados em evolução, mas outros livros como o Quando Éramos Peixes: Uma viagem pelos 3,5 mil milhões de anos de história do corpo humano fazem isso muito melhor. É um conteúdo que contribui mais em um livro sobre ideias mais amplas, como o The Evolution of Everything: How New Ideas Emerge que citou ele, do que como uma obra em si.
February 22, 2016
Deeply disappointing both as a guide to current thinking and theory in evolutionary theory, and as a popular science book. Wagner is very bad at explaining things, even when those things are his professional opinions on evolution.
A key problem for the reader is that Wagner can't seem to pitch his discussion at a consistent level. He spends far too many pages describing unremarkable and widely understood principles so that he can set these scarecrows up to be knocked down by his sneeringly presented Big Insight; this is especially true when his objection is banal and under-described.
Take for example the whole mess of the Metaphor of The Library. Wagner devotes dozens of pages describing how the Library of Congress System is organized, then many pages more on how the analogous genetic library he proposes would look in that context, then tells us in a sentence that the library is a terrible metaphor because the genome works nothing like a library anyway. And then refers back to the genetic library metaphor constantly after that. This means that Wagner objects entirely to his own choice of metaphor. Yes, he does. It only gets worse from here. Granted, Wagner gives us this lengthy and confusing explanation to illustrate his research finding that there is more than one possible genotype to express the same phenotype. He appears to think that his proof is a sea change in genetic understanding rather than an unproven near certainty for many decades.
Then there is the problem of needless information. Wagner includes a long chapter on the origins of life at the smoky vents deep in the ocean, then introduces nothing about his topic of evolutionary fitness. Darwin and Mendel are propped up as strawmen for Wagner to tut over, as is the "new synthesis", as are dozens of other tangential theories and scientists, possibly to add some historical weight to this otherwise lightweight and needlessly obscure book.
For my critique of his actual science project to make sense, I will need to reveal Wagner's Big Idea. For anyone who either hasn't read this book, or was understandably confused by it, this is Wagner's book in one sentence:
Wagner used some 450 pages of wandering prose poems to gift us with just that.
Problem is this what is called a tautology (x=x), and worse it is a tautology that continues to beg the question of where these qualities come from since one innovation often needs be matched with other innovations to provide robustness. No one innovation is immediately "fit" on Wagner's terms, but it is graced with qualities that make it survive and superior over other discarded mutations. Wagner makes some attempts (via the library metaphor) to paper over the definitional circularity of his argument, but if you read closely there is no essential difference between his mechanism of evolutionary processes as described here and those of the gradualists he mocks except that Wagner energetically insists they are very, very different. Worse, his tautology seems to land him dangerously close to an argument that evolution has a direction, a goal, a map of how to get from squid to albatross.
In short: Don't bother.
A key problem for the reader is that Wagner can't seem to pitch his discussion at a consistent level. He spends far too many pages describing unremarkable and widely understood principles so that he can set these scarecrows up to be knocked down by his sneeringly presented Big Insight; this is especially true when his objection is banal and under-described.
Take for example the whole mess of the Metaphor of The Library. Wagner devotes dozens of pages describing how the Library of Congress System is organized, then many pages more on how the analogous genetic library he proposes would look in that context, then tells us in a sentence that the library is a terrible metaphor because the genome works nothing like a library anyway. And then refers back to the genetic library metaphor constantly after that. This means that Wagner objects entirely to his own choice of metaphor. Yes, he does. It only gets worse from here. Granted, Wagner gives us this lengthy and confusing explanation to illustrate his research finding that there is more than one possible genotype to express the same phenotype. He appears to think that his proof is a sea change in genetic understanding rather than an unproven near certainty for many decades.
Then there is the problem of needless information. Wagner includes a long chapter on the origins of life at the smoky vents deep in the ocean, then introduces nothing about his topic of evolutionary fitness. Darwin and Mendel are propped up as strawmen for Wagner to tut over, as is the "new synthesis", as are dozens of other tangential theories and scientists, possibly to add some historical weight to this otherwise lightweight and needlessly obscure book.
For my critique of his actual science project to make sense, I will need to reveal Wagner's Big Idea. For anyone who either hasn't read this book, or was understandably confused by it, this is Wagner's book in one sentence:
Define "evolutionary fitness" as Robustness and Openness to Improvement (or what Wagner calls "Evolvability") and the problem of how life innovates goes away.
Wagner used some 450 pages of wandering prose poems to gift us with just that.
Problem is this what is called a tautology (x=x), and worse it is a tautology that continues to beg the question of where these qualities come from since one innovation often needs be matched with other innovations to provide robustness. No one innovation is immediately "fit" on Wagner's terms, but it is graced with qualities that make it survive and superior over other discarded mutations. Wagner makes some attempts (via the library metaphor) to paper over the definitional circularity of his argument, but if you read closely there is no essential difference between his mechanism of evolutionary processes as described here and those of the gradualists he mocks except that Wagner energetically insists they are very, very different. Worse, his tautology seems to land him dangerously close to an argument that evolution has a direction, a goal, a map of how to get from squid to albatross.
In short: Don't bother.
December 30, 2015
I am a developmental geneticist and even had the privilege to have contributed a few scientific results discussed in the book. I also know how difficult it is to teach biological concepts and what the author coins the innovability of evolution to first year biology and chemistry students. For me this book has been very inspiring. It provides mathematical insights into how innovability works. Wagner reduces the complexity of this process to three interconnected processes of protein structure, metabolic networks and gene regulatory networks. The three are arranged in multidimentional libraries which the 10^30 organisms on earth have explored for 3.5 billion years by moving - one mutations at a time - from one book in these libraries to the next. Experimental evidence by the author's group and others shows that the adjacent books in the libraries are diverse and that there many different solutions to a given problem (eg ability to live in a specific environment or to specify a certain shape limb). Combined with redundancy conferring robustness and natural selection's power to preserve small innovations we have the ingredients for the diversity of live. In the final chapter Andreas Wagner describes how Boolean Logic can be used to model the behavior of these networks and he shows parallels with the architecture of modern computers.
Andreas Wagner's writing is crisp and his analogies and examples from nature are excellent and engaging. I have read many book by Richard Dawkins. Wagner does not have to shy comparison with Dawkins also in literary style. As a computational and molecular biologist he brings the knowledge of modern systems biology that Dawkins is lacking. In summary this is an excellent and up to date book on biology. I will recommend it to my students and anyone interested in biology. I listened to the audio version. Sean Pratt does an excellent job!
Andreas Wagner's writing is crisp and his analogies and examples from nature are excellent and engaging. I have read many book by Richard Dawkins. Wagner does not have to shy comparison with Dawkins also in literary style. As a computational and molecular biologist he brings the knowledge of modern systems biology that Dawkins is lacking. In summary this is an excellent and up to date book on biology. I will recommend it to my students and anyone interested in biology. I listened to the audio version. Sean Pratt does an excellent job!
February 1, 2015
Nice piece! I can see lots of care and courage put into the text. This is the beginning of evolution theory of the "whole" - the animate, the inanimate, and all, have to be seen as deeply connected in order to understand how evolution could possibly work at the observed pace. He has a really neat research paradigm to mathematically formalize and actually get one's hands dirty with the relationship between micro structure and macro function across different scales of the universe as time progress. Maybe, what's beautiful about evolution is indeed the math - what high dimensional function maps between the relative micro-macro worlds can create such intricate/entangled topology? Has he solved it? I think not. But at least we are learning how to ask the question.
March 30, 2015
I am having some difficulty in identifying exactly what underwhelmed me about this book. The premise and subject matter are interesting. The research presented is important. Perhaps the metaphor of the library was either overused or not sufficiently elucidating?
This is still worth reading if you are interested in evolutionary theory. It is not a definitive treatment of the questions it tries to address (it would benefit from a less lofty subtitle). There is a lot more to say about the mechanisms of variation and the odds of useful adaptations arising.
This is still worth reading if you are interested in evolutionary theory. It is not a definitive treatment of the questions it tries to address (it would benefit from a less lofty subtitle). There is a lot more to say about the mechanisms of variation and the odds of useful adaptations arising.
June 29, 2016
The theory of evolution answers many questions about the growing and winnowing of the tree of life, but it does not answer questions about "innovability" - how advantageous phenotypic changes are initiated in the first place. This book goes a long way in answering that question. Complex at times, but well worth the read.
May 10, 2017
Highly recommended!
February 17, 2023
So I think my brother got this book as a gift at some point in the past and never finished it. It sat in my parent's house for a while before I noticed it and its nice looking cover and compelling blurb and decided to take it for myself. Then it sat on my shelf for about 3 years. So goddamnit, I better just get this thing done at some point.
The two stars are for the main subject material of the book being interesting and well explained . I can't give it anything more than that because this book should have been 50 pages instead of nearly 300. The text takes countless unnecessary and long detours, repeats itself several times and tries too hard to sound smart but also cool. I started a technique where when I sensed I was in a particularly tedious section I would just skim the first and last sentence of every paragraph, which helped and tellingly did not seem to affect my comprehension.
On the bright side, learning about the amazing proprties of life from RNA and amino acids up to the "gene networks" that regulate the ultimate form and function of any organism, and specifically how the math of the sort of system all of this is basically operating on works out to enable life to innovate from the first simple cells into incomprehensibly complex creatures, was cool.
The two stars are for the main subject material of the book being interesting and well explained . I can't give it anything more than that because this book should have been 50 pages instead of nearly 300. The text takes countless unnecessary and long detours, repeats itself several times and tries too hard to sound smart but also cool. I started a technique where when I sensed I was in a particularly tedious section I would just skim the first and last sentence of every paragraph, which helped and tellingly did not seem to affect my comprehension.
On the bright side, learning about the amazing proprties of life from RNA and amino acids up to the "gene networks" that regulate the ultimate form and function of any organism, and specifically how the math of the sort of system all of this is basically operating on works out to enable life to innovate from the first simple cells into incomprehensibly complex creatures, was cool.
February 16, 2021
Wonderful and vivid exploration of the phase space of amino acids, proteins and genes, and how small changes in this enormous multidimensional space are closely interconnected, like a sponge of viable life filled with little holes of death.
November 2, 2021
อธิบายเรื่องวิวัฒนาการได้ดี เข้าใจง่ายสำหรับคนที่เจอเป็นครั้งแรก แต่ถ้าเคยผ่านมาแล้วข้อเสนอในเล่มนี้ก็ไม่ได้มีอะไรใหม่มาก เแต่จะเน้นอธิบายงานวิจัยที่เป็นหลักฐานสนับสนุน
July 31, 2020
This recent publication redeems itself from being merely another entry in the seemingly endless series of popular expositions of evolutionary biology and Darwinism by the circumstance that its author, Andreas Wagner, happens to be a professional biologist who can back up his ideas with reference to significant original research, unlike armchair speculators of the likes of Richard Dawkins who have done precious little laboratory work (would we could pass over as unworthy of mention even worse literary men like Christopher Hitchens, who ignorantly suppose they can advance an impressive case in favor of atheism by trotting out stale arguments from natural selection in a field in which they enjoy no competence whatsoever!). The first two chapters of the work under review disappoint, however, and have almost nothing to say that would be unfamiliar to someone knowledgeable in the literature. It may be a failing common to popular science writing that the author will ever be constrained to rehearse well-known details for the benefit of the uneducated reader he must assume. All Wagner does here is to repeat the story of the discovery of Mendelian genetics and its implications for the so-called new evolutionary synthesis of the 1930’s, in the first chapter, and in the second, to review speculations on the origin of life, the Miller-Urey experiment, hydrothermal vents, the metabolism-first versus replicator-first debate and so forth. He really gets underway in the third and later chapters. The third chapter, on the ‘universal library’, introduces the concept of a space of all possible designs for single-celled organisms. The metabolic genotype specifies precisely which among the several thousand known reactions can, in fact, take place in the cell (i.e., for which the genome codes appropriate protein catalysts). The explosion of data collected in recent decades makes it possible to explore this space—on the computer—as never before. The findings are novel and buttress Wagner’s thesis throughout this work on the nature of innovation. Biological innovation through deep evolutionary time has long been a puzzle because one finds it hard to expect the observed rate of diversification, even given the prodigious number of mutants with which natural selection has to contend. The metabolic space turns out to have a quite surprising topological structure. It is connected in the sense that one can get from one organism to another, seemingly very different one via a sequence of incremental steps, each changing a single reaction among the entire network of reactions taking place in the cell, in such a way that function is preserved along the way. Even closely related organisms, for instance strains of E. Coli, can have dramatically different metabolic texts, differing by up to twenty percent of the enzymes they produce. In the succeeding chapters, Wagner investigates along similar lines the space of all possible amino acid sequences that code for proteins and finds it to have a similarly interconnected structure. Wagner comments on the possibilities for biological innovation this implies for enzyme catalysis of needed reactions in chapter four and for regulation of genetic expression in chapter five, with clear implications for the program of embryogenesis according to the genetic blueprint. One could regret that Wagner’s treatment of evolutionary developmental biology—a fascinating field in its own right—is rather too sketchy. The heart of the book lies in chapter six, where Wagner sets forth his ideas on how biological innovation takes advantage of the self-organized multidimensional fabric of genotype networks (what he discovered along with collaborators in his original research) to respond to environmental change, in an ever-ascending spiral of complexity and innovability. These genotype networks, with their remarkable interconnectivity, afford just the right balance between order and disorder. The final chapter looks to some potential technological applications of what we have learned about how evolution works in nature. All around, an excellent read; despite a slow start, it proves meatier in content than one might have judged from its title and cover!
September 28, 2015
now it's a trilogy. in order to understand how life arose on earth:
1. the origin of the species by charles darwin
2. the selfish gene by richard dawkins
3. arrival of the fittest by andreas wagner
Every iteration brings us closer to understanding how it actually works. we can now prove mathematically just how life could have found its myriad forms - and can model the progress of evolution from its origins to its current manifestations.
if you imagine a library filled with every possible configuration of dna letters (ATCG) or every possible metabolic reaction or every possible gene regulation circuit, it would fill a hyperastronomical number of volumes, too much for live to navigate since the beginning of the universe. based on this fact, it is highly unlikely that life would ever have originated, much less evolved to such variety as we see today. through computation and computer modeling, we can now show that life can find adaptations in the immediate neighborhood of whatever starting configuration life chose.
science man.
1. the origin of the species by charles darwin
2. the selfish gene by richard dawkins
3. arrival of the fittest by andreas wagner
Every iteration brings us closer to understanding how it actually works. we can now prove mathematically just how life could have found its myriad forms - and can model the progress of evolution from its origins to its current manifestations.
if you imagine a library filled with every possible configuration of dna letters (ATCG) or every possible metabolic reaction or every possible gene regulation circuit, it would fill a hyperastronomical number of volumes, too much for live to navigate since the beginning of the universe. based on this fact, it is highly unlikely that life would ever have originated, much less evolved to such variety as we see today. through computation and computer modeling, we can now show that life can find adaptations in the immediate neighborhood of whatever starting configuration life chose.
science man.
October 19, 2014
In my opinion, Evolution and, more specifically Natural Selection, is the most powerful force in Nature and our understanding of it, starting with Darwin, is probably humanities greatest insight into the world around us. But one thing that Darwin recognized his theory could not explain was where new things, innovations, come from. It would simply take too many random mutations to explore the space of possibilities. Andreas Wagner's book, does an excellent job of presenting the challenge. The solution, as he presents it, is more difficult to understand, but he does a fair job.
March 30, 2016
Hardly readable and completely unlistenable. An example of how not to approach popular scientific writing. Any reader with even the slightest experience with popular science will be able to spot where the ghost writer added some flavour to the raw dullness of this text and the editor's fingerprints are all over the book. A real disappointment as the topic is highly interesting. For those who feel courageous and want to know more about innovation in nature: don't bother reading the entirety of this horrendous volume, just skip straight to the final two chapters.
January 4, 2015
Interesting concept. I enjoyed reading about various studies and theories, but the author lost credibility when he insulted people who disagree with him. While I too find monotheism impossible, I wouldn't call believers such insults. You aren't going to convert people with name calling. A man of this supposed caliber should be above that. Perhaps the publisher should edit that out in future editions.
January 24, 2018
Takes awhile to hit its stride.
September 5, 2015
**I read Wagner's Arrival of the Fittest, John Tyler Bonner's Randomness in Evolution, and David Deamer's First Life: Discovering the Connections between Stars, Cells, and How Life Began subsequently, so my review of this book is meant to be read relative to the other two as all three overlap in subject matter. (This paragraph appears in all three reviews). I am reading these books after reading several on cosmology.* I wanted to move beyond what cosmologists say (with disagreement) about the formation of the universe to see how it could be compatible with what chemists and biologists say about the beginning of life. Alan Lightman writes in the Accidental Universe that "Science can never know how universe was created," and I find that to be echoed in these books -- science can never know or prove how exactly life began (Deamer states this outright). Exactly what chemicals were available on earth to mix in what quantities to randomly create a reaction between molecules that led bonds to form, information to be transmitted, and growth to begin? All of the hypotheses presented in the books require certain laws of physics and nature to hold but I have not found any who attempts to explain how those laws arose in the first place. Why are these laws what they are? Call this the Paul Davies critique.
Deamer acknowledges that it's possible a creator put those laws into existence, but the other two avoid the subject. None of the three seem to recognize that chance is not a causal force, so time + chance cannot explain anything. Where did light come from and how did it contain information? How did cells know that it contained information and figure out a way to receive and decode it? How do "regulator cells" operate according to these laws? What is consciousness and at what point is life "life" such that it has "value?" All three of the authors reach the same conclusion as the cosmologists above-- we are a random collection of atoms that will one day be scattered, nothing more nothing less. Life has no meaning outside of a debatable definition regarding complex molecular processes, and any sentiment we attach to it is illogical-- there is no soul in science. I do not, therefore, understand how Lightman, Hawking, Richard Dawkins, etc. can argue that scattering people's atoms is "wrong," or where they get ethics. We're not special, only lucky in the sense of randomness.
These three biochemist authors, however, engage in less armchair philosophy than Hawking et al, and (unlike string theorists Hawking and Green) argue that science requires testable hypotheses and that the universe had a beginning. Each of these books have a good look at what actual laboratory research looks like. These are not just men working equations at a desk all day, although there is some of that. They're often out traveling the world in search of mineral samples and in the laboratory mixing chemicals in the search for the genesis of life. My next set of books will be on the scientific understanding of consciousness-- something these books do not address.**
Andreas Wagner is a professor in the Institute of Evolutionary Biology and Environmental Studies at the University of Zurich in Switzerland. From the cover: "Using experimental and computational technologies that were heretofore unimagined, (Wagner) has found that adaptations are not just driven by chance, but by a set of laws that allow nature to discover new molecules and mechanisms in a fraction of the time that random variation would take." This "set of laws" already found in nature seems to me to fall under the "Davies critique"-- who or what created those laws, where did they come from?
Wagner briefly touches on the debate in biology between the "neutralists" - those who put more weight on random processes, like John Tyler Bonner in Randomness in Evolution, and "naturalists," those who put more weight on natural selection, that cells were somehow smart enough to figure out what adaptation would be best to keep.
While this book is interesting, it is an uphill climb for someone who has not had many courses in biology. If you're like me, you had to Google "phenotype," and note it's hard to nail down a definition. The simplest I can understand it is that phenotypes are the uniquely distinct results of geneotypes interacting with the environment.
Wagner's research focuses on phenotypes and his book uses his research to hypothesize how organisms began such that they could survive. Natural selection explains the survival, but what explains the arrival? Evolution was not a new idea when Darwin wrote The Origin of Species, and Darwin had no idea how information was transmitted through generations-- genes and laws of inheritance would be discovered later. Wagner is concerned with where phenotypes come from. While we may have mapped genomes, "the road from genotype to phenotype has not been mapped."
The author writes that genome mapping is, in a sense, "useless," and much less helpful than the popular media seems to think. It has little predictive value, can only help calculate some probabilities of genetic likelihoods. "Nature never ceases to surprise" and science cannot predict any single innovation or random mutation. Laboratory experiments on RNA did not help the researchers predict even though they had a great amount of data from nature. Genomics is no help in studying phenotypes. Where do phenotypes come from? We do not have the ability to decode the amino acid chain, but Wagner hypothesizes that we may not need to map all amino acids to draw the map.
Wagner's quest, ultimately, is to find a molecule that replicates itself perfectly due to a random mix of chemicals and energy believed to exist on earth 14 billion years ago. How did life form? It formed before there were genes. He goes step-by-step through what is needed, from an "enormous" food supply for the self-replicating molecules which depends on the rate of metabolism to the catalysts that make metabolism possible. He examines various hypotheses about the "primordial soup" that resulted in the first randomly reproducing cells that eventually formed bonds. Chemical biology has gotten a big boost from the discovery that meteorites crashing into earth contain amino acids and other substances required for life, resulting in further hypotheses and experiments that have produced inconclusive results.
Some of the mature processes are seen in science today, the citric acid cycle for one example, and these are believed to contain clues or echoes from the genesis of reproduction. There had to be many available metabolisms to survive on glucose. Molecules spontaneously change shape, and among multiplying cells there appear to be "regulator cells" that determine what cells will form. Proteins have to fold in precise shapes. It was this "self-organization" that "guided our formation" many years ago. Chapter 5 deals specifically with the "regulation" of molecular development.
Many genes apparently have no role at all which begs the question: why do they still exist? Wagner writes that robustness allows a gene to change an organism without fundamentally changing the organism. The environment matters and old environments where certain genes would have been necessary for survival explain now useless "junk genes." Wagner briefly touches on the debate between those in the natural selection camp and "neutralists" who put much more weight on random processes at work.
Wagner gives insights into his own research comparing genotypes, and using random walk models on computers to determine whether certain structures remain viable. These models generate results that "surprise" researchers. Cells form bonds that would not have been predicted. This is interesting and also questionable as a replacement for actual laboratory experimentation.
Chapter 7 is on "technology and nature," how modern software designers and entrepreneurs have seemingly "discovered" from biochemists the solution to certain problems. We can learn a lot from the random processes and adaptability of nature in designing various routes in software and circuit design. "Evolutionary algorithms" play a roll in machine learning. To Wagner, biology demonstrates the truth often neglected in business schools that innovators crowd source or rely on the crowd/market for signals and ideas. There is a myth about Thomas Edisons of the world locked in their office working on inventions, when in reality those people outsource a lot of the work to other innovators in their laboratory who are collaborating on results and experiment with things hundreds of ways before something finally "works." So it is in nature, Wagner writes.
Wagner appears to embrace randomness, but not at the level of John Tyler Bonner nor deal much with Bonner's criticisms of the "naturalists." He also does not deal with the delicateness (and debates in the field of biology) of the definitions of words like "life" as David Deamer does in First Life. Where there is overlap between the three works, Wagner appears to have left out some relevant research by others. I found the experimentation and Monte Carlo modeling interesting, but I don't find an answer to the "Davies critique" in the book, and so it's therefore somewhat lacking. 3 stars out of 5.
* Books I had read previously which are tangentially related:
Brian Greene - Fabric of the Cosmos, The Hidden Reality, The Elegant Universe
Stephen Hawking - Black Holes and Baby Universes, The Universe in a Nutshell, The Grand Design
Alan Lightman - The Accidental Universe
Lee Smolin - The Trouble with Physics
Richard Dawkins - The God Delusion
Charles Darwin - The Origin of Species
Deamer acknowledges that it's possible a creator put those laws into existence, but the other two avoid the subject. None of the three seem to recognize that chance is not a causal force, so time + chance cannot explain anything. Where did light come from and how did it contain information? How did cells know that it contained information and figure out a way to receive and decode it? How do "regulator cells" operate according to these laws? What is consciousness and at what point is life "life" such that it has "value?" All three of the authors reach the same conclusion as the cosmologists above-- we are a random collection of atoms that will one day be scattered, nothing more nothing less. Life has no meaning outside of a debatable definition regarding complex molecular processes, and any sentiment we attach to it is illogical-- there is no soul in science. I do not, therefore, understand how Lightman, Hawking, Richard Dawkins, etc. can argue that scattering people's atoms is "wrong," or where they get ethics. We're not special, only lucky in the sense of randomness.
These three biochemist authors, however, engage in less armchair philosophy than Hawking et al, and (unlike string theorists Hawking and Green) argue that science requires testable hypotheses and that the universe had a beginning. Each of these books have a good look at what actual laboratory research looks like. These are not just men working equations at a desk all day, although there is some of that. They're often out traveling the world in search of mineral samples and in the laboratory mixing chemicals in the search for the genesis of life. My next set of books will be on the scientific understanding of consciousness-- something these books do not address.**
Andreas Wagner is a professor in the Institute of Evolutionary Biology and Environmental Studies at the University of Zurich in Switzerland. From the cover: "Using experimental and computational technologies that were heretofore unimagined, (Wagner) has found that adaptations are not just driven by chance, but by a set of laws that allow nature to discover new molecules and mechanisms in a fraction of the time that random variation would take." This "set of laws" already found in nature seems to me to fall under the "Davies critique"-- who or what created those laws, where did they come from?
Wagner briefly touches on the debate in biology between the "neutralists" - those who put more weight on random processes, like John Tyler Bonner in Randomness in Evolution, and "naturalists," those who put more weight on natural selection, that cells were somehow smart enough to figure out what adaptation would be best to keep.
While this book is interesting, it is an uphill climb for someone who has not had many courses in biology. If you're like me, you had to Google "phenotype," and note it's hard to nail down a definition. The simplest I can understand it is that phenotypes are the uniquely distinct results of geneotypes interacting with the environment.
Wagner's research focuses on phenotypes and his book uses his research to hypothesize how organisms began such that they could survive. Natural selection explains the survival, but what explains the arrival? Evolution was not a new idea when Darwin wrote The Origin of Species, and Darwin had no idea how information was transmitted through generations-- genes and laws of inheritance would be discovered later. Wagner is concerned with where phenotypes come from. While we may have mapped genomes, "the road from genotype to phenotype has not been mapped."
The author writes that genome mapping is, in a sense, "useless," and much less helpful than the popular media seems to think. It has little predictive value, can only help calculate some probabilities of genetic likelihoods. "Nature never ceases to surprise" and science cannot predict any single innovation or random mutation. Laboratory experiments on RNA did not help the researchers predict even though they had a great amount of data from nature. Genomics is no help in studying phenotypes. Where do phenotypes come from? We do not have the ability to decode the amino acid chain, but Wagner hypothesizes that we may not need to map all amino acids to draw the map.
Wagner's quest, ultimately, is to find a molecule that replicates itself perfectly due to a random mix of chemicals and energy believed to exist on earth 14 billion years ago. How did life form? It formed before there were genes. He goes step-by-step through what is needed, from an "enormous" food supply for the self-replicating molecules which depends on the rate of metabolism to the catalysts that make metabolism possible. He examines various hypotheses about the "primordial soup" that resulted in the first randomly reproducing cells that eventually formed bonds. Chemical biology has gotten a big boost from the discovery that meteorites crashing into earth contain amino acids and other substances required for life, resulting in further hypotheses and experiments that have produced inconclusive results.
Some of the mature processes are seen in science today, the citric acid cycle for one example, and these are believed to contain clues or echoes from the genesis of reproduction. There had to be many available metabolisms to survive on glucose. Molecules spontaneously change shape, and among multiplying cells there appear to be "regulator cells" that determine what cells will form. Proteins have to fold in precise shapes. It was this "self-organization" that "guided our formation" many years ago. Chapter 5 deals specifically with the "regulation" of molecular development.
Many genes apparently have no role at all which begs the question: why do they still exist? Wagner writes that robustness allows a gene to change an organism without fundamentally changing the organism. The environment matters and old environments where certain genes would have been necessary for survival explain now useless "junk genes." Wagner briefly touches on the debate between those in the natural selection camp and "neutralists" who put much more weight on random processes at work.
Wagner gives insights into his own research comparing genotypes, and using random walk models on computers to determine whether certain structures remain viable. These models generate results that "surprise" researchers. Cells form bonds that would not have been predicted. This is interesting and also questionable as a replacement for actual laboratory experimentation.
Chapter 7 is on "technology and nature," how modern software designers and entrepreneurs have seemingly "discovered" from biochemists the solution to certain problems. We can learn a lot from the random processes and adaptability of nature in designing various routes in software and circuit design. "Evolutionary algorithms" play a roll in machine learning. To Wagner, biology demonstrates the truth often neglected in business schools that innovators crowd source or rely on the crowd/market for signals and ideas. There is a myth about Thomas Edisons of the world locked in their office working on inventions, when in reality those people outsource a lot of the work to other innovators in their laboratory who are collaborating on results and experiment with things hundreds of ways before something finally "works." So it is in nature, Wagner writes.
Wagner appears to embrace randomness, but not at the level of John Tyler Bonner nor deal much with Bonner's criticisms of the "naturalists." He also does not deal with the delicateness (and debates in the field of biology) of the definitions of words like "life" as David Deamer does in First Life. Where there is overlap between the three works, Wagner appears to have left out some relevant research by others. I found the experimentation and Monte Carlo modeling interesting, but I don't find an answer to the "Davies critique" in the book, and so it's therefore somewhat lacking. 3 stars out of 5.
* Books I had read previously which are tangentially related:
Brian Greene - Fabric of the Cosmos, The Hidden Reality, The Elegant Universe
Stephen Hawking - Black Holes and Baby Universes, The Universe in a Nutshell, The Grand Design
Alan Lightman - The Accidental Universe
Lee Smolin - The Trouble with Physics
Richard Dawkins - The God Delusion
Charles Darwin - The Origin of Species
June 6, 2021
A refresher course on Highschool Biology, but more!
Learning about DNA, RNA, replication, citric acid cycle, ribosomes, enzymes, etc in highschool was mostly just about memorising and being amazed at how complex and organised life is. But I never thought of these in lights of the origin of life.
All the theories like Darwin's evolution, natural selection, Mandellian inheritance, etc. I took for granted, and never once thought of the missing puzzles, of how one theory neatly lies on top of another eventually leading up to the massive body of knowledge that we have now, and of how mathematics -- my absolute favourite -- was involved in everything.
The book helps me see the world differently, yet again, through a pair of more refined lenses. It gave me a deeper sense of appreciation and gratitude for the opportunity to experience life as is, and to participate in evolution.
I also can't help but realise how innovation in general - be it in business or tech - generally mimics the way life innovates. It gives light to what I will do in my business venture in the future, and once again showed that we should not limit ourselves to learn only from a certain stream but be bold enough to venture farther and wider, one little step at a time. Although the basic philosophy of life is "simple", the complex creation that results help life survives, leading to the eventual arrival of the fittest.
Learning about DNA, RNA, replication, citric acid cycle, ribosomes, enzymes, etc in highschool was mostly just about memorising and being amazed at how complex and organised life is. But I never thought of these in lights of the origin of life.
All the theories like Darwin's evolution, natural selection, Mandellian inheritance, etc. I took for granted, and never once thought of the missing puzzles, of how one theory neatly lies on top of another eventually leading up to the massive body of knowledge that we have now, and of how mathematics -- my absolute favourite -- was involved in everything.
The book helps me see the world differently, yet again, through a pair of more refined lenses. It gave me a deeper sense of appreciation and gratitude for the opportunity to experience life as is, and to participate in evolution.
I also can't help but realise how innovation in general - be it in business or tech - generally mimics the way life innovates. It gives light to what I will do in my business venture in the future, and once again showed that we should not limit ourselves to learn only from a certain stream but be bold enough to venture farther and wider, one little step at a time. Although the basic philosophy of life is "simple", the complex creation that results help life survives, leading to the eventual arrival of the fittest.
November 28, 2017
Overall, this is an excellent introduction to the topic. Early on, the author presents what is perhaps the most stunning argument in favor of creationism and goes on to demonstrate the many ways in which that argument has been chipped away by some of the recent findings in systems biology.
As a pop-science book, it is extremely approachable. In fact, I probably would have appreciated a bit more depth on the information theory side of the text. The repetition in the process of exploration could have allowed for deeper detail as the chapters progressed. I think this is a missed opportunity and had me spending a fair bit of time doing my own deeper research in a few areas.
Lastly, I think the closing remarks of the book could benefit from some revision. What's missing here is an argument from the amazing progress that has been made in machine learning recently with more robust architectures. Deep Neural Networks are immediately obvious, but even random forests and simulated annealing demonstrate similar applications of robustness to the circuit networks that are discussed. This is doubly interesting because while Andreas Wagner focuses on hypothetical opportunities from robotics, these applications of the principle are at work in industry today.
As a pop-science book, it is extremely approachable. In fact, I probably would have appreciated a bit more depth on the information theory side of the text. The repetition in the process of exploration could have allowed for deeper detail as the chapters progressed. I think this is a missed opportunity and had me spending a fair bit of time doing my own deeper research in a few areas.
Lastly, I think the closing remarks of the book could benefit from some revision. What's missing here is an argument from the amazing progress that has been made in machine learning recently with more robust architectures. Deep Neural Networks are immediately obvious, but even random forests and simulated annealing demonstrate similar applications of robustness to the circuit networks that are discussed. This is doubly interesting because while Andreas Wagner focuses on hypothetical opportunities from robotics, these applications of the principle are at work in industry today.
February 24, 2022
Good introduction, but too basic for working biologists, who know most of this and might be disappointed there's not enough depth in the interesting parts. Nothing wrong with that given its intended audience for whom most is new.
A bit too enamoured with enormous combinatorial counts. After the first couple, we get it, focus instead on how these counts are reduced explicitly by genotypic networks. This is there, but not so clearly connected to the counts.
Robustness as the result of changing environments does not seem mechanistic enough. Changing environments will maintain the ability to use alternative metabolic pathways as the need pops up, each with their multistep pathways some steps of which are novel. But that does not go far enough to explain robustness itself, unless robustness is treated as simply a side effect of having multiple multistep pathways. I'd see robustness as the shadow of natural selection of the past in response to changing environments, maintaining evolvability. Endoparasites like Buchnera simplify because of a much more predictable environment, but that doesn't necessarily mean that robustness is lost, or at least the loss or maintenance of robustness would be a separate question that depends on how often the composition of the endoenvironment changes.
A bit too enamoured with enormous combinatorial counts. After the first couple, we get it, focus instead on how these counts are reduced explicitly by genotypic networks. This is there, but not so clearly connected to the counts.
Robustness as the result of changing environments does not seem mechanistic enough. Changing environments will maintain the ability to use alternative metabolic pathways as the need pops up, each with their multistep pathways some steps of which are novel. But that does not go far enough to explain robustness itself, unless robustness is treated as simply a side effect of having multiple multistep pathways. I'd see robustness as the shadow of natural selection of the past in response to changing environments, maintaining evolvability. Endoparasites like Buchnera simplify because of a much more predictable environment, but that doesn't necessarily mean that robustness is lost, or at least the loss or maintenance of robustness would be a separate question that depends on how often the composition of the endoenvironment changes.
January 25, 2019
The premise is that the Theory of Evolution describes 'survival of the fittest' (that's a very overly simplified meme-like explanation) but not the 'arrival of the fittest'. In other words, evolution describes adaptations as they exist but not how they came to exist. Wagner argues that random mutations in DNA, genes, proteins, amino acids, etc. cannot be the driving force behind evolution's adaptations because 3.8 billion years is not enough time. There must be another mechanism that nature uses to parse through all the possibilities of adaptations with great efficiency and speed. With the help of computational power now available to scientists, Wagner concludes that nature does indeed have a way to create trillions of different adaptations in relatively short periods of time. This book is a fascinating journey into the machinations of nature and the creation of life. It is also a sobering look at how the mysteries of life have been solved. Astoundingly, nearly 40% of Americans still do not believe in evolution's tenets. Hopefully, books like this one will continue to help reduce that percentage.
June 12, 2023
As a non scientist, and someone who is not knowledgeable at all about science, I found this book very interesting. The author has a recent book on evolution and I read this one to expand my knowledge, knowing it was written over a decade ago. The principles have not changed. In the past few years, Nobel Prizes and huge battles over licensing intellectual property have dominated the news. A best-selling book was written about Jennifer Doudna, famous for her gene-splicing technology. Yet the average person has no idea about what is happening. Wagner attempts to explain the extreme complexity of the chemical processes, animo acids and proteins that determine the genome of every living organism.
I thought one statement early in the book is so elegant in its simplicity (at least for this non scientist): life = metabolism + replication. He has a few analogies in the book that become more difficult to understand, mainly because the possible combinations of strings of data quickly become huge beyond ordinary experience, but even these chapters impress upon one the complexity of life.
I thought one statement early in the book is so elegant in its simplicity (at least for this non scientist): life = metabolism + replication. He has a few analogies in the book that become more difficult to understand, mainly because the possible combinations of strings of data quickly become huge beyond ordinary experience, but even these chapters impress upon one the complexity of life.
July 22, 2018
数学，进化，哲学
01达尔文进化论的局限
达尔文进化论的局限在于，它无法解释遗传现象。生命起源于何处？更好、更强的适者从何而来？大自然如何无中生有，如何创新？达尔文的进化论是人类历史上杰出的学术成就，但生物进化的秘密远不是达尔文进化论所能穷尽的。生物学在20世纪发生了翻天覆地的变化，现代技术得以带领我们探索生命进化的动力和起源。
02新性状的起��
新性状的出现有赖于新的分子和合成这些新分子的化学反应的存在。生命以及生命背后驱动新性状出现的动力并不是神秘莫测的东西，这种动力本身和生命一样古老。我们还不知道生命到底是如何从最简单的形式进化出了如此高的复杂性，���我们知道，生命的开端不是一个自我复制的分子，而是一张新陈代谢的网络。
03宇宙图书馆
一种生物所具有的全部生化反应构成了这种生物的新陈代谢。新陈代谢进化的本质在于重新组合。生命时刻在尝试每一种可能的基因新组合，重新解读，重新编译，然后重新布局代谢遗传，毫不停歇，从而造就并提升着代谢的多样性。新的代谢能力是不断驱动生命拓展最前沿阵地的引擎。
04构型之美
蛋白质是生命的驱动者。每种蛋白质的构型都高度复杂，与它们执行的功能相适应。蛋白质的构型维持着生命世界的运转。大自然可以用蛋白质书写不同的文本，更多的文本就意味着更多的构型，参与更多的催化反应，执行更多的功能和完成更多的任务。
05命令与操控
无论多复杂的生物，它的形态和功能都受到调节因子的控制。调节因子占据着某个基因相��的一小段DNA，一旦它们遇上特定的DNA序列，就会与之结合。调节因子与相应的DNA需要在形态上互补。有些基因表达能被调节因子抑制，有些基因则需要它们激活。调节因子指导着所有生物的发育。调节因子之间相互调控，形成了复杂的网络。
06神秘的建筑师
多变的环境催生了生物的复杂性，而复杂性促成了发育稳态，发育稳态继而造就了基因型网络，后者让进化成为可能，使得生物能够通过演变适应环境的变化、提高自身的复杂性，循环往复，生物进化通过这种方式螺旋上升。这种进化方式的核心在于处在多维空间的基因型网络的自组织性。自组织性是生命绚烂光彩背后的支持者，它是隐藏的生命建筑师。
07从大自然到工程技术
自然进化和技术创新有诸多共同之处，促进自然进化的基因型网络在人类技术进步中同样存在。与自然界类似，科研人员也总是行进在各自领域的最前线，他们依赖不断的试错、
人海战术、多起源策略和组合优化，模仿自然的创造能力，实现技术突破和创新。技术发明的精简主义和高雅主义，深深隐藏在现实世界的背后。
后 记 柏拉图的洞穴
01达尔文进化论的局限
达尔文进化论的局限在于，它无法解释遗传现象。生命起源于何处？更好、更强的适者从何而来？大自然如何无中生有，如何创新？达尔文的进化论是人类历史上杰出的学术成就，但生物进化的秘密远不是达尔文进化论所能穷尽的。生物学在20世纪发生了翻天覆地的变化，现代技术得以带领我们探索生命进化的动力和起源。
02新性状的起��
新性状的出现有赖于新的分子和合成这些新分子的化学反应的存在。生命以及生命背后驱动新性状出现的动力并不是神秘莫测的东西，这种动力本身和生命一样古老。我们还不知道生命到底是如何从最简单的形式进化出了如此高的复杂性，���我们知道，生命的开端不是一个自我复制的分子，而是一张新陈代谢的网络。
03宇宙图书馆
一种生物所具有的全部生化反应构成了这种生物的新陈代谢。新陈代谢进化的本质在于重新组合。生命时刻在尝试每一种可能的基因新组合，重新解读，重新编译，然后重新布局代谢遗传，毫不停歇，从而造就并提升着代谢的多样性。新的代谢能力是不断驱动生命拓展最前沿阵地的引擎。
04构型之美
蛋白质是生命的驱动者。每种蛋白质的构型都高度复杂，与它们执行的功能相适应。蛋白质的构型维持着生命世界的运转。大自然可以用蛋白质书写不同的文本，更多的文本就意味着更多的构型，参与更多的催化反应，执行更多的功能和完成更多的任务。
05命令与操控
无论多复杂的生物，它的形态和功能都受到调节因子的控制。调节因子占据着某个基因相��的一小段DNA，一旦它们遇上特定的DNA序列，就会与之结合。调节因子与相应的DNA需要在形态上互补。有些基因表达能被调节因子抑制，有些基因则需要它们激活。调节因子指导着所有生物的发育。调节因子之间相互调控，形成了复杂的网络。
06神秘的建筑师
多变的环境催生了生物的复杂性，而复杂性促成了发育稳态，发育稳态继而造就了基因型网络，后者让进化成为可能，使得生物能够通过演变适应环境的变化、提高自身的复杂性，循环往复，生物进化通过这种方式螺旋上升。这种进化方式的核心在于处在多维空间的基因型网络的自组织性。自组织性是生命绚烂光彩背后的支持者，它是隐藏的生命建筑师。
07从大自然到工程技术
自然进化和技术创新有诸多共同之处，促进自然进化的基因型网络在人类技术进步中同样存在。与自然界类似，科研人员也总是行进在各自领域的最前线，他们依赖不断的试错、
人海战术、多起源策略和组合优化，模仿自然的创造能力，实现技术突破和创新。技术发明的精简主义和高雅主义，深深隐藏在现实世界的背后。
后 记 柏拉图的洞穴
July 21, 2017
This book gives a clear, readable presentation of genetic and biochemical networks.
The book is valuable in informing a layperson about very recent developments in evolutionary theory going beyond pure natural selection with random mutations alone.
The first 40 pages are a basic primer on biology along with some potted history. Someone with such basic background do be well to skip to p. 40 or so. There the action really begins and is well worth following.
The only fault, I would say, is that in making the book popular he overdoes it with metaphors. Metaphors are useful and needed for explanation and understanding in popular science writing, but the author is guilty of the sort of thing that the New Yorker magazine used to ridicule in sidebars titled "block that metaphor." He borrows metaphors from other popularizers of biology without credit and piles on metaphors. Despite this the rest of the writing is very clear and helpful.
The book is valuable in informing a layperson about very recent developments in evolutionary theory going beyond pure natural selection with random mutations alone.
The first 40 pages are a basic primer on biology along with some potted history. Someone with such basic background do be well to skip to p. 40 or so. There the action really begins and is well worth following.
The only fault, I would say, is that in making the book popular he overdoes it with metaphors. Metaphors are useful and needed for explanation and understanding in popular science writing, but the author is guilty of the sort of thing that the New Yorker magazine used to ridicule in sidebars titled "block that metaphor." He borrows metaphors from other popularizers of biology without credit and piles on metaphors. Despite this the rest of the writing is very clear and helpful.
January 4, 2018
An interesting, conceptual treatise on how innovation happens at the genetic level. Wagner demonstrates how mutations are not as "random" as conventionally thought, but are informed by what he describes as a "genetic library" which informs the ways in which the coding of enzymes and proteins may change and innovate while still maintaining the overall fitness of the organism, what Wagner calls "innovability." Because the ideas he discusses are fundamentally mathematical in nature, trying to find metaphors or analogies to explain the goings-on is a bit like telling a story to explain quantum mechanics. It kind of works, but not really. An interesting, albeit abstract, look at the bioinformatics of mutation.
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