The Arrival of the Fittest: a book review

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Andreas Wagner’s book,The Arrival of the Fittest has been mentioned many times (just try a site search as I’ve just done) since it was published. Petrushka pointed it out in a comment

For anyone interested in whether RMNS can create stuff, I recommend a relatively new book, Arrival of the Fittest. I just bought the Kindle version an haven’t finished, but it has a lot to say about how goldilocks mutations occur.

Much later Mung writes:

Reminds me of petrushka, who is always plugging Andreas Wagner’s Arrival of the Fittest, but will never post an OP on it for discussion.

So I’ve taken the hint and bought the book at last. I can see why people have recommended it.

Wagner writes clearly and fluidly. The first chapter is an outline of the history of evolutionary biology, from Darwin to today, and the related fields of genetics, biochemistry and molecular biology. He considers the modern synthesis and how, while hugely successful in dealing mathematically with the genotype and selection, fails to get to grips with the phenotype and sources of innovation. Hopes were raised with the new discipline of evolutionary developmental biology (evo-devo) but Wagner observes:

Where the modern synthesis has a theory without phenotypes, the embryologists have phenotypes without a theory.

Wagner suggests biochemists have begun to bridge the gap by showing that proteins build the phenotype. Wagner mentions the fact that whilst we now have the technology to sequence genomes and construct 3D models of proteins in complete atomic detail, we as yet cannot predict the folding and functionality of novel protein sequences. Later in the chapter, he remarks that unlike, say, advances in physics, advances in evolutionary biology have left the core concepts intact. (Professor Moran may disagree!)

Chapter 2, entitled The Origin of Information, is a review of “origin-of-life” hypotheses. Wagner favours RNA world, hydrothermal vents and the citric acid cycle as primordial. He points out that the citric acid cycle produces a lipid precursor; lipids, he points out, having the emergent property of self-organising into membranes and vesicles in an aqueous medium. Continuing the chemical pathway theme, Wagner moves on to the universal energy molecule, adenosine triphosphate (ATP). He ends the chapter by listing his list of essential ingredients for life to emerge from non-life. First, some chemistry needs to happen prior to becoming life – involving simple catalysts such as metal complexes and then we need innovative reactions, innovative biological catalysts to speed those reactions and regulatory elements to coordinates the reactions.

Chapter 3, The Universal Library, discusses cell biology and the fact that at least 5,000 different chemical reactions occur in at least one organism, somewhere. No single organism performs all 5,000 but some bacteria perform many. E. coli manages more than a thousand. Wagner goes on to explain the idea of the metabolic genotype, a comparison based on which metabolic pathways an organism is able to perform and the “geniuses” of innovative metabolic pathways are prokaryotes. Wagner attributes this to horizontal gene transfer being rife across bacterial species and their very rapid generation time (twenty minutes for E. coli).Wagner points out the variability in stains of E. coli which can be 25% of their genome. Wagner goes on to describe his research using computer analysis that shows the staggering variation in closely related bacteria.Wagner finds there are many solutions to a metabolic pathway, rebutting the “needle in a haystack” canard.

Chapter 4 is entitled Shapely Beauties and is an in-depth look at cell biochemistry for the interested layman. He touches again on the “needle in a haystack” argument when discussing finding functional proteins in among the theoretical number of all possible proteins and describes Keefe and Szostak’s experiment to find functional proteins. He mentions that insects and plants both have oxygen-binding globins that have similar shapes and folds, do similar jobs, yet differ in 90% of their amino acid sequences. There’s also a digression into RNA world. He describes further work at his lab developing the concept of genotype networks.

Chapter 5, Command and Control,is about gene regulation and the field of systems biology which marries experimental data with mathematics and computing. Wagner talks about his collaboration with Olivier Martin, a statistical physicist. Again, he demonstrates the robustness of regulatory processes and the huge amount of viable variation.

Chapter Six, The Hidden Architecture, develops the idea of <i>robustness</i>, resilience in the face of change. For example, the protein lysozyme, contained in tears and saliva, is a bactericide. Scientists have engineered some 2,000 variants involving one altered amino acid and 80% of those variants still kill bacteria. Another example Wagner uses are crystallins, that form transparent lenses for eyes. Their refractive index is ideal for the job. Yet crystallins also perform metabolic functions. Wagner mentions the selectionist neutralist controversy and disputes Kimura’s suggestion that most genetic variation is neutral but agrees that some neutral variation is necessary to his idea of genetic networks.

The final chapter, From Nature to Technology, is on a theme of “trial and error” and the phenomenon of exaptation, where some organ or system becomes redundant for it’s original purpose and gets reworked for a new one. A digression into Boolean algebra, truth tables and computing was helpful to me but I probably need to read it again.

Then we come to the epilogue Plato’s Cave. Thankfully, no mention of Kairosfocus! It’s Wagner’s advocacy for mathematical modelling and computing as a tool that should bring powerful insights into biology.

Summing up, a good read, wide-ranging and informative for the lay reader. I recommend it.

111 thoughts on “The Arrival of the Fittest: a book review”

  2. In 2014, Denyse O’Leary hilariously mistook Arrival of the Fittest for an anti-Darwinian book:

    Evolution driven by laws? Not random mutations?

    Denyse:

    One thing for sure, if an establishment figure can safely write this kind of thing, Darwin’s theory is coming under more serious fire than ever. But we knew, of course, when Nature published an article on the growing dissent within the ranks about Darwinism.

    Never mind that it took me less than ten minutes of Googling (I hadn’t yet read the the book) to find an interview in which Wagner stated:

    The book shows principles that are in agreement with Darwinism, but go beyond it.

    Mung, unsurprisingly, followed Denyse off the cliff.

  3. Wagner mentions the selectionist neutralist controversy and disputes Kimura’s suggestion that most genetic variation is neutral

    What is his argument?

  4. There isn’t much of a disagreement. Wagner writes:

    But back to biology, where the neutralists’ most outspoken proponent was the Japanese scientist Motoo Kimura, who had developed a sophisticated and successful mathematical theory to explain the evolutionary fate of such neutral mutations. Kimura asserted that most genetic variation seen in nature is neutral. The genomic era has taught us that he was wrong on that count— neutral variants are no more frequent than those providing an advantage. However, his hunch of neutral change’s being important was dead on, though it took another few decades to understand why.

  5. keiths:
    There isn’t much of a disagreement.Wagner writes:

    “…neutral variants are no more frequent than those providing an advantage.”

    Where does he get this? Does he say anything whatsoever in support of that claim? It seems exceedingly bizarre to me.

  6. Other than the bit I quoted, I don’t remember seeing Wagner arguing the point in his book. Maybe Alan does, since he just finished reading it.

    But I am aware of some earlier work that Wagner did on the subject:

    Rapid Detection of Positive Selection in Genes and Genomes Through Variation Clusters

    Abstract

    Positive selection in genes and genomes can point to the evolutionary basis for differences among species and among races within a species. The detection of positive selection can also help identify functionally important protein regions and thus guide protein engineering. Many existing tests for positive selection are excessively conservative, vulnerable to artifacts caused by demographic population history, or computationally very intensive. I here propose a simple and rapid test that is complementary to existing tests and that overcomes some of these problems. It relies on the null hypothesis that neutrally evolving DNA regions should show a Poisson distribution of nucleotide substitutions. The test detects significant deviations from this expectation in the form of variation clusters, highly localized groups of amino acid changes in a coding region. In applying this test to several thousand human–chimpanzee gene orthologs, I show that such variation clusters are not generally caused by relaxed selection. They occur in well-defined domains of a protein’s tertiary structure and show a large excess of amino acid replacement over silent substitutions. I also identify multiple new human–chimpanzee orthologs subject to positive selection, among them genes that are involved in reproductive functions, immune defense, and the nervous system.

  7. keiths: Mung, unsurprisingly, followed Denyse off the cliff.

    Some doubt was expressed that you’d ever actually read the book. Has something changed that you’d now like to share?

  8. keiths,

    That abstract is talking only about non-silent mutations in protein-coding sequences, which make up a tiny percentage of the average genome. If that’s all he means, his statement in the book is very poorly written.

  9. Mung,

    Of course I hadn’t read it. I had just learned about it.

    That’s why I searched online and found the Wagner interview. As you know perfectly well.

    Man, what a waste of time you are. It’s time for you to go searching for “that integrity thingy” again.

  10. John:

    If that’s all he means, his statement in the book is very poorly written.

    I don’t know whether that’s all he means. Just thought I’d mention the paper since I was aware of it and it seemed relevant.

  11. keiths,

    My point is that considered on its face, the statement is absurd. 90% of the human genome is junk. Of the 20+ million point fixations in the human lineage, how many would Wagner think were fixed under positive selection? Of the umpteen million polymorphic sites in the current population, how many would Wagner think are currently under positive selection? If it’s anything at all near half, that’s just crazy.

  12. keiths: Man, what a waste of time you are. It’s time for you to go searching for “that integrity thingy” again.

    lol. I wasn’t the one who went about dredging up an old link that demonstrated another instance of “skeptic who hadn’t read the book.” Without which, I might add, we wouldn’t be having this particular digression from the OP.

  13. Thanks Alan. Nice summary. Didn’t petrushla claim the book is some sort of magical “ID killer” or some such?

    I’m hoping someone will raise things from the book relevant to ID, since it seems to come up as a book that ID’ists really ought to read. My questions is why?

    You didn’t see anything at all anti-Darwinian about the book? Did it challenge any of you beliefs about evolution? You didn’t say.

    Or is evolution now even more God-like than ever. 🙂

  14. Mung,

    lol. I wasn’t the one who went about dredging up an old link that demonstrated another instance of “skeptic who hadn’t read the book.”

    Actually, it was an instance of “skeptic who had actually read Wagner’s words (in an interview) correcting an IDiot who was basing his claim on a marketing blurb.”

  16. John,

    My point is that considered on its face, the statement is absurd.

    I agree. I’m not defending the claim. I’m just pointing out what I think Wagner might have been thinking of when he made it.

  17. In the Prologue Wagner refers to “the biblical accounts asserting that the earth was only six thousand years old.” Of course, he fails to provide a footnote, or quote, or any way at all to substantiate his claim. I wonder why that is.

    Wagner also states that “the processes of random mutation and selection now had the time needed to create life’s enormous complexity and diversity.” But then goes on to immediately question the idea. Apparently he thinks otherwise.

    He writes that “The number of potential proteins is not merely astronomical, it is hyperastronomical, much greater than the number of hydrogen atoms in the universe. … They would never have found the one opsin string. There are a lot of different ways to arrange molecules and not nearly enough time.”

    Getting to the crux of the book:

    The power of natural selection is beyond dispute, but this power has limits. Natural selection can preserve innovations, but it cannot create them. And calling the change that creates them random is jsut another way of admitting our ignorance about it. Nature’s many innovations – some uncannily perfect – call for natural principles that accelerate life’s ability to innovate, its innovability.

    If natural selection has limits then Darwin was wrong.

  19. The title of the first chapter is What Darwin didn’t Know. But who cares about that, am I right? Because Darwin got right the only thing that matters, no Designer required. Well, that’s what some people say anyways. 🙂

    So what was it that Darwin didn’t know?

    …biology has been transformed by a revolution… This revolution has revealed a world as inaccessible to Darwin as outer space was to cavemen. And it has helped to answer the single most important question about evolution, the question that Darwin and generations of scientists after him did not, could not touch. How does nature bring forth the new, the better, the superior? How does life create?

    … Darwin’s theory surely is the most important intellectual achievement of his time, perhaps of all time. But the biggest mystery about evolution eluded his theory. And he couldn’t even get close to solving it.

    Makes you want to cringe, doesn’t it?

  21. keiths, there’s an open invitation to anyone to take an argument from the book they find compelling and defend it. You could start with his discussion of intelligent design, if you can find it.

  22. Authors should have their drafts read by Moran, Harshman, and Joe F, et al, before publishing.

  24. Mung,

    Instead of this inane running commentary, why not step away from the keyboard and finish the book first? At that point, if you still don’t understand — or won’t admit that you understand — why the book is bad news for ID, I’ll be happy to explain.

  25. Promises. Promises. keiths.

    And we know how good you are at keeping those.

    This thread is your chance to shine. You and Petrushka. Have at it.

  27. Mung,
    Once you’ve read the book I’d be interested to know if you still stand by your statements in that thread?

    That’s about as non-darwinian as you can get.

    ?

  28. I bought the book over two years ago and I don’t recall anything in it that addressed intelligent design. But now that Alan’s brought it up I’m reading it again. Who knows, maybe I missed something. The book has an awful lot of highlighting in it for a book I’ve never read.

    Looks like some people would rather do anything other than making the case that the book somehow poses a challenge to intelligent design. Even the OP doesn’t make that claim.

    petrushka and keiths, you either have the goods or you don’t. Here’s your big chance and you’re going to squander it. How about you OMagain, have you read it, or would you rather discuss a thread from UD from over two years ago?

    keiths, if it helps, pretend that I’ve read the book.

  29. Let me provide an example:

    …regulatory circuits…hint at a deep unity between the material world of biology and the conceptual world of mathematics and computation.

    Not exactly the sort of the stuff to make an IDist lose sleep at night.

  30. John Harshman,

    I paraphrased badly for which my apologies. Here’s what he actually writes (page 181):

    …the neutralists’ most outspoken proponent was the Japanese scientist Motoo Kimura, who had developed a sophisticated and successful mathematical theory to explain the evolutionary fate of such neutral mutations. Kimura asserted that *most* genetic variation seen in nature is neutral. The genomic era has taught us that he was wrong on that count – neutral variants are no more frequent than those providing an advantage. However his hunch of neutral change’s being important was dead on, though it took another few decades to understand why.

    One reason is that neutral change is critical for navigating genotype networks. Neutral change provides the browsers of nature’s libraries with a safe path to innovations through treacherous territory of meaningless texts. Without genotype networks and the neutral changes they allow, the exploration of nature’s libraries would be just about impossible.

  32. Mung:
    Thanks Alan. Nice summary.

    Thanks and thanks to all who let me sneak back and correct a bunch of typos without having them pointed out.

    Didn’t petrushla claim the book is some sort of magical “ID killer” or some such?

    My take is that Wagner is proposing genomic networks as a perfectly Darwinian process by which cell biochemistry could evolve. A sort of riposte to the “too complex to have evolved” negative argument favoured by ID proponents.

    I’m hoping someone will raise things from the book relevant to ID, since it seems to come up as a book that ID’ists really ought to read. My questions is why?

    Can’t say other than perhaps to come across new ideas. I don’t think Wagner is trying to refute “Intelligent Design”. The phrase does not occur in the book; nor does he refer to Creationism.

    You didn’t see anything at all anti-Darwinian about the book?

    Absolutely not.

    Did it challenge any of your beliefs about evolution? You didn’t say.

    Again, no. (Insofar as evolution is a belief system 😉 )

    Or is evolution now even more God-like than ever.

    Something that was never anything cannot be more anything. 😉

  33. John Harshman,

    Well, it is intended to be a popular book pitched at the layman. Also I suspect he is not thinking of eukaryotes at this point but the much slimmer genomes of prokaryotes.

  34. Alan Fox: Something that was never anything cannot be more anything.

    Then how do you explain my posts here and the responses they get? 🙂

  36. For what it’s worth, my own take on why people think Wagner’s book is devastating to ID is because they think it dispenses with the entire “islands of function” metaphor.

    What do others who have actually read the book think?

  37. Alan Fox:
    John Harshman,
    Well, it is intended to be a popular book pitched at the layman. Also I suspect he is not thinking of eukaryotes at this point but the much slimmer genomes of prokaryotes.

    I hope you don’t think “it’s a popular book” is a valid defense of egregiously incorrect statements. If he’s talking solely about prokaryotes the statement is only somewhat less incorrect, but is he really? It certainly isn’t what Kimura was talking about.

  38. John Harshman: I hope you don’t think “it’s a popular book” is a valid defense of egregiously incorrect statements.

    Absolutely not*. Whether Wagner is egregiously incorrect is above my pay grade.

    If he’s talking solely about prokaryotes the statement is only somewhat less incorrect, but is he really?

    He seems to be generally talking about the billion years or so of evolution prior to the emergence of eukaryotes. Horizontal gene transfer is a large component of his exposition of genomic networks.

    It certainly isn’t what Kimura was talking about.

    Molecular clocks in non-functional DNA?

    ETA a rather important “not”.

  39. John Harshman: I hope you don’t think “it’s a popular book” is a valid defense of egregiously incorrect statements. If he’s talking solely about prokaryotes the statement is only somewhat less incorrect, but is he really? It certainly isn’t what Kimura was talking about.

    Maybe it would be better to ask what objections have been raised to Kimura’s major arguments. Has subsequent research undermined those arguments in some important way?

  40. Mung: For what it’s worth, my own take on why people think Wagner’s book is devastating to ID is because they think it dispenses with the entire “islands of function” metaphor.

    His ideas certainly address the problem of how 5,000 chemical reactions can evolve in prokaryotes. If there were only one RNA or protein sequence for each enzyme/ribozyme activity then evolutionary theory would be in trouble. Wagner demonstrates this is not so quite elegantly.

  41. Alan Fox: Molecular clocks in non-functional DNA?

    ETA a rather important “not”.

    I’m unable to parse this bit. Perhaps you could expand.

  42. For those who haven’t read the book I actually recommend that you start with the last chapter [ETA: Epilogue]. For those who have read the book I suggest that you explain the last chapter [ETA: Epilogue].

    For example, why does it [ETA: the Epilogue] carry the title Plato’s Cave and why does it end with the following sentence:

    And we learn that life’s creativity draws from a source that is older than life, and perhaps older than time.

    Make’s me shiver. That. Maybe I’ll give up ID altogether and become a Creationist instead.

    ETA: By “last chapter” I meant to refer to the Epilogue. I guess technically the last chapter is chapter 7. For those who think pedantry is a virtue.

  43. I thought Kimura was instrumental in developing the idea of molecular clocks. Where sections of non-functional DNA accumulate errors at a fixed rate as there is no selective pressure to eliminate changes.

  44. Alan Fox:
    I thought Kimura was instrumental in developing the idea of molecular clocks. Where sections of non-functional DNA accumulate errors at a fixed rate as there is no selective pressure to eliminate changes.

    True. Still looking for a point here. If you could try being a little bit less elliptical, we could have a better discussion.

  46. Mung:
    For what it’s worth, my own take on why people think Wagner’s book is devastating to ID is because they think it dispenses with the entire “islands of function” metaphor.

    What do others who have actually read the book think?

    IDC isn’t a scientific endeavor, so no scientific evidence is going to be “devastating” to it. Creationists will believe what they want to believe.

    That being said, Wagner does provide strong evidence against the “islands of function” argument that is occasionally raised by some IDCists.

  47. Patrick: Care to support that bare assertion?

    I’ll put it on my rather lengthy to do list. Right after “inflate Patrick’s sense of the value he places on my responses.”

  48. Mung:

    Care to support that bare assertion?

    I’ll put it on my rather lengthy to do list. Right after “inflate Patrick’s sense of the value he places on my responses.”

    At least you’re achieving your goals here.

  49. Patrick: Care to support that bare assertion?

    Given that supporting it could mean just linking somewhere, it’s obvious Mung is just bluffing as usual.

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