The Arrival of the Fittest: a book review

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”

  1. RumraketRumraket

    Mung: 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.

    That sentence is incomprehensible. Even if we overlook the obvious logical contradiction in something being “older than time”.

  2. MungMung

    “…innovation in nature and innovation in technology show many parallels.” – Andreas Wagner

    That has to be an IDist’s worst nightmare. Am I right?

  3. MungMung

    “The nineteenth century’s Lord Kelvin used the laws of thermodynamics – and his Christian faith – to underestimate the age of the earth more than a hundredfold.”

    I guess Lord Kelvin was only partially impressed by the biblical statements that the earth is only 6000 years old. Anyone care to comment on how Lord Kelvin’s Christian faith influenced his calculation of the age of the earth? Why didn’t he jsut go by what the bible says?

  4. MungMung

    The OP hardly does justice to Chapter 7, From Nature to Technology, and like the Epilogue, it is utterly ID-friendly. Did the ID critics here who actually read the book simply ignore Chapter 7 and the Epilogue?

    So while I wait for the “skeptic’s” here to address just how the book is hostile to ID, I’ll continue to show how it is rather just the opposite.

    Just keep in mind though, that I haven’t actually read the book. 😉

  5. keithskeiths

    Mung,

    Alan’s review barely touches on what I think are the most important ideas in the book: those concerning the “libraries”, the “networks”, and the extent to which the networks extend across the libraries.

    How about summarizing those ideas for us in your own words? That will serve the dual purpose of 1) filling a gap in Alan’s review and 2) demonstrating that you actually understand what Wagner is saying.

    Having summarized those ideas, if you still don’t (or pretend not to) understand the implications for ID, I’ll help you out.

  6. Alan FoxAlan Fox Post author

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

    Frankly, I’m probably projecting my scepticism about drift on to Wagner. Maybe, if I can find time to read through and digest the material Larry Moran provided, I should start another thread.

  7. Alan FoxAlan Fox Post author

    keiths: Alan’s review barely touches on what I think are the most important ideas in the book: those concerning the “libraries”, the “networks”, and the extent to which the networks extend across the libraries.

    Indeed true, the nub of the book is his idea of metabolism as a network of chemical reactions and making comparisons using the deceptively simple concept of representing the presence or absence of a particular metabolic pathway by 0 or 1 as a way of representing these “genomic networks” between multiple bacterial strains and species. Oh, and developing computer systems to handle and analyse this data to find evolvable routes through the network.

  8. petrushka

    I think isolated islands is the only concept that keeps ID alive.

    If genomic word laddering is possible, evolution is possible, and there is no need for “that hypothesis”.

  9. MungMung

    keiths, I’m not here to carry water for you. You can take a position and defend it or not. I really don’t care.

  10. keithskeiths

    Mung,

    Did you even understand the book?

    That’s why I’m asking for the following:

    Alan’s review barely touches on what I think are the most important ideas in the book: those concerning the “libraries”, the “networks”, and the extent to which the networks extend across the libraries.

    How about summarizing those ideas for us in your own words? That will serve the dual purpose of 1) filling a gap in Alan’s review and 2) demonstrating that you actually understand what Wagner is saying.

    Having summarized those ideas, if you still don’t (or pretend not to) understand the implications for ID, I’ll help you out.

    Think of it as being similar to an ideological Turing test. I’d like to see if you even bothered, or were able, to understand the book before dismissing it as no threat to ID.

  11. MungMung

    Pretend that someone else is reading this thread and wondering why keiths won’t explain why this book [allegedly] poses such a challenge to ID.

    Wagner claims evolutionary innovations are discovered by searches through nearly infinite libraries. How much more ID friendly can you get?

  12. petrushka

    Evolution doesn’t search an extraordinarily large space. It only searches the vivinity immediately adjacent to what currently exists and works.

    Glad to see mung acknowledge that I started an OP on this two years ago, which garnered several hundred posts. This is not the first time I’ve linked to it.

  13. keithskeiths

    Why the squirming, Mung? I promised to help you out, and I will. I just want you to make a good faith effort first.

    Try to summarize the crucial ideas I mentioned above, so I can find out whether you understand them. If you don’t, I’ll need to teach them to you first before I can explain why the book is bad news for ID.

    Mung:

    Wagner claims evolutionary innovations are discovered by searches through nearly infinite libraries. How much more ID friendly can you get?

    Oh, dear. This is not a promising start.

    Maybe you should read the book (again?) before summarizing those ideas.

  14. PatrickPatrick

    Mung:
    Pretend that someone else is reading this thread and wondering why keiths won’t explain why this book [allegedly] poses such a challenge to ID.

    Wagner claims evolutionary innovations are discovered by searches through nearly infinite libraries. How much more IDfriendly can you get?

    Wagner demonstrates that functional sequences are widely connected in sequence space. That destroys the “islands of function” argument used by IDCists so that they can no longer use the “evolution needs to search the whole space” claim. Exploring near known functional sequences, as evolution does, discovers new functional sequences just fine.

  15. colewd

    Patrick,

    Wagner demonstrates that functional sequences are widely connected in sequence space. That destroys the “islands of function” argument used by IDCists so that they can no longer use the “evolution needs to search the whole space” claim. Exploring near known functional sequences, as evolution does, discovers new functional sequences just fine.

    I think that his claim is about metabolic pathways. He does not address the islands of function issue since they are a piece of the metabolic pathway.

    Regardless, since there are many more ways to arrange a functional sequence then function (Szostak) random change will drift toward non function. Living organisms don’t drift toward non function because of repair mechanisms that keep the genome in a very tight window.

  16. petrushka

    Patrick: Wagner demonstrates that functional sequences are widely connected in sequence space.

    Which is why “searching” only the adjacent phase space works. there are always workable alternative sequences just one mutation away.

    For various definitions of mutation.

    In a population of some size, every individual has numerous differences, and some sequences can be two or three steps away from the typical sequence. That’s why adaptations that require two steps happen in real life.

  17. keithskeiths

    Patrick:

    Wagner demonstrates that functional sequences are widely connected in sequence space. That destroys the “islands of function” argument used by IDCists so that they can no longer use the “evolution needs to search the whole space” claim. Exploring near known functional sequences, as evolution does, discovers new functional sequences just fine.

    colewd:

    I think that his claim is about metabolic pathways.

    You didn’t make it very far into the book, did you?

    He does not address the islands of function issue since they are a piece of the metabolic pathway.

    What does that even mean?

  18. PatrickPatrick

    colewd:

    Wagner demonstrates that functional sequences are widely connected in sequence space. That destroys the “islands of function” argument used by IDCists so that they can no longer use the “evolution needs to search the whole space” claim. Exploring near known functional sequences, as evolution does, discovers new functional sequences just fine.

    I think that his claim is about metabolic pathways.He does not address the islands of function issue since they are a piece of the metabolic pathway.

    That is not accurate. You need to read the book before making claims about it.

    Regardless, since there are many more ways to arrange a functional sequence then function (Szostak) random change will drift toward non function.Living organisms don’t drift toward non function because of repair mechanisms that keep the genome in a very tight window.

    There’s the whole issue of selection that you like to ignore.

  19. colewd

    keiths,

    In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell. The reactants, products, and intermediates of an enzymatic reaction are known as metabolites, which are modified by a sequence of chemical reactions catalyzed by enzymes.[1] In a metabolic pathway, the product of one enzyme acts as the substrate for the next. These enzymes often require dietary minerals, vitamins, and other cofactors to function.

    The island of function refers to a single enzyme. How can a mutation of a single enzyme substantially change the function of the entire pathway.

  20. colewd

    Patrick,

    There’s the whole issue of selection that you like to ignore.

    Can you give me an example of a gene mutating and finding reproductive advantage inside a multicellular organism?

  21. keithskeiths

    colewd,

    How to you propose that a changing or improving enzyme i.e. moving up the functional landscape translates to reproductive advantage in a multi cellular organism?

    Not sure why you’re fixated on enzymes. Any change that moves higher on the fitness landscape increases fitness and thereby “reproductive advantage”.

  22. keithskeiths

    Mung,

    Perhaps you could start your summary by

    1) telling us what “libraries”, “networks”, and “readers” are; and

    2) explaining how the networks factor in to the readers’ explorations of the libraries.

  23. PatrickPatrick

    colewd:

    There’s the whole issue of selection that you like to ignore.

    Can you give me an example of a gene mutating and finding reproductive advantage inside a multicellular organism?

    “I am not able rightly to apprehend the kind of confusion of ideas that could provoke such a question.”

  24. petrushka

    Take any genetic trait in any multi cellular organism and ask if it exists to varying degrees in members of that species. By genetic trait, I simply mean any trait that is observed to breed true. Do such variations confer advantage or disadvantage in various environments and under various challenges?

  25. colewd

    Patrick,

    “I am not able rightly to apprehend the kind of confusion of ideas that could provoke such a question.”

    Abstracthttp://www.pathlights.com/ce_encyclopedia/Encyclopedia/10mut10.htm#Speeding%20Up

    This is the creation argument. Can you counter it? When mutation is accelerated the organism breaks down.

  26. Alan FoxAlan Fox Post author

    colewd: When mutation is accelerated the organism breaks down.

    Is there a Creationist publication detailing the problem and some evidence to support it?

  27. Allan Miller

    colewd,

    This is the creation argument. Can you counter it? When mutation is accelerated the organism breaks down.

    Uncloaking just long enough to point and laugh …

    Bashing people hard causes them to become unconscious. Therefore you can’t even touch them. Drowning people causes them to become dead. Therefore water is toxic.

    There’s such a thing as a problem of rate, y’know … ?

    Zorro – awaaaay!

  28. AhmedKiaan

    lewis grizzard wrote that joke decades ago. After some study along the lines of “rats fed 12,000 doses of aspartame got cancer” he said (paraphrasing) “Any day now scientists are going to hold rats underwater for three hours and conclude that water is dangerous for your health.”

  29. petrushka

    My Chernobyl point is that doubling or tripling the mutation rate seems to be compatible with survival of mammal species.

    It seems likely that some rate will be incompatible. But observed facts override simulations.

  30. colewd

    petrushka,

    My Chernobyl point is that doubling or tripling the mutation rate seems to be compatible with survival of mammal species.

    It seems likely that some rate will be incompatible. But observed facts override simulations.

    The DNA repair mechanism is pretty accurate. As long as the mutation rate is low enough it can reverse them. The problem hits when the repair mechanism gets damaged. Many cancers are the result of mutated repair genes.

  31. MungMung

    petrushka: I agree with Keiths. Wagner’s book is death to ID. The only way it isn’t death to ID is if it’s factually wrong. Which is why gp has to assert it’s factually wrong.

    Well, there you have it! I guess we can all go home now.

  32. colewd

    Allan Miller,

    Bashing people hard causes them to become unconscious.

    So mutations are like head injuries? If you bash softly a new organism poofs into existence.:-)

  33. colewd

    Mung,

    petrushka: I agree with Keiths. Wagner’s book is death to ID. The only way it isn’t death to ID is if it’s factually wrong. Which is why gp has to assert it’s factually wrong.

    I vote for this as the ballziest claim of the last 12 months 🙂

  34. newton

    colewd: So mutations are like head injuries? If you bash softly a new organism poofs into existence.:-)

    It helps if you sing it a little song.

  35. keithskeiths

    Mung,

    Well, there you have it! I guess we can all go home now.

    Oh, no. Not yet. We’re still awaiting your summary of some crucial ideas from the book, plus we haven’t settled the question of whether Mung v. Wagner will be as embarrassing for you as Mung v. Weasel was.

    This statement of yours…

    Wagner claims evolutionary innovations are discovered by searches through nearly infinite libraries. How much more ID friendly can you get?

    …indicates that you either didn’t read, or didn’t understand, the book. Are you reading (or rereading) it now? When should we expect your summary?

  36. petrushka

    Wagner seems to be a litmus test tha can separate those who can summarize the way evolution works from those who can’t. It’s really quit stunning.

  37. Allan Miller

    colewd,

    So mutations are like head injuries? If you bash softly a new organism poofs into existence.:-)

    I offered two analogies, in fact. Evidently, it cannot be like both in every single respect, while simultaneously being like itself. That’s analogy for ya.

    The point was about extrapolating a severe rate change to cover the entirety of the mutational spectrum. If I remove a trillion cells an hour from your body, you might struggle to survive the onslaught. Does that mean I can’t even remove one an hour? (That, incidentally, is another analogy).

  38. Allan Miller

    What’s particularly dense about this line of reasoning – the fruit fly experiment proferred routinely by the Creationist crowd – is that it supposes a particularly limited God. He can’t somehow arrange things such that genome space is mutationally explorable without the constant surreptitious shove of the Divine Hand? Why?

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