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p.5 The power of natural selection is beyond dispute, but this power has limits. Natural selection can preserve innovations, but it cannot create them.
p.8 How does nature bring forth the new, the better, the superior? How does life create?
p.11 natural selection... this process helps explain all of life's diversity, so much so that the geneticist Theodosius Dobzhansky could say in 1973 that "nothing in biology makes sense except in the light of evolution."
p.13 In today's language, a genotype comprises all genes of an organism, all its DNA, whereas the phenotype comprises everything else you could observe about the organism: its size, its color, whether it has a tail, or feathers, or a carapice. To see this distinction is crucial, because it allows us to tell cause from effect when organisms change.
p.14 Where do innovations come from? Where do the new variants come from that selection needs? ...natural selection is not a creative force. It does not innovate, but merely selects what is already there.
p.14 consider that every one of the differences between humans and the first life forms on earth was once an innovation: an adaptive solution to some unique challenge faced by a living being.
p.15 A few decades after Darwin, Hugo de Vries expressed it best when he said that "natural selection may explain the survival of the fittest, but it cannot explain the arrival of the fittest" (emphasis added). And if we do not know what explains its arrival, then we do not understand the very origins of life's diversity.
p.15 Life can innovate, it has innovability. What is more, it can innovate while preserving what works through faithful inheritance. It can explore the new while preserving the old. It can be progressive and conservative at the same time.
p.17 The real mystery of evolution is not selection, but the creation of new phenotypes.
p.22 Evo-devo [evolutionary developmental biology], however, has taught us an important lesson. To understand innovability we cannot ignore the complexity of phenotypes. We must embrace it.
p.39 Life wasted no time, and appeared almost as soon as it could appear.
p.58 an innovation without an innovator
p.64 All organisms on the planet, from single-celled bacteria to the blue whale, use a standard means to store energy, the molecule adenosine triphosphate (ATP).
p.65 Living things have adopted ATP as the universal energy storage standard... Every organism living today can trace its descent from the inventor of life's most successful power storage innovation.
p.83 Everywhere on this planet, a relentless shuffling and mixing and recombining of genes takes place.
p.135 Such surprises occur time and again in laboratory evolution experiments... nature never ceases to surprise... although we failed to predict a specific solution, we had managed to predict something more important: that a genotype network could accelerate the population's discovery of this solution. And this prediction was right on target. We can predict innovability even if we cannot predict individual innovations... Science can explain general principles of innovability even if it cannot predict any individual innovation. Understanding innovability can leave the magic of innovation intact.
p.137 Regulation has come a long way from its murky origins in the first cells... More than three billion years later, regulation is shaping the bodies of every living thing on the planet. And no understanding of innovability would be complete without grasping how new regulation appears.
p.141 If regulation matters because it avoids waste, then it should be everywhere. And indeed it is... This is perhaps the most convincing evidence for regulation's importance: Life has invented a dozen different ways of doing it.
p.142 Regulatory recipes are the business of developmental biology... regulation... guides the development of all organisms.
p.144 And what regulates the regulators? Simple: more regulators.
p.145 regulation can get much more complicated: Regulators form not just linear chains but complex regulator circuits where regulators regulate each other.
p.147 regulation circuits can shape a body incredibly rapidly.
p.154 How exactly these innovations originated may be forever lost in the mists of life's deep history, but one principle is crystal clear: They originated through changes in regulation. The same principle is just as clear in other, more ancillary innovations.
p.156 Each time this innovation required changes in regulation.
p.156 These examples and hundreds more illustrate the power of regulation to innovate... A half century of research has told us how important regulation is to building bodies old and new.
p.157 No list of examples, however long, could tell us how innovation through regulation is even possible.
If the problem is familiar, so is the solution: Study not just one circuit but many, an entire library of circuit genotypes and their expression phenotypes. [JLJ - this effectively happens when you create a competition involving hundreds of games. A tournament of hundreds of games presents a variety of positions which demand general-purpose innovation. Successful performance in this kind of tournament of games must involve creating successful innovations - or at least regulates our use of time in a way that allows innovations to emerge from a competition of collective-maybe moves - the innovative emerges from an intelligent developmental exploration of the maybe, the what about this, the possibly next best and the keep an eye on the not-yet-but-still-might-turn-around.]
p.170 a biological phenomenon... so widespread that it deserves to be called a hallmark of life: robustness, the persistence of life's features in the face of change.
p.171 C. H. Waddington... called the phenomenon through which development can produce "one definite end-result regardless of minor variations in conditions" canalization - another word for robustness.
p.172 life is robust... What mechanism creates robustness?
p.174 The most obvious benefit of such robustness is that it keeps organisms alive.
p.175 all organisms, their structures and activities, are to some extent robust, and it is precisely this robustness that allows populations to explore nature's enormous libraries.
p.179 Many mutations neither harm nor help when they first arise. Such neutral changes are a consequence of life's robustness and the disorder it allows.
p.181 a change that is neutral when it first appears doesn't have to stay that way. Once-neutral changes can turn into essential parts of innovations
p.188 Anybody who has struggled to understand living beings, and has despaired at their complexity, will sympathize with this yearning for simplicity. Life seems unnecessarily complex... Why doesn't ruthlessly efficient nature get rid of all this complexity?
The answer is "the environment" - or rather, "the environments." What looks like a wastefully complex suite of genes is actually the secret to survival in more than one environment... In biology, increased complexity means increased robustness to environmental change.
p.189 even though engineers prize simplicity, they must also design for changing environments. [JLJ - what also seems to matter is performance in the changing environment]
p.193 One lesson from such minimal metabolisms is that living in many environments generally requires complexity... Life's complexity and robustness increase with its exposure to environmental change.
p.194 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.
p.196 innovation in nature and innovation in technology show many parallels.
p.196 Thomas Edison... One of the dozens of quotations attributed to him sums it up: "I have not failed. I have just found ten thousand ways that do not work." The quote reminds everyone that trial and error - especially error - is as crucial to technological innovations as to biological ones... John Backus, a co-creator of the highly successful computer programming language Fortran... said that "you need the willingness to fail all the time. You have to generate many ideas and then you have to work very hard only to discover that they don't work. And you keep doing that over and over until you find one that does work."
p.200 Edison said it well: "To invent, you need a good imagination and a pile of junk." [JLJ - perhaps instead, to invent you need a bunch of tricks or rules for combining old things into new that sometimes work, and a period of time to try lots of combinations. One is rarely aware of the tricks - perhaps obtained through experience - that are used when doing the combining - these appear instead to be imagination.]
p.200 Darwin... reminded the Origin's reader that "an organ originally constructed for one purpose... may be converted into one for a widely different purpose."
p.200 Innovation is combinatorial. It combines old things to make the new.
p.201 in biology... All evolutionary innovations, discovered as they are in searches through nearly infinite libraries, are combinatorial, just as new books combine old letters into new meanings.
p.201 Trial and error. Populations. Multiple origination. Combination. With all these parallels between technology and nature, it is little surprise that technologists would try to mimic nature's innovability.
p.202 Technologists... realized that evolution follows an algorithm, a recipe so simple and stereotypical that it could be executed by a machine. By altering DNA, mutations create organisms with new phenotypes, and selection allows some of them to survive and reproduce. Mutate. Select. Repeat over and over... evolutionary algorithms: recipes that use some form of mutation and selection to solve really difficult real-world problems, entirely inside a computer.
p.205 Standards that make recombination mindlessly easy do not just exist in proteins... If we could take a small number of different objects, create a standard way to link them, and recombine them into every conceivable configuration - mindlessly - our powers to innovate could be just as immeasurable as those of nature.
p.215 When Karthik analyzed logic circuits that differed in their complexity - their number of logic gates - he found that the simplest circuits could not be rewired without destroying their function... Such simple circuits have no innovability, because they cannot explore new configurations and computations. For rewiring, one needs more complex circuits. The more complex they are, the more rewiring they tolerate.
p.215 Just as in biology, innovability comes from complexity, apparently unnecessary, but actually vital. This is one of nature's lessons for innovable technologies: If we want to open nature's black box of innovation, Ockham's razor is much too dull. Like oil and water, simplicity and innovability don't mix.
p.219 genotype networks are the common origin of the different kinds of innovations - in metabolism, regulation, and macromolecules - that created life as we know it.
p.219 organisms are robust, a consequence of the complexity that helps them survive in a changing world
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