Wednesday, January 28, 2015

What We're Reading: New Science Books

Arrival of the Fittest:
by Andreas Wagner

Wagner begins his book with an overview of life’s amazing diversity, and the problem he poses concerning the Darwinian mechanism of natural selection is this:

"Selection did not---cannot---create all this variation. 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.' And if we do not know what explains its arrival, then we do not understand the very origins of life’s diversity."

The real mystery of evolution, Wagner argues is not selection, but the creation of new phenotypes (the physical expressions that genes encode). Mere randomness in mutations is insufficient as an explanation because ..…given the staggering odds, selection is not enough. We need a principle that accelerates innovation.” Life has what Wagner calls “innovability,” the ability to find solutions to changes in environment and challenges to viability and survival that, compared to the adaptations that might be “discovered” by mere random mutation alone, occur at warp speed. This book explains how this is so.

This idea itself should be enough to draw in the reader, because, while modern biology as a science may have moved on to a new understanding of how life works, popular notions--the ones that most of us have grown up with--change more slowly. They are changed by books like this, where research scientists try to explain to a lay audience what they have discovered and what the implications of that discovery are for our understanding of life. Major scientific ideas create new paradigms that with time come to permeate our thought and culture. We take scientific ideas and make them into analogies and algorithms that we use to explain more than the physical world alone, using their concepts to explain the workings of our cultural and social lives. They frame our idea of what life is and how it works, and what our place is in the universe. So it has been with the Copernican Revolution, Newton’s physical laws, Darwin’s explanation of where species come from. The influential paradigm with which most of us have grown up, the one that remains in popular culture, is that we live in a random universe, that life is what it is by chance, by the random alterations that occur to DNA and to genes, the codes that are the key to how life and its diverse forms has evolved. This is an exciting book because it challenges that notion with recent research and discoveries. If you are a creationist, don’t get too excited: Wagner’s argument is that there is a self-organization to life that follows “rules” of mathematical organization, rules that allow it to develop a special robustness through complexity and to achieve an extraordinary ability to uncover useful innovations while maintaining viability.

Wagner treats us to an interesting exploration of where “innovation” in life began, and speculates about what kind of environments might have been most conducive to the origin of life. Wagner is very interested in the environment of deep sea vents. There is also an interesting exploration of a version of the “which came first, the chicken or the egg?” conundrum concerning the development of early life, or in this case, what came first in the development of life’s two necessary features of viability: metabolism and reproduction? Wagner argues that “life started not with a replicator, but with a metabolism.” He explores the “innovability” of metabolism in bacteria and also the frequency of horizontal gene transfer in some of the simpler and original organisms that still thrive on the planet.

The major discovery Wagner is interested in explaining to us in this book is that of genotype networks, arguing that those genotype networks are "the common origin of the different kinds of innovations---in metabolism, regulation, and macromolecules---that created life as we know it.” Their discovery came about as a result of the mathematical perspective of systems biology, the intertwining of biology and mathematics, which has also revealed the conceptual and physical architecture of the ”libraries” of life that genotypes are able to explore, demonstrating how they can accumulate innovations while still maintaining their viability and “phenotypic” meaning. Wagner reveals for us a portrait of life that is astonishingly more robust and complex than we imagined, one in which life can explore a variety of innovations without those mutations being fatal to the life of the organism. We learn how an organism has backup systems--a variety of ways to solve the same environmental problem it might face, part of the redundancy and complexity that comprises the variability which will allow it to sustain life.

Part of the scientific paradigm we grew up with was that DNA was a key that (in a rather straightforward way) encoded certain physical traits, and that mapping the human genome would allow us to unlock all kinds of secrets about physical development, among them allowing us to predict the likelihood of disease. But the reality, as Wagner explains, is that we have discovered that life is unimaginably more complex than this, that the relationship between genotype and phenotype is moderated by entire circuits of regulatory genes that influence the way any gene is ultimately expressed. Yes, Wagner shows us that life is more complex than we had imagined, but he also shows us that it follows rules, that there is an organization and architecture that can be explored, and he shows us how those rules, rather than randomness, mutation, and natural selection alone, explain life’s remarkable ability to adapt and to endure. The computationally challenged should not despair--Wagner has an exceptional ability to give us a picture of all of this by using analogies that take us from the familiar to the new world he wishes to show us. This is exciting and effective popular science writing, and it’s a book that may change your ideas about the way life “works.”

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