Saturday, September 05, 2015

Arrival of the Fittest by Andreas Wagner (Book Review #68 of 2015)

Arrival of the Fittest: Solving Evolution's Greatest Puzzle
**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

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