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A Rock-Solid Mathematical and Conceptual Foundation for Genetics
on November 21, 2011
About 7 years ago I waded into the huge subject of evolution and origin of life. As an electrical engineer I was quickly appalled at the confusion, the endless opining, indulgent name-calling, and quantity of intellectual slop that passed for science in biology.
This was one of the first books I found that brought the level of rigor to biology that people in the hard sciences (Physics, Engineering, Computer Science) are accustomed to. If most discussions about biology seem "squishy" to you, that's because they are. This book is a refreshing departure.
Others here have complained that Yockey is dogmatic. He is, and he's earned the right to be. Most of what Yockey says is as right and as black and white as 1's and 0's. Claude Shannon's 1948 model for digital communication laid the foundation for our modern digital age and Shannon's work is flawless. In this book Yockey shows that the genome is *isomorphic* (structurally identical) with Shannon's model for digital communication.
Yockey says, "Information, transcription, translation, code, redundancy, synonymous, messenger, editing, and proofreading are all appropriate terms in biology. They take their meaning from information theory (Shannon, 1948) and are not synonyms, metaphors, or analogies."
This isomorphism is crucial to establishing any rigorous mathematical framework for modeling evolution in software. It's a required assumption for studying evolution as a computational process; for establishing a sound mathematical framework for the history of evolution (which still for the most part does not exist), and for clarifying the difference between assumptions and truth in evolutionary theories.
Yockey rightly points out that the laws of the genetic code are not derivable from physical laws and that even the simplest genome contains more information than all the laws of physics put together. This is why he says, "I have no doubt that if the historic process leading to the origin of life were knowable it would be a process of physics and chemistry. Thus the process of the origin of life is possible but unknowable."
For this reason he takes the position that the existence of the genetic code must be taken an axiom, a required but unprovable assumption. He shows the vast chasm exists between life and non life. Any attempt to argue otherwise muddles definitions and conflates the laws of physics with the freely chosen rules of codes. As a communications engineer, I understand that two could not be more different. Yockey puts it this way:
"The existence of a genome and the genetic code divides living organisms from nonliving matter. There is nothing in the physico-chemical world that remotely resembles reactions being determined by a sequence and codes between sequences."
The book does contain a few statements I disagree with. Crick's central dogma, which Yockey espouses, has since been shown to be wrong; cells do modify their own genomes based on inputs from the environment. The genome is a read/write storage system, not read-only. And evolution is not a random walk; it is driven by transposition, horizontal gene transfer, symbiogenesis, epigenetics and whole genome duplication, all of which are non-random. Authors like Lynn Margulis, Barbara McClintock and James Shapiro elaborate on these points in detail. However, the mechanisms of evolution are not the focus of this book so this is only a minor issue.
Engineers have very high expectations of theoretical models. As well they should; if they don't, bridges and buildings fall down and people die. Yockey brings the standards that are normally found in engineering to biology. Some biologists will be offended at this; that can only be expected when someone ushers in knowledge from outside their field that highlights the shortcomings of their assumptions.
In any case this book is a tremendous contribution to the field because it opens the door for a systems view of biology, in contrast to the traditional straitjacket of insisting that "it's all just complex physics and chemistry." It's not all just physics and chemistry because genomes literally and not figuratively process information. Living things are information driven and systems oriented. Little progress can be made without a solid foundation in digital communication. Yockey's work lays that foundation.