Genome complexity: probabilistic (Introduction)

by David Turell , Friday, May 12, 2017, 15:04 (2889 days ago) @ David Turell

David Comment: Of course there are 'functional reasons' for changes. They require planning. The big black box in our discussions is our lack of knowledge. We can tell which genes control what function or what appears in embryogenesis but we have no idea how the controls work, how the gene actually does its direction through chemical action.

Here is an article, very long, on gene networks and the fact that we know very little about how it all results in functions, traits, even free will and consciousness. We do have a few specifics:

https://aeon.co/essays/dna-is-the-ruling-metaphor-of-our-age?utm_source=Aeon+Newsletter...

"Sounds simple enough, but what if we need to predict the specific outcome of a large number of such flips, somewhat like the challenge we face in predicting, from a person’s genotype, the risk of life events such as a heart attack or diabetes? Each of us has a unique set of variants in perhaps hundreds of different genes that separately contribute to the probability of disease. What will each one do? Will they flip as ‘illness’ or ‘health’? Is that even a realistic question?

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"What role do genes play in non-physical traits such as behavior, or even the ultimate questions of consciousness and free will? Here, the metaphoric replacement of ‘soul’ by ‘gene’ works in a different way. How much of our feelings, thoughts and behavior is actually determined from the moment we are conceived, and could in principle be read like a computer program from our genome?

"The extent to which we have free will is a fundamental aspect of how we view our ‘selves’, and for many religions, relates to whether we can be held responsible for our moral behavior. The scientific view, on the other hand, goes something like this: we live in a totally material world made of matter, energy, and the forces that connect them. Since genes are the fundamental causal elements of life, it would seem inevitable that, if we knew enough, we could predict everything about all of us — our health, our behavior, and our ideas. The alternative would seem to be mysticism — invoking some sort of immaterial something-or-other that we can’t measure but that affects who and what we are.

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"Evolutionary determinism was the first thread of the gene metaphor. Natural selection preserves only what is inherited from the successful organisms in the past.....Mendel identified a pattern of inheritance that provided perhaps the most powerful tool for research design in the history of science. The genetic research that followed eventually led to the identification of the nature of DNA, the locations and structure of genes in DNA, and the understanding of how they code for proteins. But that same Mendelian thinking made us conceptual prisoners of the deterministic, law-like interpretation of genetic function.

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"Genomic studies searching for causal genes have grown ever larger and more expensive, but commensurately important results have yet to roll in. Most of the estimated overall genetic influence on the traits or diseases of interest is still unidentified. What we’re finding instead is ‘polygenic’ causation, that is, that many different parts of the genome contribute mainly trivial individual effects.

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"Instead of the widespread view of life as raw, relentless Darwinian competition leading to a single ‘fittest’ way to be, a far better way to see it is in terms of cooperation. By cooperation we do not necessarily mean the social, emotional variety. Cooperation describes the way in which a trait is produced by many factors, the countless genes and lifestyle aspects that contribute to the trait.

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"... genes are molecules and hence fundamental causal agents of life, yet their effects are highly probabilistic and very hard to pin down or predict.

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"conceptually, we have not advanced very much in our understanding of what are deeply puzzling aspects of the way the cosmos — including life — works.

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"that is perhaps why the metaphor of the gene as the atom of causation in life is so easy to absorb, and its subtleties so easy to overlook. We are made very uneasy by things that are only probabilistic unless, as in coin-flipping, we can sense what’s going on. When we can’t see it, and causation is many-to-many, that is far too much for our minds to deal with easily. Yet that seems to be the reality of the world."

Comment: Very long article worth reading. We know so little. Like quantum theory.