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genes as codes vs. genes as templates: information theory in the Companion to the Philosophy of Biology

First: that the classical understanding of genes is more problematic than I previously knew.  The same gene, may, on different occasions, because of other factors, be the source of coding for different proteins (this is called "alternative splicing").  Different gene combinations may be read the same way in the sense that they may be used to code for the same protein.  RNA does other things than just translate DNA into proteins.  And then there are other factors than genes that influence inheritance. And finally, some proteins may be modified after translation.

The author of the related section in Companion to Philosophy of Biology says that the discovery of these complicating factors (covered in proteomics rather than genomics) has somewhat problematized the notion of the gene as the unit of inheritance.  For there is not always a one-to-one relationship between genotype and phenotype.  To the degree that these non-DNA factors figure in the formation of phenotypes, that formation process looks unlike the reading of DNA as a kind of code.  As the author says, DNA is more like a tool kit and/or set of templates that are used when needed.

What significance would this deviation from the notion of DNA as code have for the proposal that genes can be thought of as selfish? 

Perhaps someone interested in this problem should write a book titled The Useful Gene?

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Yet another thought.  Perhaps there are two ways to read the word "information": one, more mechanistic and the other more.... hermeneutical.   The more mechanistic usage would carry with it the expectation that one could plug it into an algorithm to predict outcomes.  The other would be messier, noisier, as it were; for the meaning of the so-called information would vary according to context, and the unifying factor among these various contexts would not be the sort of thing one could measure.  The telos.

The alternative way of looking at epigenetics is to say that its a complex system with many interacting individual components.  DNA may now look more like a toolkit than a blueprint.  But there is, from the perspective of molecular biology, no goal-driven tool-user to be singled out.

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Yet another thought: this link discusses epigenetics, the name for the study of what this post is talking about: http://nautil.us/issue/2/uncertainty/the-genome-in-turmoil

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