Oh, that's right -- that's what philosophers are good for. They're really good at questioning models. John Wilkins has been busily dismantling the cheap and easy metaphors we use to describe molecular biological concepts in a series of posts, taking on genes as language, other popular gene myths and metaphors, and explaining why genes aren't information. The problem is that when we explain stuff we know well to students, we use metaphors and analogies to get across the initial ideas, and unfortunately, because scientists are human, the metaphors take on a life of their own and sometimes become the dominant paradigm for understanding the reality. And that can be hazardous.
I've lived through the era in which everyone started thinking of the genome as an elaborate computer program -- we still have lots of people thinking that way, and in some ways it's gotten worse as bioinformatics has brought in a synergy with computer science. But it's not! It's nothing like a series of instructions! This model has become a serious impediment to getting the new generation of advanced students to understand the biology, and worse, they try to shoehorn the biology into how they think a sophisticated computer program ought to work.
We've also got the problem of naive idiots thinking the metaphor is the thing and drawing false conclusions. The genome is a recipe, and every recipe needs a cook, therefore God, etc., etc., etc., ad nauseam.
Genes and DNA are one important component of a complex of compartmentalized biochemical reactions, in which every reaction product interacts with and influences the state of the whole. We're seeing an excessive reductionism borne of the last 50 years of success in molecular biology, and it's about time the pendulum swung back to a more balanced perspective. One gene tells us very little; you need to step back and look at the interactions of networks of gene products in a complex environment to understand what's going on in the cell, and then you have to step back further to look at patterns of interactions between cells, and then further still to see how individuals interact with one another and the environment, and then you have to step way back to see how populations interact, and then, maybe then, you're really talking about evolution.
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I think that metaphors are invented words or references for describing the little that a person can see/touch from a whole that he/she can not see/touch. The little thing that one see is used for trying to explains the whole. It can works when the whole is simplest, but it never works when the whole is complex, because the little saw thing does not repeats the whole image/functioning.
The most astounding metaphors that I know is the Genesis account, at the Bible. My personal investigation has suggested an astronomical model of the state of the world before life's origins, which I can explain each small detail with words and concepts from Physics, Astronomy, Genetics, etc., and the theories of thermodynamics. But, my big surprise was discovering that we describe it also using the symbols used by the authors of Adam/Eve and the Paradise. The snake, the tree, the primordial shapes of the male and female forces, a closed system as a paradise that is eternally under the state of orgasm.. And calculating how that state of the world could creates biological systems inside it, we see an event just as described in The Fall, but explained with words from the second law of thermodynamics and the process of entropy creating chaos and developing into order. .
This is a fascinating discover, the problem now is testing it, if right or wrong, and it is scientifically falsifiable. My suggestion is that the ancient astronomical state of the world is registered into our RNA/DNA which are at the center of our neurons, so, certain altered states of brain can produces flashes of memories, images, at random, but, the observer needs to connect those flashes into a whole picture. The result can be the metaphorical description at Bible ( far away from the real picture) or the metaphorical description of human nowaday knowledge ( far away also but a little bit closer).
Metaphors has origins at any human baby stage, when imagination take places of natural reasoning. This process is projected as big wave encompassing the whole human species still baby stage of collective consciousness. But it must be deconstructed like the adult shape always deconstructs the infantile imaginations. For instance, the metaphors about genes and DNA:
Each lateral pair of nucleotides is a specific and unique reproduction of a functional system that's the building block of all natural systems, from atoms to galaxies to human bodies. Like each human being is a specific and unique copy with some different detail from the others 8 billions human beings. The final product of each internal DNA chemical reactions is like the final product of each human species activity. So, is it right to say that the whole set of human kind is a "code", or a computer program? These names avoid the student to understand the real thing. ( from Matrix/DNA Theory)
http://theuniversalmatrixtheory.blogspot.com/ - Na Luta para Desmascarar os Falsos