Pharyngula

What would analog genetics look like?

How about another of those non-awkward Dawkins Twitter questions? Although this one actually is kind of awkward, in a non-offensive way. I don’t quite know what it means.

Does evolution rely upon digital genetics? Could there be an analogue genetics? What features of life have to be true all over the universe?

I don’t understand what ‘digital genetics’ is…it sounds very Mendelian, I think. There is a reasonable but overly simplistic perspective on genetics, a very old school way of thinking, that mutations are binary — you’ve either got a trait or you don’t. We also use a linear sequence of nucleotides that get translated into a linear sequence of amino acids, and it all looks very much like a digital computation…and can be modeled reasonably well with a computer. So in a very narrow sense, I suppose you could argue that earthly genetics is ‘digital’.

But it’s also analog. It’s all chemistry, so reaction kinetics and concentrations and equilibria drive everything. I also think it’s a flaw of that old-school classical genetics that subtle quantitative variations are difficult to detect — people were always looking for mutations with distinctive phenotypic effects. Look at the Drosophila eye mutations, for instance: white was discovered first. Wild type flies have brick red eyes, while the mutant has obvious white eyes. A single gene can flick the color between red and white.

But here’s a qualifier: it’s not simply binary, a choice between white and wildtype. FlyBase tells me there are 1060 published, classical alleles of white. The gene behind it is an ATP-dependent transporter protein — so it’s an enzyme, with analog chemical properties.

Further, when I think of all the other things that can modulate genes, it’s hard to retain an image of them being digital. Codon usage in the gene can have quantitative effects on rates of translation. Position effects — what genes or other DNA are in the neighborhood of the gene in question — can modify the regulation of the gene. The number of copies of a gene can have effects — there are lots of experiments in gene dosage in flies, and we know that humans have copy number variants.

We also know that many genes generate phenotypic effects with concentration gradients, not digital at all. In flies, bicoid is the canonical morphogen — its RNA product is concentrated at the head end of the embryo, and its protein diffuses away to form a gradient from high at the head to low at the posterior, and this gradient is read by other genes, like orthodenticle, hunchback, and knirps, to determine whether they should be switched on or off. We can push around boundaries of anatomical features in the larvae by changing the concentration of bicoid.

bicoid

To make it all fuzzier still, that gradient is also a product of other cooperating genes, like stauffen and valois, that localize bicoid.

So I guess my answer to that question is that we already know what an analog genetics would look like — we just have to look at ourselves.

Comments

  1. #2 Justin Payne
    United States
    August 21, 2014

    But it’s also analog. It’s all chemistry, so reaction kinetics and concentrations and equilibria drive everything.

    …Ok, yeah, but all digital electronics are analog, too, they’re just analog circuits overdriven to extremes of high (1, or V+) and low (0, or GND). But we say “digital” (and “binary”) because we’re talking about elements that are, in normal function, always in one of two discrete, unambiguous states.

    So, too, with genetics. It’s not so much that you always have a mutation or you don’t, but it’s that at Locus L of a given Chromosome C, you have Base B = A or C or G or T. Unambiguously. You can’t have half-an-A on a specific locus of a specific molecule. It’s digital in that sense – genomic information is discrete, not continuous.

    That’s what Dawkins is saying – not that genomes are like computation. (They’re not.)

  2. #3 Rosie Redfield
    http://www.coursera.org/course/usefulgenetics
    August 21, 2014

    Genotypes are digital (quantized), but phenotypes are analog (have continuous variation).

  3. #4 Brian Blais
    August 23, 2014

    In one of Dawkins talks he refers to this, and compares it to the difference between mixing blue and red paint vs blue and red marbles. If genetic mixing is like paint, then all traits will eventually “wash out” and become homogenous – you will lose genetic variation over time through averaging. Thus, natural selection would break down over time because it wouldn’t have anything to act on. If genetic mixing (as it actually is) is more like marbles, you can maintain genetic variation over time. You also won’t get male+female = semimalefemale and things like that.

    Dawkins is asking if one could come up with a “continuous” DNA code – not 4 letters, or a finite countable set of letters – perhaps something to the effect of the density of a chemical, and still have natural selection work.

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