I was going to talk about a cool recent paper that described the evolution of novelties by way of modifying modular gene networks, but I started scribbling it up and realized that I was constantly backtracking to explain some fundamental concepts, so I stopped. I was concerned because one of the most common sources of confusion I've found in my students in the past was difficulty in distinguishing phenotypes from the complexities of the underlying genotype, and I have to be slow and thorough in setting up those differences early on until it sinks in, a habit I'm continuing here. It's so easy for students to reify a trait, like eye color, into a single discrete property that must be somewhere on a chromosome. It's not. It's so much messier than that.

Let's talk about eye color in flies. Drosophila eyes have a characteristic brick red color, and the most famous mutation in flies is white, which produces distinctly white-eyed flies. Eye color is too complex to be described as the product of a single locus and only two alleles, though: there's actually a whole battery of genes that work together to produce eye color.

For example, the specific color of the eye is the product of mixing two pigments, drosopterin and xanthommatin, in appropriate proportions in the pigment cells of the eye. So we've actually got at least two genes, brown or bw for short, that is part of the pathway that makes drosopterin, a bright red pigment from guanine, and scarlet or st, that's part of the pathway to make xanthommatin, the brown pigment. Each of these pigments is produced in a more complex way than is illustrated here — xanthommatin is produced from the amino acid tryptophan by a series of enzymes, tryptophan pyrrolase, formamidase, kynurenine-3-hydroxylase, and phenoxazinone synthetase — but this story is already complicated enough, so in this diagram we reduce all that to just a couple of arrows.

So there are two parallel pathways to produce the eye color. There is a brown pathway that produces a red pigment, and a scarlet pathway that produces a brown pigment. The names might be a bit confusing (they always are for my students), but it's part of a standard genetics convention: the genes are named for their effect in mutants, not wild type forms. If you knock out the brown gene with a mutation, the fly will be unable to make the red pigment, but it will still make the brown pigment, so the eye will look brown. See? Makes perfect sense.

Conversely, if you knock out the scarlet gene with a mutation, the fly will not be able to make the brown pigment, but it will continue to produce the red pigment, so the eye will look bright red.

All you have to do is think about genetics for a few years, and don't worry, this inversion of names will someday begin to seem perfectly natural. It's just another peculiarity of the genetical mind that makes geneticists weirdos on campus.

Now for the test: if you knock out both the brown and the scarlet genes, what do you get? They don't make the brown pigment, and they also don't make the red pigment, so the eye color would be…?

If you realized it would be unpigmented or white, give yourself a kewpie doll. Eye color is primarily the product of two gene products, a red and brown pigment, which are produced by multi-step enzymatic reactions that offer multiple points for possible disruption. This one trait is the outcome of a whole series of genes.

I mentioned at the beginning that the white-eyed fly was the most famous Drosophila mutant. Have we just explained how that mutant was created? No we have not. As it turns out, the white mutation was in a single gene, but again, not a gene that directly makes a pigment. White is a mutation that makes a defective a transporter protein — the mutant blocks the transport of the precursors tryptophan and guanine into the cell, so it has no raw materials to make the pigments. In the wild-type fly, there is a complex sequence of events that results in the ultimate production of two pigments in the eye.

Defects in white, scarlet, and brown disrupt different events in the sequence, with white upstream, or epistatic, to the other two. White affects both branches of the pathway, while scarlet and brown each affect one.

Whoa, so this is already getting complicated, and we haven't even dug into the details of each pathway. The proportions of the two pigments that end up in each eye are dependent on the relative rates of each of the two branches, so subtle mutations can change the hue of the eye; variations in intermediate steps can produce aberrant byproducts with odd colors; and of course, this whole collection of genes has to be regulated to be expressed in the right place. The whole fly isn't brick red, just the eyes, so this process has to be switched on in only a subset of cells.

At this point, you could just give up, if you were a creationist. It's too complex, there are too many bits and pieces, and everything is interlinked — even if you could get it too evolve, the interdependencies must lock the whole grand network into one rigid pattern where you can't break one thing without the whole thing collapsing like a house of cards. But you'd be completely wrong.

It's counter-intuitive, but it turns out that this complexity actually enables the evolution of interesting novelties. I'll get to that either tomorrow or the day after…be patient.

Diagrams are from Klug, Cummings, Spencer, and Palladino, Concepts of Genetics, 9th edition.

(Also on FtB)