The phoebe is on her nest. She stands her ground now (or rather sits her wattle and daub) when I enter the root cellar where she has built her nest, six tiny white eggs under her warm body. Does she know what's coming, or when? There is so much we don't understand about animal intelligence and instinct.
But this we do know: She is born with the instinct to build a nest, incubate her eggs, feed her chicks. Somehow that knowledge is in her DNA, as a sequence of four chemical bases. The DNA spins out proteins on cue as the phoebe embryo develops. My God, what a mystery! It was all so much easier to understand when we imagined that the phoebe was divinely ensouled with knowledge.
One cell, two, four, eight, sixteen. The earliest cells, the so-called stem cells, have the potential to become any other kind of cell -- feather, muscle, bone, brain. What they become depends upon which genes are expressed at each stage of development, and that in turn is sensitive to what has already been expressed. It's a bootstrap process. The phoebe pulls herself into being.
Her DNA is not quite a blueprint, because there's no builder to follow the plan. It's not quite a computer program, because there's (initially) no hardware to run it.
Here's how geneticist Enrico Coen puts it in his book, The Art of Genes: 'The software, the program, is responsible for organizing hardware, the organism. Yet throughout the process, it is the organism in its various stages of development that has to run the program. In other words, the hardware runs the software, whilst at the same time the software is generating the hardware."
Sounds terribly circular, and the metaphor is unsatisfactory. Metaphorical thinking is always perilous. There is really nothing else quite like what happens in the developing organism. And yet, and yet -- the phoebe knows.