You seem fixated on 'programming'. Biological cycles are based on biological clocks, sometimes adjusted by the light & dark changes between day & night (
circadian clocks). Many simple creatures orient or move according to light & dark cycles, tidal cycles, or lunar cycles, and the mechanism by which they do so have been explained - they use biochemical oscillators, sequences of chemical reactions that periodically repeat, such as
oxidation–reduction cycles of peroxiredoxin proteins. In more complex creatures like mammals, these cycles are adjusted and managed via genetic feedback loops.
Here's a video of a chemical oscillator for your enjoyment:
You can call it a machine, and claim it works by programming designed into it, but that doesn't change the fact that, given the fundamental laws of physics we observe in the universe, and a high-energy, low-entropy, start to the universe as we know it, the rest of what you call a 'machine' emerges quite naturally, with no need for explicit design or programming. The strong and weak nuclear forces hold together the elementary particles that make up the elements, the electromagnetic force binds elements into compounds, and gravity pulls it all together on a large scale, into galaxies, stars, and planets.
You can certainly claim that the laws of physics we observe, and the initial state of the universe as we know it, were created or configured by some inexplicable creator or designer before the universe got going - as I mentioned earlier, there's no shortage of fanciful origin myths, with or without an intelligent designer; but from that point (i.e. the 'big bang') on, to paraphrase Laplace, "We have no need of that hypothesis".