My money is on the structure that the genome produces. The genome produces the brain, the most complex structure known, albeit with the help of information and additional "programming" from the environment.
How complex, really, is your brain? Sure, there's a great deal of complexity from genes through neurons and synapses and such, but all of this is pretty mcu auitomatic as far as we know. It's simple complexity contributing to greater complexity, but then there's the matter of your conwsciousness. That's really pretty simple when you try to use it to comprehend the complexity of itself. It's really error prone.
The entire system growing around the genome necessarily includes the relationships among genes/letters, which subsumes a lot of relationships with things outside of the genome. If you consider the relationship of genes or letters with things outside of the genome, it is probably included in the relationships among genes/letters - but not necessarily so I mention it separately. I don't think I need to prove that that system probably subsumes the human nervous system.
But that's not what you were asking. You asked which is more complex, the nanocomputer or the machine itself. But that makes me wonder - what is the nanocomputer that you refer to? The genome doesn't function without the machines it builds. You must mean the program itself, the DNA and perhaps the reproductive machinery. I think it is less complex than the machine it builds when defined mathematically. It is a virtue of DNA that it produces a lot of complexity from very little complexity. But that's just a guess.
For those who don't want to read through the tedious details that follow, here's the take-home message: if you want to store the data in a raw format for later re-analysis, you're looking at between 2 and 30 terabytes (one terabyte = 1,000 gigabytes). A much more user-friendly format, though, would be as a file containing each and every DNA letter in your genome, which would take up around 1.5 gigabytes (small enough for three genomes to fit on a standard data DVD). Finally, if you have very accurate sequence data and access to a high-quality reference genome you can squeeze your sequence down to around 20 megabytes.
pretty good size to performance ratio. i don't think this represents the interaction or even the presence of epigenes. i have read epigenes represent orders of magnitude increased complexity
with or without baggage?
supposedly the nano has some element of immortality or at least in some cases a half-life surviving partial death, I'd say that additional information counts for something, but isn't nano and mach partners or something, there may be some inner rivalry going on and such, but in some cases they are like teammates, not so much competing for the complexity crown but aiding and abetting each other, kind of like driver and cart, and I heard you don't have to put the cart in front.