> We propose a theoretical formalism, molecular finite automata (MFA), to describe individual proteins as rule-based computing machines. (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070173/)
A textbook I read several years ago on cellular mechanics inspired my thoughts on this, unfortunately I'm not able to find it right now. I was blown away at the time, the chapter on dna transcription strongly reminded me of programming.
People like to think of blobs interacting and not interacting, but really a cell is more of a crowded mess, see this image for a sense of scale:
http://media.tumblr.com/525082e14ba810bc539c61a646fdba93/tum...
Now picture everything in that image swirling around incredibly fast, with some parts of it (the yellow fibers) more stationary and everything else randomly zooming/bouncing around. There is no equivalent in computation.
A logic may appear to emerge from that jumble, but it's not going to behave very predictably. It takes years of work to be able to predict mechanistically just a tiny aspect of one system, much less the whole cell.
The DNA example you describe is a fascinating area, but it took ~30-50 years to get that understanding, and we still find out new things about it all the time! Now that's a really easy system to study, you can isolate its components, you have clean readouts (new DNA generated, sequencing etc.). How about everything upstream of that? The signaling chain going from the cell surface to the DNA to turn on a gene is quite long, picture at least 3 links with yet another 3 links each, which themselves have separate, independent links back into the DNA.
That's not to say we can't make assumptions and make some progress, see Marcus Colvert's lab:
But it's really, really hard, and an FSA is a quite incomplete way of describing it. Looking at the paper you sent, a useful MFA would have to be insanely large to be useful, and defining all the terms is just an impossibly large task.
Honestly, tomatoes are really efficient as is. They grow huge amounts of fruit per acre; they grow in preposterous conditions, like people's windowsills, greenhouses, fields across the world, etc. I don't mean to pick on your particular choice of example, but you really got to get into the weeds to really understand the efficiencies of agriculture.
Indeed, there's consensus that the greatest threat to agricultural efficiency are all the weaknesses of a highly-engineered monoculture. Imagine the devastation of the Florida orange harvest a few years ago due to frost, but due to a single weed.
> a cell is basically a huge finite state machine
There is a huge amount of research to create an "algebra" of synthetic biology, which is really fascinating stuff. You'd love it! You're right that a lot of what you're describing is inevitable, but there's a huge grind to get there, solving engineering problems totally orthogonal to the theoretical biology of it all.
do you have links to such research?
The fact is, even with a perfectly engineered tomato, it's hard to beat the low cost of dirt+sun.
Photosynthesis is actually fairly efficient.
As for the whole cells-are-state-machiines, while that's technically true, the state vector has a trillion parameters.
Lygos is the first step towards the above scenario happen. At its heart, a cell is basically a huge finite state machine. It is programmed both through dna and proteins. Some day (and maybe Lygos already has something like this) we'll have a programming/description language to describe what a cell does/how it works. It would start with the basics. (When you see this molecule, attach this other molecule to it. When concentration of this gets too high, start doing this.) It would also have a basic support structure (nucleus/ribosomes) needed to be a functioning call. On top of this, you could program it to produce what you needed.
I never supported Trump, but I'm severely disappointed in the direction his administration is going. If he wants to make America great again, lets start researching projects like what I described above. There was a pdf posted in yesterdays posting on Germany's fusion reactor, talking about the private companies that were helping to build it. They had to come up with new manufacturing skills and tools, and are now able to use those in other jobs. That is how you make America great again.