You can implement A simulation. But that simulation having anything to do with any particular thing that has existed in the real world is harder.
Physics itself is not hard. Applying it to large numbers of particles is hard.
As for non-DNA molecules, there are all kinds of small molecule metabolites which are constantly being converted back and forth, some of which are very important (they bind to the big molecules, are part of metabolism, and I have seen some brand new research about particular proteins that only fold properly around a 'nucleus' formed by a particular 6-carbon molecule). But my main point I was trying to make was more along the lines of (addressing the third bullet):
Shape is more detailed than general cell shape. There is fine structure in terms of internal fibers, distributions of molecules, impermiable barriers that segregate things, etc. Some of this, like the aforementioned membranes in bacteria, the self-perpetuating but never-made-from-scratch compartments that distill out their components from the general cell mileu, don't necessarily have the DNA as a determinant but rather as something that sets up the circumstance in which it is stable. Other things like the amounts and simple distributions of molecules all come from pervious states and most possible distributions dont correspond to any real state (though doubtless many of them would be unstable and collapse down to one attractor or another that normally exists once you instantiate them).
I have a hard time trying to think of the nature of the correspondence between these things and bits for a simulation besides positions of molecules, and I'm not sure in what context those bits are specified. A little help?
I have a hard time trying to think of the nature of the correspondence between these things and bits for a simulation besides positions of molecules, and I'm not sure in what context those bits are specified. A little help?
What you do is write a program that generates a set of particles and places them into the simulated cell, such that the resulting cell is viable and functionally equivalent to the original cell. Take the program and count its length in bits. If you haven't programmed before you may not have much intuition about this. In that case thin...
I changed the old topic because it was misleading and did not convey the questioning intention of this post. Sorry about that.
The point of this post is to examine the proposition that people underestimate the complexity of living beings from examining them through the complexity of their functional DNA included in the genome alone. I don't have sufficient information to answer the question, but I have just about enough information to ask the question, so if you can do a better job drawnig a conclusion that'd be great. Also if you could point out technical errors that'd be nice too.
Genome
The genome contains the DNA which contains each invidual gene and serves as the currency of inherited qualities of the organism. That is evolutionary theories calculate around the frequency of genes and create formalisms, mathematical laws and so forth to predict and understand the phenomenom of natural selection or natural reproduction.
Nothing wrong with this so far. But when it comes to actually thinking about the genes and the protein sequences, it seems to me that often it is forgotten that the entire cell which contaisn the DNA and the mitochondrial DNA and the intracellular devices are part of this replicatory system.
To draw an unreliable surface analogy you could compare the replicatory process to a cellular automata you could think of the system as a generator which accepts a string of numbers to operate the generator. In this surface analogy the entire system is the final organism, the product of the automata, the invidual genes represent the fed in string of numbers and the other parts of the cell - DNA excluded - function as the generator which accepts the string of numbers. This analogue is poor because the distinction isn't real. But it only serves to illustrate a point. Which is that if you have just the string of genome that is contained in the DNA of a human being - you can not make a human being. Something is missing. The devices inside the cells, the mitochondrial DNA, the initial position - which is a fertilized ovum in a suitable environment like the womb.
The point of the post and the proposition is the following:
The genome (mathematically) contains a smaller amount of data than is actually required for an organism as complex as the phenotype produced with the help of it to develop. To illustrate this with the previous surface analogy of a generator and a feed, the complexity of the generator contributes to the complexity of the final product with the fed string. And this leads to cognitive oversimplifying the complexity of an organis. But that analogue is inaccurate, and this proposition could be too.
So can you tell if this proposition is correct or incorrect?
I don't have sufficient knowledge in biology, evolutionary theory, mathematics and I just pretty much can't tell if this is true or completely false, but I'm intuitively anticipating a systemic underevaluation of the complexity of organisms in relation to the complexity of it's genome on these grounds. Note however I'm not saying that people think organisms as less complicated than they're, but in terms of mathematics when extrapolating from the genetic complexity, they'd underestimate their predictions. So what do you think?