How do most of these objections not apply also to computer programs? Computer programs are physical objects, and what the program actually does depends entirely on the physical machinery that runs it.
I would say the main difference is that computer systems work to embody the same bit string in widely varying substrates and perform the same logical operations on it. It doesn’t matter if a program is stored on magnetic domains in a tape drive and executed in vacuum tubes, or if it is stored in electrons trapped in flash memory and executed in a 22 nanometer process CPU, the end result of a given set of logical operations is the same. In biology though there really isn’t a message or program you can abstract away from the molecules bouncing around, there is only one level of abstraction. You cannot separate ‘hardware’ and ‘software’.
Assuming “bit string” means “machine code”, this isn’t true. The same machine code will not result in the same logical operations being performed on all computers. It may not correspond to any logical operations at all on other computers. And what logical operations are carried out depends entirely on “the molecules bouncing around” in the computer. You aren’t making DNA sound different from machine code at all.
Good point regarding machine code, I wasn’t thinking at that level of detail. But at this point the similarity is metaphorical at best.
The metaphor fails to go far enough, I think, because the non-DNA context and the DNA are working at the same level. Both are objects with shapes that interact. Yes, software is always embodied in matter, and yes processing happens in matter rather than some kind of abstract logical space, but part of the point of most computers is that the same matter can carry all kinds of different patterns. In biology the DNA builds the context and the context builds the DNA, and both of them alter each other when they interact. The interations also produce effects that tend to much more closely resemble physics-model-type actions—of he sort that can be modeled via differential equations when you are at a large enough scale that the single-molecule variances average out—rather than really embodying particular operations or logics.
I get the feeling there is an inferential gap happening here...
How do most of these objections not apply also to computer programs? Computer programs are physical objects, and what the program actually does depends entirely on the physical machinery that runs it.
I would say the main difference is that computer systems work to embody the same bit string in widely varying substrates and perform the same logical operations on it. It doesn’t matter if a program is stored on magnetic domains in a tape drive and executed in vacuum tubes, or if it is stored in electrons trapped in flash memory and executed in a 22 nanometer process CPU, the end result of a given set of logical operations is the same. In biology though there really isn’t a message or program you can abstract away from the molecules bouncing around, there is only one level of abstraction. You cannot separate ‘hardware’ and ‘software’.
Assuming “bit string” means “machine code”, this isn’t true. The same machine code will not result in the same logical operations being performed on all computers. It may not correspond to any logical operations at all on other computers. And what logical operations are carried out depends entirely on “the molecules bouncing around” in the computer. You aren’t making DNA sound different from machine code at all.
Good point regarding machine code, I wasn’t thinking at that level of detail. But at this point the similarity is metaphorical at best.
The metaphor fails to go far enough, I think, because the non-DNA context and the DNA are working at the same level. Both are objects with shapes that interact. Yes, software is always embodied in matter, and yes processing happens in matter rather than some kind of abstract logical space, but part of the point of most computers is that the same matter can carry all kinds of different patterns. In biology the DNA builds the context and the context builds the DNA, and both of them alter each other when they interact. The interations also produce effects that tend to much more closely resemble physics-model-type actions—of he sort that can be modeled via differential equations when you are at a large enough scale that the single-molecule variances average out—rather than really embodying particular operations or logics.
I get the feeling there is an inferential gap happening here...