“Now with DNA, the mutation rate is fixed at ~10^-8.”
Well no, it isn’t. Not to get too complicated, usually the mutation rate is lower than that, but occasionally things happen that bring the mutation rate rather higher. We have things like DNA repair mechanisms that are mutagenic and others that are less so, and when the former get turned on we get a burst of mutations.
“Since we need to be able to weed out bad mutations, this imposes an upper bound of ~10^8 on the number of functional base pairs.”
Definitely no more than 10^8 sites that would mutate into dominant lethals. For lesser deleterious mutations it gets murkier.
But there’s nothing special mathematically about the constant 10^-8 -- that (unless I’m mistaken) is just an unwelcome intruder from physics and chemistry. So by using an error-correcting code, could we make the “effective mutation rate” nonzero, but as far below 10^-8 as we wanted?
Yes, and it happens some.
Indeed we could! Here’s my redesigned, biology-beating DNA that achieves this. Suppose we want to simulate a mutation rate ε<<10^-8, allowing us to maintain ~1/ε functional base pairs in a steady state. Then we simply stick those 1/ε base pairs (in unencoded form) into our DNA strand, and also stick in “parity-check pairs” from a good error-correcting code. These parity-check pairs let us correct as many mutations as we want, with only a tiny probability of failure.
It’s been years since I’ve looked at this. I may have some of it wrong and it might have changed while I wasn’t looking. But one way we used to handle that was to keep track of which strand of DNA is the old known strand and which is the new one. Then if there’s a mismatch, you repair the new one instead of the old one.
If you have two copies of the DNA sequence and one of them is being replicated while the other waits, and there’s an error, you can copy DNA from the reserve copy and splice it into one or both of the new ones.
Since each DNA repair system might possibly do misrepair under some circumstance, and since they are potentially disruptive, it makes some sense that they would only be activated when needed.
“Now with DNA, the mutation rate is fixed at ~10^-8.”
Well no, it isn’t. Not to get too complicated, usually the mutation rate is lower than that, but occasionally things happen that bring the mutation rate rather higher. We have things like DNA repair mechanisms that are mutagenic and others that are less so, and when the former get turned on we get a burst of mutations.
“Since we need to be able to weed out bad mutations, this imposes an upper bound of ~10^8 on the number of functional base pairs.”
Definitely no more than 10^8 sites that would mutate into dominant lethals. For lesser deleterious mutations it gets murkier.
But there’s nothing special mathematically about the constant 10^-8 -- that (unless I’m mistaken) is just an unwelcome intruder from physics and chemistry. So by using an error-correcting code, could we make the “effective mutation rate” nonzero, but as far below 10^-8 as we wanted?
Yes, and it happens some.
Indeed we could! Here’s my redesigned, biology-beating DNA that achieves this. Suppose we want to simulate a mutation rate ε<<10^-8, allowing us to maintain ~1/ε functional base pairs in a steady state. Then we simply stick those 1/ε base pairs (in unencoded form) into our DNA strand, and also stick in “parity-check pairs” from a good error-correcting code. These parity-check pairs let us correct as many mutations as we want, with only a tiny probability of failure.
It’s been years since I’ve looked at this. I may have some of it wrong and it might have changed while I wasn’t looking. But one way we used to handle that was to keep track of which strand of DNA is the old known strand and which is the new one. Then if there’s a mismatch, you repair the new one instead of the old one.
If you have two copies of the DNA sequence and one of them is being replicated while the other waits, and there’s an error, you can copy DNA from the reserve copy and splice it into one or both of the new ones.
Since each DNA repair system might possibly do misrepair under some circumstance, and since they are potentially disruptive, it makes some sense that they would only be activated when needed.