You say that, but you go on to contradict it.
If I were you, I would now spend some time trying to work out just what it is you actually believe because by now it’s clear you have no idea.
Not FI, no. It has zero bits of FI. None of it. Because if the sequence is lacking anything for function, it has zero bits of FI. It doesn’t have “most of” the bits required for the function, it has zero. None.
My feud is pretty simple: You and Gpuccio aren’t using FI correctly as it is defined by Hazen et al 2007. You are assigning FI values above zero to nonfunctional molecules, which is incorrect. Despite your protestation above, you go on to do exactly that here below. As I will show now again.
No, wrong. It means ALL the bits necessary for function are missing. If the system cannot perform the function, then no matter how much of the system is in place, it has NONE of the bits necessary for function. NONE. Yes, despite it missing just a single mutation and yet the entire rest of the sequence is there, if that sequence before mutation cannot perform the function, then is below the minimal threshold for function, is therefore nonfunctional, and therefore has zero bits of FI.
You started by acknowledging exactly that:
“It is exactly what I said for I explicitly recognized that a system (or a sequence) unable to perform the function has zero FI.” - You.
This is from Hazen et al 2007:
In this formulation, functional information increases with degree of function, from zero for no function (or minimum function) to a maximum value corresponding to the number of bits necessary and sufficient to specify completely any configuration of that system.
In other words, how much of the system is present is irrelevant if it fails to perform the function of interest, then it has zero bits of FI.
Functional information is defined only in the context of a specific function x. For example, the functional information of a ribozyme may be greater than zero with respect to its ability to catalyze one specific reaction but will be zero with respect to many other reactions.
So if the system does not perform the function of interest, despite the (in this case enzyme) having a sequence, it has no FI with respect to that function.
Functional information therefore depends on both the system and on the specific function under consideration. Furthermore, if no configuration of a system is able to accomplish a specific function x [i.e., M(Ex) = 0], then the functional information corresponding to that function is undefined, no matter how structurally intricate or information-rich the arrangement of its agents.
So basically a system incapable of performing the function regardless of it’s configuration, is undefined in terms of FI. So FI can go from undefined to however much -log2[M(Ex)/N] is if the system is altered such that it functions.
It may have a lot of information by some other definition of information, but if it doesn’t perform the function of interest, if it fails to meet M(Ex), aka the minimal threshold for function, then it has zero bits of FI.
Not FI, no. Because that one mutation (amino acid) is incapable of performing the function alone, so the FI doesn’t increase by 4.3 bits. It may increase by 4.3 bits of information by some other measure of information, but not according to FI.
Supposing the functional molecule in total scores 300 bits of FI, you are saying it goes from 295.7 bits in it’s nonfunctional state, then 4.3 bits of FI are added by that one mutation, and then it becomes a 300 bit FI molecule. But that’s wrong, because the nonfunctional sequence before the mutation has ZERO BITS of FI.
It goes from zero for the nonfunctional molecule, to however many bits it is given -log2 of the ratio of functional to nonfunctional sequences of that length. That one mutation doesn’t add 4.3 bits of FI, because the molecule before the mutation is incapable of performing the function. Then it by definition has zero bits of FI.
Yes, and if it cannot, then it has none of them. Not 4.3 bits(or however much) less than required, it has none of it.
