Gpuccio: Functional Information Methodology

[gpuccio]

@swamidass

No, I’m just using a particular definition of function, which parallels yours in biology. If you don’t want me to use my definition, I am not sure you can use yours.

@swamidass

It seems you are defining function by the already observed configuration of proteins in extant biology. This does not take into account the configurations that would produce the same high level functions, but we just don’t see because it is not what happened.

@swamidass

It is subjective how we define function. I chose a definition of function that paralleled yours in biology, so I am not sure how you can object to me “breaking the rule” while breaking yourself with your own definition!

Yes, this highlights the problems with using FI as a way of determining if something is designed or not

This is bad. Frankly, I would probably not even answer this kind of arguments, if they did not come from you.

I don’t know if you really believe that the stars in the sky exhibit high values of FI, or if you are only provoking (without any good reason, IMO).

If you really believe that, there is proibably no purpose in continuing any discussion about FI.

If you are provoking, it’s not a good sign just the same.

However, here is a brief answer.

The simple rule I have described (and which is rather obvious in any possible serious discussion about FI) is that we cannot use the observed bits to define the function. The function must be defined undependently from the knowledge of the observed bits.

So: “a configuration of stars that favors storytelling” is valid. But probably almost all possible configurations would do that.

While “a confifuraion of stars where the first has these celestial coordinates, the second these other ones”, and so on for all 9000 visible stars, is not valid.

So, a binary number of 100 digits is a good definition. And, of course, has no relevant FI.

A binary number that is 00110100… is not a valid definition. It can be used only as a pre-specification.

This is the rule, and I have never broken it. I have never defined a protein function that says: “a protein with the following sequence: …” I have always used for proteins the function described in Uniprot for the observed protein, or something like that. IOWs, a protein which can do this and that. Never: “a protein with this sequence”.

But you say: no, I wnat the stars that must have exactly the position that we know. That is breaking the rules. You are using the bits. I have never done that.

You say:

"It seems you are defining function by the already observed configuration of proteins in extant biology. "

Not at all. That statement is unfair, wrong and confounding.

I am always defining function as what a protein can do. I am using observed configurations, in a precisely described way and accordign to well explained assumptions, only to estimate FI in proteins, not to define function. You are equivocating, and rather badly.

You raise the problem of other sequences that could implement the function. But my methodology is aimed exactly at that: having an estimate of the target space. If you do the math, you will see that the estimates of the target space in my results are very big.

Of course, there is always the problem of possible alternative solutions, similarly complex, but completely different. Those cannot easily be anticipated. They certainly exist, in some measure.

That is a completely different problem. It has nothing to do with the definition of the function, but rather with the estimate.

I have discussed that problem in detail in the past. You will find a long discussion about that in this OP and in the following thread:

Defending Intelligent Design Theory: Why Targets Are Real Targets, Probabilities Real Probabilities, And The Texas Sharp Shooter Fallacy Does Not Apply At All.

Look at the part about clocks.