Good question. I still believe that gpuccio gave you the right scenario given a single AA change.
I don’t think you can but is any of this relevant.
I think the more important issue is treating those with different points of view with respect.
Then we are done. Your bad excuses are of no value or consequence here.
but you are in reality only adding 4.3 bits by adding an amino acid.
No. If the sequence can not perform the function of interest, it has zero FI with respect to that function.
If one amino acid substitution turns it into a functional sequence, then the FI of that sequence is the number of sequences that meet M(E_X) divided by the total number of possible sequences of that length.
The balance of the functional information was already in the AA sequence.
There is no such thing as “the balance of the functional information in the AA sequence”. You’re making stuff up Bill, and it’s nonsense.
If this is not true then you have no way to differentiate a garbage sequence then one that is only 1 AA away from function.
Except empirically of course. Test them. Which is actually the only way to do it, which is why Gpuccio’s extrapolation method based on the diversity of sequences present in known life doesn’t work. It doesn’t tell us what is out there in the space that has not been sampled.
If adding 1 AA or 4.3 bits could change any sequence into functioning ubiquitin then you would have a better case that the mutation was adding more than 4.3 bits of FI.
Bill, think, please just think. Take the ubiquitin sequence as-is, then find out which amino acid substitution renders it nonfunctonal. Presumably there is such a substitution which, if it happens, causes ubiquitin to become nonfunctional. You agree with this, right? There is such a thing as a mutation that can potentially destroy ubiquitin’s ability to function.
Okay, now pretend this mutation has happened. You now have a sequence that is not a functional ubiquitin sequence. It is one substition away from becoming a functional ubiquitin sequence if the right one(a reversal) happens.
What is the FI of the nonfunctional, mutated ubiquitin-sequence? Well since is can not perform the function of interest, it is zero. It’s level of function is below the minimal threshold, it is outside the “target set”(to borrow Gpuccio’s terminology). FI is calculated by taking -log2 of a ratio. The ratio is the number of sequences that can perform the function, divided by the total number of sequences of equal length.
Any sequence that can not perform the function, no matter how close it is in sequence space to one that can, is not included in the number of sequences that can perform the function. So only sequences that can perform the function, by definition, have any FI. The rest do not.
Edit: Edited for spelling.
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I thought it was the creationists that crapped on the chess board and declared victory 
Yeah I emplore you to stop doing it. Please.
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You may have spotted a weakness in the H and S definition of function as it cannot differentiate between garbage and almost function. That does not make Gpuccio’s answer stupid or it does not indicate that he does not know what he is talking about.
Your logic is fine based on strict definition in this case.
Bill instead of you playing this silly go-between game with gpuccio at UD why don’t you invite him back here? Ask him why he’s afraid to defend his own ideas in a venue which isn’t heavily censored and controlled like the UD site he is hiding. Let us know his reasons, OK?
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Why is that a weakness Bill? Just because it shoots down gpuccio’s argument? If gpuccio is free to make up his own custom definitions different from the accepted scientific ones then science is perfectly free to laugh at him then ignore him.
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He is working on other stuff to answer your first question. H an S definition does not differentiate between almost functional sequences and garbage sequences. This does not affect gpuccio’s measurements it simply showed up in T’s question and the answer becoming illogical based on H and S’s strict definition.
There is no need to change the definition but only to recognize the weakness.
You haven’t shown any weakness in it Bill. It’s their definition and they based their work around it. Like always you confuse your ignorance based personal opinions with fact.
You are gpuccio are free to make up your own pet definition and have it peer reviewed and published, but you won’t. Gpuccio couldn’t even deal with the criticisms of his claims he got here.
I think we have common ground I said there is no need to change the definition. If you think a definition that does not differentiate garbage sequences from almost functional is fine that’s up to you.
How do you differentiate between functional sequences and almost functional sequences Bill? You don’t even have a clue how many functional sequences exist, let alone how many almost functional sequences exist, or sequences with different functions which can be co-opted to perform the function of interest.
That’s a problem, isn’t it? For you, that is.
You say the protein, after the deletion that renders it non-functional, still contains FI, because it still has most of the structure of the functional protein.
But how would you detect all this FI if you only evaluate the sequence after the deletion, without knowing that it used to be part of a functional sequence? And if you cannot answer this question, then how can you answer it of any of the other trillions of variants in sequence space that have no discernible function?
This is just another way of asking you to acknowledge that problem that you have been trying to avoid all along. Maybe you could just actually answer it this time?
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We’re discussing a hypothetical that is not part of the real argument. If you and Tim really want to discuss this further please do among yourselves. I have made my argument.
More important than answering people’s questions honestly instead of running off to another forum to tell lies about them?
I respectfully disagree.
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A crucial part of your argument is the definition of functionality as a proportion of total sequence space. You must be able to answer this question in order to make that assessment. Of course, you are free to run away from answering the question yet again. We are all reasonably intelligent adults here, and are able to figure out how to interpret your refusal to answer.
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Pigeon chess again.
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As I said Fazil the definition from H and S is fine for gpuccio’s work. Have read their paper?
Please answer this question. I’ll make it as simple as I can:
Is it important for the argument you are trying to make that you be able to calculate the FI of a DNA sequence?
It’s the FI of an amino acid sequence.
You forgot to answer this question Bill.
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