Comments on Gpuccio: Functional Information Methodology

With all due respect, you are completely wrong here, as explained by @gpuccio below.

I was indeed wrong, but a lot less wrong that @gpuccio.

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If the scenario that you describe is real then the FI was already in the previous application as far as I can tell.

Who ever ends up being right is immaterial as the conversation is going to improve our understanding of functional information. Thanks for the thoughtful posts.

@gpuccio here is a reference point for the discussion. This definition is from Hazen and Szostak.

I(Ex) = ?log2[F(Ex)], where F(Ex) is the fraction of all possible configurations of the system that possess a degree of function ? Ex. Functional information, which we illustrate with letter sequences, artificial life, and biopolymers, thus represents the probability that an arbitrary configuration of a system will achieve a specific function to a specified degree. In each case we observe evidence for several distinct solutions with different maximum degrees of function, features that lead to steps in plots of information versus degree of function.

The safes example assumes independence (see 1 below). That is, the combinations and rewards (hence in $dollars) are part of a whole, not 101 independent parts. Each safe has $1. The firt safe has a 1-but combination the second a 2-bit combo, etc., up to a 100-bit combo for the last safe.
The first small safe with a 1-bit combination is quickly opened by thief, who gains $1 and 1-bit of the combination to the next safe. The second safe has a 2-bit combination, but using his 1-bit knowledge he only needs one more bit! The second safe is also soon opened gaining another $1 and 1 more bit. The thief proceed to open each safe in turn until all the safes are open, and walks out with $100.

Let’s make this harder - The thief does know how the safes are ordered, so it is not clear what order he should proceed.
He starts by entering “0” as the combination for all 100 safes, if one of the does not open, he goes around again and enters “1” as the combination, and one must open. The thief has gained $1 and 1-bit. 99 safes remain.
The thief repeats his task, starting with the bit(s) he knows and and adding 1-bit at a time until all the safes are open.

Additional notes:

  1. I am making the error of assuming only a single function, or a single set of safes, when the thief may have many to choose from. A combination that does not open a safe for a particular function might open a safe containing some other new and unexpected function.

  2. Another error! There is not just a single thief, but a population of thieves, each working to open the safes and sparing information.

  3. If the safe combinations allow extra bits beyond the correct combination, the thief can guess the next two or three bits, possibly opening several safes with each pass, greatly speeding his task.

  4. The thief ought to be flipping coins to choose bits instead of sequentially trying “0” and “1” bits. The thief will average 2 attempts per bit, but this does not substantially change the point I am making so I’m not going back to fix it! :wink:

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Gpuccio is, I think, assuming there is nothing for the thief can gain until some substantial number of correct bits are known. We could modify the example so the thief needs to guess more than 1-bit, at least at first. That would mitigate some of the easy gains for the thief I demonstrated, but opening the safes and gaining $100 is still far easier than claimed. I’m willing to give our busy thief a well earned rest. :slight_smile:

Looking at the original CARD11 example: The actual function of the matching protein in Saccoglossus kowalevskii seems to be unknown at this time, as it is only a predicted protein from analysis of the genome sequence (if I understand correctly). However, if it does have an analogous function, isn’t the divergence in sequence between Saccoglossus kowalevskii and humans suggestive of low functional information (as defined), since two very different proteins can achieve the same function? And if the two proteins don’t have analogous functions and we are just looking for the raw material to mutate into something that can carry out the function in humans/vertebrates, don’t we need to look at the DNA level rather than the protein level?

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The situation is a little more dynamic that this. The environment/ecosytem changes (change in weather, animal migration patterns, pathogens etc).

So it more like the safes code keeps changing every once in a while.
This is why evolution is a process that depended so much on “contingencies”.
In short biodiversity is a miracle that normally shouldn’t have happened.

How do you know?

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No, that’s not what I’m saying. I’m saying why can’t the accumulation in the same protein continue? There’s an antibody, it has some sequence. It mutates in the hypervariable region in a stretch of 6-10 amino acids, and over the course of a few weeks 50 FI (or whatever) is generated. Why could a larger portion of the antibody not continue mutating?

Why could the same thing not happen to 200 residues, out of a 600 amino acid protein over the course of 500 million years? In fact, isn’t this exactly what phylogenetics reveals to us has happened? We create a large tree of homologous proteins, and we see that along some lineages lots of mutations have accumulated in the protein during this time period?

Natural selection fixed the mutations in the antibody. Why can’t natural selection have fixed the mutations in the larger protein?

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Why doesn’t it? It seems to me that it does. There is an enormous amount of evidence that this has in fact happened to most proteins. You pull up a phylogeny of a large protein family with a common ancestral protein a billion years ago and you’ll see that has pretty much happened across every lineage leading to all the modern, extant members of the family we see today. Many substitutions have happened, some have had deletions, or insertions, or both.

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That does not follow logically.

It would be more correct to say that many of the errors made by creationists arise from their viewing contingencies as necessities.

This is a general statement. How did natural selection fix the the sequence?

Some mutants leave more offspring than others. You know, the usual way.

There’s a big population, they reproduce. Some in the population have deleterious mutations, some have neutral mutations, some have beneficial mutations. Those with beneficial mutations leave more offspring. Over time, they take over the population. Meanwhile, new mutations keep occurring, etc. etc.

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We are talking about an environment of antibodies right?

Bill there’s no reason for us to go through how mutations in antibodies affect the proliferation of successful antibody mutants in the immune system. You can go read about that on wikipedia.

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After close to a week it looks like we have ascertained the following:

  1. There is lots of evidence natural processes can produce over 500 bits of FI and no evidence it can’t.

  2. Gpuccio’s calculations are based on a strawman version of evolution which has nothing to do with actual evolutionary processes.

It seems Gpuccio’s FI hypothesis is dead in the water. The interesting thing will be to see if he attempts to modify it based on the fatal flaws it currently has.

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I am sure you feel this way Tim. You should read @swamidass last post very carefully.

Bill, what do you think I’m saying that is relevant? I can’t see any contradiction with what @Timothy_Horton wrote. Can you?

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