Comments on Gpuccio: Functional Information Methodology

You said nothing at all about VDJ recombination. That’s what “omitting” means.

Note your statements:

You should really get together with yourself and sort this one out. If you thought that the immune system generates large amounts of FI (note: not “has” high FI content – generates high FI content), what was the point of posting a calculation purporting to show that it only generates 12 bits of FI?

Which is the kind of circular logic that discredits ID. Claim: “Only intelligent designers can create objects with lots of FI”. Response: “The suite of antibodies in an adult have lots of FI, and the immune system is not an intelligent designer.” ID conclusion: “See, that just proves the immune system was designed.”

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This is a generic statement. The devil is in the details. :slight_smile:

I think you are ignoring the cumulative nature of mutations. As the old saying goes, a walk of a thousand miles begins with one step.

If this process repeats over and over, as it does in life, then why wouldn’t this type of FI start to accumulate until we hit the 500 bit threshold?

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Yes. This one is so obvious it’s a mystery to me why many can’t see it. Mutations accumulate, they’re subject to natural selection, so their functions are selected and their information accumulates. The genetics of replication is EXACTLY the kind of thing that would produce a gradual increase in information, genes, functions, and so on.

Mutations even come in exactly the types required to sample the space of genetic solutions: Duplications, rearrangements, transpositions, substitutions, insertions, deletions.

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How would you measure the FI in a newly emerged protein that is found in a single species with no variation? It would be near zero, wouldn’t it? You only get increases in FI as the gene is passed down to subsequent populations and diverges in lineages that split from one another.

Why isn’t evolution searching for any genetic change that increases fitness? You need to explain this.

That’s what @glipsnort said:

What does evolve is just one possible solution that increases fitness. You seem to think that what we see is the ONLY possible solution. That’s the problem.

How many genes and species does Behe look at? I don’t see how looking at a handful of examples allows anyone to make general statements about all of biology.

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A post was split to a new topic: More questions for Gpuccio: biological or non-biological functional information?

Read up on open ended evolution in EAs. I think there are still prizes available for achieving it.
Not to mention the billions of dollars in business potential.

That would be omitting the step that generates the most FI.

It doesn’t make any sense.

No, they usually ignore it, as I don’t know of any who make such a claim.

So you are claiming that there is active design involved in all of the VDJ recombination going on in your body all the time? That seems to be trivializing ID.

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I[quote=“glipsnort, post:280, topic:7560”]
Note your statements:

Giltil:

The bottom line is that the amount of new FI produced by the immune system is, to say the least, ridiculously low compared to the 500 bits threshold required to draw a design inference.

Giltil:

Now, I don’t dispute the fact that the IS has high FI content. In fact, the FI of the IS is huge, no doubt about that. And no doubt that VDJ recombination contributes very significantly to this huge FI.

You should really get together with yourself and sort this one out. If you thought that the immune system generates large amounts of FI (note: not “has” high FI content – generates high FI content), what was the point of posting a calculation purporting to show that it only generates 12 bits of FI?
[/quote]

As far as the Immune system is concerned, two FIs are to be distinguished. The first one (let’s call it FIa) is the FI that is present BEFORE a given antigen has entered the body. The second one (let’s call it FIb) is the NEW FI produced AFTER the antigen has entered the body. What I said is that FIb is entirely produced during the somatic hypermutation process and has nothing to do whatsoever with the VDJ recombination process, so that charging me of omitting to mention VDJ recombination in my assessment of FIb is like charging me of omitting to mention Pinocchio!
The bottom line is that my two statements are not contradictory at all; I was referring to FIb in the first one and to FIa in the second one. I hope things are clear now.

Now, I would like to clarify a point regarding FIb. My calculation of FIb at 229 is wrong. I estimated it to be around 12 bits but it is clearly much higher, probability around 50 bits. This is quite a large amount of FI that the IS could not produced by a random walk. The trick here is that it succeeds in this task by resorting to the old friend of darwinists, ie., natural selection!

If natural selection can add 60 bits of FI in a few weeks, why can’t it add 500 bits of FI over the course of (say) 20 million years?

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This is a good question. I am wondering if @gpuccio, @glipsnort @swamidass or @Joe_Felsenstein can answer it.

And you didn’t mention the first one in any way until we pointed out that you had omitted any mention of VDJ recombination.

Even when @glipsnort mentioned VDJ recombination, you did not address it, while claiming that you were addressing “the immune system.” Limiting your reply to what happens in a first encounter with a foreign antigen omits much of what the immune system does.

That’s simply false. New FIa is CONSTANTLY being generated in our bodies. This fact alone falsifies @gpuccio’s hypothesis.

You never said anything of the sort. You did not mention VDJ recombination.

No, it is simply true. Your post hoc rationalization for omitting it makes no sense. Language differences don’t explain your omission, as French has the identical verb, omettre.

You are giving a very strong impression of evasiveness, because you’ve given zero justification for omitting FIa in your initial response, just as you’ve given no justification for not mentioning VDJ recombination, followed by your false denial of omitting it.

FIb is much smaller, but as @glipsnort showed, it easily exceeds 500 bits if one accurately describes the multiclonal nature of the immune response, which you also omitted.

I would like you to calculate FIa, including an explicit mathematical treatment of the fact that it is being increased in everyone’s bodies daily. If that’s design, we now have “when” answered; all the time. If this is scientific, what are your hypotheses for “who” and “how”?

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Bill,

Since you do applied math, why don’t you calculate the FI generated by constant VDJ recombination in real time?

I am confident that it dwarfs Gilbert’s FIb.

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If something like ubiquitin came about through a single mutation, what would be the measured FI for that new ubiquitin gene after that single mutation?

FI does not depend on the numer of steps that were needed to find the target. So, the FI would be the FI of ubiquitin, either it was found in 1 step or in 1 billion steps.

Of course, it is 1 billion times more likely to find the target in 1 billion steps then in 1 step.

You must not confound the FI with the probabilistic resources of the system. They are both important, but they are two different things.

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From my understanding, the FI calculation for ubiquitin includes all of the sequence variation seen in different species. Is that correct?

If we take all of that variation away and look at just pre-ubiquitin, a single mutation, and functional ubiquitin, what would the FI measurement be?

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The change in FI would be about 4.3 bits, at most, if I understand well what you are asking.

What is your calculation for the constant increase in FI for an individual human from VDJ recombination for immunoglobulin and T-cell receptor genes?

A daily value would be a good increment, don’t you think?

This whole discussion seems so far removed from how actual biological systems behave as to be completely meaningless.

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Then evolution would only need to produce 4.3 bits of FI in order to produce the functions you claim require 500 bits, correct?

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