Comments on Gpuccio: Functional Information Methodology

I’d certainly be surprised if there ability to develop catalytic antibodies were a significant selective factor at the organismal level.

Well as stated earlier in the thread, binding exists on a continuum, and it’s almost never zero. Molecules always have some weak affinity to each other to begin with. If you’re going to say that this means an antibody recognizing a novel antigen can never amount to new FI, then the same will apply to basically any molecular interaction between molecules. Entire families of transcription factors, literally hundreds of DNA binding proteins that regulate different downstream genes, now contain no new FI, because they all evolved from previous DNA binding proteins by duplication and divergence.

Clearly there’s something fishy about the way you define the relationship between “new” FI and the actual functions of molecules, if you can say that several hundred different proteins contain no new FI because they all do the same thing: Bind DNA.

How much FI in this one gene? Well lets say 400 bits. Okay, so how about these two hundred and seventy other, equally complex genes? Still just 400 bits.


You could do the same with enzymes: Enzymes all catalyze chemical reactions, as in they speed them up and discriminate against side reactions. That’s the basic function of any enzyme. So tens of thousands of enzymes catalyzing novel chemical reactions can evolve by duplication from already existing enzymes, and you’d say no new FI is being created.

Tens of thousands of enzymes, tens of thousands of novel chemical reactions, radically different changes in chemistry. ZERO NEW FI.

There’s something wrong with your concept of functional information. There’s this thing wrong with it that, it’s obvious it’s been invented and defined in a way that allows you to always wiggle out of admitting that new FI has evolved.

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rumraket. i think that you missed my comment above.

I’m satisfied that the comment of mine you responded to explains why your subsequent comment is wrong. I don’t feel the need to rehash that any further.

The Tierra instruction set contains of 32 instructions. Any evolved Tierra ‘organism’ of length n will thus contain nlog(2)32 = 5n bits of information, so an ‘organism’ of length 100 will contain 500 bits of information. It’s not hard to adjust the Tierra settings* so that ‘organisms’ of that length evolve, including organisms with no redundant instructions (so they’re all functional) - especially if you start with a seed organism that uses a less compact reproduction algorithm* than the default one.

The ‘organisms’ generated by Dave Thomas’s Steiner tree GA consist of 4 3-digit numbers and 45 Boolean values, which works out at just under 85 bits of information - all of it functional. But that’s for a Steiner tree for ten nodes (six fixed, four variable) - it’s easy to modify the GA* for more nodes, and the 500-bit threshold would be exceeded by setting the GA to look for a Steiner tree connecting 32 nodes.

Similar to finding Steiner trees is the travelling salesman problem. This has been addressed by many different GAs, including at least one interactive web-based one that I can’t find at the moment. There are more than 10^130 possible traverses for a 100-city travelling salesman problem, so specifying any individual path takes more than 500 bits of information, and any path evolved by such a GA would likewise have more than 500 bits of non-redundant information.

Here is a report on successfully using a GA to create an algorithm to play checkers/draughts. It uses a neural network of 50 internal nodes and more than 1700 weighting values - so each possible network contains well in excess of 500 bits of information. Determining what proportion of that information is actually necessary (functional) is probably impossible, but even one bit per connection (e.g. on/off) would exceed 500 bits.

The GA I posted yesterday that finds routes from a starting point to a distant location represents routes by a series of angles representing directions to take. They’re specified in degrees, so have 6+ bits per angle. The version I posted generates paths that are typically 10 steps long, which is only about 60 bits per ‘organism’, but it can easily be updated* to generate paths that are 80+ steps long,** which require more than 500 bits - and they’re all functional, since without at least that number of steps the paths wouldn’t get close to the destination.

None of the ‘organisms’ produced by these GAs are designed, and none of them are biological. All of them contain more than 500 bits of information, and most wouldn’t work with less than that. In every case the search space exceeds 10^130 possibilities, and the target space is many orders of magnitude smaller.

I submit that these GA-generated ‘organisms’ are all non-biological, non-designed objects that exhibit high FI.

*I’ve done these things.
**It actually generated paths more than 200 steps long, which required considerably more than 500 bits to represent each path, but I’d hesitate to say it was all functional.


Gpuccio: “So why the many questions about ID theory, which I have been answering?”

I beg to differ. I’ve seen lots of hand waving, lots of repetition and restating of the original ID claims but none of the critical questions about ID have been answered.


Wow. As @glipsnort pointed out, you’re completely ignoring the literal generation of massive FI produced by recombination of V,D, and J segments in the germline.

That’s a truly staggering omission.

Why wouldn’t you look at the NEW FI produced by VDJ recombination?

No, most of the NEW FI is produced by recombination after birth. Why are you ignoring it?

The bottom line is that you’re ignoring the new FI produced by VDJ recombination. Why?

I do, however, give you credit for at least trying to address this.

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Arithmetic time.

The number of possible combinations of 28 letters/spaces is more than 10^40.
“METHINKS IT IS LIKE A WEASEL” is only one of those possible combinations.

The ratio of target space to search space is thus less than 1/10^40. This is about 120 bits of FI according to gpuccio’s definition.

Extending the quote to this: “METHINKS IT IS LIKE A WEASEL TO ME IT LOOKS LIKE A WEASEL IT IS BACKED LIKE A WEASEL IT DOES HAVE A BACK LIKE A WEASEL” gives a ratio of target space to search space of less than 1/10^166 - more than 500 bits of FI.

My python weasel implementation found it easily.*

No doubt gpuccio would say that this is possible because I knew the target sequence. Unfortunately for him it would work just as well if I didn’t know the target sequence - if it was generated randomly, for instance, or typed by some-one else.

*mutation frequency 5%, population 1000, no ratchet, 422 generations.

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So the scholarly discussion has been going on for a while, and I think it can be summarized briefly: @gpuccio is committing the Texas Sharp Shooter fallacy, a bunch of informed and experienced scholars are trying to explain this to him, and he cannot or will not get this.

Is that accurate?

No that’s not what I said. Just read the discussion and my comments in context.
I would just say that scientific explanations are incomplete and insufficient in themselves to explain life/biological diversity.
I think @Rumraket would acknowledge the possibility that scientific explanations are or atleast could be incomplete, while asserting that they are sufficient to account for the bio diversity observed.
@Rumraket can correct me if he disagrees.

I am not sure how @swamidass would put it. So I won’t make an attempt.

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That agrees with what I’ve seen.


I’m not sure.

I think it’s more that he doesn’t believe that the smoothness and continuity of a search space can make it much easier to find a target in it.

As some-one once said to me: “cold, cold, getting warmer, warm, very warm, hot, very hot, yes!”

Only partially. The much larger problem you are eliding is that there are multiple peaks of function and you are falsely assuming that there can be only a single one when you limit your observations to conservation. Catalytic antibodies are a fine example that refutes that assumption, as are regular antibodies.

Why don’t you try it with real-world, real-time data from catalytic antibodies?

Then it seems surprising to me that you would not have done so before going public.

I look forward to it. In the latter case, please don’t do as @Giltil just did and omit VDJ recombination and the fact that hundreds of B-cell clones react with a single antigen.


Gpuccio called for non-biological examples of systems exhibiting FI. I see nothing in his methods that makes any restrictions to semantic information.

Here is the original request:

And the request restated more clearly:

Any semantic property of FI, if there was any to start, is removed by expressing the information as a probability or “bits”.


@Mercer Please stop posting on the main thread. This is not your first offense. This goes for other people too.

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I disagree that it takes a mind to calculate, but I am applying the standard from computational theory, and you may have another standard?. I already stated that I cannot defend “evolution is calculating life”, that’s just the best description I can offer.

Randall Munroe has a much better description:

xkcd: A Bunch of Rocks.

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GA’s can also find good solutions to problems that do not have specific targets. There are many examples. I’ve used a GA for constrained maximization problems, resulting in unexpected answers.

I have an issue with your issue - where is there any requirement for a translated sequence. Star positions change over time, just very slowly as we see them. Weather configurations change very quickly!

“This change” is the difference from a hypothesis of random generation, which in no way resembles evolution. All it means is that natural selection is unlikely to be a purely random process. Do No Even Think About Moving The Goal Posts To Abiogenesis, that is not the current discussion.
The comparison here is to a strawman of a “normal expectation of randomness”, but no one expects evolution to be random.

This seems obvious to me, yet it comes up over and over. Perhaps a new thread is in order? (I might start one later, or you can).

It seems obvious because if I generate a sequence by flipping a coin 500 times, or any equivalent random series, I will have just exceeded the probabilistic resources of the universe.

You may respond that I haven’t specified the pattern in advance, but neither does this common argument from ID. Independent specification after the fact is difficult, since there may be patterns providing the same function that are never observed.

On a grander scale, the question of the Design or evolution of life itself, I seriously question the possibility of any independent specification when that specification is conditional on our own history and current existence. Our ability to ask these questions constitutes after the fact information, and no post hoc specification can be independent of our existence.

There will be limits to any physical system, true. If we applied an EA to some mathematical maximization problem, the algorithm may happily climb to infinity (or unto someone stops a runaway process). It would be better to say that FI will be monotonically increasing with time.

If we consider the history of aviation as an analogy to evolution, we see LOTS of feedback and selection from the first gliders to the most modern aircraft.

Are you sure about that? That’s surprising because it should be simple to demonstrate. It’s not really worth arguing about, or I’d bet I could Google some examples. ($20 maximum)

I didn’t omit VDJ recombination at all. I simply noted that this since this process doesn’t occur at the moment the humoral response is triggered by an antigen but has occurred before that event independently of the antigen, no NEW FI is produced by the Immune System (IS) at this step. That’s all. Would you dispute this rather obvious point?
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. This is why IDers would probably claim that the IS has been designed.
I am also looking forward @gpuccio’s analysis of the IS. No doubt it’s going to be an exciting and rewarding read.

Yes, but intelligent agents were not inactive during this process, were they?:wink:

I’m old enough to have seen previous rounds of “I have a theory”. This is (this is my theory which is mine) going nowhere.

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