Does gpuccio’s argument that 500 bits of Functional Information implies Design work?

On Uncommon Descent, poster gpuccio has been discussing “functional information”. Most of gpuccio’s argument is a conventional “islands of function” argument. Not being very knowledgeable about biochemistry, I’ll happily leave that argument to others.

But I have been intrigued by gpuccio’s use of Functional Information, in particular gpuccio’s assertion that if we observe 500 bits of it, that this is a reliable indicator of Design, as here, about at the 11th sentence of point (a):

… the idea is that if we observe any object that exhibits complex functional information (for example, more than 500 bits of functional information ) for an explicitly defined function (whatever it is) we can safely infer design.

I wonder how this general method works. As far as I can see, it doesn’t work. There would be seem to be three possible ways of arguing for it, and in the end; two don’t work and one is just plain silly. Which of these is the basis for gpuccio’s statement? Let’s investigate …

A quick summary

Let me list the three ways, briefly.

(1) The first is the argument using William Dembski’s (2002) Law of Conservation of Complex Specified Information. I have argued (2007) that this is formulated in such a way as to compare apples to oranges, and thus is not able to reject normal evolutionary processes as explanations for the “complex” functional information.  In any case, I see little sign that gpuccio is using the LCCSI.

(2) The second is the argument that the functional information indicates that only an extremely small fraction of genotypes have the desired function, and the rest are all alike in totally lacking any of this function.  This would prevent natural selection from following any path of increasing fitness to the function, and the rareness of the genotypes that have nonzero function would prevent mutational processes from finding them. This is, as far as I can tell, gpuccio’s islands-of-function argument. If such cases can be found, then explaining them by natural evolutionary processes would indeed be difficult. That is gpuccio’s main argument, and I leave it to others to argue with its application in the cases where gpuccio uses it. I am concerned here, not with the islands-of-function argument itself, but with whether the design inference from 500 bits of functional information is generally valid.

We are asking here whether, in general, observation of more than 500 bits of functional information is “a reliable indicator of design”. And gpuccio’s definition of functional information is not confined to cases of islands of function, but also includes cases where there would be a path to along which function increases. In such cases, seeing 500 bits of functional information, we cannot conclude from this that it is extremely unlikely to have arisen by normal evolutionary processes. So the general rule that gpuccio gives fails, as it is not reliable.

(3) The third possibility is an additional condition that is added to the design inference. It simply declares that unless the set of genotypes is effectively unreachable by normal evolutionary processes, we don’t call the pattern “complex functional information”. It does not simply define “complex functional information” as a case where we can define a level of function that makes probability of the set less than $2^{-500}$.  That additional condition allows us to safely conclude that normal evolutionary forces can be dismissed — by definition. But it leaves the reader to do the heavy lifting, as the reader has to determine that the set of genotypes has an extremely low probability of being reached. And once they have done that, they will find that the additional step of concluding that the genotypes have “complex functional information” adds nothing to our knowledge. CFI becomes a useless add-on that sounds deep and mysterious but actually tells you nothing except what you already know. So CFI becomes useless. And there seems to be some indication that gpuccio does use this additional condition.

Let us go over these three possibilities in some detail. First, what is the connection of gpuccio’s “functional information” to Jack Szostak’s quantity of the same name?

Is gpuccio’s Functional Information the same as Szostak’s Functional Information?

gpuccio acknowledges that gpuccio’s definition of Functional Information is closely connected to Jack Szostak’s definition of it. gpuccio notes here:

Please, not[e] the definition of functional information as:

“the fraction of all possible configurations of the system that possess a degree of function >=
Ex.”

which is identical to my definition, in particular my definition of functional information as the
upper tail of the observed function, that was so much criticized by DNA_Jock.

(I have corrected gpuccio’s typo of “not” to “note”, JF)

We shall see later that there may be some ways in which gpuccio’s definition
is modified from Szostak’s. Jack Szostak and his co-authors never attempted any use of his definition to infer Design. Nor did Leslie Orgel, whose Specified Information (in his 1973 book The Origins of Life) preceded Szostak’s. So the part about design inference must come from somewhere else.

gpuccio seems to be making one of three possible arguments;

Possibility #1 That there is some mathematical theorem that proves that ordinary evolutionary processes cannot result in an adaptation that has 500 bits of Functional Information.

Use of such a theorem was attempted by William Dembski, his Law of Conservation of Complex Specified Information, explained in Dembski’s book No Free Lunch: Why Specified Complexity Cannot Be Purchased without Intelligence (2001). But Dembski’s LCCSI theorem did not do what Dembski needed it to do. I have explained why in my own article on Dembski’s arguments (here). Dembski’s LCCSI changed the specification before and after evolutionary processes, and so he was comparing apples to oranges.

In any case, as far as I can see gpuccio has not attempted to derive gpuccio’s argument from Dembski’s, and gpuccio has not directly invoked the LCCSI, or provided a theorem to replace it.  gpuccio said in a response to a comment of mine at TSZ,

Look, I will not enter the specifics of your criticism to Dembski. I agre with Dembski in most things, but not in all, and my arguments are however more focused on empirical science and in particular biology.

While thus disclaiming that the argument is Dembski’s, on the other hand gpuccio does associate the argument with Dembski here by saying that

Of course, Dembski, Abel, Durston and many others are the absolute references for any discussion about functional information. I think and hope that my ideas are absolutely derived from theirs. My only purpose is to detail some aspects of the problem.

and by saying elsewhere that

No generation of more than 500 bits has ever been observed to arise in a non design system (as you know, this is the fundamental idea in ID).

That figure being Dembski’s, this leaves it unclear whether gpuccio is or is not basing the argument on Dembski’s. But gpuccio does not directly invoke the LCCSI, or try to come up with some mathematical theorem that replaces it.

So possibility #1 can be safely ruled out.

Possibility #2. That the target region in the computation of Functional Information consists of all of the sequences that have nonzero function, while all other sequences have zero function. As there is no function elsewhere, natural selection for this function then cannot favor sequences closer and closer to the target region.

Such cases are possible, and usually gpuccio is talking about cases like this. But gpuccio does not require them in order to have Functional Information. gpuccio does not rule out that the region could be defined by a high level of function, with lower levels of function in sequences outside of the region, so that there could be paths allowing evolution to reach the target region of sequences.

An example in which gpuccio recognizes that lower levels of function can exist outside the target region is found here, where gpuccio is discussing natural and artificial selection:

Then you can ask: why have I spent a lot of time discussing how NS (and AS) can in some cases add some functional information to a sequence (see my posts #284, #285 and #287)

There is a very good reason for that, IMO.

I am arguing that:

1) It is possible for NS to add some functional information to a sequence, in a few very specific cases, but:

2) Those cases are extremely rare exceptions, with very specific features, and:

3) If we understand well what are the feature that allow, in those exceptional cases, those limited “successes” of NS, we can easily demonstrate that:

4) Because of those same features that allow the intervention of NS, those scenarios can never, never be steps to complex functional information.

Jack Szostak defined functional information by having us define a cutoff level of function to define a set of sequences that had function greater than that, without any condition that the other sequences had zero function. Neither did Durston. And as we’ve seen gpuccio associates his argument with theirs.

So this second possibility could not be the source of gpuccio’s general assertion about 500 bits of functional information being a reliable indicator of design, however much gpuccio concentrates on such cases.

Possibility #3. That there is an additional condition in gpuccio’s Functional Information, one that does not allow us to declare it to be present if there is a way for evolutionary processes to achieve that high a level of function. In short, if we see 500 bits of Szostak’s functional information, and if it can be put into the genome by natural evolutionary processes such as natural selection then for that reason we declare that it is not really Functional Information. If gpuccio is doing this, then gpuccio’s Functional Information is really a very different animal than Szostak’s functional information.

Is gpuccio doing that? gpuccio does associate his argument with William Dembski’s, at least in some of his statements.  And William Dembski has defined his Complex Specified Information in this way, adding the condition that it is not really CSI unless it is sufficiently improbable that it be achieved by natural evolutionary forces (see my discussion of this here in the section on “Dembski’s revised CSI argument” that refer to Dembski’s statements here). And Dembski’s added condition renders use of his CSI a useless afterthought to the design inference.

gpuccio does seem to be making a similar condition. Dembski’s added condition comes in via the calculation of the “probability” of each genotype. In Szostak’s definition, the probabilities of sequences are simply their frequencies among all possible sequences, with each being counted equally. In Dembski’s CSI calculation, we are instead supposed to compute the probability of the sequence given all evolutionary processes, including natural selection.

gpuccio has a similar condition in the requirements for concluding that complex
functional information is present:  We can see it at step (6) here:

If our conclusion is yes, we must still do one thing. We observe carefully the object and what we know of the system, and we ask if there is any known and credible algorithmic explanation of the sequence in that system. Usually, that is easily done by excluding regularity, which is easily done for functional specification. However, as in the particular case of functional proteins a special algorithm has been proposed, neo darwininism, which is intended to explain non regular functional sequences by a mix of chance and regularity, for this special case we must show that such an explanation is not credible, and that it is not supported by facts. That is a part which I have not yet discussed in detail here. The necessity part of the algorithm (NS) is not analyzed by dFSCI alone, but by other approaches and considerations. dFSCI is essential to evaluate the random part of the algorithm (RV). However, the short conclusion is that neo darwinism is not a known and credible algorithm which can explain the origin of even one protein superfamily. It is neither known nor credible. And I am not aware of any other algorithm ever proposed to explain (without design) the origin of functional, non regular sequences.

In other words, you, the user of the concept, are on your own. You have to rule out that natural selection (and other evolutionary processes) could reach the target sequences. And once you have ruled it out, you have no real need for the declaration that complex functional information is present.

I have gone on long enough. I conclude that the rule that observation of 500 bits of functional information is present allows us to conclude in favor of Design (or at any rate, to rule out normal evolutionary processes as the source of the adaptation) is simply nonexistent. Or if it does exist, it is as a useless add-on to an argument that draws that conclusion for some other reason, leaving the really hard work to the user.

Let’s end by asking gpuccio some questions:
1. Is your “functional information” the same as Szostak’s?
2. Or does it add the requirement that there be no function in sequences that
are outside of the target set?
3. Does it also require us to compute the probability that the sequence arises as a result of normal evolutionary processes?

1,971 thoughts on “Does gpuccio’s argument that 500 bits of Functional Information implies Design work?

  1. vjtorley:
    Hi RoyLT.

    Are you kidding me? If we found a signal from interstellar space consisting of a short, repeating sequence of the first 100 primes, you would NOT infer that an intelligent being sent that signal until you found out how it was produced?

    So, do you really believe that people like Joe Felsenstein, John Harshman, Jerry Coine, PZ. Myers, Richard Dawkins, Larry Moran and many, many other sceptics would believe that the signal of repeating sequence of the first 100 primes, sent from interstellar space originated with intelligence, if its source could only be traced back to supernatural?

  2. J-Mac: So, do you really believe that people like Joe Felsenstein, John Harshman, Jerry Coine, PZ. Myers, Richard Dawkins, Larry Moran and many, many other sceptics would believe that the signal of repeating sequence of the first 100 primes, sent from interstellar space originated with intelligence, if its source could only be traced back to supernatural?

    Why does God need a starship?

  3. J-Mac: if its source could only be traced back to supernatural?

    Given that nothing in the entirety of human history has ever been “traced back to the supernatural” what makes you think that’s their position?

    Quotes or admit you are in error.

  4. colewd: High degree of function compared to what?

    Compared to the competing sequences in the population.

    colewd: Enrich means that the sequences are better then the previous ones.

    It means there will be more of them. Use another word if you don’t like the connotations.

    colewd: Where did these enriched sequences come from?

    They were already in the population. Ultimately, they originated in a mutational event.

    colewd: Can you make a real world example of how this works?

    Pretty much any example of natural selection you can think of, as they all result in an increase of the frequency of alleles that are associated with the fitter phenotype. Note that sometimes populations end up in an evolutionary cul-de-sac, showing that this process occurs without consideration of some ultimate target.

  5. gpuccio@UD

    First question: “I am very interested whether cnidarians have a functional copy of TRIM62 for example”

    Answer: The best hit in Cnidaria is 84.7 bits, and the lowest among the first 100 hits is 54.3 bits. The E-values are 2e-16 for the best hit, 8e-07 for the lowest.

    Not much, but enough to detect homology, due mainly to the RING finger domain. The proteins involved are labeled as:

    “tripartite motif-containing protein 3-like [Stylophora pistillata]”

    or:

    “E3 ubiquitin-protein ligase TRIM71-like [Stylophora pistillata]”

    or:

    “RING finger protein nhl-1 [Exaiptasia pallida]”

    and so on.

    So, to answer Corneel’s question, TRIM 62 as we oberve it in humans, a 475 AAs long protein with about 1000 bits of total potential functional information in BLAST comparisions, is not present in cnidaria, even if a low homology can be detected with other proteins having a similar RING finger domain.

    As already said, TRIM 62 appears rather suddenly in cartilaginous fish:

    E3 ubiquitin-protein ligase TRIM62 [Rhincodon typus]

    with 823 bits of homology and 80% identities to the human protein. That’s a jump indeed!

    Second question. “how they [cnidaria] pull that off without all the conserved information that humans have”

    Maybe I am missing the brilliant, subtle wisdom in this question.

    My simple answer is: because that protein is not needed in cnidaria. What’s the problem?

    Here is a paper about TRIM 62 (aka DEAR1):

    DEAR1 is a Chromosome 1p35 Tumor Suppressor and Master Regulator of TGF?-Driven Epithelial-Mesenchymal Transition

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4107927/

    And here is the OMIM page about the protein:

    https://www.omim.org/entry/616755

    Now, I would suggest an idea to Corneel, hoping that it is not too devastating for his worldview:

    Is it possible, maybe, that cnidaria are functionally different from vertebrates?

    Let’s see what he thinks.

    Thanks for answering my questions. However, I still cannot fully wrap my head around your scenario.

    First observation: you acknowledge homology, but say nothing about function. Since you are claiming that your definition of FI is close to that of Hazen-Szostak, that is a peculiar omission, and it was actually the precise function that was bothering me. Let me explain:

    You answer that the three homologs in cnidarians are not “TRIM62 as we oberve it in humans”. Well, no kidding. I do not think you are denying that the cnidarian homologs function as E3 ubiquitin-protein ligases and that they are capable of binding specific substrates (as they have the conserved RING-domain). That is, cnidarians do not carry around non-functional sequences that they inherited because they share some early part of the human evolutionary traject (which would be a ridiculous claim). But you deny that these genes function at the same degree of function as their human counterpart. Otherwise, why did they need to have added additional functional information? What was being added?

    So we move on to the next problem. Somehow I suspect your function incorporates the binding to specific human substrates. Of course, TRIM62 did not evolve from a protein that specifically binds a human protein, because the ancestor was not a human. But now I wonder: How could setting this function in your calculations of FI, instead of the generic function, NOT be Texas Sharp Shooting? After all, cnidarians (and many other orgaisms) are evidence that the specific human function of TRIM62, though strongly conserved, is completely dispensible in a eukaryotic cell with a fully functional ubiquitin system. That is an empirical observation 😉

    You failed Joe’s challenge to defend a general version of the 500-bit rule, but it looks like cannot even defend the 500-bit rule for your little castle of the ubiquitin system, since in that case it seems to depend on a little sleight of hand with regard to the definition of function in your functional information. Now, I could be misinterpreting your position. But I fail to see what functional information was being added in the human lineage, and you fail to make it explicit. If that function is not an improvement of E3 ubiquitin-protein ligase activity, but concerns the specific situation we happen to observe in humans, then how can you possibly avoid the allegation of Texas Sharp Shooting?

  6. So if there’s a version of the protein that is highly conserved, this proves it couldn’t evolve. Because reasons.

    But if the protein isn’t highly conserved and more divergent similar proteins exist, then this isn’t actually a similar protein at all (so not homologous, haven’t diverged from a common ancestor) and so both of them must have been conjured into existence because they couldn’t have evolved.

    LOL. Well played Gpuccio, well played.

    He’s basically looking at the two end-points at branches that diverged (connect to a node) over 700 million years ago, and saying: Look, these two proteins are very different, so couldn’t have evolved.

    I do wonder if Gpuccio thinks there’s some sort of cutoff. If I can find proteins with similarities to TRIM62 at say ~80%, 60%, 50%, and 30% similarity, does this then just mean there are MORE GAPS to fill in and so all of these distant similarities must each have been conjured into existence, or is that evidence the protein has just been diverging in sequence and function in the diversity of life over deep time?

  7. Corneel,

    After all, cnidarians (and many other orgaisms) are evidence that the specific human function of TRIM62, though strongly conserved, is completely dispensible in a eukaryotic cell with a fully functional ubiquitin system. That is an empirical observation

    Do you think it is completely dispensable in a human eukaryotic cell?

    We are observing a jump in information yet there seems to be no reason for the jump in your opinion.

    You seem to be trying to ignore an observed sequence. How well do you understand the function of the ubiquitin system?

  8. Corneel,

    colewd: Can you make a real world example of how this works?

    Corneel
    Pretty much any example of natural selection you can think of, as they all result in an increase of the frequency of alleles that are associated with the fitter phenotype.

    I can think of very few. This appears to be the exception and not the rule.

  9. colewd: Do you think it is completely dispensable in a human eukaryotic cell?

    We are observing a jump in information yet there seems to be no reason for the jump in your opinion.

    You seem to be trying to ignore an observed sequence. How well do you understand the function of the ubiquitin system?

    I think you misunderstood his point.

    He’s not saying eukaryotic cells can do just fine without a ubiquitin system, he’s saying the particular homologoue TRIM62 (found in humans, and homologous of it in many animals) is not critical for the existence of eukaryotic life (as cnidarians, aka jellyfish, have a very distant homologue of it known by another name). The fact that it isn’t called TRIM62 is irrelevant.

    So it doesn’t matter how conserved the category of proteins someone has decided to label as TRIM62 is, when you can find proteins at ~25% sequence similarity doing essentially the same job in animal life we share ancestry with 700-800 million years ago.

  10. colewd: Do you think it is completely dispensable in a human eukaryotic cell?

    No (at least not all of them). So what is special about that? Would you have predicted a protein with the specific substrate affinity of human TRIM62 to arise a priori, 700 million years ago, when we parted way with cnidarians? Or is that a contingent result?

    colewd: We are observing a jump in information yet there seems to be no reason for the jump in your opinion.

    Not quite true.

    You have not been following the discussion on FI very closely, have you? When you speak about “information”, do you mean the same thing that gpuccio means with it? Is that the functional information that we have been discussing and calculating? For a jump in functional information sensu Szostak to have taken place, the modern human copy needs to have acquired a higher degree of function. So what is that function in TRIM62?

    Whatever it is, gpuccio believes he can measure it by scoring the “human conserved functional information”. As has been explained to you (by Entropy, I believe), gpuccio simply blasts proteins and uses similarity to the modern human sequence. He assumes that conserved pieces are functionally important. That means that, in effect, the function we are looking at is “being similar to the modern human sequence”. That looks an awful lot like another weasel to me 🙂

    But to remain fair: some of the sequence similarity has been acquired a long time ago, so is probably conserved by purifying selection. I have no problem accepting that some proteins have rapidly acquired sequences that are currently subject to purifying selection in humans. I do have some doubts that gpuccio’s figures can show us if and when such episodes have taken place. But if they exist, they pose no threat to evolutionary theory, as they are compatible with episodes of rapid adaptive evolution.

    colewd: You seem to be trying to ignore an observed sequence. How well do you understand the function of the ubiquitin system?

    Getting better. And I have also invested in learning a bit about functional imformation. How about you?

  11. Rumraket,

    So it doesn’t matter how conserved the category of proteins someone has decided to label as TRIM62 is, when you can find proteins at ~25% sequence similarity doing essentially the same job in animal life we share ancestry with 700-800 million years ago.

    What makes you think it is doing the same job?

  12. Corneel,

    Getting better. And I have also invested in learning a bit about functional imformation. How about you?

    It is very surprising that you don’t believe new information was added to the ubiquitin system in the vertebrate lineage. I have studied it enough that I understand it is a regulation mechanism for proteins.

    As you add a new protein that needs to be regulated by the ubiquitin system you need to add a protein to the ubiquitin system in order to bind to and control that protein. An example is tagging the protein for destruction. This is the additional information we are observing in Trim 62.

  13. colewd: It is very surprising that you don’t believe new information was added to the ubiquitin system in the vertebrate lineage. I have studied it enough that I understand it is a regulation mechanism for proteins.

    You are mistaken about my beliefs. I do believe new information was added to the ubiquitin system in the vertebrate lineage. Heck, I will even say that it is functional information. What I am getting at is, if you can only describe the new function after it has arisen, it isn’t really that portentous any more. Pretending that it is, rightly deserves you the accusation of committing the lottery fallacy.

    colewd: As you add a new protein that needs to be regulated by the ubiquitin system you need to add a protein to the ubiquitin system in order to bind to and control that protein. An example is tagging the protein for destruction. This is the additional information we are observing in Trim 62.

    Quite right, but that is the additional information that we observe in every E3 ubiquitin-protein ligase. Each and every one of them brings the loaded E2 ubiquitin-conjugating enzyme in proximity of some substrate S. So if that is the function you describe in your functional information, than verily no information has been added whatsoever.

    Consider this: in order to acquire substrate specificity for the modern human substrate, the early precursor of TRIM62 probably lost affinity for a number of other potential substrates, losing functional information as it did. So what is so special about the functional information it acquired?

  14. vjtorley: Are you kidding me? If we found a signal from interstellar space consisting of a short, repeating sequence of the first 100 primes, you would NOT infer that an intelligent being sent that signal until you found out how it was produced?

    I’m not kidding at all, but you’ve just changed the example. The example we discussed in the previous comment was something (e.g. a wormhole) that we have no understanding of or ability to build ourselves. I’d still like an answer as to why you would personally draw a design inference in the case of multiple wormholes near habitable planets when you wouldn’t with a single one.

    We as humans have a ton of experience generating repeating sequences (with caveats as petrushka mentioned). So, sure, SETI receiving a repeating signal of the first 100 primes would be viewed as evidence of intelligence. But that is a very different example since we already have personal experience with a type of being that broadcasts repeating non-random signals (who), some of the methods used to broadcast such signals (how), and the motivation for broadcasting such signals (why).

    Without knowledge of who/how/why (as in my wormhole example), I don’t think that a design inference would make sense and it would certainly have no explanatory power as we wouldn’t have the slightest clue where to look for more information.

  15. J-Mac: …and many, many other sceptics would believe that the signal of repeating sequence of the first 100 primes, sent from interstellar space originated with intelligence, if its source could only be traced back to supernatural?

    Care to explain how we could trace something back to the supernatural?

  16. Corneel,

    What I am getting at is, if you can only describe the new function after it has arisen, it isn’t really that portentous any more. Pretending that it is, rightly deserves you the accusation of committing the lottery fallacy.

    Are you condemning all historical sciences?

  17. Corneel: Consider this: in order to acquire substrate specificity for the modern human substrate, the early precursor of TRIM62 probably lost affinity for a number of other potential substrates, losing functional information as it did.

    If fewer sequences meet the minimum degree of function then the FI is higher.

  18. Corneel: But if they exist, they pose no threat to evolutionary theory, as they are compatible with episodes of rapid adaptive evolution.

    I’ll have some of that too please.

  19. colewd: Me: What I am getting at is, if you can only describe the new function after it has arisen, it isn’t really that portentous any more. Pretending that it is, rightly deserves you the accusation of committing the lottery fallacy.

    Are you condemning all historical sciences?

    Damn, they are on to me!

  20. Mung: If fewer sequences meet the minimum degree of function then the FI is higher.

    What function would that be?

  21. Corneel: What function would that be?

    It depends. It’s all relative.

    Pick one of the following:

    the early precursor of TRIM62 probably lost affinity for a number of other potential substrates

    So you appear to be defining it as affinity to some specific substrate which you didn’t name.

  22. Mung: It depends. It’s all relative.

    Pick one of the following:

    the early precursor of TRIM62 probably lost affinity for a number of other potential substrates

    So you appear to be defining it as affinity to some specific substrate which you didn’t name.

    Exactly. Note that the functional information we have been using requires you to specify the function you are interested in (and be able to quantify it). Gpuccio likes to set it to “binding the substrate it binds now” because then the FI went UP, by definition. To demonstrate how arbitrary this is, I just set it to “binding the substrate it used to bind”, because then the FI went DOWN, by definition.
    So what makes the former special? E3 ubiquitin-protein ligases need to bind some substrate, right?

  23. Corneel: Gpuccio likes to set it to “binding the substrate it binds now” because then the FI went UP, by definition.

    No, that is incorrect. He is allowed to pick the function and threshold that he wants to without naysaying from the naysayers. Unless you care to say that there are more sequences that match the function he chose and exceed the threshold he chose (iow, more sequences “above the plane” than he is allowing for).

    To demonstrate how arbitrary this is, I just set it to “binding the substrate it used to bind”, because then the FI went DOWN, by definition.

    It’s ALL arbitrary. You can choose your function and your threshold but it it no way
    invalidates his.

    Your’s doesn’t make the FI go down. Your’s is just as arbitrary, and perhaps even more so, because you don’t know the ancestral function nor the ancestral threshold for binding. Your’s is pure handwaving.

  24. keiths: Damn, Mung. After all this time, you still don’t understand how Weasel works?

    Damn, keiths. After all this time, you still don’t understand how logic works?

    No, Weasel doesn’t work by climbing steps to the top of a mountain.

  25. colewd: Are you condemning all historical sciences?

    As far as I’m aware they have been functionally characterized for at least some species.

    But if we suppose they don’t perform the same ubiquitylation-related functions in cnidarians that implies they don’t have a ubiquitylation-system at all, which means there are eukaryotes that can live without it.

  26. Mung: It’s ALL arbitrary. You can choose your function and your threshold but it it no way invalidates his.

    Your’s doesn’t make the FI go down. Your’s is just as arbitrary, and perhaps even more so, because you don’t know the ancestral function nor the ancestral threshold for binding. Your’s is pure handwaving.

    Precisely right *. But at least I am not trying to accumulate a gazillion bits of “functional information” (without clearly specifying which function) just to get above some arbitrary 500-bit threshold. If gpuccio had made it clear that the amazing 680 bit jump that occurs in TRIM62 in the transition to the vertebrate lineage was mostly caused by a simple shift in substrate affinity, but that it still functions as an E3 ubiquitin-protein ligase, just like it had always done, then it wouldn’t have looked quite so impressive, would it? Especially since we know that most E3 ubiquitin-protein ligases bind multiple substrates, many of them spuriously (gpuccio is denying this of course, saying this is all specific).

    Specifying the function in functional information matters, Mung. Otherwise it is just obfuscation.

    ETA: * (except the arbitrary threshold part)

  27. Corneel: If gpuccio had made it clear that the amazing 680 bit jump that occurs in TRIM62 in the transition to the vertebrate lineage was mostly caused by a simple shift in substrate affinity

    Note that I am giving gpuccio a LOT of leeway here. So far the only function he has characterized is “resembling the modern human sequence”. That is essentially the same as the weasel.

  28. Mung: If fewer sequences meet the minimum degree of function then the FI is higher.

    Why does that matter to the question of whether it could have evolved? The minimum degree of function is, as you say, just arbitrarily declared.

    What use is it to arbitrarily define the minimum degree of function against a specific substrate such that only a particular subcategory of E3 ubiquitin-protein ligases that we label “TRIM62” meet it, and then declare that because this arbitrarily defined limit entails >500 bits of FI, then it couldn’t have evolved from an ancestor with a broader, or even less substrate specificity?

    The TRIM62 homologoues found in vertebrates apparently evolved from an even older common ancestor that also functioned as an E3 ubiquitin-protein ligase, given that similar proteins exist in species as divergent as prokaryotes (archaea). Why can’t that have happened gradually over deep time under natural selection? How does arbitrarily deciding on a minimun degree of function that entails 500 bits FI imply it couldn’t have evolved?

    I don’t see how this whole information-gibberish even advances the design argument at all. It doesn’t tell us anything meaningful or useful. It just appears like fancy technobabble designed to make the idea of a “design inference” sound sciency. It’s pretension. Like dressing up in a lab coat and getting a “doctorate” from a creationist diploma mill. In the end the IDcreationist argument from information is no less a ridiculous act of theater designed to impress faithheads than fucking Kent Hovind and his “PhD” from “patriot bible university“.

  29. Rumraket: Why does that matter to the question of whether it could have evolved?

    Your guess is as good as mine.

    The minimum degree of function is, as you say, just arbitrarily declared.

    It seems we once again manage to find ourselves in agreement.

  30. dazz: Poor Mung doesn’t understand FI, nor the weasel, of course

    Did you miss the part where DNA_Jock said that you were committing the TSS?

  31. Corneel: Specifying the function in functional information matters, Mung.

    Of course it does. And I have always said it does. Did DNA_Jock specify a function or a metric?

    Is there some disagreement about whether gpuccio specified a function or not? You seem to be accepting that he has done. So where’s the problem?

    You realize, don’t you, that whether some sequence can serve some other function is irrelevant.

  32. Rumraket: What use is it to arbitrarily define the minimum degree of function against a specific substrate such that only a particular subcategory of E3 ubiquitin-protein ligases that we label “TRIM62” meet it, and then declare that because this arbitrarily defined limit entails >500 bits of FI, then it couldn’t have evolved from an ancestor with a broader, or even less substrate specificity?

    I give up. What use is it?

    Why can’t that have happened gradually over deep time under natural selection?

    Do you believe it did? Is this another one of those cases where the evidence has been lost? Why can’t that have happened gradually over deep time under neutral evolution?

    How does arbitrarily deciding on a minimun degree of function that entails 500 bits FI imply it couldn’t have evolved?

    The implication is that there has not been enough time or resources to perform a search requiring that many bits of information.

  33. Rumraket: I don’t see how this whole information-gibberish even advances the design argument at all. It doesn’t tell us anything meaningful or useful.

    We already know that life is designed, so I agree with you that we’re not learning anything we don’t already know.

    🙂

  34. Mung: We already know that life is designed, so I agree with you that we’re not learning anything we don’t already know.

    Thank you for once again uttering that completely unsupported opinion. If all your “methods” used to support that claim to knowledge are actually vacuous then one wonders how it is you “know” life was designed. Please give me your best argument for the design of life. How do you know it was designed?

  35. Rumraket: How do you know it was designed?

    Some things are just blatantly obvious. Haven’t we already had this conversation?

  36. Mung: Do you believe it did?

    Is this another one of those cases where the evidence has been lost?

    No that evidence actually exists: The fact that homologous ubiquitylation systems pretty much exists across the diversity of life.

    Why can’t that have happened gradually over deep time under neutral evolution?

    Good point, I don’t think blathering about “bits” makes you able to rule that out either. it is entirely plausible that in large part the various ubiquitylation proteins have been drifting apart over deep time, not necessarily been forced apart by positive selection.

    The implication is that there has not been enough time or resources to perform a search requiring that many bits of information.

    That is the claim, it’s just not obvious what supports it. It seems to be based primarily on our purported ignorance of ancestral states. Basically the ID argument says that if we can’t show how those 500 bits evolved, we should a priori conclude design.

    Even more preposterously, if we CAN show a gradual increase in function Gpuccio will claim it doesn’t exhibit 500 bits of FI.

  37. Mung: Rumraket: Why does that matter to the question of whether it could have evolved?

    Your guess is as good as mine.

    The minimum degree of function is, as you say, just arbitrarily declared.

    It seems we once again manage to find ourselves in agreement.

    Good, have you asked Gpuccio why he puts the limits where he does?

  38. Rumraket: Even more preposterously, if we CAN show a gradual increase in function Gpuccio will claim it doesn’t exhibit 500 bits of FI.

    I would probably disagree with him over that, esp if we are talking Hazen/Szostk FI. It’s obvious that as the required specificity increases the FI value will be higher. But we always have to remember that the FI is always relative to a specific function.

    Rumraket: The fact that homologous ubiquitylation systems pretty much exists across the diversity of life.

    I don’t think gpuccio disagrees with that. Doesn’t he look at the homologs and calculate the FI for them as well?

  39. Mung: I don’t think gpuccio disagrees with that. Doesn’t he look at the homologs and calculate the FI for them as well?

    Yes and no, he arbitrarily sets a limit (somewhere above 80% similarity) where only the version of the protein called TRIM62 qualifies (so he does include homologous proteins above a certain threshold). If it has lower similarity (like 25-30% for TRIM71 and others), he simply discounts them.

  40. Joe Felsenstein: I sense that maybe Mung’s problem is that Mung thinks that when we say “function” we mean only nonzero function.

    I think my problems go far deeper than that. I am a middle child.

  41. Mung,

    We already know that life is designed, so I agree with you that we’re not learning anything we don’t already know.

    Large information jumps is additional evidence of how life was designed. Somehow I don’t think I am saying anything new to you:-)

  42. Hi RoyLT,

    We as humans have a ton of experience generating repeating sequences (with caveats as petrushka mentioned). So, sure, SETI receiving a repeating signal of the first 100 primes would be viewed as evidence of intelligence. But that is a very different example since we already have personal experience with a type of being that broadcasts repeating non-random signals (who), some of the methods used to broadcast such signals (how), and the motivation for broadcasting such signals (why).

    That’s not how Carl Sagan portrayed the discovery of the sequence in his novel Contact (Simon & Schuster, 1986):

    “No, look at it this way,” she said smiling. “This is a beacon. It’s an announcement signal. It’s designed to attract our attention. We get strange patterns of pulses from quasars and pulsars and radio galaxies and God-knows-what. But prime numbers are very specific, very artificial. No even number is prime, for example. It’s hard to imagine some radiating plasma or exploding galaxy sending out a regular set of mathematical signals like this. The prime numbers are to attract our attention.”

    But what for?” he had asked, genuinely baffled.

    I don’t know. But in this business you have to be very patient. maybe in a while the prime numbers will turn off and be replaced by something else, something very rich, the real message. We just have to keep on listening.”

    This was the hardest part to explain to the press, that the signals had essentially no content, no meaning – just the first few hundred prime numbers in order, a cycling back to the beginning, and again the simple binary arithmetic representations: 1, 2, 3, 5, 7, 11, 13, 17, 19, 23, 29, 31,…

    She tried to make a bigger leap, into the mind of someone who was enormously, orders of magnitude, more intelligent than she was, smarter than Drumlin, say, or Eda, the young Nigerian physicist who had just won the Nobel Prize. But it was impossible. She could muse about demonstrating Fermat’s Last Theorem or the Goldbach Conjecture in only a few lines of equations. She could imagine problems enormously beyond us that would be old hat to them. But she couldn’t get into their minds; she couldn’t imagine what thinking would be like if you were much more capable than a human being. (pp. 85-87)

    So, no “who” and no “why,” and the bare minimum on “how” – and yet the inference to an intelligent source is readily made. (By the way, as you’ve probably noticed, Sagan makes a couple of mathematical mistakes in the passage quoted above: he counts 1 as a prime and claims falsely that there are no even primes, overlooking the number 2.)

    I’d still like an answer as to why you would personally draw a design inference in the case of multiple wormholes near habitable planets when you wouldn’t with a single one…

    Without knowledge of who/how/why (as in my wormhole example), I don’t think that a design inference would make sense and it would certainly have no explanatory power as we wouldn’t have the slightest clue where to look for more information.

    If all wormholes turned out to be near habitable planets, that would be a very striking fact, not at all to be expected under the hypothesis that they arose naturally. If, however, they were created by aliens, then that would be precisely what you would expect. Using Bayes’ Theorem, one can show that given enough such wormholes near habitable planets, the design hypothesis would become the more probable one.

    As to where to look for more information: I’d look for wormholes located near old stars, until I found the oldest one in the galaxy. That would tell us when and where the technology was invented. Next, I’d try to ascertain whether the alien technology was transmitted to other civilizations, or discovered by them independently, by looking at the spatial distribution pattern of wormholes in the galaxy. That might give us a hint.

    Hope that helps.

  43. Hi J-Mac,

    So, do you really believe that people like Joe Felsenstein, John Harshman, Jerry Coyne, PZ. Myers, Richard Dawkins, Larry Moran and many, many other sceptics would believe that the signal of repeating sequence of the first 100 primes, sent from interstellar space originated with intelligence, if its source could only be traced back to supernatural?

    Richard Dawkins is not 100% sure that God does not exist, and Jerry Coyne has acknowledged that there is scientific evidence which would make him believe in God, at least provisionally. PZ Myers, on the other hand, has said that nothing could convince him of the existence of God: he thinks the very concept is self-contradictory, as does the philosopher A. C. Grayling. I’m not sure what the other individuals you listed think, regarding the possibility of scientific evidence for the supernatural.

  44. vjtorley: So, no “who” and no “why,” and the bare minimum on “how” – and yet the inference to an intelligent source is readily made.

    vjtorley: “This is a beacon. It’s an announcement signal. It’s designed to attract our attention. We get strange patterns of pulses from quasars and pulsars and radio galaxies and God-knows-what. But prime numbers are very specific, very artificial.

    “It’s designed to attract our attention” sounds very much like a ‘why’ to me. Sending a very conspicuously non-random signal like that into space has a very clear motivation – to ‘Contact’ life on other planets. And while the identity of the sender is unknown, the type of being (intelligent, corporeal) is obvious within the context of the example.

    ETA- Corporeal was probably too specific as a software based AI being would probably be a candidate as well.

  45. vjtorley: If all wormholes turned out to be near habitable planets, that would be a very striking fact, not at all to be expected under the hypothesis that they arose naturally. If, however, they were created by aliens, then that would be precisely what you would expect

    I would certainly be inclined to agree with you on this. However, my reason for agreeing is primarily that a clear correlation between wormholes and habitable planets would suggest some possible motivations (seeding life, monitoring) for their placement, whereas a single anomaly would not.

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