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. DNA_Jock: I don’t see how this will help, but here goes: 99.8% of sequences in the space have no effect on apoptosis. 0.1% have an adaptive effect. Minus logbase2(1/1000) = 10

    I don’t see how that helps either. 🙂

  2. Joe Felsenstein: I am just puzzled why they think that evolution is unable to climb the nearest peak in the fitness surface, but once it is there, that after a while it has somehow explored all the others, so we can use that as evidence that they don’t exist.

    I know, right? It’s like looking at a microwave radio tower on a mountain peak and then exclaiming “look at all the other peaks it could have been on!”

    TSS indeed.

  3. Corneel: Difficult, because gpuccio does not explicitely state that he excludes FI introduced by natural selection.

    I don’t blame him. There is no such thing as FI introduced by natural selection.

    Joe gets that.

  4. Joe Felsenstein: So they are not using Szostak’s definition, but instead one that, among other things, calculates a totally useless quantity.

    And the quantities given us by using the Szostak definition are useful for what?

  5. colewd: Since cytochrome c has very little sequence conservation across living organisms gpuccio will also get a low bit score. Lots of different workable solutions seems to correlate with low sequence preservation.

    So 83% identical between humans and corbicula fluminea (the freshwater clam) is “very little sequence conservation”. Or were you perhaps thinking of a different protein?

    Additionally, he needs to demonstrate that he’s done the calculation for all relevant functions.

    Enough that he has captured most the variation. Statistical samples and such.

    ROFL. The thing with “statistical samples”, Bill, is that they have to be *representative*. “Functions that gpuccio thought of” don’t cut the mustard. At all. You have admitted that any protein might have additional “specified” functions about which we know nothing. Makes figuring out how many sequences have a minimal selectable function that leads to the observed sequence tricky…

  6. Mung:

    Joe Felsenstein: So they are not using Szostak’s definition, but instead one that, among other things, calculates a totally useless quantity.

    And the quantities given us by using the Szostak definition are useful for what?

    Szostak’s definition does not pretend to say anything about Design.

    My complaint about uselessness was not compared to Szostak, but compared to what gpuccio and colewd think their version does for us. They argue that 500 bits of FI implies design. But by calculating it only after they have us determine that the adaptation cannot have happened by ordinary evolutionary processes, they require us to reject evolutionary processes by some other unspecified means, before we get to calculate the quantity whose size indicates that evolutionary processes can be rejected.

    So the number becomes a useless tack-on to their own agument.

  7. Mung: I know, right? It’s like looking at a microwave radio tower on a mountain peak and then exclaiming “look at all the other peaks it could have been on!”

    TSS indeed.

    No, that’s not at all what gpuccio and colewd are doing.

  8. DNA_Jock,

    So 83% identical between humans and corbicula fluminea (the freshwater clam) is “very little sequence conservation”. Or were you perhaps thinking of a different protein?

    Yet 30% ID with bacteria. Guess that apoptosis function is adding a butt load of FI:-)

  9. Joe Felsenstein,

    They argue that 500 bits of FI implies design. But by calculating it only after they have us determine that the adaptation cannot have happened by ordinary evolutionary processes, they require us to reject evolutionary processes by some other unspecified means, before we get to calculate the quantity whose size indicates that evolutionary processes can be rejected.

    So are you making the positive claim that evolutionary processes can produce 500 bits of FI? Are you making the claim that evolutionary processes can produce unlimited FI?

  10. DNA_Jock,

    You have admitted that any protein might have additional “specified” functions about which we know nothing. Makes figuring out how many sequences have a minimal selectable function that leads to the observed sequence tricky…

    Are you saying that finding additional function on proteins makes your claim that evolution can build 500 bits of functional information easier?

  11. colewd,

    they require us to reject evolutionary processes by some other unspecified means,

    The means is the observation of a functional protein with 120 conserved AA’s across species over deep time. This causes rejection of the null. You may not agree but gpuccio has clearly articulated the method.

  12. colewd:
    The means is the observation of a functional protein with 120 conserved AA’s across species over deep time. This causes rejection of the null.

    The null being that the two proteins are that similar by chance. Since that’s rejected, they must be that similar for some other reason, the most reasonable being that they share common ancestry.

    colewd:
    You may not agree but gpuccio has clearly articulated the method.

    And the method has fundamental problems. For one, as I and Rum keep repeating, that it measures the conservation of proteins that diverged from a protein that was already at a local minimum. We should therefore expect them to have a tendency towards being conserved if they keep performing the same, or a similar, function. There’s other problems, but let’s see if we can get you to understand this one. What say you?

  13. colewd: Yet 30% ID with bacteria. Guess that apoptosis function is adding a butt load of FI:-)

    No, 82%.
    Like I said, perhaps you were thinking of a different protein?

  14. colewd: Are you saying that finding additional function on proteins makes your claim that evolution can build 500 bits of functional information easier?

    You fail to comprehend. I am saying that the more paths there are to a particular protein, the more difficult it will be for gpuccio to figure out whether evolution could do it or not.
    But, since you mentioned it, it is also true that the more paths there are, the easier it is to evolve to something that gpuccio would score as 500 bits of gpuccio-FI.

  15. Entropy,

    And the method has fundamental problems. For one, as I and Rum keep repeating, that it measures the conservation of proteins that diverged from a protein that was already at a local minimum. We should therefore expect them to have a tendency towards being conserved if they keep performing the same, or a similar, function. There’s other problems, but let’s see if we can get you to understand this one. What say you?

    At some point E you need to explain the origin of the sequence that common ancestry is preserving. You can start with the beta chain of F1 of ATP synthase.

    300 AA sequences preserved over a billion years and your explanation is that it fell in that hole where that hole is the size of a pin and the space it is traversing is the size of the universe.

  16. colewd: 300 AA sequences preserved over a billion years and your explanation is that it fell in that hole where that hole is the size of a pin and the space it is traversing is the size of the universe.

    The mouth of the hole is wider than the bottom of the hole, and the mouth of the hole is surrounded by a big bowl.
    The lack of freedom at the bottom of the crevice is not indicative of the landscape above. We’ve been trying to get you to look at the Hayashi figure for a while now.

  17. DNA_Jock,

    The mouth of the hole is wider than the bottom of the hole, and the mouth of the hole is surrounded by a big bowl.
    The lack of freedom at the bottom of the crevice is not indicative of the landscape above. We’ve been trying to get you to look at the Hayashi figure for a while now.

    The mouth is the pinhead the bottom is a proton. The visual of the Hayashi paper is more than misleading conceptually.

  18. DNA_Jock,

    But, since you mentioned it, it is also true that the more paths there are, the easier it is to evolve to something that gpuccio would score as 500 bits of gpuccio-FI.

    So given 70 randomly generated AA’s you would bet on it binding to two different substrates over 1?

  19. colewd: So given 70 randomly generated AA’s you would bet on it binding to two different substrates over 1?

    ROFL no.
    Your strawman is “Linda is a bank teller.”
    Given a particular optimized sequence, I would be less surprised by its existence if there were multiple ways that it could have evolved.
    Your strawman is precisely backwards, temporally.

    colewd: The mouth is the pinhead the bottom is a proton. The visual of the Hayashi paper is more than misleading conceptually.

    Yet the authors state:

    The evolvability of arbitrary chosen random sequence suggests that most positions at the bottom of the fitness landscape have routes toward higher fitness.

    Strange, that.

  20. DNA_Jock,

    The evolvability of arbitrary chosen random sequence suggests that most positions at the bottom of the fitness landscape have routes toward higher fitness.
    Strange, that.

    Yet a library of 10^70 to find the wild type with 35 specific required AA”s.

    The beta chain we have been discussing has north of 300 preserved AA’s over 1 billion years.

  21. DNA_Jock,

    Given a particular optimized sequence, I would be less surprised by its existence if there were multiple ways that it could have evolved.

    How much less surprised?

  22. colewd:
    At some point E you need to explain the origin of the sequence that common ancestry is preserving.You can start with the beta chain of F1 of ATP synthase.

    I’m certainly curious about that, and I think there’s plenty of explanations. However, instead of showing you things we have explained before, I’d rather ask you to acknowledge that you understand the problem (if you do understand it). If you don’t understand the problem, then we should fix that first. rather that having you avoiding it, only to keep insisting that gpuccio’s analysis shows something it doesn’t show. Do you understand this?

    colewd:
    300 AA sequences preserved over a billion years and your explanation is that it fell in that hole where that hole is the size of a pin and the space it is traversing is the size of the universe.

    It is painfully obvious that if two homologous sequences perform the same function, and they share 300 preserved amino-acids (out of some higher number), then the sequences diverged from a common ancestor that was already performing that function, and thus, was already at a local minimum. It doesn’t matter how it got there for this to be a problem with gpuccio’s analysis.

    From those conserved amino-aicds, however, you cannot say anything about the depth, shape, and size of the “hole.” You cannot say anything about the number of holes either. All you can talk about is the relative time since those sequences diverged, and the amount of room at the bottom of their particular “hole.”

    I thus insist, it’s not the same to dance around a local minimum, as getting to a local minimum.

    Do you understand the problem yet?

  23. Entropy,

    From those conserved amino-aicds, however, you cannot say anything about the depth and size of the “hole.” All you can know is the relative time since those sequences diverged, and the amount of room at the bottom of that “hole.”

    So, do you understand the problem yet?

    There is empirical data telling us about the depth and size of the whole with highly preserved sequences. In the Hayashi paper a wild type protein required 35 specific AAs. The beta chain requires 300 specific AAs. When a substitution occurs so does purifying selection.

  24. Yikes, Bill,

    No, that’s not what I am saying. Did I say anything about binding two proteins? Did I say anything about having to perform two functions? Really, get a grip.

    I am enjoying your claim that (in gpuccio-speak) there is a massive (and unexplained by apoptosis) injection of FI between Caldithrix abyssi and Herbaspirillum rubrisubalbicans (“Still just a bacterium”) and then scarcely any change at all from Herbaspirillum through clams and crocodiles, baboons and humans. Positively weird, that.
    ETA: I note that colewd has edited his post to remove the “Having to bind two proteins” idiocy that he originally posted, and I replied to. There’s hope for him yet…

  25. colewd:
    There is empirical data telling us about the depth and size of the whole with highly preserved sequences.

    Again, no. The preserved sequences only show you the amount of dancing around a local minimum. Nothing about the depth shape, and size of the hole. Again, the most it would tell you is the relative time since divergence and a bit of information about the shape of the bottom of the hole.

    colewd:
    In the Hayashi paper a wild type protein required 35 specific AAs.

    I don’t think you’re reading that paper correctly. But I prefer to keep the focus on the problem I’d like you to understand:

    colewd:
    The beta chain requires 300 specific AAs.When a substitution occurs so does purifying selection.

    You don’t know if it requires that number of amino-acids, but if so, it requires them to keep at its local minimum. That, again, doesn’t tell you anything about whether there’s other holes or not. Nothing about the depth and nothing about overall shape of that particular hole.

    Really, Bill, this is like saying that because I dance around at the bottom of a hole, you could guess the number of holes in the landscape, the depth of the one I’m dancing around, the size and shape of the opening, etc. All from just looking at me dancing at the bottom.

    Do you really not see the problem?

  26. Entropy,

    You don’t know if it requires that number of amino-acids, but if so, it requires them to keep at its local minimum.

    It requires them to produce enough ATP for the organism to survive. We are talking about perhaps 1/13 of ATP synthase. What is happening here for 300 possible single mutations that can kill the organism or prevent it from developing? It is telling us that for these 300 AAs the proper binding to the alpha chain is right on the edge and there is no tolerated sequence variation to bind to the alpha chain and allow ATP synthase to function. If those AAs are not in that exact fixed condition the cell dies. This is what the empirical evidence is telling us. Gpuccio is exactly right in his FI calculation which is conservative as it ignores other restrictions.

    Do you really not see the problem?

    The problem from my perspective is that you don’t see how small in relation to total sequence space that the empirical evidence is telling us these holes really are.

  27. DNA_Jock,

    I am enjoying your claim that (in gpuccio-speak) there is a massive (and unexplained by apoptosis) injection of FI between Caldithrix abyssi and Herbaspirillum rubrisubalbicans (“Still just a bacterium”) and then scarcely any change at all from Herbaspirillum through clams and crocodiles, baboons and humans. Positively weird, that.

    I thought you would bury you head in the sand on this one 🙂

    ETA: I note that colewd has edited his post to remove the “Having to bind two proteins” idiocy that he originally posted, and I replied to. There’s hope for him yet…

    I read through the exchange and realize you had pivoted. I fouled with a strawman. I apologize. For what its worth, nice pivot.

  28. colewd: So are you making the positive claim that evolutionary processes can produce 500 bits of FI? Are you making the claim that evolutionary processes can produce unlimited FI?

    I’m making the claim that you and gpuccio have no argument showing that evolutionary processes cannot produce 500 Bits Of FI.

    Unless you redefine FI so that it only exists if evolutionary processes can’t produce it. Then of course, you win the argument, by definition, and the argument is also a useless tack-on only used after, by some other means, we have drawn the conclusion that evolutionary processes can’t do the job.

    I’ve said this many times.

  29. colewd: It requires them to produce enough ATP for the organism to survive. We are talking about perhaps 1/13 of ATP synthase. What is happening here for 300 possible single mutations that can kill the organism or prevent it from developing? It is telling us that for these 300 AAs the proper binding to the alpha chain is right on the edge and there is no tolerated sequence variation to bind to the alpha chain and allow ATP synthase to function.

    No, it doesn’t tell us that at all. All it tells us is that the sequences we see have higher fitness than the sequences further away, and the difference is high enough to be visible to selection. It doesn’t tell us whether sequences further away are still capable of supporting life.

    An organism that can generate enough energy to divide once every month, has higher reproductive success than an organism that can generate enough energy to divide once a year in the same environment. An organism that can divide once a week is better than once a month. An organism that can divide once pr day is better than once pr week. And so on. Did you know there are species of prokaryotes that divide on average once pr. century or even less?

    You can’t derive the conclusion that because ATP synthases in extant life have X level of efficiency, therefore life couldn’t even exist at less than X activity. Nor can you derive the conclusion that there is no slope for selection to climb from much less than X.

  30. colewd: Apoptosis in yeast

    Not wanting to deny you your well-deserved warm ale. But picking Saccharomyces as an example of a unicellular organism was cheating a bit; Baker’s yeast forms multicellular structures, like colonies and biofilms. Therefore yeasts are teetering at the brink of multicelularity (unsurprising given that they are related to multicellular fungi). I also found that the paper you cited describes a mutant strain with an unusual phenotype.

    Truly unicellular organisms do not have apoptosis. That doesn’t make sense.

  31. colewd: DNA_Jock,

    You have admitted that any protein might have additional “specified” functions about which we know nothing. Makes figuring out how many sequences have a minimal selectable function that leads to the observed sequence tricky…

    Bill: Are you saying that finding additional function on proteins makes your claim that evolution can build 500 bits of functional information easier?

    Yes, Bill. The presence of multiple functions (I’ll drop the superfluous “specified”, if you don’t mind) makes co-option of existing molecular function a plausible scenario, like the recruitment of the Wnt signaling pathway in very different biological contexts clearly shows.

    I suspect though that gpuccio has a different view than you. Instead of trying to define an overarching function for the whole family, he has been isolating the function of each and every (human) protein from that of closely related proteins (like in the case of TRIM62). FWIW, I think your approach makes more sense (re-use of parts and all that), whereas gpuccio is transparantly trying to artificially inflate the number of bits of human proteins by defining arbitrary and unreasonably narrow “specified” functions.

  32. Mung: I don’t blame him. There is no such thing as FI introduced by natural selection.

    Is that true? gpuccio accepts some limited examples of natural selection (like you do) and I vaguely remember him calculating the increase in FI for that (a few bits).

  33. colewd:
    It requires them to produce enough ATP for the organism to survive.

    As I said. To keep itself at that local minimum.

    colewd:
    We are talking about perhaps 1/13 of ATP synthase. What is happening here for 300 possible single mutations that can kill the organism or prevent it from developing?

    You don’t have the data to support that all 300 positions are immutable. You only know they have been preserved so far between two lineages. As I said, there’s two components: [1] The time since divergence, and [2] The sequences representing a dance inside a local minimum. Only the second relates to whether the positions are immutable or not, and then, it only reflects the amount of dancing around the local minimum.

    colewd:
    Gpuccio is exactly right in his FI calculation which is conservative as it ignores other restrictions.

    Nope. The only thing he’s calculating is the proportion of amino-acids necessary to keep some sequence dancing around a local minimum. From that FI cannot be estimated, since that number doesn’t tell anybody if other sequences could have done the job, or how probable it is for a sequence to evolve into an effective enough ATP synthase. Again, you cannot tell any of that from looking at a sequence dancing around a local minimum.

    colewd:
    The problem from my perspective is that you don’t see how small in relation to total sequence space that the empirical evidence is telling us these holes really are.

    How could I see such a thing unless I had the proper data to see such a thing? The gpuccio analysis looks at the bottom of a hole. A local minimum. I understand that pointing to a local minimum doesn’t tell me anything about how small or large or numerous these holes might be. The real problem is that you seem unable to understand that you’re making an assumption from the wrong data. I thus insist: dancing around a local minimum is not the same as getting into a local minimum. The most it could tell you, if we were sure that mutations have explored the area well enough, is the area of that particular local minimum. AKA, the area at the bottom of that particular “hole.” However, there’s no way in Hell that could tell you the overall shape of the hole the sequences are in. Nor can it tell you anything about the landscape.

    I’m astounded that you don’t understand this problem.

  34. Corneel:

    Mung: I don’t blame him. There is no such thing as FI introduced by natural selection.

    Is that true? gpuccio accepts some limited examples of natural selection (like you do) and I vaguely remember him calculating the increase in FI for that (a few bits).

    If you have a single mutant, and it has a higher level of function, and because of that a higher fitness, then as it increases in gene frequency in the population the Functional Information of the population increases.

    I suppose the only defenses possible of Mung’s statement are these, and we’ve heard them all before here:
    1. Yes, the FI increases but it was not “introduced by” natural selection — mutation did that, all natural selection did was increase the frequency of the mutation, or
    2. Natural selection doesn’t exist — yes, genotypes can differ in viability or in fertility, but there is no such thing as natural selection so you can’t talk of it “introducing” anything, or
    3. Natural selection is not a “force” so it can’t “introduce” anything (of course by the same argument, natural processes such as erosion or Mendelian segregation are also not “forces” so they can’t “do” anything, but somehow the same people who say this about natural selection never deal with those cases).

    All of these are word games. The fact is, in a situation with just two alleles, the average calculated FI of genotypes in the population increases.

  35. Joe Felsenstein,

    I’m making the claim that you and gpuccio have no argument showing that evolutionary processes cannot produce 500 Bits Of FI.

    The observation of 300 preserved AA’s across two very different populations supports this claim.

    Natural selection cannot function in a static environment and is useless unless there are other functional sequences in the population to select from and they are realistically attainable from a sequences current position.

    We have a significant amount of AA’s that cannot mutate and the only possibility is that in some past life they could. So far no one has even surfaced a “just so” story to support this hypothesis.

  36. Joe Felsenstein,

    If you have a single mutant, and it has a higher level of function, and because of that a higher fitness, then as it increases in gene frequency in the population the Functional Information of the population increases.

    I don’t think this claim is well supported.

    Copying existing information is not increasing information. The mutation could have decreased FI and created higher fitness. There is no way for you to know.

  37. Corneel,

    Yes, Bill. The presence of multiple functions (I’ll drop the superfluous “specified”, if you don’t mind) makes co-option of existing molecular function a plausible scenario, like the recruitment of the Wnt signaling pathway in very different biological contexts clearly shows.

    So can you show me the recruitment office that nabbed the WNT 🙂
    How do you explain cooption without design or design changes?

  38. colewd:
    The observation of 300 preserved AA’s across two very different populations supports this claim.

    For the millionth time. No it doesn’t. In combination with the less preserved amino-acids, it just tells you about how much those sequences have danced around a local minimum. Really Bill. Come on. How hard is this to understand?

  39. Entropy,

    it just tells you about how much those sequences have danced around a local minimum.

    With 300 fixed AAs, that local minimum is a tiny fraction of total sequence space. How do you explain that the 500 original AA sequence found it?

  40. colewd:
    Entropy,

    With 300 fixed AAs, that local minimum is a tiny fraction of total sequence space.How do you explain that the 500 original AA sequence found it?

    I swear if you were any more stupid you’d have to be watered every other day

  41. colewd:
    With 300 fixed AAs, that local minimum is a tiny fraction of total sequence space.

    That’s why it’s called a local minimum. You’re missing the point though: dancing around a local minimum is not the same as finding a local minimum.

    colewd:
    How do you explain that the 500 original AA sequence found it?

    I could explain, but you’d miss the point again. I therefore insist: dancing around a local minimum is not the same as finding a local minimum. The dance cannot tell you if getting to any local minimum is hard or easy. It can only tell you how much those sequences have danced around their particular local minimum. That’s it. Starting to understand this yet?

  42. colewd: The mutation could have decreased FI and created higher fitness. There is no way for you to know.

    And vice versa the Designer could have introduced enormous amounts of FI only to create terribly maladapted failures.There is no way for you to know.

  43. colewd: We have a significant amount of AA’s that cannot mutate and the only possibility is that in some past life they could.

    But you have zero evidence that they can’t mutate. The evidence you have is that among the ATP synthase subunits you have seen, there have not been mutants among them at the sites in question. That doesn’t mean they can’t mutate, but it does imply that those mutants are selected against.

    Being selected against doesn’t mean an organims with those mutations couldn’t possibly exist, it probably just has lower fitness in comparison to the extant sequences.

    So far no one has even surfaced a “just so” story to support this hypothesis.

    We don’t need to explain how X evolved when the evidence we have doesn’t in any way imply it couldn’t evolve. The problem is you don’t even understand what the evidence we have implies. You are drawing a conclusion that the data simply cannot support. A completely unwarranted extrapolation. You’d need to actually do a huge screening of mutants and measure their fitness in order to be able to say that the data supports the conclusion that the known sequences couldn’t have evolved from areas of lower fitness.

  44. Entropy,

    I could explain, but you’d miss the point again. I therefore insist: dancing around a local minimum is not the same as finding a local minimum.

    We are not observing AA’s “dance”. We are observing a preservation of AA sequences over deep time. The challenge is explaining the origin of the sequence that can no longer generate mutations that remain in two completely different populations and two completely different species.

  45. colewd: So can you show me the recruitment office that nabbed the WNT 🙂
    How do you explain cooption without design or design changes?

    Oh nonono. The question is: How are YOU going to exclude all possible evolutionary paths into a complex biological system, if any participating protein can potentially have been performing some other ancestral function? Co-option has been demonstrated. Omnipotent designers creating biological organisms, not so much.

    Don’t blame me. That is the burden of endorsing a completely negative argument.

  46. Rumraket,

    Being selected against doesn’t mean an organims with those mutations couldn’t possibly exist, it probably just has lower fitness in comparison to the extant sequences.

    This assumes the fitness criteria in bacteria is the same as advanced eukaryotic cells. This is not a realistic assumption.

  47. Corneel,

    Don’t blame me. That is the burden of endorsing a completely negati.ve argument.

    Hey, only studs or the extremely stupid will take on this challenge. According to Dazz I am the later:-)

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