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An attempt at computing dFSCI for English language

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In a recent post, I was challenged to offer examples of computation of dFSCI for a list of 4 objects for which I had inferred design.

One of the objects was a Shakespeare sonnet.

My answer was the following:

A Shakespeare sonnet. Alan’s comments about that are out of order. I don’t infer design because I know of Shakespeare, or because I am fascinated by the poetry (although I am). I infer design simply because this is a piece of language with perfect meaning in english (OK, ancient english).
Now, a Shakespeare sonnet is about 600 characters long. That corresponds to a search space of about 3000 bits. Now, I cannot really compute the target space for language, but I am assuming here that the number of 600 characters sequences which make good sense in english is lower than 2^2500, and therefore the functional complexity of a Shakespeare sonnet is higher than 500 bits, Dembski’s UPB. As I am aware of no simple algorithm which can generate english sonnets from single characters, I infer design. I am certain that this is not a false positive.

In the discussion, I admitted however that I had not really computed the target space in this case:

The only point is that I have not a simple way to measure the target space for English language, so I have taken a shortcut by choosing a long enough sequence, so that I am well sure that the target space /search space ratio is above 500 bits. As I have clearly explained in my post #400.
For proteins, I have methods to approximate a lower threshold for the target space. For language I have never tried, because it is not my field, but I am sure it can be done. We need a linguist (Piotr, where are you?).
That’s why I have chosen and over-generous length. Am I wrong? Well, just offer a false positive.
For language, it is easy to show that the functional complexity is bound to increase with the length of the sequence. That is IMO true also for proteins, but it is less intuitive.

That remains true. But I have reflected, and I thought that perhaps, even if I am not a linguist and not even a amthematician, I could try to define better quantitatively the target space in this case, or at least to find a reasonable higher threshold for it.

So, here is the result of my reasonings. Again, I am neither a linguist nor a mathematician, and I will happy to consider any comment, criticism or suggestion. If I have made errors in my computations, I am ready to apologize.

Let’s start from my functional definition: any text of 600 characters which has good meaning in English.

The search space for a random search where every character has the same probability, assuming an alphabet of 30 characters (letters, space, elementary punctuation) gives easily a search space of 30^600, that is 2^2944. IOWs 2944 bits.

OK.

Now, I make the following assumptions (more or less derived from a quick Internet search:

a) There are about 200,000 words in English

b) The average length of an English word is 5 characters.

I also make the easy assumption that a text which has good meaning in English is made of English words.

For a 600 character text, we can therefore assume an average number of words of 120 (600/5).

Now, we compute the possible combinations (with repetition) of 120 words from a pool of 200000. The result, if I am right, is: 2^1453. IOWs 1453 bits.

Now, obviously each of these combinations can have n! permutations, therefore each of them has 120! different permutation, that is 2^660. IOWs 660 bits.

So, multiplying the total number of word combinations with repetitions by the total number of permutations for each combination, we have:

2^1453 * 2^660 = 2^2113

IOWs, 2113 bits.

What is this number? It is the total number of sequences of 120 words that we can derive from a pool of 200000 English words. Or at least, a good approximation of that number.

It’s a big number.

Now, the important concept: in that number are certainly included all the sequences of 600 characters which have good meaning in English. Indeed, it is difficult to imagine sequences that have good meaning in English and are not made of correct English words.

And the important question: how many of those sequences have good meaning in English? I have no idea. But anyone will agree that it must be only a small subset.

So, I believe that we can say that 2^2113 is a higher threshold for out target space of sequences of 600 characters which have a good meaning in English. And, certainly, a very generous higher threshold.

Well, if we take that number as a measure of our target space, what is the functional information in a sequence of 600 characters which has good meaning in English?

It’s easy: the ratio between target space and search space:

2^2113 / 2^ 2944 = 2^-831. IOWs, taking -log2, 831 bits of functional information. (Thank you to drc466 for the kind correction here)

So, if we consider as a measure of our functional space a number which is certainly an extremely overestimated higher threshold for the real value, still our dFSI is over 800 bits.

Let’s go back to my initial statement:

Now, a Shakespeare sonnet is about 600 characters long. That corresponds to a search space of about 3000 bits. Now, I cannot really compute the target space for language, but I am assuming here that the number of 600 characters sequences which make good sense in english is lower than 2^2500, and therefore the functional complexity of a Shakespeare sonnet is higher than 500 bits, Dembski’s UPB. As I am aware of no simple algorithm which can generate english sonnets from single characters, I infer design. I am certain that this is not a false positive.

Was I wrong? You decide.

By the way, another important result is that if I make the same computation for a 300 character string, the dFSI value is 416 bits. That is a very clear demonstration that, in language, dFSI is bound to increase with the length of the string.

Comments
DNA_Jock:
The catalytic activity is an attribute of the enzyme. When we say “An enzyme with kcat > 1000 /s” the phrase within quotation marks is the specification. The catalytic activity is NOT the specification; the words that describe the catalytic activity are the specification.
Sorry to but in again, yet, I must comment here. You're correct in saying this is "the nub of the problem." I'll use an analogy to try and get at what I think the disgreement hinges on. In special relativity, one is always concerned with "frames of reference." What looks like "motion" in one frame, might look like the complete absence of "motion" in another, if one frame is in motion relative to the other. The point here is that "observers" in two different systems see things differently. Your position on "specification" says that it is the "words that describe the catalytic activity" form the basis of the specification. This is from the "frame of reference" of human beings. With this, I don't disagree. However, what about the "frame of reference" of the cell itself? From the point of view of an "observer" on a 'ribosome,' the m-RNA looks like a 'formula' for producing a certain "specified" protein, and enzyme, which, as it turns out, will have a certain type of activity within the cell. But, as far as the "observer" in/on the 'ribosome,' it sees nucleotide bases calling for the positioning of particular a.a. in a particular sequence of linkages, which forms an a.a. string that 'we,' "observers" in the external "frame of reference" refer to as an "enzyme with kcat > 1000 /s.” Our definition is not critical; but the "specification" of the m-RNA strings of nucleotide bases is. Let me just leave off here.PaV
November 17, 2014
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Gpuccio, I know that you are hopelessly wrong on this. I think we do agree on one thing: there is no hope. I think the problem is that you are incapable of seeing the difference between the attributes of an object, and the way we describe and delimit the attributes of an object.
No. The function is the specification. We describe the function. We don’t invent it.
This is the nub of the problem. The function is NOT the specification. This is so monumentally wrong that it hurts. The function exists (or not), whether you describe it or not. The catalytic activity is an attribute of the enzyme. When we say “An enzyme with kcat > 1000 /s” the phrase within quotation marks is the specification. The catalytic activity is NOT the specification; the words that describe the catalytic activity are the specification. We may specify an enzyme in terms of its activity, but that does not mean that the activity is the specification. We could specify an enzyme in terms of its tryptic fingerprint, or molecular weight, or migration under PAGE. In each case, the specification is a group of words that describes the requirements of the specification. Consider, for a moment, a cat. It exists. I can refer to it as follows = A cat = A grey cat. = A grey long-haired cat = A grey, four-year-old long-haired cat = A grey, four-year-old double-pawed long-haired cat = A grey, four-year-old double-pawed long-haired cat called Sox = A cat with RFID implant #15479364413 Each of these phrases is a specification for the cat. The cat is not the specification. The cat has not changed. The specification lists attributes that some cats may possess, others not. (As an aside, we could additionally specify all sorts of other things about the cat that would not change the membership of the set that meets the specification -- the cat does not have eight legs, the cat has not graduated from UCLA, etc, etc -- such aspects would only serve to make the specification longer, which some find confusing.[aardvark!]) We use the specification to specify :) which cat(s) we are talking about. The same event can be described in different ways, depending on the specification used. “Hey DNA Jock, I just crushed a [insert cat specification here]” Notice how the probabilities change, depending on the specification used.DNA_Jock
November 17, 2014
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me_thinks says, Unitary consciousness too has been mathematically defined by various authors (including in the paper you cited !!). I say I agree that it has been mathematically defined. However There is an infinite gap between defining something mathematically and proving it. You can fit all the digits of pi in that space. You say. The dispute is in the concept and whether the input signals received by brain are decomposable. If it is decomposable then, unitary concept doesn’t exist. I say, That is just restating the original point. If human consciousness can be computed algorithmically then human consciousness is not unitary. But we all know it is!!!! peacefifthmonarchyman
November 17, 2014
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keith s: This comment bears repeating: "Just to be clear. I have already answered your “objections”. I will not do it again. You seem to love repetitions. I don’t."gpuccio
November 17, 2014
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Gary S. Gaulin: I agree with you on the huge complexity of the interaction between consciousness and algorithmic complexity. That is a fascinating field. I need some time to read your material, and my time in this moment is absorbed by many thing, some of which can be seen here. But this is an important issue. I don't want that anyone think that my firm conviction that consciousness is the primary reality, and cannot be explained by configurations of matter, makes me in ant way not interested to the fascinated interplay between the conscious subject and its manyfold representations, many of which are algorithmically evolving. One of the most interesting aspects of consciousness is that it always react to the things it represents in two different modalities, which are indeed so connected that they can be probably considered as the two faces of one reality: one is cognition (meaning), and the other if feeling (purpose). I believe that we cannot represent anything without reacting to it as meaning something, and at the same time as being good or bad, desirable or painful. Design is a very good epitome of all that: it is essentially a meaning used to implement a purpose.gpuccio
November 17, 2014
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gpuccio, This comment bears repeating:
Gpuccio also fails to see that when speaking of evolution, the only target specification that ever makes sense is “changes that improve reproductive success”. Evolution wasn’t shooting for “ATP synthase” or “traditional ATP synthase”. It was searching for anything that would improve fitness. And even if he were to use this corrected specification, dFSCI would still be useless, because taking the ratio of target space to total space only makes sense if you are talking about a purely random search. Gpuccio has been reminded over and over that evolution is not a purely random search. It includes selection, which is highly nonrandom. P(T|H), where H includes “Darwinian and other material mechanisms”, is the stumbling block. Dembski cannot calculate it. Neither can gpuccio or KF.
keith s
November 17, 2014
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DNA_Jock: You say:
I made two objections to your 3-protein fit: #1 that the sequence conservation around an optimum tells you about the sequence constraint around an optimum, nothing more. #2 that you should have aligned all 23,949 sequences. #1 is the killer, making #2 moot. Sorry if you did not pick up on this – I probably could have expressed myself more clearly. You can’t use Durston’s method.
My recent posts about my new calculations were, explicitly and declaredly, only an answer to your #2. #1 and the validity of the Durston method I will discuss later, when we discuss the protein space. One thing at a time.gpuccio
November 17, 2014
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DNA_Jock: "The bullet did not hit a target that already existed. You do not ‘observe’ the target. All of the bullet holes, both the ones we have noticed and the ones that we have not noticed, were present before any humans existed. Humans arrive after the fact and apply paint. What you are doing is imbuing the wall with a new and wonderful property – saying in effect that particular spots on the wall are super-special, and the bullets, amazingly, hit these super-special spots." Here your error is obvious. For me: A bullet is: Any sequence of AAs which comes from random variation Any sequence of random characters which comes from a random character generator Any ticket which is extracted in a lottery A target is: A sequence of AAs with an enzymatic activity A sequence of characters which has meaning in English An extracted ticket which belongs to the brother of the functionary who presides to the extraction. So, both the bullets and the targets were there before we observed the before and before we described the target. This is simply true. You say that we paint the targets, "imbuing the wall with a new and wonderful property – saying in effect that particular spots on the wall are super-special" So, you are saying that an enzymatic activity is "a new and wonderful property", that English meaning is not "super-special" if compared with a meaningless random sequence, and that the brother of the functionary becomes his brother only because we are biased. Again: I really think that you are deeply wrong on this point.gpuccio
November 17, 2014
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DNA_Jock: "You appear to be completely unable to distinguish the function from the specification that delineates the function. These are two different things." No. The function is the specification. We describe the function. We don't invent it. If you cannot agree on that, there is no hope. Again, the brother is the brother. We acknwoledge that simple and meaningful fact. What are we "delineating"? The rules which make some sentence meaningful in English are the result of two set of functional principles: 1) The rules of English language. 2) The general rules of meaning, if they exist. Both existed before Shakespeare, or anyone else, wrote the sonnet or any other piece of English language. Again, what are we delineating? You can say that we choose some function rather than another one. That is true. Or some level of function rather than another one. That is true. That is the problem we will discuss in our discussion about our original b) (if we arrive there). For now, we are discussing a). The function must be something that existed before our observation of the specific object which implements it. That is independent of the specific object which implements it. We cannot invent a function. A function is objective, in the sense that it is something which can really be done with the object, or with other different objects, which share the same functionality. We are absolutely bound, in describing the function, by what it really is. Again, this is completely different from choosing one function over others, or defining the minimal level of the function for the inference. That is b). a) is another thing. I really think that you are deeply wrong on this point.gpuccio
November 17, 2014
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Bob O'H: I said: "It is a specification which, although formulated after having observed a result (so, after the “event” which originated the result), was equally true before that event." You said: "How can a specification be true?" What I mean is: My specification is: Being the brother of the functionary who presides to the extraction (and therefore apt to be an accomplice to him). Is that true now? Yes. Was that true before the extraction? Yes. My specification is: Having good meaning in English. Are the rules by which a sentence has good meaning in English different before and after I read the specific sentence (for example, Shakespeare's sonnet)? No. An enzyme accelerates 1000 times a reaction. It does that now, after I have observed it. Did it do that a million years ago, when no human observed it? Yes. I set a random sequence, after having observed it, as the password for my safe. My specification is: Being a password for my safe. Can I use that as a post-specification, to infer that an I got a complex sequence randomly (which I did) which is functionally specified as being the password for my safe? No, because now that sequence is the password for my safe, but it was not when I first observed it. The functional link between the sequence and its function has been created after the random generation of the sequence. This kind of specification can only be used as a pre-specification, for a new random search. It's rather simple, after all. What is the problem?gpuccio
November 17, 2014
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gpuccio @584 -
It is a specification which, although formulated after having observed a result (so, after the “event” which originated the result), was equally true before that event.
How can a specification be true? I think you're saying the same thing as me, i.e. a post-specification is valid if it's the same as the specification we would get if we had made a pre-specification, but I'm not sure, and would like to get this clear before going any further.Bob O'H
November 17, 2014
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gpuccio, re your 570, I made two objections to your 3-protein fit:
#1 that the sequence conservation around an optimum tells you about the sequence constraint around an optimum, nothing more. #2 that you should have aligned all 23,949 sequences.
#1 is the killer, making #2 moot. Sorry if you did not pick up on this - I probably could have expressed myself more clearly. You can't use Durston's method. Also Frequentist approach with post-hoc specs is deeply, deeply problematic. I think the term I used was "garbage".DNA_Jock
November 17, 2014
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Gpuccio, I share Bob's confusion with what "something that was equally true before the event as it is after the event" means. You appear to be completely unable to distinguish the function from the specification that delineates the function. These are two different things.
IOWs, we must observe both the bullethole and the target. The bullethole is our object. The target is a function defined independently from it. And the bullethole is in the target, but not because we have painted it after the bullet hit the wall. IOWs, the position of the bullethole has not generated the target, the bullethole has only hit a target which already existed.
Yet again repeats your TSS fallacy. The bullet did not hit a target that already existed. You do not 'observe' the target. All of the bullet holes, both the ones we have noticed and the ones that we have not noticed, were present before any humans existed. Humans arrive after the fact and apply paint. What you are doing is imbuing the wall with a new and wonderful property - saying in effect that particular spots on the wall are super-special, and the bullets, amazingly, hit these super-special spots. You genuinely believe that these spots are special; that you are guided by the texture of the wall when you choose where to apply paint. But you are not. As you have demonstrated twice on this thread, you are applying paint where you have observed bullet holes.DNA_Jock
November 17, 2014
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Bob O'H: Please, read #584. If you still have doubts, or objections, try to specify them. #581 was just an introduction.gpuccio
November 17, 2014
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DNA_Jock (and Bob =’H): Another premise is that what I will discuss about a) and b) is, among other things, an answer to the "Texas sharpshooter" argument. I have already debated with you (DNA_Jock) about the fact that the "Texas" argument is applied, in different ways, to two different problems: 1) Painting targets around random bulletholes which were aimed at no target. 2) Painting wrong targets instead of correctly describing the targets which were already there. Point 1) more or less corresponds to a), while point 2) is relevant to b). I paste here, as an introduction, what I had already written to you (DNA_Jock) in another thread:
The specification is made post-hoc, in the sense that the description of the function is given after we observe it, but the function is not post-hoc: the function exists independently. I think that you are strangely mixing two different problems. One is that the definition of the function of a protein is done from the observation of the protein. As I have said, this is post-hoc only in a chronological sense, not in a logic sense: we are not imagining the functionality because we see it. We realize that the functionality exists because we see it. There is an absolute objectivity in the ability of an enzyme to accelerate a reaction, like there is an absolute objectivity in the ability of a text to covey meaning. These things are not “painted” post hoc. So, your interpretation of the need to explain them as a fallacy is really a fallacy. The second aspect is what I call “the problem of all possible functions”.
. So, for the moment, let's detail better a). What is a valid post-specification? It is a specification which, although formulated after having observed a result (so, after the "event" which originated the result), was equally true before that event. From this concept derives a very simple consequence: we cannot use the contingency in the result to post-specify. That contingency can only be used for a pres-specification (IOWs, to compute the probability of a new independent recurrence of the outcome). Let's take the sequence with good meaning in English. What has good meaning in English is valid at any time (with possible variations as the language changes), not only after having read a specific sequence with good meaning. But that is only true since English exists. So, let's say that I generate a random sequence of 600 characters, and then I build a new language which uses the specific configurations in that sequence so that they become part of a correct meaning in the new language I have creates. That is Teas sharpshooting. I am painting a target which did not exist before around a random bullethole. This is the main meaning of the fallacy. And that is the reason why we cannot use the contingency in the outcome to post-specify. Interestingly, the only real attempts to offer a "false positive" to my dFSCI procedure derive from this fallacy. Mark has tried something like that (again, in perfect good faith). So, when I post-specify, I must refer to some function in the object that is not the mere sequence of its bits. I cannot say: well, I have this random sequence, now I set it as a password for my safe, so now it is specified. This is a fallacy. But when I say: "this sequence has good meaning in English", or, more generally: "this sequence is made of English words", I am not using any specific contingency in the observed sequence to define the function. Even before the emergence of that specific sequence, what has meaning in English and what words are English words was well defined. My specific example does not contribute to the definition, nor changes it. That's what I mean when I say: "The specification is made post-hoc, in the sense that the description of the function is given after we observe it, but the function is not post-hoc: the function exists independently." IOWs, we must observe both the bullethole and the target. The bullethole is our object. The target is a function defined independently from it. And the bullethole is in the target, but not because we have painted it after the bullet hit the wall. IOWs, the position of the bullethole has not generated the target, the bullethole has only hit a target which already existed. I am not discussing here how likely that was. IOWs, I am not discussing here how many targets existed, how big they are, and how likely it was to hit one of them without aiming. That will be part of the discussion about b). This is a). The only relevant thing here is: the target existed before the bullethole. It was not painted after, using the contingent information about its position on the wall. OK, the discussion is open on a).gpuccio
November 17, 2014
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gpuccio @ 581 -
So, in brief, I want to discuss two important aspects which must be very clear when we use post-specifications in our reasoning: a) A post-specification is valid only if it refers to something that was equally true before the event as it is after the event.
I'm sorry, I don't follow what you mean here. Can you explain?Bob O'H
November 17, 2014
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fifthmonarchyman @ 579 and 580,
There is no direct way to prove it mathematically because to prove it would be to compute it and that was the whole point in the first place. Nevertheless we all know unitary Consciousness exists because we experience it directly in our own lives. Don’t get lost in the weeds here You already accept the reality lots of things that can’t be “proven” empirically to actually exist. Things like Pi and e.
Both Pi and e are mathematical concept of irrational number and have been computed (of course since they are irrational, the decimals don't end). Unitary consciousness too has been mathematically defined by various authors (including in the paper you cited !!). The dispute is in the concept and whether the input signals received by brain are decomposable. If it is decomposable then, unitary concept doesn't exist.Me_Think
November 17, 2014
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DNA_Jock (and Bob ='H): I obviously disagree with most of what you say at post #556. Not all. I certainly agree that a good understanding of the system is fundamental. For any inference about a system, not certainly only for ID or for Bayesian reasoning. That said, I would like to go on this way. I will not answer directly your arguments, at least at the beginning, but just go on discussing the methodology appropriate for post specification based inferences, given that Both you and Bob O'H have graciously acknowledged that post specifications are not a logical fallacy in themselves, although . So, I start. To discuss with order, a few premises. First of all, we are discussing the general methodology here, so for the moment no digression to problems of the protein space. I have already admitted that understanding the system is always fundamental, and therefore all the issues about the specific protein space are legitimate when we make inferences about the protein space. But I want to go on with order. First the general methodology, which is valid for any space. Then, the specifics of proteins. So, please no digressions for the moment. I will also stick to a frequentist approach, because I am convinced that it works very well if the necessary cautions are applied. However, I will try to answer your specific objections during the discussion. So, in brief, I want to discuss two important aspects which must be very clear when we use post-specifications in our reasoning: a) A post-specification is valid only if it refers to something that was equally true before the event as it is after the event. I suppose that is more or less what Bob means when he says: "I think the way to make a post-specification valid is to try to make it as close as possible to a pre-specification. Would you agree?" And, if that is what you mean, Bob, I agree. b) The second point I want to discuss is about the choice of the target space among all possible target spaces. But I will detail that after I have discussed a). OK? So, let's start.gpuccio
November 17, 2014
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Me_thinks, Don't get lost in the weeds here You already accept the reality lots of things that can't be "proven" empirically to actually exist. Things like Pi and e. In the end this entire business was anticipated by Godel and ultimately by Plato Peacefifthmonarchyman
November 17, 2014
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Me_thinks said Unitarity of consciousness is not proven, so we can’t conclude that it is not computable. I say, Unitary consciousness existence is proven intuitively. There is no direct way to prove it mathematically because to prove it would be to compute it and that was the whole point in the first place. Nevertheless we all know unitary Consciousness exists because we experience it directly in our own lives. It's a paradox. Sort of like Descartes "I think therefore I am". peacefifthmonarchyman
November 17, 2014
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keith s:
Evolution is not a purely random search.
It isn't even a search.
It includes selection, which is highly nonrandom.
LoL! Natural selection is non-random in a most meaningless way- that being not every individual has an equal probability of being eliminated. Why keith s thinks that saves unguided evolution is beyond me.Joe
November 17, 2014
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Gary S Galuin The eureka moment in this whole enterprise came when I realized that all Dembski was doing with CSI was looking for a better more objective Turing Test. That simple realization moved ID from interesting apologetics to a very practical straight forward scientific endeavor in my mind. Peace PS I might be asking for your coding assistance at some point :-)fifthmonarchyman
November 17, 2014
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DNA_Jock: Errata corrige! In my post #570, the reference to percentiles is completely wrong! I must have rushed it in a moment of complete mental confusion. :) So, I am changing the phrase: "IOWs, by my “cherry-picking” I have caught approximately the 90% percentile of the general conservation as ascertained in the whole set of sequences. Not a bad result, I would say, for a quick approximation." as follows: "IOWs, by my “cherry-picking” I have essentially caught those positions which retained a very high conservation (more than 90%) when ascertained in the whole set of sequences. Not a bad result, I would say, for a quick approximation." The concept remains absolutely valid: it is a very good result. But I apologize for the error. This remains for the record of my sins!gpuccio
November 17, 2014
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Keith S
If gpuccio isn’t aware of how it could have evolved, then it must be designed.
And are you aware how it evolved? How did it just emerge? Can you give us some insight on this emergence mechanism that unguided evolution has?Andre
November 17, 2014
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Keith S
And that is why the numerical value produced by your dFSCI computation is irrelevant. Evolution is not a purely random search.
So its not unguided? mmmmmmmmmmm yet unguided evolution is the best explanation for guided searches? You are in over your head here......Andre
November 17, 2014
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gpuccio,
I refer only to the probability of finding the target space by a random search.
And that is why the numerical value produced by your dFSCI computation is irrelevant. Evolution is not a purely random search. You take selection into account in the other part of dFSCI -- the boolean part -- but the way you do so is pitiful. It amounts to this: If gpuccio isn't aware of how it could have evolved, then it must be designed. It sounds a lot better to say "it has 759 bits of dFSCI", doesn't it? Too bad that doesn't mean anything useful.keith s
November 17, 2014
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Learned Hand:: Maybe this simple comment can help: I define specification as nay rule which generates a binary partition in the search space (target space vs non target). I refer only to the probability of finding the target space by a random search. I support the validity of the procedure empirically, as shown by its absolute specificity as estimated by a 2x2 verification table in all possible tests, and not as a logical necessity.gpuccio
November 17, 2014
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Learned Hand: I never refer to Dembski's last paper on specification. I don't criticize it: I simply don't understand it, so I can neither refer to it for my reasoning, nor criticize it. That's why I never use the P(T|H) formalism in my reasoning. Keith has kindly reposted a brief summary of my empirical procedure in post #15 of this thread. You can refer to that, as a first approach. There is no P(T|H) formalism in it. I am ready to discuss any part of my approach as I have detailed it.gpuccio
November 17, 2014
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DNA_Jock: For the moment, I am not (yet) discussing here the validity of the dFSCI computation in ATP synthase to infer design. I want to discuss before the methodological aspect, and that I will do later in the day. I am just asking if you agree with a simple fact: that my "cherry-picking" of three distant sequences and my shortcut of referring only to absolutely conserved positions in them was not so unreasonable and, as I expected, had given a serious underestimation of the complexity as estimated by the Durston method. Do you agree with that? As an interesting aside, I have checked another aspect of the results of the multiple alignment. 167 positions have a conservation, in the whole group of sequences, higher than 90%. That is very near to the number of absolutely conserved positions in my three distant sequences (176). IOWs, by my “cherry-picking” I have essentially caught those positions which retained a very high conservation (more than 90%) when ascertained in the whole set of sequences. Not a bad result, I would say, for a quick approximation. And, as I expected, the overestimation of the complexity in the "ultraconserved" positions is vastly compensated by the underestimation of the complexity of all the other positions (which, in my shortcut, was set to 0), with a global "loss" of functional complexity of about 719 bits in the first evaluation. So, this is just an answer to your previous comment: "Thank you REC @ 209 for running the alignment on a decent number of ATPases. 12 residues are 98% conserved. I suspect he might have been better off going with his Histone H3 example, but H3 doesn’t look complicated. Re your reply to him at 232. I won’t speak for REC, but I am happy to stipulate that extant, traditional ATP synthase is fairly highly constrained; you could return the favor by recognizing that this constraint informs us about the region immediately surrounding the local optimum, nothing more. Rather , I think the problem is with your cherry-picking of 3 sequences out of 23,949 for your alignment, which smacks of carelessness. Why not use the full data set?" Well, now I have done exactly that.gpuccio
November 16, 2014
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I'm sorry I missed most of this conversation. gpuccio, you mentioned on the other thread that you had explained elsewhere why you feel that P(T|H) can be omitted from your version of the CSI calculations. Would you mind linking to that explanation?Learned Hand
November 16, 2014
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