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 
. 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?
He returned when he said he would. But that is past, not future. So you are half-right.
Reputation preceding you much?
Mung,
No, he did not.
No chance of dust ever returning I’m afraid.
And changing the function is not moving the goalposts?
OK, so I was wrong about Meyer. There was one other prominent IDer who claimed this though I cant remember who, and I could swear that Meyer sat on a panel with Nelson who claimed this and didnt object.
I dont think that the identity of the designer is irrelevant to discussions of design. If that seems to be the case thats only because in most of these sorts of discussions the existence (or at least the plausibility) of the designer can be taken for granted. But in cases where the designers existence is in question we cant consider ‘designer’ or ‘designed-object’ in isolation. We have to consider the plausibility of the existence of the designer along with everything we know about designers and how and why they design. Genuine evidence for design will always tell us something about the designer and if it doesn’t that should strongly suggest that ‘design’ is just an ad hoc explanation in this case.
Get back to me when you understand what functional information is and where it comes from.
Yes I could. I read it from their paper. Which is why I didn’t accuse Rumraket of making it up.
It evolved from another location in sequence space. Look at the graph DNA_Jock linked you. Actually I’ve modified that graph by drawing on it and writing an explanation that should clarify what we mean. Please take a look at this picture. In the original the spike which is occupied by the wild-type protein isn’t shown as that peak is much taller than the peaks found by Hayashi et al so I had to draw it on. It’s not to scale.
When colewd asked you about the origin of the spliceosome you referred him to a phylogenetic analysis of eukaryotes. Did you not? The implication is that you thought such an analysis addressed his question about the origin of the spliceosome.
Is it your contention that we cannot make factual statements about the past without having been present to directly witness them?
If we find a crater on the moon, is it reasonable to state as fact that an impact happened? If you live in a house, you own a cat, it has a cat’s door and there’s muddy imprints on the floor that look like they were made by a cat and it’s muddy and raining outside, can you reasonably infer that sometime in the recent past your cat came in with wet dirty feet from outside?
This is where we are at.
Past events leave evidence behind, evidence that would be unlikely to exist and be of the particular nature it is, if those past events did not take place.
So it is with particular sequences of DNA in the genomes of living organisms. They constitute a record of past events. When analyzed, we can some times reconstruct the past by comparing DNA sequences and making phylogenetic trees. Past DNA sequences can be recreated in the laboratory and tested for how they function by putting them in living organisms in place of their modern counterparts, and seeing their effects. Tests can be done to ensure the results of those tests aren’t statistical or experimental artifacts. If those tests are passed, we can be reasonably certain that we have correctly inferred past events. We can be reasonable in saying that we know for a fact that X happened.
That’s how it works. Get over it.
Could you pencil in the Szostak line?
No. lol
Where the fuck have you seen this take place?
No. I’m saying you accept it as “fact” because you want to believe it is “fact.”
And yes, you raise a very interesting question. What qualifies as a fact. Do you believe that they have shown what actually took place in the far distant past to the point of it being indisputable? They locked it down. There is no other alternative. It’s wicked to deny it?
Except when they don’t.
Which is why I think evolutionists talk out both sides of their mouth. I can’t even begin to count the number of times I’ve been told that I could not expect evolution to leave behind evidence of what took place in the past.
What a convenient theory. You want to have your cake and eat it too. I get it.
You think inferences are facts. I don’t.
ETA:
I’ll take that to mean that you have no idea what “new & original function” means in terms of FI, thanks anyway
In different posts Bill Cole has asked for evidence of intermediary stages in the evolution of the spliceosome (which was what I was answering there), and for evidence of the origin of the spliceosome. Those are not the same things.
In fact in the post of mine where I answer Bill Cole, I have broken up his post into several pieces and give answers to the different points and questions he make. What you quote me for is in answer to this specific part:
Bill Cole: “If you knock out PRP8 from a eukaryotic cell it will not function. Where is the evidence for intermediate steps?“
So you have completely misread what was asked for and answered with. In that particular answer I am not in any way attempting to give an account for the origin of the the spliceosome.
And that is exactly what I said to you. That your response had nothing to do with the origin of the spliceosome.
So you could have said back then that you agreed with me but that my objection was not relevant because you weren’t addressing that. But I’ll take your word for it now that you have clarified. Thanks. 🙂
I thought you were saying that you had explained where it came from (“exactly that”).
That is what I mean. Care to explain why not?
Because FI in that sense is not something that is gained or lost. FI in that sense is not something that comes about via mutation and selection. It just is and the amount of it depends on where you set the threshold, not how it evolved.
So you agree that in the WEASEL example there’s no gradual or cumulative increase in FI as the generated strings approach the target string, right?
This is why Joe is misguided. You can lead a horse to water … or try to.
So if you start with sequence A, and you measure it’s FI for a certain function to be say 100, and after a number of iterations of mutation/selection you get sequence B, with 600 bits of FI, you mean to tell us there wasn’t a 500 bit increase in FI in the process? Okay then
No, I do not agree. The threshold is simply set to decide upon the set of sequences that exceed a certain information content, which is required to perform the calculation. There is no doubt that “METHINKS IT IS LIKE A WEASER” (27 matches) has a higher information content than “HELP I M TRAPPED IN A WEASEL” (11 matches), because there are fewer strings that have 27 or more matches to the target than strings that have 11 or more matches. This should be obvious as the former is a subset of the latter.
The weasel demonstrates an increase in FI when more and more matching characters accumulate in the string, because fewer and fewer strings can be found in the total set that can match the acquired level of function.
Then you do not understand Functional Information.
That is incorrect. The procedure is not to calculate the “information content” of each string and then to decide on a minimum threshold.
There is only ONE string that is an exact match and you already agreed that the calculation of FI was based on an exact match to that one string.
If you are gong to allow for partial matches then you have to define what you mean by “level of function” relative to the number of partial matches and RECACULATE the FI. IT is a mistake to think that METHINKS IT IS LIKE A WEASER has one FI value and that METHINKS IT IS LIKE A WEASEL has a different FI value and that HELP I M TRAPPED IN A WEASEL has yet another FI value.
There is no such thing as in increase in FI when more and more matching characters accumulate in the string. That is something you made up based upon a misunderstanding of FI. Sorry.
Let’s say that we define a threshold level of function of at least one match to the phrase “METHINKS IT IS LIKE A WEASEL.” Then we calculate the number of strings that meet that defined threshold of function. Then we can calculate the FI. But the FI is not something that is associated with any particular string and it doesn’t change depending on the string.
It changes if we redefine the threshold.
So if we change the threshold to strings with at least three matches, then yes the FI will be higher, because fewer strings will meet the threshold while the possible strings of that length does not change. But it’s not because those strings have a higher “information content,” it’s because we changed the threshold.
I hope that helps. This while things about “increasing function” and like nonsense is just so much of a red herring.
The functional information, I(Ex), for a system that achieves a degree of function, ≥Ex…
That’s greater than or equal to, not less than or equal to. People here appear to think that is a less than sign. It’s not.
Now in Corneel’s extended WEASEL example, in order to calculate the FI we’d need to know how he defined the degree of function of his candidate solutions. If it is anything at all like the original Dawkins program, all it needs is a single letter match.
So the actual FI is far lower than we’ve been led to think.
Right Corneel?
Well, from the link posted by Joe on Szostak’s FI:
http://molbio.mgh.harvard.edu/szostakweb/publications/Szostak_pdfs/Szostak_2003.pdf
It is important to note that
functional information is not a property of
any one molecule, but of the ensemble of all
possible sequences, ranked by activity
So looks like Mung is right on that one. But doesn’t Puccio claim there have been FI “jumps” in some transitions, like in the vertebrates one?
I honestly do not see the relevance of the monkey/Shakespeare model of cumulative selection (not cumulative natural selection, as Dawkins explains).
Functional information is defined on events, not on processes in which those events might occur. If you’re thinking “displacement problem” and “search for a search regress,” then you need to stop. Dembski generated that blather without working through the details. His vague ideas never panned out. He and Marks subsequently reattached the rhetoric to active information, which is defined on processes.
Don’t get angry with me for pointing this out. Dembski and Marks ought to have given an account of why the change was necessary. They have instead done their damnedest, from 2008 to the present, to make it appear that they’re saying what Dembski has always said. Decent grassroots proponents of ID like you should be speaking in opposition to the dishonesty of the leading proponents of ID. If ID is ever to be taken as science, then its “scientists” have got to stop behaving as activists advancing a socio-political cause.
Functional information cannot serve as a replacement for complex specified information in ID arguments. The fundamental reason is that the “target” event in the measurement is specified after the fact of its occurrence. In Dembskian terms, the target is painted around the arrow shot by a blind archer. There is no argument to be made that the sort of biological functions discussed in this thread have detachable specifications. The way that living systems function at the molecular level is weird and surprising and messy and often arbitrary. We have discovered by scientific investigation that life works in ways we never would have imagined, let alone have specified when engineering a system.
It’s an embarrassment to the UD community that no one has informed the self-styled sage gpuccio that Dembski’s 500-bit threshold makes no sense at all when an observed function is merely described, rather than associated with a specification that an engineer conceivably sought to satisfy in designing the system that has been observed to realize the function.
Rereading this, I’m struck by the fact that it could be worked into a celebration of God’s glory. In all honesty, I recall being awestruck by organisms when I was a child, and even when I was a young adult. I recall grokking on the unimaginability of building such things. It’s not an empty slur when I say that it is the Christians attempting to reduce the Creator to an engineer who are, in the words of Dembski, robbing him of his glory. (I recall hearing a priest/scientist from the Vatican Observatory say much the same, though of course not as confrontationally.)
Many years ago, watching The Passion of Joan of Arc, I was floored by Joan’s observation, when called to account for the strangeness of her personal relationship with God, “His ways are not our ways.” (Her lines in the movie are supposed to have come from the records of her trial.) Those of you who are genuine in your Christianity would do well to contemplate why I, an over-intellectualizing Ph.D. who doesn’t know how he could know God, am vastly more impressed by simple and transparent expressions of faith, coming from people who admit that they cannot explain everything, than by the dandiest of apologetics.
Which would be idiotic as THAT PARTICULAR PART of my response was addressing Bill Cole’s question concerning the EVIDENCE OF INTERMEDIATE STAGES in the evolution of the spliceosome.
In the part of Bill Cole’s posts where he questions THE ORIGIN of the spliceosome I answer that it evolved from Group II self-splicing introns.
So I invite you to go back and read the entire exchange and stop this idiotic trolling. You can’t just lift my responses out of the context and then pretend they are not in answer to specific relevant questions nor that they are in answer to other questions which they aren’t. I usually quote what I am responding to, and I break up larger posts into smaller pieces to answer particular points.
Actually he has asked questions about BOTH. And I have correctly addressed the individual questions with relevant answers. At not point have I answered a question about the spliceosome’s origin by referring to evidence for the gradual evolutionary history of an already existing spliceosome, nor the other way around.
So when you implied that “once there was a spliceosome, it evolved” was an answer I gave in response to the question “how did the spliceosome come to exist in the first place?” that is simply a product of your own lack of reading comprehension. Thank you.
How about you just read what Bill Cole writes, and what I write in response? Why do I have to waste time rehashing an interaction you can just read yourself when that alone should clarify all your confusions? Read for comprehension rather than a search-for-reasons-for-dismissal mindset. Your objections (if any) are also going to make more sense then.
Yeah, that’s where I explain that the evidence indicates that it evolved from Group II self-splicing introns. I have in fact given that answer as a response to the question about the spliceosome’s origin all the way back on page 2 of this thread. And again on page 3. So I have in fact done exactly that.
I even clarify that to you directly in this post on page 3.
I’ve been thinking along similar lines lately. I don’t understand why ID proponents don’t take a “fine-tuning approach” to the possibility of evolution, rather than the strange interventionist that has to occasionally zap a flagellum or spliceosome into existence, that they seem to be advocating.
What I mean is, rather than argue that “new and original proteins/functions”, or particular amounts of “functional information” can’t possibly evolve by a gradual process of blind sampling through mutation and selection, why not instead argue that the fact that such a thing is even possible, is where God’s handiwork lies?
That the setting up of the physical laws of a universe that makes it possible for random sampling of an unimaginably vast space of arbitrary physical “solutions” to “problems” of living organisms is God’s role in the story.
Strangely enough IDcreationists of many stripes are already hooked on the idea that God has fine-tuned the physical laws to allow physical life to exist in the first place, but they’re vehemently against the idea that those laws could also allow life to originate and evolve through or because of those laws. Why? Is there some scriptural interpretation that demands such a theology? That God has made it impossible for life to originate and evolve without his direct intervention and meddling?
Perhaps, but I am not yet convinced that your understanding of it is correct either 🙂
I agree with most of what you wrote here. When I said that “METHINKS IT IS LIKE A WEASER” has a higher information content than “HELP I M TRAPPED IN A WEASEL”, I was being sloppy. Functional information I(Ex) describes the information content of populations of strings, not individual strings. Correction accepted.
What I do NOT agree with is that this somehow invalidates the idea that the amount of functional information is gradually increased during a typical run of the weasel program.
The function x that I am considering is the number of matches a string has to the given target string. This is a continuous trait which is quantifiable for any given string, as is required to be able to calculate FI. The information that determines how well a string can perform that function is carried by the specific combination of characters in the string.
Now if I accept your description of FI, then a typically weasel run will show a succession of strings that are all members of the set that fails to meet the arbitrary threshold, and therefore the system shows no increase in functional information. Then, all of a sudden there is an enormous leap, when a string is introduced that does make the cut and displays at least a level of function Ex. And thereafter nothing happens anymore, not even when a string matches the target string. I would say that is nonsensical. Especially as during the run we see a continuous improvement of the ability of strings to perform function x. I would expect that that is somehow reflected in our measure of functional information. And it is, because every improvement in function allows us to set a more stringent threshold, so the strings become members of more and more exclusive sets. This reflects the gradual accumulation of functional information, as I see it.
Only if we doggedly cling to a fixed threshold level, which would defeat the purpose of trying to quantify the information needed to fulfill a given level of function.
Uh-huh, but that’s just flat out wrong I’m afraid.
Does something have to be indisputable to a degree where it would be wicked to deny it, for it to be called a fact?
Everything can be disputed, but is it rational to do so? Can disputing it be done rationally?
It doesn’t matter that they some times don’t when in this case they did. It is that very evidence that makes the inference possible in this particular case.
Which is absolutely true, there is no necessary entailment that evolution preserve any and all historical events in the DNA record.
But WHEN it does, we CAN analyze it and make evidentially well-justified inferences about past events.
Of course you do, you just haven’t thought about it until my very next sentence. You think the existence of atoms is a fact (I guess you can reveal just now nuts you are by correcting me that you don’t consider the existence of atoms to be a fact). Yet they have never been observed. They are inferred to exist from all sorts of indirect evidence collected over the course of a century. The theory of atoms explains an incredible number of observations, none of which are a direct picture of them. Even the best scanning tunneling microscopic pictures will reveal a lumpy surface that is inferred from the electrostatic behavior of an ultra-thin rod of a platinum/iridium alloy. It’s inferences all the way down.
There are probably thousands of trivialthings you consider facts by simple inferences that you’ve just never thought about as being based essentially on simple everyday inferences. You’re just playing your usual butthurt contrarian here.
That is an interesting letter, dazz. Thanks. And it confirms my intuition that we can tell that functional information is gradually increased in a run of the weasel program, because of its relation to the level of function, which also increases gradually. There is even a handy figure!
Jerry Coyne is a determinist. From that it follows that everything from the first moment that physical laws exist is inevitable. There are some religious views compatible with that.
Far be it from me to get angry with you. 🙂
I’m trying to use it as a teaching device, like Dawkins did.
I’ve been talking about the Hazen, Szostak, et al. version. It’s not defined on events or processes.
That’s what we are exploring. Whether or not it can. I agree with your that it would not be the same as the Dembski argument, and gpuiccio does not say that it is.
If I knew of a case of dishonesty I would. Or are you saying the entire “movement” is dishonest?
I have and do take that approach. Like you with your bridges between islands and floating islands that just happen to bump into each other. There’s no reason to expect those in a randomly generated fitness landscape. The paths have to be “just right” for evolution to work.
It’s design all the way down. 🙂
There is no reason to not expect those things either without assuming the conclusion of design.
Of course even random generated fitness landscape could be designed.
It is always design all the way down.
But you have misinterpreted the figure! You are reading it as if it is referencing a single function but that is not what it depicts.
All possible sequences,. Any activity. Not at all the same as your WEASEL example.
So let’s revisit it. What is the function you have defined and what percentage of generated strings can fulfill that function? All of them?
In the original WEASEL even a single letter match was considered functional. So we’d need to identify the number of strings that would have one or more letters that match and then we could calculate the FI. Do you agree?
And I assume the run you did with the longer string had the same definition of a functional string. As long as at least one letter matched it was considered functional.
So we are no where near 500 bits of FI. We need to get 500 bits of FI and THEN see if the program can find it.
Actually you seem to be arguing both positions in different posts. If you really accept the reality that the laws of physics make evolution possible, shouldn’t you be calling out those who arguing against it like Gpuccio and Bill Cole?
Good point, he has been showing “information jumps” by plotting the accumulation of conserved AA that eventually result in human proteins with a certain level of function. But of course, he knowns zip about the level of function of the ancestral proteins, so this has nothing to do with Szostak’s FI.
Pondering on it a bit more, I think there is some seriously weird stuff going on in those calculations. Gpuccio has been plotting the accumulation of conserved AAs that lead to some human *incredibly-complex-gene* and claims to demonstrate that these are introduced in large jumps. He assumes that these proteins only become fully functional when the entire protein has been assembled in its current form (no ladders). But there are organisms that do not have all of those human-conserved AAs otherwise he would not have been able to show those jumps. But that is weird, since the orthologous genes must surely serve some function in all extant organisms in which they are found, right? Yet gpuccio insists that the proteins that those orthologs encode can not have a function that is useful to a living cell!
No, not any activity. Yes, a single well-defined function, like ATP-binding, catalyzing a specific reaction, perform addition for as many times as possible, or spell out a naughty word (Phe-Ala-Arg-Thr will do nicely). Look in the Hazen paper; it has several nice examples.
But there is variation in the efficiency in which various strings accomplish their function. The function is quantitative, not qualitative. Hence the requirement to set thresholds.
Knock yourself out, and don’t forget to inform gpuccio that the ubiquitin system does not have 500 bits of information because he forgot to include all configurations that are capable of activity … any activity.
Heads I win tails you lose.
Are you saying I ought to Rumraket, that I have some moral obligation?
You’re a funny guy.
The level of function of “the ancestral proteins” has nothing to do with calculating Szostak’s FI. Any protein, “ancestral” or otherwise, that met the qualification of the chosen threshold of function is what is relevant to calculating the FI. Whether it is ancestral or not is totally irrelevant. All that matters is degree of function above a threshold.
If both the ancestral protein and the modern human protein are functional to the same degree, no increase in functional information can be said to have taken place.
As far as I can see, to ask about Functional Information in the Weasel case we count the matches of the current string, use that number as the threshold, then compute the fraction of all strings that would have greater than that number of matches (call it P) and compute
. The fraction 
is pretty easy to compute using tail probabilities of binomial distributions, in this case with a Heads probability of 1/27 and 28 tosses. As the current string changes through time we do that each time we want to know the FI. The FI could either go up or go down, but mostly it will go up. A Weasel-like model with a longer string could easily get to 500 bits of FI.
Of course over at UD gpuccio tries to pull the rug out from under all this by crying out:
Of course gpuccio would say this of any computer simulation of natural selection, because its behavior is inherent in its computer program. I assume Mung doesn’t agree, else why would Mung bother to ask about computing FI for a simulation?
To me, the question was legitimate and the answer is not that the FI is already all there. The Weasel is a simulation showing how fast a simple system with cumulative selection works, and if you want to do the above calculation, that’s legitimate.
It’s also funny that nonlin.org made the argument about the nonexistence of fitness and of phenotypes over at Uncommon Descent as well. The local denizens are busy rejecting it and getting really frustrated with nonlin (in gpuccio’s Texas Sharpshooter thread, see especially comments starting at #212). They are doing a fairly good job over there of pointing out why nonlin.org is “out to lunch”. I would not have expected that they could do that well, given their usual reluctance to acknowledge that natural selection is able to do much of anything.
According to the example we’ve been working with you want me to accept that the string GTAFSDRNJPGOZXDQBQBRWHHPODLL has some degree of function relative to METHINKS IT IS LIKE A WEASEL because one letter matches, which is pretty far afield considering the examples given by Hazen et al.
eg, FYRE and FIRE or MANE and MAIN.
I just want to know where you set your threshold that’s all. Then we can try to figure out how many strings are in and how many are out and THEN we can figure out whether the FI is 500 bits or not.
Yeah, I don’t see a problem with it. It appears to me to be what Hazen et al. were doing though they weren’t trying to “evolve” a string with more and more FI in it.
The more specific something is, the more it needs to be specified, the more information “content” it could be said to have, and that is consistent with Hazen.
METHINKS IT IS LIKE A WEASEL where an exact match is required at each location in the string is far more specified than only requiring an exact match at 80% of the positions. And the FI will be different i each case. It’s back to the single target vs. multiple targets that we always get into in these discussions.
But this helps clarify that if you add more potential targets then the FI goes down. Hopefully everyone can agree on that!
So you can’t add more targets and maintain the same FI. To do that you’d have to increase the set of possible strings that are not a valid target. So the problem is the same whether a single target or multiple targets because it’s relative the the size of the search space.
Starting from where?
But it did not have a 500 bit FI threshold. And I am saying that neither did the one that Corneel put together.
From any string whatsoever.
Corneel gave the example of the string “TO BE OR NOT TO BE THAT IS THE QUESTION WHETHER TIS NOBLER IN THE MIND TO SUFFER THE SLINGS AND ARROWS OF OUTRAGEOUS FORTUNE OR TO TAKE ARMS AGAINST A SEA OF TROUBLES” which I make out to have 167 characters.
is a bit bigger than 
so finding this string would lead to an FI of about 794 bits.
Or do you think that somehow once it gets past 499 bits a Weasel-like program wouldn’t find the target string?