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?
Entropy,
I think you want your conclusion to be true also. 4 years ago we would have been on the same side. I think there is evidence from observation of our universe that the cause of what you call nature is design or conscious intelligence. This includes the 4 forces, atomic particles, molecules and living organisms.
Then why all the talking about biology?
Please find a forum for physicists (and theologians).
And? What did you conclude from that? In particuar:
* Why do these simple single-celled bacteria need this bewildering variation of ATP synthase beta subunits whereas animals make do with so few?
* Why do alpha-proteobacteria, just simple single celled organisms, need a protein that is very similar to ours, whereas actinobacteria need a completely different one?
* Why do green plants, in addition to that, need a second variant, that happens to be very similar to the one used by cyanobacteria [I checked that, try it yourself, just plug the FASTA sequence into Rum’s tree]?
I have an explanation for that. Do you? Demonstrate to us the amazing explanatory power of the Design inference.
Yes why would large multicellular animals be more similar in protein sequence? Why would dropping the more distantly related worms from the comparison bring the identity up? Why would mice and humans be almost identical? Hmm…can anyone help me with this?
Design!
Design explains this, and here is the explanation: The designer designed it that way.
But tinkering with existing proteins by changing their amino acid sequence is, and that happens to be what we were discussing. If the Designer can create FI that way, then any process that results in changes in AA sequences can as well. I am still waiting for you to retract your statement that mutations cannot create FI “of any amount”.
There is something else going on as well. I think (Mung, correct me if I am wrong) that Mung fails to realize that a population carries a sample of the sequences in sequence space, with replacement. That is; most populations carry multiple copies of a single specific sequence (let’s call them alleles, shall we 🙂 )
After all, even if we consider a binary function with a fixed threshold value (E.g. antibiotic sensitive and resistant alleles), mutation and natural selection can easily increase the average FI of a population.
Especially when gpucicio has explicitly said that they can.
Here’s an inference to the best explanation: 4 years ago, Billy swapped churches for a more fundamentalist one
I don’t see why that matters. How does it enter into the calculation of the FI for the hypothetical population you mention?
What is the meaning of “the average FI of a population” and how does one measure it?
You’re joking, right? It can explain anything, and that sir, is powerful!
I’m hoping that Joe will address the contradictions in his calculations of FI.
First he tells us that the FI for the two sequences 00000000 and 11111111 is 7 bits. But then shortly thereafter he tells us that the FI for those same two sequences is 0 bits. Which is it?
I’m also hoping that DNA_Jock will tell us what term he’d prefer us to use in place of “minimum threshold.”
You should pay some more attention to what Joe says. 😉
There’s an actually reasonable explanation: natural processes. “Deterministic” phenomena, very importantly energy flow, with a pinch of randomness. Scientists understand what that can do in terms of generic and functional information. Your ignorance and extreme skepticism about nature cannot trump proper thinking. Sorry.
On the other hand, the “design” thing is unreasonable from the very foundation. As I already explained.
An “inference” based on ignorance sitting on top of poor philosophical and scientific foundations cannot be called “powerful.” It can only be called fallacious. Again, why do you have such a low standard for this, while remaining unreasonably skeptical about nature? How come you don’t notice this discrepancy?
Nope. I just want to have some understanding. unlike you, I don’t lower my standards for the sake of religion though.
I doubt it. That would require much better understanding on your part. If you don’t haver that understanding now, you didn’t have it before.
More cart-before-the-horse here. Extending your philosophical problems into the whole universe doesn’t improve your position. It makes it much worse (if that’s even possible).
No doubt. But if you are going to adopt his argument shouldn’t you understand it and be able to explain it?
I don’t argue that 500 bits of FI gives reason to infer design because I couldn’t, for myself, explain why. If I can’t explain it to myself, I can hardly explain it to others.
For Joe, each individual sequence in a population has its own value for FI. Presumably, all other sequences with the same “degree of function” would have that same value of FI.
But how does he calculate the FI for each individual sequence and how does he calculate the average FI of the population as a whole?
On the bright side, at least I now know how Joe is calculating FI for an individual sequence.
He picks a sequence. Decides on its degree of function. Sets the threshold to that degree of function. Calculates the FI of “the system [1].” Then says that value is the FI of that sequence.
1. What would DNA_Jock call it?
Correct. We just map the degree of function to a FI value that quantifies how likely we are to find that degree of function (or better) in a randomly chosen sequence of total sequence space.
That can turn out to be very useful: What seems at first glance a minor increase in degree in function may be very hard to reach because only very few sequences possess this level, or OTOH a major increase in function may be very easy because a lot of sequences with a higher degree are very abundant (and hopefully close) in sequence space (e.g. require only a single substitution @Bill: co-option baby).
See?
ETA: minor correction
Mung,
The only way to calculate FI, that’s what I would call it.
FI is a function* of the level of activity that a sequence has. To calculate the FI of a sequence, you compare it’s activity with the activities of all possible sequences in the sequence space.
FI = -log2(1-percentrank)
You appear to have conceptual difficulty understanding percentiles and inequalities.
Do I need to understand those to understand how to calculate FI?
Then we are not talking about the same thing.
Q: What are we calculating the FI of?
Mung: “the system”
DNA_Jock: We are calculating the FI of the only way to calculate FI.
And that’s nonsensical.
Here’s Hazen:
So it seems to me we have two fundamental questions.
1. What is it that we are we measuring (e.g., the information content)?
2. What is the measurement being performed on (e.g., a complex system)?
I’d like to know how you and Joe answer those two questions. If you don’t mind.
Corneel,
Do share 🙂
That “quote” was never said. If people said the things you are claiming they said why not actually quote and link?
And to think I had actually thought you were changing your ways.
Corneel,
The statement was that mutations cannot create FI of any amount from scratch.
Can you give me a well argued reason to retract it?
Szostak:
That ought to settle it, but it won’t.
DNA_Jock claims that FI is not a property of the ensemble of all possible sequences, ranked by activity, but rather a property of each individual molecule (sequence).
Szostak says the exact opposite.
Yep, it’s that simple.
Define “from scratch” and perhaps that reason will become obvious?
OMagain,
A sequence that does not require the pre existence of another sequence such as the one you generated above.
Hint: endyosyboitisc
Waiting for the alternative from the design inference …
LoL. Did you just accuse OMagain of originality?
Corneel,
You have a small hurdle called the prokaryotic eukaryotic transition.
I saw the data for the first time last night and am grateful that you guys brought it to light.
Mung,
I know. I ran it through my plagiarism software program with no matches 🙂
You have a small hurdle called: “I am still waiting for the explanatory power of the design inference”.
This is the moment to win us over.
Corneel,
You mean that it explains the origin of the FI to build ATP synthase is not enough. You guys are really picky 🙂
The irony is unbearable [emphasis mine]. 🙁
Joe Felsenstein,
Because that is where the smoking gun was found…….FI
The FI for a system. There ought be nothing odd or remarkable about my using the same language.
Mung,
We have covered this already. System has been used ambiguously; in your quote above, the task is described as “To determine the functional information of any particular sequence we must specify three parameters:”.
It isn’t nit-picking and it does describe a real error of understanding on your part.
I will re-consider iff you can provide an example where Hazen ascribed an FI value to the set of all possible sequences?
Can you provide a reference that it is a smoking gun from the creators of the metric we’re talking about? Or is that simply your spin?
OMagain,
It was answering Joes question of why biology is important in the origins discussion. Thats where we find functional information thats only known true abundant source is conscious intelligence.
Except that’s not true. You have no idea where the FI came from, it is merely a weak claim that it comes from conscious intelligence unsupported by any evidence.
Even if we grant that evolutionary processes cannot generate FI in biology that does not endow the explanation that “conscious intelligence” created it with legitimacy.
What else is left, I hear you ask? Well, you do not have a full accounting of the laws of the universe and as such you cannot make any determination that sufficient non-conscious processes have been ruled out to only leave intelligence as the only candidate.
Also noted you have modified your claim to include “abundant” now that you are aware that gpuccio says that evolution can create small amounts of FI.
Given that we have never observed the creation of FI, when it is created by your conscious intelligence how is it created? Are individual atoms manipulated by this conscious intelligence? Or are the laws of physics changed? Is probability manipulation part of it?
How confident are you that this “conscious intelligence” is anything like us, given it can act over billions of years undetectably (I’m assuming you won’t be able to derive an experement to detect it’s creation in situ)?
In short, you are full of shit.
OMagain,
I am quite sure the above FI came from you. So the rest of your claim is nonsense.
Natural selection, too.
Anyway, this seems to be the reverse of what creationists usually do. When asked to be specific about why they think that biological adaptations must have arisen by Design, they take the goalposts and zoom them off to the Oirign Of Life or to the Origin Of The Universe. To which the proper response of the biologist is to say “then why the $#&@! don’t you go bother organic chemists, planetary scientists, cosmologists and/or theologians with this, and leave us alone?”
In this case the argument from the OOL or the OOTU is what convinced the creationist, who then decided that the people who most needed to be bothered were … biologists.
They don’t, of course (unless you count the Emin case we previously discussed). And I’ve never said that they do. Nor have I said that by “the system” I mean strictly “the set of all possible sequences.” Are you simply striving to misunderstand?
The set of all possible sequences alone is not sufficient for any calculation of the FI for the system. For that says nothing about function or degree of function, or, to follow his imagery, where the plane intersects the cone.
Given Szostak’s clear an unequivocal use of “the FI for a system” you should focus more on what that means and less on the fact that I use the same terminology.
When I ask you what term we should use in place of “minimum threshold” why do you remain silent? Do you just not know what we are referring to?
When I ask you what term I should use in place of “the system” why do you remain silent? Let agree on the same set of terms and make sure we’re talking about the same thing when we use them.
Ah. Now I see your error. You should have read further.
“Functional information is determined by identifying the fraction of all sequences that achieve a specified outcome.”
Plus, you can see from looking at the equations that it is not the FI for a particular sequence.
You simply cannot escape this DNA_Jock. Even after he still says “particular sequence” what follows is anything but that and he continues to speak in terms of systems.
The functional information, I(Ex), for a system that achieves a degree of function, ≥Ex, for sequences of exactly n letters is therefore …
The formulation of functional information also applies to systems in which sequences of varied lengths are combined…
ETA:
No need to calculate the FI for any particular sequence, at all.
Another inconsistency in DNA_Jock’s argument arises from the fact that Joe can speak of the FI of populations and it raises not even a squeak from DNA_Jock, the champion of the FI of a “particular sequence” view.
And obviously Joe disagrees with DNA_Jock.
What’s up with that?
I blame Richard Dawkins. And biology teachers. And lawyers. Especially the lawyers.
But not random genetic drift. That’s cumulative non-selection and it can’t possible give the appearance of design.
False. We see FI arising all the time without the interference of any intelligent beings. Intelligence itself only comes after lots of FI is put together by natural phenomena. Thus, the only known true abundant source of FI cannot be intelligence. It can only be natural phenomena, including those necessary for intelligence to arise in the first place. No amount of vacuous claims can change the facts. Nature is first by eons and immensity. Intelligence is but a much later and tiny product of nature.
Mung,
So, no reason to re-consider then. Cool.
Mung doesn’t understand, that’s what.
As we have explained repeatedly, Joe was talking about populations of sequences, each one of which has an associated FI value. As the allele frequency changes, the average FI changes.
He and I agree absolutely. So, no squeaking from me, just smiling and nodding.
I’m neither surprised nor disappointed. The facts though are staring you in the face. Take their discussion of Avida.
No particular sequence either mentioned or required. And they are obviously not calculate the FI for some particular sequence. All you have to do is look at their examples. The only ones that refer to a particular sequence (not any particular sequence) are ones that have a 1 in the numerator. Not exactly what Joe had when he allegedly calculated the FI for a particular sequence.
All the facts speak to the same thing, and all you can do is fail to address it.
That’s two things, not three.
Besides, if I was wrong, keiths would say so. 😉
ETA: And those “two things” are “attributes, they say. Attributes of what? You’ll figure it out.
This is patently false. There would be no FI without intelligent beings to make it up.