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?
So?
DNA_Jock,
This is your “I can’t estimate the water volume of the ocean” because a grain of sand fell in it argument 🙂
All science is tentative and all measurements have error factors.
keiths:
Mung:
Good to see you rubbing his face in it.
dolt.
a stupid person.
Good to see the mods letting all the personal attacks slide and your willingness to teach how it is done.
Bill obviously meant natural selection. So why are you pretending that he meant something else, oh paragon of intellectual honesty?
No, and you comment is dumb. As in stupid. Like something a dolt would say.
Rumrraket gets it. Why doesn’t keiths get it?
LoL. Your post was about protein design. Now you’re going to deny that?
Why wouldn’t Bill Cole just make stuff up? Well when he can count on backup from the likes of Gpuccio and yourself(?) no matter how galactically inane his output is then I suppose you’re right, there’d be no reason for him to police his actions for hypocricy, misrepresentation, or just blatant stupidity.
Are you asking rhetorically, or merely trolling, or are you genuinely unable to see a value in intellectual integrity?
That makes no sense whatsoever as a response to what DNA_Jock said.
Good to see someone is being honest here. 🙂
Mung,
Are you arguing that your comment should have been guanoed, since you confirmed Bill’s lack of intellectual integrity?
Dear Jesus,
I know Voltaire asked you to make his enemies ridiculous, but could you make mine a little less so?
Muchas gracias,
keiths
I can see a value in it. But if it doesn’t harm you or your loved ones, why do you care? And how is Bill obligated to align himself to the moral whims of keiths?
You have to actually read the context in which I responded to Bill. Bill was claiming that a mutation+selection process would be an inefficient way for a designer to make a functional sequence, and I explained to him that that is explicitly how it is done in practice by actual intelligent designers.
You can put the label “protein design” on that all you want but it is still an evolutionary process. It has the components of an evolutionary process(random mutants subjected to selection on their effects), and there is no target sequence, only a desired function.
Just as the biochemists who use evolution to design proteins don’t actually care about the sequence, so it is with evolution where only the function of the molecule (it’s effect on reproductive success) is what matters.
If you want to see which comments I think ought to be guanoed lobby for me to be an admin. 🙂
Exactly. Protein Design. And all those people who thought we don’t know how people design things.
Don’t blame me. You were the one who called it protein design. And rightly so.
No, it is a design process. And you know it is, so why deny it? keiths might get upset with you.
Also, an evolutionary process doesn’t have “selection for” some function in the mind of the designer. Or do you claim it does?
You guys are the ones feeding him. Don’t blame me. LoL.
And I thought making shit up was a “bad thing” that people ought not do. Silly me.
Which involves the very evolutionary process Bill Cole says is an inefficient way for a designer to design a protein sequence. And yet they do, and they don’t have a target sequence, there is just selection for function.
Your labeling obsession is neither here nor there. You get to call it whatever you want Mung.
Designers with minds can use evolutionary processes, that doesn’t somehow magically make them not be evolutionary processes. Nor does that mean evolutionary processes necessarily require minds.
Whether that which is selected for is being done consciously so, or whether it is a mindless emergent property of the selected function’s effect on reproductive success, it is still selection. It is still differential reproduction where some variations are less likely to make it to the next generation, and other variations are more likely to make it to the next generation. There really isn’t any essential difference.
Then why do you object when I call “design” what you call “evolution”? There’s no essential difference after all.
The fact is there are several essential differences, so why on earth would you claim otherwise?
For example, in the design process there is foresight, and a goal or target, and a plan to reach it. None of which allegedly exist in an evolutionary process. Now if you admit those into the evolutionary process, I don’t have a problem with that. Is that what you want to do, allow teleology back in?
I am unsure as to what you are complaining about here. It appears to me, that you are reacting to my 20 ~= 26 comment, and asserting “Yes, that’s close enough!”. If this is the case, I suggest you try re-reading what I wrote. I was agreeing that 20 is approximately the same as 26, and that therefore the size of protein space is roughly the same as the size of letter space (give or take 10^35 for strings 300 long, which is a small error in gpuccio math…)
That was the gist of my original comment : “Don’t worry Rum, Bill is only drawing a parallel between the sizes of protein and letter space. He’s not making any claim about navigation!”
I was, evidently, wrong. You are making a claim about navigability. In which case, the appropriate comparison would be “You can’t estimate the amount of salt in the ocean unless you measure the salinity.”
Volumes and grains of sand don’t enter into it.
It’s pretty weird though, even when I am agreeing with you and attempting to defend you, you still feel the need to react with content-free snark. There’s an impressively deep lack of comprehension there.
You are being naughty again, Mung. You claimed that it was not an evolutionary process.
[emphasis in original]
You need to pay attention. He claimed there is no essential difference. So my argument is if there is in fact no essential difference, he should not mind if I say “design” where he says “evolution.” Yet he does mind. So there is a difference and he knows it.
So you’re naughty for calling me naughty and for not calling Rumraket naughty. 🙂
Or keiths. Or Entropy. Or dazz.
naughty? I’m more inclined to call you retard.
I claimed what is not an evolutionary process? First things first.
DNA_Jock,
Navigability is not the issue. Function is the issue or N. If N is a grain of sand or smaller in the ocean (who’s function is displacement) then it is no longer important to the analysis or measurement of the quantity of the water.
Oh Mung,
I have been paying attention.
For instance, I know that text that appears in blue is typically a link. Click on it to see what you claimed is not an evolutionary process. You were obviously wrong about that, and Rumraket corrected you.
The issue is that the conclusion that you derive from that, that there are no functional sequences outside of the ones we currently observe in vertebrates, is clearly falsified by the sequence diversity we observe in a wider sampling of organisms. Your “functional requirements” are merely a rather smallish fig leave to hide that fact. Jock’s appraisal of gpuccio’s argument as TSS is absolutely justified.
Also, I propose that your “being blindly lead” accusation is adopted by all psychology textbooks as a classical example of projection.
Corneel,
When did I make this claim? I think your arguing against yourself again.
That is what I read from this statement.
If I misinterpreted that, then you need to explain what you think gpuccio’s claim is.
Corneel,
Yes, you misinterpreted it. I brought up the possibility of different functional requirements between bacteria and vertebrates. Singled celled organism having a different power requirement then a multicellular organism with several trillion cells each cell substantially more complex than its prokaryotic precursor.
You dismissed this out of hand.
You also make no attempt to explain 400 million years of preservation.
Gpuccio’s claim was about preservation over deep time and the evidence that supports that using a limited set of animals. TSS was a strawman argument.
Jock manufactured the fallacy by changing gpuccio’s argument from measuring a select group of animals to measuring all animals and similar structures and claiming that this is a requirement. It was a quite cleaver use of a logical fallacy.
The real issue is that Jock wanted to use the word fallacy which damns gpuccio’s argument up front. Jock is skilled in political type arguments.
He could have simply argued that the measurement was inaccurate due to too narrow a measurement. I do agree this subject is debatable but at the end of the day gpuccio’s claim is probably valid as Jock’s claim eventually ends up amounting to “a grain of sand in the ocean invalidating the water volume estimation.”
An additional issue is that the beta chain is only one of the complex proteins gpuccio has analyzed and we see deep preservation with few if any exceptions with proteins like PRPF8.
Yet there is no division between single celled and multicellular organisms. The beta chain of ATP synthase from your mitochondria is more similar to that of members of alpha-proteobacteria then either one is to that of say, Streptomyces. Hence, the solution you proposed doesn’t comport with the facts. That is the sole reason I dismiss it.
How quickly they forget. We discussed purifying selection at length previously, remember? In addition, both Rumraket and Entropy have explained to you why sequence divergence is more shallow in vertebrates, with pictures and everything.
And you still haven’t brought even a single piece of experimental evidence for it. It just remains your mere assumption that the diversity of sequences we see are due to unique functional requirements or constraints in different species. That’s a nice hypothesis, where’s the evidence?
This is just your rationalization, nothing more. Where’s the evidence Bill? You make shit like this up all the time on zero evidence. No experiments, no observations, just some ad-hoc excuse you make up on the fly.
Oh gee I just can’t figure out why vertebrate sequences would be more similar to each other, than to bacterial sequences, or why some bacterial sequences would be more dissimilar than any two arbitrary vertebrate sequences. Hmmm how to make sense of that.
No, gpuccio’s claim is that function is exceedingly rare in total protein space and conservation of some selected proteins is an argument that is supposed to support that claim. The Texas Sharp Shooter is a valid objection to gpuccio’s habit of setting unreasonably narrow definitions of specific function in order to be able to exclude similar proteins that inconveniently pop up. Yes, that is a fallacy, and yes, gpuccio has been committing it. Measurement error has nothing to do with that.
That is false too. There are numerous proteins that are polymorphic both among as well as within species.
Corneel,
How much closer?
Purifying selection as a result of?
Corneel,
How have you determined they are unreasonably narrow?
How do you validate this assertion?
Aligning Homo sapiens mitochondrial ATP synthase subunit beta to alphaproteobacterial species Candidatus Pelagibacter gets an identity score of ~73%.
Aligning Homo sapiens mitochondrial ATP synthase subunit beta to Streptomyces gives an identity score of 56%.
It’s effect on reproductive success of course. Nobody is saying ATP synthase isn’t important to the organism. Obviously there’s selection to remove mutations that keep it from functioning well. It isn’t evolving at a neutral rate. But it also isn’t immutable. The magnitude of the differences still correlate with increasingly distant relationships. It will generally be the case that the older the divergence of the species, the more change has had time to accumulate. And that is what we see.
I have tried to improve my drawing to make the time dimension and differences more explicit (click for larger version):
Rumraket,
We agree on this.
Pretty close to immutable over 400 million years. Only 10% wiggle room while you had 40000 different species form with a huge variation in morphology. This supports gpuccio’s analysis of a high content of FI for the beta chain. There is a huge variation in the species yet high conservation in this protein.
Rumraket,
90% preservation with 400 million years of DNA mutations at a reasonable rate looks like a mutation that causes AA substitutions in the fixed group is causing failure right in the germ-line at reproduction. Apoptosis may be occurring, or failure to form a fertilized egg.
Thanks Rum, I will just be adding the missing alignment of the two bacteria with an identity score of 60%.
That blows Bill’s different “functional requirements between bacteria and vertebrates” out of the water as a viable explanation. So much for the explanatory power of the design inference.
The memory is going a bit, isn’t it? A major red flag should be the fact that the definitions are adjusted everytime somebody comes up with some inconvenient data. DNA_Jock explained this to you previously.
Trust me, I am a biologist 😉
Honestly, this is not some arcane fact, but textbook stuff. Before PCR changed molecular biological research, allozymes (protein variants being pulled at different speeds through an agarose gel) were the way how biologists studied molecular variation. They are not rare at all.
What would be the function that is quantified by the FI here? Hey, that wouldn’t be fitness would it? Why yes, it must be, because you invoke conservation by purifying selection. Did you notice several people in this thread going on and on about “dancing around an optimum” not being the same as “the width of the local minimum of selectable function” like a million times? Do you understand that argument, Bill? Could you reproduce it in your own words, please?
Oh look, it’s the argument from The Feelies. I feel like a small amount must have a tiny effect tolerance, or something (consult the graph). It’s “only” 10% wiggle room. That’s not an argument. And it sure as hell isn’t science.
What is meant by a “reasonable rate”? Rate of what? Reasonable to whom? What are you talking about?
Are you blathering again without having clue? That’s a rhetorical question.
What’s a “fixed group”? Is this just more blather?
Where’s the experimental evidence? Surely you must have numerous articles you can link which document observations of ATP synthase variants not normally observed in vertebrates that cause “failure right in the germ-line at reproduction”, that “apoptosis is occurring”, or “failure to form a fertilized egg”.
You wouldn’t just be making shit up again right Bill? That was also a rhetorical question.
Corneel,
So your assertion is supported up by Jocks assertion? A funny assertion at that 🙂
Thats an answer 🙂
If you’re not an indoctrinated biologist it would be producing ATP for cellular energy 🙂
Rumraket,
No its an argument from the alignment data.
The mutation rate 10-^8 mutations per generation. Enough to explore the whole genome over 400 million years.
The alignment data.
Corneel,
How does it ” blow away” the different functional requirement claim?
I thought that would be obvious. Remember that we set out to explain the fact that the sequence variation of the beta chain of ATP synthase among bacteria is much greater then among vertebrates. If your explanation were correct:
… then we would expect a separation between single cell and multicellular organisms. Yet this is not borne out by the sequences we have looked at so far, which show that there are groups of bacteria with a higher overall similarity to vertebrate sequences than to more distantly related groups of bacteria. I will not rule out that some different functional requirements exist in multicellular organisms that give rise to shared protein features (you have yet to produce evidence for them), but the large sequence variation in bacteria, and the nesting of vertebrate sequences within them, is best explained by the phylogenetic pattern, regardless of functional requirements.