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?
Gathered Bill. gathered. I depended on loads of FI in order to be able to do that. Not by choice, but as an inescapable necessity out the way nature works.
That’s been done already. I know, you think that providing a target is cheating. But you’re doing two things there. 1. moving the goalposts, you said mutations, selection and energy. That’s done. The weasel program and similar can do that. Mutations, selection and energy. 2. You’re forgetting that we’re dealing with information understandable by humans. Letters on screens. It’s only natural that we’d need a target understandable by humans. That doesn’t change the fact that the bits can be transformed by mutation selection and energy.
In non-human-made systems the “targets” are environments. No need for intelligences to provide those targets.
I think you’d do better if you read all those explanations for comprehension, rather than trying to make excuses to keep yourself from understanding something that goes against your preferred conclusions. This way, at least, you’d keep your faith in all honesty, for no reason but faith alone, rather than lying to yourself that science supports it.
Bill,
You specified the problem. I provided a solution that met your requirements.
You thought your challenge couldn’t be met, but I met it easily.
As I said, you’re always five steps behind. You’re so lost that you can’t even pose a successful challenge.
keiths,
Yes you did Keith, and you also supported my argument by providing a solution that required conscious intelligence. Thanks 🙂
Bad assumption
Entropy,
Sure, and with a target provided by conscious intelligence this process can work. Your dependent on this mechanism when you’re trying to find function through a long sequence.
Pointing out that Keiths solution required conscious intelligence is hardly moving the goal posts.
keiths:
colewd:
It sure was. You foolishly assumed that your opponents would have trouble with your challenge, when in fact it was easily addressed.
Poor Bill. You were hoping to show that FI couldn’t be produced by mutation and selection, and your challenge completely backfired on you.
When you open your mouth (or type on a keyboard), your incompetence makes you a liability to the causes you care about, including ID and Christianity. When will you learn to remain silent?
keiths,
Again thanks for supporting my argument:-)
colewd, then:
colewd now, dishonestly trying to move the goalposts:
Bill,
The funniest part is that even if it hadn’t been a goalpost move — and it obviously was — you’ve still failed. After all, here’s your reasoning:
But mutation and selection can easily generate FI without requiring a target provided by a “conscious intelligence”. See these threads:
You’ve failed again. If Team Jesus actually had a living coach, you’d be on the bench for sure, with your mouth duct-taped closed.
Has anybody mentioned quantum functional information on this OP yet?
After almost 1700 comments, somebody must’ve mentioned it…
How about Joe Sombrero?
Different … functional requirements? Bacterial ATP synthase has a different function than ours?
Oh boy, I hope the Designer could just add some bits of FI, and wasn’t compelled to do the whole thing from scratch again.
No actually all you need is differential survival and reproduction. There doesn’t have to be someone deciding on a target. The fitness landscape can be an emergent property of interactions between the environment and the evolving phenotype. Whatever sequence evolves is a result of that interaction, not a pre-specified target.
That’s what happens in Avida. It’s also what evolves in BoxCar2D. There is no target sequence, nor a target car architecture, in BoxCar2D.
And of course, that is what happens in nature.
ROFL. It can do nothing else you dolt. That is literally what it does. Find local minimums. How can you not know this? How can this not be immediately apparent to you?
Just like the natural processes work with “targets” provided by nature.
Bill, please. Don’a pretend not to understand something this obvious.
I wonder if you stopped reading, because I explained this. Of course we’d be dependent of such thing for a sentence. Sentences are human-related things, thus the target has to be a human-related thing. What else but a human can provide the target?
In nature it’s nature-related things. So the targets are nature-related things, such as environments.
It’s moving the goal posts to add a complain about targets after you asked for mutations, selection and energy. But that’s the least of your problems. The most important one is distinguishing contexts.
Nah. Team Jesus depends on their players to be blind to the amount strikes they get. They just keep playing as if nothing happened.
Corneel,
Since when is a “different functional requirement” the same as a “different function”. You just can’t help yourself 🙂
Entropy,
You are right. I asked for mutation, selection and energy. So Keith supplied mutation, selection, energy and conscious intelligence. You don’t see the irony here?
The english language has a similar sequential space as proteins. Thats why Dawkins used it to simulate protein cumulative selection.
You are claiming that nature can do this without a target sequence. Can you state a clear hypothesis? A hypothesis you can model? A hypothesis you can test?
What is your actual evidence of that? It’s just another thing you write without having the slightest clue if it is even true. Some excuse you make up to try to handwave away the evidence.
The difference between older branchings of bacterial clades, is greater than the deepest branches of vertebrate clades, because bacteria predate vertebrates by at least 3,000 million years. Oh gee it’s not like that makes perfect goddamn sense. Bacteria is a much older clade, there are much older bifurcations on the bacterial branch. The deepest branches in the bacterial clade go back almost to the universal common ancestor something like 3,800 million years ago, while vertebrates go back how far? At most 600 million years or so.
Here’s a drawing for you(click link for larger version). How much time has there been for sequence divergence in vertebrates, compared to how much time there has been for sequence divergence in bacteria?
Ah, sure. Silly me. It has different functional requirements, but that doesn’t mean it doesn’t fulfill the same function, right?
No sorry, you lost me again. Could you tell me what you mean by “different functional requirements”?
Corneel,
-energy usage
-speed of reaction
-maximum allowable error rates
-raw supply of ADP
-charge differential supplied by the cell
-etc
Yeah so those would be different functional requirements. Now where is you evidence that it actually has those different functional requirements? You’re just assuming it. You must have copious amounts of experimental evidence for it right?
What I see is that you continue reading partially, rather than for comprehension. The word “selection” implies that there must be something to select for. So Keith gave you what you asked. Mutation, selection, energy. You complained because there’s something for the program to select. Not only that, but something that should be expected since you’re talking about sentences in English.
That the target would be human-supplied is implicit in your request Bill. Not something Keiths added to it. If you ask for a different sentence, then, of course the final product will be a human-readable sentence. So you gave me a “problem” where the final product is a human-understandable sentence, then you complained because Keiths gave you exactly what yo asked for.
If so, then the program is demonstrating that mutation, selection, energy works for that FI gathering thing all right. Right?
If you say so.
Of course! The target is not a sequence, but a function. That makes it easier for the “mutation, selection, energy” process than the “sentence” problem. The functions can be performed by many different sequences, instead of been limited to a single answer.
Has already been done multiple times Bill. Tested in many different ways. Sometimes in the lab, sometimes in the wild, sometimes by checking new evidence, sometimes by looking for “smocking guns.”
What do you mean by that? Do you even know?
It’s like your bad habit of blurting out vacuous nonsense is getting worse and you’re just piling on with crap that is half-way incoherent, and the other half is just vacuous.
Rumraket –
I think he merely means that there are ~20 amino acids and ~26-27 distinct characters in English, and 20 ~= 26.
Given that he then references Dawkins [=> Weasel], it is clear that he is NOT making a claim about sparseness or connectivity of function in the two sequence spaces. That would be gpuccio’s favorite fallacy, not Bill’s…
OTOH, the idea that Dawkins was modeling specifically protein cumulative selection looks like a whole new misunderstanding.
Entropy,
I was delighted that he brought a solution to the table that required conscious intelligence. I tried to thank him twice for being a great wing man.
As long as conscious intelligence is involved.
Are you claiming that all protein solutions contain less then 300 bits of FI? 500 bits? I asked for any coherent comment and you could select and fix any english word that was found by mutation. There are 177k words in the english language so the FI here is under 300 bits.
Then you should be able to state a clear hypothesis of how nature creates FI.
I may have over-estimated Bill.
Bill,
Don’t you ever tire of being a punchline?
DNA_Jock,
Dawkins was modeling an inefficient way for an intelligent agent to create a sequence.
DNA_Jock,
actually Jocks fallacious naming of a fallacy when he misunderstands what gpuccio is doing.
Now you’re insulting my intelligence Bill. You brought a problem with a human-related target, therefore “intelligence” was necessarily involved. That doesn’t mean that the method required the intelligence to be involved in the way IDiots pretend their gods to be involved. Namely, this is not direct transformation of a sentence into another, it’s done by “mutation, selection, energy,” a procedure that doesn’t require intelligence. It only requires a target. It was the procedure that was in question Bill, not the target. The procedure worked.
The procedure was in question Bill, not the target. The target was already set as being human-related by yourself. The procedure worked.
I don’t know how many bits are involved, or whether the solutions have less or more than those bits. I know, however, that the energy to produce those amounts are orders upon orders of magnitude more than enough. Otherwise we, ourselves, would be unable to gather that amount of information. We would not even have the intelligence to plan the gathering of that information.
You first claimed that my sentence had more than 300 bits, now it contained less? Which is it? Then you asked if my sentence could be transformed into another with the same amount of information by mutation, selection, energy, and the answer was yes.
Joe gave you a theoretical example that you don’t understand, and I gave you the general features of nature that do that. I also mentioned that lots of hypothesis testing have been done. They’re called evolutionary studies. All of them have concluded not only that nature gathers FI, but has done so for billions of years.
In other areas of research they don’t talk in those terms (FI), but what they get is also information gathered by the natural processes involving a pinch of randomness (nothing would work without that pinch), plus the phenomena we model as natural “laws.” For example, the sorting of stones by size by the waves in a beach, or the forming of the solar system by gravitation acting on unevenly distributed matter (unevenly because of that pinch of randomness), thus resulting in accession discs, condensation of matter, and ending in planets circling the largest mass where a star is formed.
Stop missing the point Bill. It’s embarrassing that you’d twist things that way when you question was about the procedure to get to a target, not about the target itself. It’s even more insulting that you’d ignore that the environment can be a target without any intelligence being involved. So, please, I really prefer to keep things respectful between us, but you’re making it very hard.
Mutation and natural selection. It’s trivial actually.
Genetic sequences accumulate mutations over many generations. When lineages diverge because different subpopulations get reproductively isolated, different mutations accumulate in each for obvious statistical reasons.
Those that negatively affect function are removed by purifying selection, and the degree of their negative effect and the effective population size determines how effective purifying selection will be. Over long time periods (millions of generations), gene-duplications of already existing genes are slowly rewritten in their nucleotide sequences and those changes are subject to natural selection and drift. The duplicates diverge in sequence and function (just like we see in comparative genetics). So-called superfamilies of proteins have diversified through this process. Similar genes from different species gradually diverge with increasingly distant relationships.
So just as a teaching example, (to keep it simple, I can’t be bothered writing hundreds of nucleotides) there is this starting sequence. Let’s just say it’s a gene:
CGGATGAAAGCCGCT
This gets duplicated, so there are two of them (the second copy isn’t necessarily placed in extension of the first, it can be elsewhere in the genome):
CGGATGAAAGCCGCT CGGATGAAAGCCGCT
Generations later, a mutation happens in the copy
CGAATGAAAGCCGCT
Along the way, other mutations happen that negatively affect the organism that get these mutations which probably makes it selected against:
CGGATGATAGCCGCT
But there are millions of individuals in the population, so there are still many others that don’t get the lethal/deleterious mutation.
Then many generations later, another mutation happens in the copy
CGAATGAAAGTCGCT
Again many generations later, another mutation happens in the copy
CGAATGAAAGTCGAT
…
…
And so on until many many thousand of generations later, an entirely new piece of gene-sequence has been written that can end up almost completely dissimilar to the original:
GTAGCTCCGATACAA
That’s how evolution produces FI (any particular mutation that results in neofunctionalization can have this effect). The combination of mutations that accumulate, the novel functional effects of those mtuations, and natural selection on their effects, produced a new functional gene-sequence.
There isn’t a coherent definition of FI that could meaningfully say the first and original gene-sequence constitutes a genuine case of FI, but that a functional mutated copy generations later, does not. Any rational person can see that all it takes for FI to be created by an evolutionary process, is mutations accumulating over time, those mutations having novel functional effects, and their effects filtered through natural selection. Of all the IDiot arguments vented here through the years, the one that says there isn’t a process that can create FI is among the most obviously false.
accretion discs.
That’s cute.
gpuccio claims that the FI seen in the function “a sequence having a good meaning in English” is a good analogy for the FI seen in a protein.
You are claiming that gpuccio is correct. Please support this claim with evidence regarding the sparseness and connectivity of function in these two sequence spaces (English and proteins). If you are unwilling or unable, please concede that you were making stuff up.
DNA_Jock, to colewd:
That would require intellectual integrity. Not a Bill thing.
DNA_Jock,
I understand you disagree with gpuccio on this. You have a disagreement and you label your opponents position a fallacy. You think you cannot estimate FI by looking at sequence preservation over deep time and basing FI on preserved AA sequences.
If we can then, using the english language is a relevant analogy given an equivalent number of bits of FI. It also brings to light the difficulty of generating FI.
As you label your opponents position a fallacy I label your failed attempt to support your claim resulted in creating your own fallacy. Simply raising measurement uncertainties does not eliminate the ability to estimate FI.
Now please refrain from the lecture on islands of functions and local minimums unless you can provide evidence for their existence for the proteins that are being evaluated.
Sorry Bill, but this takes the cake. If you don’t understand the conceptual framework of this discussion, then it’s you who should refrain from lecturing anybody about anything.
If now we had to start by explaining why this request of yours is nonsensical, we’d have to start by explaining what local minimum means, and that might be very difficult given the misunderstanding/ignorance that your request reveals. Worse, it reveals that your “answers” have been given within an ocean of ignorance that’s worse than we could possibly have anticipated, and thus we should not be surprised of the lack of advance in this conversation. You’re using terms you don’t understand. You’re complaining about things that you don’t understand at the most basic level either. All while being quite adamant about how this or that “supports” your position. But you have no idea. You’re unfit for the conversation, and we’ve been wasting a lot of time thinking we were talking to someone who was using words that he understood, but actually didn’t.
The proper action when you’re out of your league is to say so, and stop pretending to lecture others Bill. I’m sorry, but I’m out of this conversation. No point if you will pretend to understand, ignore lots of explanations out of incompetence, yet lecture us by using words whose meaning you have no idea about.
Which we technically can’t, since we don’t know how many other possible functional variants are out there that evolution never “found”, or have been discarded in favor of the ones we see because the ones we see just have higher fitness.
Seeing a handful of sequences used in extant life doesn’t tell you the density, or number of functional islands in the fitness landscape of sequence space. It doens’t tell you how big the island is they sit on, or how far there is another island. It doesn’t tell you how tall the extant island is compared to others.
You think there are no other functional islands out there, and you think there is no slope for selection to climb because we see some degree of sequence conservation. But that could just as well tell you that there IS a slope for selection to climb, but extant sequences just sit on a local optimum with sequences further away having lower fitness in comparison. Fitness that would still be viable and allow an organism to exist and reproduce, but be outcompeted by extant sequences.
You’re claiming that isn’t the case, despite the fact that you can’t. We have asked you over and over again how you know this, and all you seem to be able to do is to brainlessly regurgitate that extant sequences are “preserved” to some degree.
But as just explained, and previously explained like fifteen times, your conclusion doesn’t follow from the premise.
It.
Just.
Doesn’t.
Follow.
We are explaining to you why it doesn’t follow, and you keep coming back with the same claim on repeat. Will you allow yourself to think at some point or is this same stupid regurgitation of the same endlessly refuted point all you have?
Equivalent number of bits of FI of what? Do you even fucking know what you are saying? Here you seem to be confusing FI, Functional Information, with the size of the english and the amino acid alphabet.
Those are two very very different things.
Why do you persist in blathering about a subject you’re not equipped to discuss? Get a fucking education.
Well since Dawkins already knew the target, then there’s no reason to “generate” it using his Weasel algorithm.
But when the target sequence isn’t known, only the function is, then an evolutionary process is one of the best ways to “design” proteins that humans have alighted upon. That is how human biochemists who make proteins for use in the biotech industry actually “design” new protein sequences. Because it is extremely difficult to predict from first principles how a protein with a desired function “should look”. It is actually much easier to just generate a large collection of randomized and shuffled sequences and submit them to multiple iterations of mutation +selection for the desired function, then pick the best candidates from the results. The sequence that results from this isn’t known beforehand.
Fascinating. Do go on.
I’ll pick “maximum allowable error rates” if you please (gee, I wonder what that means too). Tell me how are maximum allowable error rates different between E. coli and humans on the one hand, and oh.. just pick some gram-positive bacterium of your liking on the other for comparison. Bonus points if you can point out the sequence differences that correspond to the differences in that functional requirement.
To be honest, I firmly believe you just made that stuff up without checking whether variation in any of those requirements really correlates with sequence differences in the beta chain of ATP synthase, but who knows, we might get pleasantly surprised by the amazing explanatory powers of the design inference.
Exactly. I wonder what experiments researcher Bill Cole, PhD in bullshitology, has performed where he functionally analyze ATP synthase mutants, where he determined which residues have which particular effect(s).
Or perhaps he can link us some actual articles where such work has been performed. Surely he wouldn’t just be making stuff up right? Note that we are asking not because we think none of the mutations that separate different ATP synthase homologues have any functional effects. I’m certain some of them do.
But Bill’s rationalization is that different ATP synthases cluster into different clades because their differences must be due to unique functional constraints that must have been designed and couldn’t plausibly have evolved from common ancestors. In order to be able to make such a claim with evidential justification(as opposed to just blatant assumption), Bill must have copious amounts of experimental evidence that exchanging ATP synthase subunits results in unconditional lethality for species with mutationally divergent subunits. And of course it should follow that the more divergent they are, the more likely they are to be unable to be exchanged without unconditional lethality. Or alternatively, he must be aware of articles that document tests involving huge libraries of inferred ancestral states where it is demonstrated these are unconditionally lethal and nonfunctional.
True, I do think that. I am correct, for reasons that have been explained to you multiple times by multiple posters, including most recently Rumraket above.
Sorry, Bill, but this makes zero sense. This is terrible, even by your standards. You are claiming that IF AA preservation over deep time offers a useful insight into protein FI, THEN the English language is a good analogy for the sparseness and connectivity of protein space.
Why even bring it up?
</Pa Grape>
Well, ‘raising measurement uncertainties’ degrades the ability to estimate FI, obviously. To the point where gpuccio’s efforts are useless. And we have explained why.
Well, I was talking about how navigable the two spaces (good meaning in English and protein) were; ‘sparseness and connectivity’, remember? YOU brought up local minimums (‘preserved AA sequences’), but I am not allowed to talk about how you are wrong? Seems a mite unfair. Not to worry, though — the other commenters here have done a bang-up job explaining why you are wrong.
In order to defend your claim that my statement about the sparseness and connectivity of protein space was fallacious, you must explain how the sparseness and connectivity of the two spaces are analogous, and support your explanation with evidence. To do that, you are going to have to display expertise in BOTH linguistics and biochemistry.
Or, you could admit that you were just making stuff up.
Bill is quite enamored by gpuccio’s english language metaphor, to the point where he was planning to run a simulation of gpuccio’s one-paragraph-transforming-into-another-one analogy. This discussion took place in the “cosmic consciousness 2” thread, starting around here.
To expand on this. it would be even more impressive if Bill could show articles where a particular F-type ATP synthase was completely transferred from one species to another that had it’s own ATP synthase genes knocked out or deleted, where such an exchange was demonstrated lethal under a range of plausible physiological conditions. Since Bill’s argument is, in essence, that there are unique functional requirements in species A which produce constraints on the sequence of ATP synthase genes such that an ATP synthase from species B could not replace it.
Corneel,
Yikes.
I have over-estimated Bill.
I note that Rumraket was a party to that ‘Cosmic Consciousness’ conversation, so he knew that Bill was in fact offering English sentences as an analogy for the navigability of protein space.
My apologies.
DNA_Jock,
First: nice post.
The sparseness is the issue when we are talking about large spaces. I think your point is right that the connectivity would be different for different functions but again if the space is large enough this is moot.
Sure but when the spaces get large enough the uncertainties begin to become a minor issue. They are just error factors that become minor.
This is the unsupported claim that taints your analysis.
DNA_Jock,
Or maybe you have over-estimated yourself. Time will tell.
Corneel,
I have done nothing more then state functional constraints as a possible cause of the variation. This is not the issue as many have been blindly lead by Jock down the TSS diversion non sense.
The issue is we see 400 million years of preservation between groups of species and thats the evidence to be explained and not dismissed because it is an inconvenient truth for the evolutionists.
Why not?
That’s not an evolutionary process Rumraket, that’s a design process.
ETA: Unbelievable.
So, the entirety of your basis for considering the analogy a good one is that both spaces are “large”.
Ack!
So, I was in fact correct when I stated that you were merely claiming that 20 ~= 26, and you have no idea about sparseness, nor connectivity.
Here’s a tip, Colewd, if the space is well-connected, then its size is virtually moot.
I would offer up an example, but I doubt it would help any.
You can assert that as many times as you desire, but we have given you two reasons, either one of which is sufficient to destroy gpuccio’s “conservation implies levels of FI that are unreachable via RM+NS” calculation: the existence of other peaks, and peak shape, both of which are supported by the experimental data.
If the space is well-connected then obviously it was designed to be like that. 🙂