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?
Interesting Nolin,
So, are you implying that in both cases/sides some kind of faith is required?
There’s a conceptual problem there. A sequence can be conserved by natural selection even if the mutations in it are (say) only 1% lower in fitness. The mutant sequence could be the next-to-last step on a path leading to the current sequence. Once you get to it, slightly-lower fitnesses of mutants will eliminate them and prevent the current sequence from changing.
Huh? You have proof for that? Or are you speculating as usual and pretend that your speculations are scientific? It’s easy to prove me wrong, Joe.. I don’t think you can do it….
Faith is ALWAYS required for anything we do: if you go to sleep and think you will wake up tomorrow, if you watch weather forecast, if you go to school to get a good job, if you think gravity will work the same from now on, etc. But that’s an entirely different discussion: http://nonlin.org/philosophy-religion-and-science/
Is it speculative or is it, in fact, occurring (albeit as an exception)? If it is the latter, then you admit that mutation and NS can, in principle, add functional information into the genome. Gpuccio felt compelled to add the “new and original” qualifier to help us …ahhhh avoid wrong interpretations. So help me avoid wrong interpretations and tell me how we can tell apart new and original designed information from haphazard non-designed functional information, please.
Or say we lay a blanc sheet of paper on the table and wait for some invisible Designer to write the string down? What would that tell us? Right: nothing. So why should we disregard the effect of NS?
You have the weasel program on your computer. Just feed in some more-than-106-character target string and watch “blind search and random sampling” shatter the 500 bit limit:
TO BE OR NOT TO BE THAT IS THE QUESTION WHETHER TIS NOBLER IN THE MIND TO SUFFER THE SLINGS AND ARROWS OF OUTRAGEOUS FORTUNE OR TO TAKE ARMS AGAINST A SEA OF TROUBLES
** Gen: 1156 Dif: 0 Fit: 1.0000 Bene: 0.0125 Detr: 0.9625 Neu: 0.0250 Unchanged: 13
Whaddaya know: 168 characters in a little over a 1000 generations. It doesn’t work without natural selection, Mung.
Thanks, Joe.
Joe Felsenstein,
The data is telling us it is not moving up or down it stuck in a fixed sequence for a billion years across all life forms yet the DNA is mutating. There are many other proteins gpuccio has identified with this behavior.
In the Hayashi case the wild type required 10^70 trials. How is it we are observing the wild type?
Corneel,
I am not sure that given a mutation natural selection is working on additional information but I do believe genetic changes can improve fitness. The fitness improvement can be the result of a loss of information.
If a sequence is in an optimized state any change will decrease functional information. What we appear to be observing is lots of optimized sequences.
“Intelligent design” is, for the most part, creationism in a cheap tuxedo. I’m not saying that absolutely nothing new has come of it. The reason that ID is mostly a shabby revamp of creationism is simple: IDists are mostly creationists doing a bad job of hiding the fact that they are creationists.
It seems to me that gpuccio has merely cast protein families as created kinds. He is saying that evolution cannot change one kind into another, and cannot give rise to an entirely new kind, though it can account for novelty within kinds.
Gpuccio obviously has no genuine involvement in the measurement of functional information. It’s just science-y window dressing. He obviously has no justification for the 500-bit threshold. He simply took it from Dembski, without considering that Dembski required that the event have a detachable specification, and that he does not. (It’s impossible to provide detachable specifications for most biological functions. No one would ever have dreamed of them prior to scientific investigation of what actually occurs in living systems.)
By the same token, some scientists are bad at hiding the fact that they are atheists. But does that fact, on its own, disqualify their work in science? Of course not.
You guys are pathetic, unscientific liars. True scientists (atheist or not) don’t need to pretend to be doing science, you do
Dazz
If ID is not science, then, please, be so kind to point out the lies and mistakes. My simple point, in response to Tom English, is that ID cannot be discarded solely on the basis of the perceived world view of its proponents/adherents.
Not a single attempt at explaining anything, no theory, nothing but negative arguments, stupid analogies, and lots of unfounded assertions.
Oh, and no “new, original” information for centuries, just the same rehashed shit, you all sound like tard-bots
Tom English,
His interest is in information jumps over long evolutionary periods. I don’t believe he thinks in terms of created kinds at all. His hypothesis on information increase relies on common descent.
His work is trying to find an empirical measurement based on preserved sequences. His working assumption is that if information (AA sequences) is preserved over hundreds of millions of years and across many animal types despite saturated DNA mutations then the sequence is required for the function now and you can measure the information required for that function in bits.
The proteins he has identified are typically pieces of multi protein complexes where they are just a piece of an overall function and it looks like they’re binding specificity is very tight.
The 500 bit limit has an enormous error margin given that the total number of evolutionary searches is 120 bits over the history of life. I think you are correct in saying that he borrowed this number from Demski.
I think what is interesting about his work is identifying large jumps in information during evolutionary history. As more data is collected the pattern he has identified will prove informative.
And what is the ID explanation for such conservation over long periods of time? We have natural selection operating on functional constraints, which makes complete sense. You have nothing but bullshit
ID argues that certain features of the universe and of living things are best explained by an intelligent cause rather than an undirected process.
I take it that, according to you, explaining something by referring to an “intelligent cause” is no explanation at all.
Before I respond, would you care to elucidate your idea of what qualifies as an explanation and what does not?
That’s your problem right there, ID “argues” (and fails) but doesn’t explain in any way worth calling science. So the ID “explanation” is that “certain features” are best explained by ID, how fucking explanatory! Hilarious
You dimwits don’t even know the first thing about science.
Take Puccio’s nonsense for example: he claims proteins are engineered in non coding DNA. If it takes 400 million years for neutral evolution to erase all sequence similarity, a Designer that knows his target can also reach any region of sequence space in that time, actually he could engineer vertebrate ATP synthase in a much shorter time with no sequence similarity to E-Coli’s by producing only the necessary mutations towards the desired target: ID does not entail sequence conservation and can’t explain it (just like everything else)
But of course your response will be that ID is not about figuring out how the designer operates, which clearly shows that you’re not in the business of explaining stuff: ID has no entailments, no scientific content and you don’t even see the problem
ID is indeed creationism in a cheap tuxedo
ID invokes an “intelligent cause” as the best explanation for certain features of the universe and of living things. You apparently do not think that an “intelligent cause” qualifies as an explanation. Can you explain what leads to you to this conclusion, rather than stating that an intelligent cause is no explanation?
I am trying to understand your point. Are you arguing that science does not accept an intelligent cause as an explanation for certain things?
Fwiw, I think everyone should do science as if atheism were true. Not because it necessarily is, but because the scientific method ought not to leave dummy variables around for miraculous occurrences.
Origenes,
Invoking an undefined “intelligent cause” explains nothing. The book of Genesis contains some actual explanations with entailments. All debunked by the evidence, of course, but still.
No one stops you from providing actual explanations based on that intelligent cause, but you refuse to characterize the designer, even though we all know it’s your sky daddy. Go ahead and explain something based on your intelligent cause, no one’s stopping you, so stop whining and lying
Imagine if Newton formulated his gravitational theory the way creotards do: “Gravitation argues that certain features of the universe are best explained by a gravitational force, rather than non-gravitational processes.”
-How does that work Mr Newton?
-Gravity is not a mechanistic theory, and it’s not Gravity ’s task to match your pathetic level of detail in telling mechanistic stories
woo-hoo! science 101!
Walto & Dazz
Walto, notwithstanding the theistic inclination of the vast majority of IDists, ID is compatible with atheism. Moreover, biological ID is (even) compatible with materialism, in which case an ‘intelligent cause’ is a placeholder for a ‘material brain’ — a scenario where aliens seed the earth with life comes to mind.
ID essentially argues that intelligent design is a categorically separate causal explanation from undirected physical processes. According to ID, every post on this forum, the computer in front of you, science and so forth are best explained by an intelligent cause, rather than undirected physical processes.
This follows from, as Dazz correctly points out, ID’s neutrality on the identity of the designer.
I am a theist, and I suppose that the vast majority of IDists is too. However, that does not imply that ID is exclusively compatible with theism.
I propose that an intelligent cause, rather than undirected physical processes is the best explanation for your posts. Also, any scientific research is best explained by an intelligent cause(s).
Yeah, we’ve heard it all before. And you think that’s a killer argument. How cute.
Meanwhile, @ UD
You guys still don’t see that if that was such a damning problem, evolution would be impossible regardless of mechanism. You guys are closet special creationists
What’s the difference between claiming “intelligent cause” with no additional information and claiming “MAGIC”? Both have the identical explanatory and predictive powers.
Walto made a similar remark about “miraculous occurrences”. I do not quite understand what you mean. Sure, we do not know how intelligent design works. How we ourselves design things is a mystery. All we know is that intelligent design can accomplish things with ease that undirected physical processes can never bring about. In that sense every post on this forum is “magic” and a “miraculous occurrence”. If that is what you mean, then, surely, I can agree.
(Just saw this)
I think this is the only case where the calculations of the IDers are valid. Whenever they see a complex entity they assume that it exists in an island of function that exists at a minimum of 500 bits from complete non-function. IIRC the number is so large that we’d never expect to find a single example in all of the natural world. Its like a lottery that no one could ever win even if everyone on earth played.
We know a lot about how *we* design stuff, and not a single thing about any other kind of design. That’s one of the reasons why ID is anti-scientific: you guys avoid detail at all cost. You NEED to make vague and useless claims/analogies that get us nowhere in terms of added knowledge, just to conceal what is plain to see anyway: that ID is creationism without mentioning god. It’s stupid and dishonest
No, that’s not what I mean. Merely offering “Intelligence caused biological life” as ID-Creationists do is as scientifically worthless as offering “MAGIC caused biological life. ID-Creationists provide zero details, have no testable hypotheses, and indeed haven’t done the slightest bit of work which could possibly provide any details. ID-Creationism is about as scientifically and intellectually impotent as it gets.
ID could be science in the same way that archaeology is a science. Contrary to what Nelson, Meyers and other IDers say science is perfectly capable of considering design. When design is the causal explanation the type of questions asked and answered will be very different from when natural phenomena are the explanation. To understand that watch any good documentary on how the pyramids, Stonehenge or Easter Island statues were built. If there were any evidence at all that living things were designed we wouldn’t need ID because biology would already be working in ‘design’ mode and biologists would seem more like archaeologists.
If ID were valid it would be great to be an ID scientist. They could work on anything they wanted and would be fantastically productive. They would be like the first biologists to land on an alien world filled with life. And yet they dont take the first step to legitimize their assertion that life was designed.
Why do you suppose that is?
No one knows how God creates.
Unfortunately, from a materialist perspective, we do not know anything. First, conscious experience is utterly mysterious — the hard problem. Second, how quadrillions of tiny particles, which make up the brain, work in concert thinking about stuff, while none of them is rationally motivated, is equally mysterious.
This is a well-known complaint. Eric Anderson once answered thusly:
I have clearly stated that I am a theist, and that I suppose that the vast majority of IDists is too. However, as argued, it also true that ID is not only compatible with theism. The basic idea of ID, that intelligent design can do things that undirected physical processes cannot, is not an article of faith, but, instead, common knowledge, based upon our uniform and repeated experience.
Good to point this out. However you are mistaken if you hold that your observation goes against what ID proponents say. For instance, Stephen Meyer:
And being a theist ,you know the answer to those mysterious things?
Which is nothing more than a rewording of Dembski’s infamous “pathetic level of detail” quote, so still no new original information there,why should I believe that was designed? You are too stupid to notice, but that is a tacit admission of defeat right there. Thanks for playing
If requires faith to believe an omnipotent being is choosing to direct physical processes.
I agree. However, ID is neutral on the identity of the designer, which means that it does not posit an omnipotent being. This should be OLD news.
Again Stephen Meyer:
After all these years, can TSZ drop this pointless “argument”?
If the omnipotent being can, and possibly chose, not to direct some of the physical processes, does it make Him impotent?
What else are the retired farts going to do? Feed the bird in the park while awaiting the inevitable?
It does not posit an omnipotent being could be the designer? It may claim neutrality but logically an undesigned intelligence is required at some point.
Only by design.
Are you sure that it is neutral?
If it is neutral, then it should be considering the theory of evolution as giving an account of at least one possibility for the designer.
Somehow, I am not seeing that kind of neutrality.
ID does give the theories of evolution its due and acknowledges change over time… This is not what ID has been questioning and this is not what the theory of evolution predictions, Neil. It reaches beyond that: new, different body plans evolutionists call explosive…
The only problem is to move beyond speculations..
How do you give due respect to say… population genetics?
How should ID acknowledge mutagenesis experiments that have never proven the evolutionary predictions?
Most evolutionists are underwhelmed by ID arguments about body plans.
Most? Why not all?
Emphasis added.
I know a biology professor (an immunologist) who believes, on faith, that the earth is young. When I asked one of the members of his department whether there’d been any problems with his tenure review, she responded immediately, “It was a snap.” I’m not qualified to judge his research, but I can tell you that he’s got an outstanding publication record.
I really like the guy, as do his colleagues. I won’t call him a YEC, because, while he thinks that science might provide evidence to support his beliefs, he acknowledges that he doesn’t have adequate evidence. He owns his faith as faith — and humbly, I should add.
What disgusts me to no end in ID is the deceitful presentation of articles of faith as though they were conclusions arrived at by scientific investigation. It is no mystery as to why IDists do this. ID is a socio-political movement designed by a law professor in response to a Supreme Court decision. The court ruled against teaching “creation science” as an alternative to “evolution science” in public schools, and religious adversaries of “evolution science,” led by Phillip Johnson, scrambled to throw together a seemingly not-so-religious alternative. The approach of the movement has never been to say that there might be a science of ID. It has always been to claim that there already exists a science of ID. That is an utter fucking lie.
It is not impossible for utter fucking liars to do science. But it is not hard to see that utter fucking liars are constitutionally unsuited to scientific investigation. They do much better as shysters (of which there are considerably more in the ID movement than biologists).
I must emphasize that I have never made a blanket judgment that ID proponents are utter fucking liars. I insist on treating people as individuals, and I’m actually quite good at it. Furthermore, I’ll allow that ID might be able to gain some credibility as science. The very first, and absolutely necessary, step is to repudiate YECism. Of course, many more proponents of ID are YECS than are not, and there’s no way that the ID movement is going to disenfranchise them. So I’m going to keep identifying ID as the socio-political movement that it is, and not as science.
Again, this does not mean that no IDist will manage to do some science along the way. Each published paper must be judged on its own merits. And that gets us to the supreme irony of the matter: Guys like Joe Felsenstein and me are the ones digging into the papers. The ID crowd is constantly oohing and aahing over papers they don’t begin to understand. A fundamental problem with gpuccio is that he doesn’t have all that good a grasp of ID. He, like GEM, is much more interesting is spinning his own tales than in studying published papers.
Oh boy! It’s time to remove that earning, Tom… It looks like it pricked not only though your brain, but also through your consciousness….