Does gpuccio’s argument that 500 bits of Functional Information implies Design work?

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 2^{-500}.  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?

1,971 thoughts on “Does gpuccio’s argument that 500 bits of Functional Information implies Design work?

  1. Origenes: 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).

    I propose that you drop the dodgy rhetoric, designed for use in legal testimony, and say straight out that intelligence creates physical information out of nothing.

  2. Adapa: Merely offering “Intelligence caused biological life” as ID-Creationists do is as scientifically worthless as offering “MAGIC caused biological life.

    The great disappointment for students taking a first course in artificial intelligence is that they never learn the secret of programming intelligence into the computer. In fact, different types of “intelligent” processing in AI work very differently from one another. Study of brains gives us no reason to believe that we’re missing some unifying principle.

    In psychology (my major as an undergrad, and not a bad way to prepare for AI), intelligence, like thirst, is treated as a hypothetical construct. No one believes that animals literally have intelligence. A big part of the rhetorical game of ID is to make it seem perfectly obvious that the cause of special things that people do is their intelligence. Just about everyone accepts, uncritically, that s/he literally has intelligence. So it’s easy to get away with telling them that their intelligence is the cause of the intelligent things that they do.

  3. Origenes,

    This is a well-known complaint. Eric Anderson once answered thusly:

    ID is not an attempt to answer all questions. It is a limited inquiry into whether something was designed.

    Well, this is false. ID is a commitment to demonstrate that life and, perhaps, the whole universe, was designed. Not “whether,” not “limited,” not just “something.”

    Questions about who, why, how, when are all interesting second-order questions that can be asked only after an inference to design is drawn.

    This shows very poor thinking, if not plain stupidity. An “enquiry” about “whether” something was designed has to start by showing that there’s some designer to do the designing. There can be no design without designers, so there’s nothing second rate about this question.

    You may want, deeply in your heart of hearts, for ID to answer all of those questions. But that is a failure of your expectations, not ID itself.

    Of course it’s a failure of ID, a failure ironically introduced by design to hide the real goal of the movement: to introduce god-did-it into the science classroom. This stupid attempt at denial backfires.

  4. Origenes:
    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.

    While this might sound reasonable to you, it isn’t. What we know about intelligence is about us. We know that all those features that ID is committed to prove as being the product of ID are necessary for our own intelligence to work. Therefore, there’s a cart-before-the-horse problem right there.

    Thus, positing an alien invites the questions: if our intelligence can only operate thanks to ID, then how come those aliens’s intelligences don’t have any need for being intelligently designed? If those intelligences are independent of ID, then why would our intelligences not be independent of ID? Why not approach the problem by assuming what we see: that our intelligence requires those features, therefore, those features are not the product of intelligence. Even if we didn’t have an answer to the origin of these features, we’d save the embarrasment of proposing a cart-before-the-horse scenario with no basis (no intelligent designers, no tools, no methods, no nothing but ID-did-it!).

    ID essentially argues that intelligent design is a categorically separate causal explanation from undirected physical processes.

    This one contains problems so profound that it gives me a headache. What do you mean by undirected physical processes? I ask because having a direction does not mean that intelligence is involved. Actually, the only way intelligence can exist is if there’s “direction” in the first place. So, again, cart-before-the-horse. We’d be indefinitely asking what gives direction to whatever makes this imaginary Designer’s intelligence work. Another 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.

    Sorry, but this is false. While I think you honestly believe this, I doubt that you have thought about it carefully enough. Once the ID claims are examined carefully. There’s no proper scientific/philosophical way to get to ID. The only way is religious.

  5. Tom English: The great disappointment for students taking a first course in artificial intelligence is that they never learn the secret of programming intelligence into the computer. In fact, different types of “intelligent” processing in AI work very differently from one another. Study of brains gives us no reason to believe that we’re missing some unifying principle.

    In psychology (my major as an undergrad, and not a bad way to prepare for AI), intelligence, like thirst, is treated as a hypothetical construct. No one believes that animals literally have intelligence. A big part of the rhetorical game of ID is to make it seem perfectly obvious that the cause of special things that people do is their intelligence. Just about everyone accepts, uncritically, that s/he literally has intelligence. So it’s easy to get away with telling them that their intelligence is the cause of the intelligent things that they do.

    There is so much wrong in what you said in a few posts. Seeemly off thread but these threads of hundreds of posts are always off thread I note.

    ID is not cheap suit creationists.
    I am a creationist. I wish the leaders and most famous, prestigious, ID thinkers were YEC creationists. They are not or just a few.
    ID folks seem to believe in a creator but thats not a creationist as understood by the courts or social-political movements. its just everybody who ever thought there was a creator and the fingerprints is in nature.
    This is functionally erroneous.

    ID is successful, as the reason for this forum proves, because they have intelectualy killer knownk down better conclusions for natures origins/mechanism and criticisms of the wrong ideas in the story. Its an intellectual adventure for ID. They are still in the pink of health.!

    What in the world Tom English are you teaching about intelligence.
    AI is not intelligence but merely memory operations. No more intelligent playdoe taking a image.
    YES! People are right to think they have intelligence and spectrum/score amongst humans.
    God has intelligence and so does his people made in his image.!
    Intelligence is not really a thing. Its Wisdom, understanding, knowledge, as the bible says God said.
    I insist a greater intelligence, w, u, not k, is , on a curve, amongst ID /YEC folks and this a reflection on greater demographics. More republican then democrat for example.
    Its unlikely , on a curve, ID/YEC will fail to prevail in many/most of its criticisms.
    You can calculate probability after all. Probability is on the side of the aggresive rejection of a claim scientific theory and on the criticism of a rejection of a intelligent creator.
    TOM is your side being persiuasive on this forum when i8t should be dominant? NO! There is no persuasion as i see it on the main points.
    The others here are not all that either and could do better but they are giving fair fight.
    Error has a innate attrition within its dna.!

  6. Tom English: 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.

    This reminds me of Dembski’s famous, “Intelligent design is just the Logos theology of John’s Gospel restated in the idiom of information theory.”

    Dembski evidently thought he was on to some Next Big Thing that would launch a new scientific and philosophical paradigm. Too bad for him that he never got the gist of neither science, philosophy, or of theology. Even in theology you can’t just assume stuff.

  7. Origenes: I propose that an intelligent cause, rather than undirected physical processes is the best explanation for your posts.

    That’s nice. Perhaps you can demonstrate the truth of that proposal scientifically?

    http://www.conservapedia.com/Explanatory_filter

    Or, you know, at least as scientifically as possible for ID. Care to try to use the EF to demonstrate that claim?

  8. colewd: 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.

    It’s not clear what you are saying here. Are you suggesting that non-designed mutations never involve gains of functional information? By which you mean molecular function, I guess?

    It is true that we know of cases where loss-of-function mutations turn out to be adaptive (which can result both from deletions as well as insertions, the latter adding information in the colloquial sense). Perhaps less well known to you is that most novel gain-of-function mutations (where function is enhanced, or a novel function is acquired) are also bad news to the organism that carries it. They can lead to immune deficiencies and cancer for example. Are those mutations designed? If not, will you let go of the idea that random mutations can not introduce functional information?

    colewd: 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.

    Optimized to what? What will happen when an organism needs to deal with a novel environmental challenge? How does it adapt?

  9. Origenes as quoted by dazz: Origenes: “Obviously, function is a called “function” because it serves a larger whole — the organism. So, changing the function puts the whole in harm’s way. How can one, while driving a car, change (or improve) the motor and retain its function?”

    That is interesting, as I just asked Bill Cole about disease variants that result from gains-of-function. Do the affected proteins cease to have “function”? What IS the relationship between molecular function and fitness in ID science, I wonder?

  10. Origenes: This is a well-known complaint. Eric Anderson once answered thusly:

    ID is not an attempt to answer all questions. It is a limited inquiry into whether something was designed. Questions about who, why, how, when are all interesting second-order questions that can be asked only after an inference to design is drawn. You may want, deeply in your heart of hearts, for ID to answer all of those questions. But that is a failure of your expectations, not ID itself.

    I certainly note how all those IDers are wary about accepting the design inference. Best to put off those second-order questions until you are really really REALLY sure.

  11. Origenes

    Questions about who, why, how, when are all interesting second-order questions that can be asked only after an inference to design is drawn.

    Entropy

    This shows very poor thinking, if not plain stupidity. An “enquiry” about “whether” something was designed has to start by showing that there’s some designer to do the designing. There can be no design without designers, so there’s nothing second rate about this question.

    I’m sorry, but I’m going to have to side with Origenes here. Think of the Monolith On The Moon in 2001: A Space Odyssey. The design inference comes first, and it’s a mathematical inference based on the simple fact that the likelihood of any unguided natural process generating an object like that is astronomically low. Questions about the identity or even the current existence of the designer (who might have lived and died billions of years ago) come second.

  12. vjtorley,

    I think the stronger point against Origines is that his argument for the possibility that the designers were aliens is self-contradictory. If we infer design based on the impossibility of a natural origin of life or humans, then the same argument applies to the origin of the aliens, and so we have a regress back to something that doesn’t need an origin, i.e. a first cause or deity. (Let’s set aside for the moment problems with the very notion of uncaused first cause or deity, which is likely also incoherent.)

    If, on the other hand, we allow that aliens might have originated naturally, there is no reason to suppose that life on earth could not have also.

  13. Origenes: Questions about who, why, how, when are all interesting second-order questions that can be asked only after an inference to design is drawn

    For the sake of argument let’s assume we grant you Design has been inferred. What now? If you had access to the best scientific lab in the world with unlimited funding how would you go about investigating “design”? What testable hypotheses would you perform experiments on? How would you go about determining the answers to the when, where, how, and by who critical questions?

  14. Adapa:
    Origenes: Questions about who, why, how, when are all interesting second-order questions that can be asked only after an inference to design is drawn

    For the sake of argument let’s assume we grant you Design has been inferred. What now?

    I think this approach is reasonable. I agree that we start by drawing testable inferences, and then we test them. I recall reading somewhere that the substantial majority of scientific hypotheses prove incorrect under rigorous testing (or partially correct, but for unanticipated reasons).

    The inevitable problem here, as always, is that testing requires operational definitions, which divine design is lacking. So we bat the question of testing back and forth a few times, until we are obliged to concede that divine design is in fact NOT a testable inference, but rather a non-negotiable presumption, based on emotional need rather than any sort of probability estimate.

  15. John Harshman: If, on the other hand, we allow that aliens might have originated naturally, there is no reason to suppose that life on earth could not have also.

    Exactly

  16. vjtorley: it’s a mathematical inference based on the simple fact that the likelihood of any unguided natural process generating an object like that is astronomically low

    We observe natural processes generating life every day, not many monoliths. The “unguided” qualifier seems superfluous… and negative. What does guided mean in this context?

  17. vjtorley: Think of the Monolith On The Moon in 2001: A Space Odyssey. The design inference comes first, and it’s a mathematical inference based on the simple fact that the likelihood of any unguided natural process generating an object like that is astronomically low.

    ID’ers got basic science upside down. Always, invariably, and obstinately.

    The thing that comes first is a hypothesis, not an inference. And no, it’s not mathematical, because (assuming that we are indeed talking about what comes first) you don’t have any data yet to compute with. Dembski’s (and gpuccio’s) 500 whatever is nonsense out of thin air.

    Prove me wrong. Mathematically.

  18. Just noticed that gpuccio is eavesdropping on the conversation here:

    Corneel at TSZ proudly walks Dawkins’ silly steps:

    [ Quoting my comment to Mung about the weasel program ]

    So, this is his idea of NS: having an oracle that already knows the solution.

    As I have already said, if you already have the full solution ready, why pretend to find it in 1156 generations? Isn’t that completely stupid?

    Boy, it sure is. Say, who was inserting all that functional information during the course of millions of generations into the to-become-human genome? Wasn’t that an omnipotent designer with all-knowing foresight?

    That was a rather disingeneous comment, gpuccio. I never argued that weasel programs have a realistic fitness function, but Mung and I actually discussed specifically the limits of those type of programs. If you want to discuss with me, I’d appreciate if you respond to the criticisms I raised against your arguments, instead of intercepting and misinterpreting my dialogue with others. Thanks.

    Here is a question specially for you: How do we partition functional information into “new and original” functional information sensu gpuccio that the Designer put in and the boring ol’ functional information that mutation and natural selection introduced into the genome?

  19. Corneel,

    It’s not clear what you are saying here. Are you suggesting that non-designed mutations never involve gains of functional information? By which you mean molecular function, I guess?

    Do you consider genetic recombination a mutational event?

    Perhaps less well known to you is that most novel gain-of-function mutations (where function is enhanced, or a novel function is acquired) are also bad news to the organism that carries it. They can lead to immune deficiencies and cancer for example. Are those mutations designed? If not, will you let go of the idea that random mutations can not introduce functional information?

    I think this statement is self contradictory. If something is bad for an organism it is hard to claim you have increased information.

    Optimized to what? What will happen when an organism needs to deal with a novel environmental challenge? How does it adapt?

    Optimized to perform its intended function? Your cell phone number is optimized to call you. If you have a mutation what happens?

    Adaption is a function of the adaptive immune system. Adaption occurs as a result of systems engineered specifically for adaption. It can also occur from genetic recombination over time where features are modified in populations.

  20. colewd:
    Corneel,
    .If something is bad for an organism it is hard to claim you have increased information.

    Here’s a simple example to show what a dumb claim that is.

    Suppose we have a large island with a mountain chain running down the middle. The average temperature in the mountains is 70F. One side of the island is heated by warm tropical air and has as average temp of 80F. The other side is cooled by a northern sea current has as average temp of 60F

    On that mountain are born two identical twin mammals with a mutation which gives them longer warmer fur. One mammal walks to the cooler side where the warmer fur is beneficial. The other walks to the warmer side where the warmer fur is deleterious.

    Did the identical mutation increase information in the beneficial case and lose information in the deleterious case?

  21. colewd: Optimized to perform its intended function? Your cell phone number is optimized to call you. If you have a mutation what happens?

    Intended by whom?

  22. Adapa,

    Did the identical mutation increase information in the beneficial case and lose information in the deleterious case?

    What is your argument that the information content changed at all? Prior to the mutation the animal still had fur.

  23. colewd: Do you consider genetic recombination a mutational event?

    Not in itself, although it occasionally does give rise to genetic mutations. It can also increase genetic variation by creating novel allelic combinations. Will you be answering my question?

    colewd: I think this statement is self contradictory. If something is bad for an organism it is hard to claim you have increased information.

    Yet if you define FI in terms of some quantifiable task, e.g. protein binding affinity or enzymatic reaction rate (which Szostak’s definition does), it follows that there is some optimum you can exceed. There simply is no perfect correlation between molecular function and organismal performance. Too much of anything is bad for you. If you don’t like that, you need to define FI in terms of survival or fitness. I strongly encourage that you do, because it makes more sense when you invoke purifying selection as a means to preserve function.

    colewd: Optimized to perform its intended function? Your cell phone number is optimized to call you. If you have a mutation what happens?

    There are quite some implicit assumptions in that example, don’t you agree? Not biting.

    colewd: Adaption is a function of the adaptive immune system. Adaption occurs as a result of systems engineered specifically for adaption.

    Only vertebrates have an adaptive immune system, and it will only deal with pathogens, not adaptation in the general sense. In addition, many genes involved in immunity are notorious for being incredibly polymorphic (e.g. human HLA genes), so there does not seem to be a single optimal solution. Note that that runs counter to the scenario that gpuccio presents.

    colewd: It can also occur from genetic recombination over time where features are modified in populations.

    Now this is by far the most interesting comment you have made. Recombination between what? No variation is tolerated, because most sequences were optimized remember? Recombination without genetic variation doesn’t make sense.

  24. gpuccio@UD

    It’s really telling what most commenters at TSZ are trying to do.

    They usuallly try to simply deny that functional information exists.

    Now, as the current thread has been initiated by Joe Felsestein, who is much more reasonable than the average there, and who knows perfectly well that functional information exists and is important, and relies on a definition of functional information by none the less than Szostak, they have changed their strategy.

    OK, functional information exists, but it seems that it is impossible, or useless, to measure it, or to assess if there are useful thersholds in its values that can inform us about its origin.

    Their arguments are pitiful at best.

    Again, I exclude Felsestein, who is trying to discuss. But the others, who just state meaningless “ideas” about the 500 bit threshold, which is of course an arbitrary and very high threshold meant to ensure specificity, or simply relive the Weasel, or the cheap tuxedo, are a complete disappointment.

    This is deeply moving, gpuccio. It is so unfair how people insist on misunderstanding you. But I do hope you don’t mind if I don’t sympathise too much. The discussion of the weasel was in fact started by Mung, who suggested it was a good exercise for calculating functional information (which it was, because the system is tractable). It was you that misattributed the view to me that this is an accurate portrayal of how natural selection works in protein evolution. So the “reliving the Weasel” is a ghost of your own making. May I also take this opportunity to point out that the premise of the weasel program, that there is only one single target sequence, and a preset goal, is in fact closer to your view than to mine?

    Now if you would please stop the sobbing and address some of the valid criticisms please?

    It’s also interesting to note that the possible existence of imaginary and never observed pathways for whose existence there is no rationale at all remains their only argument. That’s the only thing that has come from Felsestein and Corneel.

    Since you are relying on the hollow logic of the design inference which can only survive if those pathways are not there, it is little wonder that this where all of the criticisms are aimed at, don’t you think? If you don’t like that, I suggest you seek out a positive argument.

    Oh wait, you don’t have any. These are all second-order questions of course. Silly me.

  25. gpuccio,
    I’m sure it would help if you were to create a single version of his argument that can be easily referenced instead of spreading it out over many OP’s and comments that are easily lost in the 100’s of other comments.

    I’m sure a page could be created as a sub page in this section: https://www.conservapedia.com/Intelligent_design

    And I’m sure they would give him sole edit rights, but I don’t really know how it works over there.

    And, perhaps, if the invisible pink unicorn gods are smiling, such a page could be used as the foundation for a formal paper that demonstrates that all biological constructs with a certain configuration must be designed.

    The problem is gpuccio, is that these discussions exist only in the minds of the participants and the dozen or so readers who are following along. If you want to convince others who are too busy to follow along extended discussions those discussions should end with the new knowledge generated being formalized and stored.

    I find it odd that this has not already happened. It would help you differentiate your output gpuccio from Kariosfocus’ whose work is obviously of a culture war nature rather then an attempt at elucidating the ideas behind Intelligent Design. He could never be published in a scientific journal. Assuming you are genuine in your desire to convince scientists that your ideas have scientific merit gpuccio, you should present them in the manner scientists are used to seeing them in. And this is not that.

    Otherwise one could argue that you know that your ideas cannot stand that level of formal scrutiny, so you are happy to keep it casual on blogs with a mostly unscientific audience who arrived as believers and continue to believe regardless. I’m sure you will say you don’t have time or don’t have an interest in such. But it’s plain you have the time. In fact you’d have more time, as rather then argue with people you can simply provide a citation to where that question is answered. And it’s plain you have the interest. You’ve been making these same arguments for years.

    So if you are not using quite the definition of information you claim you are actually using I’m sure peer review will sort all things like that out before they become a real problem.

    What’s to be afraid of?

    All ID needs is a couple of people to step into the void Dr Dr Dembski left when he abandoned ship.

  26. vjtorley:
    I’m sorry, but I’m going to have to side with Origenes here.

    Are you seriously saying that the identify of the designers is secondary?

    vjtorley:
    Think of the Monolith On The Moon in 2001: A Space Odyssey. The design inference comes first, and it’s a mathematical inference based on the simple fact that the likelihood of any unguided natural process generating an object like that is astronomically low.

    Sorry, but you’re talking about very different things. The monolith was not about the likelihood of “unguided” natural processes generating such a thing. It’s, even as a fantasy, a much more obvious case than the mere calculation of probabilities.

    (ETA: Actually, the only reason we know that monolith was designed is because Arthur told us so, and we learned all that the monolith could do, and even had a messages from the designers themselves. It was not merely, wow, it looks designed, therefore it is.)

    Even then, I doubt that if we found some mechanical, technologically advanced, objects we’d consider the question as to who are those designers as secondary. We’d still consider it of utmost importance. So, no, the design “inference” doesn’t come first unless we had no other option. I’d rather discover designers than discuss endlessly about whether something was designed or not.

    vjtorley:
    Questions about the identity or even the current existence of the designer (who might have lived and died billions of years ago) come second.

    Why would those questions come second? Why is that so unimportant except because IDiots want to get their bullshit taught in schools?

    P.S. I suggest you to read the comment right after the one you quoted from.

  27. colewd:
    Adapa,

    What is your argument that the information content changed at all?Prior to the mutation the animal still had fur.

    The length and thickness of the fur increased due to a new mutation. Are you saying that happened with no change in information?

    You make up this shit as you go along, don’t you?

  28. Corneel: Since you are relying on the hollow logic of the design inference which can only survive if those pathways are not there, it is little wonder that this where all of the criticisms are aimed at, don’t you think?

    The pathways could be there, by design.

    I see selectable pathways as nothing short of miraculous.

    🙂

  29. dazz: We observe natural processes generating life every day…

    Those are supernatural processes.

  30. colewd: If something is bad for an organism it is hard to claim you have increased information.

    Not really. Did you lose information when you learned not to touch a hot stove?

    Seems to me like that would be a useful gain of information.

  31. John Harshman: …and so we have a regress back to something that doesn’t need an origin, i.e. a first cause or deity. (Let’s set aside for the moment problems with the very notion of uncaused first cause or deity, which is likely also incoherent.)

    You just demonstrated that the idea is not incoherent John. And better philosophers than you have found nothing incoherent about either a Deity or a First Cause.

  32. Mung: You just demonstrated that the idea is not incoherent John. And better philosophers than you have found nothing incoherent about either a Deity or a First Cause.

    How did I demonstrate this? Who are these better philosophers and what are their justifications?

  33. Tom English: I propose that you drop the dodgy rhetoric, designed for use in legal testimony, and say straight out that intelligence creates physical information out of nothing.

    There is no such thing as “physical information.”

  34. dazz: Does that make any sense?

    No. It was a nonsense question. FI is not something that is “produced” except by the mind of the person deciding what the function is and what the threshold is. One can choose any function and any threshold for that function. To then later change the threshold is to move the goalposts.

  35. Joe Felsenstein: The cumulativeness is not owing to some mysterious property — it simply is the consequence of the fact that each generation starts from where it is at, rather than back where the starting generation was at.

    But that’s true even if selection is not operating. So your attempt at a distinction is hardly helpful. The “accumulation” happens either way.

  36. Corneel: 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.

    If you mean functional information in the Hazen, Szostak, et al. sense, then no.

  37. vjtorley: I’m sorry, but I’m going to have to side with Origenes here. Think of the Monolith On The Moon in 2001: A Space Odyssey. The design inference comes first, and it’s a mathematical inference based on the simple fact that the likelihood of any unguided natural process generating an object like that is astronomically low.

    I think this is valid but part of the calculation includes the likeliness of the designer. Consider 4 examples.
    1. You find a sphere of relatively pure iron about 1 ft in diameter in the woods in New England. This is as simple an object as you can get yet natural processes probably cant produce it. Its very likely that it was produced by some anonymous blacksmith nearby within the last 250 years.
    2. What looks like a stone tool is found buried on an uninhabited Pacific island in strata dated to a few thousand years before islands in the Pacific were settled. After weighing the various evidence that it was in fact a tool ( the likelihood of its shape, marks, locality of rock-type etc) we consider the designer- does it point to a designer where previously we thought there were none? We know that humans made stone tools, that they made boats and traveled in the Pacific. This would just change the timing of those events.
    3. A year or 2 ago there were very anomalous readings from a star that some astronomers said could be explained by a very large object built by aliens occluding the star. Without other evidence of aliens at that location and knowing how exceedingly rare we expect life, and especially intelligent life to be in the universe, this should be our explanation of last resort. Even if we independently established the existence of said aliens (by receiving radio waves etc) this still wouldn’t prove they were the cause of the readings but it would make the explanation more likely. At least aliens aren’t a completely unreasonable explanation. They would be, like us, creatures that evolved on the surface of a planet, and extrapolating into the future we might one day make objects that could be detected from distant stars.
    4. The life on earth appears to have been evolving by incremental steps for 3.5 billion years. When we have the evidence those steps are perfectly consistent with natural phenomena and there is no evidence for a designer. The designer invoked to explain life was originally part of a bronze age mythology and our concept of this designer has been evolving for millenia as our knowledge of the world and ourselves has increased. This should make us very suspicious. There are many qualities attributed to this designer which are clearly ad hoc, inconsistent or outright nonsensical: the designer loves us, the designer exists outside of space and time etc etc. In this case the evidence doesn’t add up to evidence for a designer, though in principle it could.

  38. Tom English: IDists are mostly creationists doing a bad job of hiding the fact that they are creationists.

    I am a New Creationist.

  39. dazz: You guys are pathetic, unscientific liars.

    All of us?

    dazz: You guys are pathetic, unscientific liars.

    Is that better or worse than being a pathetic, scientific liar?

    dazz: You guys are pathetic, unscientific liars.

    So?

  40. dazz: And what is the ID explanation for such conservation over long periods of time?

    If it ain’t broke don’t fix it. But maybe you will invent a better wheel.

  41. RodW: 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.

    Biology does and always has worked in “design” mode and biologists are just like archaeologists.

  42. Mung: Rumraket: That portrayal follows from nothing I’ve said.

    That statement is false. It directly follows from what you wrote.

    Stop just stupidly making contradictory statements please when you can’t back them up.

    One can’t fail to notice how you completely skipped all this: “The spliceosome evolved from group II self-splicing introns which exist in prokaryotes (and some eukaryotic organelles). Group II self-splicing introns are not “a spliceosome”. Unless you have your own personal definition of “spliceosome” whereby any putative ancestral entity from which a spliceosomal component of some sort evolved, is also a spliceosome. Is that the case?”

    Only by deliberately ignoring this can you somehow maintain the delusion that I have even implied that once there already was a spliceosome, then it evolved.

    It began with your claim that phylogenetics can tell us how things evolved

    Which it can.

    and continued with your claim about the phylogenetic analysis of the spliceosome in eukaryotes.

    An analysis that depends on something that already exists (the spliceosome) in eukaryotes.

    At no point have I stated or even insinuated that the origin of the spliceosome can be elucidated only from an analysis of eukaryotes. That’s just false.

    Stop saying obviously and provably false things.

    IOW, it tells us about the evolution of the spliceosome in eukaryotes, but nothing about its purported origin from prokaryotes.

    Doh. Who the hell has said otherwise? Not me. Disagree? Then quote me stating that we can know how the spliceosome originated without looking at prokaryotes.

    Rumraket: “The spliceosome evolved from group II self-splicing introns which exist in prokaryotes (and some eukaryotic organelles). Group II self-splicing introns are not “a spliceosome”.”

    Mung: “You don’t get that from a phylogenetic analysis of the splicesosome in eukaryotes.”

    And I haven’t claimed that. So why are you telling me? You are trying to saddle me with a particular chain of reasoning I have not engaged in, nor even implied anywhere. Why Mung? Why?

  43. Mung: Rumraket: To pick an example, the Thornton lab has elucidated how the GK protein-interaction domain (GK-PID) family evolved from the guanylate kinase family of enzymes sometime around the origin of multicellular animals.

    Mung: No, they didn’t.

    Strong rebuttal, you really changed minds there. A few more posts like that and evolutionary biology the world over is want to collapse any day.

  44. Tom English: The very first, and absolutely necessary, step is to repudiate YECism.

    I repudiate YECism. It’s based on a faulty hermeneutic. And Jesus did not return in 1988. Or 1914.

  45. Rumraket: A few more posts like that and evolutionary biology the world over is want to collapse any day.

    My goals are far more modest. Why do they claim as fact something which they cannot possibly demonstrate to be factual and why are you suckered into it unless it’s because you just believe what you want to believe?

  46. Once you observe the asymmetry regarding what Mung says and what people say to Mung his choice is clear.

    He responds to cogent, lucid well argued attempts to educate him with one liners or stupid questions. It is pearls before swine and I wonder why anybody still bothers.

    Mung: No, they didn’t.

    And Jesus never returned and never will. Checkmate.

  47. Rumraket: At no point have I stated or even insinuated that the origin of the spliceosome can be elucidated only from an analysis of eukaryotes. That’s just false.

    Stop saying obviously and provably false things.

    At no point did I claim or even insinuate that you stated or even insinuated that the origin of the spliceosome can be elucidated only from an analysis of eukaryotes.

    FFS

  48. Mung,
    Believing what you want to believe is your lot’s trick. If you have a better explanation as to the origin of the GK protein-interaction domain (GK-PID) family then feel free to share it.

    And here we are again.

    Why do they claim as fact something which they cannot possibly demonstrate

    Could you quote where they claim they have shown it for a fact? Their “demonstration” would need to take what form to satisfy you? A video recording?

    Your denial of your stupidity on the moderation thread is belied by your basic error here regarding what science is and what it is not.

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