Two forthcoming peer-reviewed pro-ID articles in the math/eng literature

_{William Dembski

January 20, 2009

Informatics, Intelligent Design}

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The publications page at EvoInfo.org has just been updated. Two forthcoming peer-reviewed articles that Robert Marks and I did are now up online (both should be published later this year).*

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“Conservation of Information in Search: Measuring the Cost of Success”
William A. Dembski and Robert J. Marks II

Abstract: Conservation of information theorems indicate that any search algorithm performs on average as well as random search without replacement unless it takes advantage of problem-specific information about the search target or the search-space structure. Combinatorics shows that even a moderately sized search requires problem-specific information to be successful. Three measures to characterize the information required for successful search are (1) endogenous information, which measures the difficulty of finding a target using random search; (2) exogenous information, which measures the difficulty that remains in finding a target once a search takes advantage of problem-specific information; and (3) active information, which, as the difference between endogenous and exogenous information, measures the contribution of problem-specific information for successfully finding a target. This paper develops a methodology based on these information measures to gauge the effectiveness with which problem-specific information facilitates successful search. It then applies this methodology to various search tools widely used in evolutionary search.

[ pdf draft ]

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“The Search for a Search: Measuring the Information Cost of Higher Level Search”
William A. Dembski and Robert J. Marks II

Abstract: Many searches are needle-in-the-haystack problems, looking for small targets in large spaces. In such cases, blind search can stand no hope of success. Success, instead, requires an assisted search. But whence the assistance required for a search to be successful? To pose the question this way suggests that successful searches do not emerge spontaneously but need themselves to be discovered via a search. The question then naturally arises whether such a higher-level “search for a search” is any easier than the original search. We prove two results: (1) The Horizontal No Free Lunch Theorem, which shows that average relative performance of searches never exceeds unassisted or blind searches. (2) The Vertical No Free Lunch Theorem, which shows that the difficulty of searching for a successful search increases exponentially compared to the difficulty of the original search.

[ pdf draft ]

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*For obvious reasons I’m not sharing the names of the publications until the articles are actually in print.

Comments

gpuccio, I welcome the nonsense we get here even if it is frustrating. It shows two things First, the level of information that the anti ID people think they can bring against ID. It is pretty pathetic. Second, the character of the individuals who do it. To me this is most interesting thing about the debate. Why do they do it? IQ wise they are not dumb but they sure can act the part really well when they try to debate here. The real audience are the lurkers who come here to get information so trying to convince those who support the Darwinian paradigm for everything is useless. They are not going to change since this commitment is based on ideology which must be defended at all cost. As opposed to many of us who would accept the Darwinian paradigm if there were evidence for it and thus, our position is not based on ideology. We have the advantage since if someone shows us some facts and good reasoning we will agree with them. And they paint themselves into absurd corners as they defend something their ideology requires.jerry_{January 29, 2009
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"It odd how powerful metaphors can be. “Hurdles” imply barriers on a route to somewhere. Evolution does not have to find or get over hurdles. It just exploits opportunities to go to somewhere completely unplanned." The metaphor is a teaching mechanism. The hurdles metaphor indicates that there are some places naturalistic processes just can not get to. You seem to quibble over the obvious. Are you trying to understand anything?jerry_{January 29, 2009
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gpuccio @214
Isn’t anybody else tired of reading “inconsistent and intellectually frustrating” posts from a couple of people? I am.
I am as well. The kind of unsupported, overbroad assertions made by some long time participants here do the ID cause no favors. JJJayM_{January 29, 2009
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Re #211 Gpuccio You can probably see where I am going. As you know, it is my belief that ID is entirely negative. It only comprises evidence against Darwinism. So I am interested to know what evidence for ID, if any, would remain if Darwinism was established as plausible. If you take away the evidence against Darwinism - what's left? Re #212 Tribune - my post was a question not a statement. As it happens I don't think the evidence for ID would be changed one jot. A designer of undefined power and motives is always the perfect explanation for everything and might well have designed things to look like Darwinism.Mark Frank_{January 29, 2009
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Isn't anybody else tired of reading "inconsistent and intellectually frustrating" posts from a couple of people? I am. And yes, this is a totally unsupported claim. Interested people will have to read the posts themselves to judge.gpuccio_{January 29, 2009
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Jerry If you give the MET a very low bar to hurdle it will succeed but if it has to find some medium or high hurdles it has a tough time getting over them. It odd how powerful metaphors can be. "Hurdles" imply barriers on a route to somewhere. Evolution does not have to find or get over hurdles. It just exploits opportunities to go to somewhere completely unplanned.Mark Frank_{January 29, 2009
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Mark Frank -- Suppose that biologists eventually produce such a model and were consistently able to produce such models for favourite ID examples such as the cliched flagellum. Mark, you have made the point that ID is falsifiable and hence legitimate science. Well done :-)tribune7_{January 29, 2009
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Mark (#204): That would certainly be a very hard blow for ID, and would make the darwinian theory much more credible. But not necessarily true. There would probably be still much space for discussion. But it would certainly change things very much.gpuccio_{January 29, 2009
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Mark Frank @202
All this talk of islands of function in the sea of possible proteins (or DNA) made me think that it would be more appropriate to talk of evolution exploring the functional space rather than searching it. Evolution is not looking for something. It is stumbling across things that are useful or just different (genetic drift). I don’t think it makes the maths any more or less relevant but it is a more appropriate metaphor.
This is an excellent point. Many ID proponents think naturally in along telic lines. We need to remind ourselves that the only goals within the MET framework are immediate reproductive success. MET mechanisms do, in fact, explore very limited regions of viability without concern for an end goal. Unfortunately, this makes it more difficult to tie Dr. Dembski's papers (the original source of this thread, if I remember correctly) to the ID controversy. The search that he discusses isn't obviously analogous to the exploration performed by MET mechanisms. JJJayM_{January 29, 2009
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gpuccio @203

His point, as I understand it, is that the “search strategy” provided by MET mechanisms explores only very small regions around the current, known viable, point. Since viable points in genome space are not uniformly distributed, this search doesn’t need to look at all possible sequences. It works because it is so limited.
Nonsense. No search needs to look at all possible sequences. In a random search, it is just a question of reasonable probabilities. And a search limited to the surroundings of what already exixts will never find anything distant.
Exactly! This is why Dr. Dembski's two papers don't appear to be "pro ID." The MET mechanisms are not a random search on a uniformly distributed genome space. Far from being nonsense, djmullen explained what is observed in real organisms.

He is explaining exactly what we observe.
I was not aware that we have been observing natural history.
The scientists studying MET mechanisms at the cellular level are observing exactly what djmullen described. That is the evidence we have to explain as well or better than MET for ID to be a real scientific theory. Those scientists are also extrapolating backward through history. If we want to challenge them on the validity of those extrapolations, we need to do so based on the evidence, not on baseless claims.
As far as I know, I can assert what I like. . . . I can make all the claims I want . . . I don’t think you are in the best position to decide what claims ID supporters should make. ID supporters can decide for themselves.
You can indeed make all the claims and assertions you like. So long as they are unsupported, though, you are giving ID opponents more ammunition. They can point at ID proponents who make baseless claims and use them to discredit or ignore the whole theory.

There’s no need for name calling, this is supposed to be a collegial environment.
It was not meant as name calling.
Ah, clearly it's my misinterpretation. "Stupid" can't be in any way considered offensive.
You decide your strategy for yourself. And obviously, research is always welcome.
The research must come before the claims or we will be rightfully ignored by the scientific community. There is much that ID can validly claim, with support. Your overbroad claims in this thread are not in that set. JJJayM_{January 29, 2009
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"what evidence leads you to believe that evolution cant get over a mdedium or high hurdle?" Human nature. The fact that there is no example where it has ever been shown to happen. Other wise humans being humans would not be letting us forget about the one let alone myriad of examples that exist. I suggest you read Silver Blaise and the famous incident of the "Dog barking in the Night." But the dog didn't bark. Precisely. And so do the evolutionist fail to bark.jerry_{January 29, 2009
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Jerry, what evidence leads you to believe that evolution cant get over a mdedium or high hurdle?djmullen_{January 29, 2009
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"Evolution is not looking for something. It is stumbling across things that are useful or just different (genetic drift)." Genetic drift is not exploring or searching or different but cuddling up in a cave and never coming out again. The MET says that evolution is stumbling but the question is how often is what is found useful, or really "how" useful. It finds useful things but can it find combinations that are novel complex and functional. If you give the MET a very low bar to hurdle it will succeed but if it has to find some medium or high hurdles it has a tough time getting over them. That is the issue, has it ever gotten over a medium hurdle let alone a high hurdle. So far the evidence say no.jerry_{January 29, 2009
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gpuccio [118]: "Now you state the most incredible thing: that when a bacterium duplicates its DNA, there is no search necessary. That is incredible, not because it is not true, but because it is so trivial that I really can’t understand why you have to state it." I have to state it because Dembsk and Marks seem to have missed it altogether. Remember, their papers describe searching for this protein amongst the uncountable gazillions of possible proteins of the same length when the truth is that organisms just copy what they already have. gpuccio [149] "There are single point mutations which are incompatible with life. Much more difficult would be to find a single point mutation which gives a reproductive advantage to a complex organism." Easy: http://www.circ.ahajournals.org/cgi/content/full/104/20/2498 "Apolipoprotein A-IMilano is the result of a point mutation, with an arginine to cysteine substitution at position173" Humans are complex organisms. This is a point mutation which gives a reproductive advantage to a complex organism. A few decades ago, a family in Milano, Italy was found to almost never have heart attacks. The cause of their good fortune was tracked down to a single point mutation in the DNA that codes for Apolipoprotein A-I. The new molecule, Apolipoprotein A-Imilano removes cholesteral and atherosclerotic plaque. Better yet, scientists have discovered that injecting it directly into the blood stream also works its wonders in people who were born without that single point mutation too! I can't wait for that drug to hit the market! gpuccio [150] "Let’s take the example of myoglobin. At some point in natural history, this protein appears. It is about 154 aminoacids long. Where did it come from?" http://www.hawaii.edu/microbiology/Alam/downloads/Evolutionary%20implications%20myoglobin-like%20proteins%20found.pdf "UH researchers find myoglobin-like proteins in ancient microorganisms A University of Hawaii research team has discovered a new class of myoglobin-like proteins in ancient microorganisms. In animals, myoglobin (found in muscle) and its close relative hemoglobin (the main protein in the red blood cell) play an essential role in oxygen transport and storage. The newly identified proteins may be the evolutionary ancestors of proteins involved in oxygen sensing as well as transport and storage." "...djmullen’s statement that DNA replication was not a search was suspiciously trivial. Maybe he (and you) have not well considered that the search happens before, when you have to find the information, and not when you simply copy or transmit it?" Searching in the immediate vicinity of a known good genome is what lowers the odds enough to make it possible. gpuccio [167] "There is nothing in the homologies which shows incremental change in the sense of a gradual modification of the function." Ahhh... you're searching through proteins in current organisms, right? So if the proteins diverged hundreds of millions of years ago and the intermediate forms have long since gone extinct, what would you expect to find in current proteins? gpuccio [171] "First of all, my expertise in proteins is not your business. This is a blog, and not a scientific journal. And I, and all the other sincere people who come here, have never spoken “from authority”, or requested any academic title or position from others." Since all you give us is your opinions on proteins and BLAST, your argument is entirely an argument from authority except that you haven't established your authority. "Second, I feel honored of being compared to Salvador Cordova." Well, you're going a long way towards emulating him. Salvador's greatest blunder was to take Avida, a program he knew nothing about, set the single point mutation rate to about 99% and triumphantly announce that the organisms were still growing and that Avida was bunk. Unfortunately for him, one of the readers showed his comment to one of the authors of Avida who dug into it and discovered that every single organism was being blasted to pieces in the first generation and that the poor program was counting fragments of the defunct digital organisms as living, giving the false count. Since typical mutation levels in real life are far under one percent and no real researcher had ever been foolish enough to set it to "puree", Salvador basically just proved that Avida wasn't fool proof. You, on the other hand, are taking a program, BLAST, which was invented to find relationships between proteins and is used for that purpose every day. (Wikipedia says the article introducing BLAST was the most widely citedpaper published in the 90s.) Take my advice, don't let people who understand and use BLAST every day hear that you've used it to prove that proteins can't possibly be related to each other. Or, if you do, ignore whatever they say and take a page from Salvador's book: He keeps telling people how he found a serious problem in Avida, one that even the authors didn't know was there. Works for him, might work for you too.djmullen_{January 29, 2009
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Gpuccio While I think of it - I have a queston - arising from what you said in post #167. But there is no model which can explain the step by step derivation of myoglobin from some other simpler protein with a different function. And remember, such a model should explain not only the variations in aa sequence, but also the variations in function which allow the selecrion and expansion of each single intermediate. Again, that’s why I am in ID, and not in the darwinian field. Suppose that biologists eventually produce such a model and were consistently able to produce such models for favourite ID examples such as the cliched flagellum. You imply that you would then move to the Darwinist camp. But would there still be any evidence for design or would this wrap it up?Mark Frank_{January 29, 2009
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JayM (#194): In brief: "His point, as I understand it, is that the “search strategy” provided by MET mechanisms explores only very small regions around the current, known viable, point. Since viable points in genome space are not uniformly distributed, this search doesn’t need to look at all possible sequences. It works because it is so limited." Nonsense. No search needs to look at all possible sequences. In a random search, it is just a question of reasonable probabilities. And a search limited to the surroundings of what already exixts will never find anything distant. "He is explaining exactly what we observe." I was not aware that we have been observing natural history. "That’s the point under discussion. Personally, I am interested in finding where the limits of MET mechanisms lie. I think that is the most fertile ground for ID research. However, no one currently knows where those limits are, so you can’t simply assert that they are insufficient to produce the structures you note. We have to prove that limits exist and determine where they are." As far as I know, I can assert what I like. We are debating scientific theories here. The fact that we don't exactly know something is exactly the reason why we build theories for the best explanation. And scientific theories do not prove anything (they are not mathemathical theorems). They suggest a possible best explanation. Please, check your scientific epistemology. "As long as a possible path from one genome to another can be hypothesized (and the literature is full of examples where researchers looked at families of proteins coded for by those genomes and found homologs) and as long as that path doesn’t violate any known natural laws, the argument that MET mechanisms are in principle unable to take that path is refuted. We need hard evidence before making the claims that you do above." I can make all the claims I want, and suggest that they are the best explanation fot known data. Anybody can judge how good an explanation they are. The fact that other explanations, possible "in principle", but empirically unsupported and unrealistic, are suggested by others means only that we are in a free world, and thyat different scientific theories are competing for explanation of what we know. I am perfectly fine with that. And no one can simply affirm that his antagonists need "hard evidence", while he can stick to explanations which are possible "in principle". "Again, that isn’t his claim. He simply noted that observation shows that populations evolve in very small steps. Since viable genomes are clustered rather than uniformly distributed, this results in finding new viable genomes much, much more efficiently than random search." Again, nonsense. The fact that viable genomes are clustered (true) does not mean that they are all in the same spot of the space. It just means that they are clustered, and that the clusters are interspersed in the space. So, the kind of search that you describe is efficient only to remain in the same cluster. "There’s no need for name calling, this is supposed to be a collegial environment." It was not meant as name calling. Please notice that I explicitly refer to "what you say", and was preceded by a long and explicit "if", which gave space to the possibility that I was misunderstanding your statements. Anyway, if you just object to the terms as too rude a comment for an expressed idea, then I apologize. Sometimes I am really primitive. Let's say that "then what you say is both inconsistent and intellectually fristrating". "You have shown, at best, that there are a wide variety of proteins in existing organisms." That's exactly what I wanted to show. "You have not shown that the islands of viable genomes are too dispersed to permit all that diversity to have arisen from a common ancestor via MET mechanisms." That was not my point, nor was it the subject of djmullen's affirmations. "That would be a phenomenal achievement and a huge amount of work." And we are working at it. "Until that work is done, though, ID supporters shouldn’t make overarching claims about the existence of those limits. This is especially true given the extensive research being done to trace proteins back in history." I don't think you are in the best position to decide what claims ID supporters should make. ID supporters can decide for themselves. You decide your strategy for yourself. And obviously, research is always welcome.gpuccio_{January 28, 2009
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An aside. All this talk of islands of function in the sea of possible proteins (or DNA) made me think that it would be more appropriate to talk of evolution exploring the functional space rather than searching it. Evolution is not looking for something. It is stumbling across things that are useful or just different (genetic drift). I don't think it makes the maths any more or less relevant but it is a more appropriate metaphor.Mark Frank_{January 28, 2009
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"Personally, I am interested in finding where the limits of MET mechanisms lie." There are no limits according to the MET. I assume that is what this thread is about. To show that the MET has limits. Let me provide what I believe the MET says. When a population has offspring and the environment is stable then the variation of the offspring will be limited by this stability or I guess as one person put it here, it stays within the sweet spot. I am not sure that is a good term but you can use it. This doesn't say that some offspring cannot be born that are far away from this sweet spot. Probabilites say that such a thing could happen and the organism could be viable. It just says that given the current environment most of these will not likely be able to move the average genome far away from the original population average. Unless there is an extremely useful variation in these offspring, gene flow will bring future offspring back into the fold. It is possible that some characteristics that push an offspring outside the so called "sweet spot" will take hold and the new average for the population will move slightly away. And that is the MET in a nutshell. If a sub population separates from the main population and encounters a new environment, then the sweet spot may not be so sweet anymore and offspring outside the sweet spot may become dominant because of natural selection in the new environment. Now if one wants to say that the sweet spot includes all these new populations then one has to deal with the potential that the average genome may keep moving and soon a new population cannot inter breed with the old population and so is now on its own moving slowly away from the original. So I am not sure sweet spot is a meaningful concept for the MET though the idea explains why species do not vary much over time. But it fails to take into account outliers and their ability to change a population or a sub population. Now these outliers may result from variation that is due to recombination, or a mutation or they could just be due to a unique shuffling of the genes that are currently in the gene pool that now exist but have never appeared in any offspring before. The later case can be seen in artificial selection or breeding to get to some combination that is possible but would not show up in any natural way and has to be intelligently guided even though there is always a probability that it could happen naturally. After all Chihuahuas and Great Danes are both dogs. Over time MET predicts these isolated populations will diverge even more. By the way a sub population could be within spitting distance of its parent population and not interact. Some insects that are just one generation away from its parents may find a certain new plant to live on and because of this new plant may never go back home and thus form a new species within just a few feet of it original population. Mammals need a much greater distance to form a sub population. Anyway that is the theory but the changes that can happen has limits as Behe has shown in the Edge of Evolution and discussed in a great book by Ray Bohlin and Lane P. Lester called he Natural Limits to Biological Change. I assume all these searches discussed in this thread is about the same thing or the possible movement of a genome away from an original to another which has some element that provides a new functional capability that is not just trivial but complex in nature. The future will show the way as new mappings of genomes and more understanding of the function of non coding elements will tell one how feathers are formed and bats have radar and why mammals do not lay eggs etc. Then one will be better able to see what must have taken place in a Darwinian sense to get to these new complex and functional capabilities and whether the creeping of a genome over time could be the answer or rather whether massive relocations of the genome had to have taken place. Based on the logic of what is presently know, neither will be a viable option and then a new escape will have to be planned for the Darwinist to move on. One of the things that recent threads has revealed is that these discussions are not about data and logic and a striving to learn but overt attempts to preserve one's current ideological turf through whatever methods one thinks will work. Different people choose different tactics including civility but all this has been seen before and what is interesting is how they play out in different people. One of the ways it nearly always plays out is in ad hominems.jerry_{January 28, 2009
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JayM, Apologies. I copied my response to Khan, along with additional comments, so parts of it didn't connect to what you were saying. My main point is that it's much more practical and feasible to provide a single reasonable hypothesis than it is to wade through the entire data set for biology to prove that none exists. We should be looking at what we know now. What you are talking about is gathering the knowledge of all genomes and completing the project we call biology.
While I think that ID theory has considerable promise, I have yet to see how it could be falsified.
Personally I consider theistic evolution to be ID-compatible, although people like Ken Miller would disagree. And while many ID-compatible ideas are very much open to falsification I'd agree that there are some ID-compatible ideas that are not.
We need to identify the real edges of evolution, both in terms of limits of the MET mechanisms and disconnected islands of viability in the genome space.
Long term, yes. I just disagree that the evidence we do have now is not enough to make certain claims.Patrick_{January 28, 2009
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Patrick @196
We are merely asking that the grand claims be verified in ANY manner. Essentially, you’re asking us to accept as an article of faith that pathways of hundreds and thousands of informational bits leading to an irreducible core are as easily achieved as pathways consisting of less than 50 informational bits (and IC is often not an issue at all)
I'm not asking any such thing. My point in that section of my post was to note that overbroad claims do not do the ID movement any favors. When someone claims that "ID means that X could never happen." and an ID opponent says "Actually, it could have happened in any of these ways....", we all lose credibility.

Until that work is done, though, ID supporters shouldn’t make overarching claims about the existence of those limits.
It’s long been stated the design inference is open to falsification
That's a separate, but also important issue. Stating something is easy, supporting it is more difficult. While I think that ID theory has considerable promise, I have yet to see how it could be falsified. That's one reason I hopped into Dr. Fuller's thread related to learning about the designer. If the designer is not bound by any constraints, voluntary or otherwise, I don't see how to falsify the design inference. If literally anything is possible, any observations can be claimed to support the theory, which makes it unfalsifiable.
I’ve elaborated at greater length about this, but I’m open to the potential that the only instantiation of Design is OOL and the configuration of the system (code/language conventions, limited foresighted mechanisms, etc.) allows unguided processes to largely work from there, but for the reasons gpuccio has already given this seems unlikely.
I agree, although not for gpuccio's reasons. We need to identify the real edges of evolution, both in terms of limits of the MET mechanisms and disconnected islands of viability in the genome space. Until we have real evidence, we need to be circumspect in our claims if we want to be taken seriously. JJJayM_{January 28, 2009
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CJYman:
Simply put, the foundational randomness and chaos from which everything arises would be uniform and would not be biased toward any specific outcome.
I misinterpreted this statement in the post above and falsely accused it of being self-contradictory. My sincere apologies. But it raises the question: If other distributions arise from that foundational randomness, shouldn't they be uniformly distributed? In other words, we would expect the vast majority to be non-uniform and biased toward their intrinsic targets.
The implications of this would be that there has always been an infinite regress of bias in the foundational search space to produce our universe, life, evolution, and intelligence. However, that infinite regress of active info is only one of the options which I have discussed in my comment #122
According to the principle of indifference, each of your n options has a 1/n chance of being correct. ;-) And how do you know that "life, evolution, and intelligence" is the target? Maybe the Designer was trying to create a sterile universe, but some replicators arose accidentally and infected a planet with life. In that case, where's the active info? I'm being tongue-in-cheek, but the point is that we're dealing with ultimate questions that can be answered by neither science nor math. BTW, I find it strange that talk of design regress is verboten on this board, but it's okay to talk about probability hierarchies that regress to before the universe existed.
and if there is indeed “uniform randomness,” then the ID position becomes more of an obvious and accurate choice.
There is not uniform randomness, regardless of whether the ID position is true or not.
One way to begin to answer if the preceding assumptions are justified is to “test randomness” and see if it has any tendency to match non-uniform search spaces with search algorithms to generate active information.
If this "randomness" is over M(omega) as Marks and Dembski define it, then obviously it will have no such tendency, although it doesn't tend very far in the other direction, as Prof. Olofsson has pointed out. How do you propose we apply this mathematical fact to reality?R0b_{January 28, 2009
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ROb[195], CJYman claims a "non-arbitrary uniform probability distribution" but as ROb points out, it is determined by the choice of metric, thus not unique.Prof_P.Olofsson_{January 28, 2009
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As long as a possible path from one genome to another can be hypothesized
Does such a hypothetical non-trivial pathway even exist?
(and the literature is full of examples where researchers looked at families of proteins coded for by those genomes and found homologs)
These basic comparisons do not meet the same standards for a hypothesis for what you then write:
and as long as that path doesn’t violate any known natural laws, the argument that MET mechanisms are in principle unable to take that path is refuted.
There's a reason I kept referring to previous discussions:
You have not shown that the islands of viable genomes are too dispersed to permit all that diversity to have arisen from a common ancestor via MET mechanisms. That would be a phenomenal achievement and a huge amount of work.
This discussion has reached the same point as my discussion with Khan. Yes, let's MERELY calculate every single potential indirect stepwise pathway and set that as the milestone that the ID community must meet in order to qualify itself. Yes, that's sarcasm. For the Darwinist "[a] single plausible pathway will do, which does not require analyzing ALL possibilities. And if this pathway happens to consist of processes that act uniformly in regards to other biological objects, then a large chunk of most design hypotheses would be falsified. But if you plan on verifying whether a plausible pathway does not exist at all, then indeed we’d need to calculate every single potential pathway. We are merely asking that the grand claims be verified in ANY manner. Essentially, you’re asking us to accept as an article of faith that pathways of hundreds and thousands of informational bits leading to an irreducible core are as easily achieved as pathways consisting of less than 50 informational bits (and IC is often not an issue at all)" which are all within local genome space.
Until that work is done, though, ID supporters shouldn’t make overarching claims about the existence of those limits.
It's long been stated the design inference is open to falsification. I've elaborated at greater length about this, but I'm open to the potential that the only instantiation of Design is OOL and the configuration of the system (code/language conventions, limited foresighted mechanisms, etc.) allows unguided processes to largely work from there, but for the reasons gpuccio has already given this seems unlikely.Patrick_{January 28, 2009
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CJYman:
First, those assumptions could be a part of an hypothesis which incorporates the math within these papers. As such, until the assumptions are falsified or the math is shown to be incorrect, we have a standing scientific hypothesis.
An active info analysis requires, according to Dembski, "a search space omega, a metric D that induces a compact topology on omega, a target T included in omega, a uniform probability measure U on omega induced by D, and an arbitrary probability measure phi on omega." In order to come up with those parameters, we need to make assumptions about how the underlying phenomenon should be modeled. We may also have to make assumptions about the phenomenon itself. Only the latter type of assumptions can be falsified.
You seem to be saying that these assumptions have to do with how we measure active information by individuating the possibilities, yet I don’t see this as a problem at all, since the probability of a pattern is measured against a non-arbitrary uniform probability distribution.
But how do we define the space over which this uniform distribution sits? It depends on how we individuate the possibilities. To borrow an example from Dembski, what is the endogenous information in a roll of a die? That depends on whether we define the die landing on the floor as a different outcome than the die landing on the table.
Breaking up the pattern and convoluting it into a couple of different searches would be the arbitrary action, and I’m not sure that would even return a different measurement when these separate searches are each measured against a uniform probability distribution.
Actually, we're not talking about breaking anything into different searches. The point is that the active info measure depends on how we individuate the possibilities, contra Dembski's earlier position on how information should be measured. And I should qualify my usage of arbitrary. It's arbitrary according to the mathematical framework, which doesn't dictate how to model things. But if we want to use the framework as a tool and draw conclusions from it, then our modeling choices may be determined by what we're trying to find out. So in that sense it could be non-arbitrary (although I'd love to see an example with a modicum of rigor). But if all we're trying to find out is the amount of active info in something other than a pre-defined mathematical model of a search, then it's arbitrary.
As far as I understand, Active info = probability associated with bit operations taken to find the pattern – probability of pattern measured against a uniform distribution. Neither the number of bit operations nor the uniform probability distribution are arbitrary figures, so neither is their difference (active info) arbitrary.
They aren't arbitrary given omega, D, and T, but how do we non-arbitrarily come up with those parameters? That's one of the questions we'll need to answer if we want the framework to tell us anything meaningful about reality. For instance, how do you non-arbitrarily define T when you model biological evolution as a search?
Actually no, that would not be a non-uniform distribution of distributions, if *everything* is characterized by a uniform distribution. If you actually mean *everything*, then that would include the distribution of distributions.
Exactly. It's logically impossible for everything to be characterized by a uniform distribution. Which renders your subsequent statement self-contradictory: "Simply put, the foundational randomness and chaos from which [b]everything[/b] arises would be uniform and would not be biased toward any specific outcome." (emphasis mine) This post is too big. More later...R0b_{January 28, 2009
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gpuccio @192
Let’s not play games, please. If djmullen is saying that, as long as living beings just reproduce themselves with very minor changes, they remain the same and are in the same “sweet spot” of the search space, and so no search is necessary
That's not what he is saying. Here is an exact quote:
In practice, they do this by making only small changes to the DNA they hand down to their offspring. This keeps the results of their so-called “search” either inside the sweet spot or very close to it. No other “search strategy” is necessary.
His point, as I understand it, is that the "search strategy" provided by MET mechanisms explores only very small regions around the current, known viable, point. Since viable points in genome space are not uniformly distributed, this search doesn't need to look at all possible sequences. It works because it is so limited.
he is saying something literally true, but completely trivial, and which does not correspond to what we onserve in natural history
He is explaining exactly what we observe.
and does not explain in any way the appearance of new proteins, new functions, new body plans, new species, and so on.
That's the point under discussion. Personally, I am interested in finding where the limits of MET mechanisms lie. I think that is the most fertile ground for ID research. However, no one currently knows where those limits are, so you can't simply assert that they are insufficient to produce the structures you note. We have to prove that limits exist and determine where they are. As long as a possible path from one genome to another can be hypothesized (and the literature is full of examples where researchers looked at families of proteins coded for by those genomes and found homologs) and as long as that path doesn't violate any known natural laws, the argument that MET mechanisms are in principle unable to take that path is refuted. We need hard evidence before making the claims that you do above.
But if, as I believe, djmullen (and probably you) are affirming that all the proteins and functions and body plans and information we find in the living world were generated starting from a simpler ancestor without the need for any search
Again, that isn't his claim. He simply noted that observation shows that populations evolve in very small steps. Since viable genomes are clustered rather than uniformly distributed, this results in finding new viable genomes much, much more efficiently than random search.
because all the transitions happened in the same sweet spot of the search space, then what you say is both stupid and irritating. I have shown clearly that proteins, as we know them, are interspersed in the ocean of possible sequences.
There's no need for name calling, this is supposed to be a collegial environment. You have shown, at best, that there are a wide variety of proteins in existing organisms. You have not shown that the islands of viable genomes are too dispersed to permit all that diversity to have arisen from a common ancestor via MET mechanisms. That would be a phenomenal achievement and a huge amount of work. Until that work is done, though, ID supporters shouldn't make overarching claims about the existence of those limits. This is especially true given the extensive research being done to trace proteins back in history. JJJayM_{January 28, 2009
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Re #188 First - I am sorry - my comment in #187 was more suitable for a private e-mail than a public forum - sometimes my frustrations spill over. The issue of uniform probability distributions has been done to death here and elsewhere. For example, the calculation that goes: (Number of functional outcomes(/(number of trials) = (probability of functional trials) relies on a uniform probability distribution.Mark Frank_{January 28, 2009
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JayM: Let's not play games, please. If djmullen is saying that, as long as living beings just reproduce themselves with very minor changes, they remain the same and are in the same "sweet spot" of the search space, and so no search is necessary, he is saying something literally true, but completely trivial, and which does not correspond to what we onserve in natural history, and does not explain in any way the appearance of new proteins, new functions, new body plans, new species, and so on. So, if djmullen (and you) want to spend your time accumulating tautologies which do not mean anything, you're welcome, but I will not follow you any more. But if, as I believe, djmullen (and probably you) are affirming that all the proteins and functions and body plans and information we find in the living world were generated starting from a simpler ancestor without the need for any search, because all the transitions happened in the same sweet spot of the search space, then what you say is both stupid and irritating. I have shown clearly that proteins, as we know them, are interspersed in the ocean of possible sequences. That is simply true. See also my answer to rna. So, one of two things: a) a lot of search was necessary, and the ocean of possible sequences has been traversed a lot of times (which is the opposite of what you seem to say) or b) no search was necessary, because all the proteis we know were already present in LUCA, as we know them or in a very similar form (which is simply wrong and foolish) And that's enough, for me. Unless you say something new and sensible, I don't think I will answer any more to that kind of nonsense.gpuccio_{January 28, 2009
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gpuccio @167
I appreciate your efforts, but I am afraid I can only repeat for you what I have already said about djmullen: your characterization is inaccurate.
In the interests of brevity, I'm going to focus just on djmullen's original statement:
But every living organism that exists is the product of organisms that are already in that tiny proportion of the possible genomes and if they successfully reproduce then their DNA is already in it too. In practice, they do this by making only small changes to the DNA they hand down to their offspring. This keeps the results of their so-called "search" either inside the sweet spot or very close to it. No other "search strategy" is necessary.
This is an entirely accurate representation of the MET position. Let's take it step by step so you can point out where you disagree: 1. Every living organism is in a viable point in genome space. This is true by definition, else the organism wouldn't be living. 2. Changes in DNA between generations are small. This is observed. 3. Living offspring are in viable points in genome space. This is true by definition, like 1. 4. The points in genome space occupied by offspring are very close to those occupied by their parents. This is a result of 2 and is also observed. From these four points, we can see that: 5. The viable regions in genome space are not uniformly distributed. If they were, the odds of getting viable offspring would be vanishingly low. And so we come to djmullen's conclusion:
Evolution says that every living organism since the first self-reproducing molecule is already in the genomic sweet spot and all they have to do is keep their offspring in it too.
That follows logically from the earlier points. Now, you and I may disagree with djmullen about the probability that all life, from the very first common ancestor 3.8 billion years ago to today, is in a connected network of viability within genome space, but you can't say that his characterization of MET is "inaccurate." What is your precise objection to what he said? JJJayM_{January 28, 2009
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CJYman @161

That’s great, but it still seems to cede the field of biology to modern evolutionary theory.
It cedes biology to evolution and it takes evolution for itself.
That's an interesting and refreshing view, that seems to stretch even the ID community's Big Tent. While I personally think that ID research would be most profitable in identifying exactly where the "edge of evolution" lies and why, I share your respect for the work done by scientists. In order for ID theory to replace MET, it needs to explain everything that MET does, and then prove itself to have greater predictive power. We're not going to get to that point by ignoring the knowledge already gained by evolutionary biologists. So, although I don't agree that we need to cede biology to ID opponents, I find your position thoughtful and rational.

An aside due to my inner geek: Is there a formal proof that CSI cannot be generated from evolution simulations?
The only formal proof presented is that CSI won’t generate itself through only chance and law and this is implicit within these two papers.
I was hoping for something more explicit. CSI isn't even mentioned in either paper.
Since CSI is a measurement of finding a specified or pre-specified pattern at better than chance performance, problem specific information is required to find it (according to NFLT). Problem specific information is measured as active information within these two papers.
The reason why I still don't see how either of these papers can be claimed to be "pro ID" is that active information can be transferred to the genome from the environment via MET mechanisms. This is why GAs work so much better than random search. From this, the papers could be said to be "pro MET."

I don’t believe that "all simulations of evolution require foresight." We’ve discussed several different genetic algorithms in recent threads here and Dawkin’s Weasel is the exception rather than the rule.
My apologies for not being clear. If we are discussing any simulation relevant to biology, then evolution is the discovery and increasing of CSI. Can you provide any simulation of biological evolution which discovered CSI from initial conditions that were not programmed with any consideration for future results?
I'm not sure I understand the constraints you're specifying. There are a number of GAs documented on the web that simulate a small subset of MET mechanisms and generate complex, previously unknown solutions to the problems they are posed. One of my favorites is the evolution of antenna designs done at MIT. Another interesting one is Thomas Ray's Tierra. While we're on the topic, I would be very interested in modifying one of those GAs to address your questions. How would you go about measuring the CSI for the results of one of those, then finding the source of it? JJJayM_{January 28, 2009
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Mark Frank [187], The last claim in the video is indeed classic confusion of conditional probabilities: "It was about 10^80000 times more probable that ID was required..." Sigh. You're probably right, better not waste too much time. I'll read the article when I have time though because tibrune is such as nice person!Prof_P.Olofsson_{January 28, 2009
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