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Why ID Advocates Downplay Our Disagreement With Them

Posted 8 November 2015 by Joe Felsenstein

Last March Tom English and I posted an argument here here at Panda's Thumb analyzing an argument by William Dembski, Winston Ewert, and Robert Marks. They had made an argument that evolutionary "search" would not do better than blind search; we proved that their argument showed no such thing. In response to our analysis here of the Dembski-Ewert-Marks paper, Winston Ewert has replied at Evolution News and Views. As that site does not allow comments, I have finally gotten around to posting a response here (six months late). Tom has now put up a related thread at The Skeptical Zone; I will try to comment in both discussions. Ewert rather dramatically reveals that Tom and I do not actually disagree with any of the theorems in their paper. And he's right about that. How did they discover this remarkable fact? Perhaps it was by reading our post, where we said
We're not going to argue with the details of their mathematics, but instead concentrate on what in evolutionary biology corresponds to such a choice of a search.
or by reading a comment in that thread where I also said:
As theorems they may be mathematically true, but the average poor performance of searches is true only because so many irrelevant and downright crazy searches are included among the set of possible searches.
Ewert is right that we did not question their theorems. Instead we concentrated on what would follow from their theorems. We showed in a simple model that once there are organisms that reproduce, with genotypes that have phenotypes and fitnesses, that evolution will find higher fitnesses much more effectively than random guessing. So is it true that having what they call Active Information, embodied in a fitness surface and in a reproducing organism whose genotypes have those fitnesses, requires that there be Design Intervention to set up that system? The issue is not the correctness of their theorems but, given that they are correct, what flows from them. Dembski, Ewert, and Marks (DEM) may object that they did not say anything about that in their paper. We don't think that it is a stretch to say that DEM want their audience to conclude that Design is needed. Let's look at what conclusions Dembski, Ewert, and Marks draw from their theorems. There is little or no discussion of this in their paper. Are they trying to persuade us that a Designer has "frontloaded" the Universe with instructions to make our present forms of life? Let's look at what Dembski and Marks have said about that (below the fold) ... Our analysis of what kinds of "searches" would be achieved by a reproducing organism that has fitnesses led us to this simple conclusion (summarized in a comment of mine in the thread following our post):
1. Their space of "searches" includes all sorts of crazy searches that do not prefer to go to genotypes of higher fitness -- most of them may prefer genotypes of lower fitness or just ignore fitness when searching. Once you require that there be genotypes that have different fitnesses, so that fitness affects survival and reproduction, you have narrowed down their "searches" to ones that have a much higher probability of finding genotypes that have higher fitness. 2. In addition, the laws of physics will mandate that small changes in genotype will usually not cause huge changes in fitness. This is true because the weakness of action at a distance means that many genes will not interact strongly with each other. So the fitness surface is smoother than a random assignment of fitnesses to genotypes. That makes it much more possible to find genotypes that have higher fitness.
In short, with their theorems, Design is not needed to explain why a reproducing organism whose genotypes have fitnesses might be able to improve its fitnesses substantially. Just having reproducing organisms, and having the laws of physics, gets an evolving system much farther than a random one of DEM's "searches". But here's what William Dembski said about this in his interview at the Best Schools website:
The term "evolutionary informatics" was chosen deliberately and was meant to signify that evolution, conceived as a search, requires information to be successful, in other words, to locate a target. This need for information can be demonstrated mathematically in the modeling of evolutionary processes. So, the question then becomes: Where does the information that enables evolutionary searches to be successful come from in the first place? We show that Darwinian processes at best shuffle around existing information, but can't create it from scratch. ... I see this work as providing the theoretically most powerful ID challenge against Darwinian evolution to date. As for the attention this work has garnered, there has been some, but Darwinists are largely ignoring it. I'm justified in thinking this is because our methods leave them no loopholes. We're not saying that evolution doesn't happen. We're saying that even if it happens, it requires an information source beyond the reach of conventional evolutionary mechanisms.
and here's what Robert Marks said at his Evolutionary Informatics Lab website (http://evoinfo.org) (copied 7 Nov 2015):
By looking to information theory, a well-established branch of the engineering and mathematical sciences, evolutionary informatics shows that patterns we ordinarily ascribe to intelligence, when arising from an evolutionary process, must be referred to sources of information external to that process. Such sources of information may then themselves be the result of other, deeper evolutionary processes. But what enables these evolutionary processes in turn to produce such sources of information? Evolutionary informatics demonstrates a regress of information sources. At no place along the way need there be a violation of ordinary physical causality. And yet, the regress implies a fundamental incompleteness in physical causality's ability to produce the required information. Evolutionary informatics, while falling squarely within the information sciences, thus points to the need for an ultimate information source qua intelligent designer.
In case there is any doubt, here is what Marks said in an "ID The Future" podcast (This is available at Marks's Evoinfo.org website, but for some reason not at the Discovery Institute's "ID The Future" website).
[Minute 13:28] Luskin: What is Active Information, and why does it point to the need for Intelligent Design to solve a problem, rather than an unguided evolutionary process? Marks: Well the idea actually goes back to Bill Dembski's book entitled "No Free Lunch", which shows that, remarkably, if one is a doing a search and designing something, then one search, or one process, is on average as good as any other process if you have no idea about the problem you're solving, in other words, the search is undirected -- and that its blind search. [I omit his Wierd Al Yankovich blind Rubik cube scene description. JF] Marks: That's an example of a blind search. And without information to guide you where you want to go, one search is as good as another search, which on the average is as good as blind search. [I omit banter with Luskin about liking stupid movies and stuff about algorithmic information theory pioneer Gregory Chaitin liking their paper. JF] Luskin: ... Well, we appreciate the work that you're doing and the papers that you're publishing analyzing many of these evolutionary algorithms and asking whether they support a Darwinian view of life or an Intelligent Design view of life. "Dr. Robert Marks, Active Information in Metabiology" 2014-05-31 16:00. Discovery Institute, Center for Science and Culture, Copyright Discovery Institute, 2014
Ewert himself, in his reply, uses the evolution of birds as an example:
While some processes are biased towards birds, many others are biased towards other configurations of matter. In fact, a configuration biased towards producing birds is at least as improbable as birds themselves, possibly more so. Having postulated Darwinian evolution, the improbability of birds hasn't gone away; we've merely switched focus to the improbability of the process that produced birds. Instead of having to explain the configuration of a bird, we have to explain the configuration of a bird-making process.
This example leaves it unclear what the "process" is. The reader may be tempted to conclude that it is the process that models an evolving population. And then the reader may think that if this evolutionary process succeeds in improving fitness, that some outside force is needed to set up the process so that it succeeds. But for their theorem to apply, the processes considered must include processes that make no sense as models of evolution. Processes that wander around among genotypes randomly, without being more likely to come up with higher fitnesses. Even processes that prefer to find genotypes with lower fitnesses. All of those are among the processes that must be eliminated before we get to processes in which genotypes have fitnesses, and those fitnesses affect the outcome of evolution. But after narrowing the searches down to those that have organisms with fitnesses, the probability of success is much improved. And no designer needs to intervene to get that improvement. All that occurs even when the fitness surfaces are extremely rough, with nearby genotypes having wildly different fitness. But the laws of physics strongly suggest that fitness surfaces will be much smoother than that. That smoothness is a further reason for evolutionary processes to succeed far better than blind searches. In his reply, Ewert invokes the smoothness of the fitness landscape, and considers the smoothness to result from "laws or self-organization"
It is not sufficient to invoke the three-fold incantation of selection, replication, and mutation. You must also assume a suitable fitness landscape. You have to appeal to something beyond Darwinism, such as laws or self-organization, to account for a useful fitness landscape.
He does not seem to realize that those "laws" might simply be the laws of physics, and that the "self-organization" can simply be self-reproduction, something that all organisms do. By simply declaring that we do not disagree with their mathematics, Ewert is avoiding the issue of what flows from those theorems. In their subsequent statements, Dembski, Ewert, and Marks have made clear that they regard those theorems as evidence for Design. It is clear from these examples that Dembski and Ewert mean their theorems to be read as evidence for an Intelligent Designer either frontloading the evolutionary process, or for an Intelligent Designer intervening in it. But Tom English and I have shown that their Active Information can come about without that. It can come about simply by having a reproducing organism which has different genotypes, which have different phenotypes, and these have different fitnesses. And further Active Information can also come about by the predisposition of the laws of physics to bring about fitness surfaces smoother than "white noise" fitness surfaces. Could that Active Information be enough to explain the evolution of, say, a bird? Do they have some argument that further "configuration of a bird-making process" is needed beyond that? There is actually nothing in their argument that requires that there be further Intelligent Design. This is bad news for the implications that they have drawn from their theorems. To say that is to disagree fundamentally with Dembski, Ewert, and Marks, however little we have questioned the validity of their theorems. As usual, I will "pa-troll" this thread aggressively and send off-topic comments by our usual trolls (and replies to those comments) to the Bathroom Wall.

86 Comments

Mike Elzinga · 8 November 2015

The 2013 Nobel Prize in chemistry went to three scientists whose work on the computer modeling and characterizing of molecular assemblies originated back in the 1960s and 70s. Those computer algorithms were developed over a period of something like 50 years, and they are based on the fundamental laws of physics applied to atomic and molecular interactions.

Also, ID/creationism begin formally in 1970 when Henry Morris and Duane Gish set up ID/creationism's rules for the properties and behaviors of atomic and molecular assemblies using junkyard parts in a tornado as the definitive ID/creationist model. Yet Morris and Gish didn't get any Nobel Prize for their assertions.

I have only one question for Dembski, Ewert, and Marks: Why didn't that Nobel Prize go to the mathematical development of CSI and the search "theorems' of Dembski, Ewert, and Marks; or whichever three ID/creationists want to take credit for taking logarithms to base 2 of the number of trials multiplied by the probability per trial, labeling that "information," and then applying that mathematics to atomic and molecular assemblies?

eric · 8 November 2015

We’re not saying that evolution doesn’t happen. We’re saying that even if it happens, it requires an information source beyond the reach of conventional evolutionary mechanisms.
It seems to me that this is just the "(natural) laws require a lawmaker" argument tarted up with a lot of math. The 'information' they're talking about comes from the laws of physics. They are right that the Theory of Evolution doesn't explain where those come from. But there's nothing in their math that says where those laws come from, either.

Mike Elzinga · 8 November 2015

Joe Felsenstein asks:

Could that Active Information be enough to explain the evolution of, say, a bird? Do they have some argument that further “configuration of a bird-making process” is needed beyond that? There is actually nothing in their argument that requires that there be further Intelligent Design.

Suppose we ask this question about the determination of the sex of, say, some lizard or other animal during incubation. Where does the "Active Information" come from - or disappear to - when a modest change in temperature produces a different sex in the hatchlings from what occurs at a another temperature? When the physical processes that take place in animals are shown to be extremely temperature dependent, how is one justified in ruling out physics and chemistry and replacing it with "active information?" How does "active information" push atoms and molecules around?

harold · 8 November 2015

Simple but basically valid mathematical model of evolution -

"Roll 100 dice, select out the sixes, put them aside, do it again, inevitably you eventually have all sixes."

Dembski's model -

"Keep rolling 100 dice. The probability of getting all sixes on any given roll is 1 in 6^100. This is a small number. It's so small that in some engineering applications it might be taken as approximately zero. Therefore it is zero. Therefore you need magic to get 100 sixes."

I strongly defend this terse summary as a basically accurate paraphrase of all ID probability based models that have ever been proposed, including the one under discussion here.

Joe Felsenstein · 8 November 2015

harold, I'm not sure I agree. Dembski's use of the Universal Probability Bound is basically saying that a result this good (say, this well adapted) is very improbable even once in the history of the known universe. That is not saying that is absolutely impossible, but I don't find this extreme improbability argument to be an unreasonable argument. If it were true you would worry.

The place where it falls down is when you calculate the probability for pure mutational processes without natural selection, then argue that you have some proof that natural selection cannot make the event probable. (Or his more recent version where you ask the user to calculate the probability of an event this good happening, but don't tell them how to do that).

harold · 8 November 2015

The place where it falls down is when you calculate the probability for pure mutational processes without natural selection, then argue that you have some proof that natural selection cannot make the event probable. (Or his more recent version where you ask the user to calculate the probability of an event this good happening, but don’t tell them how to do that).
I feel that we are saying the same thing. I should note that we are being relatively kind to ID/creationists. I feel as if we are saying, and I feel that this is true of Dembski, that Dembski gets the random sampling from a distribution part of a mathematical model of evolution acceptably right, but misrepresents the selection part. (I've noted many times here that mutations are almost ideally modeled by random variables; we know the frequency with which many type of mutation should occur, but cannot predict exactly when and where they will occur; this is the definition of a random variable. Saying that mutations are well modeled as random variables in no way implies that all individual types of mutation have equal frequency.) I feel that this is a commonality among ID/creationists. I said we are actually being kind, because I also feel that it is fairly common for ID/creationists to also misrepresent how random sampling works. I don't have an example at my fingertips but feel confident that one will shortly be provided. I don't mean to disparage the necessary and valuable work of challenging each new manifestation of ID/creationism in detail. I'm just noting a commonality.

Joe Felsenstein · 8 November 2015

harold said: ... I feel that we are saying the same thing. I should note that we are being relatively kind to ID/creationists. I feel as if we are saying, and I feel that this is true of Dembski, that Dembski gets the random sampling from a distribution part of a mathematical model of evolution acceptably right, but misrepresents the selection part. (I've noted many times here that mutations are almost ideally modeled by random variables; we know the frequency with which many type of mutation should occur, but cannot predict exactly when and where they will occur; this is the definition of a random variable. Saying that mutations are well modeled as random variables in no way implies that all individual types of mutation have equal frequency.) I feel that this is a commonality among ID/creationists. I said we are actually being kind, because I also feel that it is fairly common for ID/creationists to also misrepresent how random sampling works. I don't have an example at my fingertips but feel confident that one will shortly be provided. I don't mean to disparage the necessary and valuable work of challenging each new manifestation of ID/creationism in detail. I'm just noting a commonality.
Well, your comment here sounded like you wanted to make a big distinction between an event that is impossible, and an event that has probability so small that it is improbable that it happened even once in the whole history of the universe. That is quite different from my complaints about Dembski's argument.

Mike Elzinga · 8 November 2015

Joe Felsenstein said: Well, your comment here sounded like you wanted to make a big distinction between an event that is impossible, and an event that has probability so small that it is improbable that it happened even once in the whole history of the universe. That is quite different from my complaints about Dembski's argument.
Lest we forget; Dembski lifted that "Upper Probability Bound" from the abstract of a paper by Seth Lloyd that appeared in Physical Review Letters. I personally doubt that Dembski ever read that paper or has the capacity to understand what Lloyd was doing. Dembski was merely reaching for a maximum number of trials, N, that could take place in the universe against which he could calculate probabilities, p, of specified events such that Np < 1. (Forget all that stuff about Dembski's taking the logarithms to base 2 and calling it "information:" that is a totally irrelevant obfuscation.) Lloyd did a perfectly legitimate calculation of the number of logical operations that a perfect quantum computer would have to do in order to model the entire universe as we know it. What Dembski missed by not plowing through Lloyd's calculations is that that number Lloyd came up with is an upper bound that applies to our known universe, which is a universe that already contains life. Lloyd's calculation is interesting because it deals with the actual energies involved in flipping quantum bits; so it has nothing to do with Dembski's CSI or anything that ID/creationists claim they are calculating when they come up with a probability for the occurrence of some specified assembly of atoms and molecules. Dembski's ploy is an example of pseudoscience attempting to appear legitimate by riding on the back of a legitimate scientist doing a perfectly legitimate scientific calculation. Whatever Dembski attempts to make of Lloyd's calculation has absolutely nothing to do with the probabilities of molecular assemblies or the occurrence of life in the universe. It is pure gaseous emission.

eric · 8 November 2015

Mike Elzinga said: Suppose we ask this question about the determination of the sex of, say, some lizard or other animal during incubation. Where does the "Active Information" come from - or disappear to - when a modest change in temperature produces a different sex in the hatchlings from what occurs at a another temperature?
The air molecules around the lizard. And the solar photons absorbing into its body.
When the physical processes that take place in animals are shown to be extremely temperature dependent, how is one justified in ruling out physics and chemistry and replacing it with "active information?"
I think its basically the same thing. Active Information (the way they're using it) smooths out the search landscape and allows some searches to do better than others. This is basically identical to "reasonably stable physical laws and environment" (respectively). At least that's my best guess. It kinda makes sense in a very meta or theoretical way: any boundary conditions on a problem are, technically, 'information' you're given about that problem. The laws of physics are the boundary conditions in which other processes operate in our universe.

Joe Felsenstein · 8 November 2015

I knew Dembski's calculation came from Lloyd, but I hadn't realized that Lloyd's use of it was so interesting. Nevertheless, I do do not see anything wrong with Dembski's use of it to get a conservative low probability value that would be disturbing if we actually see events that have such low probabilities of being that good.

Nor does it matter whether the Universal Probability Bound is 10 to the minus 120 or 10 to the minus 150. The real problem with his use of that bound is

(1) If he calculates the probability only for a random process like mutation, without natural selection, and has no way of ruling out natural selection, he has not made a useful argument, and

(2) If he says that the probability calculation is to be done using not just mutation, but also natural selection, we are entitled to wonder how that is to be done. If it is known how to do it, then we have the answer we need, and no calculation of Specified Complexity adds anything to it -- we have what we need without SC.

It is here that the Specifed Complexity argument falls down, and badly.

But the UPB calculation that he makes ought to be noncontroversial, and its exact value is unimportant.

Mike Elzinga · 9 November 2015

Joe Felsenstein said: I knew Dembski's calculation came from Lloyd, but I hadn't realized that Lloyd's use of it was so interesting. Nevertheless, I do do not see anything wrong with Dembski's use of it to get a conservative low probability value that would be disturbing if we actually see events that have such low probabilities of being that good. Nor does it matter whether the Universal Probability Bound is 10 to the minus 120 or 10 to the minus 150. The real problem with his use of that bound is (1) If he calculates the probability only for a random process like mutation, without natural selection, and has no way of ruling out natural selection, he has not made a useful argument, and (2) If he says that the probability calculation is to be done using not just mutation, but also natural selection, we are entitled to wonder how that is to be done. If it is known how to do it, then we have the answer we need, and no calculation of Specified Complexity adds anything to it -- we have what we need without SC. It is here that the Specifed Complexity argument falls down, and badly. But the UPB calculation that he makes ought to be noncontroversial, and its exact value is unimportant.
Well, given the size and the age of the universe relative to the time that life has existed on this planet, the number of logical operations is quite irrelevant to what Dembski claims to be doing. Knowing that there is an "upper bound" to the number of trials it takes to get life going on this planet - or to form some specified form of life - has no bearing on the actual probabilities of such events. Those probabilities are determined by the local environment in which the constituents that go into the processes of making complex systems exist. And that local environment includes not only all those constituents, it also includes whatever energy cascades are taking place and the temperatures of the environments in which developing systems anneal and become stable. There are some empirical ways that these can be estimated using experiments and models; but those methods have to include the processes that are actually observed to take place; not some assumed tornado-in-a-junkyard type of argument. We already have plenty of evidence that atoms and molecules don't behave like junkyard parts. It is remarkable that ID/creationists don't demonstrate that they know any of this. Natural selection occurs at every level of the condensation of matter. It involves competitions between thermal kinetic energies and binding energies of the atoms and molecules as well as those energy cascades that are required to construct the more tightly bound building blocks that make up the final systems. Nothing in the calculations by Dembski or any of his followers includes temperatures, binding energies, and natural selection; but the calculations and computer algorithms of those 2013 Nobel Prize winners in chemistry do. When one folds in the mathematical physics of atomic and molecular interactions, all that is included. And, if you look at what those chemists actually did, you will see the shading and blending of quantum calculations into classical calculations in which wells become smooth and rounded and not isolated and spiky. Most of the limitations in the modeling of complex systems these days are in the areas of speed, memory, precision and resolution, and the ability to do parallel operations in computers. Lloyd's calculation is an example of how physicists go about exploring future needs in computer processing to get a complicated job done. Not only are more precise and efficient algorithms being developed, but future computer architectures and quantum computing are also being explored and developed. This is all part of a multi-pronged attack on making the computer modeling of complex systems more and more realistic. Dembski, Ewert, and Marks are totally out of the ballpark when it comes to knowing how to use computers to model complex systems. Their "math" is far too immature and amateurish. Natural selection is real; it is observed at every level of complexity.

TomS · 9 November 2015

What puzzles me is how Fred Hoyle could come up with the wind storm in a junkyard analogy.

He surely knew about the energy differences between microscopic and macroscopic systems.

And the model of random collisions of atoms has been around since the ancient atomists.

TomS · 9 November 2015

What puzzles me is how Fred Hoyle could come up with the analogy of a windstorm in a junkyard.

Surely he knew about the differences in energy levels between microscopic and macroscopic systems.

And the model of random collisions between atoms has been around since the ancient atomists.

Joe Felsenstein · 9 November 2015

The windstorm seems to have duplicated your comment.

TomS · 9 November 2015

Joe Felsenstein said: The windstorm seems to have duplicated your comment.
Yes, sorry. Now, what is the probability of that happening without intelligent design?

Joe Felsenstein · 9 November 2015

Mike Elzinga said: Well, given the size and the age of the universe relative to the time that life has existed on this planet, the number of logical operations is quite irrelevant to what Dembski claims to be doing. Knowing that there is an "upper bound" to the number of trials it takes to get life going on this planet - or to form some specified form of life - has no bearing on the actual probabilities of such events. Those probabilities are determined by the local environment in which the constituents that go into the processes of making complex systems exist. ... Dembski, Ewert, and Marks are totally out of the ballpark when it comes to knowing how to use computers to model complex systems. Their "math" is far too immature and amateurish. Natural selection is real; it is observed at every level of complexity.
Dembski's use of the UPB is just that he wants to find a number that is so small that an event that improbable is unlikely to have occurred even once in the history of the universe. It is then rather easy to show that finding a specific 250-base nucleotide sequence is less probable than that, when mutation is the only mechanism available. The UPB works fine for that -- I do not disagree with his computation. But once one brings in natural selection, the numbers change -- a lot. In his 2002 book No Free Lunch he had a Law of Conservation that was supposed to rule out natural selection being able to make events probable enough. This Law turns out to be wrongly applied. In 2005 the whole computation was recast. Now he wanted you to have done the calculation, including taking natural selection into account. So he never even attempted to provide any general machinery to calculate. (The closest he came was an unconvincing bound on the probability that a bacterial flagellum would arise de novo). In its post-2005 incarnation, the Specified Complexity calculation assumes you already know the number. It avoids the calculation, pushes it off on the user. And then all it comes up with is a declaration that this number is too small for the event to be plausible. All of the physical and chemical considerations are thus left to the user -- say, to Mike Elzinga. Which makes it easy for Dembski but useless to the user.

Joe Felsenstein · 9 November 2015

TomS said:
Joe Felsenstein said: The windstorm seems to have duplicated your comment.
Yes, sorry. Now, what is the probability of that happening without intelligent design?
Well, actually it is a nice example. If a bunch of monkeys with typewriters typed the second comment, what is the chance that it would be identical in all of its 289 characters? 1 in 27 raised to the 289th power, which is less than 10 to the minus 952. Thus an event has occurred that is so improbable that it must have been either miraculous or carefully designed by you.

eric · 9 November 2015

Joe Felsenstein said: Thus an event has occurred that is so improbable that it must have been either miraculous or carefully designed by you.
Ha! So we live in the matrix and the screwy things that happen in our reality are due to either (a) sever glitches or (b) higher order beings impatiently clicking the "submit" button multiple times because the first time it didn't seem to work. :)

harold · 9 November 2015

Well, your comment here sounded like you wanted to make a big distinction between an event that is impossible, and an event that has probability so small that it is improbable that it happened even once in the whole history of the universe. That is quite different from my complaints about Dembski’s argument.
I did mildly critique the use of "upper" ("lower"?) "probability bounds" in creationist work, because they, not I, tend to represent such bounds as literally, not approximately, equal to zero. However, I agree that approximating an insanely low probability to "zero" is not necessarily wrong in many contexts, and certainly is not the main problem with Dembski's work. The main point of my comment is that all models of evolution that show it as random sampling, but ignores or understate the role of selection, will always show adaptations as "extremely unlikely". This is obvious, yet this is a common feature of ID/creationist models of evolution. Science has never modeled biological evolution as random mutation without significant selection, and in fact, Origin of Species itself makes extensive use of the concept of selection. At a higher level, those of us who don't have an ideological issue can recognize that random factors like genetic drift play a key role in evolution, too. But to make up a model of evolution that inappropriately ignores selection, and then declare this a problem for scientific understanding of evolution, is silly. Infinite variations on this theme are possible, but they all have exactly the same flaw.

rew · 9 November 2015

In addition, the laws of physics will mandate that small changes in genotype will usually not cause huge changes in fitness
I'm not sure what you mean here but I think I disagree with it. The laws of physics have nothing do to with the fitness landscape. It has more to do with the particular genetic and protein network architecture that makes up living things. Two different networks might perform the same function but have very different topologies having to do with the number of nodes, numbers and nature of connections etc. One network might give a very different output even after minor tweaking of its connections. Another might be buffered against such changes. The second network would be much more evolvable. I think observation supports the notion that the networks that control animal development at least are in the second category.

TomS · 9 November 2015

harold said:
Well, your comment here sounded like you wanted to make a big distinction between an event that is impossible, and an event that has probability so small that it is improbable that it happened even once in the whole history of the universe. That is quite different from my complaints about Dembski’s argument.
I did mildly critique the use of "upper" ("lower"?) "probability bounds" in creationist work, because they, not I, tend to represent such bounds as literally, not approximately, equal to zero. However, I agree that approximating an insanely low probability to "zero" is not necessarily wrong in many contexts, and certainly is not the main problem with Dembski's work. The main point of my comment is that all models of evolution that show it as random sampling, but ignores or understate the role of selection, will always show adaptations as "extremely unlikely". This is obvious, yet this is a common feature of ID/creationist models of evolution. Science has never modeled biological evolution as random mutation without significant selection, and in fact, Origin of Species itself makes extensive use of the concept of selection. At a higher level, those of us who don't have an ideological issue can recognize that random factors like genetic drift play a key role in evolution, too. But to make up a model of evolution that inappropriately ignores selection, and then declare this a problem for scientific understanding of evolution, is silly. Infinite variations on this theme are possible, but they all have exactly the same flaw.
The probability that an agency which is apt to do any one of an infinite number of things, with no preference among them ... isn't that probability zero?

harold · 9 November 2015

rew said:
In addition, the laws of physics will mandate that small changes in genotype will usually not cause huge changes in fitness
I'm not sure what you mean here but I think I disagree with it. The laws of physics have nothing do to with the fitness landscape. It has more to do with the particular genetic and protein network architecture that makes up living things. Two different networks might perform the same function but have very different topologies having to do with the number of nodes, numbers and nature of connections etc. One network might give a very different output even after minor tweaking of its connections. Another might be buffered against such changes. The second network would be much more evolvable. I think observation supports the notion that the networks that control animal development at least are in the second category.
I guess it depends on what is meant by "small" and what is meant by "usually". A point mutation at a particular locus can have huge impact on fitness. But most point mutations won't be at such loci, and most point mutations at those loci won't have huge impact. So it may be safe to say that more extensive mutations are more likely to impact on phenotype and thus fitness. With the strong caveat that some deletions or duplications of large amounts of the genome will have no effect and some point mutations will have major effects.

Mike Elzinga · 9 November 2015

Joe Felsenstein said: All of the physical and chemical considerations are thus left to the user -- say, to Mike Elzinga. Which makes it easy for Dembski but useless to the user.
I am juggling a complex schedule at the moment, so I may not be giving this enough attention to make my point clear. But let me oblige with a bracketing calculation. It is important to understand what Seth Lloyd did. His is considering a quantum computer that flips quantum bits. Therefore it is operating at a level that can count bit flips for everything that occurs in our known universe. The energy levels at which these bits are flipped are the average system energies above the ground state; so they include the process in chemistry and condensing matter. Think of the universe as being the result of a simulation by such a computer. Let the number of logical operations required by that computer to produce the entire universe be NU. This is the upper bound of that number, which Lloyd estimated to be 10^120 (approximately 2^500). Let the number of logical operations required to produce any proper subset of that universe be NS; which is strictly less than NU. Ignore all of Dembski's obfuscations of taking logs to base 2 and calling it "information." The expected number of occurrences of an event in N trials at probability p per trial is Np. The probability of that subset of the entire universe being produced is therefore greater than or equal to 1/NS which, in turn, is greater than 1/NU. Life and all of its complexity is a subset of the universe being simulated by Lloyd's quantum computer. Therefore, the probability that life occurs in the universe is greater than 1/NU. Dembski didn't read Lloyd's paper or understand any of its implications; he just lifted 10^120 from the abstract and used it as a number against which to calculate probabilities using methods that have absolutely nothing to do with the physical processes involved in producing atomic and molecular assemblies.

JimV · 9 November 2015

Google tells me that a blind search, or uninformed search, is one that lacks any information about the search space, except for the goal state.

Then it seems to me that biological evolution is a blind search. Each time a genome is modified, searching for an improvement in reproductive fitness (the goal state), the modification is made randomly (within the constraints of the existing structure), without knowing what effect it will have. So praise for blind, random searches (which, yes, work as well or better than any other kind of search when the search space can be anything) is praise for biological evolution.

It also seems to me that IDer's are looking at the issue wrongly by 180 degrees. They claim that the only instances of successfully producing working ideas and designs, in human experience, is by something magic which they call "intelligent design" (whose workings they cannot explain). In fact, the only way working ideas and designs have ever been produced by humans has been by the evolutionary process. Cars have evolved, phones have evolved, computers have evolved, and scientific theories have evolved, by trial and error and survival of the fittest. We have also evolved meta-evolutionary methods, such as lab experiments and computer simulations, to speed up the process, but we have yet to match the capability of biological evolution, in its current, massively-parallel state. For example, it took us about 100,000 years of technological development to produce the synthetic fiber called nylon. It took bacteria less than 40 years to invent a way to digest it.

News flash for IDers: Paley's watch did not poof into existence ex nihilo; it evolved.

Henry J · 9 November 2015

As I understand it, blind search means starting from scratch each time. Adding changes to something that's already successful isn't starting from scratch.

Joe Felsenstein · 9 November 2015

rew said: [I said in the post]
In addition, the laws of physics will mandate that small changes in genotype will usually not cause huge changes in fitness
I'm not sure what you mean here but I think I disagree with it. The laws of physics have nothing do to with the fitness landscape. It has more to do with the particular genetic and protein network architecture that makes up living things. Two different networks might perform the same function but have very different topologies having to do with the number of nodes, numbers and nature of connections etc. One network might give a very different output even after minor tweaking of its connections. Another might be buffered against such changes. The second network would be much more evolvable. I think observation supports the notion that the networks that control animal development at least are in the second category.
The argument based on the paper by Dembski, Ewert, and Marks assumes that smooth fitness landscapes can arise only by Design. An infinitely rough fitness surface means that there is tight interaction between all pairs of genes (and all combinations of higher order as well). Making a change in one gene will then almost always reduce the fitness to that of an organism so bad that it is just like one produced by changing all sites in the DNA at the same time. However sensitive networks of gene interaction can be, they don't interact that strongly. That is because different genes can have effects on different parts of the organism, at different times. Real fitness surfaces are not that rough at all. And at least part of that smoothness comes from the weakness of effects at a distance in real physics. It mandates that genes acting in the production of my toenail and genes acting in the connection of nerves in my brain probably do not interact a lot. DEM assume, in effect, tight interaction between everything and everything else, as their default. Real genes do not act like that.

Joe Felsenstein · 9 November 2015

Henry J said: As I understand it, blind search means starting from scratch each time. Adding changes to something that's already successful isn't starting from scratch.
Search can be blind if there is no feedback from fitness to where the search goes next, even if it starts from the previous result. As a population moving on a fitness surface is biased toward preferentially moving to nearby states with higher fitness, I wouldn't call the search blind.

TomS · 10 November 2015

JimV said: News flash for IDers: Paley's watch did not poof into existence ex nihilo; it evolved.
Paley's watch did not poof into existence ex nihilo. It was produced. In the case of the living analog of the watch, it was reproduced. If one thinks that the analogy shows that materialist, naturalistic explanations are not enough, one doubts reproduction.

Rolf · 10 November 2015

harold said: Simple but basically valid mathematical model of evolution - "Roll 100 dice, select out the sixes, put them aside, do it again, inevitably you eventually have all sixes." Dembski's model - "Keep rolling 100 dice. The probability of getting all sixes on any given roll is 1 in 6^100. This is a small number. It's so small that in some engineering applications it might be taken as approximately zero. Therefore it is zero. Therefore you need magic to get 100 sixes." I strongly defend this terse summary as a basically accurate paraphrase of all ID probability based models that have ever been proposed, including the one under discussion here.
What I understand is that we don't need to search for a predefined combination, all combinations have equal probability of occurence. We may strike lucky and get the 'right' one at our first throw. Life and evolution probably was inevitable, Dembski notwithstanding. I once won 20.000 NOK on Lotto because I by accident happened to have two identical coupons just that time. But in the past 40 years I've won only a few times, about NOK 50 or so each time. I now have decided it is a waste of money

Rolf · 10 November 2015

Mike Elzinga said: Dembski didn't read Lloyd's paper or understand any of its implications; he just lifted 10^120 from the abstract and used it as a number against which to calculate probabilities using methods that have absolutely nothing to do with the physical processes involved in producing atomic and molecular assemblies.
That, as far as I am concerned, sums it up quite nicely. Not only Dembski, unless otherwise proven, ID proponents generally are quite lacking in knowledge and understanding of physics and chemistry. That's where we find the ingredients and processes required for life and evolution. We have plenty of evidence of what nature can do. Where's the evidence of what magic can do, or does?

TomS · 10 November 2015

Rolf said:
harold said: Simple but basically valid mathematical model of evolution - "Roll 100 dice, select out the sixes, put them aside, do it again, inevitably you eventually have all sixes." Dembski's model - "Keep rolling 100 dice. The probability of getting all sixes on any given roll is 1 in 6^100. This is a small number. It's so small that in some engineering applications it might be taken as approximately zero. Therefore it is zero. Therefore you need magic to get 100 sixes." I strongly defend this terse summary as a basically accurate paraphrase of all ID probability based models that have ever been proposed, including the one under discussion here.
What I understand is that we don't need to search for a predefined combination, all combinations have equal probability of occurence. We may strike lucky and get the 'right' one at our first throw. Life and evolution probably was inevitable, Dembski notwithstanding. I once won 20.000 NOK on Lotto because I by accident happened to have two identical coupons just that time. But in the past 40 years I've won only a few times, about NOK 50 or so each time. I now have decided it is a waste of money
I don't think anyone has mentioned this problem: The number of combinations which result in life, or a viable living thing, is not just one out of the vast number of possibilities. It isn't as if evolution is successful only when it produces the species of platypus. That is no big deal, but it just one more item in the list of things which are wrong with the probability calculation which shows that it is not worth the effort. Except it can be used as a teaching tool to explore the subtleties of probabilities, showing where one can go astray if one is not careful.

TomS · 10 November 2015

Rolf said:
Mike Elzinga said: Dembski didn't read Lloyd's paper or understand any of its implications; he just lifted 10^120 from the abstract and used it as a number against which to calculate probabilities using methods that have absolutely nothing to do with the physical processes involved in producing atomic and molecular assemblies.
That, as far as I am concerned, sums it up quite nicely. Not only Dembski, unless otherwise proven, ID proponents generally are quite lacking in knowledge and understanding of physics and chemistry. That's where we find the ingredients and processes required for life and evolution. We have plenty of evidence of what nature can do. Where's the evidence of what magic can do, or does?
Rather, I suggest, where's the description of what magic can do? How does an agency which is not involved in nature have an effect in nature? What happens when such an agency results in something in the world of life? When and where? Until we have some idea of what were looking at, it is pointless to expect evidence for it.

eric · 10 November 2015

TomS said: Rather, I suggest, where's the description of what magic can do?
Intelligent Design answer: Genesis 1"ID is not a mechanistic theory, and it’s not ID’s task to match your pathetic level of detail in telling mechanistic stories."

harold · 10 November 2015

Rolf said:
harold said: Simple but basically valid mathematical model of evolution - "Roll 100 dice, select out the sixes, put them aside, do it again, inevitably you eventually have all sixes." Dembski's model - "Keep rolling 100 dice. The probability of getting all sixes on any given roll is 1 in 6^100. This is a small number. It's so small that in some engineering applications it might be taken as approximately zero. Therefore it is zero. Therefore you need magic to get 100 sixes." I strongly defend this terse summary as a basically accurate paraphrase of all ID probability based models that have ever been proposed, including the one under discussion here.
What I understand is that we don't need to search for a predefined combination, all combinations have equal probability of occurence. We may strike lucky and get the 'right' one at our first throw. Life and evolution probably was inevitable, Dembski notwithstanding. I once won 20.000 NOK on Lotto because I by accident happened to have two identical coupons just that time. But in the past 40 years I've won only a few times, about NOK 50 or so each time. I now have decided it is a waste of money
The point of my simple model is to show how random mutation with selection leads to results that would be very unlikely to arise without the selection, that is all. It has nothing to do with abiogenesis, although the same general principles might apply, and it is not intended to imply that evolution is "looking for" anything. Just to show that a correct model of biological evolution must include both variation and selection. Denying or distorting either simply produces an incorrect model.

harold · 10 November 2015

The argument based on the paper by Dembski, Ewert, and Marks assumes that smooth fitness landscapes can arise only by Design. An infinitely rough fitness surface means that there is tight interaction between all pairs of genes (and all combinations of higher order as well). Making a change in one gene will then almost always reduce the fitness to that of an organism so bad that it is just like one produced by changing all sites in the DNA at the same time. However sensitive networks of gene interaction can be, they don’t interact that strongly. That is because different genes can have effects on different parts of the organism, at different times. Real fitness surfaces are not that rough at all. And at least part of that smoothness comes from the weakness of effects at a distance in real physics. It mandates that genes acting in the production of my toenail and genes acting in the connection of nerves in my brain probably do not interact a lot. DEM assume, in effect, tight interaction between everything and everything else, as their default. Real genes do not act like that.
It's important to do that hard, necessary work of tearing these deliberately complicated and obfuscating models apart in detail, and my terse summaries are not intended to disparage that in any way. It's also valuable to note that they all amount to repetitions on basic mistaken themes. This amounts to a variant of the "no beneficial mutations" argument. Dembski is ultimately saying that if the surrounding environment is "natural" any mutation whatsoever will be harmful (because of its impact on other genes). Therefore "the designer" must constantly be changing the environment to accommodate mutations. The semantics are obscure and dissembling, but he's essentially saying that mutations can't be adaptive in a "natural" environment. He "concedes" that mutations lead to adaptations but counters "Oh yeah, well then the designer must be designing the environment instead of the mutations, so there!". It's interesting to note how perverse ID/creationist "models". In normal life, if you make a model and it doesn't conform to observations, you have to concede that it was a bad model. If I make a model to predict the stock market and it doesn't work, I have to admit that it doesn't work. An ID/creationist, on the other hand, sets out to, in this analogy, "prove" that the stock market must be driven by magic. So they make a deliberately bad model that doesn't even incorporate what academic finance actually does know about stock market behavior. Then they say "if the stock market was 'materialist' it would conform to my model; since my model doesn't work, it proves that the stock market is driven by magic". But who is the magician? How does the magician do it? When did the magician start doing it? What, obviously useful question, will the magician do next? How can this conclusion help us to better understand the stock market? These questions must not be answered. Ironically, the only way an ID/creationist model of evolution can make them happy is if it doesn't work and they offer no suggestion for improvement. They can't try to identify or explain the designer, because that would either fail to disguise their religious motivations, or identify the wrong designer, or involve conceding that they can't identify a designer. If their models worked, designer forbid, they'd actually be helping us to understand evolution. So all they can do is make up models that are designed not to work, and then say "If my model doesn't work, it must be magic".

Mike Elzinga · 10 November 2015

harold said: So all they can do is make up models that are designed not to work, and then say "If my model doesn't work, it must be magic".
It is also important to note that these are the kinds of "models" they expect their opponents to agree on in a public debate. ID/creationists have a long history of attempting to drag their debating opponents onto ID/creationist territory using ID/creationist concepts and definitions. If they are successful in doing that, then they assure themselves of a satisfying "gotcha" victory in front of the kinds of sectarian audiences they prefer. They can't get away with this kind of arguing in front of an assembly of expert scientists. Experts can spot the errors instantly. This tactic by ID/creationists is simply another example of the fact that ID/creationism is a socio/political movement being performed on a public stage.

Mike Elzinga · 10 November 2015

Rolf said:
Mike Elzinga said: Dembski didn't read Lloyd's paper or understand any of its implications; he just lifted 10^120 from the abstract and used it as a number against which to calculate probabilities using methods that have absolutely nothing to do with the physical processes involved in producing atomic and molecular assemblies.
That, as far as I am concerned, sums it up quite nicely. Not only Dembski, unless otherwise proven, ID proponents generally are quite lacking in knowledge and understanding of physics and chemistry. That's where we find the ingredients and processes required for life and evolution. We have plenty of evidence of what nature can do. Where's the evidence of what magic can do, or does?
Abstracts of papers are usually shown on line, and unless one is a member of the professional society with access to the text of the paper, one has to pay a fee for the paper. I'm guessing that Dembski found the abstract on line, saw that number in the abstract, and figured it would give him some scientific credibility for his number of trials in the history of the universe. If Dembski actually held that paper in his hands, then I can only surmise that he had absolutely no comprehension of the fact that Lloyd was demonstrating the physical connections between energy and the processes involved in building up the complex systems we see in the universe. Dembski was like a dog sniffing a huge diamond, licking off some scent he thought he liked, and then walking away from it as being of no further interest.

Paul Burnett · 11 November 2015

eric said:
Mike Elzinga said: Suppose we ask this question about the determination of the sex of, say, some lizard or other animal during incubation. Where does the "Active Information" come from - or disappear to - when a modest change in temperature produces a different sex in the hatchlings from what occurs at a another temperature?
The air molecules around the lizard. And the solar photons absorbing into its body.
The eggs are underground...no solar photons, and stagnant air at best. The temperature gradient in the egg pile is the determinant of gender in the embryos - males at the top, females at the bottom.

Tom English · 11 November 2015

Apologies to Joe, and to all at PT, for being so slow with my post at The Skeptical Zone:

The Law of Conservation of Information Is Defunct

A relatively unimportant section is sketchy, and I hope to complete it tomorrow. I think there's plenty of interest to the folks who have commented here.

Joe nailed ID with his analysis of the GUC Bug. Dembski et al. have made some huge concessions. I hope you'll have a better appreciation of that after reading my post.

eric · 12 November 2015

Paul Burnett said:
eric said:
Mike Elzinga said: Suppose we ask this question about the determination of the sex of, say, some lizard or other animal during incubation. Where does the "Active Information" come from - or disappear to - when a modest change in temperature produces a different sex in the hatchlings from what occurs at a another temperature?
The air molecules around the lizard. And the solar photons absorbing into its body.
The eggs are underground...no solar photons, and stagnant air at best. The temperature gradient in the egg pile is the determinant of gender in the embryos - males at the top, females at the bottom.
Dembski is equating 'active information' with some sort of required intelligent action but he's never shown this to be true. Active information is supposed to be the "numerical measure of the amount of problem-specific information resident in the search algorithm" [secondary citation]. In the case of sex choice during development, the "search algorithm" is genes activating with some temperature dependence and the "active information" is the temperature dependent instructions. The insulation and thermal contribution from the environment trigger certain developmental pathways vice others. So the real science question his idea poses is; how did these genetic phenotypic instructions become temperature dependent? How did temperature dependence become resident in the search algorithm? Dembski's implication that design is needed amounts to saying that temperature dependent DNA reactions cannot evolve. That seems highly dubious given the role temperature plays in practically every chemical and biochemical reaction, including organic ones. The other possibility is that active information (such as temperature dependent reactions) can evolve and thus is not an indication of design - which undermines his entire design inference.

Joe Felsenstein · 12 November 2015

eric said: In the case of sex choice during development, the "search algorithm" is genes activating with some temperature dependence and the "active information" is the temperature dependent instructions. The insulation and thermal contribution from the environment trigger certain developmental pathways vice others. So the real science question his idea poses is; how did these genetic phenotypic instructions become temperature dependent? How did temperature dependence become resident in the search algorithm? Dembski's implication that design is needed amounts to saying that temperature dependent DNA reactions cannot evolve. That seems highly dubious given the role temperature plays in practically every chemical and biochemical reaction, including organic ones. The other possibility is that active information (such as temperature dependent reactions) can evolve and thus is not an indication of design - which undermines his entire design inference.
I wonder. In the papers of Dembski, Ewert, and Marks the "search" is both the association of fitness with genotypes and the populatiion-genetic process of change that results. The point Tom English and I are making is that just having genotypes, phenotypes, and fitnesses, whatever they might be, buys you a lot of DEM's "Active Information". The default assumption that they are implicitly making is that interactions of genes are as complex as they could be, and that the process of change in populations is most likely paying no attention to the fitnesses. As complex as gene interactions may be in temperature-dependent sex determination, DEM's default is much more complex interaction. And that the genetic system is probably not even tending to go uphill on the resulting fitness surface.

eric · 12 November 2015

Joe Felsenstein said: I wonder. In the papers of Dembski, Ewert, and Marks the "search" is both the association of fitness with genotypes and the populatiion-genetic process of change that results. The point Tom English and I are making is that just having genotypes, phenotypes, and fitnesses, whatever they might be, buys you a lot of DEM's "Active Information".
Yup; the example Mike Elzinga originally gave is not a great fit to a discussion of RM+NS as mechanism or fitness, because RM+NS isn't what's happening in the case of sex determination in incubating lizards. I was trying to work as best I could with that example though, to show how it might work in Dembski's framework. If I mistranslated some ideas, mea culpa.

harold · 12 November 2015

eric said:
Joe Felsenstein said: I wonder. In the papers of Dembski, Ewert, and Marks the "search" is both the association of fitness with genotypes and the populatiion-genetic process of change that results. The point Tom English and I are making is that just having genotypes, phenotypes, and fitnesses, whatever they might be, buys you a lot of DEM's "Active Information".
Yup; the example Mike Elzinga originally gave is not a great fit to a discussion of RM+NS as mechanism or fitness, because RM+NS isn't what's happening in the case of sex determination in incubating lizards. I was trying to work as best I could with that example though, to show how it might work in Dembski's framework. If I mistranslated some ideas, mea culpa.
It should be noted that ID/creationists do spend a lot of time making arguments that either only apply to abiogenesis, and/or are actually arguments that apply more to development than to evolution. The general idea that specialized cellular adaptation cannot occur without "intelligent" (i.e. supernatural) guidance is an argument against development as much as against evolution. Of course, if ID/creationists begin to say "we admit it happens but say it can't happen without magic", they make, as this discussion suggests, a significant concession. To use gravity as an analogy, the movement began by arguing that apples fall up, and claiming that scientific evidence shows that apples fall up (creation science). Then they moved into the classic phase of ID, circa 1995-2005, during which they gained much public exposure for "proofs" that, although apples seem to fall down, it's "theoretically impossible" for them to do so according to "information science", so we can ignore biased reports of apples falling down from atheist scientists, and feel secure that they only fall up, and we can teach this in public schools because nobody said a word about the Bible. We all know how that worked out. Now Dembski seems to be doing the equivalent of admitting that apples fall down, but "proving" with "information science" that apples fall down, but can only do so because angels are pushing them. I guess even anti-evolution can evolve.

TomS · 12 November 2015

harold said:
eric said:
Joe Felsenstein said: I wonder. In the papers of Dembski, Ewert, and Marks the "search" is both the association of fitness with genotypes and the populatiion-genetic process of change that results. The point Tom English and I are making is that just having genotypes, phenotypes, and fitnesses, whatever they might be, buys you a lot of DEM's "Active Information".
Yup; the example Mike Elzinga originally gave is not a great fit to a discussion of RM+NS as mechanism or fitness, because RM+NS isn't what's happening in the case of sex determination in incubating lizards. I was trying to work as best I could with that example though, to show how it might work in Dembski's framework. If I mistranslated some ideas, mea culpa.
It should be noted that ID/creationists do spend a lot of time making arguments that either only apply to abiogenesis, and/or are actually arguments that apply more to development than to evolution. The general idea that specialized cellular adaptation cannot occur without "intelligent" (i.e. supernatural) guidance is an argument against development as much as against evolution. Of course, if ID/creationists begin to say "we admit it happens but say it can't happen without magic", they make, as this discussion suggests, a significant concession. To use gravity as an analogy, the movement began by arguing that apples fall up, and claiming that scientific evidence shows that apples fall up (creation science). Then they moved into the classic phase of ID, circa 1995-2005, during which they gained much public exposure for "proofs" that, although apples seem to fall down, it's "theoretically impossible" for them to do so according to "information science", so we can ignore biased reports of apples falling down from atheist scientists, and feel secure that they only fall up, and we can teach this in public schools because nobody said a word about the Bible. We all know how that worked out. Now Dembski seems to be doing the equivalent of admitting that apples fall down, but "proving" with "information science" that apples fall down, but can only do so because angels are pushing them. I guess even anti-evolution can evolve.
I wish that there was more attention drawn to the arguments which are supposedly against evolution, but are at least as appropriately against reproduction, genetics, development or even metabolism. Many of the arguments (for example, irreducible complexity - although not by that name) were used in the 18th century against reproduction (and in favor of preformation). How often do we hear the complaint that if I am evolved then I am not something special. Or how evolution says that humans evolve from a single cell. Or that evolution relies on chance (think of the role of chance in genetics).

harold · 12 November 2015

TomS said:
harold said:
eric said:
Joe Felsenstein said: I wonder. In the papers of Dembski, Ewert, and Marks the "search" is both the association of fitness with genotypes and the populatiion-genetic process of change that results. The point Tom English and I are making is that just having genotypes, phenotypes, and fitnesses, whatever they might be, buys you a lot of DEM's "Active Information".
Yup; the example Mike Elzinga originally gave is not a great fit to a discussion of RM+NS as mechanism or fitness, because RM+NS isn't what's happening in the case of sex determination in incubating lizards. I was trying to work as best I could with that example though, to show how it might work in Dembski's framework. If I mistranslated some ideas, mea culpa.
It should be noted that ID/creationists do spend a lot of time making arguments that either only apply to abiogenesis, and/or are actually arguments that apply more to development than to evolution. The general idea that specialized cellular adaptation cannot occur without "intelligent" (i.e. supernatural) guidance is an argument against development as much as against evolution. Of course, if ID/creationists begin to say "we admit it happens but say it can't happen without magic", they make, as this discussion suggests, a significant concession. To use gravity as an analogy, the movement began by arguing that apples fall up, and claiming that scientific evidence shows that apples fall up (creation science). Then they moved into the classic phase of ID, circa 1995-2005, during which they gained much public exposure for "proofs" that, although apples seem to fall down, it's "theoretically impossible" for them to do so according to "information science", so we can ignore biased reports of apples falling down from atheist scientists, and feel secure that they only fall up, and we can teach this in public schools because nobody said a word about the Bible. We all know how that worked out. Now Dembski seems to be doing the equivalent of admitting that apples fall down, but "proving" with "information science" that apples fall down, but can only do so because angels are pushing them. I guess even anti-evolution can evolve.
I wish that there was more attention drawn to the arguments which are supposedly against evolution, but are at least as appropriately against reproduction, genetics, development or even metabolism. Many of the arguments (for example, irreducible complexity - although not by that name) were used in the 18th century against reproduction (and in favor of preformation). How often do we hear the complaint that if I am evolved then I am not something special. Or how evolution says that humans evolve from a single cell. Or that evolution relies on chance (think of the role of chance in genetics).
And of course to the less biased mind, this draws attention to the fact that these things are intimately associated. It's actually kind of hard to come up with a "pure" claim that evolution is impossible, without making an argument against development, reproduction, genetics, or possibly even metabolism. After all, the current forms of reproduction and development on Earth are the product of evolution. And evolution happens because of the way reproduction and development work.

JimV · 12 November 2015

Henry J said: As I understand it, blind search means starting from scratch each time. Adding changes to something that's already successful isn't starting from scratch.
Then you have an argument with Google, whose 2nd and 3rd top hits are (the first does not give a definition): http://cse.unl.edu/~choueiry/S03-476-876/searchapplet/ Blind Search Algorithms Blind search, also called uninformed search, works with no information about the search space, other than to distinguish the goal state from all the others. http://www.cs.nott.ac.uk/~pszgxk/courses/g5aiai/003blindsearches/blind_searches.htm Blind Searches Introduction A blind search (also called an uninformed search) is a search that has no information about its domain. The sites go on to list several different ways of doing a blind search. There are many methods. One of them is biological evolution. As far as evolution being biased towards higher fitness, all blind searches (indeed, all searches) are biased toward their goal states. This has nothing to do with their being blind. (I think Dr. Dawkins would agree with me, e.g., "The Blind Watchmaker".)

JimV · 12 November 2015

TomS said: Paley's watch did not poof into existence ex nihilo. It was produced. In the case of the living analog of the watch, it was reproduced. If one thinks that the analogy shows that materialist, naturalistic explanations are not enough, one doubts reproduction.
My point was that timekeepers/clocks evolved over a long period of time (which continues today) and Paley's pocket watch was not the result of some intelligent designer sitting down with a blank piece of paper and drawing the first, last, and only viable watch design by some magical process. The trees of the forest evolved and so did the watch that Paley found there (in his thought experiment). If you want to say that the trees were grown from acorns and the watch was made in a factory, true, but that obscures the point. Engineering and science are not magic, and in fact bacteria do them better than us (in terms of quick and novel results). There may be other factors involved, but I think I come much closer to the truth in evoking the evolutionary algorithm to explain engineering and scientific progress than ID does with its magic.

Henry J · 12 November 2015

Well, as a search, evolution has information about its history (although just the latest results of that history). I'm not sure if that would be considered part of its domain or not.

harold · 13 November 2015

Blind search, also called uninformed search, works with no information about the search space, other than to distinguish the goal state from all the others.
It seems that perhaps bothering to argue about the definition and characteristics of a blind search is a distraction, perhaps one intentionally created by ID/creationists. Biological evolution does not have a human-perceptible "goal" of course. Alleles change in frequency in populations, but no human-perceptible scheme to promote certain alleles over others exists. Therefore, it makes more sense to say that evolution does not have a goal. It really does not make sense to model specific adaptations as goals, because adaptations, although contingent on past events, are not planned in advance, Whether an inscrutable divine being has set things up so that to the best observations of the human brain there is no goal, but that being the end result is intended in a way that humans can never perceive, is a question that cannot be answered by scientific methodology, and which is not relevant to science classes, but may be of interest to some philosophers. Here's a very crude but somewhat reasonable model of evolution. Roll one die. Note the result. Then roll 100 die. Whichever of the 100 have the value "seven minus the original roll" set them aside. For example if the original roll was a three you would set fours aside. If your first roll of the 100 dice produces 18 fours, set them aside and roll the remaining 82, again setting the fours aside, and so on. This model is crude but incorporates the fact that what is to be selected for is itself not planned by humans or any other demonstrable entity, plus random variation and selection. The elements, which can be and are frequently modeled in a much more sophisticated way than this (even simple improvements using dice are obvious but would waste space here, for example the fact that more than one adaptation will be selected for), are that something we don't control determines what will be adaptive, and then random variation and selection of what is adaptive, contingent on prior results, with the caveat of abundant random variation, including some random increase of things that are neutral or even anti-adaptive may sometimes occur, especially at small population numbers. Sophisticated models are possible but the basic way if works is clear. Inappropriate models that do not make use what is known serve no purpose. Any model that sets present adaptations as an "ultimate intended goal" and attempts to show the "improbability", from the perspective of the distant past, of seeing the exact adaptations we see now, is completely stupid, because current adaptations were not an a priori goal, to best human observation.

Joe Felsenstein · 13 November 2015

JimV said:
Henry J said: As I understand it, blind search means starting from scratch each time. Adding changes to something that's already successful isn't starting from scratch.
Then you have an argument with Google, whose 2nd and 3rd top hits are (the first does not give a definition): http://cse.unl.edu/~choueiry/S03-476-876/searchapplet/ Blind Search Algorithms Blind search, also called uninformed search, works with no information about the search space, other than to distinguish the goal state from all the others. http://www.cs.nott.ac.uk/~pszgxk/courses/g5aiai/003blindsearches/blind_searches.htm Blind Searches Introduction A blind search (also called an uninformed search) is a search that has no information about its domain. The sites go on to list several different ways of doing a blind search. There are many methods. One of them is biological evolution. As far as evolution being biased towards higher fitness, all blind searches (indeed, all searches) are biased toward their goal states. This has nothing to do with their being blind. (I think Dr. Dawkins would agree with me, e.g., "The Blind Watchmaker".)
Both of these definitions of "blind search" say that the only information that the search can have about the surface is to distinguish the goal state from all others. In other words to be told that it has arrived at the goal state. Although JimV quotes the second citation as saying that the search "has no information about its domain", when I go to that page it also says that "The only thing that a blind search can do is distinguish a non-goal state from a goal state." So they are consistent with each other. Neither of these pages mentions evolution. In the examples given on those pages, the search can retain information about where it has been, including the "cost" of traveling between nodes. But for none of them is the search given any feedback information about how well it is doing, aside from being told whether or not it has now arrived at the goal. From this I conclude that any model of evolution as a search is not using a blind search, since fitnesses of non-optimal genotypes affect the movement on the search space. I do not know why JimV said that one way of doing a blind search was "biological evolution". Neither of the references he gives say that.

stevaroni · 13 November 2015

Joe Felsenstein said: From this I conclude that any model of evolution as a search is not using a blind search, since fitnesses of non-optimal genotypes affect the movement on the search space. I do not know why JimV said that one way of doing a blind search was "biological evolution". Neither of the references he gives say that.
Also, it's important that the "goal state" of evolution is pretty damned flexible. Contrary to the creationist claim that the goal of evolution is to "produce animal X", the actual goal is the much simpler "live long enough to produce viable offspring". In practice, in a world of competition and predation, this usually translates to "get eaten last", but even that solution space is much, much larger than the one-solution-a-bajillion strawman of creationist wet dreams.

Mike Elzinga · 13 November 2015

JimV said:
TomS said: Paley's watch did not poof into existence ex nihilo. It was produced. In the case of the living analog of the watch, it was reproduced. If one thinks that the analogy shows that materialist, naturalistic explanations are not enough, one doubts reproduction.
My point was that timekeepers/clocks evolved over a long period of time (which continues today) and Paley's pocket watch was not the result of some intelligent designer sitting down with a blank piece of paper and drawing the first, last, and only viable watch design by some magical process. The trees of the forest evolved and so did the watch that Paley found there (in his thought experiment). If you want to say that the trees were grown from acorns and the watch was made in a factory, true, but that obscures the point. Engineering and science are not magic, and in fact bacteria do them better than us (in terms of quick and novel results). There may be other factors involved, but I think I come much closer to the truth in evoking the evolutionary algorithm to explain engineering and scientific progress than ID does with its magic.
Paley's watch is another example of the inappropriateness of using inert objects blown about by tornados as stand-ins for the properties and behaviors of atoms and molecules. Junkyard parts, watch parts, or battleship parts do not have charge-to-mass ratios. They do not get their shapes from interatomic and intermolecular interactions. They do not have binding energies; nor do their constituent parts have thermal kinetic energies comparable to their binding energies. Their parts don't crawl over themselves and plop into mutual potential energy wells as they are being jostled by their thermal kinetic energies. Their final configurations are not determined by quantum mechanical rules that apply to atoms and molecules. If the masses of junkyard parts and watch parts had charge-to-mass ratios comparable to those of protons and electrons, then 1 kg masses separated by a meter would have interaction energies on the order of 10^26 joules, or roughly 10^10 megatons of TNT. ASCII characters, dice, flipped coins, junkyard parts, the stones of Stonehenge, and all other artifacts built by humans do not have any of the properties of the building blocks of living organisms; and they do not self assemble in any of the configurations found in complex molecular assemblies. Atoms and molecules bind in ways that are determined by the type of atom and by quantum mechanical rules; and some configurations are far more probable than others. ASCII characters don't have any such forces and rules of interaction; there are no Periodic Tables for ASCII characters, watch parts, and junkyard parts. Watches, battleships, 747s, cathedrals, are not sculpted and assembled by any of the kinds of forces and rules that apply to atoms and molecules. There are no covalent bonds, or ionic bonds, or hydrogen bonds, or Van der Waals forces among them. Furthermore, ID/creationists do not use "information" in any sense that applies to the physical world. In the real world of physics and chemistry, information is physical. Whenever an atomic or molecular bond is formed, energy is released. Each and every atomic and molecular configuration is a collection of bonds, each of which released energy in the form of a photon, a phonon, or another particle that carried energy to some other location in space and time. Each and every configuration represents a collection of energy states and potential energy wells that forms a "template" for subsequent interactions with other systems in the environment. ASCII characters, junkyard parts, and coin flips never behave that way. "Information" in ID/creationism has no correspondence with energy states. ID/creationist "information" is nothing more than arbitrary counting of arrangements of inert things and then taking logarithms to base 2. There is no regard whatsoever for energies of interaction among themselves or with an environment. In physics and chemistry, every bit that is flipped is paired with a "packet" of energy. In physics and chemistry, entropy can be mapped onto bits because each bit represents a one-to-one correspondence with a physical energy state that is related to temperature, pressure, volume, and real physical processes in which energy and momentum are exchanged among particles and the environment. Real living organisms are made of atomic and molecular assemblies that interact and exchange energy with a real physical world. Those interactions are crucial in their evolution over time. In the real world, information is always paired ultimately with energies of interaction among constituents and with the surrounding environment. It is temperature dependent. The mere fact that ID/creationist "information" is never temperature dependent means that ID/creationist "information" has nothing to do with the physical world but instead exists only in ID/creationists' imaginations.

stevaroni · 13 November 2015

Mike Elzinga said: Paley's watch is another example of the inappropriateness of using inert objects blown about by tornados as stand-ins for the properties and behaviors of atoms and molecules.
Again, I will point out that the reason we can instantly know that Paley's watch was intelligently designed is not because it is very complex, but rather because it is composed of parts that we know are artificial. If we lived in a world of living, reproducing machines, where you could leave two eager alarm clocks in a room overnight and find a litter of fresh wristwatches in the morning, a planet where you couldn't turn over a rock in the forest without finding a nest of wriggling machine screws, then you would no longer be able to make that determination. The thing is, obviously, as soon as you start using Paley's watch as a proxy for evolution, then we do live on that planet of living machines and watches in the sand become a lot less definitive.

Mike Elzinga · 13 November 2015

stevaroni said:
Mike Elzinga said: Paley's watch is another example of the inappropriateness of using inert objects blown about by tornados as stand-ins for the properties and behaviors of atoms and molecules.
Again, I will point out that the reason we can instantly know that Paley's watch was intelligently designed is not because it is very complex, but rather because it is composed of parts that we know are artificial. If we lived in a world of living, reproducing machines, where you could leave two eager alarm clocks in a room overnight and find a litter of fresh wristwatches in the morning, a planet where you couldn't turn over a rock in the forest without finding a nest of wriggling machine screws, then you would no longer be able to make that determination. The thing is, obviously, as soon as you start using Paley's watch as a proxy for evolution, then we do live on that planet of living machines and watches in the sand become a lot less definitive.
Like the frog that popped out of a clock in response to the words, "Plunk your magic twanger, Froggy!"?

phhht · 13 November 2015

Mike Elzinga said: Like the frog that popped out of a clock in response to the words, "Plunk your magic twanger, Froggy!"?
Thanks for that. It took me back to childhood.

TomS · 13 November 2015

stevaroni said:
Mike Elzinga said: Paley's watch is another example of the inappropriateness of using inert objects blown about by tornados as stand-ins for the properties and behaviors of atoms and molecules.
Again, I will point out that the reason we can instantly know that Paley's watch was intelligently designed is not because it is very complex, but rather because it is composed of parts that we know are artificial. If we lived in a world of living, reproducing machines, where you could leave two eager alarm clocks in a room overnight and find a litter of fresh wristwatches in the morning, a planet where you couldn't turn over a rock in the forest without finding a nest of wriggling machine screws, then you would no longer be able to make that determination. The thing is, obviously, as soon as you start using Paley's watch as a proxy for evolution, then we do live on that planet of living machines and watches in the sand become a lot less definitive.
From one 19th century theologian:
I have not insisted on the argument from design, because I am writing for the 19th Century, by which, as represented by its philosophers, design is not admitted as proved. And to tell the truth, though I should not wish to preach on the subject, for 40 years I have been unable to see the logical force of the argument myself. I believe in design because I believe in God; not in a God because I see design. John Henry Newman letter to Brownlow, April 13, 1870

Richard B. Hoppe · 13 November 2015

Apropos of Harold's remark concerning goals (or the lack thereof) in evolution, I have to repeat once more: Modeling adaptive evolution--the interactions of random (with respect to fitness) mutations and natural selection--as a search process is a snare and a deception. It leads one down garden paths to fairy land.

TomS · 14 November 2015

Richard B. Hoppe said: Apropos of Harold's remark concerning goals (or the lack thereof) in evolution, I have to repeat once more: Modeling adaptive evolution--the interactions of random (with respect to fitness) mutations and natural selection--as a search process is a snare and a deception. It leads one down garden paths to fairy land.
Yes. Like so much else in the world of creationism, it is full of bad arguments for empty assertions, begging for attention as if it were worthy of serious discussion.

harold · 14 November 2015

stevaroni said:
Joe Felsenstein said: From this I conclude that any model of evolution as a search is not using a blind search, since fitnesses of non-optimal genotypes affect the movement on the search space. I do not know why JimV said that one way of doing a blind search was "biological evolution". Neither of the references he gives say that.
Also, it's important that the "goal state" of evolution is pretty damned flexible. Contrary to the creationist claim that the goal of evolution is to "produce animal X", the actual goal is the much simpler "live long enough to produce viable offspring". In practice, in a world of competition and predation, this usually translates to "get eaten last", but even that solution space is much, much larger than the one-solution-a-bajillion strawman of creationist wet dreams.
Semantics, but I would prefer to say it isn't a goal. Mutations neither know in advance whether or not they will increase fitness, nor have any inherent sense of motivation to do so. Mutations happen when nucleic acids replicate. Mostly they don't even affect the phenotype. If they affect the phenotype they frequently do so in a neutral way, relative to the environment. But sometimes they lead to a phenotypic variation that is, in a stochastic sense, selected for or selected against. Some mutations are fatal or cause infertility, but often even if a mutation affects phenotype, chance plays a role. We've all seen the image of turtle hatchlings scrambling to the sea before they are eaten by predators, with only a small percentage making it. Imagine a little turtle with a powerful positive mutation. With no downside, he has the ability to scramble to the sea twice as fast. Rerun this scenario thousands of times and that allele will overall be selected for. But just because he can scramble twice as fast doesn't mean he won't usually get eaten. So usually, the allele is adaptive but in the individual case often won't actually be selected for because of random chance. Alternately suppose the beach is on an island, and a group of humans have arrived in an outrigger canoe. They don't bother with turtles but ate all the predatory seabirds. All the turtles make it to the sea. Now the allele won't be selected for, again, because the environment shifted. It no longer confers a relative advantage, because scrambling speed doesn't matter any more. Seeing a "goal" is, to me, excessively teleological thinking. Of course, I have no major argument with Stevaroni about the actual mechanisms of evolution. Sterile semantic debate about the exact meaning of the word "goal" is of limited value. Still, to me, that word implies "somehow planned or wanted by someone before it happened". As I said, I don't deny that in a Last Thursday sense a divine being COULD "intend" the outcomes of evolution, or could have "set off the big bang" with the intention of eventual biological evolution, or whatever, but those are not scientific issues. From the perspective of what we can objectively observe and test, there is no human-perceptible advance goal driving biological evolution.

Joe Felsenstein · 14 November 2015

As an aside to this discussion, I want to quibble a bit with some statements about the "goal" of evolution. For example stevaroni says that
the actual goal is the much simpler “live long enough to produce viable offspring”.
I have to differ with that. If we have two genotypes, one which survives 100% of the time and produces 2 offspring per survivor, and another which survives 95% of the time and produces on average 2.2 offspring per survivor, it is the second genotype that has the higher fitness. There are similar issues with statements that organisms are selected to do well enough, not perfectly. Even if they're doing well enough, one that does a little better than that will have a higher fitness. I do realize that the points being made here are not dependent on these technical details, but technical details is what I do for a living.

Mike Elzinga · 14 November 2015

Teleological language in science is shorthand language for complex processes that would require paragraphs rather than a single sentence to describe.

Such language is used even in the most basic descriptions in physics and chemistry when, for example, someone says that a rope suspended from both ends "seeks" to minimize internal kinetic and potential energies, or when they say about a chemical reaction that an atom "seeks" to complete its outer shell with electrons by taking them away from another atom that "seeks" to give them.

There is no "seeking" in any of this. Processes in this universe - no matter how complex and no matter how complex the systems in which they are taking place - are taking place in a net direction in which momentum is transferred - from higher energy to lower energy - and in a net direction that dissipates energy, such as falling into potential energy wells and staying there. Matter is condensing. Any system that does not dissipate energy cycles repeatedly through a finite number of energy states. Processes in dissipative systems proceed in a net direction from higher energy to lower energy. That's the way our universe works; otherwise, there would be no universe as we know it, and we wouldn't be around to know anything.

These processes manifest themselves in the nervous systems of sentient animals as "wants" or "seeking" or "needs" or as "instinctive behaviors" that, in the context of a much larger environment, produce populations of such systems that are the most consistent with the surrounding environment in terms of those more fundamental physical and chemical processes. No complex system or collections of such systems, living or not, works against those fundamental processes.

"Survival of the fittest" is shorthand for the above paragraphs.

Frank J · 15 November 2015

Intelligent Design answer: Genesis 1“ID is not a mechanistic theory, and it’s not ID’s task to match your pathetic level of detail in telling mechanistic stories.”

— eric
I’m not sure of your reason for writing, then crossing out “Genesis 1,” but it is appropriate, and not for the reason that most people think. Genesis (1 and 2) invokes the Judeo-Christian God, but the DI never tried to hide the fact that they encourage the audience to infer that the designer they claim to have caught is that God. They never denied the Wedge document, and Demsbki (2010) even encouraged belief in a global flood, despite admitting that there’s no evidence of it. That presents a huge dilemma for the DI. How can they make a case that the evidence for evolution is weak, when they know that the evidence for the “what happened when” account of Genesis – 1 or 2, old earth or young earth version - is infinitely weaker, and suffers from fatal, embarrassing contradictions to boot? Oh, they can have it both ways with the ~30% that are committed to believing their version of Genesis, and don’t care what the evidence supports. But they need to fool another 30-40, in order to get their scam taught in public schools. Those “fence sitters” are already convinced that “God did it,” and tend to say “it could be evolution, or something like it,” They rarely give 5 minutes thought to geologic time or common descent, and the DI is determined to keep it that way. Otherwise they would clearly see that those mutually-contradictory, long-discredited “theories” have not earned the right to be taught anywhere, on the public dime or not. And that would deprive the DI of their best opportunity to spread their authoritarian paranoia to a captive audience of impressionable children. Now imagine if there were a shred of evidence for independent origin of “kinds” – even an old-earth version, which, contrary to popular belief, is what a majority of self-described Genesis literalists favor – what would the DI do? Given their talent for being absurdly selective with the evidence to make evolution look “weak” (at least to nonscientists), wouldn’t they jump at the opportunity to do the same to make a Genesis-like account look convincing – at least to nonscientists? I have zero doubt. Plus there would be no need to mention creation or design, as a great majority, including critics, would infer that anyway, as well as the designer’s identity. And no need for the pathetic objection (Dembski, 2002) that “ID is not a mechanistic theory…” As it stands, the lack of any evidence that would comfort their target audience forces the DI to take no official position “what happened when,” and thus deprives them of anything that would make their arguments credible to scientists (even failed hypotheses are better than chronic avoidance of even stating some). But in fairness, individual IDers have stated personal speculations. In 1996 Behe admitted ~4 billion years of common descent, and speculated a “designed” ancestral cell. In 2001 Dembski admitted that ID can accommodate all the results of “Darwinism,” and on another occasion speculated that the design could have been “front loaded” into the universe itself at the Big Bang. Not much comfort there for Genesis literalists, most of whom insist that there was no Big Bang. But the DI doesn’t lose sleep over that. They know that most critics will ignore that, and look for any statement, however vague, that appears sympathetic toward Genesis literalists. Which is just what the DI wants.

Joe Felsenstein · 15 November 2015

Frank J, as much fun as it is to bash the Discovery Institute over the issue of evidence for religious beliefs, and as much as it is done around here, your points are Off Topic in this thread. If this thread develops into a big discussion of evidence for the Genesis account, I will move that whole part of the thread to the Bathroom Wall.

Bill Bigge · 16 November 2015

"As theorems they may be mathematically true, but the average poor performance of searches is true only because so many irrelevant and downright crazy searches are included among the set of possible searches. "
A handy analogy I found to explain this to people who don't understand - Its like claiming that a car is useless as a form of transport because if you average its performance across all possible forms of landscape (like mountains, the ocean, the surface of the sun), it ends up appearing to be no better than walking.

eric · 16 November 2015

harold said:
stevaroni said:
Joe Felsenstein said: From this I conclude that any model of evolution as a search is not using a blind search, since fitnesses of non-optimal genotypes affect the movement on the search space. I do not know why JimV said that one way of doing a blind search was "biological evolution". Neither of the references he gives say that.
Also, it's important that the "goal state" of evolution is pretty damned flexible. Contrary to the creationist claim that the goal of evolution is to "produce animal X", the actual goal is the much simpler "live long enough to produce viable offspring". In practice, in a world of competition and predation, this usually translates to "get eaten last", but even that solution space is much, much larger than the one-solution-a-bajillion strawman of creationist wet dreams.
Semantics, but I would prefer to say it isn't a goal.
IMO here is another example of the 'translation problem' - i.e., correctly translating the implications of Dembski's math into viable biological inferences. Since the 'goal' of a search algorithm is to produce a good mathematical fit to some genetic or phenotypic fitness surface, translating that into biology means there are many goals and they are things like "I'm nocturnal...and develop night vision" or "I spend most of my time in water...and mutate to be able to extract oxygen from it." A jagged landscape (the ones Dembski et al tout because they make evolutionary algorithms less viable) represents localized ecosystems so different from each other that it's instant death (or at least lack of offspring) when a species gains a mutation that alters how it behaves in its environment. Its like claiming that if lions adapt to prey behavior by starting hunt at night, or learn to swim so they can hunt in swamps, they will die or at least stop having any offspring before things like night vision or swim folds in paws ever have a chance to develop. Or claiming that if some lion is born with exceptional night vision, it couldn't possibly respond to that adaptation by hunting at night because "hunting at night" will prevent it from passing on its genes amongst the normal day-hunting lions. This is, of course, nonsense. As Joe has pointed out with great patience, our real life fitness landscapes are largely smooth. Animals often behaviorally shift ecosystems due to external pressures and survive, and those changes to their 'working environment' will then alter the fitness value of different (future) adaptations. In Dembski speak, they often cross small fitness landscape valleys - something that should be impossible in a highly jagged model. Or the reverse can also happen, where some random mutation changes the benefits of different behavior, essentially shifting it to a slightly varied 'ecosystem' compared to others of its species. But again, this can happen and the animal yet survives and leaves offspring. We probably have some real life examples of jagged fitness landscapes which serve to illustrate that the vast majority of life on earth isn't constrained to such situations. Deep sea smokers/vents, where the temperature and chemical makeup of the water may change radically across a small distance. The aerobic/anaerobic boundary layer in some lakes might be another: these environmental boundaries are pretty biologically sharp/discontinuous, meaning there are few or no genetic or phenotypic mutations that could allow an organism in one environment to move to the other and survive long enough that it's offspring start climbing the new hill. Consequently we can expect it might take a long long time, with lots of failures produced, for evolution to work its way across them. But the vast majority of life on earth doesn't live in such discontinuous environments; most organisms can survive small 'dislocations' in their genetic fitness surfaces. We know this because we watch it happen: they either (1) get pushed into a valley through external pressures, but survive to climb a different genetic hill, or (2) they internally develop some genetic trait that would allow them to climb a different hill higher, so they move across the intervening valley.

Mike Elzinga · 16 November 2015

eric said: A jagged landscape (the ones Dembski et al tout because they make evolutionary algorithms less viable) represents localized ecosystems so different from each other that it's instant death (or at least lack of offspring) when a species gains a mutation that alters how it behaves in its environment.
I recognize that I may seem like a narrow-minded physicist who turns every biology discussion into a physics discussion; but biological systems are subject to the laws of physics and chemistry. Biological systems, as we know them here on this planet, are bound together by potential energies slightly above that of liquid water; something on the order of 0.01 to 0.02 electron volts. Living organisms are approaching their extreme limits at the ends of this range (think of what is like to be immersed in either freezing or boiling water). It is absolutely and physically impossible for such soft-matter systems to exist and evolve on a "spiky fitness landscape;" period. Such a landscape is an example of how one destroys a living organism; and this is what the ID/creationists are asserting. They are revealing that they know absolutely nothing about the basic physics and chemistry of living organisms. No surprises there. The internal molecular assemblies that form the templates for what any given organism actually is at any given time in its history simply cannot make a sudden change without destroying the organism. Subsequent developments over the course of reproduction are slight modifications of those templates; and that always means locally smooth fitness surfaces all the way down to the level of the basic chemical building blocks of the organism. Living organisms don't suddenly produce an entirely different organism any more than clocks suddenly give birth to frogs.

Joe Felsenstein · 16 November 2015

Mike Elzinga said: ... The internal molecular assemblies that form the templates for what any given organism actually is at any given time in its history simply cannot make a sudden change without destroying the organism. Subsequent developments over the course of reproduction are slight modifications of those templates; and that always means locally smooth fitness surfaces all the way down to the level of the basic chemical building blocks of the organism. Living organisms don't suddenly produce an entirely different organism any more than clocks suddenly give birth to frogs.
I guess that the one thing that worries me about that account is that a modest change of one chemical, say having cytosine instead of thymine at a particular point in the DNA, can be a mutant and can have a large effect on the phenotype of an organism. When Dembski and co. make a default fitness landscape in which there is no correlation between fitnesses of neighboring sequences. they are assuming that every mutation is a complete disaster, and all pairs of mutations, even when they are in different genes, interact maximally. That is much much more dramatic.

Mike Elzinga · 16 November 2015

Joe Felsenstein said: I guess that the one thing that worries me about that account is that a modest change of one chemical, say having cytosine instead of thymine at a particular point in the DNA, can be a mutant and can have a large effect on the phenotype of an organism. When Dembski and co. make a default fitness landscape in which there is no correlation between fitnesses of neighboring sequences. they are assuming that every mutation is a complete disaster, and all pairs of mutations, even when they are in different genes, interact maximally. That is much much more dramatic.
But swapping C and T changes the underlying template; and those changes affect the details of the secondary, tertiary, and higher level structures of the DNA. But the coiled structure of DNA molecules consists of a huge number of molecules that are being jostled in a heat bath that not only smears out the potential wells that bind them together, but also jockeys these structures into their minimum free energy configurations consistent with the underlying template. One of the important early findings by organic chemists was that the properties of organic molecules were determined more by structure than by the specific atoms - or groups of atoms - at specific positions in the structure. It is a smooth transition from swapping atoms and molecules within a large, soft-matter structure to the changes in the properties of the structure as manifested by its interactions with its surrounding environments. There is a consistent general rule about potential wells in complex structures; proceeding up the hierarchy of complexity means the potential wells that bind the structure together in secondary, tertiary, and higher level structures get shallower and smoother. Quarks are held together by bonds on the order of hundreds of millions of electron volts. Nuclear binding energies are on the order of a few tens of MeV. Stripping an electron completely off a hydrogen atom takes 13.6 eV. Chemistry takes place on the order of an eV. Solids such as iron are bound at roughly 0.1 eV. Liquid water is on the order of 0.01 eV. Soft matter of living organisms is bound together on the order of 0.01 to 0.02 eV. The metabolic processes taking place within a cell and switching of signals within in the nervous systems of a complex organism are in the range of 0.002 eV. When looked at from the perspective of energy windows, life as we know it exists within an extremely narrow energy range of about 0.01 to 0.02 eV. Everything that happens within that window involves energy states that can exist only within that narrow window. Any larger kicks outside that energy window - e.g., cosmic ray events that disrupt critical structures - destroy the organisms or cause mutations that may be passed on to subsequent generations. Such events may be one of the reasons that speciation becomes "locked in" after a considerable time of drift and separation. But, as is always the case in complex structures, large energy kicks cascade into a "shower" of smaller and smaller energy events; and this is again the second law of thermodynamics at work. Life could not exist without the second law of thermodynamics. If this explanation is a bit too many words, I extend my apologies. But you as a modeler of biological systems need not apologize for invoking physics as the reason for the smoothness of fitness landscapes. If DE&M and the rest of the ID/creationists don't get it - and it certainly appears that they don't - that is their fault. We already know that their comprehension of physics, chemistry, and biology falls all apart at the high school level.

Joe Felsenstein · 17 November 2015

Quibble: Mike, the effect of having C instead of T that I was thinking about is not on the higher-order structure of the DNA molecule, but what happens when it gets replicated into RNA, and then that gets translated into a protein that now has a different amino acid in one position, and hence may function differently.

Mike Elzinga · 17 November 2015

Joe Felsenstein said: Quibble: Mike, the effect of having C instead of T that I was thinking about is not on the higher-order structure of the DNA molecule, but what happens when it gets replicated into RNA, and then that gets translated into a protein that now has a different amino acid in one position, and hence may function differently.
Well, certainly; but I am unaware of any instances in which that produces a completely different organism. Genetic "defects" can make an organism less viable - or perhaps more viable, depending on the environment in which it is immersed - but we never see any of the kinds of creatures in Duane Gish's menagerie. In Dembski's scheme of calculating, clocks really can give birth to frogs, or vice-versa, however improbable. Sheesh; even Lucretius knew better.

Marilyn · 17 November 2015

What isn't intelligent about an atom or a molecule. I might not be intelligent, my spelling comes to mind, but I do think the atom and molecule seem to be a very intelligent idea.

eric · 17 November 2015

Mike Elzinga said:
Joe Felsenstein said: Quibble: Mike, the effect of having C instead of T that I was thinking about is not on the higher-order structure of the DNA molecule, but what happens when it gets replicated into RNA, and then that gets translated into a protein that now has a different amino acid in one position, and hence may function differently.
Well, certainly; but I am unaware of any instances in which that produces a completely different organism.
I'm not sure that's the point. Dembski et al.'s assumption of a spiky fitness landscape is based on the concept that small changes to the genome will always cause changes to fitness that are very large. I don't think your argument regarding energy regimes really answers that assertion because it is certainly possible for a small change in the genome to do that. Some changes do in fact have the property Dembski claims - any relatively small mutational change in DNA that caused the mother's body to consider the zygote to be unhealthly/foreign and miscarry it would count as such a change. Where Dembski et al. fall down is in thinking every change is like that when in fact there are many genetic changes that are not like that at all. The obvious counter-example is a genetic letter mutation that codes for the same amino acid. With 64 possible 3-letter combinations but only 21 amino acids used (plus a few extra things like stop codons), it should be obvious to Dembski et al. that the real life eukaryote genetic landscape is not that spiky. But they continue to promote the spiky model because its the only one under which they can claim evolution wouldn't work within the timespans we have.

TomS · 17 November 2015

Mike Elzinga said:
Joe Felsenstein said: Quibble: Mike, the effect of having C instead of T that I was thinking about is not on the higher-order structure of the DNA molecule, but what happens when it gets replicated into RNA, and then that gets translated into a protein that now has a different amino acid in one position, and hence may function differently.
Well, certainly; but I am unaware of any instances in which that produces a completely different organism. Genetic "defects" can make an organism less viable - or perhaps more viable, depending on the environment in which it is immersed - but we never see any of the kinds of creatures in Duane Gish's menagerie. In Dembski's scheme of calculating, clocks really can give birth to frogs, or vice-versa, however improbable. Sheesh; even Lucretius knew better.
What did Lucretius think about spontaneous generation? What did he think about the difference between butterflies and caterpillars?

DS · 17 November 2015

So Dembski has proven rigorously and mathematically, to his own satisfaction, that evolution absolutely, positively cannot work the way he thinks it does. Good to know. When he starts using an appropriate model of evolution, maybe someone will pay attention. Until he does, that Noble prize will continue to elude him. The only question is whether or not he realizes how ridiculous his characterization of evolution is, or whether he really believes that it works that way. You would think that he would realize that he doesn't know what he is talking about, but with creationists you can never really tell.

TomS · 17 November 2015

One major problem in dealing with evolution phobia is that there is so much that goes wrong with it. To begin with, it is only negative. It is against evolution, not for anything - but which branch should we follow - pointing out that it has no positive substance, or pointing out the straw man version of evolution, or even pointing out that the attacks are as much against reproduction (or genetics, development, metabolism, etc.). Or should we show the technical mistakes in presenting the attacks?

DS · 17 November 2015

I know, how about if Dembski specifies under what conditions the search would be effective. Then he could compare the required conditions to those actually found in nature and determine if evolution was theoretically possible or not, at least according to his model. Now I wonder why he doesn't take that approach? Maybe he already did. OR maybe he just can;t figure out what is actually likely to happen in nature and he knows it.

Mike Elzinga · 17 November 2015

TomS said: What did Lucretius think about spontaneous generation? What did he think about the difference between butterflies and caterpillars?
I probably should not have mentioned Lucretius. I was thinking of his observation that all the various creatures in the world produce offspring like themselves and then using that observation to argue that atoms come in different forms. Obviously that same argument would not allow for evolution to occur or for caterpillars "turning into" butterflies. The Greek Atomists had a number of good insights that led them to infer the existence of atoms, but many of their other speculations were, as would be expected, quite off the mark. Dembski's search strategies have the implicit assumption that everything possible must be allowed in the search; so, for example, a clock producing a frog is not ruled out. The infinite spikiness of Dembski's landscape is due to the fact that every possible combination of atoms must be explored - as though they are all equally likely - in order to find a specific pattern. So, according to ID/creationist thinking, evolution is a blind search for a specified arrangement of atoms and, "therefore" (gotcha), cannot arrive at that combination in the lifetime of the universe. At least the Greek Atomists argued for human atoms, sheep atoms, frog atoms, and so on.

eric · 17 November 2015

TomS said: One major problem in dealing with evolution phobia is that there is so much that goes wrong with it. To begin with, it is only negative. It is against evolution, not for anything
Indeed. One amusing thing about Dembski's claims is if we take the extreme version of his claim seriously - i.e., that no search algorithm outperforms random search across fitness landscapes - then that would imply ID couldn't work either, because 'an intelligence considers the possible outcomes and makes a decision based on prior knowledge' is just another type of search algorithm. And that makes intuitive sense also; if we consider all possible fitness landscapes at once, induction can't work (because the fitness landscape you were evaluating a moment ago may bear no relation to the fitness landscape under consideration now) and intellectual analysis would not provide any advantage over choosing randomly.

Mike Elzinga · 17 November 2015

eric said: I'm not sure that's the point. Dembski et al.'s assumption of a spiky fitness landscape is based on the concept that small changes to the genome will always cause changes to fitness that are very large. I don't think your argument regarding energy regimes really answers that assertion because it is certainly possible for a small change in the genome to do that. Some changes do in fact have the property Dembski claims - any relatively small mutational change in DNA that caused the mother's body to consider the zygote to be unhealthly/foreign and miscarry it would count as such a change. Where Dembski et al. fall down is in thinking every change is like that when in fact there are many genetic changes that are not like that at all. The obvious counter-example is a genetic letter mutation that codes for the same amino acid. With 64 possible 3-letter combinations but only 21 amino acids used (plus a few extra things like stop codons), it should be obvious to Dembski et al. that the real life eukaryote genetic landscape is not that spiky. But they continue to promote the spiky model because its the only one under which they can claim evolution wouldn't work within the timespans we have.
The binding energies of base-pairs are important for understanding mutations. A quick search can find other research along the same lines. Here is a Wikipedia article. Stepping back and taking a broader view from the perspective of energy; the energy window in which these events are taking place limits what remains viable after a mutation. And that means that viable structures - or even partially viable structures - cannot deviate grotesquely from their original template. Every DNA strand is composed of bonded pairs that have a range of binding energies somewhat higher than the binding energies of the soft-matter components comprising the rest of the organism. And given that these molecules - and all the molecules of life - exist in a heat bath clustered within a few degrees around 37 Celsius means that the thermal kinetic energies available to move nucleic acids from position to position are not going to produce changes that will convert a given creature into something entirely different. The changes will affect primarily viability and the ability to reproduce. The ID/creationist model of tornado-in-a-junkyard assembly - and starting over again if a specified assembly is not produced - has no energy constraints on where to begin the next round of the "search". There are no binding energies and kinetic energies among ASCII characters, dice, and junkyard parts. The "search" resumes anywhere, without regard to what happened in the previous trial. On the other hand, real organisms in the real world cannot energetically deviate greatly from their original template in any given reproductive cycle without being destroyed. Jumping to an extremely distant configuration, especially one that is equally or more viable, has essentially a zero probability. In nearly all cases, the original form or phenotype can be modified only within a narrow energy window; otherwise the organism comes all apart. Any large energy kicks coming from outside that window - e.g., cosmic rays - may or may not produce significant changes; but if the changes are large, the organism is unlikely to survive and/or reproduce. That narrow energy window - roughly within the range in which water remains a liquid - is the reason why the soft-matter systems that exist within that window don't jump all over a spiky landscape but, instead, creep to nearby local configurations on a smooth terrain. This isn't any new idea I am elaborating here. Physicists, chemists, engineers and other researchers and developers are extremely familiar with these constraints when building atomic and molecular structures and using techniques like annealing, quenching, and other forms of gentle molecular "nudging" to get the structure into the desired configuration. Within the last 20 or 30 years, a lot of research has gone into soft matter systems, and some of that is motivated by the possibility of growing artificial organs.

TomS · 17 November 2015

eric said:
TomS said: One major problem in dealing with evolution phobia is that there is so much that goes wrong with it. To begin with, it is only negative. It is against evolution, not for anything
Indeed. One amusing thing about Dembski's claims is if we take the extreme version of his claim seriously - i.e., that no search algorithm outperforms random search across fitness landscapes - then that would imply ID couldn't work either, because 'an intelligence considers the possible outcomes and makes a decision based on prior knowledge' is just another type of search algorithm. And that makes intuitive sense also; if we consider all possible fitness landscapes at once, induction can't work (because the fitness landscape you were evaluating a moment ago may bear no relation to the fitness landscape under consideration now) and intellectual analysis would not provide any advantage over choosing randomly.
One of the characteristics of many of the arguments against "naturalistic evolution" is that they don't tell us how ID does any better. Yes, I know that they have told us that they are under no obligation to provide "petty details" - like who, what, where, when, why or how. But when they claim that such-and-such provides a fatal failure for evolution, wouldn't anyone want to point out how they are not subject to the same?

Mike Elzinga · 17 November 2015

TomS said: One of the characteristics of many of the arguments against "naturalistic evolution" is that they don't tell us how ID does any better. Yes, I know that they have told us that they are under no obligation to provide "petty details" - like who, what, where, when, why or how. But when they claim that such-and-such provides a fatal failure for evolution, wouldn't anyone want to point out how they are not subject to the same?
From what I have observed of their "scientific" arguments over the past 50 years, I suspect that there is no hope of their even getting a glimmer of what a scientific concept is and how science explains. There is simply no vocabulary of science that we could work with that they would understand. They have spent their entire lives bending scientific definitions and concepts to fit their sectarian beliefs. So I think such a question doesn't even compute in their minds. One needs only to look at the Uncommonly Dense website and the endlessly repeated misconceptions of their dear leaders to see this phenomenon still going on in real time.

harold · 17 November 2015

IMO here is another example of the ‘translation problem’ - i.e., correctly translating the implications of Dembski’s math into viable biological inferences. Since the ‘goal’ of a search algorithm is to produce a good mathematical fit to some genetic or phenotypic fitness surface, translating that into biology means there are many goals and they are things like “I’m nocturnal…and develop night vision” or “I spend most of my time in water…and mutate to be able to extract oxygen from it.”
Eric makes may intelligent comments that show an excellent understanding of evolution. Possibly some legitimate groups model evolution as a search algorithm. I am not a professional evolutionary biologist. As an interested amateur, though, I profoundly disagree with doing so, for two reasons. 1) Organisms do NOT "develop night vision" "because they are nocturnal". That is NOT how it works. Mutations that impact multicellular phenotypes in a heritable way have to occur in germ cells. They occur because of the chemical properties of nucleic acids in the particular environment. They are independent of the human-perceived "needs" of the organism. If they impact phenotype of offspring, they may have an impact on fitness. Their impact is constrained by context. For example, imagine two species of blind cave fish and a big-eyed species of nocturnal primate with excellent night vision. One species of cave fish has lost a gene for a basic light receptor protein. The other species of cave fish has, like the primates, a gene that codes for a homologue of this protein. One species of cave fish can't get a mutation in this gene (they don't have the gene anymore). In the other, they can get a mutation, but in them, that particular gene could be described as "junk" DNA, they have no eyes to express it in, so mutations in that gene are highly unlikely to be selected for one way or the other in offspring. In the primate a mutation at the same amino acid locus could have dramatic impact on fitness, even of a heterozygote. However, barring details like variations in DNA repair mechanisms, the primate is no more or less likely to get a point mutation in that gene than is the blind cave fish. Furthermore, the primate is just as likely to get a mutation in some common gene that is of little importance in their lineage but part of a critical system for the fish. A "designer" does not need to reach in and mutate the primate's visual genes more often because the "need" night vision. Why the hell did they "need" it more than the fish in the first place? They share a common ancestor with the fish. At that common ancestor stage, did some magical being decide "this little hatchling 'should' give rise to a lineage of nocturnal primates, so she 'needs' mutations in those visual system genes, but this little hatching 'should' give rise to blind cave fish descendants so she 'needs' different mutations?" Possibly, but we can explain it without need for that supernatural step. Let theologians deal with theology and scientists can deal with science. It's a feedback loop between random mutations, and subsequent stochastic selection of phenotypes, which sets the stage on which subsequent mutations occur. 2) Why not model evolution as evolution? It isn't the search for something that fits a pre-determined goal, and calling the goal a set of multiple acceptable pre-determined goals doesn't change that. There is no predetermined goal. Calling a "result" a "goal" is simply not helpful for anything. Adaptation is a result, not the goal, of biological evolution.

Joe Felsenstein · 17 November 2015

harold said: ... 2) Why not model evolution as evolution? It isn't the search for something that fits a pre-determined goal, and calling the goal a set of multiple acceptable pre-determined goals doesn't change that. There is no predetermined goal. Calling a "result" a "goal" is simply not helpful for anything. Adaptation is a result, not the goal, of biological evolution.
Dembski and Marks argue that biologists do analogize evolution to a search. What the situation is, is that most models have genotypes and fitnesses, and some space of population composition such as a set of gene frequencies, some at each locus. The population will often (not always) move in an uphill direction on that surface. Mutation, migration and genetic drift can push it off any local maximum mean fitness. So D&M might then say see, it is going uphill on that surface, so that is a "search" and a "target". Of course, as you know, the process does not see further, and there might be much higher peaks a little further out, perhaps in another direction, and it won't always find them. However, it is definitely not a search which has a goal that's the best peak in the space. On the whole, then, population geneticists do not describe this as a search.

TomS · 18 November 2015

I am not a scientist, but ISTM that the Principle of Least Action provides a similar case where one informally says that nature is engaging in seeking a "goal". For example, that a ray of light finds the shortest path. No one seriously takes that as an indication of intelligent design.

DS · 18 November 2015

TomS said: I am not a scientist, but ISTM that the Principle of Least Action provides a similar case where one informally says that nature is engaging in seeking a "goal". For example, that a ray of light finds the shortest path. No one seriously takes that as an indication of intelligent design.
My good man, I believe you underestimate the propensity of the human mind for self deception. But seriously, most children do tend to describe things in terms of teleology. The purpose of fire is so we can cook food, and rocks are pointy so no one will sit on them, that kind of thing. Of course, as we mature, we usually begin to see the world around us more clearly and eventually realize that to anthropomorphize all of nature is a drastic mistake. However, when emotional and intellectual development is stunted, you often get the kind of thinking that sees evolution as having a goal that it is seeking. Usually that goal is to make things just the way we see them now, as if there were something special about that particular outcome. Oh well, if it makes you feel special, I guess you just can't resist.

Henry J · 18 November 2015

Re "Oh well, if it makes you feel special, I guess you just can’t resist."

Resistance is futile!!111!!eleven!!