Professor Olofsson on probability, statistics, and intelligent design

If you stuck these guys heads into 100% proof of evolution they still wouldn't change. There is no way that expert rebuttal of their arguments is going to do any good.

Olofsson's observations are the simplistic, but most elegant, probabilistic and statistical refutations of ID's main "concepts". How Dembski can still claim to call himself a mathematician with a background in statistics is quite a mystery to me, especially when he has all but admitted to me - both in person and in e-mail - that he can't calculate the confidence limits to his explanatory filter.

Now Behe is changing his definitions like Dembski? There goes my last ounce of respect for Behe as a scientist.

cimple?

alhypotheses?

appoach?

contasnts?

Moverover?

elimative?

Interesting essay. Shoulda run it through a spell-checker.

Jon,

There is a link to the properly proofread and spell-checked Chance article here:

http://ramanujan.math.trinity.edu/polofsson/research/ID.html

Cheers,

PO

Olofsson's argument with Dembski is about whether one can really reject "chance" in favor of "design". It has been pointed out that Dembski's Explanatory Filter does work -- but that the alternative to "chance" could be natural selection, not just Intelligent Design. Dembski invokes his Law of Conservation of Complex Specified Information, which supposedly makes it impossible to explain adaptive information, when we see it, by natural selection. Thus when he rejects "chance", all that is left is Intelligent Design, in his view. However Elsberry and Shallit (2003) and I (2007) have each found major holes in Dembski's LCCSI. Dembski's Explanatory Filter does reject "chance", but it leaves us with ordinary evolutionary mechanisms as the major alternative.

Joe F,

Depends on what you mean by "chance." Demsbki routinely uses it as a synonym for the uniform distribution but in general
it means any stochastic mechanism for example mutation + natural selection. The problem Dembski has is then how to rule
out every possible chance explanation, not merely the uniform distribution.

PO

In response to Jon Fleming's comment: Thanks for pointing to the typos in Olofsson's essay posted on Talk Reason. I've forwarded your comment to Talk Reason's technical editor with a request to promptly spellcheck the text and fix all errors. I am sure she'll do it. Usually she has been very thorough, but this time she had serious reasons to do the job in a hurry, for which I apologize on behalf of Talk Reason team.

Regarding Joe Felsenstein's comment: I take the liberty of disagreeing with his statement that Dembski's Explanatory Filter "works." I believe such an assertion cannot be made, as the infamous filter readily produces false positives and false negatives in too many situations, so its conclusions (in particular conclusions asserting design, regardless of the design's nature) are unreliable (not to mention its many other shortcomings). I had discussed these points in detail already in my book of 2003, as well as both before and after that in various posts and printed articles.

Peter Olofsson said: Joe F, Depends on what you mean by "chance." Demsbki routinely uses it as a synonym for the uniform distribution but in general it means any stochastic mechanism for example mutation + natural selection. The problem Dembski has is then how to rule out every possible chance explanation, not merely the uniform distribution. PO

JPS,

The idea behind Dembski's "explanatory filter" is to assume a "chance hypothesis" and argue that, under this assumption, the
observed biological phenomenon is so unlikely we cannot possibly believe it happened by chance.

In his biological example of the bacterial flagellum, he argues that if all the proteins needed are
assembled randomly, odds are solidly against anything useful being formed. This conclusion of his is correct
but no biologist have ever claimed that the flagellum has come about in such a way. Rather than using this particular
chance hypothesis, Dembski ought to form a hypothesis involving mutation and selection, and under this hypothesis compute
the probability of the flagellum evolving. I claim that this task is more or less impossible.

PO

JPS said: What all this leaves me with is a curiosity about who Dembski thinks his audience is. (This is also true of Behe.) It isn't likely to convince anyone with the requisite mathematical or scientific training, and it isn't likely to be understood by anyone without it.

Peter Olofsson said: JPS, The idea behind Dembski's "explanatory filter" is to assume a "chance hypothesis" and argue that, under this assumption, the observed biological phenomenon is so unlikely we cannot possibly believe it happened by chance. In his biological example of the bacterial flagellum, he argues that if all the proteins needed are assembled randomly, odds are solidly against anything useful being formed. This conclusion of his is correct but no biologist have ever claimed that the flagellum has come about in such a way. Rather than using this particular chance hypothesis, Dembski ought to form a hypothesis involving mutation and selection, and under this hypothesis compute the probability of the flagellum evolving. I claim that this task is more or less impossible. PO

Depends on what you mean by “chance.” Demsbki routinely uses it as a synonym for the uniform distribution but in general it means any stochastic mechanism for example mutation + natural selection. The problem Dembski has is then how to rule out every possible chance explanation, not merely the uniform distribution.

Regarding Joe Felsenstein’s comment: I take the liberty of disagreeing with his statement that Dembski’s Explanatory Filter “works.” I believe such an assertion cannot be made, as the infamous filter readily produces false positives and false negatives in too many situations, so its conclusions (in particular conclusions asserting design, regardless of the design’s nature) are unreliable (not to mention its many other shortcomings). I had discussed these points in detail already in my book of 2003, as well as both before and after that in various posts and printed articles.

Nice article. I think that Peter dismisses specification a bit too quickly. I agree it is a meaningless term, especially as applied to biological outcomes, but Dembski does go a bit further than "the type of pattern that highly improbably events must exhibit....". In Specification: The Pattern That Signifies Intelligence" he tries to define specification in terms of simplicity which roughly corresponds to what is the minimum number of concepts you can use the describe the pattern. The whole thing falls apart with a bit of analysis and doesn't even get off the ground when applied to biology - but I think it is important to take into account what he wrote.

As for Dembski's treatment of hypothesis testing and Bayesian inference. I find it hard to read it without feeling slightly embarrassed for the poor man.

The perspective that both Dembski and Behe bring to their analyses has its roots in the egregious misconceptions about chaos and randomness that have been abused repeatedly among the ID/Creationists. These misconceptions are characteristic identifying features of ID/Creationism.

"Also, I don't view ID as creationist."

What all this leaves me with is a curiosity about who Dembski thinks his audience is. (This is also true of Behe.) It isn’t likely to convince anyone with the requisite mathematical or scientific training, and it isn’t likely to be understood by anyone without it.

— JPS

What all this leaves me with is a curiosity about who Dembski thinks his audience is. (This is also true of Behe.) It isn’t likely to convince anyone with the requisite mathematical or scientific training, and it isn’t likely to be understood by anyone without it.

One problem that is not sufficiently discussed is that ID does not present an alternative, and does not even make an attempt at a calculation of the probability for any alternative to evolutionary biology.

To take the "ballots" case as an example. (Assuming that the facts are as usually presented. I don't know anything about the real case. I'm not going to use his name, because I don't want to gossip about someone I know nothing about.) Suppose that we knew some different facts about the suspect. The suspect could be a Republican, or it could be that he didn't like some of the candidates. It could be that he had no responsibility for the production of the ballots. And what if we learned that he thought that names at the bottom of the ballot tended to get more votes? Information like that would surely change our estimate of whether the suspect "designed" the ballots.

No matter how unlikely it is that the ballots turned out as they did by "pure chance", is it any more likely that he designed them? If he had no opportunity or no means to design the ballots, then, no matter how unlikely it is that the ballots turned out that way by "pure chance", he didn't do it. If he had no motivation (because he would favor Republicans, or because he was ignorant of the results of ballot-placement), then we can't say that he did it.

In the case of ID, what do we know about "Intelligent Designers" that makes us believe that they would "design" bacterial flagella?

The answer is, of course, that ID does not tell us anything about the opportunity, means, or motivation of the "intelligent designers", so we have no idea at all whether "intelligent design" is more likely than "pure chance" as a reason for bacterial flagella.

No matter how slim the odds that something happened by chance, we cannot reach a conclusion just on that basis. We have to compare the probability with the probability of the alternatives.

So if Intelligent Design Theory isn't Creationism, then what is it? Prominent Intelligent Design proponents have even admitted that Intelligent Design is neither scientific nor a legitimate alternative explanation. And then there is the distinct problem that all of the so-called "arguments" proposed by Intelligent Design Theory have all been recycled from Creationism.

Amadán said: It seems that while the Know-Nothings remain a political force in your country, no politician will tackle them head-on. Have none of the biotech companies ever raised concerns about the collapse in educational standards that would probably happen if the likes of the Discovery Institute got its way?

Dear Stanton,

You forget that the DI is promoting actively its rather peculiar brand of mendacious intellectual pornography elsewhere in the English-speaking world, especially in the United Kingdom, Canada and Australia. That is why ID has become an issue lately in the United Kingdom.

John

FL said: Mike said,

The perspective that both Dembski and Behe bring to their analyses has its roots in the egregious misconceptions about chaos and randomness that have been abused repeatedly among the ID/Creationists. These misconceptions are characteristic identifying features of ID/Creationism.

I'm just surfing through Dr. Olofsson's arguments and statements, (it's gonna take a while), but I am happy to report one thing: In a previous (July 31) dialogue at Uncommon Descent, Dr. Olofsson said:

"Also, I don't view ID as creationist."

That's important. (And refreshing as well.) I'm hoping that Dr. Olofsson's clear refusal to conflate ID and creationism will provide motivation for other evolutionists to seriously think about and follow his example. FL

Mark Frank said: Nice article. I think that Peter dismisses specification a bit too quickly. I agree it is a meaningless term, especially as applied to biological outcomes, but Dembski does go a bit further than "the type of pattern that highly improbably events must exhibit....". In Specification: The Pattern That Signifies Intelligence" he tries to define specification in terms of simplicity which roughly corresponds to what is the minimum number of concepts you can use the describe the pattern. The whole thing falls apart with a bit of analysis and doesn't even get off the ground when applied to biology - but I think it is important to take into account what he wrote. As for Dembski's treatment of hypothesis testing and Bayesian inference. I find it hard to read it without feeling slightly embarrassed for the poor man.

Stanton said: So if Intelligent Design Theory isn't Creationism, then what is it? Prominent Intelligent Design proponents have even admitted that Intelligent Design is neither scientific nor a legitimate alternative explanation. And then there is the distinct problem that all of the so-called "arguments" proposed by Intelligent Design Theory have all been recycled from Creationism.

Tom S. said: To take the "ballots" case as an example...If he had no opportunity or no means to design the ballots, then, no matter how unlikely it is that the ballots turned out that way by "pure chance", he didn't do it.

Amadan said: Have none of the biotech companies ever raised concerns about the collapse in educational standards that would probably happen if the likes of the Discovery Institute got its way?

Dear Peter:

I believe Wesley Elsberry and others have addressed the issue of Dembski's inappropriate usage of Bayesian Inference in several articles published earlier in the decade. Alas I don't have the references handy, but I am sure Wesley could provide you with a bibliography.

John

John Kwok said: Dear Peter: I believe Wesley Elsberry and others have addressed the issue of Dembski's inappropriate usage of Bayesian Inference in several articles published earlier in the decade. Alas I don't have the references handy, but I am sure Wesley could provide you with a bibliography. John

Mark Frank said: (snip)In Specification: The Pattern That Signifies Intelligence" he tries to define specification in terms of simplicity ...(snip)

Dr. Olofsson, let's see how IDC is creationism. This comes through clearly to people familiar with the phenomenon. We should drop the "literal interpretation" and Genesis hangups. The words "literal" and "interpretation" don't go together well. There are Old Earth, Young Earth and ID no earth creationists. IDCs tell religious audiences and readers that ID = the Gospel of John expressed in mathematical information theory (among other things). This covers Genesis while leaving interpretation unspecified. Dembski, accused by YEC master Henry Morris of stealing his and other IDC's ideas, said IDists take these ideas and make them rigorous. [Can someone please find the reference for this?] As a mathematician you will be sensitive to the difference between making an argument more formal as Dembski does, and rigor. But Dembski did not try to tell Morris that no, these are new ideas.

Reluctantly, I'd like to argue against Peter's opinion regarding the legitimacy of the term "creationism" as applied to ID advocates. To my mind ID "theory" can be, to all intents and purposes, referred to as creationism (perhaps qualifying it, when it can be confusing, by using it in the form "ID creationism.") Here is why.
Of course, generally speaking, any definition is a matter of consensus. Hence, the distinction between various definitions of the same object may be viewed as a question of pure semantics, and as such not really crucial. However, to be useful, a definition must reasonably reflect, at least partially, the real features of the defined subject. Say, we want to provide a definition of what is a semi-conductor. Nobody can prevent us from arbitrarily choosing for a definition, for example, the sentence "semi-conductor is a metal that is red," and having agreed on that definition, to use it in the further discussions. Will such a pseudo-definition, even being a result of a consensus, useful? I don't think so, because it, by its utter arbitrariness and being contrary to the factual contents of the concept of a semi-conductor, would be misleading and counter-productive. Semi-conductors are not metals and are not red. The proper definition can be chosen in many ways, but must preferably reflect some actual properties of the defined concept, in this case a semi-conductor. One such definition may be "a semi-conductor is material whose electric resistivity decreases with temperature."

Back to creationism, its definition likewise should reflect its contents, and if chosen in a very narrow way, would be not very useful. If we define creationism as adherence to a belief in the literal truth of every word in the book of Genesis, then ID "theory" as such indeed can be construed as being distinctive from creationism, because ID advocates, even those of them who in fact do believe in the Bible's inerrancy, usually do not use such beliefs as arguments, turning instead to seemingly "scientific" and/or "mathematical" arguments. (The same is, however, also true for many YEC frank creationists, but they do not object to being called creationists, and neither do their critics avoid such a term). I think that the appropriate definition of creationism more reasonably should be less narrow. ID advocates' views, after all their "mathematical" and "scientific" arguments have been dealt with, boil down to the assertion that the universe in general (and biological life in particular) was "created" by a mysterious "Designer." Therefore there is a good reason to refer to them as creationists, albeit not forgetting about the secondary distinctions between various brands of creationism, of which there are many. Feverish denials of some ID advocates of being "creationists" make me shrug (actually some of them frankly admit being creationists).

Therefore to my mind Peter's asseveration about ID advocates not being creationists, while being a choice to which he is entitled, is not very useful.

Frankly, if people can twist reality enough to differentiate ID from creationism, then I don't see how the battle can ever be won.

I mean, people are able to ignore:

- the wedge document, which basically says 'WE ARE CREATIONISTS AND WE INTEND TO MANUFACTURE SOME FAKE SCIENCE TO FURTHER OUR CREATIONIST GOALS'
- the fact that this document was made by the organisation behind ID.
- the fact that all the arguments, even the very core of ID, are the same as creationist arguments. Irreducible Complexity, for example, I saw in a 1980s creationist magazine.
- the fact that ID hinges on naturalistic evolution being false, which is exactly what creationists would like.
- the fact that 'creationism' can be replaced with 'intelligent design' in a textbook with ease.
- the fact that IT WAS.
- the fact that pretty much all the ID proponents and supporters won't shut up about Jesus.
- the fact that ID is used the world over BY CREATIONISTS AND NO ONE ELSE.
- the fact that the ID people have said no word about this (sure, it's not their fault, but they haven't done much to eliminate this suspicion).

There's probably more. What can you do against that? People dismiss every single one as circumstantial, which is kind of odd for people who love to argue from improbability.

I also prefer to tackle ID people on their arguments instead of their obvious affiliation, but sheesh, why bother? How do you convince people of science when they fall for such obvious trickery?

I think the label issue is water under the bridge. Anti-evolutionists have moved on to the 'strengths and weaknesses' and 'academic freedom' arguments now. I think some of the media quotes from the Texas Citizens of Science show those guys know exactly the right way to refute the ignorance. Focus on the specific arguments anti-evolutionists are making instead of what they call themselves, and you will find that today's weaknesses are the same as yesterday's design arguments and last week's creationist arguments. And courts will recognize the relabeling as a sham.

Mark, Thanks for the comment on Bayesian inference which I don’t think has been addressed before. The filter has been debated ad nauseum and I included it because of the target audience of Chance readers were not likely to have heard of it. The Bayesian part and the criticism of Behe’s “The Edge” are new.

well of course. The only people who will criticise ID are those who are against it (neutral scientists likely don't care, since they have real science to be busy with), so any criticism can be dismissed as an anti-ID attack.

is ID Creationism? yes and no.
ID proponents want to distance themselves from the terms 'creationism' and 'creation science' because court cases have explicitly named those terms and effectively outlawed curricula based on 'creationism' in schools. In the Kitzmiller case it was shown that the terms 'ID', 'intelligent design', and 'design' was substituted for 'creation' etc in a proposed textbook WITHOUT otherwise changing the content of the book - in the case of "Of Pandas and People" ID=Creationism

the concept as proposed by Demski, Behe et al is not the same as creationism - but in application is a not so subtle bait and switch. Publish a popular book (vs scientific journal entries) establishing ID as a 'scientific' critisism of Modern Evolutionary Theory (MET) and then propose ID as an 'alternate' to evolution or as a critsism of evolution or as a way to evaluate the 'strenghs and weaknesses' of evolution in public schools- but with a wink - all of the same proponents of 'creationism' would endorse 'ID' and the 'ID' curriculum would be the same 'creationism' curriculum that was previously outlawed. - so IN APPLICATION and De Facto ID=Creationism

interestingly - as professor Olaffson's article shows - there is a major difference between ID and Creationism - ID has a veneer of scientic sounding truthiness that can be picked apart and debunked using good, basic, logic/math/science - It boils down to ID, from the scientific point of view, having zero content. ID's lack of content is used by ID proponents to have it be defined however they decide for it to be defined at that time (and change it's definition, and the definition of its components on a whim, whenever convienient)

this is how ID is NOT creationism - creationism is specific- 'scientific creationism' makes specific claims than are falsifiable (and are false) -

One more difficulty with the "probability" argument.

Consider the probability that (1) the various measurements of the age of the universe would agree on billions of years (2) all forms of life on earth would fit into the nested hierarchy of the tree of life or (3) that the bodies of humans would be so very similar to the bodies of chimps and of other primates. The complexity of the evidence for life being related by common descent with modification is much greater than the complexity of the bacterial flagellum. It is far less likely that that evidence is a matter of chance. It is also "specified", in the sense that it regularly makes predictions about what will be discovered, much more so than any predictions made about "the bacterial flagellum is complex". If this "specified complexity" is not due to some regularities of nature, such as real descent with modification, then - was it purposefully designed that way? Is there some "intelligent designer" who wanted it to look as if evolution were true? Is there some "intelligent designer" who had some purposes in common for humans and chimps? If our designer wanted it to look that way, wouldn't we be opposing the wishes of our designer not to "believe" in evolution? If our designer wanted similar purposes for us and chimps, shouldn't we obey his wishes, and act like chimps?

Pete Dunkelberg said:Dembski, accused by YEC master Henry Morris of stealing his and other IDC's ideas, said IDists take these ideas and make them rigorous. [Can someone please find the reference for this?] As a mathematician you will be sensitive to the difference between making an argument more formal as Dembski does, and rigor. But Dembski did not try to tell Morris that no, these are new ideas.

By contrast, much of my own work on intelligent design has been filling in the details of these otherwise intuitive, pretheoretic ideas of creationists. ... Nonetheless, I found the probabilistic reasoning in the creationist literature incomplete and imprecise. For instance, authors often referred to the probability of the chance formation of a particular protein, but failed to note that the relevant probability was that of any protein that performed the same function (this is a much more difficult probability to calculate, and one with which recent ID research has been having some success). Another problem was taking the small probability of events as sufficient reason to rule out their chance occurrence without acknowledging that small probability by itself is not enough to rule out chance. What else is needed? In my theory of design detection, I argue that what's needed is a specification, that is, a type of pattern with certain mathematical and logical characteristics.

In contrast to ID, creationism is scientific and provides an alternative explanation!

— Peter Olofsson

Peter Olofsson said:

FL said: Mike said,

The perspective that both Dembski and Behe bring to their analyses has its roots in the egregious misconceptions about chaos and randomness that have been abused repeatedly among the ID/Creationists. These misconceptions are characteristic identifying features of ID/Creationism.

I'm just surfing through Dr. Olofsson's arguments and statements, (it's gonna take a while), but I am happy to report one thing: In a previous (July 31) dialogue at Uncommon Descent, Dr. Olofsson said:

"Also, I don't view ID as creationist."

That's important. (And refreshing as well.) I'm hoping that Dr. Olofsson's clear refusal to conflate ID and creationism will provide motivation for other evolutionists to seriously think about and follow his example. FL

If one by creationism means the belief that the Bible presents a literal account of how species were created, then I don't view ID as creationism. One might of course claim that a "designer" is also a "creator" at least if the design leaves the drawing board and results in an object. As neither Behe nor Dembski refer to the book of Genesis, I prefer to address their arguments rather than try to figure out what to call them. If they call themselves ID proponents, so be it.

Dave Scot recently posted a response to Prof. Olofsson's article on Uncommon Descent. Some initial howlers:

1. "The second thing I’d like to thank him for is describing ID as a valid scientific hypothesis in the discussion of the explanatory filter and the flagellum."

Prof. Olofsson nowhere describes ID as a "valid scientific hypothesis."

2. He compares his own claim, "There are no unintelligent processes which can [my emphasis] produce a complex machine (like a flagellum) in nature” with Popper's example "There are no black swans in nature." Evidently he doesn't see that his claim is about possibility while Popper's example is about an empirical fact, and so the two claims are falsified differently.

He also has some argument about chloroquine resistance but I can't really follow his logic. As far as I can tell he seems to be arguing that the evolution of chloroquine resistance in malaria does not demonstrate evolution via natural selection because the change is too small. Uh?

Dembski, accused by YEC master Henry Morris of stealing his and other IDC’s ideas, said IDists take these ideas and make them rigorous. [Can someone please find the reference for this?]

Actually, Henry Morris specifies what the Creationism Model is, and it’s very very clear that ID is differentiated from creationism. It’s two different gigs, NOT the same gig, NOT conflatable.

— FL

....“creationism” has come to mean any design-based pseudoscience that centers on promoting unreasonable doubt of evolution, and that includes ID.

Clearly, if the definition of "Creationist" can include a proponent of Darwinian evolution, then the definition adds smoke, not light, to the debate. --- Mike Gene

FL said:

....“creationism” has come to mean any design-based pseudoscience that centers on promoting unreasonable doubt of evolution, and that includes ID.

That also includes theistic evolution. Just ask Kenneth Miller. He's been publicly called a creationist by his fellow evolutionists. Twice, even.

Clearly, if the definition of "Creationist" can include a proponent of Darwinian evolution, then the definition adds smoke, not light, to the debate. --- Mike Gene

Pete Dunkelberg said: Dr. Olofsson, let's see how IDC is creationism. This comes through clearly to people familiar with the phenomenon. We should drop the "literal interpretation" and Genesis hangups. The words "literal" and "interpretation" don't go together well. There are Old Earth, Young Earth and ID no earth creationists. IDCs tell religious audiences and readers that ID = the Gospel of John expressed in mathematical information theory (among other things). This covers Genesis while leaving interpretation unspecified. Dembski, accused by YEC master Henry Morris of stealing his and other IDC's ideas, said IDists take these ideas and make them rigorous. [Can someone please find the reference for this?] As a mathematician you will be sensitive to the difference between making an argument more formal as Dembski does, and rigor. But Dembski did not try to tell Morris that no, these are new ideas.

Mark Perakh said: Reluctantly, I'd like to argue against Peter's opinion regarding the legitimacy of the term "creationism" as applied to ID advocates. To my mind ID "theory" can be, to all intents and purposes, referred to as creationism (perhaps qualifying it, when it can be confusing, by using it in the form "ID creationism.") Here is why. Of course, generally speaking, any definition is a matter of consensus. Hence, the distinction between various definitions of the same object may be viewed as a question of pure semantics, and as such not really crucial. However, to be useful, a definition must reasonably reflect, at least partially, the real features of the defined subject. Say, we want to provide a definition of what is a semi-conductor. Nobody can prevent us from arbitrarily choosing for a definition, for example, the sentence "semi-conductor is a metal that is red," and having agreed on that definition, to use it in the further discussions. Will such a pseudo-definition, even being a result of a consensus, useful? I don't think so, because it, by its utter arbitrariness and being contrary to the factual contents of the concept of a semi-conductor, would be misleading and counter-productive. Semi-conductors are not metals and are not red. The proper definition can be chosen in many ways, but must preferably reflect some actual properties of the defined concept, in this case a semi-conductor. One such definition may be "a semi-conductor is material whose electric resistivity decreases with temperature." Back to creationism, its definition likewise should reflect its contents, and if chosen in a very narrow way, would be not very useful. If we define creationism as adherence to a belief in the literal truth of every word in the book of Genesis, then ID "theory" as such indeed can be construed as being distinctive from creationism, because ID advocates, even those of them who in fact do believe in the Bible's inerrancy, usually do not use such beliefs as arguments, turning instead to seemingly "scientific" and/or "mathematical" arguments. (The same is, however, also true for many YEC frank creationists, but they do not object to being called creationists, and neither do their critics avoid such a term). I think that the appropriate definition of creationism more reasonably should be less narrow. ID advocates' views, after all their "mathematical" and "scientific" arguments have been dealt with, boil down to the assertion that the universe in general (and biological life in particular) was "created" by a mysterious "Designer." Therefore there is a good reason to refer to them as creationists, albeit not forgetting about the secondary distinctions between various brands of creationism, of which there are many. Feverish denials of some ID advocates of being "creationists" make me shrug (actually some of them frankly admit being creationists). Therefore to my mind Peter's asseveration about ID advocates not being creationists, while being a choice to which he is entitled, is not very useful.

Mark Perakh said: Reluctantly, I'd like to argue against Peter's opinion regarding the legitimacy of the term "creationism" as applied to ID advocates. To my mind ID "theory" can be, to all intents and purposes, referred to as creationism (perhaps qualifying it, when it can be confusing, by using it in the form "ID creationism.") Here is why. Of course, generally speaking, any definition is a matter of consensus. Hence, the distinction between various definitions of the same object may be viewed as a question of pure semantics, and as such not really crucial. However, to be useful, a definition must reasonably reflect, at least partially, the real features of the defined subject. Say, we want to provide a definition of what is a semi-conductor. Nobody can prevent us from arbitrarily choosing for a definition, for example, the sentence "semi-conductor is a metal that is red," and having agreed on that definition, to use it in the further discussions. Will such a pseudo-definition, even being a result of a consensus, useful? I don't think so, because it, by its utter arbitrariness and being contrary to the factual contents of the concept of a semi-conductor, would be misleading and counter-productive. Semi-conductors are not metals and are not red. The proper definition can be chosen in many ways, but must preferably reflect some actual properties of the defined concept, in this case a semi-conductor. One such definition may be "a semi-conductor is material whose electric resistivity decreases with temperature." Back to creationism, its definition likewise should reflect its contents, and if chosen in a very narrow way, would be not very useful. If we define creationism as adherence to a belief in the literal truth of every word in the book of Genesis, then ID "theory" as such indeed can be construed as being distinctive from creationism, because ID advocates, even those of them who in fact do believe in the Bible's inerrancy, usually do not use such beliefs as arguments, turning instead to seemingly "scientific" and/or "mathematical" arguments. (The same is, however, also true for many YEC frank creationists, but they do not object to being called creationists, and neither do their critics avoid such a term). I think that the appropriate definition of creationism more reasonably should be less narrow. ID advocates' views, after all their "mathematical" and "scientific" arguments have been dealt with, boil down to the assertion that the universe in general (and biological life in particular) was "created" by a mysterious "Designer." Therefore there is a good reason to refer to them as creationists, albeit not forgetting about the secondary distinctions between various brands of creationism, of which there are many. Feverish denials of some ID advocates of being "creationists" make me shrug (actually some of them frankly admit being creationists). Therefore to my mind Peter's asseveration about ID advocates not being creationists, while being a choice to which he is entitled, is not very useful.

Mark Frank said:

Mark, Thanks for the comment on Bayesian inference which I don’t think has been addressed before. The filter has been debated ad nauseum and I included it because of the target audience of Chance readers were not likely to have heard of it. The Bayesian part and the criticism of Behe’s “The Edge” are new.

Peter I did have a rather amateur go at Dembski's argument that inference from comparative likelihood presupposes specification about 18 months ago here. I guess others must have done the same somewhere. But you have done it much more authoritively and completely. I have never seen your criticism of Behe before. The frustrating thing is that it makes no difference. The ID community seems to just ignore these criticisms even when they come from real experts in the field such as yourself.

The label issue is of course semantics, but there is the
issue of whether the "ID community" and the creationist
community are separate entities.

I do believe that some ID advocates, Behe comes to mind,
at least started out thinking they were going to do
something new and different. This ran into two problems.
The first was that the number of anti-Darwin arguments
is actually somewhat limited -- Paley fallacy ("if it's
complex it must have been designed"), monkeys & typewriters,
lottery winner fallacy, all mutations are bad,
second law of thermo, gaps, and so on. Once you've hit
the basic set all you can do is rephrase them -- second
law argument reconfigured as law of conservation of information, all mutations are bad becomes "genetic
entropy", and so on.

Modern evolutionary science is somewhat counterintuitive
(in much the same way that the fact that Earth goes around
the Sun is counterintuitive, our senses saying it's the
other way around) and such advocates start out thinking
they have a clear shot. The reality is that all they
end up doing is rehashing one of the old arguments --
Behe's work is essentially an updating of the Paley
fallacy. And they run out of steam so fast that they
then increasingly mine the set of standard anti-Darwin
arguments.

The second problem is that there is no real audience
for something really new and different.
The DI does not reflect a new movement; the
anti-Darwinists among the general community are
overwhelmingly straightforward creationists, and to
the extent they are receptive to the DI message, it is
only to help muddy the waters. To the extent the DI
message has subtleties they go right past that receptive
public. It is hard to believe that the DI doesn't know
this, but even giving them the benefit of the doubt,
the DI and the general anti-Darwin public share a major
common subset of arguments and have effectively the
same goal -- assaulting the teaching of modern evo
science in the public schools.

White Rabbit (Greg Goebel) http://www.vectorsite.net/gblog.html

FL said: Creationism ... is totally dependent on acceptance of Genesis' supernatural claims as the starting point of the "Creation Model."

(1) Scientific creationism (no reliance on Biblical revelation, utilizing only scientific data to support and expound the creation model).

FL said: Likewise, you don't have to subscribe to the Gospel of John prior to placing the ID hypothesis under serious consideration as a scientific hypothesis.

That also includes theistic evolution. Just ask Kenneth Miller. He's been publicly called a creationist by his fellow evolutionists. Twice, even.

— FL

The second problem is that there is no real audience for something really new and different. The DI does not reflect a new movement; the anti-Darwinists among the general community are overwhelmingly straightforward creationists, and to the extent they are receptive to the DI message, it is only to help muddy the waters.

— iml8

The question of whether ID is creationism really has two answers, depending upon context.

In the wake of Barbara Forrest's research, I think that we can take it as established that ID was developed by creationists as a rebranding of creationism in order to further the political goals of the Discovery Institute. Its fundamental arguments are ones that were originally advanced by creationists. So politically and legally speaking, ID is creationism.

Philosophically, however, one can allow for the possibility that somebody might subscribe to the concept of intelligent design without embracing creationism, although so far as I can tell, none of the prominent ID advocates fall into this category, displaying zero interest in non-supernatural "design" hypotheses such as alien intervention or Matrix-style simulated worlds. So in principle, one could say that all creationism is necessarily ID, but it is possible to have ID that is not creationist. It's just that non-creationist ID advocates seem to be virtually nonexistent in actual practice.

trrll said: ... In the wake of Barbara Forrest's research, I think that we can take it as established that ID was developed by creationists as a rebranding of creationism in order to further the political goals of the Discovery Institute. Its fundamental arguments are ones that were originally advanced by creationists. So politically and legally speaking, ID is creationism. ...

trrll said: The question of whether ID is creationism really has two answers, depending upon context.

386sx said: Get rid of the "irreducible complexity" stuff, and then maybe ID wouldn't be all about creationism. But good luck with that, because "irreducible complexity" and fightin' the Devil are practically all that ID is about.

FL said:

....“creationism” has come to mean any design-based pseudoscience that centers on promoting unreasonable doubt of evolution, and that includes ID.

That also includes theistic evolution. Just ask Kenneth Miller. He's been publicly called a creationist by his fellow evolutionists. Twice, even.

Frankly, if people can twist reality enough to differentiate ID from creationism, then I don’t see how the battle can ever be won.

— Venus Mousetrap

FL said: PS.....If the ID hypothesis (particular the Dembski/Behe 3-point ID hypothesis) survives falsification, THEN a rational person can indeed conclude, as Dembski does, that ID is the Logos concept stated in the NT, restated in the idiom of information theory. But here's the kicker: that hypothesis does NOT require you to assume or accept any of the Gospel of John's claims (nor the Logos claim or any other Bible claim) at any point of the hypothesis. THAT's the difference Pete.

FL said: PS.....If the ID hypothesis (particular the Dembski/Behe 3-point ID hypothesis) survives falsification, THEN a rational person can indeed conclude, as Dembski does, that ID is the Logos concept stated in the NT, restated in the idiom of information theory.

Joe Felsenstein said: If we make a Filter that detects whether the DNA sequence (of some part of the genome) is in the top 10^-150 of fitnesses of all sequences of that length, is this unlikely? Yes, if the mechanism imagined is just mutation and other evolutionary forces, but does not include natural selection. No, if it includes natural selection. So depending on whether or not you take the "chance" mechanism to include natural selection, you either have a Filter that is so vague as to be unworkable (Olofsson and Perakh) or one that works but then can't rule out natural selection as the cause of the adaptation (me). Dembski imagined that he had a proof that natural selection could not do the job, but his proof was wrong, and also was of the wrong theorem that could not do the job, even if it had been provable.

Dembski claims that he can ignore natural selection because of the No Free Lunch theorems. Those theorems deal with genetic algorithms and state that, averaged over all fitness landscapes, a random search is as effective as any other search strategy. The obvious problem here is, to what extent the NFL theorems apply to biological evolution. If the NFL theorems do not apply to biological evolution, then Dembski’s calculations just don’t apply either.

pwe said: Dembski claims that he can ignore natural selection because of the No Free Lunch theorems. Those theorems deal with genetic algorithms and state that, averaged over all fitness landscapes, a random search is as effective as any other search strategy. The obvious problem here is, to what extent the NFL theorems apply to biological evolution. If the NFL theorems do not apply to biological evolution, then Dembski's calculations just don't apply either. For an illustration, consider a binary decision tree. It has a root with two branches, each branche ending in a node, which in turn is the root of a subtree, and so on, until a non-branching node, called a leaf, is reached. Say a tree has 1024 (= 2¹⁰) leaves. Then the tree has 2047 nodes. Assume we are to find the way from the root to a specific leaf. A random search will on the average have to visit half of those nodes, which is 1024 nodes, if we round up. However, the height of the tree is 10, so a more informed search can go straight from the root to that specific leaf in 10 steps. But, would Dembski ask, from where does that information come? From the environment, will the evolutionist answer. But, would Dembski ask, who put the information into the environment. And so on. As for the use of a uniform distribution in the case that the real distribution is not known, there is some merit to that, since a uniform distribution will have the least maximum error. From a scientific point of view, that isn't good enough, but would simply call for more research into the actual distribution. However, for Dembski it is quite ok to replace missing information with, what he considers the most optimal guess, rather than to do any research. - pwe

I said "where “nearby” means one mutation away from a currently occupied node...". I should had said "one or a few mutations away from a currently occupied node." Mutations don't necessarily occur at a rate of one per offspring. (Offspring are biological systems' way of sampling new nodes.) Nevertheless, that expands the neighborhood from which samples are drawn only a bit. Sampling is still from a tiny neighborhood of nearby nodes, not from the whole of geno-space.

The fallacy of Dembski's treatment of the NFL theorems had been demonstrated immediately after his infamous No Free Lunch book appeared (for example, see here and here). Later some other publications (like those by Olle Haggstrom and others) added more arguments showing the utter lack of rationale in Dembski's attempts to use the NFL theorems to support ID. It is amazing that this point is being addressed, often without a reference to the earlier stuff, time and time again, as if all those earlier publications did not exist.

I am sorry to have failed to mention in my preceding comment that the very first (and very apt) demolition of Dembski's misuse of the NFL theorems was perhaps that by Richard Wein (see, for example here).

I have apparently misspelled the URL's of the posts critical od Dembski's misuse of the NFL theorems. Here are the amended links: (1) this and (2) this. (the link to Wein's post was OK). AR

The links seem to be faulty again. I am trying one more time.
(1) this, and (2) this.

I’m hoping that Dr. Olofsson’s clear refusal to conflate ID and creationism will provide motivation for other evolutionists to seriously think about and follow his example.

Because that will give people like FL yet another excuse to avoid having to demonstrate any actual validity for either one.

ID, by contrast, doesn’t depend on nor assumes nor requires ANYBODY’s religious writings or texts. No supernatural or God prerequisites or pre-assumptions.

First, as was demonstrated at the Dover trial, ID is merely creationism with the specific names and religious references removed to make it look more science-y. Second, your assertion of "No supernatural or God prerequisites or pre-assumptions" is a flat-out lie: the basic thrust of ID is that life as we see it could never have evolved without intervention from an intelligent being with supernatural powers. (Yeah, yeah, you say it "could" be space-aliens too, but those would be physical creatures whose powers would be limited, and whose actions would have left physical traces that could be found; and you never really pretend you're looking for such traces, do you?)

ID hypothesis starts ONLY with observation of the biological world (looking for the presence of specified or irreducible complexity) and goes on from there.

How can you "look for" something you have never bothered to define or quantify, and have no means of measuring? The answer is simple: you can't. ID pretends to observe, then pretends to find something that can't be defined or verified, when the pretense of finding it can be used to support the creationists' preferred conclusion.

Once again, a YEC who worships a deceiver-God shows his true colors.

Here's the real difference between ID and creationism: creationism is what the radical right want to teach our kids, and ID is the transparent -- and repeatedly debunked and discredited -- pretense of scienciness they need to get creationism past the courts.

Or, to put it in the language of this election year: creationism is the pig; ID is the lipstick and the laughably overpriced set of clothes that don't fool anyone.

Here’s the real difference between ID and creationism: creationism is what the radical right want to teach our kids, and ID is the transparent – and repeatedly debunked and discredited – pretense of scienciness they need to get creationism past the courts. Or, to put it in the language of this election year: creationism is the pig; ID is the lipstick and the laughably overpriced set of clothes that don’t fool anyone.

— Raging Bee

In order to make remarks about biological evolution based on the mathematical literature of search techniques requires that the model take those specific characteristics of biological evolution into account. Nothing in Dembski’s (or anyone else’s) work of which I’m aware comes anywhere near to doing so.

— RBH

What an interesting discussion. I wonder if anyone has realized that this all rests on the controversial traditional understanding of probability anyway? And there is dwindling certainty when controversial claims presuppose other controversial claims. I try to avoid this in my own work except in rare instances of massive mutual explanatory force. I guess I'm a Coherentist in that way.

So anyway, it seems like Dembski & co. are virtually always conceding and/or shifting ground, and almost never gaining ground. This is not good news for them!

No free lunch indeed!

NS
http://sciencedefeated.wordpress.com/

Mike Elzinga said: Your list captures some of the requirements that are needed in a realistic modeling of evolution. There are many complex physical systems that have had effective modeling techniques applied to them over the years. Many of the mathematical techniques are discussed in such journals as Computers in Physics (now Computers in Science and Engineering). Len Sander at the University of Michigan , who I know personally, has been working in these areas for decades.

pwe said:

Joe Felsenstein said: If we make a Filter that detects whether the DNA sequence (of some part of the genome) is in the top 10^-150 of fitnesses of all sequences of that length, is this unlikely? Yes, if the mechanism imagined is just mutation and other evolutionary forces, but does not include natural selection. No, if it includes natural selection. So depending on whether or not you take the "chance" mechanism to include natural selection, you either have a Filter that is so vague as to be unworkable (Olofsson and Perakh) or one that works but then can't rule out natural selection as the cause of the adaptation (me). Dembski imagined that he had a proof that natural selection could not do the job, but his proof was wrong, and also was of the wrong theorem that could not do the job, even if it had been provable.

Dembski claims that he can ignore natural selection because of the No Free Lunch theorems. Those theorems deal with genetic algorithms and state that, averaged over all fitness landscapes, a random search is as effective as any other search strategy. The obvious problem here is, to what extent the NFL theorems apply to biological evolution. If the NFL theorems do not apply to biological evolution, then Dembski's calculations just don't apply either. For an illustration, consider a binary decision tree. It has a root with two branches, each branche ending in a node, which in turn is the root of a subtree, and so on, until a non-branching node, called a leaf, is reached. Say a tree has 1024 (= 2¹⁰) leaves. Then the tree has 2047 nodes. Assume we are to find the way from the root to a specific leaf. A random search will on the average have to visit half of those nodes, which is 1024 nodes, if we round up. However, the height of the tree is 10, so a more informed search can go straight from the root to that specific leaf in 10 steps. But, would Dembski ask, from where does that information come? From the environment, will the evolutionist answer. But, would Dembski ask, who put the information into the environment. And so on. As for the use of a uniform distribution in the case that the real distribution is not known, there is some merit to that, since a uniform distribution will have the least maximum error. From a scientific point of view, that isn't good enough, but would simply call for more research into the actual distribution. However, for Dembski it is quite ok to replace missing information with, what he considers the most optimal guess, rather than to do any research. - pwe

If what Dembski said was true then Physicists wouldn’t find much utility in techniques like simulated annealing or GA’s. As discussed, the issue boils down to the type of landscape, and Dembski would need to prove that the landscape is more like a Devil’s Staircase rather than the smoother topologies we tend to find in dealing with real world systems. I wish him luck with that.

The fallacy of Dembski’s treatment of the NFL theorems had been demonstrated immediately after his infamous No Free Lunch book appeared (for example, see here and here). Later some other publications (like those by Olle Haggstrom and others) added more arguments showing the utter lack of rationale in Dembski’s attempts to use the NFL theorems to support ID. It is amazing that this point is being addressed, often without a reference to the earlier stuff, time and time again, as if all those earlier publications did not exist.

In particular, the argument that the No Free Lunch theorem does not establish that natural selection cannot do better than pure random search was also made by Wein 2002, Rosenhouse 2002, Perakh 2004b, Shallit and Elsberry 2004, Tellgren 2005, and Häggström 2007.

Joe Felsenstein said: Stuart Weinstein noted that

If what Dembski said was true then Physicists wouldn’t find much utility in techniques like simulated annealing or GA’s. As discussed, the issue boils down to the type of landscape, and Dembski would need to prove that the landscape is more like a Devil’s Staircase rather than the smoother topologies we tend to find in dealing with real world systems. I wish him luck with that.

Interestingly, Dembski's recent work with Robert Marks tries to establish that the information that natural selection puts into the genome is already present, lying around in the adaptive landscape, the more the smoother that landscape is. Which some of us might argue with, but anyway it's completely irrelevant. The issue was whether natural selection can explain adaptation. If our planet is predisposed to this by having unusually smooth adaptive landscapes, that may be of interest to cosmologists (or to theologians) -- but it still means that on our planet, in our universe, natural selection works. Which is what he was originally trying to argue against. In effect the new argument throws in the towel and says "OK, yes, it does work, but only because God set the planet up that way."

Now its sounds as though the argument has regressed to a fine-tuning argument.

Stuart Weinstein said: Now its sounds as though the argument has regressed to a fine-tuning argument.

the most the fine-tuning argument buys (theologically) is a sort of fuzzy deism.

Interestingly, Dembski’s tries to establish that the information that natural selection puts into the genome is already present, lying around in the adaptive landscape, the more the smoother that landscape is.

Henry J said:

Interestingly, Dembski’s tries to establish that the information that natural selection puts into the genome is already present, lying around in the adaptive landscape, the more the smoother that landscape is.

How is that different from saying that the information was in the environment in which the species lives? Henry

Information theorists since Kelly [19] have observed that in special circumstances, information value and information theoretic measures may be related. Here we argue that these special circumstances are exactly those about which biologists should be most concerned: the context of evolution by natural selection. We address the question “how much is information worth to living organisms?” and show that the answer turns out to be a striking amalgam of mutual information and the decision-theoretic value of information.

Yes, it’s perfectly compatible with theistic evolutionism. Dembski can’t be very happy to end up so close to Ken Miller’s position.

— Joe Felsenstein

I don’t have all the references at my fingertips, but my impression is that Dembski has been “all over the map” since the beginning.

— Frank J

Isn't this entire discussion falling into the creationists' honeytrap?

Creationism is a political movement. The real debate is political, not scientific. The battle must be won on the political field.

Intelligent design was concocted as a trojan horse for creationism. It has no other basis, no other raison d'etre. To dignify it with reasoned discussion is to be lured by the creationists' honey trap, to allow these liars the unearned dignity and respectability of scientific debate.

The challenge must surely be: if you ID/creationists reckon your field is scientific, you do the science and publish it properly. You prove it.

But the fraudulent crapmeisters Dembski and Behe weave around tickling your funny bones with their featherweight arguments and you guys are falling for it!

Who is going to actually be swayed by this paper? ID/creationists will ignore it, rationalists and scientists already know what's going on. Nice arguments, complete waste of time.

This is a perfect example of the perils of avoiding scientific peer review. The result is a whole sequence of “oh crap, I screwed up and now it’s out there for everyone to see” moments.

— Mike Elzinga

Isn’t this entire discussion falling into the creationists’ honeytrap?

— Sam Centipedro

Frank J said: Any reaction to any "kind" of pseudoscience runs that risk. But not responding also runs a risk. Anti-evolutionists are still spinning how "evolutionists" didn't show up at the 2005 Kansas Kangaroo Court, while conveniently ignoring how they did show up at the real trial (Kitzmiller v. Dover) a few months later. Where they convinced a conservative, Christian, GWB-appointed judge that ID/creationism has no place in science class.

One of the long list of refutations of Dembski's attempts to apply the NFL theorems is that NFL only applies if you average over all possible fitness landscapes. Whatever biological evolution does, it certainly doesn't do that! Ergo NFL tells us nothing about biological evolution. Moving on!

Clearly Prof. Olofsson doesn't understand biology:

http://kairosfocus.blogspot.com/2008/11/follow-up-blog-visit-report-deleted.html

[Nov 26, 2008, UD thread on Prof PO's ID critique paper at http://www.uncommondescent.com/intelligent-design/some-thanks-for-professor-olofsson/ ]

[comment] 16 [deleted]

gpuccio

11/25/2008

6:38 pm

I have read Peter Olofsson’s essay on Talk Reason titled “Probability, Statistics, Evolution, and Intelligent Design” and, while recognizing the correctness of the general tone, I am really disappointed by the incorrectness of the content. With this I do not mean, obviously, that PO does not know his statistics, but that he uses it completely out of context. And many of his errors derive essentially from not being apparently really familiar with biology.
I will try to make some comments.

PO’s arguments are essentially dedicated first to Dembski, and then to Behe. I think he fails in both cases, but for different reasons.

In the first part, he argues against Dembski’s approach to CSI and his explanatory filter.

The first, and main, critic that he does is the following: “He presents no argument as to why rejecting the uniform distribution rules out every other chance hypothesis.”

I’ll try to explain the question as simply as possible, as I see it.

Dembski, example, when applied to biological issues like the sequence of aminoacids in proteins, correctly assumes a uniform probability distribution. Obviously, such an assumption is not true in all generic statistical problems, but Dembski states explicitly, in his works, that it is warranted when we have no specific information about the structure of the search space.

This is a statistical issue [e.g. cf here, here, here and here], and I will not debate it in general.

I will only affirm that, in the specific case of the sequence of aminoacids in proteins, as it comes out from the sequence of nucleotides in the genome through the genetic code, it is the only possible assumption. We have no special reason to assume that specific sequences of aminoacids are significantly more likely than others.

There can be differences in the occurrence of single aminoacids due to the asymmetric redundant nature of the genetic code, or a different probability of occurrence of the individual mutations, but that can obviously not be related to the space of functional proteins. There is really no reason to assume that functional sequences of hundreds of aminoacids can be in any way more likely than non functional ones. This is not a statistical issue, but a biologic one.

So, PO’s critic may have some theoretical ground (or not), but it is totally irrelevant empirically.

His second critic is the following:

“As opposed to the simple Caputo example, it is now very unclear how a relevant rejection region would be formed. The biological function under consideration is motility, and one should not just consider the exact structure of the flagellum and the proteins it comprises. Rather, one must form the set of all possible proteins and combinations thereof that could have led to some motility device through mutation and natural selection, which is, to say the least, a daunting task.”

In general, he affirms that Dembski does not explicitly state how to define the rejection region.

Let’s begin with the case of a single functional protein. Here, the search space (under a perfectly warranted hypothesis of practically uniform probability distribution) is simply the number of possible sequences of that length (let’s say, for a 300 aa protein, 20^300, which is a really huge space). But which is the “rejection region”? In other words, which is the probability of the functional target? That depends on the size of the set of functional sequences. What is that size, for a definite protein length?

It depends on how we define the function.

We can define it very generically (all possible proteins of that length which are in a sense “functional”, in other words which can fold appropriately and have some kind of function in any known biological system). Or, more correctly, we can define it relatively to the system we are studying (all possible proteins of that length which will have an useful, selectable function in that system). In the second case, the target set is certainly much smaller.

It is true, however, that nobody, at present, can exactly calculate the size of the target set in any specific case. We simply don’t know enough about proteins.

So, we are left with a difficulty: to calculate the probability of our functional event, we have the denominator, the search space, which is extremely huge, but we don’t have the numerator, the target space.

Should we be discouraged?

Not too much.

It is true that we don’t know exactly the numerator, but we can have perfectly reasonable ideas about its order of magnitude. In particular we can be reasonably certain that the size of the target space will never be so big as to give a final probability which is in the boundaries, just to make an example, of Dembski’s UPB.

Not for a 300 aa protein. And a 300 aa protein is not a very long protein.

(I will not enter in details here for brevity, but here the search space is 20^300 [NB: ~ 2.037*10^390; the UPB of odds less than 1 in 10^150 as the edge of reasonable probbaility is based on the fact that there are less than 10^150 quantum states of all atoms in the observable universe from its origin to its end, so odds longer than that exhaoust its available probabilistic resources]; even if it were 10^300, we still would need a target space of at least 10^150 functional proteins to ensure a probability for the event of 1:10^150, and such a huge functional space is really inconceivable, at the light of all that we know about the restraints for protein function.)

That reasoning becomes even more absolute if we consider not one protein, but a whole functional system like the flagellum, made of many proteins of great length interacting for function. There, if it is true that we cannot calculate the exact size of the target space, proposing, as PO does, that it may be even remotely relevant to our problem is really pure imagination.

Again, I am afraid that PO has too vague a notion of real biological systems.
So, again, PO’s objections have some theoretical grounds, but are completely irrelevant empirically, when applied to the biological systems we are considering.

That is a common tactic of the darwinian field: as they cannot really counter Dembski’s arguments, they use mathematicians or statisticians to try to discredit them with technical and irrelevant objections, while ignoring the evident hole which has been revealed in their position by the same arguments. PO should be more aware that here we are discussing empirical science, and, what is more important, empirical biological science, which is in itself very different from more exact sciences, like physics, in the application of statistical procedures.

The last point against Dembski regards his arguments in favor of frequentist statistics against the Bayesian approach.

This part is totally irrelevant for us, who are not pure statisticians. Indeed, it will be enough to say that, practically in all biological and medical sciences, the statistical approach is Fisherian, and is based on the rejection of the null hypothesis.

So, Dembski is right for all practical applications.

Indeed, PO makes a rather strange affirmation: “A null hypothesis H0 is not merely rejected; it is rejected in favor of an alternative hypothesis HA”. That is simply not true, at least in biology and medicine. H0 is rejected, and HA is tentatively affirmed if there is no other causal model which can explain the data which appear not to be random. So, the rejection of H0 is done on statistical terms (improbability of the random nature of the data), but the assertion of HA is done for methodological and cognitive reasons which have nothing to do with statistics.

The second part of PO’s essay is about Behe’s TEOE, and the famous problem of malaria resistance.

Here, PO’s arguments are not only irrelevant, but definitely confused.

I’ll do some examples:

“The reason for invoking the malaria parasite is an estimate from the literature that the set of mutations necessary for choloroquine resistance has a probability of about 1 in 10^20 of occurring spontaneously.”

Yes, Behe makes that estimate from epidemiological data of the literature.

But he also points out that the likely reason for that empirical frequency is that chloroquine resistance seems to require at least two different coordinated mutations, and not only one, like resistance to other drugs. Indeed, Behe’s point is that the empirical occurrence of the two kinds of resistance is in good accord with the theoretical probability for a single functional mutation and a double coordinated functional mutation.

Again, PO seems to be blind to the biological aspects of the problem.

“Any statistician is bound to wonder how such an estimate is obtained, and, needless to say, it is very crude. Obviously, nobody has performed huge numbers of controlled binomial trials, counting the numbers of parasites and successful mutation events.”

But Behe’s evaluation is epidemiological, not experimental, and that is a perfectly valid approach in biology.

“Rather, the estimate is obtained by considering the number of times chloroquine resistance has not only occurred, but taken over local populations — an approach that obviously leads to an underestimate of unknown magnitude of the actual mutation rate, according to Nicholas Matzke’s review in Trends in Ecology & Evolution.”

Here PO seems to realize, somewhat late, that Behe’s argument is epidemiological, and so he makes a biological argument at last. Not so relevant, and from authority (Matzke, just to be original!). But yes, maybe there is some underestimation in Behe’s reasoning. Or maybe an overestimation. Thats’ the rule in epidemiological and biological hypotheses. nobody has absolute truth.

“Behe wishes to make the valid point that microbial populations are so large that even highly improbable events are likely to occur without the need for any supernatural explanations.”

No, he only makes the correct point that random events are more likely to occur in large populations than in small populations. If they are not too “highly improbable”, of course. In other words, a two aminoacid coordinated functional mutation “can” occur (and indeed occurs, although rarely) in the malaria parasite. But it is almost impossible in humans.

What has that to do with supernatural explanations? [NB: Cf my discussion here on the misleading contrast natural/supernatural vs the relevant one: natural/artificial, and the underlying materialist agenda that is too often at work, here.]

“But his fixation on such an uncertain estimate and its elevation to paradigmatic status seems like an odd practice for a scientist.”

Uncertain estimates are certainly not an odd practice for a biologist. And anyway, Behe does not elevate his estimate to “paradigmatic status”: he just tries to investigate a quantitative aspect of biological reality which darwinists have always left in the dark, conveniently for them I would say, and he does that with the available data.

“He then gores on to claim that, in the human population of the last 10 million years, where there have only been about 10^12 individuals, the odds are solidly against such an unlikely event occurring even once.”

For once, that’s correct.

“On the surface, his argument may sound convincing.”

It is convincing.

“First, he leaves the concept “complexity” undefined — a practice that is clearly anathema in any mathematical analysis.”

That’s not true. He is obviously speaking of the complexity of a functional mutation which needs at least two coordinated mutations, like chloroquine resistance. That is very clear if one reads TEOE.

“Thus, when he defines a CCC as something that has a certain “degree of complexity,” we do not know of what we are measuring the degree.”

The same misunderstanding. we are talking of mutational events which require at least two coordinated mutations to be functional, like chloroquine resistance, and which in the natural model of the malaria parasite seem to occur with an approximate empirical frequency of 1-in-10^20.

“As stated, his conclusion about humans is, of course, flat out wrong, as he claims no mutation event (as opposed to some specific mutation event) of probability 1 in 10^20 can occur in a population of 10^12 individuals (an error similar to claiming that most likely nobody will win the lottery because each individual is highly unlikely to win).”

Here confusion is complete. Behe is just saying a very simple thing: that a “functional” mutation of that type cannot be expected in a population of 10^12 individuals. PO, like many, equivocates on the concept of CSI ([with bio-] functional specification [being particularly in view]) and brings out, for the nth time, the infamous “deck of cards” or “lottery” argument (improbable things do happen; OK, thank you, we know that).

“Obviously, Behe intends to consider mutations that are not just very rare, but also useful,”

Well, maybe PO understands the concept of CSI, after all. [NB: cf. "useful" and "[bio-] functional."] But then why does he speak of “error” in the previous sentence?

“Note that Behe now claims CCC is a probability; whereas, it was previously defined as a mutation cluster”

That’s just being fastidious. OK, Behe meant the probability of that cluster…

“A problem Behe faces is that “rarity” can be defined and ordered in terms of probabilities; whereas, he suggests no separate definition of “effectiveness.” For an interesting example, also covered by Behe, consider another malaria drug, atovaquone, to which the parasite has developed resistance. The estimated probability is here about 1 in 10^12, thus a much easier task that chloroquine resistance. Should we then conclude atovaquone resistance is a 100 million times worse, less useful, and less effective than chloroquine resistance? According to Behe’s logic, we should.”

Now I cannot even find a logic here. What does that mean? Atovaquone resistance has an empirically estimated probability of 1 in 10^12, which is in accord with the fact that it depends on a single aminoacid mutation. What has that to do with “usefulness”, “effectiveness”, and all the rest?

“But, if a CCC is an observed relative frequency, how could there possibly have been one in the human population? As soon as a mutation has been observed, regardless of how useful it is to us, it gets an observed relative frequency of at least 1 in 1012 and is thus very far from acquiring the magic CCC status.”

Here, Po goes mystical. CCC is an observed relative frequency in the malaria parasite. That’s why we cannot reasonably “expect” that kind of mutation an empirical cause of functional variation in humans. What is difficult in that? Obviously, we are assuming that the causes of random mutations are similar in the malaria parasite and in humans. Unless PO want to suggest that humans are routinely exposed to hypermutation.

“Think about it. Not even a Neanderthal mutated into a rocket scientist would be good enough; the poor sod would still decisively lose out to the malaria bug and its CCC, as would almost any mutation in almost any population.”

I have thought about it, and still can find no meaning in such an affirmation. The point here is not a sporting competition between the malaria parasite and the human race. We are only testing scientific hypotheses.

“If one of n individuals experiences a mutation, the estimated mutation probability is 1/n. regardless of how small this number is, the mutation is easily attributed to chance because there are n individuals to try. Any argument for design based on estimated mutation probabilities must therefore be purely speculative.”

That’s just the final summary of a long paragraph which seems to make no sense. PO seems to miss the point here. we have two different theories which try to explain the same data (biological information). The first one (darwinian evolution) relies heavily on random events as causal factors. Therefore, its model must be consistent with statisticalm laws, both theoretically and empirically.

Behe has clearly shown that that is not the case.

His observations about true darwinian events (microevolution due to drug pressure) in the malaria parasite, both theoretical (number of required coordinated functional mutations and calculation of the relative probabilities) and empirical (frequency of occurrence of those mutations in epidemiological data) are in accord with a reasonable statistical model.

The same model, applied to humans, cannot explain the important novel functional information that humans exhibit vs their assumed precursors.

Therefore, that functional information cannot be explained by the same model which explains drug resistance in the malaria parasite.

Does that seem clear?

It is.

In the end, I will borrow PO’s final phrase:

“Careful evaluation of these arguments, however, reveals their inadequacies.”

Unlike ID creos, we let the critics of our position to freely express themselves on PT threads. The lengthy dissertation presented by the commenter signed as "Nils Ruhr" as a comment on this tread is an illustration of our policy.

In all of "Nils Ruhr"s endless post there is one correct statement - it is his assertion that biology is an empirical science and therefore its problems can't be solved by purely mathematical argument. True! Indeed, such an argument has been offered more than once before, and legitimately it has to be addressed to Dembski in the first place. As an example, one may look up this post wherein the notion of mathematical arguments being intrinsically incapable of repudiating the empirical data was evinced, thus making "Nils Ruhr"s thesis late by nearly five years.

It is Dembski who has devoted his career to repudiation of evolution theory by supposedly mathematical, in particular statistical "arguments." It is only natural that real experts in mathematics, seeing Dembski's awkward attempts to "demolish" evolution theory by means of obviously inadequate mathematics, analyze Dembski's mathematical discourse and demonstrate its utter fallacy, leaving biological aspects of the matter to biologists. The main thesis of "Nils Ruhr" is hence first of all applicable to ID advocates' output, Dembski's including.

In view of that "Nils Ruhr"s pseudo-sophisticated notions, rooted in biology, are irrelevant insofar as Olofsson's article is in question. As to the validity of Dembski's and Behe's arguments, they have been shown to be utterly wrong many times over, so continuing the debate with Dembski and Behe looks to me as beating a dead horse, but I also can understand the desire to pounce time and time again upon those two ID advocates whose output, while patently wrong, is invoking the continuing debate simply because of the arrogance and impudence of their behavior.

Frank J said:

This is a perfect example of the perils of avoiding scientific peer review. The result is a whole sequence of “oh crap, I screwed up and now it’s out there for everyone to see” moments.

— Mike Elzinga

You don't seriously think that Dembski lost a minute of sleep over what mainstream science thinks of his antics? ...

The pseudo-science “rebuttal” of Peter Olofsson’s article is a copy/paste by “Nils Ruhr” of a comment on 11/28/2008 by “Gordon” on the kiarofocus.blogspot.com website.

It is complete gibberish, and is a nice example of the tactics of pseudo-scientists who try to make it appear that they are knowledgeable and on top of the science.

Word salads, especially long ones, are clear indications of hocus-pocus. Digging into them and looking for meaning is time-consuming, but always comes up with nothing, as was the case with this one. Going over it line-by-line will simply derail this thread.

I suggest taking one and only one specific argument he makes and taking it, and only it, apart in detail. Ignore any commentary he may make in rebuttal that is not specific to that point. The creationists take advantage of people thinking in anecdotes, so it is time we adopted that tactic as well. As Sam correctly pointed out earlier, this battle is political, not scientific, so our weapons need to be political too. So prove one thing wrong and keep throwing it in their faces.

gpuccio (via Nils Ruhr) said: That is a common tactic of the darwinian field: as they cannot really counter Dembski’s arguments, they use mathematicians or statisticians to try to discredit them with technical and irrelevant objections, while ignoring the evident hole which has been revealed in their position by the same arguments.

As Sam correctly pointed out earlier, this battle is political, not scientific, so our weapons need to be political too. So prove one thing wrong and keep throwing it in their faces.

— Science Avenger

I must say this is a very interesting essay.

Zepp said: I must say this is a very interesting essay.

Sam Centipedro said: Isn't this entire discussion falling into the creationists' honeytrap? Creationism is a political movement. The real debate is political, not scientific. The battle must be won on the political field. Intelligent design was concocted as a trojan horse for creationism. It has no other basis, no other raison d'etre. To dignify it with reasoned discussion is to be lured by the creationists' honey trap, to allow these liars the unearned dignity and respectability of scientific debate. The challenge must surely be: if you ID/creationists reckon your field is scientific, you do the science and publish it properly. You prove it. But the fraudulent crapmeisters Dembski and Behe weave around tickling your funny bones with their featherweight arguments and you guys are falling for it! Who is going to actually be swayed by this paper? ID/creationists will ignore it, rationalists and scientists already know what's going on. Nice arguments, complete waste of time.

gpuccio (via Nils Ruhr) said: The first, and main, critic that he does is the following: “He presents no argument as to why rejecting the uniform distribution rules out every other chance hypothesis.” I’ll try to explain the question as simply as possible, as I see it. ... There can be differences in the occurrence of single aminoacids due to the asymmetric redundant nature of the genetic code, or a different probability of occurrence of the individual mutations, but that can obviously not be related to the space of functional proteins.

We can rule out every chance hypothesis because we can rule out more than one chance hypothesis? I can't tell if that is gpuccio's argument or not.

BTW, different mutations can be related to the space of functional proteins: a base pair change is far more likely to yield a functional protein than a base pair deletion. That is, if they are acting on a pre-existing genome rather than a random sequence of nucleotides.

peter olofsson said:

gpuccio (via Nils Ruhr) said: That is a common tactic of the darwinian field: as they cannot really counter Dembski’s arguments, they use mathematicians or statisticians to try to discredit them with technical and irrelevant objections, while ignoring the evident hole which has been revealed in their position by the same arguments.

A most astute observation! I am indeed a member of Team Darwin's Revolutionary Math Guard and have been sent out by my masters to present technical and irrelevant objections. PO

Peter Olofsson said:

Zepp said: I must say this is a very interesting essay.

Which one? Mine or gpuccio's (via Nils) reply? PO

Are you aware that the Uncommon Descent thread devoted to you just shrank considerably, with most of the “descenting” opinions consigned to the bit bucket.

Henry J said: Somebody took some bytes out of that thread? That's not descent of them.

On said thread, there is an interesting comment by Bill Dembski in post 169, part (1).

Regarding the latest comment by Peter Olofsson: he shied away from explaining what precisely was interesting in Dembski's comment, thus sending PT's visitors to delve into the garbage can named Uncommon Descent. There is, though, no need to go there: Wesley Elsberry provided the necessary clarification in a post titled "Vindication" on this blog (dated Dec 4, 2008). The "interesting" point Peter had in mind is Dembski's admission that his Explanatory Filter (EF) is not up to the task he until now persistently maintained to be within the filter's abilities. Of course, Dembski has not acknowledged multiple critiques of his EF, as if he came to its rejection completely on his own. Also, he asserts now that the better argument is a direct application of his CSI ("complex specified information") concept. Everybody familiar with the long history of the debate about ID knows that the the concept of CSI, as rendered by Dembski, is not any better than his EF. I believe I have shown (in an article published in the Skeptic magazine in 2005, see here ) that CSI argument in fact is nothing more than a slightly disguised argument from improbability. A detailed critique of CSI was also offered in the excellent article by Elsberry and Shallit (see here).

Mark Perakh said: Regarding the latest comment by Peter Olofsson: he shied away from explaining what precisely was interesting in Dembski's comment, thus sending PT's visitors to delve into the garbage can named Uncommon Descent. There is, though, no need to go there: Wesley Elsberry provided the necessary clarification