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Some Thanks for Professor Olofsson

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I’m halfway through mathematics Professor Peter Olofsson’s essay titled Probability, Statistics, Evolution, and Intelligent Design which originally appeared in the journal Chance.

The first thing I want to thank PO for is stating this early on:

Although [religion] is of interest in its own right, in fairness to ID proponents, it should be pointed out that many of them do not employ religious arguments against evolution and this article does not deal with issues of faith and religion.

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. PO brings up the same argument I’ve always pointed out when he talks about the rejection region for biological applications of the filter and the inability to bound it without doubt. I describe the same problem as that of, I think, a better term also used by Dembski called “probabilistic resources”. How can we ever possibly know some undiscovered pathway for law and chance to have assembled the flagellum doesn’t exist? The short answer is we cannot. We don’t know what we don’t know and we can’t calculate a probability for an unknown. This is in fact employing a valid “chance of the gaps” argument by PO.

The thing of it is there are lots of theories and hypotheses in science that are not provable because it is impossible in principle to rule out the unknown or the unobserved. Karl Popper famously stated how something cannot be provable but remain a valid scientific hypothesis. He illustrated it famously with a then mythical black swan. He gave the hypothesis “There are no black swans in nature.” He said this was a valid hypothesis because while it could never be proven true, that it was impossible to say all of nature was searched and no black swan possibly overlooked, the hypothesis can be disproven (falsified) by the observation of just one single black swan. In the meantime it was a valid hypothesis because it explained the known facts – millions of swans observed and none were black. A black swan in fact was eventually observed and science worked as it should – the black swan hypothesis was falsified.

So we have the ID hypothesis for the flagellum stated as “There are no unintelligent processes which can produce a complex machine (like a flagellum) in nature”. I have stated the ID hypothesis this way many times here. It is a perfectly valid scientific hypothesis which cannot be proven but can be falsified by observing just one unintelligent process producing such a machine. In the meantime we know that intelligence can produce complex machines. You’re reading this on one example of a complex machine which the explanatory filter would also predict is virtually impossible to have come about by law and chance alone.

I just glanced at the second half of the PO essay which addresses Behe’s “The Edge of Evolution”. I trust it rests on the same argument that the failure to observe any novel complex machines arising in the malaria parasite does not prove anything. I agree that it proves nothing. However, that doesn’t mean it doesn’t offer more evidence in favor of the ID hypothesis stated in the paragraph above. ID predicts that no complex machines would originate in even 10^30 reproductive opportunities for mutation and selection. Law and chance handily explains what was observed and what was observed fell far, far short of producing any significant machine-like complexity. What this represents is what Behe describes as probably the biggest real world test of evolution by chance and necessity ever witnessed. It validated microevolution by producing some small useful novelties but failed utterly to produce anything greater than what was predicted by known law and chance. No unknowns showed up. No black swan was observed.

The observations surrounding the malaria parasite could have, at least in principle, falsified the ID hypothesis. But it didn’t. So chalk up a successful prediction for ID.

Comments
This discussion continues at a new thread Barry A created. Thanks, Barry.Sal Gal
December 7, 2008
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IDskeptic[344], It's free, it's online, and it might end abruptly at any time! :)Prof_P.Olofsson
December 7, 2008
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gpuccio, if you're still around: I intended to reply to all your criticism but we haven't even made it to Behe yet. It usually happens and the last time I debated at UD, we set a length record (the "Archie Bunker" thread). I have comments about Behe as well but I think we'll take them "off the air" if you're still interested.Prof_P.Olofsson
December 7, 2008
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I'd love a free online statistics correspondence course...IDskeptic
December 7, 2008
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RoyK[341], I know, but I have already explained to him in an email the difference between a rejection region and a "rejection region." He said I shouldn't expect a reply but I still hope he read it. We can also look back at Mark Frank's comment [237] or my comments [276] and [280]. I said I wouldn't continue this debate but I reneged because PaV asked questions that I can answer. We'll see how much stamina I have!Prof_P.Olofsson
December 7, 2008
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By the way, what's often done in screenings for a disease is to first use a test with high sensitivity (will catch most disease cases but also many normal cases). Then the positive cases are restested with another test that has higher specificity (will weed out most false positives). The reason for not using the second test from the beginning is that it's more expensive or time-consuming. I have personal experience in testing for TB for my green card application. First I tested positive with the skin test because I'd been vaccinated which gives a lot of false positives. Then I was cleared with a chest X ray. More specific because it actually looks at the lungs and is not affected by previous vaccinations.Prof_P.Olofsson
December 7, 2008
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PO, you see where PaV is going here. By getting you to admit that you would "reject" if p=.1, or .2 or .3 or .4, he will say that these constitute an implicit "rejection region." Can you please respond to this "implicit" logical trap?RoyK
December 7, 2008
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PaV[336], Pleae ignore [338], I pressed return by mistake. You write
When the conditional hypothesis assumes a ‘normal’ population, then why would you want to accept false positives.
Well, you wouldn't, but everybody isn't normal. You have a population that is composed of normals and schizophrenics and you have two conditional probabilities, one for normals and one for schizophrenics. Among the normals, 3% test positive and among the schizophrenics, 97% test positive. As there are so few schizophrenics, most positive cases are actually miclassified normals. It's a common problem in any type of screening.
(1) According to Shandin, the true probability of getting a false positive is around 60%. Does that mean if the test were conducted twice on the same individual that the likelihood of that person getting a false positive 36%.
Good question. No, the 36% (60% of 60%) would assume independence. Here, an individual tested twice would likely get the same test result twice (although that of course depends on the test and I don't know what it is) so the false-positive rate would still be 60%. (2) Yes.Prof_P.Olofsson
December 7, 2008
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I challenge the notion that there can be any empirical basis for saying that something that is not empirically observable causes the empirical distribution to deviate from the average. In the scenario of an indifferent creator of distributions, the uniform distribution is no more likely than any other. One must actually violate the Principle of Indifference to say that the data should be distributed in one way, and not another. But there is a reality and this includes the existence of design. Attempts to quantify it are certainly not beyond the pale. And I suspect Dembski's methods have grounds for improvement -- it is a fairly new thing, after all -- but it is a pretty solid at bat. You have to bring something non-empirical to the table to argue that empirical distributions should “look” one way and not another. Sal Gal, that almost sounds like something Godel would say :-) But then again he went ahead and proved God anyway. I am here to say that the only important things I know are unspeakable absurdities. They are a matter of private experience, not empirical observation or proof. I agree with this. And unlike Godel, ID will not prove God nor is it designed to do so. It will, however, illustrate the dangerous and cruel absurdity that society should be predicated on the belief that everything happened by accident and that there is no absolute purpose for our existence.tribune7
December 7, 2008
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PaV[336],you won’t accept false positives.
When the conditional hypothesis assumes a ‘normal’ population, then why would you want to accept false positives.
Prof_P.Olofsson
December 7, 2008
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gpuccio [329,326] I wrote: "I hope you didn’t mean that humans have some general ability to distinguish compressible sequences from non-compressible ones, because no such ability exists anywhere." Let it not be said I can't comprehend someone else's point of view. Upon reflection, I do understand that humans see patterns (compressible sequences) in things. We look for patterns. If we don't discern a pattern in something, then for us it is noise (i.e. uncompressible) whether it is in reality or not. Furthermore, it seems to me that the patterns we perceive are often internal to us, that is we see patterns dictated by the patterns inherent in our internal coginitive and sensory makeup, which serve to filter out all but what they are capable of detecting. This is all mechanistic, not some unexplained attribute of a nonmechanism, i.e. "Intelligent Agency", IMO.JT
December 7, 2008
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PO[302]:
We catch most cases of schizophrenia but also get a lot of false positives. If we use a very low significance level, such as the UPB, we would not classify anybody with schizophrenia so we’re missing the 2% that are schizophrenic and get no false positives.
If you are willing to accept a test that is 97% reliable, then you will get false positives 3% of the time. If you use the UPB, you're saying you won't accept false positives. When the conditional hypothesis assumes a 'normal' population, then why would you want to accept false positives. Two questions for you: (1) According to Shandin, the true probability of getting a false positive is around 60%. Does that mean if the test were conducted twice on the same individual that the likelihood of that person getting a false positive 36%. (2) For the posterior distribution you graphed, you've said that the cumulative porbability for p<=1/2 of 10^-11 is a level you consider too low to be likely. IOW, you reject it. Now the cumulative probability for p=.1, or p=.2 or .3 or .4 would all be lower. Would you reject those probabilities as well?PaV
December 7, 2008
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I have to clarify the following as well or someone will misunderstand [329]: "If the sequence can be produced by a simplistic process then its only the probability of that simplistic process that is relevant, IMO - not the uncompressed length of the output." By simplistic process I don't mean flipping a coin. I mean any simplistic process that could generate the string 100% of the time. "Necessity" in ID parlance.JT
December 7, 2008
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gpuccio: another clarification [329] I wrote: That I believe is where the argument from ignorance comes in in ID. Dembski would grant that “Sure a mechanism could cause this - but if you think there is one, you have to point it out, otherwise we’re going to assume its Intelligence”, where for him, Intelligence is something other than mechanism (or at least historically it has been for him). Sometimes I think I actually agree with Dembski, and he is just incapable of expressing his ideas in a succinct way. I understand, as I alluded to in 316, that if you trace back the mechanistic causes for something, that you will eventually hit something that wasn't caused by a mechanism. At that point I do agree that all you have left as an explanation is blind chance or something else. If ID want's to call this "something else" "Intelligent Design" that's fine. But that doesn't mean humans themselves operate on the basis of some nebulous unspecifiable thing. And let's be clear - for ID, Intelligence is unspecifiable as it cannot be characterized as a mechanism for them. And just to repeat what I said in 316, whatever that first cause is it could have just existed forever, so you don't even have to invoke "Intelligent Design" as a cause for it. OK that's it hopefully.JT
December 7, 2008
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clarification: I said: "If the sequence can be produced by a simplisitic process then its only the probability of that simplistic process that is relevant, IMO - not the uncompressed length of the output." I meant that that is what is relevant in reality, not the design inference. But I guess you've given me some information I solicited previously if you're confirming that the size (in bits) of a process capable of generating a string is not relevant in I.D, only the uncompressed length of the generated string itself.JT
December 7, 2008
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Sal Gal[321], Let me repeat Demsbki's answer: we rule out all hypotheses with p>1/2 by taking Caputo's word (my emphasis because I think it's pretty weak). My answer is that we can't rule out all these hypotheses but it doesn't matter, because he could also have cheated by using nonuniform chance. There is no need to insist on ruling out all chance hypotheses and infer "design" but that's what the EF insists upon.Prof_P.Olofsson
December 7, 2008
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tribune7[323], You say that they are, Dembski says that they are not. I can only conclude that you disagree.Prof_P.Olofsson
December 7, 2008
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StephenB[320], No hurt feelings here. Now, you write
The original point of the EF exercise was, after all, was to show that that, regardless of the method he used, Caputo was almost certainly cheating
which is still not true. The original point was to ask how the EF is applied. As it requires all chance hypotheses to be rejected, (1) how do we reject those with p>1/2 and (2) why do we need to? I have now repeated the two questions many times. Any answers?Prof_P.Olofsson
December 7, 2008
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gpuccio [326]: Thanks for your thoughtful reply. Dembski considers all forms of specification. Compressibility is one of them. A sequence like the one you cited is highly compressible. Highly compressible sequences are a tiny subset of the whole search space, and are easily recognizable by intelligent beings. As far as I can see (and do correct me if I'm wrong by giving specific quotes) the only type of specification that Dembski mentions in that entire paper (the one he mentioned above and which I've made repeated reference to) is compressibility. They are specified and, if complex, they cannot come out of purely random causes. Its not a matter of them being complex. If they're of a certain uncompressed length and described by a simple pattern, then to Dembski they're created by something other than chance and Dembski's term for "Not chance" is "Intelligence". I understand that you have your own interpretation of what he says - I don't think its what he says. In that case we have to consider the whole complexity of the sequence, and not the “compressed” complexity. In other words, you will never obtain that sequence of 01 by flipping a fair coin. If the sequence can be produced by a simplisitic process then its only the probability of that simplistic process that is relevant, IMO - not the uncompressed length of the output. But the problem with compressible sequences is that they can often be the product of necessity. that would be the case if the sequence of 01 were the output of a computer program. So, to define such a sequence as specified one must be sure that no necessary cause is present. That I believe is where the argument from ignorance comes in in ID. Dembski would grant that "Sure a mechanism could cause this - but if you think there is one, you have to point it out, otherwise we're going to assume its Intelligence", where for him, Intelligence is something other than mechanism (or at least historically it has been for him). I think that Dembski correctly analyzes all forms of specification because that’s important for his general theory. Moreover, compressible sequences are specially interesting for the fact that they are easily recognized by consciousness. They're also recognizable by mechanisms, if by "recognize" you mean a change in behavior closely correlated with encountering some specific compressible sequence. If you mean "have a subjective experience of the sequence", well who knows what that means. But I hope you didn't mean that humans have some general ability to distinguish compressible sequences from non-compressible ones, because no such ability exists anywhere. But, that said, we must remember that all that has no real importance for the question of biological information. In fact, the specification in biological information is of the functional type, and is not linked to compressibility. Functional specification is much easier to treat, and can easily be considered out of the range of necessary laws. It bears no relationship to compressibility. So, functional sequences are really pseudo-random: only their functional meaning in a specific context defines them as “different”. To the best of my knowledge, you are absolutely wrong on this. The only type of specification that Dembski considers is compressibility. IOW, that is what he is exploiting for the purpose of his specific arguments. The only thing relevant about "biological information" from the standpoint of Dembski's arguments is that such information is compressible. I stand ready be corrected if you can provide specific quotes from that paper (which after all he identified in this thread as the most up to date statement regarding what CSI is all about.) Note: I'll carry this discussion on for as long as you want I guess. I had statements I wanted to make previously - I sincerely hope they were comprehended. I am certainly willing to clarify them. I should be willing to defend them as well, but its not like I'm itching for a debate. (Note: I have idea how the formatting of this will turn out because I'm not getting the preview function currently.) RegardsJT
December 7, 2008
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gpuccio, Quick response. I'll check back in the wee hours.
Functional specification is much easier to treat, and can easily be considered out of the range of necessary laws. It bears no relationship to compressibility.
You've strayed onto my turf. Dembski is not the only one who has his uses for Seth Lloyd. Even taking gravitational degrees of freedom into account, Lloyd bounds at about 2^400 bits the information storage capacity of the known universe. Let's consider a physical box that takes seven 64-bit numbers as inputs and supplies a single 64-bit number as output. There are (2^64)^(2^448) possible functions implemented by the box. It follows from basic coding theory that almost all of those functions require about 2^454 bits to encode, no matter how clever you are with the design of the code. That is, for a fixed representation, almost all functions are incompressible in the sense that the description of the function requires about as many bits as an explicit listing of all the input-output pairs. Only a minuscule fraction of the functions "fit" in the known universe. With some technical argument, I can get to the statement that the box can implement only functions with highly compressible descriptions. (The technical mess relates to non-uniqueness of the representation, and that different functions have descriptions of different length in different representations.) Now there is nothing exceptional about the class of functions I just described. And when you speak of biological function, you are not that far removed from my physical box. Perhaps you meant something I did not understand. But I have just shown that implemented functions have highly compressible specifications (descriptions).Sal Gal
December 7, 2008
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tribune7,
So why do we axiomatically rule out design when dealing with proteins, flagellum etc.?
In 321-322, I challenge the notion that there can be any empirical basis for saying that something that is not empirically observable causes the empirical distribution to deviate from the average. In the scenario of an indifferent creator of distributions, the uniform distribution is no more likely than any other. One must actually violate the Principle of Indifference to say that the data should be distributed in one way, and not another. You have to bring something non-empirical to the table to argue that empirical distributions should "look" one way and not another. Juergen Schmidhuber is well aware of this. He applies a speed prior in inductive learning of programs to describe data and solve problems. This amounts, in his mind, to saying that the Great Programmer does things in a particular way, and he owns up to it as an essentially religious belief. This brings me back to something I have said in various incarnations at UD -- empirical science and logic will never "prove" the existence of the non-material. It should be evident at this point that I know a fair amount of math and science. I am here to say that the only important things I know are unspeakable absurdities. They are a matter of private experience, not empirical observation or proof. I object strenuously to the devaluation of knowledge that is not of a sort that permits public argument for its correctness.Sal Gal
December 7, 2008
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JT: Dembski considers all forms of specification. Compressibility is one of them. A sequence like the one you cited is highly compressible. Highly compressible sequences are a tiny subset of the whole search space, and are easily recognizable by intelligent beings. They are specified and, if complex, they cannot come out of purely random causes. In that case we have to consider the whole complexity of the sequence, and not the "compressed" complexity. In other words, you will never obtain that sequence of 01 by flipping a fair coin. But the problem with compressible sequences is that they can often be the product of necessity. that would be the case if the sequence of 01 were the output of a computer program. So, to define such a sequence as specified one must be sure that no necessary cause is present. I think that Dembski correctly analyzes all forms of specification because that's important for his general theory. Moreover, compressible sequences are specially interesting for the fact that they are easily recognized by consciousness. But, that said, we must remember that all that has no real importance for the question of biological information. In fact, the specification in biological information is of the functional type, and is not linked to compressibility. Functional specification is much easier to treat, and can easily be considered out of the range of necessary laws. It bears no relationship to compressibility. So, functional sequences are really pseudo-random: only their functional meaning in a specific context defines them as "different". We can call functional CSI as FSCI (functionally specified complx information). That is obviously a subset of CSI proper, but practically the only subset which is really relevant for biological issues.gpuccio
December 7, 2008
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Thus there is no empirical basis for inferring intelligent design here. That would only be because it involves New Jersey. We should be polite and simply refer to it as design. :-)tribune7
December 7, 2008
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tribune7, it was Dr. Dembski himself who said above that chance, design and necessity are not mutually exclusive. My guess is that was his euphemistic way of saying he finally realized that design and necessity are indistinguishable (with necessity being his term for mechanism).JT
December 7, 2008
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tribune7,[315], Sorry, I don’t quite understand your quasi-semantic point. You said chance, design, necessity are not mutually exclusive. They are. While something could have come about by a combination of chance/design/necessity the part that came about by chance did not come about by design, and vice versa. So chance could have come about in the development of the flagellum as we know it without ruling out design. So why do we axiomatically rule out design when dealing with proteins, flagellum etc.?tribune7
December 7, 2008
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A related note for readers familiar with Dembski's technical papers: Dr. Dembski likes to invoke the Principle of Indifference to justify his analyses in terms of uniform distributions on sample spaces. But the idea in that principle is that a modeler in some sense "adds information" if s/he arbitrarily selects another distribution. To my knowledge, Dembski has never attempted to justify turning the Principle of Indifference on its head and asserting that something has "added information" to the data-generating machinery if the distribution of the data diverges from the uniform. Now reexamine what I said about Caputo, keeping in mind that his choice of data-generating machinery may in fact reflect indifference to making the random distribution of the data equal to a particular distribution. The uniform distribution is just the average of all distributions. If the actual distribution is not average, why should we attribute this to intelligence rather than indifference?Sal Gal
December 7, 2008
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Suppose that New Jersey law called only for random ordering of candidates' names on the ballot, and that Caputo used an American roulette wheel as Prof. Olofsson indicated (Republican first if and only if the outcome is 00). Then Caputo satisfied the letter of the law. Our feeling that Caputo violated the spirit of the law indicates our biased interpretation of "random" as "uniformly at random." We can argue that he "added information" only by invoking our bias in favor of the uniform and by imputing intention to Caputo as an agent. Consider that any formal calculation of CSI cannot take properties of an intelligence into account, and that swapping the Democrats and Republicans on the ballots cannot change the CSI. Why would we not convict Caputo for violation of election law if he listed Republicans first 40 times, and a Democrat first just 1 time? He would in fact be guilty if he believed mistakenly that the second position is better for the candidate. If he did not believe this, then was he inept, or was he capricious, in the performance of his duty? The only way to know if Caputo caused the probability of listing a Republican first deviated from .5 by intelligent design is to read his mind. Thus there is no empirical basis for inferring intelligent design here. By the way, if you did not know that ignorant voters tend to select the first candidate on a ballot, would you not be inclined to say that the one anomalous ballot was an error?Sal Gal
December 7, 2008
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Professor O: I am sorry if I upset you. It was not my intention to hurt your feelings. The objective was simply to call attention to the fact that it is possible to obsess over the math and lose track of the reasons for using it. The original point of the EF exercise was, after all, was to show that that, regardless of the method he used, Caputo was almost certainly cheating. Your example made it appear that he may well have been innocent and that he could have used a perfectly valid method for arriving at his skewed result. Obviously, that is not the case, and since we all now agree that your example was inappropriate, nothing more need be said. So I will be happy to withdraw my comment about your objectivity, since it is not needed to make the point. We will just shrug it off as on oversight.StephenB
December 7, 2008
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tribune7,[315], Sorry, I don't quite understand your quasi-semantic point.Prof_P.Olofsson
December 7, 2008
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correction: you will eventually have to hit a point of origin, where nothing preceded it by blind chance or something else should read: you will eventually have to hit a point of origin, where nothing preceded it but blind chance or something elseJT
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