Durston Cont’d

_{Barry Arrington

February 3, 2009

Intelligent Design}

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Kirk Durston‘s Thoughts on Intelligent Design

In this thread, I would like to lay out my own thinking regarding a method to detect or identify examples of intelligent design. I then would like to unpack my thinking in a slow, meticulous (pedantic perhaps?) way and, if we can get that far, apply it to a few examples, including a protein, and the minimal genome.

Defining ‘Intelligent Design’:

I commonly see the term ‘intelligent design’ used in two ways. An example of the first way is in a magazine headline I saw this morning:

‘Evolution by Intelligent Design’

The above example is similar to the way ‘planning’ is used in, ‘Success through good planning.’

In this sense, we can define Intelligent Design as the ability of a mind to produce an effect that both satisfies a desired function or objective and might not otherwise likely occur. This ability emerges out of what we understand to be intelligence, defined in <a href=”http://en.wikipedia.org/wiki/Intelligence”>Wikipedia</a> as the capacities to reason, to plan, to solve problems, to think abstractly, to comprehend ideas, to use language, and to learn.

The second way I see the term intelligent design used is:

‘That traffic control system is a beautiful example of intelligent design.’

The usage of ‘intelligent design’ in the above sentence is similar to the usage of planning in, ‘That rescue operation was an excellent piece of planning.’

In this second type of usage, we can define intelligent design as an effect that satisfies a function or objective and requires a mind to produce. Other examples of intelligent design are the Sphinx and the Microsoft Vista operating system.

In the first sense, ‘intelligent design’ is an ability and in the second sense, ‘intelligent design’ is an effect, or result of that ability.

With this in mind, the definition of intelligent design that I will be using in this discussion is as follows:

Intelligent Design: 1 the ability of a mind to produce an effect that both satisfies a desired function and might not otherwise occur. 2. an effect that performs a function and that requires a mind to produce.

I realize that there are other definitions out there, some of which I do not at all agree with (e.g., Wiki’s). In general, most of the definitions of intelligent design that I see are actually specific examples, applications or results of intelligent design, rather than the defining essence of intelligent design. Ultimately, what I want to argue is that examples of intelligent design all required a mind to produce. I then want to argue that intelligent design is the most rational explanation for the protein families and the minimal genome. I will pause here in case anyone wishes to raise a question about what I’ve covered thus far. Then I will proceed to the next step.

Comments

In the previous post, I presented Hypothesis H: a unique property of intelligence is the ability to produce significant levels of functional information. I then suggested that an essential property of functional anomalies is the functional information required to produce them. Thus, we have a link between intelligence and functional anomalies. We now need a method to quantify these functional anomalies in terms of functional information. In a recent paper in PNAS, Hazen et al, propose a method to measure the functional information encoded within biopolymers (Hazen, R.M., Griffen, P.L., Carothers, J.M. & Szostak, J.W. (2007) 'Functional information and the emergence of biocomplexity', PNAS 104, 8574-8581). This paper was an outcome of an earlier article in Nature in 2003 by one of the coauthors of the Hazen paper (J.W. Szostak (2003) ‘Molecular messages’, Nature Vol. 423, p. 689). Hazen's equation was almost identical to an earlier equation published by Leon Brillouin in 1951. In Hazen's equation, Functional information I(Ex) is defined as I(Ex) = - log2[M(Ex)/N] (1) where Ex is the degree of function x, M(Ex) is the number of different configurations that achieves or exceeds the specified degree of function x, ? Ex, and N is the total number of possible configurations, both functional and otherwise. For proteins, N is simple to compute, N=20^L where L= the length of the sequence. The problem, however, is computing M(Ex). In 2005 a paper was published that defined three subsets of sequence complexity. The three types were defined as ordered sequence complexity (OSC), random sequence complexity (RSC) and functional sequence complexity (FSC). At that time the authors were uncertain as to how to measure FSC. I contacted them with a method, and we went on to publish a paper proposing a measure of FSC . For both Shannon information and Kolmogorov information, an equivalent term is 'complexity' rather than 'information'. It is the same here. Functional complexity is equivalent to functional information. To check this, the more sophisticated equation for functional complexity presented in the Durston et al. paper can be simplified, with certain assumptions, to the Hazen et al. equation. The beauty of the Durston et al. equation, is that it can actually be evaluated using real data. I have found that if I have at least 500 aligned sequences, the sample size is starting to get large enough to adequately estimate M(Ex), although I prefer to work with at least 1,000 sequences for any protein family. For those interested in working with functional complexity, it is important to read the Durston et al. paper and get a firm grasp of the null state, the ground state, and the functional state. The functional complexity of a system is the change in functional uncertainty (defined in the paper) between the ground state and the functional state. The null state can be a special case of the ground state. Also, for basic properties determined by physics, the basic functional state is identical to the ground state, in which case zero functional information is required to produce the effect. This also holds true if the ground state is the null state. All objections I have seen result from a lack of understanding of these three states. The most common is a failure to note that if the functional state is the null state, then a vast number of possibilities are functional, but the functional information required is zero. As Abel and Trevors point out in their paper on three subsets of sequence complexity, there are only three major areas we have ever observed FSC. One is human languages, the other is human-designed software, and the third is in biopolymers such as DNA and proteins. Something to think about. We now have a method to measure functional information and can apply it to more than just sequences, but to many other artifacts, effects, and configurations as well, including uses in archeology, forensics, SETI, genetics and even suspected cases of fraud in lotteries and casinos. Once you have an estimate of M(Ex), you then have an estimate of the target size M(Ex)/N for the search. For functional folded proteins, that target size is miniscule, to the point of approaching zero for all normal scientific problems. Keep in mind, it is physics that determines which amino acid sequences have stable folds, not biology. So a biological search engine does not make proteins, it must find them and physics is the 'keeper of the combinations' that work. The next step in my method to detect examples of ID is to determine what the threshold is for nature, regarding how much functional information/functional complexity we might reasonably expect to observe within the 'noise' of the natural system. I'll pause here, however, to give people a chance to clear up any questions they may have.KD_{February 6, 2009
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gpuccio, At least you are with yourself completely.Prof_P.Olofsson_{February 5, 2009
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kirk: the previous post was obviously directed to you. It's the second time that I direct a post to myself by mistake. I am starting to be worried.gpuccio_{February 5, 2009
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gpuccio: I am with you completely. No problems up to now. And again, I like your references to "desire", which underline the role of a conscious intelligent "and" motivated agent behind the process of design.gpuccio_{February 5, 2009
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LOLOL, good one Professor O.tribune7_{February 5, 2009
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kairosfocus, You have outed Prof P as superman and as such 1000 bits of probabilistic power is nothing to the son of Sven to toss aside with a p=1.0. We need to find some kryptonite for such a powerful force.jerry_{February 5, 2009
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Prof PO: You are hereby officially outed as Superman II! (Should have thought a bit more before admitting to flying home to Sweden every night!) _______ Jerry: One more little point: FSCI does not come up for serious consideration till you are looking at 500 - 1,000 bits of info storage capacity. The latter is room for enough configs to be ten times the SQUARE of the number of quantum states of the cosmos' atoms across its lifetime. Chance based search sees a needle in a haystack problem on steroids. Reasonable minimal storage for life -- DNA -- ~ 300 k 4-state elements, 600 times the limit. So, the islands of function are credibly very sparse in the config space. Directly observed cases of FSCI all trace to intelligent design, e.g. longish posts in this thread. ________ Have fun all. GEM of TKIkairosfocus_{February 5, 2009
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tribune[30], Touche! The exchange reminded me of this oldie: http://www.youtube.com/watch?v=Xe1a1wHxTyo The "luxury" comments appears at 2:10. Sorry,I broke my promise to stay away but the thread is already so cluttered. I'll compile Kirk's comments in the end and read them through.Prof_P.Olofsson_{February 5, 2009
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KD, Thank you for you're efforts, I am following your posts with much interest. I don't want to dirty the water, but I can't help but notice how much more valuable to the process this conversation is, compared to recent material. It has been argued recently (even by people on this very thread) that design detection theory is of a lesser value if it doesn't address issues beyond the empirical evidence (such as the presence of evil in the world). I hope it becomes apparent (as if it is not already) that such claims are unecessary to design detection.Upright BiPed_{February 5, 2009
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and fly home to Sweden to care for my grandmother every night. I call BS!!! If your grandmother lives in Sweden you wouldn't have to care for her!!!!tribune7_{February 5, 2009
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Prof P, :Luxury! I have to work full time, study, run four families in different states, and fly home to Sweden to care for my grandmother every night.: Exactly what would you expect from a descendant of the mighty Sven. But not mocking. No that would make dear Sven turn in his grave. He had no need for that.jerry_{February 5, 2009
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KD, A similar discussion but not as theoretically organized as yours has been going on for some time here. It always revolves around the concept of FCSI or as kairosfocus uses FSCI. FSCI is easy to understand and the examples are powerful. The argument is that FSCI does not appear anyplace in nature except life. Now life is the issue under analysis so the argument goes, if FSCI has never been generated by nature at any level of complexity, how can one expect so much FSCI to develop in life. The answer is that life is the place where nature developed FSCI. They beg the question but to them that is the answer. They do point to the many ongoing research efforts that exist to show how life could have arisen with a cocky confidence that it is only a matter of time. They then go on to say that life which has FSCI creates new FSCI and all the complexity and function we see is the result of these processes working out over deep time. They provide no real data to support this but the answer is always the same, time will do it and the multitude of variation creation processes that change a genome is the basic mechanism and then natural selection leads to new FSCI. There is a certain logic to their arguments and is supported by the fossil record which shows the gradual increase in complexity and increasing diversity of life over deep time. That is the argument of the naturalistic thinkers simply stated. No real data but some circumstantial evidence as micro evolutionary processes exists and deep time cures all. So I do not know if your approach handles this. It sounds like it may handle an OOL ok but then the refrain will be the mantra "deep time, deep time" cures all once FSCI exists in life. I am sure you are aware of all this and it will be interesting to see how your work and ideas handle these objections. So far we like what we see.jerry_{February 5, 2009
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KD, Peter, kf, Luxury! I have to work full time, study, run four families in different states, and fly home to Sweden to care for my grandmother every night.Prof_P.Olofsson_{February 5, 2009
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KD @22
a unique property of intelligence is the ability to produce significant levels of functional information. Note that I have claimed that this property is 'unique' to intelligent agents. . . . Falsification of H: Out of the hypothesis H arises a prediction that can be falsified; mindless natural processes cannot produce significant levels of functional information. It follows, therefore, that the method that I will propose to detect examples of ID can be falsified. If anyone does not like the results of the application of my method, they have merely to falsify hypothesis H. At this point, some may be thinking that it will be easy to falsify H, but restrain yourself a bit longer until I have provided a definition of functional information.
If my understanding is correct, you are looking to mathematically quantify the limits of evolutionary mechanisms. I've long thought that this is a rich vein for ID research to mine, so I am looking forward enthusiastically to your definition. You're probably already planning on this, but your post doesn't make it clear whether or not you'll be providing positive evidence for your uniqueness claim or only predictions that could be falsified in principle. Either would be great, of course, but both would be extremely compelling. JJJayM_{February 5, 2009
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Dave, it's a shame there is not a private means of contacting each other as per FreeRepublic.tribune7_{February 5, 2009
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I guess classic design detection is something along the lines of the Explanatory Filter -- if physics can't explain it, and it couldn't happen by chance then it was designed. The problem of course is that it was found have found that for many things it was thought physical laws couldn't explain, they did. So a faith has somehow developed that the physical sciences can answer everything. OTOH, design indisputably exists. Suppose if we dump the EF as I think was discussed a few weeks back? As per Dembski, we start with a pattern first & if found to have a certain measured complexity we be be certain it is designed, after which it can be presumed that physics and chance could not have done it. This is not eliminative. It looks like Kirk is going to start with function first, which is interesting.tribune7_{February 5, 2009
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KD Like what I am seeing from you. Function-specifying complex information [FSCI] -- you and colleagues seem to have been thinking in terms of functional [as opposed to both orderly and random] sequence complexity -- is emerging in your discussion, in a very useful, empirically anchored way. I, too like the "anomaly" issue: it is not expected to see that -- it draws attention, it sticks out. It cries out for explanation per plausibly adequate causal forces, and that leads us to issues on inferences to best explanation over adequacy of mechanical vs intelligent causes on relevant aspects; the latter reflecting art as a possible force. [My own rather more modest remarks (esp. by comparison with that work in progress diss . . . I assume you are "writing up from Day 1") are in my always linked, esp. App 3 on FSCI and CSI and their roots in the 70's - 80's. If it will help you in getting a better expression than my rough notes, I also made some initial notes on functionality here.] Keep up the good work! GEM of TKI PS: I too have had to work full-time, study and try to run a family. (Sleep is the first thing that gets lost in that equation. You have my sympathy.)kairosfocus_{February 5, 2009
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To detect artifacts/effects that were likely to have required intelligence to produce, I have proposed that we must look for a special type of anomaly …. an anomaly that has some sort of function …. a functional anomaly. I have proposed that we will need two things: 1. method to measure some essential property of these functional anomalies and,? 2. a threshold within that essential property above which intelligent design is required. To do this, we need a link between the essential property of functional anomalies that we will measure, and intelligence. If you will look at the definition of intelligence, it has several properties. There is one property that I will focus on. It is an empirical fact that intelligence can produce functional information. I realize there may be some reservations about this concept of functional information, but please hold off on those questions until I have defined functional information (probably in my next post). At this point, I will propose an hypothesis as follows: H: a unique property of intelligence is the ability to produce significant levels of functional information. Note that I have claimed that this property is 'unique' to intelligent agents. The hypothesis does not suggest that mindless processes cannot produce any functional information at all but, rather, only insignificant levels within the 'noise' levels of those mindless systems. Some of you may notice that there is a beautiful symmetry about this. Before the effect existed, there was only the intelligence that desired and produced it. The intelligent agent had the ability to produce the functional information required to produce the effect that nature could not, with the result that a functional anomaly was formed. Later (whether we are looking at a signal from deep space, an archeological artifact, or a suspicious death in forensics) we see only the anomaly. We can then work backward to derive the signs of intelligence behind that anomaly by measuring the functional information required to produce it. Think about this for a bit; I believe it is quite powerful. Falsification of H: Out of the hypothesis H arises a prediction that can be falsified; mindless natural processes cannot produce significant levels of functional information. It follows, therefore, that the method that I will propose to detect examples of ID can be falsified. If anyone does not like the results of the application of my method, they have merely to falsify hypothesis H. At this point, some may be thinking that it will be easy to falsify H, but restrain yourself a bit longer until I have provided a definition of functional information. So to summarize this post, regarding (1) above, the essential property of functional anomalies that we will measure is the functional information to produce the anomaly. The threshold mentioned in (2) will be some level of functional information above which a mindless process will not be able to exceed with any reasonable probability. That level/threshold will need to be established in a future post. I'll pause here for queries before I proceed with a definition of functional information.KD_{February 5, 2009
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Kirk I like the concept of function design. It's meaning is a little clearer to me than specified complexity. My opinion has nothing to do with the fact that I am a Canadian. Also, "working full time in addition to being a full time Ph.D. candidate, plus having a family makes it difficult for me to post more often" I am working on a Masters 'full time' working full time, and have a family too. I almost understand what you are going through. My courses are at the PhD level. I thought universities do not allow PhD students to work full time. Should we keep this on the qt? :)Peter_{February 4, 2009
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Dave, that is a helpful point re. 'intelligent agency' A general comment: I welcome collegial criticisms/worries as we proceed. Folks like Prof. Olofsson, Mark and others are useful contributors in either exposing weak links or lack of clarity. My attitude is that the truth can withstand anything you can throw at it, although my grasp of the truth and ability to communicate it may be in dire need of improvement.KD_{February 4, 2009
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Kirk Just delete this comment after reading it. Use of the term intelligent agency to specify your first definition of "intelligent design" will disambiguate it. agent = the actor agency = the ability to act design = the act itselfDaveScot_{February 4, 2009
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Kirk: again, I agree with your points. Just let me point out that your concepts seem to be approximately the same, with different names, as the classical points in ID theory. In that sense, your concept of function seems the same as that of functional specification, but it is interesting how you link it to a "desire" of the intelligent agent, providing a teleological facet which is often overlooked. And your concept of "anomaly" is evidently linked in some way to the concept of complexity (in the sense of improbability) of the observed pattern. But calling it an "anomaly" is interesting in itself. I will have to think about that.gpuccio_{February 4, 2009
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Second Installment It would be helpful to construct a method that we could use to detect effects that have been produced by intelligent design (definition 1), so let us think about that for a minute. We cannot know what sort of art other intelligent agents might like, or what they would consider to be a good design. There is one type of circumstance, however, where all intelligent agents must exercise their ability for intelligent design. It occurs when the agent desires some function or objective and the physical system is not likely to cooperate by producing it. The agent then exercises that ability and what results is not only an example of intelligent design (definition 2), but an anomaly within the physical system. It is anomalous in virtue of the fact that the physical system was not likely to produce it. For example, an observer gazing at the skies between AD 1000 and the present, would have seen an empty sky save for the usual clouds, birds, etc. However, early in the 20th century, the observer would have seen something anomalous, an aircraft. People desired a function or held an objective to fly. Nature did not seem very helpful in satisfying this objective, so humans exercised their ability for intelligent design (def. 1) and produced a piece of intelligent design (def 2) that would fulfill that function. The resulting aircraft in the sky was an anomaly within the physical system. The less likely nature is to satisfy some particular desire or objective of an intelligent agent, the greater the requirement for intelligent design and the greater the resulting anomaly. Conversely, the more likely nature is to supply the desired function or meet the desired objective, the less the need for intelligent design (def 1). The intelligent agent can still exercise her or his ability for intelligent design, but the resulting effect will only be a small anomaly within the physical system. In general, we can think of examples of intelligent design as: 1. having a function of some sort even if we are unsure as to what it is 2. anomalous, to varying degrees, within the physical system Intelligent design can mimic nature, in which case the physical system can satisfy the objective and the resulting effect produces no anomaly at all. For this reason, among others, I will not concern myself with trying to detect all effects that are products of intelligent design. Rather, I will focus only on detecting those examples of intelligent design where intelligent design (def 1) was required. To do this, I will need to do two things: 1. provide a method to measure some essential property of these functional anomalies and, 2. establish some sort of threshold beyond which intelligent design is required. By 'required' I do not mean that it would be nomologically or logically impossible for nature to produce the effect. I merely mean that the probability that nature could produce the effect becomes so low within the boundary conditions of the problem that the intelligent agent must exercise intelligent design (def 1) and it would be irrational to believe otherwise. I'll pause here in case anyone wants clarification on anything. I'll try to post at least once every couple days (working full time in addition to being a full time Ph.D. candidate, plus having a family makes it difficult for me to post more often). If we can get past this post, then I will focus on (1) above in the next step.KD_{February 4, 2009
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"Kirk, I will follow your thinking to the end and not interrupt. If we open the debate already, you’ll never get through!" Prof O actually I think before going any futher it would seem to me Kirk would want to know if anyone agrees or disgrees with his opening statement before going any further. One step at a time Vividvividbleau_{February 3, 2009
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Prof. Olaf...I just read your chance.pdf paper. I'm happy to be corrected, but it seems you sell Prof. Behe short. The reason he can claim that NO mutations of probability 10^-20 will occur in a population of 10^12 individuals is because he and other biochemists are acquainted with known mutation rates per generation. Nowhere do I see the mention of mutation rates (which, in your example, might be akin to knowledge of how frequently individuals actually play the lottery) in your paper. It would seem that some knowledge of the underlying biochemical processes would be useful before running through these probability calculations.WeaselSpotting_{February 3, 2009
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Color me clueless. (Don't get old.)Adel DiBagno_{February 3, 2009
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Microsoft design would probably need a scientific theory of its own, to be explained! :-) LOL Adel, I'm confident to almost 10^150th that Barry's letting him use his name.tribune7_{February 3, 2009
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gpuccio:
Kirk, very clear and well said.
Where? When? As best I can tell, Kirk Durston hasn't made a peep on this thread.Adel DiBagno_{February 3, 2009
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trib: Microsoft design would probably need a scientific theory of its own, to be explained! :-)gpuccio_{February 3, 2009
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GP, I propose a caveat: Microsoft design does not mean intelligent design :-)tribune7_{February 3, 2009
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