Mathematically Defining Functional Information In Biology

_{January 28, 2009

Intelligent Design}

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Lecture by Kirk Durston, Biophysics PhD candidate, University of Guelph

[youtube XWi9TMwPthE nolink]

Click here to read the Szostak paper referred to in the video.

HT to UD subscriber bornagain77 for the video and the link to the paper.

Comments

DaveScot[289],
I think you’re raising natural selection to some exalted, mysterious status it doesn’t deserve. You called it reproduction and selection and said Dembski doesn’t treat it properly.
No I'm not. They're not mysterious. I only pointed out that Dembski's shopping cart model don't take them into account. I find this simple point hard to argue against. In fact, an ID supporter on this blog agrees with me (and I have also honestly admitted that I don't have a better model to suggest). Dembski does not suggest any evolutionary scenario that warrants his model so he can hardly claim to have rejected an evolutionary hypothesis.Prof_P.Olofsson_{February 3, 2009
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So even if we find an account of the evolution of the flagellum through RM+NS it is still also possible that the flagellum was designed. Do you deny this? Mark, if we should ever find this to be the case we would falsify the aspect of ID known as IC. We would not falsify God. You are conflating ID with God. They are not the same. ID is not faith.tribune7_{February 3, 2009
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Prof O I think you're raising natural selection to some exalted, mysterious status it doesn't deserve. You called it reproduction and selection and said Dembski doesn't treat it properly. What you describe is nothing more than a simple process used purposely in all kinds of situations. It's called "trial and error". The trials are generated by reproductive events and the errors are evaluated by natural selection. It's a simple search algorithm. Its power lies in big numbers - many trials conducted in parallel (populations) with many serial iterations (generations). For an organism like a bacteria the simultaneous trials number in the trillions and the number of iterations over deep time in the billions. Recombinationm, horizontal gene transfer, and a changing environment complicate matters which is why many of us prefer to focus on asexual microbes and basic mechanisms found in all organisms like the ribosome. In that case recombination is not a complicating factor and neither is the external environment. By far the best evaluation of the capabilities of trial and error with big numbers is the discussed in Behe's book "The Edge of Evolution" with the malarial parasite. Its successful and unsuccessful responses to various intense manmade and natural selection pressures is quite illuminating. Those responses also fall in line quite well with the limits predicted by the probabilistic resources (mutation rate, population size, and generations). The math and the biology is all simple, tractible, and most importantly the predicted result was essentially the same as the actual result.DaveScot_{February 3, 2009
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Barry stated in response to the request for a new thread under tighter constraints; A new thread will be started. Kirk is working on the opening.bornagain77_{February 3, 2009
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Gpuccion [#281] I only used God as an example (actually you introduced him/it in #261). All I am saying is - how do you know the designer is not responsible for any given phenomenon on earth if you don't specify the powers and motivation? As Dembski (correctly) explains - the explanatory filter can give false positives. So even if we find an account of the evolution of the flagellum through RM+NS it is still also possible that the flagellum was designed. Do you deny this? On what grounds would you prefer the RM+NS account? Bfast may describe this as "yapping in the philosophical ether" but it seems to me to go the essence of what is wrong with ID. By avoiding "how" and "why" it gives no scope for assessing it. All it does is rely on other theories failing to account for things.Mark Frank_{February 2, 2009
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http://pandasthumb.org/archives/2009/01/durstons-deviou.html As you guys probably know, PZ posted a response to this talk to the Panda's Thumb blog.Havermayer_{February 2, 2009
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gpuccio @283
We recently had a more private, long, focused and rather civil and satisfying discussion about CSI and its calculation on Mark’s personal blog, with the contribution of many good willed people from both sides (including Mark and R0b). You could probably find some interesting input there, whatever your position may be.
I found the discussion using the search terms you specified, thank you. Unfortunately, the outcome of the discussion appears to be that no one knows how to objectively compute CSI in even short bit strings, let alone real world biological constructs. At the risk of sounding like a broken record, this reinforces my view that the most fertile ground for ID research is in the limits of the mechanisms proposed by modern evolutionary theory (MET), and the disconnectedness of viable regions in genome space. JJJayM_{February 2, 2009
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IN CASE ANY ADMINISTRATORS ARE LISTENING, EVERYONE WANTS A NEW THREAD SO THAT KIRK DURSTON CAN EXTEND HIS CASE. It's a real live grass roots movement---honest!StephenB_{February 2, 2009
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B L Harville (# 278): We recently had a more private, long, focused and rather civil and satisfying discussion about CSI and its calculation on Mark's personal blog, with the contribution of many good willed people from both sides (including Mark and R0b). You could probably find some interesting input there, whatever your position may be. Just google "Mark Frank" and "Clapham Omnibus" and you will easily find it.gpuccio_{February 2, 2009
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bornagain: "DaveScot, Barry or any admin listening, Kirk Durston Has requested to start a new thread under his video lecture, that could somehow be more tightly constrained so as to be more productive and less messy." I would appreciate that too. And with the premise (or assumption, as we like) that the post stays, as far as possible, technical and focused.gpuccio_{February 2, 2009
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Mark: "Do you think that God is not capable of simulating an apparently perfect spontaneous and unguided process? Or are you saying that God would not want to do it? If you don’t know then of course it is possible." But ID theory in itself has nothing to do with the concept of God. We require a designer whose working can be "objectively" inferred. If that's not the case, we may still have a God, but we no more have an ID designer, and we no more have ID. Kenneth Miller will be happy, and I will be very, very unhappy. So, as you see, ID is taking all the responsibilities for its theory. If we lose, we lose, and if we win, we win. The game is open, and absolutely fair. Some of your objections could perhaps be valid for some form of creationism. But ID is not creationism. If you, who are intelligent and sincere, still do not acknowledge that, after all our discussions, I must really be a very bad interlocutor.gpuccio_{February 2, 2009
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R0b: Indeed, you are not treating me very fairly :-) In # 240 you reduce all to how we disambiguate things, after I have tried my best not to be ambiguous, and then you propose to calculate CSI on crystals and mandelbrots, when a very non ambiguous point in my post was: "Many times, even with you, I have suggested that, for operational reasons, we stick in our discussions of a very generic nature about ID to some very simple and unequivocal definition of CSI. As you know, my favourite one is “any string of digital information which is functionally specified (that is, for which a function can be explicitly described in a specific context) and which has a complexity (improbability of the target space) which certainly is lower than a conventional threshold (which for a generic discussion we can well assume at 1:10^150)." Where are crystals and mandelbrots a "string of digital information which is functionally specified"? I try to disambiguate things, but it seems to me that you don't cooperate... and then in # 264, you attribute to me Stephen's post (Steve, I appreciate being associated with you too, but maybe we have worked too much together recently, and have lost our separate identities?) :-) Never mind, we can always disambiguate that! :-)gpuccio_{February 2, 2009
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Mark Frank:
How would you know that intelligence had not been involved? Whatever series of events you observed they may have been designed."
Its time for you to think simply, fact-based, rather than yapping in the philosophical ether. If all evidence was consistent with a non-designed universe and biology, then there would be no good reason to hypothesize a designer. Further, any evidence that is nicely explained by non-guided means should be, and is by the majority of IDers, considered to be the product of unguided forces. So only one question remains, is there any data that is a poor to terrible fit with the available understanding of what is plausible via unguided means? Let me suggest two obvious places to look: 1 - The finely tuned big bang, 2 - the orgin of life. Do I need to list the multitude of other places to look? Now, if you can honestly suggest that the current unguided explanations for these phenomena are in any way plausible, reasonable and adequate, then you have information that should rightly shut down the entire ID movement. If not, however, I ask this, How do you know that intelligence was not involved in these phenomena -- in light of a dearth of plausible alternative explanations?bFast_{February 2, 2009
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I see numerous references to "CSI" on this website but I can't find any demonstration of a calculation of "CSI." Could someone please provide one? Thanks in advance.B L Harville_{February 2, 2009
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You might accept that ID was wrong – Mark, ID is a methodology. It is not my faith. ID could turn out to be completely unsustainable. I have no problem with that. It's not going to affect my faith. I think that's true for most of us here.tribune7_{February 2, 2009
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kairofocus: Thanks for your response, you state in post 228, "I suspect the issue over length vs fits has to do with degree of isolation: a more hard to find island of function has more info in it" The correlation being that the more functionally complex a protein is the more it will contribute to its rarity and thus to its required information content. Thus, I believe this answers my question in that this equation is not sensitive enough to provide the measure needed for Genetic Entropy on the single protein-mutation scalebornagain77_{February 2, 2009
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Great idea, JayM. I put it on the FAQ thread.tribune7_{February 2, 2009
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OK, Professor, thanks. Dittos to BA77's suggestion for a new thread for Kirk.tribune7_{February 2, 2009
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tribune7 @268

How many ID papers and research proposals have been rejected? That’s not a rhetorical question.
I’m pulling this one out so it doesn’t get lost. It’s a subject that’s often discussed here ROb.
This came up in a different thread, but got lost in the noise. Is there a website somewhere with ID friendly papers that have been rejected by mainstream, peer-reviewed journals (preferably with some indication as to why they were rejected)? That would be a great resource. JJJayM_{February 2, 2009
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Gpuccion [261] Me: “How would you know that intelligence had not been involved? Whatever series of events you observed they may have been designed.” Gpuccion: Well, again I cannot agree with you on that kind of argument. You have no faith in the objectivity and serious scientific approach of us IDists! This is nothing to do with your integrity and seriousness. I am convinced that you (singular) have both. It is a logical consequence of the ID position that the designer has undefined powers and motives. You might accept that ID was wrong –but why? It would be illogical to do so unless you have some knowledge of the powers and motives of the designer. Do you think that God is not capable of simulating an apparently perfect spontaneous and unguided process? Or are you saying that God would not want to do it? If you don’t know then of course it is possible.Mark Frank_{February 2, 2009
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DaveScot, Barry or any admin listening, Kirk Durston Has requested to start a new thread under his video lecture, that could somehow be more tightly constrained so as to be more productive and less messy.bornagain77_{February 2, 2009
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tribune[267], By Bayes' formula, the probability of guilt given the evidence, P(D|E), equals P(E|D)*P(D) / [P(E|D)*P(D)+P(E|C)*P(C )] In the court example we have P(E|D)=1 so P(D|E) equals P(D) / [P(D)+P(E|C)P(C )] so if P(E|C), the probability of the evidence under the innocence assumption, is extremely small, 1/n for some huge n, and P(D) is as small, the resulting probability P(D|E) is about 1/2.Prof_P.Olofsson_{February 2, 2009
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-----Rob: “I’m not suggesting that you accept arguments from authority. My point is relevant only if you care whether the so-called authorities eventually accept ID. I’m suggesting that if you do care, then you might want to consider whether the larger scientific community accepts your premises before you base your arguments on them.” Rob, those comments come from me not from GPuccio. I appreciate being associated with him, but I don't think we should hold him accountable for my words. In any case, here we go: We don’t want affection, approval. or appreciation from the "scientific community" at the moment. We will settle for the freedom to define our own terms, fashion our own paradigms, and establish our own methods. At a bare minimum, we would ask that the academy, the press, and the United States court system to stop lying and to desist from characterizing ID as a faith-based initiative when its methods are clearly empirically based. Apparently you haven’t noticed, but the scientific community is not open to any other premises than those embedded in their own paradigm. They have made that clear thousands of times. Are you aware of the fact that the Kansas City school system has established Darwinism as the only possible answer to the question of origins? On the other hand, neo-Darwinists proponents will not subject themselves to scrutiny from the other side. They can’t defend their position and they know it. They visit here only to criticize ID; they never provide a rational justification for their own position. They only show up on a thread like this. When the subject matter requires a defense of chance based evolution, they head for the tall grass. That goes for all of them, astronomers, STATISTICIANS, biologists, you name it. ----“In your eyes, the rejection of ID is the fault of the mainstream scientific community, the so-called authorities who have long since lost their credibility. You say: ‘Evolutionary biology is a monolithic monster that survives solely by misinforming the public about the current status of evolutionary theory and by attempting to discredit ID scientists even to the point of slander.’ ----“You might want to consider an alternate point of view: Maybe ID has simply failed to do the requisite science.” According to whom? Do you not realize that you are, once again, bootlegging the argument from authority into the discussion? Are you not aware that all progress comes from the minority and that the majority must always be dragged in kicking and screaming? In any case, which sector of the scientific community do you grant the right to define science once and for all? Is it that sector that is currently arguing that obesity is contagious and that if you don’t watch out, you will “catch it?” Or, is it the group of life scientists that seek to clone humans as sex slaves? Perhaps you will give the nod to NASA researchers who promote global warming and continually go back to touch up their past reports to make the numbers look good. Perhaps you had better identify which scientific community you refer to and explain to me where they get their authority to define science and is methods. For my part, the “scientific community” needs watching a lot more than we do. -----‘I know that some scientists are jerks, although I don’t know that the number is disproportionate. I’d be surprised if ID proponents had never been treated unfairly, but how systemic is that treatment? How many ID papers and research proposals have been rejected? That’s not a rhetorical question. Nothing personal here, Rob, but I am beginning to think that you are joking. Where were you when Baylor closed the door on Dr. Dembski and Dr. Marks? Where were you when Dr. Behe’s associates at Lehigh decided that they would never even speak to him again if they saw him in the hallway? Where were you when Dr. Gonzalas was refused tenure at Iowa State simply because he accepts and researches the “anthropic principle.” The problem is systemic in every way imaginable. Just so that you will know, 95.8% of evolutionary biologists are either agnostics or atheists, and, yes, we do have the data to support that. Is that disproportionate enough for you?StephenB_{February 2, 2009
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How many ID papers and research proposals have been rejected? That’s not a rhetorical question. I'm pulling this one out so it doesn't get lost. It's a subject that's often discussed here ROb.tribune7_{February 2, 2009
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Not necessarily. You can have an extremely low P(D|C) but if P(D) is also extremely low, these numbers work against each other. OK, I thought I was keeping up but you lost me on this one. How so?tribune7_{February 2, 2009
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The intuitive argument here is that we cant’ just compute the probability of double SIDS and base our conclusion on that. I agree. We need to compare the chance of a double SIDS to the chance of double infanticide. One of the problems with SIDS is that it is used as a cover for infanticide and child abuse.tribune7_{February 2, 2009
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trib[260],
Professor — Distilled argument: If P(E|D) is n times as large as P(E|C), you cannot conclude that P(D) is n times as large as P(C ). I’ll agree but if n is large enough it should still make you hmmmm.
Not necessarily. You can have an extremely low P(D|C) but if P(D) is also extremely low, these numbers work against each other.Prof_P.Olofsson_{February 2, 2009
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gpuccio:
You must be very new here, so I will try not to be unduly harsh.
Thanks. I'm a very sensitive soul.
Suffice it to say that we don’t accept arguments from authority on this site, because the so-called “authorities” have long since lost their credibility.
I'm not suggesting that you accept arguments from authority. My point is relevant only if you care whether the so-called authorities eventually accept ID. I'm suggesting that if you do care, then you might want to consider whether the larger scientific community accepts your premises before you base your arguments on them. In your eyes, the rejection of ID is the fault of the mainstream scientific community, the so-called authorities who have long since lost their credibility. You say:
Evolutionary biology is a monolithic monster that survives solely by misinforming the public about the current status of evolutionary theory and by attempting to discredit ID scientists even to the point of slander.
You might want to consider an alternate point of view: Maybe ID has simply failed to do the requisite science. I know that some scientists are jerks, although I don't know that the number is disproportionate. I'd be surprised if ID proponents had never been treated unfairly, but how systemic is that treatment? How many ID papers and research proposals have been rejected? That's not a rhetorical question.R0b_{February 2, 2009
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gpuccio[261],
Personally, I find that even Dembski’s model of the shopping cart is not a very satisfactory approach (on that, I have to agree with Prof. Olofsson). But the fact that something is difficult to model does not in any way mean that it does not exist.
In return, I agree with you. And as I mentioned in some post above, I don't know what type of calculations we would get from a model based on evolutionary theory. I can spot the flaws in disregarding selection and reproduction in Dembski's model, but I cannot offer a specific better alternative.Prof_P.Olofsson_{February 2, 2009
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tribune[259], You can read about the Sally Clark case on your own, there's a lot of stuff online. It's a sad story. The intuitive argument here is that we cant' just compute the probability of double SIDS and base our conclusion on that. We need to compare the chance of a double SIDS to the chance of double infanticide. Both happen, both are rare, so we need to compare how rare they are. Bayes' formula allows us to do the formal computations.Prof_P.Olofsson_{February 2, 2009
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