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

https://www.youtube.com/watch?v=XWi9TMwPthE

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

jerry[319], Yes, "behind my back" was a joke, of course. Yes, I find the discussion interesting, for the most part. No, I do not have such secret beliefs but I try to take your arguments at face value. As for my criticism, I agree that it is mostly "negative" but when claims are made by ID supporters that certain mathematical and statistical arguments discredit evolutionary theory, and I find these arguments erroneous or unconvincing, I comment. Just like a lot of ID activity is directed at criticizing evolutionary biology. We're all chipping in here and there, on both sides. I'm up for a couple of cold ones any time. You know where to find me, deep in the heart of Texas!Prof_P.Olofsson_{February 4, 2009
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JayM[318], Yes, there are some gently mocking comments but they are intended to be friendly. I do not intend to ridicule anybody or anybody's beliefs.Prof_P.Olofsson_{February 4, 2009
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Prof_P.Olofsso, you said "I didn’t know this thread was still going on. Are you talking about me behind my back?" No what I said about you in my comment I already said to you last week and knew fair well that you might still see it. The comment list on the main page is not a good indication of what has been said as it moves so fast. You also must remember the direct comment to you last week: "I do detect a small lack of constructive criticism on your part. Yours is one of pointing out the flaws in other’s arguments, which is well and good but I do not see any attempt at helping others how to solve the problem other than your criticism. For example, can the problems you raised in the past about the flagellum be solved or ameliorated somewhat if there were probability estimates of the number of potentially functional proteins from the totality of possible proteins. Now I do not know enough about the technicalities of either probability theory or the behavior or random polymers of amino acids to make any intelligent assessment but I bet that there are some that do. By the way I have hardly read all your comments so my assessment could be quite wrong. I was only using the sampling of the ones I have read to make my judgment and like any statistical analysis there is a potential error. The sampling also indicate a cordial and generally nice person." Further sampling has not changed the assessment. And we chatted quite nicely after that. All that I am pointing out is that you have indicated a lot of procedural dents in the argument but never touch the substance which is that the naturalistic processes needs a lot of incredibly improbable events to take place in order to be a legitimate explanation. If you can show why some of the arguments used to mathematically assess that proposition are not quite kosher, then you have not necessarily undermined the substance as I said. Instead of going for the substance and cutting off the life of the argument before it gets anywhere you instead nibble at the periphery. All I am doing is pointing that out. If I had the time to do the math again then I might be more effective at suggesting work arounds to your objections. Work arounds which you might be able to suggest. As I said before, I believe you know some work arounds otherwise you might jump in and show it couldn't be done and actually prove that our assumptions are fallacious. If you did that you would be a hero to the anti ID establishment because not only would you vanquish the "no nothings" but actually produce a statistical analysis that would stand as basic naturalistic dogma. But I suspect you understand the implications of what is said here and for whatever reasons you have chosen to essentially stand on the side and shoot arrows every once in awhile. If we didn't discuss ID I am certain we could have a good time over a couple cold ones. So this thread is about dead but I assume you will come back to check out if I answered you. By the way I do not believe you are here to mock us. Otherwise you are doing a poor job at it. If anything I am mocking some of the people here by pointing out the inanity of their arguments. My guess you find some of this interesting or why waste your time. I believe you secretly believe we have something.jerry_{February 4, 2009
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Prof_P.Olofsson @317

He's here to mock us.
No, that is certainly not true.
I will take your word for that (sincerely). I thoroughly enjoy your posts here, although I will say that I do interpret some of your statements as being said in a (gently) mocking tone. Your posts show good humor, and a good sense of humor, regardless.
The amount of personal attacks on me far exceed the few times I strike back, and I try to do so in good humor, which may perhaps be described as mockery.
As someone who usually watches from the peanut gallery, I agree that you take far more than you dish out.
As for substance, I think it’s a big mistake for ID supporters to accept every argument that is presented in favor of ID and dismiss any counterargument.
Unfortunately, I agree with your assessment here, as well. Scientific research is an exciting endeavor that leads to learning. Sometimes you learn things that contradict what you thought you knew before. If ID positions can't change in the face of evidence and if ID proponents aren't willing to follow all the evidence where it leads, the ID movement will stagnate and die. JJJayM_{February 4, 2009
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JayM[313],
He’s here to mock us.
No, that is certainly not true. I like most of the people here and in my entire contribution to ID, I think you will find very little mockery. Just consider this fact: Davescot (!) started a thread titled "Some thanks for Professor Olofsson" a while ago, in regards to an article I wrote. The amount of personal attacks on me far exceed the few times I strike back, and I try to do so in good humor, which may perhaps be described as mockery. I'm nicer than PZ, aren't I? As for substance, I think it's a big mistake for ID supporters to accept every argument that is presented in favor of ID and dismiss any counterargument. In this thread, and its continuation, we have discussed inference based on probabilities. I have some knowledge in this field and it is clear that the statment Kirk made in the video is not consistent with his explanations thus far in this thread. It has nothing to do with ID as such, which is why I presented the Sally Clark example in post 221. The only person in the ID camp who even tries to undesrtand my arguments is the always nice and friendly tribune7.Prof_P.Olofsson_{February 4, 2009
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jerry[311]. I didn't know this thread was still going on. Are you talking about me behind my back? Anyway, you say:
I haven’t seen anything in any of the people mentioned that has substance.
Come on, that wasn't nice! Nothing of substance? Not even in 185? Come on, please, please, acknowledge that there is a smidgen of substance in it! Otherwise I will call you a creationist nut! ;) Cheers! Olofsson, the Diverter and ConfuserProf_P.Olofsson_{February 4, 2009
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Adel DiBagno @314

Science is a nasty, mean, ugly (hat tip to Arlo) process that relies on a very aggressive marketplace of ideas.
Only to the unprepared. Otherwise, it’s remarkably collegial.
Perhaps I was overstating the adversarial nature a tiny bit for dramatic effect.... JJJayM_{February 4, 2009
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JayM:
Science is a nasty, mean, ugly (hat tip to Arlo) process that relies on a very aggressive marketplace of ideas.
Only to the unprepared. Otherwise, it's remarkably collegial. (At least in my humble experience.)Adel DiBagno_{February 4, 2009
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jerry @311

I have seen nothing in Mark Frank’s, R0b’s, or certainly Prof_P.Olofsson’s comments that warrant either of the criticisms you’ve leveled. Science is about the details and these individuals are politely yet firmly holding our feet to the fire to provide those details.
I haven’t seen anything in any of the people mentioned that has substance.
I think you need to look harder. They are carefully following the discussion and they are spending significant time analyzing our arguments and criticizing them. Are they doing so because they oppose ID? Of course! And, that's fantastic! Science is a nasty, mean, ugly (hat tip to Arlo) process that relies on a very aggressive marketplace of ideas. This adversarial approach improves good ideas and kills bad ones quickly. The gentlemen I mentioned are showing ID a great deal of respect by participating here. They're showing that it is worthy of consideration.
The nice and very civil professor throws some procedural road blocks but that is it. He has not offered anything that would undermine the substance of the argument.
That's simply not the case. He has pointed out holes in the arguments he has addressed and identified problems with at least the way certain mathematical ideas are being expressed. That's of enormous value. If ID proponents can't answer his polite questions or address his calmly presented counter arguments, there is no way we're ready to deal with the mainstream scientific community.
Nor has he offered how best to get around the procedural hurdles so that ID could be fruitfully tested.
That's not his job, it's ours.
As much as I kid with him and like him personally, he is not here to help us but to divert us or confuse us and he seems to have done that with you, judged by your comment.
Actually, I've noticed from the start that the charming Professor O isn't trying to do either. He's here to mock us. That's okay, he does it amusingly and provides value in the process.
But we are not trained scientists and here we are proclaiming on science so we make mistakes in the details.
And we should thank those who point out those errors because that enables us to correct them.
But we can see the big picture and ask for rebuttals and the people you mention don’t do that. They nit pick at the periphery and never undermine the substance.
The devil is in the details and the questions asked by these gentlemen get to the heart of the matter. Far from nitpicking, many of the comments regarding the mathematics underlying ID theory are essential to address. If CSI, for example, really is uncomputably vague, our "big picture" is wrong.
So I stand by my comments. I do not see any good will in their so called objections. If they have substantive objections we would hear them all the time. But they are silent so they much to do over nothing.
I don't care if their will is ill or good. If we can't directly and clearly address the issues raised by the people you are criticizing, then the ID movement will fail. Deservedly. JJJayM_{February 4, 2009
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As much as I kid with him and like him personally, he is not here to help us but to divert us or confuse us...
jerry, I don't think you are being fair to yourself or to Professor Olofsson. I think you have a strong enough will and intellect to avoid being diverted or confused. And I doubt that the Professor is acting in any way inconsistent with his profession. He is a scholar and a teacher.Adel DiBagno_{February 4, 2009
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"I have seen nothing in Mark Frank’s, R0b’s, or certainly Prof_P.Olofsson’s comments that warrant either of the criticisms you’ve leveled. Science is about the details and these individuals are politely yet firmly holding our feet to the fire to provide those details." I haven't seen anything in any of the people mentioned that has substance. The nice and very civil professor throws some procedural road blocks but that is it. He has not offered anything that would undermine the substance of the argument. Nor has he offered how best to get around the procedural hurdles so that ID could be fruitfully tested. As much as I kid with him and like him personally, he is not here to help us but to divert us or confuse us and he seems to have done that with you, judged by your comment. In a lot of ways we are a bunch of amateurs here. We have good minds and can see the obviousness of arguments and the shortcomings of those that are bogus. But we are not trained scientists and here we are proclaiming on science so we make mistakes in the details. But we can see the big picture and ask for rebuttals and the people you mention don't do that. They nit pick at the periphery and never undermine the substance. So I stand by my comments. I do not see any good will in their so called objections. If they have substantive objections we would hear them all the time. But they are silent so they much to do over nothing.jerry_{February 4, 2009
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Upright BiPed @302
300 posts…and still the same old tired objections. The very ones dealt with in even a modest review of ID materials.
jerry @305
You have to understand that those who are against ID have no material so they have to use tired irrelevant arguments over and over.
I think both of these comments are unfair to the ID opponents participating here, as well as the ID proponents who are trying to provide better support for ID theory, possibly in ways other than what you choose to do. I have seen nothing in Mark Frank's, R0b's, or certainly Prof_P.Olofsson's comments that warrent either of the criticisms you've leveled. Science is about the details and these individuals are politely yet firmly holding our feet to the fire to provide those details. Frankly, "a modest review of ID materials" raises more questions than it answers. We need more specifics. We need examples of CSI calculations. We need to show papers unfairly rejected from mainstream peer-reviewed journals. We need to show that ID theory explains the observations of modern biology and makes better predictions than modern evolutionary theory. Is it unfair to ask for this level of detail from ID theorists at this stage in it's lifecycle? Perhaps. Getting some of these answers takes resources that the ID movement doesn't yet have. If that's the case, though, we shouldn't be afraid to admit it. "We're working on that." (with references to the people doing the actual work, of course) is a far better answer than "Your arguments are tired and irrelevant." Sometimes the answer in science is "I don't know." And that's okay. JJJayM_{February 4, 2009
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The idea was to try and find the conditions under which the claim of design of life would be falsified. Mark, I'm guessing you don't believe life to be designed. How have you falsified it? And since it can't be overemphasized, ID can be falsified and it is not the only claim for a design of life.tribune7_{February 4, 2009
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#306 and #307 Thanks for answering these questions. The idea was to try and find the conditions under which the claim of design of life would be falsified. So far we don't seem to have found any!Mark Frank_{February 3, 2009
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Mark -- Let us assume that our RM+NS explanation does account for the organisation of the amino acids. Mark, at this point you leave biology, enter chemistry and become silly. IC is irreducible complexity -- a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. Jerry, fair point. Only IC in the flagellum would be falsified.tribune7_{February 3, 2009
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"But if you do show that the flagellum could come about by RM+NS you will have falsified IC." Not true. There are thousands of IC systems. Finding a natural explanation for one or even one as famous as the flagellum is not a major blow. Finding a natural explanation for several of the more hard core ones would be a blow. But none have been touched yet except through fanciful speculation. So we are safe for the moment.jerry_{February 3, 2009
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Upright Biped, You have to understand that those who are against ID have no material so they have to use tired irrelevant arguments over and over. It is the only way they know how to undermine the basic logic. Distract, divert, deflect, delude etc. The other technique is to find small fault with anything said but which really has nothing to do with the issue. And on other sites they would resort to mockery or some similar tactic. And they are supposedly intelligent IQ wise which is the mystery. They wouldn't stand for the same approach in some other topic area except maybe politics.jerry_{February 3, 2009
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Tribune [297] OK, the answer is yes. Design would be still preferable over chance since you would still have to account for the amino acids organizing into proper sequence to form proteins that organize into proper sequence to form the flagellum. Thanks for answering the question. Let us assume that our RM+NS explanation does account for the organisation of the amino acids. Is design still possible? If you find that inconceivable, take a non-living example, is it possible that the coast of Norway was designed by a designer with undefined powers and motives (I am Douglas Adams fan)? But if you do show that the flagellum could come about by RM+NS you will have falsified IC. I am sorry I have forgotten what IC is.Mark Frank_{February 3, 2009
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gpuccio [301] What confuses me is that I ask a question for which the answer is "yes" or "no" and you answer with 260 words and I still don't know whether the answer is "yes" or "no". Let me try to make the question as clear as I can. "For outcomes where RM+NS is shown to be a plausible explanation, is it also possible that the outcome was designed by an intelligence of undefined power and motives?" I am not asking you whether God was involved. I am not making an argument. I am just asking a question.Mark Frank_{February 3, 2009
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300 posts...and still the same old tired objections. The very ones dealt with in even a modest review of ID materials. A search for reasonable understanding? ...sure, OK.Upright BiPed_{February 3, 2009
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Mark: "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?" I am confused by your arguments. Let's start again, briefly: 1) ID is about "design detection". There are designed things where design cannot be detected. That kind of things are not the object of the ID theory and methodology. So, even if biological information were really designed, if that design cannot be detected, ID would be falsified just the same. Again, believing in a designer is one thing (whether it be God or not). Detecting design by objective methodology is another. ID is about the second thing, not the first. 2) The EF is built in a way that it can have false negatives, not false positives. If biological information were a false negative, just the same ID would be falsified, as clarified in point 1. If instead it is demonstrated to be a positive, then we believe it is a true positive, because the EF is planned not to give (empirically) false positives (false positives remain always logically possible, as discussed many times). 3) If we find an account of the evolution of biological information (obviously, the flagellum alone could not be enough, but it would certainly be an important start) through RV + NS, by definition biological information becomes a negative to the EF. Therefore ID is falsified. There is no question or doubt about that. There is nothing to "prefer". If design is not objectively detected, there is no more any ID account. I think that should be clear. If you insist with your objection, could you please specify what is not clear in the above points?gpuccio_{February 3, 2009
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gpuccio:
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…
You're right, the crystals and Mandelbrot set don't fit your personal definition of CSI, so I shouldn't have mentioned them. The point still remains that your claims about CSI haven't been tested. As far as the unequivocality of your definition, I'll have to disagree. Any physical phenomena can be represented as a "string of digital information". It just so happens that the mapping for DNA is more obvious than the mapping for, say, a rendition of Beethoven's 5th, or a tree. So how do we determine whether a given physical phenomenon fits your "digital" criterion? Is the functionality criterion a yes/no question, or are there degrees of functionality? Most importantly, as far as the improbability criterion, under what hypothesis(es) should it be improbable? I'm not trying to be a troublemaker here. I think these kinds of issues would have to be fleshed out in order to scientifically test sweeping CSI claims. I've strayed way too far. My original point was in regards to the oft-stated ID argument based on the premises that humans create CSI and nature doesn't. I merely pointed out that those premises are not a scientific given, and indeed, CSI is not generally recognized as a scientific concept. With that, I'll stop derailing this thread further. I really appreciate gpuccio, StephenB, jerry, and others for putting up with me.R0b_{February 3, 2009
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jerry:
The whole scientific community accepts the concept of functional complex specified information. They just do not call it that. If you talk about how DNA is information and is complex, they will all nod their heads yes. If you talk about how DNA specifies a protein. They will nod their heads yes and know you are talking about the translation process and transcription process.
Yes, but when the ID community says "complex" in this context, they mean "improbable under all law+chance hypotheses", or maybe "improbable under all known law+chance hypotheses", or maybe "improbable under a hypothesis of uniform chance", depending on which ID proponent you talk to and when. Outside of the ID community, "complex" usually means "complicated". What do you mean when you say "complex"? And it's interesting that you connect Dembski's idea of "specification" with the fact that DNA specifies proteins. Does the fact that DNA specifies something imply that DNA is specified? Do you think that DNA is a specifying agent?
Now I believe that Kirk Durston may be doing just what you are asking for but it won’t have much effect on people’s way of thinking.
I was asking about Dembski's specified complexity, not Durston's functional information. They're not the same.R0b_{February 3, 2009
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ROb: But I was hoping for evidence that the unfair suppression of ID is widespread. Dembski details his experiences with Baylor University What happenings when you accept a pro-ID article for publication in a referred journal And have you watched Expelled?tribune7_{February 3, 2009
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Mark If we find an account of the evolution of the flagellum through RM+NS is it also possible that the flagellum was designed? . . . If the answer is NO - why not? (the explanatory filter explicitly mentions false positives). If the answer is YES - is there any reason for preferring chance or design? OK, the answer is yes. Design would be still preferable over chance since you would still have to account for the amino acids organizing into proper sequence to form proteins that organize into proper sequence to form the flagellum. But if you do show that the flagellum could come about by RM+NS you will have falsified IC.tribune7_{February 3, 2009
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gpuccio StephenB:
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.
My apologies. Brain cramp.
We will settle for the freedom to define our own terms, fashion our own paradigms, and establish our own methods.
Done. At least in free countries.
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.
Sounds like everyone's out to get ID. Perhaps it isn't as clear to them as it is to you that ID's methods are empirically based. Publishing more data generated by empirical ID methods might help clear up this confusion.
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.
You're right, I haven't noticed that.
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?
I wasn't aware of that. That's certainly strange for a school system to take a scientific stance that a priori rejects any current or future contravening data.
According to whom? Do you not realize that you are, once again, bootlegging the argument from authority into the discussion?
When did I argue from authority before? And how am I doing so now? I'm not saying that ID is wrong because the scientific community dismisses it (that would be an argument from authority). I'm saying that maybe ID is dismissed because their output doesn't meet the standards that the scientific community has set for itself. I'm not saying it's right, and of course I'm speaking in very general terms here -- obviously there is no universal scientific organization that comes up with official definitions or sets on official standards for their stamp of approval.
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.
Why? Are there so many that I must be clueless to not be aware of them? That also is not a rhetorical question. Behe has mentioned an ID paper that got rejected. I'm sure there are others, but are there more than a handful? To make a case for unfair "expulsion", why not publish these papers on the web, with the stated reasons for rejection, so the world can see how ID is being suppressed?
Where were you when Baylor closed the door on Dr. Dembski and Dr. Marks?
I agree that it was bad form for Baylor to return funds that it had already approved. Let's put that on our list of rejected ID proposals.
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?
I'm sure that you've heard this from a good source and that you checked out both sides of the story, so I'll join with you in decrying this behavior as inexcusably rude.
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.
Whether denying Gonzalez tenure was fair or not is a matter of opinion, but it's certainly a data point. I've heard the handful of oft-repeated anecdotes from the ID side, and of course the other side has their anecdotes also. As I said, it would be very surprising if no ID proponent had ever been treated unfairly. But I was hoping for evidence that the unfair suppression of ID is widespread. Again, making rejected papers public, along with the reasons for rejection, would provide such evidence.
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?
That's certainly disproportionate.R0b_{February 3, 2009
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Tribune [290] Me: 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? tribune7: 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. This is nothing to do with God. It is a simple question. I will rephrase it very slightly. If we find an account of the evolution of the flagellum through RM+NS is it also possible that the flagellum was designed? To save some time the follow-up questions are: If the answer is NO - why not? (the explanatory filter explicitly mentions false positives). If the answer is YES - is there any reason for preferring chance or design?Mark Frank_{February 3, 2009
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DaveScot[293], What model? I'm not quite sure what we are discussing here. My original point was about Dembski's shopping cart from his book No Free Lunch.Prof_P.Olofsson_{February 3, 2009
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Prof O You are probably not applying the model correctly. Behe did it for 10^20 reproductive events focusing on genes evolving to defeat two different anti-malarial drugs. Problems involving a multitude of genes become intractible. That doesn't mean the model is wrong. Quantum mechanics is well enough established but if you try to model the precise behavior of more than a couple of particles at once the calculations become intractible. It's the same situation in molecular biology.DaveScot_{February 3, 2009
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And that should be "doesn't take them into account." Been in the South for too long I have.Prof_P.Olofsson_{February 3, 2009
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