On The Calculation Of CSI

_{March 25, 2011

Intelligent Design, Mathematics}

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My thanks to Jonathan M. for passing my suggestion for a CSI thread on and a very special thanks to Denyse O’Leary for inviting me to offer a guest post.

[This post has been advanced to enable a continued discussion on a vital issue. Other newer stories are posted below. – O’Leary ]

In the abstract of Specification: The Pattern That Signifies Intelligence, William Demski asks “Can objects, even if nothing is known about how they arose, exhibit features that reliably signal the action of an intelligent cause?” Many ID proponents answer this question emphatically in the affirmative, claiming that Complex Specified Information is a metric that clearly indicates intelligent agency.

As someone with a strong interest in computational biology, evolutionary algorithms, and genetic programming, this strikes me as the most readily testable claim made by ID proponents. For some time I’ve been trying to learn enough about CSI to be able to measure it objectively and to determine whether or not known evolutionary mechanisms are capable of generating it. Unfortunately, what I’ve found is quite a bit of confusion about the details of CSI, even among its strongest advocates.

My first detailed discussion was with UD regular gpuccio, in a series of four threads hosted by Mark Frank. While we didn’t come to any resolution, we did cover a number of details that might be of interest to others following the topic.

CSI came up again in a recent thread here on UD. I asked the participants there to assist me in better understanding CSI by providing a rigorous mathematical definition and showing how to calculate it for four scenarios:

A simple gene duplication, without subsequent modification, that increases production of a particular protein from less than X to greater than X. The specification of this scenario is “Produces at least X amount of protein Y.”
Tom Schneider’s ev evolves genomes using only simplified forms of known, observed evolutionary mechanisms, that meet the specification of “A nucleotide that binds to exactly N sites within the genome.” The length of the genome required to meet this specification can be quite long, depending on the value of N. (ev is particularly interesting because it is based directly on Schneider’s PhD work with real biological organisms.)
Tom Ray’s Tierra routinely results in digital organisms with a number of specifications. One I find interesting is “Acts as a parasite on other digital organisms in the simulation.” The length of the shortest parasite is at least 22 bytes, but takes thousands of generations to evolve.
The various Steiner Problem solutions from a programming challenge a few years ago have genomes that can easily be hundreds of bits. The specification for these genomes is “Computes a close approximation to the shortest connected path between a set of points.”

vjtorley very kindly and forthrightly addressed the first scenario in detail. His conclusion is:

I therefore conclude that CSI is not a useful way to compare the complexity of a genome containing a duplicated gene to the original genome, because the extra bases are added in a single copying event, which is governed by a process (duplication) which takes place in an orderly fashion, when it occurs.

In that same thread, at least one other ID proponent agrees that known evolutionary mechanisms can generate CSI. At least two others disagree.

I hope we can resolve the issues in this thread. My goal is still to understand CSI in sufficient detail to be able to objectively measure it in both biological systems and digital models of those systems. To that end, I hope some ID proponents will be willing to answer some questions and provide some information:

Do you agree with vjtorley’s calculation of CSI?
Do you agree with his conclusion that CSI can be generated by known evolutionary mechanisms (gene duplication, in this case)?
If you disagree with either, please show an equally detailed calculation so that I can understand how you compute CSI in that scenario.
If your definition of CSI is different from that used by vjtorley, please provide a mathematically rigorous definition of your version of CSI.
In addition to the gene duplication example, please show how to calculate CSI using your definition for the other three scenarios I’ve described.

Discussion of the general topic of CSI is, of course, interesting, but calculations at least as detailed as those provided by vjtorley are essential to eliminating ambiguity. Please show your work supporting any claims.

Thank you in advance for helping me understand CSI. Let’s do some math!

Comments

Jon S: Let me try and give you an example of what MathGrrl's request (demand) appears like to me. Let's say that you described a football field as a rectangular area, 50 x 120 yards along (including end-zones), that is striped every five yards, consisted of grass-like material, with a slope from the center to the edges of 1"/2 feet, etc. And then you say you're looking to build one. And someone says, "Oh well, come over to our house you can build it in the back yard." And then you ask, "Well, just how big is your back yard," to which they respond: "50 feet square." If they kept insisting that you could build your "football field" in their back yard, would you go over there to make sure? When, by definition, a bit sequence has to be at least 500 bits long to rank as CSI, and someone wants you to rigoruosly define CSI for a bit-string (sequence) that is 260 bits long, what would you make of it?PaV_{March 28, 2011
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Muramasa, CSI is only intended for certain circumstances- most tools are designed for certain circumstances. As for the EF answer the question- do you think scientists flip a coin or throw darts? Or do you think they have a methodology? Do you think an archaeologist can claim she is holding an artifact when a geologist can demonstrate that geological processes can account for it? Are all deaths homicides? Do you have any experience with conductiing an investigation beyond playing "hind-n-seek"?Joseph_{March 28, 2011
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Thank you, CJYman at [371]. I didn't know that you had worked out such a problem. Thanks for the link. And your analogy of Shannon information difference between the Taj Majal and CNN Tower is great. For any onlookers, the reality is as CJYman says, there are examples out there of how to calculate CSI/specified complexity. These are there to guide you. I don't see any evidence that MathGrrl sufficiently understands the concepts involved so as to justify having a meaningful conversation with her. At [368], I include quotes demonstrating MathGrrl's inability to understand vjtorley's response to her. And, I pointed out what I'm rather sure her agenda is: CSI is a moving target. It's not rigorous enough. But that seems to mean: it's not easy enough. (And it's not easy. Likely you would have to formulate some composite probability density function, and use some form of combinatorics that might be specific to the problem at hand, and so, a form you yourself would have to derive. But just because something isn't easy to achieve doesn't mean that it isn't true.) Well, it's not. But in certain situations it comes only at the end of a very long and hard search for understanding. JemimaR: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest. You have to remember: it's an entirely uninteresting problem for me (because it is an impossibility---a "tilting at windmills"). Here's an interesting problem: MathGrrl shows up with a precise "specification", including a chance hypothesis, demonstrating that she has found some instance of "specified complexity/CSI" via chance processes. I would love to debunk it. While I have zero interest the other way around, I'd debunk it for free!! Jon Spec: I'm not trying to bow out gracefully. MathGrrl, on plenty of occasions along the way, has been given her answer. That she cannot understand these answers is not my problem. You say it would be good for ID. Well, tell you what, try and get hold of Bill Dembski and see if you can interest him in that. But, tell me, would you be able to evaluate it? And if someone from the other side said Dembski's calculations were all wrong, would you know whether or not there was merit to their claim? So, then, what would be gained. CJYman has done a sample calculation. The basics are enough. Lastly, take the example of the ev program. There's a kind of subroutine to check how "correct" the "binding site" is? Well, ask yourself this? Correct compared to what? Well, obviously the actual binding site. Now, does that sound like "blind chance" to you? It sure doesn't to me. I forget the program, but years ago they said, "Oh, well you must know about so-and-so's ABC program (whatever it was) that randomly generated an electric circuit." I responded by saying, "Please don't waste my time. I don't want to go and look at it and then find out it can't do anything." "Oh, no, I was assured. It can really do what it says." So I spent quite some time meticulously going through the program, step by silly step, and what do I find out: if the program runs using information as to how the electric circuit was supposed to function (and this was specified by a "fitness function"), then, and ONLY then, did a circuit appear---something that looked like the worst case of a Rube-Goldberg machine you ever saw (highly inefficient). If you didn't feed the program this information, then NOTHING happened. Naturally when I told them what I had found that ended the discussion. But, of course, I had wasted a lot of my time. Maybe now you understand my reticence.PaV_{March 28, 2011
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CJYman provides further support for the notion that CSI, if applicable at all, can only be used in certain circumstances. Does this not render it nearly useless? Maybe a helpful intermediate step would be to list things for which CSI/specified complexity can be measured. And Joseph @373, that really isn't a specific demonstration of the explanatory filter.Muramasa_{March 28, 2011
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JR:
The explanatory filter you say kairosfocus? Would you, perhaps, be able to give a demonstration of the usage of it?
I would say it is used by anyone trying to determine how something came to be the way it is. IOW it is standard operating procedure. Do you think scientists flip a coin or throw darts?Joseph_{March 28, 2011
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CJYman, As always your efforts are appreciated. Unfortunately your efforts are wasted on those they were intended.Joseph_{March 28, 2011
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For anyone interested, here's a linklink to our previous discussion in which I gave a few more links to where I had calculated CSI for the protein Titin, explained how CSI is calculated, backed up my explanation, and showed how my calculation is derived from Dembski's lattest work on CSI in his "Specification ..." paper. Along with the work vjtorley and others have done, this shows that CSI is well defined and calculable in at least some situations. To demand that CSI be able to cover every single imaginable situation would be akin to demanding that unless one can calculate the difference in Shannon Information between the Taj Mahal and the CN Tower, then the concept of Shannon Information is not well defined. I do understand that MathGrrl would like to have CSI calculated for the scenarios that she has provided, and in principle that's great, but as PaV has noted above if she can't figuer out the examples already given her, then there is no reason to suspect that if we take the time to go through her provided scenarios she would understand the calculations any better. In fact, as a tutor, I understand very well that if you do someone's homework for them they will never understand it themselves. It would be better if she understood first what we've already tried to explain and calculate for her and then she can work on her own examples herself and ask us what we think about her calculations. Look at that, an opportunity for MathGrrl to actually engage in some ID Research. Sounds good? ... no? P.S. There is also the challenge at comment #311, referencing how law+chance absent intelligence will not produce an EA, at the above linked thread that MathGrrl has not taken up yet.CJYman_{March 28, 2011
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Jon, I believe that you’re a Creationist who doesn’t like what Dembski is doing, so that what MathGrrl is trying to do, counter-intuitively, supports your agenda.
LOL. You better have a talk with Joseph. He seems to think I am a Darwinist. If you do, though, be forewarned: he is kinda grumpy. What I am, or was, was an interested, supportive onlooker. I was interested in seeing this worked out, but it seems clear you have no intention of doing so. I can understand, if you were talking one on one with Mathgrrl, your reluctance to go through the work given that she might not accept it. But, you are on a much larger stage here and there are probably many onlookers, most remaining silent, that desparately want one of the core ID tools demonstrated in action. I just happen to be the 1 in a hundred onlooker mouthy enough to butt in. But, honestly, with your admission that you are not a scientist or a mathematician (I thought you were), I can only conclude that you probably are just looking for a graceful way out. You've done a yoeman's job thus far. Seems a shame that the real ID scientists are leaving you twisting in the wind.jon specter_{March 28, 2011
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PaV,
What she wants from us is the “chance hypothesis” for these programs. If she is willing to pay me large sums of money, I might consider showing her how its done. However, considering the time, effort and thought required, I am not willing to give it to her for free.
How much would it cost?JemimaRacktouey_{March 28, 2011
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Jon Specter [325]: So? Asking an ID scientist to demonstrate what he claims is one of the key tools in his toolbox hardly seems like some nefarious plot. The few actual scientists I know are positively giddy when asked to talk about their work. I can’t shut them up, even after the food arrives. My claim is this: Dembski's book, NFL, contains a rigorous, mathematical description/definition of CSI. MathGrrl doesn't want the definition contained there, she wants a worked-out example of CSI. Very different things. And thank you very much for elevating ID to the level of science; please inform the Darwinist community of this. PV:As I demonstrated above, she has not understood what a specification JS:Yes, and by my reading, she agrees with you on that point and has asked for help clearing it up. She has only provided what she thinks are specifications. But a specification should be linked to some "chance hypothesis". What she wants from us is the "chance hypothesis" for these programs. If she is willing to pay me large sums of money, I might consider showing her how its done. However, considering the time, effort and thought required, I am not willing to give it to her for free. Since when are we here at UD supposed to do somebody's homework assignment. If she wants help, contact Bill Dembski. He's the author of NFL. PV:The only person in the ID world providing mathematical definitions of CSI is Bill Dembski. She should have known this from the beginning. JS:It might have saved everyone alot of time and frustration if they had just said 700 comments (over two threads) ago that they can’t define CSI in an unambiguous manner. There is a great deal of rigor in both NFL and in "Specification". The definition is spelled out. MathGrrl doesn't want a DEFINITION; she wants a worked out example. If she is willing to pay me sufficiently, I might be interested. But, again, she's asking in numbers (1) and (2) for the impossible. In (1), simple duplication is tantamount to a copy machine copying multiple copies of an original. That is, there is NO NEW PATTERN! As for (2), it's length is insufficient to constitute true CSI, and therefore, "specified complexity" as well. [So, why should I even bother with them? It's obvious just looking at these "patterns". If she had even a rough idea of what CSI is, and how it works, she wouldn't be making these requests.] If she thinks OTHERWISE, then let her prove her case. Again----I don't do homework. PV:She didn’t want us to give a “rigorous mathematical definition” of CSI, she wanted us to tear apart the programs and assess it using the notions of CSI. Why should I be expected to respond to such a request on my time and energy. Am I some kind of paid consultant? JS:I, for one, was under the impression that you were an ID scientist. And, as I am led to understand, spending inordinate amounts of time developing ideas and sharing them widely is the process of science and the work of scientists. Again, thank you for elevating ID to a science. If I were a "scientist", then that would be my professional duty. I happen to not work in the sciences or in math whatsoever. As to ideas, ALL the ideas she is asking about are there in NFL and in "Specification". She's having trouble coming to grips with what all of this should look like in the cases that she's interested in. That's the problem. Again, I don't do homework. Let her figure it out herself. When I was auditing some physics classes, it was always the case that physics professors never gave their inquiring students direct answers to their questions, or else, the student would be deprived of a learning experience. PV:Why isn’t she expected to show that she understands CSI and demonstrate that understanding by, herself, anaylzing these programs. If she came up with something disproving CSI, THEN, and ONLY THEN would it be incumbent upon the ID community to rebut her findings. JS:How can she disprove what hasn’t been shown to be proven? CSI is an interesting concept. But, until someone actually shows it in action (it is easy, after all, right? You said so yourself), it seems like demands for disproof are premature. The claim is that chance processes cannot produce CSI. That is a simple claim. CSI is defined. Rigorously. Is it the duty of the ID community to prove, in every instance, that this claim is true? The way science works is that a claim is expected to work in every applicable situation. Demonstrating that it doesn't, would invalidate the claim. Again, for the umpteenth time: the calculation is easy. Setting up the equation by providing a pattern and the chance hypothesis that goes along with that, is the hard part. JV:Your demands for disproof of what you aren’t yet willing to demonstrate looks kinda like this: I claim that I am the most interesting man in the world. Now you must disprove that. And it is insufficient for you to say that I am nothing more than an internet blog troll, because someone else likely disagrees with you. You must demonstrate it with such rigor that everyone agrees that I am not very interesting. You're spilling over into the realm of the imbecilic now. I don't think any of those scenarios has any CSI whatsoever. It would take a huge amount of effort to prove so using the already existing rigorous definition of CSI. Why am I then obliged to demonstrate this to her. If she is of the mind that it does, then let her prove it. Here's a quote from MathGrrl: "For some time I’ve been trying to learn enough about CSI to be able to measure it objectively and to determine whether or not known evolutionary mechanisms are capable of generating it. Unfortunately, what I’ve found is quite a bit of confusion about the details of CSI, even among its strongest advocates." There's two parts: the first part is: "I’ve been trying to learn enough about CSI to be able to measure it objectively". Well, functional sequences are specified. That is just a given. As an example: "slltldlchd skdig;ls;s;e" wasn't helpful,was it? I typed it completely at random. But all my other words are "functional". You understand them. So, here at UD, we'll just postulate that any coding portions of the genome are "specified". And, let me go further, any coding portion sufficiently long enough would be, per NFL, CSI. So, there. It's not defined. It's a given. So all she needs to do is count. Isn't that easy enough? So now she knows "enough . . . to be able to measure it objectively." Then, the second part: "to determine whether or not known evolutionary mechanisms are capable of generating it." That's wonderful she wants to do that. Either way, whether she can determine that evolutionary mechanisms are capable of generating CSI, or not, she'd have her name in the spotlight. So, let her do it herself if she is of the mind. Why spoil her fame? PV:Even Bill Dembski can’t “agree” on a definition of CSI. He no longer is using it, in a sense. He now is using “specified complexity”. Others here at UD want to stick directly in the “information” area and have our own intuitive ideas of what CSI should look like, and what we should be looking for in biological systems. Is there something wrong with this? JS:Well, it renders your demand that Mathgrrl begone and not come back until she understands CSI a little confusing. How is she supposed to demonstrate an understanding of a central ID concept which actual ID scientists can’t agree on? Here's an exchange that took place on an earlier thread at [295]---one you are aware of since you posted at that time: vjtorley: I note that for the duplicated genome, the specified complexity Chi is much greater than 1, so Dembski’s logic seems to imply that any instance of gene duplication is the result of intelligent agency and not chance. Here's MathGrrl's response: I didn’t double check your math, but the orders of magnitude seem about right. I agree with you that by Dembski’s logic a gene duplication event generates CSI. She has either completely misunderstood vjtorley, or has twisted what he said. I don't know which. So, at the top of the thread she started, she writes: 2.) Do you agree with his conclusion that CSI can be generated by known evolutionary mechanisms (gene duplication, in this case)? This is wild. She hasn't a clue. Elsewhere in the thread I've linked to, vjtorley has directed her to Dembski's "Specification" paper. Then when vjtorley says this: the presence of bases along the gene in question, and …….. signify the rest (which are also random, let’s say), then the description of the duplicated genome will be ……..(AGTCGAGTTC)x2 instead of ……..(AGTCGAGTTC). In other words, we’re just adding two characters to the description, which is negligible. MathGrrl responds: Why are you using “x2? instead of the actual sequence? Using the “two to the power of the length of the sequence” definition of CSI, we should be calculating based on the actual length. I can see how the Kolmogorov Chaitin complexity might make more sense, but that’s not what I see ID proponents using. Yet, in Dembski's SP (=Specification Paper), when he is defining phi, which includes these kinds of duplication events, there is a footnote. In the footnote we read: "[24] There is a well-established theory of descriptive complexity, which takes as its point of departure ChaitinKolmogorov-Solomonoff theory of bit-string compressibility, namely, the theory of Minimal Description Length (MDL). The fundamental idea behind MDL is that order in data “can be used to compress the data, i.e., to describe it using fewer symbols than needed to describe the data literally.” See http:// www.mdl-research.org (last accessed June 17, 2005)." Now, if our wonderful little MathGrrl is really trying to understand CSI, then why doesn't she bother to read the footnotes? If you have a question about something, and there's a footnote, then why don't you explore it? The next footnote [25] refers her to the Design Inference. Why doesn't she try reading this stuff? That's all I've been saying. The definition is out there. Figure it out. JS:It might save you more time if you shortened your request that she go away until she understands CSI to a request that she just go away. Here's MathGrrl's true agenda----for all to see: On that earlier thread, again at [295], we have her response to vjtorley, and then her true colors shine.
VJT: Well, I’ve done the hard work. I hope you will be convinced now that fixating on a single measure of information is unhelpful. MathGrrl: Thank you, very sincerely, for your effort. The problem is, I’m not the one you need to convince.There are a number of ID proponents who continue to make the claim that CSI is a clear and unambiguous indicator of intelligent agency. They are the ones who need to be convinced to stop making those claims, that you yourself have shown to be unsupported, unless and until someone comes up with an alternative metric.
She has managed to misunderstand vjtorley (again). But it's very clear what her agenda is. And you want me to help her. No thank you. It would be best if MathGrrl went away. She's wasting our time. ---------------------- And, Jon, I believe that you're a Creationist who doesn't like what Dembski is doing, so that what MathGrrl is trying to do, counter-intuitively, supports your agenda. Please tell me I'm wrong. But be honest. __________________________ BTW, in looking over some posts, there have been some wonderful answers given to MG. Good work everyone.PaV_{March 28, 2011
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kairosfocus,
So, in the context of the explanatory filter, we may examine events, objects etc by asking on aspects, whether these are accounted for on mechanical necessity [giving rise to natural regularity], chance [giving rise to stochastic contingency on relevant distributions], or choice contingency, driven by intelligent, purposeful choice.
The explanatory filter you say kairosfocus? Would you, perhaps, be able to give a demonstration of the usage of it? You certainly talk confidently about it, as if it were trivial to apply. Perhaps then the "digital organisms" referenced in the OP might suit as a target? I'm sure there will be some reason why that's just not possible. Is the EF another CSI style mirage? Good for including in and building a complex multi-step argument, such as the tower of Babel KF is building, but it's all for naught as the foundations (CSI, the EF) evaporate away in the daylight.JemimaRacktouey_{March 28, 2011
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kairosfocus, Orgel gave a meaningful definition of specified complexity (which I think you, unlike PaV, take to be synonymous with CSI). However, his description of it was qualitative rather than quantitative. It may be that the concept is not up to mathematical precision.QuiteID_{March 28, 2011
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I think that the accusation of nonsense, takes priority over any further questions until it has been settled. And this, you know or should know. Worse, you have made a materially false assertion. One that you have had every occasion to know is materially false.
Ruh-roh. Looks like KF is getting ready to demand an apology for being slandered. Color me surprised.
this is not the inquisition, and I am no suspect heretic confined to answer quesitons as asked, however poisonously loaded.
Won't answer your questions, Mathgrrl. But, won't let you have the last word either.San Antonio Rose_{March 28, 2011
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mg @ 359 "I find your view interesting, but in this thread I am trying very hard to keep the focus on obtaining a rigorous mathematical definition of CSI and to get some detailed example calculations. Are you saying that what I am asking for cannot, even in principle, be provided?" I am saying, per my previous post, and interminable posts prior to this on other threads, that is it impossible, IN PRINCIPLE, i.e. it is logically impossible, to explain information in terms of algorithms and/or physical laws. This so obviously true that it is scarcely worth repeating. So I won't. You will sooner be able to create a square circle as to generate information with time and physics. Information is impossible without reason, language, free will, and intentionality. That is, a mind. Or Mind in the case of life.tgpeeler_{March 28, 2011
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MG: PLEASE, PLEASE PLEASE. It is you who have maintained that the undersigned, specifically, as well as others, have been "meaningless" in speaking of CSI and FSCI. Until this issue is settled, no further progress is possible. I have now any number of times pointed to Orgel and Wicken using the root of these abbreviations, and you have yet to accept that these men and others since, have been describing a significant aspect of reality, found inter alia in the living cell. I think that the accusation of nonsense, takes priority over any further questions until it has been settled. And this, you know or should know. Worse, you have made a materially false assertion. One that you have had every occasion to know is materially false. For, I took up time to address the first question of the fur you posed above, probably the most important. In so doing, I deconstructed the question, exposing the underlying issues that are begged and glided over with a glib "simple." In direct terms, MG, you have committed the fallacy of the complex, loaded question. this is not the inquisition, and I am no suspect heretic confined to answer quesitons as asked, however poisonously loaded. I have taken my privilege of intellectual liberty to analysie the quesiton, in te context of what it means to duplicate a gene. The answer in that context points in precisely the opposite way to what you seem to wish. Good day, madam. Off to my next item for the day. GEM of TKIkairosfocus_{March 28, 2011
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F/N: Pausing between meetings in a cafe, I think we need to bring a cite linked above explicitly into the discussion, from ENV; on gene duplication: ______________ http://www.evolutionnews.org/2009/10/jonathan_wells_hits_an_evoluti026791.html >> Since biology is based upon functional information, Jonathan Wells is interested in far more important questions like, Does neo-Darwinism explain how new functional biological information arises? Shallit seems interested primarly in addressing simplistic, trivial questions like how one might duplicate a string, without regard for the all important question of whether those additional characters convey some new functional message. Under Kolmogorov complexity, a stretch of completely functionless junk DNA that has been utterly garbled by random, neutral mutations might have more Kolmogorov complexity than a functional gene of the same sequence length. For example, consider the two following strings: String A: KOMOLGOROVINFORMATIONISAPOORMEASUREOFBIOLOGICALCOMPLEXITY String B: JLNNUKFPDARKSWUVWEYTYKARRBVCLTLOPDOUUMUEVCRLQTSFFWKJDXSOB Both String A and String B are composed of exactly 57 characters. String A spells a sentence in English, and String B was generated using a random string generator. Yet since many of its characters could be predicted using the grammatical rules of English, String A actually has less Kolmogorov complexity than String B (for example, we could use a data compression algorithm to shorten String A dramatically). Yet clearly String A conveys much more functional information than the String B. For obvious reasons, Kolmogorov complexity is not always a helpful metric of functional biological information. After all, biological information is finely tuned to perform a specific function, whereas random strings are not. A useful measure of biological information must account for the function of the information, and Kolmogorov information does not necessarily take function into account. In fact, Kolmogorov information is very similar to Shannon information, where "In both cases, the amount of information in an object may be interpreted as the length of a description of the object." But the length of the description says nothing about whether there is function, or how much fine-tuning is necessary for function. Thus you could have a very long random string that requires long descriptions, but it has no function. As any ID novice knows, we infer design when we find both complexity and specification. In rough terms, Shannon information or Kolmogorov information measure complexity, but not specification. Thus, such measures of information are not useful for measuring functional biological information. As a paper in the journal Theoretical Biology and Medical Modelling observes:
[N]either RSC [Random Sequence Complexity] nor OSC [Ordered Sequence Complexity], or any combination of the two, is sufficient to describe the functional complexity observed in living organisms, for neither includes the additional dimension of functionality, which is essential for life. FSC [Functional Sequence Complexity] includes the dimension of functionality. Szostak argued that neither Shannon's original measure of uncertainty nor the measure of algorithmic complexity are sufficient. Shannon's classical information theory does not consider the meaning, or function, of a message. Algorithmic complexity fails to account for the observation that "different molecular structures may be functionally equivalent." For this reason, Szostak suggested that a new measure of information -- functional information -- is required. (Kirk K. Durston, David K. Y. Chiu, David L. Abel, Jack T. Trevors, "Measuring the functional sequence complexity of proteins," Theoretical Biology and Medical Modelling, Vol. 4:47 (2007) (internal citations removed).) . . . .
Orgel captures the fact that specified complexity, or CSI, requires both an unlikely sequence and a specific functional arrangement. In fact, Orgel's "random mixture of polymers" might have extremely high Kolmogorov complexity, even though it would not be sufficiently specified to encode a functional biological life-form. Specified complexity is a much better measure of biological complexity than Shannon complexity or Kolmogorov complexity because it recognizes the highly specified nature of biological complexity . . . . ID proponents define "new" genetic information as a new stretch of DNA that actually performs some different, useful, and new function. For example, consider the following 42-character string: DUPLICATINGTHISSTRINGDOESNOTGENERATENEWCSI Now consider the following duplicate string: DUPLICATINGTHISSTRINGDOESNOTGENERATENEWCSIDUPLICATINGTHISSTRINGDOESNOTGENERATENEWCSI Whether or not we have increased the Kolmogorov complexity, we have not created any new meaning in the duplicated string. We have not increased the CSI in any meaningful sense. The above example is of course analogous to the commonly cited evolutionary mechanism of gene duplication. New functional information is not generated by a process of duplication until mutations change the gene enough to generate a new function -- which may or may not be possible . . . >> ________________ Thus, we see a second level of issues connected to the gene duplication question. In the Shannon sense of average information per symbol, i.e. the H-metric of SUM on i of pi ln pi, the highest average information per symbol occurs with zero redundancy, which implies full resistance to compression. The easiest way to get that, is to do a random string, where there is no correlation between any one digit and the next. K-complexity, similarly, would imply an increment to the algorithm to generate string X by adding to it, repeat X, once. But absent new function, we are not dealing with new information in any relevant sense. And, we observe that to get to the duplication in vivo, we are looking at exploiting a cellular replication system that (as we already saw) is brimming over with functionally specific complexity in its organisation, thus also functionally specific, complex information. In this context, the admittedly crude X-metric X = S*C*B, is enough to discern cases that are safely beyond the search capacity of our observed cosmos, acting through a blind random walk filtered by equally blind trial and error, from an arbitrary initial condition. So, in the context of the explanatory filter, we may examine events, objects etc by asking on aspects, whether these are accounted for on mechanical necessity [giving rise to natural regularity], chance [giving rise to stochastic contingency on relevant distributions], or choice contingency, driven by intelligent, purposeful choice. The original post in this thread passes the FSCI threshold, and is inferred by the explanatory filter to be an artifact of design. The protein molecule and the chromosome replicating mechanisms will pass at a similar threshold, and are inferred to also be best explained on design. The controversy over this inference, does not trace to observed cases of chance and necessity giving rise to FSCI without design, but to the a priori, Sagan-Lewontin assumption that origins are evolutionary materialistic. This assumption is then used to impose a controlling censorship on origins science. And, sadly, that is the root of ever so much of the debate we have seen, in recent years. GEM of TKIkairosfocus_{March 28, 2011
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mf @ 334 "You seem very concerned that Mathgrrl has not addressed the presence of symbols as a sign of information and therefore design." The reason that we "are very concerned" that mg has not addressed the presence of symbols is that the presence of symbols destroys the materialist project. In other words, it's not even possible for you to be right. All languages involve symbols and rules. None of which can be explained by physics. Materialism is a fool's errand. All of this nonsense about bits and bytes and how much and how many and blah blah blah is irrelevant to the fundamental issue, which no materialist seems capable of grasping, which is that physics cannot explain language. Language is required for information. Therefore, physics (the only explanatory tool in the materialist tool kit) cannot explain information. Case closed. My apologies if this is "a bit rough."tgpeeler_{March 28, 2011
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kairosfocus (339),
One of the most distressing things in the above thread (and previous ones leading up to it) is the repeated strawman — or, outright false — assertion that FSCI and/or the broader CSI cannot be worked out for real world biological cases, joined to equally predictable dismissals of observations and calculations when they are made.
You've written a considerable number of words and made a number of claims but you have not directly addressed any of my questions in the original post. What is the rigorous mathematical definition of CSI? How can I calculate it for the four scenarios I described (please show the details of your work)? What do you think of vjtorley's calculations in the previous thread? You seem to have time to participate here and you claim to be able to calculate CSI. Rather than continuing to post lots of words, please show just a bit of math.MathGrrl_{March 28, 2011
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markf (334),
You seem very concerned that Mathgrrl has not addressed the presence of symbols as a sign of information and therefore design. It seems a bit rough, as her challenge was for someone to provide a mathematical calculation of the CSI or information in certain cases. After all many leading ID proponents claim that CSI can be measured in bits. If you want to introduce a different criterion for information/design that is fair enough but it doesn’t answer her challenge and it is not necessarily an evasion on her part not to answer. She has done amazingly well to respond to so many different objections on this thread and she cannot be expected to respond to every different objection, especially when it does not answer her challenge directly.
Thank you, I am indeed resisting my usual desire to respond in detail to every point. There have been several interesting topics raised in this discussion, but I am trying very hard to keep this thread focused on getting answers to the questions I posed in the original post. I must say that I'm starting to suspect that those questions will not get answered.MathGrrl_{March 28, 2011
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tgpeeler (330),
Let’s keep this short and to the point. If we are talking about information (CSI, FSCI, or otherwise), and we are, then a language, “a system of chemical representations (symbols),” must also exist. I am saying that a materialistic explanation of language is, in principle, impossible.
I find your view interesting, but in this thread I am trying very hard to keep the focus on obtaining a rigorous mathematical definition of CSI and to get some detailed example calculations. Are you saying that what I am asking for cannot, even in principle, be provided?
This game is long over even if mg, jemima and the rest won’t get it.
What I honestly don't "get" is how ID proponents can make claims about CSI without being able to define it, let alone calculate it.MathGrrl_{March 28, 2011
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Collin (326),
I think that Mathgrrl is trying to get us to admit that CSI is not rigorously, mathematically calculable.
That would be a reasonable response, given what we've seen thus far in this thread. What I really would like, though, is a rigorous mathematical definition of CSI and detailed example calculations for the four scenarios I described. My gut instinct is that, if CSI can be rigorously defined and objectively calculated, GAs will prove to be capable of generating it. I'd very much like to test that instinct (and ID claims at the same time).MathGrrl_{March 28, 2011
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kairosfocus (320),
But, a gene DUPLICATION aint "simple"!
Gene duplications are observed in biological systems. The rest of your comment fails to provide a rigorous mathematical definition of CSI and does not provide any example calculations. Could you please do so?MathGrrl_{March 28, 2011
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vjtorley (315),
Regarding gene duplication, here’s an excellent blog post by Casey Luskin on why gene duplication doesn’t increase CSI: Jonathan Wells Hits an Evolutionary Nerve .
That article doesn't use Dembski's discussion of CSI. The calculation you performed does (with some interpretation). I find your results more compelling.
Regarding ev, PaV has already shown that it is incapable in principle of breaching Dembski’s Universal Probability Bound, so I think we can all agree it does not present a real challenge.
You grossly overstate what PaV has shown. Please see this link for a demonstration of how ev can generate that much information.MathGrrl_{March 28, 2011
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PaV (313),
And, QUITE FRANKLY, the answer to her request is that if she wants a rigourous definition of CSI then she should read NFL; and, if any questions remain, then she should email Bill Dembski. The only person in the ID world providing mathematical definitions of CSI is Bill Dembski.
In that case, ID proponents should stop making claims they can't support.
We can calculate it.
There is no evidence of that in this thread.
Even Bill Dembski can’t "agree" on a definition of CSI.
You can't agree on a definition, but you still claim to be able to calculate it?MathGrrl_{March 28, 2011
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critter (301),
I’m trying to understand all of this. MathGrrl asked for a demonstration of the math behind CSI (as defined by Dr Dembski). I too would like to see the math.
Thank you for helping to keep this discussion focused on the core issue!MathGrrl_{March 28, 2011
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kairosfocus (290),
In short, there is an intuitive, implicit appeal to the inference to design on FSCI in the heart of information theory. So, the design theory movement is doing something important in highlighting and addressing this and its significance.
ID proponents go much farther than this, though, by claiming that CSI can be objectively calculated and that it is a reliable indicator of intelligent agency. Do you reject those claims?MathGrrl_{March 28, 2011
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PaV (284),
1.) The specification of this scenario is "Produces at least X amount of protein Y." 2.) "A nucleotide that binds to exactly N sites within the genome." 3.) "Acts as a parasite on other digital organisms in the simulation." 4.) "Computes a close approximation to the shortest connected path between a set of points." The first, third, and fourth aren’t patterns.
They can easily be expressed as patterns, though. vjtorley shows this in his post 217 where he says:
Here’s the most concise English description: “stator joining two rotary motors.” This description corresponds to a pattern T
All you need to do is consider the underlying genome or bit string as the pattern. Your objection isn't reasonable.MathGrrl_{March 28, 2011
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PaV (283),
Per NFL, per the UPB found there, which is 10^150 . . . this falls woefully short of this UPB. This means that we CANNOT conclude that it is CSI.
You've only looked at one particular simulation run. Schneider has shown how to beat the UPB using ev.MathGrrl_{March 28, 2011
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Joseph (260),
MathGrrl has already made it quite clear that the book has insufficient information present to allow CSI to be calculated for the 4 examples in question.
I doubt that she has read the book. Her posts and questions tells me she hasn’t.
Your interpretation of my posts and questions is incorrect. If you feel that CSI can be rigorously defined and calculated for my four scenarios based on the discussion in No Free Lunch, please demonstrate how in this thread.
An interesting claim. But groundless without further explanation or justification.
You have it backwards- MathGrrl neds to explain how/ why her examples are good/ valid.
I'm afraid you have it backward. I'm asking for detailed clarification of a core ID concept. If you think my scenarios are somehow inapplicable, it is incumbent upon you to explain why.
Why don’t you present a few non-bogus scenarios and then calculate, if you can, the CSI present in those scenarios.
I have already told her how to do it and presented a paper in comment 12 that tells her how to do it.
As previously noted, that paper has nothing to do with CSI as described by Dembski. If you disagree, please demonstrate how they are aligned, provide a rigorous mathematical definition of CSI, and show how to calculate it for the four scenarios I described.MathGrrl_{March 28, 2011
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kairosfocus (250), You show a little math in this comment, but I don't see how it is related to Dembski's discussions of CSI, nor does it show how to calculate CSI for the four scenarios I described in the original post. Could you please just directly answer the exact questions I asked? I'll be more than happy to continue the discussion once we have that shared understanding.MathGrrl_{March 28, 2011
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