On The Calculation Of CSI

_{MathGrrl
March 25, 2011

Intelligent Design, Mathematics

4}_{Categories
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

Pardon I am a bit woozy after a fairly rocky sea-ferry ride. Yellow Hole lived up to its name. I note briefly, that MG has declared in a previous thread that the CSI concept -- especially absent a neat mathematical rigorous definition -- is meaningless. My for the record remarks above are to correct this foundational error, as if the foundation is bad, the building will be considerably weakened. I have already underscored that on observing certain realities of cell based life, Orgel and Wicken were moved to identify the concepts that lay the base for the quantities identified as complex specified information, and functionally specific, complex information [a subset of CSI, where the specification is based on observed function and vulnerability to perturbation of key elements, linguistic and/or structural]. Mathematical models, analytical techniques and metrics respond to that reality, and we must not put the mathematical cart before the reality horse. Indeed, in the iconic case of calculus, the breakthroughs happened in C17 [Newton and Leibniz in the lead], the systematisation on that success was in C19 or so. And, the limits of such systematisations were laid out in the 1930s by Godel. Mathematics is irreducibly complex and inescapably a faith venture. When it comes to CSI and the directly practically relevant FSCI, the observation came first: it was recognised by Orgel and Wicken across the 1970's, that order, randomness and organisation on specified complexity are three distinct things. Life is complex but not random, as it is functionally specific. And, in the case of DNA, we are dealing with coded digital information in data structures that specify proteins and the regulatory networks that control them. (Cf. here.) If you cannot acknowledge this as a meaningful reality that is observed before it is modelled and analysed, and measured, then forever after you will have stumbling blocks. That is why I have asked MG to answer: were Orgel and Wicken "meaningless"? In fact, the question answers itself. O & W are right, and MG has made a basic conceptual error in doing science. Or, engineering for that matter, as CSI and FSCI describe very familiar realities of technical systems. Next, there is a demand to answer to far more complex cases, when the basic ones go a begging for an answer. I think we need to learn how to crawl and stand before we try to run and fly. So, I start with a basic, practically based case of CSI using models, analysis and metrics drawn from common practices in science, technology and even mathematics. Functionally specific, complex organisation and associated information. Functional specificity is an observable. Complexity can be identified using a threshold. And specific quantum orf relevant information meeting these criteria can be identified using the basic metric, the bit. These -- as we saw above -- are related to Hartley's log metric suggestion, and the Shannon metric that ISCID conveniently summarises:
Shannon information is the type of information developed by Claude Shannon and Warren Weaver in the 1940s. Shannon information is concerned with quantifying information (usually in terms of number of bits) to keep track of alphanumeric chcaracters as they are communicated sequentially from a source to a receiver. The amount of Shannon information contained in a string of characters is inversely related to the probability of the occurrence of the string. Unlike specified complexity, Shannon information is solely concerned with the improbability or complexity of a string of characters rather than its patterning or significance.
Of course, this hints at an underlying inference to design on functional specificity. We distinguish meaningful signal from noise, and we do so in the context of signal to noise ratio, for the meaningful and functional message is based on special configurations that are unlikely by chance -- islands of function -- and are subject to corruption by the various processes that happen in information storage, processing and communication systems. 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. (Indeed, that is a key part of why my always linked note shows my road into the design theory: information and thermodynamics.) So, pardon my insistence on learning to creep first. When we can see the point of a simple, crude, brute force model and metric, then we can profitably progress to more complex cases. But, id we demand to run and fly before we can creep and stand much less walk, the exercise will be futile. So, MG: were or were not O & W "meaningless" when they spoke of specified complexity and wiring diagram based functional organisation? Good day GEM of TKIkairosfocus_{March 26, 2011
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Jemima, There are 2 questions: can CSI be recognized and can CSI be calculated. Dembski thinks that both can be done. I'm not certain about the second one, maybe he is right. But I know that you can observe specification and complexity. It's like observing light without being able to calculate its amount. People were doing it long before light was measurable in any precision.Collin_{March 26, 2011
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Pav
And that pattern has a production history behind it.
What's the "production history" behind the bacterial flagellum? DNA?JemimaRacktouey_{March 26, 2011
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Jon Specter Yet you are reluctant to put any effort into developing one of the key tools in the intelligent design toolchest. Why? Because Mathgrrl won’t believe you no matter what? No. Because she doesn't understand what a specification is. It always deals with a pattern. And that pattern has a production history behind it. It's easy to write one sentence descriptions of what you think is a 'specification'; it's quite another to actually understand what the pattern is that is involved in the program, and then to understand how it is generated. I am not of the opinion that MathGrrl is here to find out how CSI applies in each of the situations she inquires about. I think there's some ulterior motive. I again am interested in what affiliations she has, and where she now works. Hopefully she'll tell us.PaV_{March 26, 2011
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QuietID:
Joseph, I still don’t get why you think genetic changes aren’t random except that you want to think that. The evidence is that they’re random.
Again Dr Spetner wrote a book about it called "Not By Chance". And the only way you can say all mutations are random is to demonstrate that the OoL was due to random processes. Avida has nothing to do with the blind watchmaker.Joseph_{March 26, 2011
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Jon Specter [247]: In the case of ev, and from memory mostly, neither of them are complex enough, that is, show enough improbability, to exceed the UPB. I think part of what MathGrrl is getting at is that in Dembski's paper on "Specification . . " he's introduced more concepts into his reformulation of CSI, and, hence, it might seem a little unwieldy. But, to simply things---it seems it's better to approach things in a simplified form before using the more complex---we can just use the UPB, which can be used in a straightforward way. Again, neither ev nor Tierra exceed this. What I have been lamenting all along is the work that's involved in establishing the "pattern" that's involved. That's why I asked MathGrrl for an example of a "specification". Frankly, I hadn't noticed that she included a "specification" in her post. This happened because she used basically the same format as that of an earlier thread; but this time she included---she thought---a "specification" for each. In the one example where a true specification was given, that of ev, and where N is known, 16, the calculation is quite straightforward and easy. It is not CSI. In the other cases, she hasn't properly understood what a "specification" is, and so hasn't presented them properly. A "specification" always includes a pattern. It's not simply a description; although descriptions can, in the case of ev, be translated into a pattern.PaV_{March 26, 2011
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MathGrrl: Here's Dembski's brief description of "specification" from his paper: Specification denotes the type of pattern that highly improbable events must exhibit before one is entitled to attribute them to intelligence. Here are your supposed specifications: 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. The only "pattern" is that of 2.) From what I can see, N=16 in the ev program, and given that there are four, possibly five (deletion) choices for all 16 positions, the most complexity produced is going to be 2^5 x 16 power, which, again, is well below the UPB. But,ev falls apart in other ways per Dembski and Truman. Every example of a CSI calculation that Dembski has given has involved a pattern. The Caputo case dealt with 33 D's and 1 R, etc. CSI analyzes patterns, and it involves anaylzing the chance hypothesis involved in the pattern emerging. The simple descriptions you've provided don't provide any such patterns save #2. And it's not CSI. So you now have your answer.PaV_{March 26, 2011
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I've finally discovered Schneider's paper in Nucleic Acids Research where he presents his ev program and its results. I noticed this statement---which I believe to correctly summarize what he accomplished:
Second, the probability of finding 16 sites averaging 4 bits each in random sequences is 2^4X16 = 5 x 10^20 yet the sites evolved from random sequences in only ~ 10^3 generations . . .
Per NFL, per the UPB found there, which is 10^150, even if there were no other problems with ev (which there are, and can be found in the papers I linked to belonging to Dembski and Truman), this falls woefully short of this UPB. This means that we CANNOT conclude that it is CSI. That is, we CANNOT be assured that what was produced was not the result of chance. The "chance hypothesis", the null hypothesis here, CANNOT be eliminated, and thus Schneider's output does not constitute CSI. QED.PaV_{March 26, 2011
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M. Holcumbrink,
We cannot calculate anything because we are missing important information.
I'm sure that for the purposes of this thread such details will be provided if asked for and deemed relevant to the problem at hand. The objections so far seem somewhat different, e.g. Uprights demand that MathGrrl answers his questions first. Not about missing facts as such. What further details are provided is not up to me. But I'll continue to enjoy reading the thread as this develops.
No, CSI is the “filesize” with the added knowledge that the data is specific and functional, i.e. it performs a critical function within a given system.
But that added knowledge about the data can only come from knowledge that it's designed and I thought the whole purpose here was to detect design via CSI, not use the knowledge that some data is designed to say that some data is designed?JemimaRacktouey_{March 26, 2011
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Joseph, I still don't get why you think genetic changes aren't random except that you want to think that. The evidence is that they're random. The question is can they drive novel evolutionary changes? If Avida models those random changes, then functional information emerges through random changes. If Avida doesn't model those random changes, then you shouldn't cite it as a measure of functional information.QuiteID_{March 26, 2011
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QuietID, You are not paying attention. Evolutionary processes are not necessarily blind watchmaker processes. Avida is yet another targeted search.Joseph_{March 26, 2011
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Joseph, the PNAS reference you give in 12 relies on Avida, an artificial life modeling system, and seems to claim that functional information is created within the evolutionary processes of the program. Isn't that precisely what we think functional information can't do?QuiteID_{March 26, 2011
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Jemima @259: “If “CSI” objectively exists then you should be able to explain the methodology to calculate it and then expect independent calculation of the exact same figure (within reason) from multiple sources for the same artifact.” When I was in school I had to use castigliano’s theorem to generate equations for specific cases in order to do stress analysis. Some cases were much more straight forward than others, but when I came across an example where it proved exceedingly difficult for me to use the theorem to derive the specific equation needed for that situation, it did not mean that the theorem was therefore invalid. I knew that it applied, but I did not have the mental faculties to be able to use it. Likewise, CSI is a very real entity, and it has been calculated for certain situations, but that does not mean that it is not a valid concept when a less straight-forward scenario is presented. Do you deny the reality of CSI? If a man gets stuck with a knife and he starts bleeding everywhere, there is no doubt that if the bleeding is not stopped he will die, and the inability of someone to calculate the rate of blood flow out of the wound does not change the fact that he is bleeding profusely. We can see the blood, and there is a lot of it. Likewise, we can see a lot of CSI, hence the attempts to rigorously define it and calculate it. If it wasn’t there to tacitly see, we wouldn’t even be talking about it right now. Jemima: “Currently I get the impression that “CSI” is simply the (file)size of the object in question to which we add the knowledge that it was designed and so design is claimed.”…” Of course, this all seems to hinge on knowing the artifact in question is designed in advance. Which sort of defeats the entire point of CSI in the first place. Things are designed because they have lots of CSI, and CSI is only present when things are designed. Therefore design. No, CSI is the “filesize” with the added knowledge that the data is specific and functional, i.e. it performs a critical function within a given system. Then given the probability of said highly specified data, design is claimed. Jemima @265: “Ah, the “paper bluff”. If the details of how to calculate CSI for the scenarios in question are in that paper them presumably your yourself are now capable of calculating the CSI for the scenarios in question. So what’s stopping you?” We cannot calculate anything because we are missing important information. For instance, in mathgrrls scenario #1, what is the length of the gene that is duplicated? And if its duplication causes the quantity of the protein it codes for to increase within the cell, then something else is in play here, because to the best of our knowledge the gene only codes for said protein. And if its production increases due to the duplication then whatever it is that regulates the production is clearly affected by the presence of the extra gene, but we are not privy to those specifics either. We need to know the mechanism involved here, but we don’t. I figure that to be quite obvious.M. Holcumbrink_{March 26, 2011
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Here's another paper. I'm posting the link straight away since I'm having problems and don't have the time to fix them. http://www.trueorigin.org/schneider.asp#1PaV_{March 26, 2011
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kairosfocus @251, I understand how simple it is to calculate CSI in certain instances where a string of digital code is used to generate components that are unambiguously critical to the function of a system. No problem there. And after my last post, I decided that the best way to “measure” the CSI contained within one of my complex piece parts would be to take its 3D CAD file or a 2D PDF of the blueprint and apply the calculation to the amount of digital data contained therein. Not so tough after all. Regarding genetic algorithms, at what point could they be considered “artificial intelligence”? Machines make machines all the time in factories, and in some instances the processes are almost completely automated. But that of course does not mean that blind naturalistic processes are capable of making sophisticated machinery. So when software generates CSI, it seems to me that what we have is software making software. That would count as artificial intelligence, would it not? If so, then we are still stuck with intelligence being the sole originator of CSI. Intelligence by any other name is still intelligence, it seems to me.M. Holcumbrink_{March 26, 2011
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JemimaRacktouey, Are you interested in having evolutionists put their money where there mouth is? The point being is ID persists beause eolutionists have failed miserably at supporting the claims of their position. Go figure...Joseph_{March 26, 2011
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Then use those details to calculate the CSI for the examples given and prove me wrong and yourself right.
MathGrrl should be able to t do for herself-that is if her examples are valid. Why won't I do it? I say, and have explaned why, hr exampls are not valid. You, like MathGrrl, have serious issues.Joseph_{March 26, 2011
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Jemima:
The difference is that CSI is claimed to be something that can be calculated to the exact bit,
Who has made that claim? I say you made that up. I say you are full of it.Joseph_{March 26, 2011
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Joesph,
I say it provides exactly what is asked for.
One last comment to you then... Then use those details to calculate the CSI for the examples given and prove me wrong and yourself right. Why on earth would you not do so if you could?JemimaRacktouey_{March 26, 2011
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I don’t see how CSI relates to that situation at all. Illogical and irrelevant. That is beause you don't know anything about the subject. And the reasoning has been provided.
So perhaps you could calculate the CSI present in the four examples in the OP?
They are bogus and I have explained why.
It seems you are at odds with the majority of ID supporters on this thread.
What you say is meaningless. No need to engage you as you are one of the willfully ignorant.Joseph_{March 26, 2011
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Joseph,
All you have to do is demonstrate a BF can evolve via blid watchmake processes in/ from population(s) that never had one and CSI is basically refuted.
I don't see how CSI relates to that situation at all. Illogical and irrelevant. Why don't you explain in detail why that would be the case Joe?
Th point of CSI is its presence, meaning 500 or more bits of specifed information present, then all of our observations and experiences tell us tat only designing agencies are capable of such a feat.
Yes, quite. So perhaps you could calculate the CSI present in the four examples in the OP?
Nope. CSI need not be present to detect design. Counterflow is all that is required.
It seems you are at odds with the majority of ID supporters on this thread. I'll assign you as "fringe" which for ID is quite something and ignore the rest of what you have to say, unless of course you can calculate CSI for the examples given in the OP at which time I'll be happy to re-engage with you. I had wondered why most people on this thread did not engage with you, now I know.JemimaRacktouey_{March 26, 2011
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I have already told her how to do it and presented a paper in comment 12 that tells her how to do it. JemimaRacktouey Ah, the “paper bluff”. Ah the jerk response. How is what I posted a "bluff". Be specific. I say it provides exactly what is asked for. And again why/ ho are the examples valid? Why can't you tell us? Why can't MathGrrrl tell us?Joseph_{March 26, 2011
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Jemima, Specification is rigorously defined but CSI may not be. I'm not sure if CSI can be calculated, but specification and complexity can be recognized. http://www.designinference.com/documents/2005.06.Specification.pdfCollin_{March 26, 2011
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Collin
For example, psychologists measure “motivation.” Please calculate that rigorously
The difference is that CSI is claimed to be something that can be calculated to the exact bit, that it can be objectively calculated, that it can unambiguously determine if the artifact in question is designed with no prior knowledge of how it came to be and that CSI indicates intelligence. I'm not the one claiming those things, I'm just interested to see if IDers can put their money where their mouth is. A secondary reason is to see if after this thread IDers will still make the claim that CSI can be calculated for any object despite the fact nobody can actually do so. Is CSI an empty claim or one that can be backed up? What do you think Collin?JemimaRacktouey_{March 26, 2011
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JemimaRacktouey:
E.G the claims that the bac flag or the cell is “full” of CSI but no actual figure can be stated. If no figure is known, how is it known for sure that the actual value is non-zero?
All you have to do is demonstrate a BF can evolve via blid watchmake processes in/ from population(s) that never had one and CSI is basically refuted. Th point of CSI is its presence, meaning 500 or more bits of specifed information present, then all of our observations and experiences tell us tat only designing agencies are capable of such a feat.
Of course, this all seems to hinge on knowing the artifact in question is designed in advance.
That's just dumb.
Things are designed because they have lots of CSI, and CSI is only present when things are designed.
Nope. CSI need not be present to detect design. Counterflow is all that is required.Joseph_{March 26, 2011
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Joseph,
You have it backwards- MathGrrl neds to explain how/ why her examples are good/ valid.
Then I submit that the next time you claim that CSI can be calculated and is evidence for design you explain the scenarios that that cannot be applied to. Otherwise it's something of an impossible guessing game for somebody to propose a scenario and for you to simply say "nope, that's invalid" without explaining why. Why are the examples invalid Joe? You claims that they are "not valid" cuts no ice with me. Let's hear a few scenarios from you that you agree are valid for the calculation of CSI and if you calculate the CSI then perhaps a general principle can be derived.
I have already told her how to do it and presented a paper in comment 12 that tells her how to do it.
Ah, the "paper bluff". If the details of how to calculate CSI for the scenarios in question are in that paper them presumably your yourself are now capable of calculating the CSI for the scenarios in question. So what's stopping you? If you do it then you've shut up MathGrrl, provided a major boost for ID as CSI can now be calculated for arbitary scenarios and you'll probably end up as a guest blogger here. So why don't you do it Joe?JemimaRacktouey_{March 26, 2011
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For example, psychologists measure "motivation." Please calculate that rigorously... Well, they can give you statistics on what is most likely in certain situations but its hard to say what is going on in the brain of an individual. Yet measuring motivation is a worthy intellectual endeavor just like analyzing CSI.Collin_{March 26, 2011
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Colin
Whether or not CSI can be calculated, the definition is clear enough that we can at least see if there is complexity and specification.
This is the crux of the matter. If CSI cannot be calculated then the claims that it can are bogus and should not be made. If it can be calculated then it can be calculated in general and there should not be a very long thread where people are giving all sorts of reasons why in this particular case it cannot be calculated.
Do you deny that the bacterial flagellum has those things?
I don't know, define CSI and I'll tell you if it exists in the bac flag.
Even if it cannot be calculated rigorously, I think that it still leads to a valid inference of design just as Mount Rushmore leads to a valid inference of design
If you think about it that's invalid. We recognize Mount Rushmore as designed because it looks like human faces. Amongst other reasons. Yet here the claim is that "the designer" created the CSI that ID claims to observe (but cannot calculate). Given that nothing is known about this "designer" (ID is not about the designer) how can you recognize the design in the bac flag? What is you reference point? Where is the "face that looks like a human face" in the bac flag?
It’s POSSIBLE that the knife was blown by the wind in just such a way as to imbed in someone’s back, but unlikely, therefore the design inference is valid.
Or, therefore, something else entirely. Disproving one thing does not support another, positive evidence is required to do that. So it's "possible" that the bac flag evolved totally naturally and even if that is disproved it does not provide any support whatsoever for ID. How can it? There are multiple other explanations available (Craig Ventor in a time machine) so ruling out one say nothing about the probability of another being true.
Complexity and specificity, I submit, is the same thing.
Then calculate the CSI in MathGrrls examples.JemimaRacktouey_{March 26, 2011
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Collin, without calculation, the design inference is either circular or non-rigorous. We know Mount Rushmore is designed, but we can only say we know this because of complexity and specification if those are rigorously defined.QuiteID_{March 26, 2011
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QuietID, You may be correct, but I think you should consider that you are not correct. I think that complexity and specificity are well enough defined that its presence (in whatever "amount") can be reliable found. This leads to a reasonable inference of design. Remember that much of science is based on reasonable inferences. My experience is in psychology and I know that many people think that that is not a science. I'm one of them. But the world treats it as a science (especially in a court room) and what passes for science is rarely rigorously definable. Yet it receives government funding, influences public policy and is admissible as professional opinion in court. Psychologists use math, particularly statistics, but they use very fuzzy definitions; much more fuzzy and less rigorous than CSI.Collin_{March 26, 2011
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