CSI finally defined.

Not.

Incl. intelligent design, belief in divine creation

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CSI finally defined.

#1  Postby Shrunk » Mar 27, 2011 3:19 pm

The Intelligent Design website Uncommon Descent has recently included a guest post by one MathGrrl which asks a rather straightforward and, it would seem, crucial question:

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:

1. 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.”
2. 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.)
3. 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.
4. 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:

1. Do you agree with vjtorley’s calculation of CSI?
2. Do you agree with his conclusion that CSI can be generated by known evolutionary mechanisms (gene duplication, in this case)?
3. If you disagree with either, please show an equally detailed calculation so that I can understand how you compute CSI in that scenario.
4. If your definition of CSI is different from that used by vjtorley, please provide a mathematically rigorous definition of your version of CSI.
5. 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!


So far, the post has generated over 300 replies, yet no one has yet been able to provide the metric by which CSI is calculated. Of course, that doesn't stop the creationists from continuing to insist it's a really really scientificy mathematical tool that can prove evolution is just a bunch of phoney baloney hooey. It's just that no one knows how to actually measure it.

This post by JonSpector, who I gather is a mean old atheist evolutionist, in response to one of Dembski's groupies named PaV seems to give the gist of the discussion:

PAV:

So, MathGrrl’s question is not a question. It’s a demand for a demonstration, and nothing less.


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.

As I demonstrated above, she has not understood what a specification


Yes, and by my reading, she agrees with you on that point and has asked for help clearing it up.

The only person in the ID world providing mathematical definitions of CSI is Bill Dembski. She should have known this from the beginning.


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.

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?


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.

We can calculate it. But it is a very labor and time intensive operation. Why are we supposed to make this calculation?


Because, as I have been told, that is what scientists do if they want the broader world take notice of their work.

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.


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.

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.

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?

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?

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.


The whole thing can be found here. I hope someone who has the know-how can save the screen. These kind of things have a funny habit of disappearing on ID websites.
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Re: CSI finally defined.

#2  Postby Shrunk » Mar 27, 2011 3:26 pm

Another gem of a comment by one Tulse:

I’m a visitor here, so perhaps I’m not familiar with the conventions of this blog. But if this were a physics blog and an Aristotelian asked how to calculate the position of an object from its motion, I wouldn’t expect the respondents to spend time arguing about the motives of the poster, or whether objects remain in motion or naturally come to rest — I’d expect someone to simply post:

y = x + vt + 1/2at**2

where:
y = final position
x = initial position
v = initial velocity
a = acceleration
t = time

If an alchemist asked on a chemistry blog how one might calculate the pressure of a gas, one wouldn’t argue about the nobility of gold or the Philosopher’s Stone — one would simply post:

p=(NkT)/V

where:
p = absolute pressure of the gas
N = number of gas molecules
k = Boltzmann’s constant
T = temperature of the gas
V = volume of the gas

And if a young-earth creationist asked on a biology blog how one can determine the relative frequencies of the alleles of a gene in a population, one wouldn’t argue about the literal interpretation of Genesis — one would simply post:

p² + 2pq + q² = 1

where:
p = population frequency of allele 1
q = population frequency of allele 2

These are examples of clear, detailed ways to calculate values, the kind of equations that practicing scientists uses all the time in quotidian research. Providing these equations allows one to make explicit quantitative calculations of the values, to test these values against the real world, and even to examine the variables and assumptions that underlie the equations.

Is there any reason the same sort of clarity cannot be provided for CSI?
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Re: CSI finally defined.

#3  Postby Tyrannical » Mar 27, 2011 4:17 pm

I would try and test if interesting genetic events occur at a frequency higher than chance. Since anything can happen by random chance, intelligent design would be altering the probability so that the desired change would more likely occur. By examining current life now and trying to measure the likelihood of it occurring versus other outcomes you can measure the absolute influence. You could then test those results against a baseline of Brownian motion to get a simple number indicating direct influence on the probability.
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Re: CSI finally defined.

#4  Postby Shrunk » Mar 28, 2011 1:46 am

Tyrannical wrote:I would try and test if interesting genetic events occur at a frequency higher than chance. Since anything can happen by random chance, intelligent design would be altering the probability so that the desired change would more likely occur. By examining current life now and trying to measure the likelihood of it occurring versus other outcomes you can measure the absolute influence. You could then test those results against a baseline of Brownian motion to get a simple number indicating direct influence on the probability.


Well, there is a bit of problem in defining what an "interesting genetic event" might be, since that would assume one would know all the possible consequences of such an event, including in combination with other "events". But basically, it seems to me something along those lines might be interesting to pursue if the ID crowd actually believed it was possible to detect the actions of the "designer" they are convinced exists. So I wonder why they have not done anything like that? :ask:
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Re: CSI finally defined.

#5  Postby Calilasseia » Mar 28, 2011 6:31 am

Shrunk wrote:
Tyrannical wrote:I would try and test if interesting genetic events occur at a frequency higher than chance. Since anything can happen by random chance, intelligent design would be altering the probability so that the desired change would more likely occur. By examining current life now and trying to measure the likelihood of it occurring versus other outcomes you can measure the absolute influence. You could then test those results against a baseline of Brownian motion to get a simple number indicating direct influence on the probability.


Well, there is a bit of problem in defining what an "interesting genetic event" might be, since that would assume one would know all the possible consequences of such an event, including in combination with other "events". But basically, it seems to me something along those lines might be interesting to pursue if the ID crowd actually believed it was possible to detect the actions of the "designer" they are convinced exists. So I wonder why they have not done anything like that? :ask:


Because, at bottom, they're more interested in apologetics than science?
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Re: CSI finally defined.

#6  Postby Tyrannical » Mar 28, 2011 7:13 am

Because, at bottom, they're more interested in apologetics than science?


Well, now you real scientists have a target you can attempt to disprove, does God use loaded dice :ask:

If you were to shoot dice games with someone, you could eventually tell if the dice were loaded by comparing the probabilities of what did happen versus what was expected to happen. Then you measure deviation from expected outcome.

Of course envisioning and devising an experiment to test that would be difficult :think:
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Re: CSI finally defined.

#7  Postby sennekuyl » Mar 28, 2011 7:28 am

To save the page and text.

Firefox: right click, save page as..., click save.

IE: Download Firefox, Chrome, Opera, etc nearly anything except IE and Safari*. Install.
Similar process to Firefox.

* If you must use one of the to exclusions, take Safari.
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Re: CSI finally defined.

#8  Postby Shrunk » Mar 28, 2011 10:12 am

Tyrannical wrote:
Because, at bottom, they're more interested in apologetics than science?


Well, now you real scientists have a target you can attempt to disprove, does God use loaded dice :ask:


I don't see how this would "disprove God." There are literally millions of physical, chemical and biological processes that even the most committed creationists agree operate without any input from a "designer", yet that doesn't dissuade them from believing in God.
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Re: CSI finally defined.

#9  Postby Calilasseia » Mar 28, 2011 1:21 pm

To be fair, Tyrannical is merely suggesting that relevant experiments can disprove a particular hypothesis, namely that any god that happens to exist interferes directly in natural processes. This doesn't address the existence question directly. If it can be shown that some hitherto unexplained interference is taking place with testable natural processes, then the question arises, "what is the nature of this interference?" I suspect that most scientists will look for another testable natural process as the source of the interference, though, and if they alight upon one, we're back to square one. In order to establish that said interference, if it exists, is due to something other than a testable natural process, then one would have to rule out all testable natural processes - hardly a trivial task. Which again leaves IDists with a major problem. This, once again, leads to the inexorable conclusion that providing supporting evidence for a magic supernatural entity is a non-trivial problem of Nobel winning difficulty.
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Re: CSI finally defined.

#10  Postby Shrunk » Mar 28, 2011 1:25 pm

Calilasseia wrote:
Shrunk wrote:
Tyrannical wrote:I would try and test if interesting genetic events occur at a frequency higher than chance. Since anything can happen by random chance, intelligent design would be altering the probability so that the desired change would more likely occur. By examining current life now and trying to measure the likelihood of it occurring versus other outcomes you can measure the absolute influence. You could then test those results against a baseline of Brownian motion to get a simple number indicating direct influence on the probability.


Well, there is a bit of problem in defining what an "interesting genetic event" might be, since that would assume one would know all the possible consequences of such an event, including in combination with other "events". But basically, it seems to me something along those lines might be interesting to pursue if the ID crowd actually believed it was possible to detect the actions of the "designer" they are convinced exists. So I wonder why they have not done anything like that? :ask:


Because, at bottom, they're more interested in apologetics than science?


And, of course, this one of those times where the IDiocreationists tip their hands and reveal that they are not just misguided, or stupid. They know very well that they are lying and try to cover it up. There's absolutely no reason why, if the mathematical model for CSI that Dembski claims to have devised actually existed, that someone on that blog would be able to provide it to MathGrrl. The fact that no one has done so demonstrates that either a) the equation does not exist and the IDiocreationists are lying, or b) the equation does exist, but they realilze that if it is applied to MattGrrl's scenarios, it demonstrates that evolutionary processes are able to produce CSI (and the IDiocreationists are lying).
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Re: CSI finally defined.

#11  Postby Calilasseia » Mar 28, 2011 1:45 pm

In short, the IDists are fucked whichever way they turn. :mrgreen:
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Re: CSI finally defined.

#12  Postby Tyrannical » Mar 28, 2011 1:59 pm

I am disapointed that no one got my joke that I slipped in there. :(

You could then test those results against a baseline of Brownian motion to get a simple number indicating direct influence on the probability.
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Re: CSI finally defined.

#13  Postby The_Metatron » Mar 28, 2011 2:36 pm

Hey guys, none of you spelled out what exactly "CSI" stood for. Complex Specified Information.
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Re: CSI finally defined.

#14  Postby Shrunk » Mar 28, 2011 2:39 pm

Tyrannical wrote:I am disapointed that no one got my joke that I slipped in there. :(

You could then test those results against a baseline of Brownian motion to get a simple number indicating direct influence on the probability.


I still don't get it. Probably too subtle for me. :dopey:
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Re: CSI finally defined.

#15  Postby Shrunk » Mar 28, 2011 2:41 pm

The_Metatron wrote:Hey guys, none of you spelled out what exactly "CSI" stood for. Complex Specified Information.


Although where ID is involved, a Crime Scene Investigation is also apt. The crimes being those against logic and rational thought.
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Re: CSI finally defined.

#16  Postby Rumraket » Mar 28, 2011 5:45 pm

This CSI nonsense thing is the same crap Tsar tried pushing until his meltdown. What it really boils down to is the claim that evolution can not produce the increase in functional information (using the J. Szostak definition of the term) required to produce extant biodiversity, from the proposed origin of life around 3.8 billion years ago, until now, given our estimates of past and extant population sizes.
Essentially, he was trying to argue that, although Natural Selection can produce an increase in information, it can do no better than a random search, and a random search could not produce extant biodiversity in 3.8 billion years even given a colony of bacteria the size of the observable universe.

Essentially, the error lies in claiming that Natural Selection can do no better than a random search. This is simply demonstrably wrong. Tsar tried dodging all the facts thrown at him by constantly referring to Dembski's use of the "No Free Lunch Theorem", in which Dembski argued that all simulations of evolution are "smuggling the solution in through a back door" to get around it. Even this is demonstrably wrong. This has even been pointed out to Dembski, who, upon realizing it defeats his argument, simply reasserted the claim in an even more convoluted and purely obfuscatory, semantic way. It doesn't matter to him that it's false, as long as it remains sufficiently convoluted and sciency sounding, then it's enough for the "flock" and we subsequently get people like Tsar pushing the bullshit here and elsewhere.

I get a headache trying to assemble Tsar's wibblings on the subject into a coherent argument, he ran around in circles so much it was really incredible.

In any case, I think the best handlings of these insane ramblings and obfuscations have taken place on th Panda's Thump blog, where pretty much all of Dembski's bullshit has been debunked. I'm glad that page exists, in the beginning I really didn't understand much of the shit he was pushing until I went there and read all of the posts on things like evolutionary searches, searching algorithms etc. etc.
Good stuff, I would recommend it to anyone who runs into that type of "algorithmic instructional information"-wibble we see from time to time.

There is no end to the amount of bullshit terms they will make up to keep the facade that they are competent scientists on a mission from gawd. :coffee:
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Re: CSI finally defined.

#17  Postby Spearthrower » Mar 28, 2011 7:45 pm

The only mechanism for CSI is evolution via mutation and recombination sieved through a selective process. When they wake up to this, they'll change the goal posts.
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Re: CSI finally defined.

#18  Postby Calilasseia » Mar 28, 2011 11:20 pm

Spearthrower wrote:The only mechanism for CSI is evolution via mutation and recombination sieved through a selective process. When they wake up to this, they'll change the goal posts.


Haven't they done that already, courtesy of the complete abandonment of ID's assertions as the front line of attack, and instead trying to redefine "academic freedom" to mean "force-feed pupils with doctrinal assertions whilst excluding valid science"?
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Re: CSI finally defined.

#19  Postby Shrunk » Mar 28, 2011 11:34 pm

Rumraket wrote:Essentially, the error lies in claiming that Natural Selection can do no better than a random search. This is simply demonstrably wrong. Tsar tried dodging all the facts thrown at him by constantly referring to Dembski's use of the "No Free Lunch Theorem", in which Dembski argued that all simulations of evolution are "smuggling the solution in through a back door" to get around it. Even this is demonstrably wrong. This has even been pointed out to Dembski, who, upon realizing it defeats his argument, simply reasserted the claim in an even more convoluted and purely obfuscatory, semantic way. It doesn't matter to him that it's false, as long as it remains sufficiently convoluted and sciency sounding, then it's enough for the "flock" and we subsequently get people like Tsar pushing the bullshit here and elsewhere.


Jeez, you seem to have got that right. I don't read UD as a rule, and only came across this thread because it was linked on Pharyngula. But you really need hipboots,nose plugs and a good sized shovel if you step into that place. I mean, here's a post by one particularly verbose person, name of kairofocus, who's absolutely besotted with his own brilliance (Comment #320):

F/N: I pause to look at one of MG’s 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.”


1 –> But, a gene DUPLICATION aint “simple”!

(Observe: “protein” implies a cellular context of functional processes that are tightly regulated and integrated, a la the infamous Biochemist’s chart of cellular metabolic reactions. Talk about a Wicken wiring diagram well past the 1,000 yes/no decisions threshold!)

2 –> As the above implies, we are now also dealing with a regulatory process — one that will have its own Wicken wiring diagram to lay out the architecture of the control loop process [cf examples here] — that controls expression of the information in the genetic code.

3 –> So, let us ask, how do we get TO a “simple . . . duplication”? Or, more specifically, first, to the functional, controlled, regulated expression of genes and their replication when a cell divides?

4 –> ANS: By having a higher order regulatory network that responds to environmental and internal states and signals in a co-ordinated fashion. Thus, once we have gene duplication, we have already had something that regulates and expresses replication, which is itself going to be FSCI-rich, if the just linked diagrams are any indication.

5 –> That implied capacity, BTW VJT, is what seems to be pushing you over the threshold of CSI when you have such a duplication.

6 –> In other words the Dembski analysis is (correctly!) picking up that if lightning strikes the same unlikely place twice, something significant is happening.

7 –> Suppose the first protein coded for takes up say 600 bits [i.e. 300 bases, or 100 AA's].

8 –> Doubling such a short protein would jump us to 1,200 functionally specific bits, and the crude, brute force “a cubit is the measure from elbow to fingertips” 1,000 bit threshold metric would pick this up as passing the FSCI threshold, on which the explanatory filter would point to design as best explanation.

9 –> In short, (i) lightning is hitting the same unlikely place twice, which implies (ii) a capacity to target that place by replicating, regulating expression, etc, and that (iii) this is so unlikely on chance plus bare mechanical necessity, that the best explanation is design. For, (iv) designers are known to do such duplications, and to set up regulatory systems that have counting loops that control how many times something is to be expressed or done: do until, do while etc.

10 –> Of course, if a counter point in the regulatory network suffers a simple mutation that triggered the double replication of the gene, that narrow outcome is well within the range of a chance event.

11 –> But that is not a pure chance event, it is within a highly complex island of function, and so we are looking at hill climbing within such an island. (Notice the centrality of this islands of function in wider config spaces concept. Where also the focus of design theory is how do we get to islands of function, not how we move around within such an island, except that hill climbing implies a deeper level of functional complexity to promote robustness and adaptability. That holds for the FSCI X-metric and it holds for the Durston et al FSC FITS metric and it holds for Dembski’s CSI hot zone metric.)

12 –> So, by broadening the context from a protein molecule of say 100 AA’s exists, which is within threshold — so, just possibly by chance on the gamut of our cosmos, it could come about by chemistry, but of course without the cell’s context, it is not functioning, it is just an unusual molecule — to one where there is a duplication in a regulatory network, we have brought into focus a much wider set of complexity, that pushes us over the FSCI threshold.

13 –> In turn, that points to design as best explanation for the SYSTEM capable of that duplication.

14 –> This reminds me of the time I worked out and had to seriously reflect on the implications of the truth table (A AND B) => Q, namely that A => Q and/or B => Q.

15 –> Deeply puzzled [this is tantamount to saying that "Socrates is a Man" and/or "Men are Mortal" would INDEPENDENTLY imply "Socrates is Mortal"], I spoke with one of our budding mathematicians over in my next door neighbour Math Dept.

16 –> But of course, he said, blowing away my previous understanding that the interaction between the two premises was key to the syllogism. If men are mortal, Socrates is mortal. If Socrates is a man, he is mortal. (That is, the Maths was implicitly capturing a deeper reality than I had spotted.)

17 –> So, I came away with a deeper respect for the math, and a higher confidence in it.

18 –> The tickler? I was led to do the particular analysis, both by truth tables and by the Boolean Algebra, because of a theological issue over interpretation of a particular verse in the NT which in effect is of form (A AND B) => Q.

19 –> So, the deeper yet lesson is that reality — on abundant experience as well as the implication of the key first principles of right reason being models of reality — is a unified whole, and if we are capturing that reality in our models, we may be surprised by deeper connexions. But, we should respect them.

20 –> So, MG’s tickler case no 1 points to a deeper set of connexions, and the crude, brute force FSCI criterion and metric comes up trumps.


I mean seriously, WTF? How can anyone think that actually says anything meaningful.

Poor MathGrrl is doing a great job of not getting derailed, and simply repeating "Well, that might be interesting, but could you answer my question?" Unfortunately, she's starting to get a bit disillusioned (comment #360):

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.
"A community is infinitely more brutalised by the habitual employment of punishment than it is by the occasional occurrence of crime." -Oscar Wilde
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Re: CSI finally defined.

#20  Postby Bribase » Mar 29, 2011 12:51 am

What is really so astounding is that 370 odd comments, endless books, lectures, blogs, websites, documentaries, court cases and a well funded media campaign on what amounts to an argument from ignorance.

Even if CSI was true, even if the ID creationists manage to debunk the last 150 years of biology. What makes them think that the answer to the question "How does complexity arise in the natural world?" Become anything like a meaningful answer?

"I don't know"
"You don't know"
"No one knows"
"Therefore I know, it was God"
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