At Some Point, the Obvious Becomes Transparently Obvious (or, Recognizing the Forrest, With all its Barbs, Through the Trees)

_{Gil Dodgen

June 5, 2011

Intelligent Design}

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At UD we have many brilliant ID apologists, and they continue to mount what I perceive as increasingly indefensible assaults on the creative powers of the Darwinian mechanism of random errors filtered by natural selection. In addition, they present overwhelming positive evidence that the only known source of functionally specified, highly integrated information-processing systems, with such sophisticated technology as error detection and repair, is intelligent design.

[Part 2 is here. ]

This should be obvious to any unbiased observer with a decent education in basic mathematics and expertise in any rigorous engineering discipline.

Here is my analysis: The Forrests of the world don’t want to admit that there is design in the universe and living systems — even when the evidence bludgeons them over the head from every corner of contemporary science, and when the trajectory of the evidence makes their thesis less and less believable every day.

Why would such a person hold on to a transparently obvious 19th-century pseudo-scientific fantasy, when all the evidence of modern science points in the opposite direction?

I can see the Forrest through the trees. Can you?

Comments

Dr. Liddle, response to comment #5: "Well, my position is that IDists have failed to demonstrate that what they consider the signature of intentional design is not also the signature of Darwinian evolutionary processes." Darwinian processes are not known to be capable of generating functional biological systems that have a very high degree of functional specificity -- such as many protein-based systems (by functional specificity is meant a system where novelfunction is only realized by the existence of very specifically arranged and types of amino acid residues in the protein-based system). However, intelligent designers are quite capable of designing proteins that require a high degree of specificity (e.g., Kuhlman et al., 2003). And so if such systems were found in nature, this would be seem to be a signature of intelligent design -- something intelligent design can do but Darwinian processes cannot do. Such systems have been found, of course. References: Kuhlman B., et al. Design of a Novel Globular Protein Fold with Atomic-Level Accuracy. Science, 302 (5649): 1364-1368, 2003.LivingstoneMorford_{June 22, 2011
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Dr Liddle: Crick, letter to son Michael, Mar 19, 1953:
"Now we believe that the DNA is a code. That is, the order of bases (the letters) makes one gene different from another gene (just as one page of print is different from another)." [NB: From about 1961 on, that code has been identified, and is now routinely used in scientific work.]
GEM of TKIkairosfocus_{June 20, 2011
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OK, if you mean DNA is "base 4 digital" in the same sense as the English alphabet is "base 26 digital" then, fine. But I don't find it a useful description. On the other hand, I think that the way DNA is "read" can be very usefully be viewed as a digital system (on/off), indeed as a system of logic gates. But at least we agree that the thing is somewhat computer like :) Haven't forgotten your other post. Have a half-composed response, not sure when I'll get it finished, maybe tonight, maybe not for a couple of days. Cheers LizzieElizabeth Liddle_{June 20, 2011
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Hello again Dr Liddle, Quite frankly, I think you may have a bunch of people standing around looking at each other shrugging their shoulders, as if to say “What the heck is she talking about?!?!” To the best of my limited knowledge, the base of a digital coding system simply expresses the number of unique characters within the system which could occupy any given digit. A base two system such as binary code has two unique characters. In computer systems it’s either 1 or 0, but it could be any two symbols. A base four system such as quaternary code has four unique characters, such as 0, 1, 2, and 3 (or in the case of the genetic code A, T, C, and G). A base sixteen system such as hexadecimal code has sixteen unique characters, such as 0-9 plus A-F. A base sixty-four system has sixty-four unique characters, and so on. I also think you are conflating the output of a system with the coding format of a system. To put on a pot of tea and call it a base-two system because at one point it boils and at another it doesn’t … is frankly, just way out there. - - - - - - - - - I await your responses. Cheers…Upright BiPed_{June 20, 2011
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I'm currently engaged in writing a reasonably subtantive response to UBP(in between RL distractions!) but I would just like to say: I am aware that a number of people, some of whom are on "my side" have described DNA as a "Base 4 digital code". I think that is an extremely poor description, and the fact that it is given by people who should IMO know better doesn't improve it as far as I am concerned! A "four letter alphabet" is a better description, though I am also leery of language metaphors; however, language is a marginally better metaphor for DNA than "digital base 4" is, and you would not (sensibly) describe the English alphabet is not a "digital base 26" system. Like English letters, bases (in the chemical sense) are not switches, and to change the meaning of an English sentence you do not change individual letters (or very rarely). However, as I said, there is a fairly useful sense in which DNA can be regarded as a Base 2 system: at the level of the gene, we really do have a switched system, and a very fine one it is too. But it's binary - genes are switched off and on.Elizabeth Liddle_{June 19, 2011
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"I’m still not convinced that 'digital' is a good description of DNA information..."
Life, too, is digital information written in DNA. - Ridley, 2000, p.16
Mung_{June 18, 2011
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Some typical questions to be addressed in this book are: Are information and information-processing exclusive attributes of living systems, related to the very definition of life? How does information appear in Darwinian evolution? The main objective here is to show that information plays the defining role in life systems. ...information as such plays no active role in natural inanimate systems... – J.G. Roederer, Information and Its Role in Nature
Mung_{June 18, 2011
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Information is embedded in a particular pattern in space or time - it does not come in the form of energy, forces or fields, or anything material, although energy and/or matter are necessary to carry the information in question. Information always has a source or sender (where the original pattern is located or generated) and a recipient (where the intended change is supposed to occur). It must be transmitted from one to the other. And for the specific change to occur, a specific physical mechanism must exist and be activated. We usually call this action information processing. Information can be stored and reproduced, either in the form of the original pattern, or of some transformation of it. ...a fundamental property of information is that the mere shape or pattern of something - not its field, forces or energy - can trigger a specific change in a recipient, and do this consistently over and over again (of course, forces and energy are necessary in order to effect the change, but they are subservient to the purpose of the information in question). This has been called the pragmatic aspect of information. It is important to emphasize again that the pattern alone or the material it is made of is not the information per se, although we are often tempted to think that way. ...information must not only have a purpose on part of the sender, it must have a meaning for the recipient in order to elicit the desired change. – Juan G. Roederer, Information and Its Role in NatureMung_{June 17, 2011
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So what is this powerful yet "ethereal" something that resides in CDs, books, sound waves, is acquired by our senses and controls our behavior, sits in the genome and directs the construction and performance of an organism? It is not the digital pits on the CD, the fonts in the books, the oscillations of air pressure, the configuration of synapses and distribution of neural activity in the brain, or the bases in the DNA molecule - they all express information, but they are not the information. Shuffle them around or change their order ever so slightly - and you may get nonsense, or destroy an intended function! On the other hand, information can take many forms and still mean the same - what counts in the end is what information does , not how it looks or sounds, how much it is, or what it is made of. Information has a purpose , and the purpose is, without exception, to cause some specific change somewhere, some time - a change that otherwise would not occur or would occur only by chance. Information may lay dormant for eons, but it is always intended to cause some specific change. ... In summary, information is a dynamic concept. - Juan G. Roederer, Information and Its Role in NatureMung_{June 17, 2011
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I won’t be able to make a start on the coding for a week or two, but I’ll give you the odd progress report
Post any source code as you go?Mung_{June 17, 2011
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Dr Liddle,
The critical issue here is that a ribosome does not change its state as a result of reading the information. It more takes the form of an assembler, and it does something with the information it reads. Charged tRNA (providing the necessary protocols for decoding the symbols) are physically brought together with those symbols inside the ribosome, and that meeting results in the proper ordering of amino acids. The issue is not about chemicals reacting with one another to change states; it’s about the processing of information in a chemical domain. The symbols are embedded in chemistry, the protocols are embedded in chemistry, the assembler is embedded in chemistry, but the output of the system is constrained by the prescriptive and informational sequence (not by a change in states). This dynamic would of course need to be reflected in your simulation.
Yes, that’s fine, though I’d point out that this describes catalytic reactions which are not particularly mysterious. But yes, that’s fine. I will ensure that the output of my system at least leave the original informational sequence unchanged (though of course, as in life, it may deform or reform during the process of doing what it has to do – DNA is not inert as it is being “read”.)
I think we may be talking past each other here. I was indicating that the ribosome does not change its state as you had suggested in your previous post. Instead, it assembles polypeptides based upon the informational sequence given to it by mRNA. It does so by bringing the mRNA sequence together with the charged tRNA, which has an amino acid bound on one end of the molecule and an anti-codon discretely positioned on the other (isolated from the amino acid). In response to this you return to say that you’ll make sure the “original informational sequence” is left unchanged (except for any random variation that may impact it). (?!?!) What “original informational sequence” are you referring to? For there to be an informational sequence, it would require that arbitrary symbols and discrete protocols already be established – the rise of which is the very thing that you wish to demonstrate. I also cannot parse this sentence “DNA is not inert as it is being ‘read’” in order to understand what you intended to convey. The sequence within DNA is always inert, and at no time during the transcription or translation of DNA does that sequence become necessary. I am not sure where you are going with this, but it concerns me that it could have no relevance to the observed biology.
There have been numerous attempts to find a chemical basis for a particular codon being matched to a particular amino acid. All those attempts (meaning each and every one of them) has ultimately failed. The slight stereochemical affinities within the system indicate that the constituent parts are well suited to their job, but there is zero evidence that stereochemistry actually determined the full suite of associations (and even if they did, that would still not determine the sequence of codons). In the end, what can be said about the relationship of codon to AA is what can be actually observed from the physical evidence itself. The association of one codon to one amino acids is caused by the sequence of symbols in DNA which codes for the production of specialized tRNA to provide the protocol for translation. Those tRNA molecules hold the amino acid on one end of the molecule while displaying the anticodon on the other end. The amino acid and the codon do not interact. In other words, it’s the arbitrary gap in the causal chain which is bridged only by the information in DNA.
I’m not sure I buy that. But let’s leave it for now. We seem to have established a fairly usable amount of common ground
Exactly what part don’t you buy? You didn’t actually say. It’s critically important if you wish to incorporate the observed dynamics into your simulation.
One of the inferences within the design argument is that the only demonstrated source of digitized information is an intelligent agent. In the case of the genome, it is base 4 digital, read linearly.
I think this argument is fallacious. For a start, even if “digital” were a good description of DNA, it wouldn’t follow that because some known cases of digital information have been intelligently designed, all must be. But for a second, I’m still not convinced that “digital” is a good description of DNA information (for the same reasons I am uneasy about your previous point) and if it is, it isn’t in “Base 4?! Or only in the most attenuated of senses. On the other hand I am quite happy to concede that in another sense DNA is is “digital” but in Base 2 – the switching on and off of genes in response to nested contingencies really is rather like a digitized database, where the right “record” is selected according to a complicated “find” algorithm.
Referring to the symbol system in DNA as digital is not my argument – or better to say, it is my argument, but I am not the one that created it. Everyone from Richard Dawkins to Elmer Fudd has pointed to the digital nature of DNA sequencing, and I agree with them as a matter of my own observation. - - - - - - Just to be open, after reading your past couple of posts, I am concerned that what you intend to provide is not going to be a meaningful reflection of the dynamics at work. Perhaps you can describe at some sensible level of detail what you propose or expect to show, and how that incorporates the observations we've discussed.Upright BiPed_{June 17, 2011
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UBP: Just responding to the second part of your post?
Now some comments regarding your responses to my last post (points 1-9)
I am certainly happy to stipulate that information only exists when it is “recorded”. And I’d like to suggest that “recording” must involve a) the storage of the information in some form that can be “read” by another object in such a way that that object can change its own state according to the “information” read. If you are happy with this (I don’t think it’s perfect, but it’s not bad) then I’m with you. And in that context, then I would accept that DNA, for example, contains recorded information, as it can be “read” by another object (which, depending on the level of analysis, we can regard as the cell itself, or a specific ribozome) which then changes its own state (kinetically or morphologically) as a result. And if you want to call this “symbolic” then that is fine.
The critical issue here is that a ribosome does not change its state as a result of reading the information. It more takes the form of an assembler, and it does something with the information it reads. Charged tRNA (providing the necessary protocols for decoding the symbols) are physically brought together with those symbols inside the ribosome, and that meeting results in the proper ordering of amino acids. The issue is not about chemicals reacting with one another to change states; it’s about the processing of information in a chemical domain. The symbols are embedded in chemistry, the protocols are embedded in chemistry, the assembler is embedded in chemistry, but the output of the system is constrained by the prescriptive and informational sequence (not by a change in states). This dynamic would of course need to be reflected in your simulation.
Yes, that's fine, though I'd point out that this describes catalytic reactions which are not particularly mysterious. But yes,that's fine. I will ensure that the output of my system at least leave the original informational sequence unchanged (though of course, as in life, it may deform or reform during the process of doing what it has to do - DNA is not inert as it is being "read".)
Well, if we define information as recorded information, and if we define recorded information as symbolic, then this is necessarily true, indeed, circular. So obvious not falsifiable. However, if there is wiggle room between recorded information and symbolic representation, then it is not circular, but then I need to know in what way you are distinguishing recorded information from symbolic representation.
Allow me to modify my statement slightly. Matter that has been arranged to contain information is arranged to contain a symbolic representation. This is a comment about the form of the arrangement, it is symbolic.
OK.
I would certainly agree that given one nucleotide, there is no chemical grounds for predicting the next. However, I would not agree (if it were what you were saying) that a given sequence (a codon, for instance) is chemically unrelated to the amino acid that it “codes” for. Is that what you are saying? Although I might agree that a different kind of cell (perhaps on another planet) might have a different kind of ribosome that resulted in a different amino acid from the one that would result from a given codon in an earthly cell. So if that is the sense in which the codon is abitrarily assigned, then I guess I could get behind that, and concede that “symbol” is appropriate.
There have been numerous attempts to find a chemical basis for a particular codon being matched to a particular amino acid. All those attempts (meaning each and every one of them) has ultimately failed. The slight stereochemical affinities within the system indicate that the constituent parts are well suited to their job, but there is zero evidence that stereochemistry actually determined the full suite of associations (and even if they did, that would still not determine the sequence of codons). In the end, what can be said about the relationship of codon to AA is what can be actually observed from the physical evidence itself. The association of one codon to one amino acids is caused by the sequence of symbols in DNA which codes for the production of specialized tRNA to provide the protocol for translation. Those tRNA molecules hold the amino acid on one end of the molecule while displaying the anticodon on the other end. The amino acid and the codon do not interact. In other words, it’s the arbitrary gap in the causal chain which is bridged only by the information in DNA.
I'm not sure I buy that. But let's leave it for now. We seem to have established a fairly usable amount of common ground :)
A distinction is made between information presented in analog form, versus that in the genome which is a sequence of repeating digital symbols being decoded in a linear fashion following rules established by the configuration of the system (that configuration itself being determined by the information it is created to decode). What distinction? Or what distinction that matters? (Also I’m uneasy about “digital” here, but maybe it’s OK.)
One of the inferences within the design argument is that the only demonstrated source of digitized information is an intelligent agent. In the case of the genome, it is base 4 digital, read linearly.
I think this argument is fallacious. For a start, even if "digital" were a good description of DNA, it wouldn't follow that because some known cases of digital information have been intelligently designed, all must be. But for a second, I'm still not convinced that "digital" is a good description of DNA information (for the same reasons I am uneasy about your previous point) and if it is, it isn't in "Base 4"! Or only in the most attenuated of senses. On the other hand I am quite happy to concede that in another sense DNA is is "digital" but in Base 2 - the switching on and off of genes in response to nested contingencies really is rather like a digitized database, where the right "record" is selected according to a complicated "find" algorithm. But that's for another thread maybe :)
I had to rush, but I tried to cover some territory here, and hope I was successful. I look forward to your response.
And then I was slow to find your rushed response! Well, we got there, and yes, there's a lot of level playing field there that I think we can use. Thanks. I won't be able to make a start on the coding for a week or two, but I'll give you the odd progress report :) LizzieElizabeth Liddle_{June 17, 2011
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d'oh. Thanks!Elizabeth Liddle_{June 17, 2011
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Thanks. I’m not familiar with the abbreviation “IT”
IT is the word "it" in capital letters, not an abbreviation. :)Mung_{June 17, 2011
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Then, I await your results.Upright BiPed_{June 17, 2011
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@Upright BiPed #339 Thank you very much for your post, and the link to it, and apologies for the delay. I have now bookmarked this thread (which unfortunately is so long that it takes an unconscionable time to load!) and will try to check it regularly, until this conversation moves to a new thread.
Dr Liddle, To endure the amount of grief that ID proponents have to take, one would think that at the bottom of the theory there would at least be a big booming “tah-dah” and perhaps a crashing cymbal or two. But unfortunately that’s not the case; the theory doesn’t postulate anything acting outside the known laws of the universe.
Cool. Yes, I understand that.
I bring this up because you want to design a simulation intended to reflect reality to the very best of your ability, and in this simulated reality you want to show something can happen which ID theory says doesn’t happen. Knowing full well that reality can’t be truly simulated, it’s interesting that the closer you get to truly simulating reality, the more stubborn my argument becomes. Only by not simulating reality does your argument have even a chance of being true.
Heh. I recognise the sentiment. The devil is always in the details :) But we shall see.
Yet, if ID says that everything in the material universe acts within the laws of the universe, then what is it exactly to be demonstrated within this simulation? In other words, what is the IT? Of course, since this is set up to be a falsification, the IT is for prescriptive information exchange to spontaneously arise from chance and necessity. But that result may be subject to interpretation, and so consequently you want to know exactly what must form in order for me to concede that your falsification as valid.
Thanks. I'm not familiar with the abbreviation "IT" unfortunately, but I think I get your drift. I hope so. I would certainly agree that the Study Hypothesis (H1 in my language) is "for prescriptive information exchange to spontaneously arise from chance and necessity". And so to falsify the null (that prescriptive information exchange can spontaneously arise from chance and necessity) yes, I want to know the answer to that question. Good!
I intend to try and fully answer that question in this post. - – - – - – - – - – - – - I’m sure you are aware of the Rosetta stone, the ancient stone with the same text written in three separate ancient scripts. Generally, it gave us the ability to decode the meaning of the ancient hieroglyphs by leading us to the discrete protocols behind the recorded symbols. This dovetails precisely with the conversations we’ve had thus far regarding symbols, in that there is a necessary mapping between the symbol and what it is to be symbolized. And in fact, it is the prime characteristic of recorded information that it does indeed always confer that such a mapping exists – by virtue of those protocols it becomes about something, and is therefore recorded information as opposed to noise.
Trying to parse: the prime characteristic of recorded information is that it confers (establishes? requires?) a [necessary] mapping between symbol and what is symbolised. So what about these "protocols"? What I'm thinking is that in living things, the big genetic question is: by what means does the genotype impact the phenotype? And the answer is something like a protocol I like. But let me read on....
In retrospect, when I stated that recorded information requires symbols in order to exist, it would have been more correct to say that recorded information requires both symbols and the discrete protocols that actualize them. Without symbols, recorded information cannot exist, and without protocols it cannot be transferred. Yet, we know in the cell that information both exists and is transferred.
Yes. And I like that you refer to "the cell" and not simply "the DNA".
This goes to the very heart of the claim that ID makes regarding the necessity of a living agent in the causal chain leading to the origin of biological information.
Let me be clear here: by "living agent", are you referring to the postulated Intelligent Designer[s]? Or am I misunderstanding you?
ID views these symbols and their discrete protocols as formal, abstract, and with their origins associated only with the living kingdom (never with the remaining inanimate world). Their very presence reflects a break in the causal chain, where on one side is pure physicality (chance contingency + physical law) and on the other side is formalism (choice contingency + physical law). Your simulation should be an attempt to cause the rise of symbols and their discrete protocols (two of the fundamental requirements of recorded information between a sender and a receiver) from a source of nothing more than chance contingency and physical law.
Cool. I like that.
And therefore, to be an actual falsification of ID, your simulation would be required to demonstrate that indeed symbols and their discrete protocols came into physical existence by nothing more than chance and physical law.
Right. :)
The question immediately becomes “how would we know?” How is the presence of symbols and their discrete protocols observed in order to be able to demonstrate they exist? For this, I suggest we can use life itself as a model, since that is the subject on the table. We could also easily consider any number of human inventions where information (symbols and protocols) are used in an “autonomous” (non-conscious) system.
OK.
For instance, in a computer (where information is processed) we physically instantiate into the system the protocols that are to be used in decoding the symbols. The same can be said of any number of similar systems. Within these systems (highlighting the very nature of information) we can change the protocols and symbols and the information can (and will) continue to flow. Within the cell, the discrete protocols for decoding the symbols in DNA are physically instantiated in the tRNA and its coworkers. (This of course makes complete sense in a self-replicating system, and leads us to the observed paradox where you need to decode the information in DNA to in order to build the system capable of decoding the information in DNA).
Nicely put. And my intention is to show that it is not a paradox - that a beginning consisting of a unfeasibly improbable assemblage of molecules, brought together by no more than Chance (stochastic processes) and Necessity (physical and chemical properties) can bootstrap itself into a cycle of coding:building:coding:building: etc.
Given this is the way in which we find symbols and protocols physically instantiated in living systems (allowing for the exchange of information), it would be reasonable to expect to see these same dynamics at work in your simulation.
Yes, I agree. Cool!
I hope that helps you “get to the heart of what [I] think evolutionary processes can’t do”.
Yes, I think so. That is enormously helpful and just what I was looking for. This will take me some time (weeks, anyway, and I have a few RL things to do as well!) but I may pop back if I have any questions in the interim. Thanks! I'll address your responses to my other posts later (again, it may take me a while as there is a lot to chew on, and I have the weekend-from-hell on the horizon. Don't think, if I pop in and comment elsewhere, that I have forgotten the rest of your post ;) Cheers LizzieElizabeth Liddle_{June 17, 2011
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Sorry, Upright BiPed, and thanks for the link. I am reading your long post now.Elizabeth Liddle_{June 17, 2011
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Well, my position is that IDists have failed to demonstrate that what they consider the signature of intentional design is not also the signature of Darwinian evolutionary processes.
But the signature of Darwinian evolutionary processes is that they can do anything, no matter how improbable.Mung_{June 17, 2011
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And if Dr Liddle you do not intend on responding to #339 can we expect you to retract this statement: "Well, my position is that IDists have failed to demonstrate that what they consider the signature of intentional design is not also the signature of Darwinian evolutionary processes."Upright BiPed_{June 17, 2011
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Dr Liddle, do you intend on responding to post #339....or not?Upright BiPed_{June 17, 2011
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In everyday language we say we have received information, when we know something now that we did not know before. If we are exceptionally honest, or a philosopher, we assert only that we now believe something to be the case which we did not previously believe to be the case. Information makes a difference to what we believe to be the case. It is always information about something. It's effect is to change, in one way or another, the total of 'all that is the case' for us. This rather obvious statement is the key to the definition of information. – Donald M. MacKay, Information, Mechanism and Meaning
Mung_{June 15, 2011
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We shall find it profitable to ask: 'To what does information make a difference? What are its effects?' This will lead us to an 'operational' definition covering all senses of the term, which we can then examine in detail for measurable properties. - Donald M. MacKay, Information, Mechanism and Meaning
Until his death in February, Donald M. MacKay (1922-1987) was professor emeritus of neuroscience at Keele University in Staffordshire, England. He founded the Department of Communication and Neuroscience at Keele in 1960, which has become a research institute of international standing.Mung_{June 15, 2011
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ID views these symbols and their discrete protocols as formal, abstract, and with their origins associated only with the living kingdom (never with the remaining inanimate world).

Addresses numerous questions, including: Is information reducible to the laws of physics and chemistry? Does the Universe, in its evolution, constantly generate new information? Or are information and information-processing exclusive attributes of living systems, related to the very definition of life? Information and Its Role in Nature
Mung_{June 14, 2011
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Mung, Oh most definitally. ;)Upright BiPed_{June 14, 2011
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Sorry for the delay, the group that pays me to analyze data needed some data analyzed.
Would it be safe to say that the data they wanted analyzed is about something?Mung_{June 14, 2011
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Dr Liddle, To endure the amount of grief that ID proponents have to take, one would think that at the bottom of the theory there would at least be a big booming “tah-dah” and perhaps a crashing cymbal or two. But unfortunately that’s not the case; the theory doesn't postulate anything acting outside the known laws of the universe. I bring this up because you want to design a simulation intended to reflect reality to the very best of your ability, and in this simulated reality you want to show something can happen which ID theory says doesn't happen. Knowing full well that reality can't be truly simulated, it’s interesting that the closer you get to truly simulating reality, the more stubborn my argument becomes. Only by not simulating reality does your argument have even a chance of being true. Yet, if ID says that everything in the material universe acts within the laws of the universe, then what is it exactly to be demonstrated within this simulation? In other words, what is the IT? Of course, since this is set up to be a falsification, the IT is for prescriptive information exchange to spontaneously arise from chance and necessity. But that result may be subject to interpretation, and so consequently you want to know exactly what must form in order for me to concede that your falsification as valid. I intend to try and fully answer that question in this post. - - - - - - - - - - - - - I'm sure you are aware of the Rosetta stone, the ancient stone with the same text written in three separate ancient scripts. Generally, it gave us the ability to decode the meaning of the ancient hieroglyphs by leading us to the discrete protocols behind the recorded symbols. This dovetails precisely with the conversations we've had thus far regarding symbols, in that there is a necessary mapping between the symbol and what it is to be symbolized. And in fact, it is the prime characteristic of recorded information that it does indeed always confer that such a mapping exists – by virtue of those protocols it becomes about something, and is therefore recorded information as opposed to noise. In retrospect, when I stated that recorded information requires symbols in order to exist, it would have been more correct to say that recorded information requires both symbols and the discrete protocols that actualize them. Without symbols, recorded information cannot exist, and without protocols it cannot be transferred. Yet, we know in the cell that information both exists and is transferred. This goes to the very heart of the claim that ID makes regarding the necessity of a living agent in the causal chain leading to the origin of biological information. ID views these symbols and their discrete protocols as formal, abstract, and with their origins associated only with the living kingdom (never with the remaining inanimate world). Their very presence reflects a break in the causal chain, where on one side is pure physicality (chance contingency + physical law) and on the other side is formalism (choice contingency + physical law). Your simulation should be an attempt to cause the rise of symbols and their discrete protocols (two of the fundamental requirements of recorded information between a sender and a receiver) from a source of nothing more than chance contingency and physical law. And therefore, to be an actual falsification of ID, your simulation would be required to demonstrate that indeed symbols and their discrete protocols came into physical existence by nothing more than chance and physical law. The question immediately becomes “how would we know?” How is the presence of symbols and their discrete protocols observed in order to be able to demonstrate they exist? For this, I suggest we can use life itself as a model, since that is the subject on the table. We could also easily consider any number of human inventions where information (symbols and protocols) are used in an “autonomous” (non-conscious) system. For instance, in a computer (where information is processed) we physically instantiate into the system the protocols that are to be used in decoding the symbols. The same can be said of any number of similar systems. Within these systems (highlighting the very nature of information) we can change the protocols and symbols and the information can (and will) continue to flow. Within the cell, the discrete protocols for decoding the symbols in DNA are physically instantiated in the tRNA and its coworkers. (This of course makes complete sense in a self-replicating system, and leads us to the observed paradox where you need to decode the information in DNA to in order to build the system capable of decoding the information in DNA). Given this is the way in which we find symbols and protocols physically instantiated in living systems (allowing for the exchange of information), it would be reasonable to expect to see these same dynamics at work in your simulation. I hope that helps you “get to the heart of what [I] think evolutionary processes can’t do”. - - - - - - - - - - - - - In a previous post, you offered the following operational definition as a starting point.
Information is a representation of a discrete object/thing embedded in an arrangement of matter or energy, where the object/thing represented is entirely dissociated from the representation.
Perhaps that definition can be adjusted slightly to accommodate the preceding, such as: Information is a representation of a discrete object/thing embedded in an arrangement of matter or energy, where the object/thing represented is entirely dissociated from the representation, but where the association of the two can be established by means of a protocol instantiated in the receiver of the information. Personally I think the definition is a little unwieldy, but perhaps it’s workable as definition when the sender could indeed be an inanimate process instead of a living thing. Yet, even if the preceding definition were acceptable, it doesn’t capture some of the issues previously discussed. For instance it says nothing about the fact that the rise of information you are attempting to simulate is digital in form. - - - - - - - - - - - - - Now some comments regarding your responses to my last post (points 1-9)
2. The state of an object does not contain information; it is no more than the state of an object. To become recorded information, it requires a mechanism in order to bring that recording into existence outside of the object itself. As I said earlier, a carbon atom has a state which a physicist can demonstrate, but a librarian can demonstrate the information exists as well. They both must be accounted for.
OK. This is important, so I’m going to try to be as articulate as I can: I am certainly happy to stipulate that information only exists when it is “recorded”. And I’d like to suggest that “recording” must involve a) the storage of the information in some form that can be “read” by another object in such a way that that object can change its own state according to the “information” read. If you are happy with this (I don’t think it’s perfect, but it’s not bad) then I’m with you. And in that context, then I would accept that DNA, for example, contains recorded information, as it can be “read” by another object (which, depending on the level of analysis, we can regard as the cell itself, or a specific ribozome) which then changes its own state (kinetically or morphologically) as a result. And if you want to call this “symbolic” then that is fine.
The critical issue here is that a ribosome does not change its state as a result of reading the information. It more takes the form of an assembler, and it does something with the information it reads. Charged tRNA (providing the necessary protocols for decoding the symbols) are physically brought together with those symbols inside the ribosome, and that meeting results in the proper ordering of amino acids. The issue is not about chemicals reacting with one another to change states; it’s about the processing of information in a chemical domain. The symbols are embedded in chemistry, the protocols are embedded in chemistry, the assembler is embedded in chemistry, but the output of the system is constrained by the prescriptive and informational sequence (not by a change in states). This dynamic would of course need to be reflected in your simulation.
4. Matter that has been arranged in order to contain information doesn’t exist without symbolic representations. Prove it otherwise.
Well, if we define information as recorded information, and if we define recorded information as symbolic, then this is necessarily true, indeed, circular. So obvious not falsifiable. However, if there is wiggle room between recorded information and symbolic representation, then it is not circular, but then I need to know in what way you are distinguishing recorded information from symbolic representation.
Allow me to modify my statement slightly. Matter that has been arranged to contain information is arranged to contain a symbolic representation. This is a comment about the form of the arrangement, it is symbolic.
[Point #5] I would certainly agree that given one nucleotide, there is no chemical grounds for predicting the next. However, I would not agree (if it were what you were saying) that a given sequence (a codon, for instance) is chemically unrelated to the amino acid that it “codes” for. Is that what you are saying? Although I might agree that a different kind of cell (perhaps on another planet) might have a different kind of ribosome that resulted in a different amino acid from the one that would result from a given codon in an earthly cell. So if that is the sense in which the codon is abitrarily assigned, then I guess I could get behind that, and concede that “symbol” is appropriate.
There have been numerous attempts to find a chemical basis for a particular codon being matched to a particular amino acid. All those attempts (meaning each and every one of them) has ultimately failed. The slight stereochemical affinities within the system indicate that the constituent parts are well suited to their job, but there is zero evidence that stereochemistry actually determined the full suite of associations (and even if they did, that would still not determine the sequence of codons). In the end, what can be said about the relationship of codon to AA is what can be actually observed from the physical evidence itself. The association of one codon to one amino acids is caused by the sequence of symbols in DNA which codes for the production of specialized tRNA to provide the protocol for translation. Those tRNA molecules hold the amino acid on one end of the molecule while displaying the anticodon on the other end. The amino acid and the codon do not interact. In other words, it’s the arbitrary gap in the causal chain which is bridged only by the information in DNA.
7. A distinction is made between information presented in analog form, versus that in the genome which is a sequence of repeating digital symbols being decoded in a linear fashion following rules established by the configuration of the system (that configuration itself being determined by the information it is created to decode).
What distinction? Or what distinction that matters? (Also I’m uneasy about “digital” here, but maybe it’s OK.)
One of the inferences within the design argument is that the only demonstrated source of digitized information is an intelligent agent. In the case of the genome, it is base 4 digital, read linearly. - - - - - - - - - I had to rush, but I tried to cover some territory here, and hope I was successful. I look forward to your response.Upright BiPed_{June 14, 2011
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Heh. No problem. I have a fair bit of data chunking through some analysis programs myself right now :) LizzieElizabeth Liddle_{June 14, 2011
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Elizabeth Liddle, Sorry for the delay, the group that pays me to analyze data needed some data analyzed. :) I will return shortly...Upright BiPed_{June 14, 2011
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F/N: Just to make it clear that the Chi metric is not THE definition of CSI, let us look at the X-metric for functionally specific information (similar to what is in the UD weak argument correctives): X = C * S * B, in functionally specific bits C is a dummy variable that is 1/0 according as one is beyond the 1,000 bit threshold, S is a similar dummy variable on functional specificity and B is the file size or the information metric in bits. In effect if you see a Word file that takes up 197 k bits, and it is being looked at from the perspective of functional specificity, the file size recognised as functionally specific, will be reported: 197 k bits. By contrast, a random bit string of similar size will not be functionally specific and will be reported as a 0. A functionality specific file of size 90, 490 or 900 bits will similarly go to zero on the grounds that the size is insufficient to be confident that chance based processes could not have given rise to it. [Again, high contingency is seen a, on the grounds that lead us to infer to lawlike natural necessity from consistency in behaviour.) The approach is similar, but the way the result is reported is different. GEM of TKIkairosfocus_{June 14, 2011
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F/N: On operational definitions and definitionitis as a road to infinite regress and/or question-begging. One of the advantages of taking a comparative difficulties, worldviews approach to issues, is that it allows one to see the balance of different approaches on the merits, in light of factual adequacy, coherence and explanatory power [simply elegant, not simplistic or ad hoc]. So, we can easily see that one of the fundamental limits we face is that we cannot warrant everything relative to something else. If we question A, we have to move to B, then the question is why B. Thence, C, D, . . . We have but three options: (a) infinite regress -- absurd; (b) circularity -- self-defeating [and this includes systems that claim to hang together like a raft floating on a sea -- coherence is not all]; (c) grounding our systems of thought in first plausibles that are properly basic. Indeed, we are left with the often un-acknowledged importance of self-evident foundational claims. That is, things which are seen as not only so, but which, on our experience of the world and understanding of it, MUST be so, on pain of patent absurdity. In short, "rigour" has its limits, and the demand for "proof" and "definition" have even sharper limits. Not all things are capable of proof, not even mathematics -- post Godel -- is capable of proof beyond possibility of contradiction, and chains of definitions must end in accepted primitive concepts not amenable to the demand for further definition, other than in the end by pointing to examples of reality and implicitly calling on our capacity to understand; i.e. ostensive definition on key examples and family resemblance thereto. As a classic example, LIFE [the major underlying feature of our world that is at the heart of the ID controversy] is not amenable to any other definition than by pointing out key examples and calling for sufficient family resemblance. So, to then act as though other things will not end there [e.g. by dismissing an ostensive definition as an appeal to analogy or the like], is to be absurdly selectively hyperskeptical, and if one does this knowingly, one is hypocritical. Going on, we must face a critical weakness of operational definitions: they are tainted by their ancestral roots in self-refuting logical positivism, which in effect brazenly asserted that the only meaningful claims were those that could be subjected to operational tests and/or were true by being analytic statements [in effect first tautologies as in Mathematics]. The fatal flaw: this claim is self-referential and itself is -- surprise -- not subject to operational test and is plainly not analytic. It is self-refuting, as it declares itself meaningless by implication. But, as long as that self referentiality and incoherence are not spotted, it often seems invulnerable and a very handy club to knock over what one is inclined to reject. (Notice the importance of a balance of the three main worldview tests and that of self-examination of a system by bringing it too to the table of comparative difficulties.) So, we know that (while such definitions can be useful in our toolbox of concept clarifications) not everything can be operationally defined, and that many things can only be accessed in light of concepts formed on open-minded examination of key examples. In addition, mathematical models and metrics are actually quite flexible, as was discussed at length in a previous thread. The same posts showed as well that "rigour" in mathematics is subject to sharp limits in practice, so we must beware of self-refuting selective hyperskepticism in dismissal arguments. So, yes, there hsould be no double-standard of an easy pass to a favoured view, but that also means tha there should be no imposition of selective hyperskepticism, demanding: "extraordinary claims require ~~extraordinary~~ [adequate, reasonable, accessible] evidence." We must note, too that the hyperskeptic, so long as he is pointing the finger elsewhere and presenting demands for "proof" etc, can appear invincible, but so soon as s/he must now step up to the same table of comparative difficulties as the rest of us, his or her unexamined assumptions and/or self referential incoherences soon enough raise serious questions. On our experience, we know what design is. Even, to post a comment challenging the nature of design is to give an example of design -- the poster designs the comment. Similarly, we can easily enough know what complex specified information is, as the same post is an example. In Wicken's classic description in the context of living systems:
‘Organized’ systems are to be carefully distinguished from ‘ordered’ systems. Neither kind of system is ‘random,’ but whereas ordered systems are generated according to simple algorithms [[i.e. “simple” force laws acting on objects starting from arbitrary and common- place initial conditions] and therefore lack complexity, organized systems must be assembled element by element according to an [[originally . . . ] external ‘wiring diagram’ with a high information content . . . Organization, then, is functional complexity and carries information. It is non-random by design or by selection, rather than by the a priori necessity of crystallographic ‘order.’ [[“The Generation of Complexity in Evolution: A Thermodynamic and Information-Theoretical Discussion,” Journal of Theoretical Biology, 77 (April 1979): p. 353, of pp. 349-65.]
Earlier, Orgel had written:
. . . In brief, living organisms are distinguished by their specified complexity. Crystals are usually taken as the prototypes of simple well-specified structures, because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures that are complex but not specified. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity. [[The Origins of Life (John Wiley, 1973), p. 189.]
Similarly, when one composes a post, one provides a string of alphanumerical characters that must be arranged according to rules of meaningful function, and which are essentially arbitrary symbols expressing a code. So, let us have done with pretence that CSI is not real for want of sufficiently rigorous definitions, metrics etc. We know it, we cannot but exemplify it, and the same sort of examples that we provide in making posts that pretend to object to it, are to be found in the heart of the living cell's digitally coded instructions: digital, symbolic code that follows rules of meaning. But, can we so define this that we can measure it in ways that are amenable to empirical testing? Yes. And again, this has long been adequately done over and over and over again, never mind oceans of wasted ink and rivers of equally wasted digital bandwidth on all sorts of objections that ever so often fail by exemplifying what they object to: the reality of comnplex specified information, and especially of functionally specific complex information. Dembski's key contribution was to identify that if we see an informational event E that comes from a separately definable and specific set T, where T is itself in a config space, let's say W, that is sufficiently large that the set T is maximally unlikely to be chanced upon by a random walk rewarded by trial and error success, on accessible resources, then the best explanation of E from T in W is design. What this boils down to is that if we can reduce E to a string or if E is already a string of symbols, that can in turn be evaluated as a set of structured yes/no questions of sufficient length, such a random walk based search will be maximally likely to fail, as the scope of search relative to the scoe of W is so small that the search, let us call that R, rounds down to R/W --> 0. But, a random walk implies a flat random distribution and we have no right to such an assumed distribution! Not quite, it can be shown that on average, searches -- as opposed to searches designed based on knowledge of the domain being searched -- in spaces will do no better than the sort of random walk just described, providing we have a topology that does not give us clues as to the location of the target zones T unless we are already there. In short, the features of clever searches that exploit clues that point to targets, such as nice trends, will have no information fed into their search and improve modules in the algorithms [and the search for a relevant and effective algorithm is a higher order, more complex search than the direct RW based search]. Besides, the very point of something that can store symbolic information is that it must be highly contingent, so to a first approaximation, it will fit close enought to this sort of approach that the model is instructive. In this context, the reason why E is probably about 1/8 of the letters in this post and other similar texts in English is because an intelligence is following the conventional rules of English, not because of any inherent bias in the physical system. [As at now my keybpoard's E looks more like an I than an E, no prizes for guessing why.] So, we may quantify. Simplifying Demsbski's discussion, we may reduce a certain metric of such CSI as follows:
1: Where I = - log2 P, per standard definition and methods 2: Or where, as the case of Shannon showed, I may be directly estimated from the physical storage characteristics and/or the statistical patterns of symbol usage 3: And where S is a dummy variable of value 1/0 according as we have a warranted conclusion that an event E comes from a specific zone T in config space of possibilities W, e.g. on seeing the effect of modest perturbation, or on observing the specificity of the rules for a code, or by noting the specifications and tolerances to function etc [i.e. this is a definition by key case and family resemblance], 4: We see Chi_1000 = I*S - 1,000, in bits beyond the observed cosmos threshold 5: Where Chi_1000 goes positive, we are warranted to infer on best current explanation that an object or event E with that vsalue, is designed.
It is asserted that this is a well-tested metric, and that it is empirically quite reliable. For intance, it is claimed thsat all cases of at least 143 ASCII characters of meaningful text on the Internet that we know the source of, will prove to be the product of intelligences. Indeed, it is asserted that we routinely infer form say posts in this thread to intelligent posters, on intuitive grounds closely connected to this quantification. The real problem is, this suggests that certain phenomena, i.e. the living cells, are the ultimate product of design. That is, that language, intelligently designed code, algorithms, functional organisation and the like are antecedent to the cell based life we observe. But many claim to "know" that this is wrong, or that the claimed powers of chance variations and natural selection and extensions from that to origin ofr life contexts are sufficient to explain what we see without such an inference. On what grounds? a: Demonstration by example? (Genetic algorithms are usuually trotted out as a claimed example. But such are plainly intelligently designed and start inside zones T, where there are so-called fitness fucntions that provide trends pointing to peaks of performance. These are therefore actually examples of the truth of the claim they are used to object to.) b: Intelligence was not possible at the time and place in question? (On what grounds, apart from question-begging assertions?) c: We must not allow a Divine Foot in the door of the hallowed halls of science? (This is blatant question-begging materialistic prejudice and censorship that undermines the inegrity of science.) d: Maybe, we will see an explanation in the future that will solve the problem of how chance and necessity can account for CSI without appealk to design? (This is an appeal to blind faith in an IOU that has been in circulation for 150 years, and has so far not been redeemed. Backing it up by the sort of intimidatory tactics an d snide dismissals that are unfortunstely all too common does not help matters.) e: Something else will come up? (This is an appeal to blind faith.) So, now, let us look seriously at the matter, with fresh eyes. GEM of TKIkairosfocus_{June 13, 2011
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