EA nails it in a response to an insightful remark by KN (and one by Box): “the ability of a medium to store information is inversely proportional to the self-ordering tendency of the medium”

_{kairosfocus

March 23, 2013

Intelligent Design}

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Here at UD, comment exchanges can be very enlightening. In this case, in the recent Quote of the Day thread, two of the best commenters at UD — and yes, I count KN as one of the best, never mind that we often differ — have gone at it (and, Box, your own thoughts — e.g. here — were quite good too 😀 ).

Let’s lead with Box:

Box, 49: [KN,] your deep and important question *how do parts become integrated wholes?* need to be answered. And when the parts are excluded from the answer, we are forced to except the reality of a ‘form’ that is not a part and that does account for the integration of the parts. And indeed, if DNA, proteins or any other part of the cell are excluded from the answer, than this phenomenon is non-material.

KN, 52: the right question to ask, in my estimation, is, “are there self-organizing processes in nature?” For if there aren’t, or if there are, but they can’t account for life, then design theory looks like the only game in town. But, if there are self-organizing processes that could (probably) account for life, then there’s a genuine tertium quid between the Epicurean conjunct of chance and necessity and the Platonic insistence on design-from-above.

EA, 61: . . . the evidence clearly shows that there are not self-organizing processes in nature that can account for life.

This is particularly evident when we look at an information-rich medium like DNA. As to self-organization of something like DNA, it is critical to keep in mind that the ability of a medium to store information is inversely proportional to the self-ordering tendency of the medium. By definition, therefore, you simply cannot have a self-ordering molecule like DNA that also stores large amounts of information.

The only game left, as you say, is design.

Unless, of course, we want to appeal to blind chance . . .

So — noting that self-ordering is a species of mechanical necessity and thus leads to low contingency — we see the significance of the trichotomy necessity, chance, design, and where it points in light of the evidence in hand regarding FSCO/I in DNA etc. END

Comments

Thank you very much Eric. And you should know how much I have gained from your comments as well. Thanks!Upright BiPed_{April 3, 2013
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Spoofing on steroids?kairosfocus_{March 30, 2013
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UB @163: Thanks for the additional details. Incidentally, I hope it comes through in my comments, but I should say directly that you have some of the best comments on the topic of information and have obviously put a lot of thought into it. Your approach to semiotics in particular has been helpful and I've learned much from your efforts. Just a couple of quick thoughts on pheromones. Not necessarily disagreeing with your comments right now, just wanted to throw out a couple of observations as I think through this out loud, so to speak. - A pheromone might indeed tend towards its lowest potential energy state, but the pheromone is not necessarily the lowest potential energy state of the individual atoms. In other words, it may often be an uphill chemical climb to construct the actual pheromone molecule (which, once constructed, would tend towards its lowest potential energy state). The construction of a pheromone will therefore often depend on specific construction instructions and processes and will not necessarily occur through purely natural processes. - The information (signal/message) in a pheromone is really just "I'm here; I exist." As such, by itself it really only has the same amount of 'information' as any other molecule. - However, there are two aspects that make the pheromone more meaningful than any old molecule: (i) it is an arbitrary construct, meaning it generally does not otherwise exist in nature (though, to be sure, some pheromones might be similar to otherwise naturally-occurring molecules,* and (ii) the recipient understands that the simple "I'm here" carries dependent meanings that go along with it, such as "I'm available and interested in mating." Thus, when the simple "I'm here" signal is received, it ends up conveying more information than another naturally-occurring molecule might. - That said, there are lots of other (non-pheromone) molecules that also convey information in the broad sense in which you are talking right now: The bees sensing pollen, a predator sensing the scent of its prey, etc. As a result, I'll have to think through whether and in what sense these might be regarded as information. It seems that nearly any interaction between two organisms might arguably depend on some of these kinds of "signals" being conveyed and received, but it would seem they are a different kind of information than what we are talking about in a representative semiotic system? Anyway, just a couple of things to chew on. I'll think about this some more as well. ----- * Just yesterday my neighbor, a retired engineer who has been exposed to various scientific applications in his career, was telling me about how his friend created a way to protect crops from a certain pest. The short of it is that they were able to identify the pheromone that triggered the mating habits and then created a synthetic version. By spraying it all over the field (the "I'm here" signal was everywhere), the males became confused and eventually either tired or became conditioned to ignore the real pheromone. It was an overload of the pheromone -- false positives of the "information" signal -- that eventually caused the mating to fail and protected the crops.Eric Anderson_{March 29, 2013
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Eric, of course you will recognize that the DNA sequence is transcribed to mRNA. The same issues apply.Upright BiPed_{March 28, 2013
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Hi Eric, I’ll do a layman’s best. From an earlier question, I wrote:
Any material object (including any material medium) must adhere to a one of the fundamental principles of physics, often referred to as the Minimum Total Potential Energy Principle. This principle states that any physical structure (of any size, shape, or make-up) will distort and twist, and naturally orient itself to seek its lowest potential energy state. One might think of it in general terms as an object seeking a balance of all the physical forces acting upon it.
..and I gave a link HERE describing the principle. So a pheromone is a chemical substance, such as bombykol or other chemosemiotic compound, and as such, it in fact a chemical structure with specific physical and chemical characteristics. As a material structure it assumes its lowest potential energy state, and is recognizable within its system by assuming that state and those physical and chemical characteristics. In other words, it is those characteristics that make it an identifiable representation to a receptor within the system. By being a recognized structure it serves as a representation of some variable or other form. I’ve flirted with this being a prime example of analog semiosis, but have not committed to it. On the other hand, there are other mediums of information whose identifiable characteristics are not at all a result of the medium assuming it lowest potential energy state, they exist independent of it. Earlier I offered the simple example of written text. The word “apple” written in ink on a piece of paper is a material structure, and the ink will soak into the paper and together they will interact to assume their combined lowest potential energy state. However, what is recognized within the system is solely the arrangement of the ink on the paper, and that arrangement has nothing whatsoever to do with the lowest potential energy state of ink and paper. DNA exemplifies this same phenomenon. The nucleic triplet C-T-A evokes the addition of leucine to a polypeptide. But the isolated causal structure C-T-A does not exist (as it does) as a matter of the DNA molecule assuming its lowest potential energy state. The sequence of nucleotides along the backbone of DNA is not determined by this state. The nucleotides can easily be re-arranged to evoke a different response within the system. Also up-thread, I made the observation that coding systems which are state independent are also capable of encoding virtually any amount or form of information (if the appropriate protocol exist), whereas state dependent mediums are limited in comparison. The reason I brought this up in the first place was because I think your comments in the OP have great merit, and I thought you might want to consider how these observations might impact your formulation.Upright BiPed_{March 28, 2013
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UB @160: UB, can you give me a bit more detail about your pheromone example and what you mean by it being the lowest potential energy state? I'm not sure I'm clear on the example and want to make sure I understand it. Thanks,Eric Anderson_{March 28, 2013
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Eric, I'm sorry to be so late in responding, but I have now been able to snatch a few moments from a busy time in my life. You said"
The topic of this thread, and the context of the statement I made, as quoted in the OP, is the alleged possibility of self-ordering as an explanation for the origin of information-rich systems.
Eric, thank you for saying "alleged." That is a degree of modesty that one rarely encounters when a protagonist is making a sweeping claim. (I trust that you accept the characterization that your claim is bold and sweeping.)
The argument is not as you have written it. Rather, it is as follows: - The self-ordering tendency of a medium is inversely proportional to the medium’s information carrying capacity. (This is an empirical observation, as has been explained above and as can be understood by reviewing Shannon’s information metric.)
"...an empirical observation, as has been explained above..." I assume that this refers to your #20. I'm sorry, but I don't see any empirical observations in that post. I see hypothetical examples of what you seem to mean by "self-ordering," but I see no references to observations of naturally occurring phenomena that support your concept (invented, as far as I can discern) of "self-ordering." Maybe my understanding of "empirical" as you construe it is deficient. In any case, I have no idea how your concept of "self-ordering" relates to the observable world of phenomena. I'll stop here, awaiting your clarification.Daniel King_{March 28, 2013
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Groov, ”Biped declared seemingly that there were two ways to store information and seemed to distinguish between “types” of information” There are two general ways in which the identifiable characteristics of a medium may be recognized and function within its system; those that identify the medium as a matter of it assuming its lowest potential energy state (like a pheromone), and those that identify characteristics of the medium that are independent of the medium assuming its lowest potential energy state (like language). And I also stated that systems which operate independent of that state are less limited in their coding capacity. Frankly, you are sort of making my point for me. Let’s go back to your example of the light switch, where you say that finding it in its ON position tells you that ‘your wife wants the light on’. Well Groovamos, no it doesn’t. The position of the switch neither codes nor represents anything whatsoever about your wife. You added all of that as a matter of being a cognitive intelligent agent. The only thing the position of the switch represents is whether the light is ON or OFF. As a representation of a variable, that is its general limit. However, as I said earlier, adding you (and your human mind) into the system changes everything, because you (as a natural-born symbol maker) can make it represent anything you want. For instance, let us say that you want to be able to store significantly more information in a message and transfer that message to an observer. Perhaps you want to be able to use the position of the switch to answer the question “What is your name and do you like Buddy Miles” then certainly it can be done. Simply establish a protocol for encoding the information (perhaps something similar to Morse code for instance) and store your answer within a series of flips of the switch. No problem. The issue being highlighted here is that the code you create will have nothing whatsoever to do with whether the light switch is at rest in either the ON or OFF position. You can invert and/or change the code at will. The function of the system will be determined by the pattern and protocol; it will be independent of the lowest potential energy state of the switch. - - - - - - - - - - - - - - - - - - KF, I am not certain that I or Groov have made an error here. I think we are just not talking from the same frame of reference. Of course, I stand to be corrected.Upright BiPed_{March 28, 2013
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Groov: No need for CMOS, two BJT's will do. The key issue is as I said, that we need metastable states that can be triggered by surmounting potential hills, leading to controllable storage in the states. If UB has a minor error, it is correctable without loss of the fundamental point. And back on topic, EA's point is right: lack of ability to go to controllable contingent states does diminish ability to store information. KFkairosfocus_{March 28, 2013
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OK a few mistakes in last post, I was in a hurry. A bistable can be made from two CMOS inverters as well as gates. What's interesting is that whereas a spring activated switch is stable at the lowest potential energy state(s), a CMOS bistable is stable at the lowest power dissipation states, no potential energy state enters the picture as such. There is a potential energy peak as the switch changes state, there is a power peak coincident with the bistable changing state. I let myself get into this because Biped declared seemingly that there were two ways to store information and seemed to distinguish between "types" of information, based on the previous (?) two ways to store information?groovamos_{March 27, 2013
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Groov: All that is required to store information in A PRACTICAL SYSTEM is state-contingency associated with (i) controllability and reasonable change-ability of state [thus metastability which allows lowered vulnerability to noise AND change when needed], (ii) a protocol by which information is represented in a standard way, (iii) a system for storing, recognising and retrieving, transmitting and detecting the information. Debates on energy states beyond that are a distractor. KFkairosfocus_{March 27, 2013
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Biped, you used the term "store information" and this is exactly what a bistable does. OK maybe the key is that information cannot exist without a mind. dnd personally I would say this includes genetic information but I can't prove it, the is outside the reach of science possibly. An Kfocus how does what you describe above relate to one of the other ways to store energy other than a state with the lowest potential energy such as in the light switch. How about lowest power dissipation?groovamos_{March 27, 2013
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Hello groov Your first post spoke about a rusty or heat-damaged spring, and your second post didn't even mention it ... so perhaps I am not following you. I stated that mediums that are recognizable within their systems as a result of the medium assuming its lowest potential energy state are generally limited in comparison to mediums that code form independently of that energy state, and you want to demonstrate otherwise by making the human mind the reciever of the symbol - where it can literally mean anything or nothing at all, completely independent of the actual function of the lightswitch itself, having either everything or nothing whatsoever to do with whether or not the light is turned on, or off, or is even present? Is that what your response is? May I ask, do you envision this additional capacity to be the result of the spring, or the presence of the mind?Upright BiPed_{March 26, 2013
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Groov, light switches are usually the first example of digital info stred in a 2 state system used in digital electronics courses. Indeed, the basic gates [NOT, NAND, NOR] are actually switch and resistor circuits, from rail to gnd. The NOT has a voltage controlled switch, which when activated drops the o/p to low. The NAND uses two (or more) in series, and the NOR uses two in parallel. And yes, these are the "natural" gate ckts. Cross-couple a pair of NANDS or NORS, and you have the RS flipflop the first memory element. So, the light switch is a1-bit element, and uses the metastable positions on or off, transited between based on a higher energy state, which does use the spring. I thought I had said somewhat about this already. Notice, the issue of metastability. KFkairosfocus_{March 26, 2013
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Biped: I have no idea how the spring in a light switch relates to the topic of information storage or lowest potential energy state of an information-bearing medium. Well does the position of a light switch bear information? I thought this was fairly apparent but here goes - the information could take the form of: (1) My wife likes the light on. (2) If the switch is in the up position, and the light is off then there is a burned out bulb, unless (3) The circuit breaker is tripped unless (4) I just put in a new florescent bulb. In other words a binary quantity actually has informational value. Sometimes referred to as digital information as in the information age.groovamos_{March 26, 2013
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Major premise: Self-ordering and storing capacity are inversely proportional (mutually exclusive) in a medium. Minor premise: The amount of information in DNA is excessive Conclusion: DNA cannot arise by self-ordering (natural processes).Box_{March 26, 2013
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Daniel King @149: Thank you for your good faith effort. However, you seem to have missed the argument, so let me summarize it again. The topic of this thread, and the context of the statement I made, as quoted in the OP, is the alleged possibility of self-ordering as an explanation for the origin of information-rich systems. The argument is not as you have written it. Rather, it is as follows: - The self-ordering tendency of a medium is inversely proportional to the medium's information carrying capacity. (This is an empirical observation, as has been explained above and as can be understood by reviewing Shannon's information metric.) - Therefore, media with high information carrying capacity do not arise through natural self-ordering processes. As it relates to a specific system, such as DNA, we can add the following: - DNA is an information-rich medium (and, by the way, is also known to not have a self-ordering tendency of the bases). - Therefore, DNA did not arise through natural self-ordering processes. This is not circular. It is based on what we do know about information-rich systems and the constraints that exist on the storage and transmission of information. Incidentally, I have not said that DNA could not arise naturally. Only that it did not arise through any kind of self-ordering, self-organization, chemical necessity, or other law-like process. DNA could have arisen by pure chance. Indeed, that it the only possibility left on the table . . . unless one is willing to consider design.Eric Anderson_{March 26, 2013
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I'm no expert on syllogisms, but I would think a more appropriate one might be: - Information storing systems do not arise via natural self-organizing processes - DNA is an information storing system - DNA did not arise via natural self-organizing processesPhinehas_{March 26, 2013
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Eric, This thread is getting elderly by blog standards, and I don't want to prolong things, but I feel that I owe you the courtesy of trying to reply to your #144, where you update me on your revised statement @106. “By definition, therefore, you simply cannot have a molecule like DNA arise through purely natural self-organization processes and also store large amounts of information.” I don't see that this changes the concept. Consider the following syllogism, which is my good-faith effort at sorting out your argument: Major premise: Information-storing molecules like DNA cannot arise naturally Minor premise: DNA stores information Conclusion: Therefore, DNA could not have arisen naturally It appears to me that you have assumed your conclusion.Daniel King_{March 26, 2013
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F/N: Re EL
there is no evidence for anything without a brain designing anything. And no evidence for anything with a brain designing biology, at least before people came along.
1 --> This "there is no evidence" gambit is well past sell-by date. It overlooks or inappropriately brushes aside and dismisses the highly material body of evidence of cosmological fine tuning, which points to a mind beyond matter behind the observed cosmos and any wider material multiverse. 2 --> Once such a mind is even possible, evidence that per well warranted signs points to a design of cell based life and of the cosmos that hosts it, should not be overlooked or dismissed. (And it should be pointed out -- per the logic of necessity of being, which is relevant as God is envisioned as eternal -- that those who assert or imply that they know that there is no God, have taken up the task of either showing that God is not a serious candidate to be a necessary being [hopeless], or else of showing that God is an impossible being [attempted, failed since Plantinga's successful free will defense shattered the logical form of the problem of evil].) 3 --> And there is abundant such evidence in cells pointing back to the original living cells, which can be summed up under FSCO/I for short. As has been repeatedly discussed here at UD. 4 --> But if a materialistic controlling assumption is allowed to rule unquestioned, and to a priori dismiss evidence that points beyond matter to mind, then there is a subtle, underlying worldview level begging of the question at work. Such will warp the evaluation of evidence, as has here apparently happened with the issue of a fine tuned cosmos, and the linked issue of contingency vs necessity of being. 5 --> This is what I noted to Dr Liddle in the linked intro to cosmological ID thread July 19, 2011 at 8:24 am, when she said at 6:56 am the same day, to Ilion "I’d be happy to posit a First Causer of some kind. It’s calling it God and worshipping it that I don’t get." Namely:
The cosmological design inference is about the relevant causal process that gives rise to a cosmos such as we observe, with a beginning at a finite distance in the past and with evident fine tuning fitting it for C chemistry cell based life, including intelligent life. The logic of a contingent cosmos leads to looking for an explanation external to it, which at root must per logic be a necessary being. The multiverse proposal is every inch a candidate necessary being, and being lacking in empirical data, it is every inch a metaphysical proposal. The fine tuning raises the issue of design intent. Other issues come up at worldviews level, which make theism a serious candidate. cf here for a discussion. Remember, once multiverses are on the table this is now a phil discussion on comparative difficulties. Every serious alternative has a seat at that table as of right, not sufferance.
6 --> It is worth noting that EL never responded, vanished from the thread at this point. Perhaps, she will now be willing to take it up in light of the associated issues and evidence. 7 --> Notice, we are looking here at a necessary being as the causal root of the observed material cosmos and/or wider material multiverse [where per the past 100 years of physics we know matter to be contingent, try implications of E = m*c^2 for one aspect . . . ], with the knowledge, skill, power and intent to build at least one life-friendly cosmos that sits at a massively fine tuned operating point that facilitates life. A necessary being, by the logic of necessity -- having no external dependence on enabling "on/off switch" causal factors has no beginning, and cannot come to an end. 8 --> In addition, given the sorts of self-referentiality and incoherence issues implied by evolutionary materialism regarding the credibility of knowledge, reasoning and truth seeking of a mind wholly explained on a brain formed by blind chance and mechanical necessity, I would take serious pause before too closely associating brain and mind. That is why I have for years underscored the Smith cybernetic two-tier controller model. Let me add a clip from J B S Haldane thast focusses this aspect enough to show some of what I am getting at:
"It seems to me immensely unlikely that mind is a mere by-product of matter. For if my mental processes are determined wholly by the motions of atoms in my brain I have no reason to suppose that my beliefs are true. They may be sound chemically, but that does not make them sound logically. And hence I have no reason for supposing my brain to be composed of atoms. In order to escape from this necessity of sawing away the branch on which I am sitting, so to speak, I am compelled to believe that mind is not wholly conditioned by matter.” [["When I am dead," in Possible Worlds: And Other Essays [1927], Chatto and Windus: London, 1932, reprint, p.209.]
9 --> This too needs to be discussed. KFkairosfocus_{March 26, 2013
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Lizzie sez:
However, there is no evidence for anything without a brain designing anything. And no evidence for anything with a brain designing biology, at least before people came along.
And there isn't any evidence to support your position's claims so we must not exist.Joe_{March 25, 2013
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Eric has fully addressed the issue in #106 where he reworded his last sentence in order to remove any ambiguity. Perhaps Danial King will have a chance to read that reworded sentence, and can move to his next comment for EA.Upright BiPed_{March 25, 2013
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DK: it should be fairly clear how DNA stores information per how RNA works as a control tape in the ribosome etc, also having been explicitly stated above; that the chaining chemistry (which makes the string structure) is independent of the particular bases and is at right angles to the side-prong height/config due to a side chain [comparable to that on a Yale lock], which is how the info value is stored -- four values per base, due to A/G/C/T (or U for RNA) -- so that the sequence stipulates a 4-state per character code. Cf. pic, courtesy NIH. KFkairosfocus_{March 25, 2013
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DK @143: Please see my comment @106. I think the context of the original statement was rather obvious, but to address this very point I wrote #106 to make sure everyone was on the same page. Thanks,Eric Anderson_{March 25, 2013
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Eric, It was kind of you to respond so generously to my comments @112. Since I may not have time in the next day or two to answer each point, I will start with this: I had written:
The principle may apply to digital information, but it may not apply to chemical information.
The principle under discussion (as I understand it) is: ...the ability of a medium to store information is inversely proportional to the self-ordering tendency of the medium. Eric replied:
The principle applies to information storage and transmission media and it doesn’t make any difference whether the medium is nucleotides, amino acids, letters in an alphabet, digital signals in a computer or otherwise.
It's Eric's principle, which he is entitled to apply to anything he likes, but he seems to contradict himself. How can it apply to DNA, of which he said:
By definition, therefore, you simply cannot have a self-ordering molecule like DNA that also stores large amounts of information.
How can DNA store information if by definition it can't? I know I'm not the brightest candle on the tree, so please be gentle in your correction of my confusion. (Assuming that you care to respond to such a dullard.)Daniel King_{March 25, 2013
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EA is precisely correct. A physical object does not contain information by its mere existence. If it does, then everything contains information, and we'll need new words to describe and differentiate those things that are actually arranged to contain information and/or operate within systems that recognize those arrangements. Saturn's hexagon has form, but it does not contain information. That form becomes information only when it is instantiated in the arrangement of a medium. In this case, that medium resides in the sensory systems of the researcher and his instrumentation.Upright BiPed_{March 25, 2013
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And I ahve explained why I am an ID supporter. OTOH no one seems to be able to explain why they support evolutionism.
They don’t support it. They accept it as the most evidenced hypothesis currently available.
Except there aren't any testable hypotheses nor evidence that supports evolutionism. Either you are lying- most likely- or you are totally clueless. And teh fact that artificial ribosomes do not function, and have the same matter and energy configuration as ribosomes found in living organisms, tells us there is more than matter and energy at work. And my comment in 126 describes the positive part of the design inference. As I said, your ignorance is not a refutation although you seem to think that it is.Joe_{March 25, 2013
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DK @111:
If you measure the atomic coordinates of a crystal, you have acquired information about the structure. What message have you acquired?
This is a good question, but let me first dispense with the elephant in the room. Does Elzinga seriously think there is information "contained" in Saturn's hexagonal cloud structure in the same way that there is information contained in DNA? Back to your question, it is important to keep in mind the difference between information about an object and the mere existence of the object. We've discussed this on another thread, but briefly: An object does not "contain" information just by its mere existence. Using Saturn's hexagon as an example, since it was brought up, we see that there is a diffuse roughly hexagonal shape in Saturn's cloud structure. Does this hexagon contain any code, any language, any message, any instruction set? No. It is true we can use instruments to take measurements about the hexagon -- perhaps its size, location, rotational speed, dissipation/formation rate, etc. -- and those measurements are now information. And, like all information, those measurements and the related details can now be stored and conveyed in a medium, subject to the principles we've been discussing. So the observer in observing the physical phenomenon and in taking measurements creates information, which can then be stored and conveyed. But that is very different than saying the hexagon itself "contains" the information. Physical objects don't contain information in any meaningful sense of the word by their mere existence. This can be easily contrasted with DNA, for example, which clearly contains information. To be sure, we can also study the structure of DNA, as we did Saturn's hexagon, and as a result of that study also produce information about DNA -- its diameter, its length, the number of nucleotide bases, the helix structure, etc. And here is the fun part: we could then store that information in DNA. This is possible because DNA not only exists as a physical object, but has the ability to store large amounts of information. ----- Now before ending let me anticipate a quibble. Many people are confused (or purposely obtuse) about what is meant by "information" and will want to quibble and argue that the information about Saturn's hexagon is somehow "contained" in the hexagon itself. (It isn't. The information is produced by an intelligent agent in its research and study of the physical object.) But that is really a distraction for two reasons. First, it is clear to the objective observer that the kind of information found in DNA differs both in quantity and quality from any alleged information found in Saturn's hexagon. Second, it is a semantic game. If someone insists that Saturn's hexagon "contains information," we can just define that is "Information 1." We can then define the kind of information contained in DNA, in a digital code, or in a written language, as "Information 2." Then we can proceed to have a rational discussion using the term "Information 2" and it will be obvious that the kind of information "contained" in Saturn's hexagon is not Information 2. So even if someone mistakenly thinks there is some kind of meaningful information contained in Saturn's hexagon, it doesn't in any way address the kind of information contained in DNA or the issues we are discussing. Again, for the kind of information we are discussing -- complex specified information -- there is a critical distinction between information about a physical object and information contained in a physical object.Eric Anderson_{March 25, 2013
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Semi related: Top Ten Most Cited Chemist in the world wants to understand evolution but can’t – James Tour, Phd. – video http://www.youtube.com/watch?v=WCyAOCesHv0bornagain77_{March 25, 2013
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DK @112: Lots of stuff in your comments, so let's go through them.
The principle may apply to digital information, but it may not apply to chemical information.
The principle applies to information storage and transmission media and it doesn’t make any difference whether the medium is nucleotides, amino acids, letters in an alphabet, digital signals in a computer or otherwise.
What is the “instruction manual” analog in the chemical assembly of protein structures?
There is a whole suite of information involved in the building of a protein, from the nucleotide sequence in DNA, to the machinery that locates, reads, transcribes the DNA, to the mapping of the nucleotide sequence to amino acids, and so on. None of this just happens. It all occurs because the cellular machinery is following a precisely laid out instruction set.
Persons who don’t have a solid background in chemistry and physics may think that they know things that they haven’t a clue about.
Agreed. Like people who think that complex functional information-rich systems just arise through natural processes of chemistry and physics.
Spontaneous protein folding has been demonstrated. Google Anfinsen experiment. Google protein folding. The cellular machinery that assists folding is mainly “chaperonins,” which are themselves protein assemblages.
First of all, it is not clear what your point is. I have already said that there may be some spontaneous protein folding. Further, I went ahead and Googled ‘Anfinsen experiment’ and the first link I found showed that you are incorrect in your assumption. Specifically, it says: “This led to the discovery of an enzyme called protein disulfide isomerase (PDI)—an enzyme that catalyzes reduction of incorrect disulfide bonds and allows a protein trapped in an incorrect conformation to unfold and try again.” What is this review and correction process doing in what is supposed to be a purely spontaneous chemical process? Regardless, the fact of the matter remains that many (perhaps most) proteins do not just spontaneously fold into their correct shape without other machinery in place to assist in folding, check the folding, or break down incorrectly folded proteins. Furthermore, in most cases proteins work in complexes that themselves must be built in the correct way. It doesn't just happen by chemistry and physics.
That looks like a change of subject. We were discussing self-assembly and self-organization.
Then perhaps you’re misunderstanding the subject. Even if we have some cases of spontaneous protein folding, the folding would be utterly dependent on the sequence of amino acids. You seem to be very focused on the protein folding aspect, but that is only the second half of the issue. Did the amino acid sequence just poof into existence? If not, then any spontaneous or self-organization type theory about the formation of proteins and larger complex structures has to fully take into account the origin of the information needed to produce the correct amino acid sequence. Here’s a video on the subject of self-assembly: I’ve already addressed this. Very simple. (What appear to be) interchangeable parts. No function. No information. Carefully isolated from potential cross-interfering reactions, etc. This is most definitely not going to convince any thoughtful observer that proteins and viruses just automatically self assemble as a rule. Nevertheless, it bears repeating that spontaneous folding is not even the key point. We are talking about the information needed to build the system – in this case, to get the right amino acid sequence in place in the first place.Eric Anderson_{March 25, 2013
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