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”

Thank you very much Eric. And you should know how much I have gained from your comments as well. Thanks! Upright BiPed

Spoofing on steroids? kairosfocus

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

Eric, of course you will recognize that the DNA sequence is transcribed to mRNA. The same issues apply. Upright BiPed

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

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

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

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

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. KF kairosfocus

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

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. KF kairosfocus

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

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

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. KF kairosfocus

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

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

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

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 processes Phinehas

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

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. KF kairosfocus

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

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

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. KF kairosfocus

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

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

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

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

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

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=WCyAOCesHv0 bornagain77

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

Daniel King as to the Anfinsen Experiment on 'spontaneous' protein folding and the 'self assembling' of the virus,, first,,,

The Anfinsen Experiment in Protein Folding Excerpt: Anfinsen wanted to show that the information for protein folding resided entirely within the amino acid sequence of the protein. He choose ribonuclease A as his model for folding but he couldn't completely denature the protein unless he treated it with the denaturant urea plus 2ME to break the disulfide bridges. Under those conditions, the protein unfolded. It would refold spontaneously once he removed urea and 2ME from the folding solution.,,, However, recovery is not 100%. Mistakes are made in vitro and presumably in vivo as well. 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. http://sandwalk.blogspot.com/2007/02/anfinsen-experiment-in-protein-folding.html

Well Mr. King, if you are trying to the defend molecular reductionism of neo-Darwinism, then the fact that proteins folding is also critically dependent on the specific molecular context, of the cellular environment that the protein is in, ought to give you some pause as to your atheistic/materialistic philosophical starting point,,,

Now Evolution Must Have Evolved Different Functions Simultaneously in the Same Protein - Cornelius Hunter - December 1, 2012 Excerpt: LysRS has two different structural and functional states. When not phosphorylated LysRS is a crucial part of the translation process, supplying lysine amino acids to tRNA molecules. When phosphorylated it regulates gene expression. This is a major problem for evolutionary theory. http://darwins-god.blogspot.com/2012/12/now-evolution-must-have-evolved.html Human Genes: Alternative Splicing (For Proteins) Far More Common Than Thought: Excerpt: two different forms of the same protein, known as isoforms, can have different, even completely opposite functions. For example, one protein may activate cell death pathways while its close relative promotes cell survival. http://www.sciencedaily.com/releases/2008/11/081102134623.htm Genes Code For Many Layers of Information - They May Have Just Discovered Another - Cornelius Hunter - January 21, 2013 Excerpt: “protein multifunctionality is more the rule than the exception.” In fact, “Perhaps all proteins perform many different functions by employing as many different mechanisms." http://darwins-god.blogspot.com/2013/01/genes-code-for-many-layers-of.html

moreover,,

Nature Review Article Yields Unpleasant Data For Darwinism - August 2011 Excerpt: The number of possible shapes that a protein can fold into is very high and folding reactions are very complex, involving the co-operation of many weak, non-covalent interactions. A high percentage of proteins do not fold automatically into the required shape and are at risk of aberrant folding and aggregation. As the abstract to this paper states: “To avoid these dangers, cells invest in a complex network of molecular chaperones, which are ingenious mechanisms to prevent aggregation and promote efficient folding.” https://uncommondescent.com/intelligent-design/nature-review-article-yields-unpleasant-data-for-darwinism/

,,, and if the preceding does not do it for you, then the following certainly ought to divest you of any preconceived bias you have towards the neo-Darwinian molecular reductionism model you have for protein folding,,,

Physicists Discover Quantum Law of Protein Folding – February 22, 2011 Quantum mechanics finally explains why protein folding depends on temperature in such a strange way. Excerpt: Their astonishing result is that this quantum transition model fits the folding curves of 15 different proteins and even explains the difference in folding and unfolding rates of the same proteins. That's a significant breakthrough. Luo and Lo's equations amount to the first universal laws of protein folding. That’s the equivalent in biology to something like the thermodynamic laws in physics. http://www.technologyreview.com/view/423087/physicists-discover-quantum-law-of-protein/ Testing quantum entanglement in protein Excerpt: The authors remark that this reverses the previous orthodoxy, which held that quantum effects could not exist in biological systems because of the amount of noise in these systems.,,, Environmental noise here drives a persistent and cyclic generation of new entanglement.,,, In summary, the authors say that they have demonstrated that entanglement can recur even in a hot noisy environment. In biological systems this can be related to changes in the conformation of macromolecules. http://www.quantum-mind.co.uk/testing-quantum-entanglement-in-protein-c288.html

Now Mr. King all you have to do, since material particles are themselves not the cause for quantum entanglement (Bell, Aspect, Zeilinger, Leggett), is find a 'non-local', beyond space and time cause, for the quantum entanglement we find in proteins. I already have my beyond space and time cause Mr. King! As to the 'self assembling' virus video you referenced. (the one with magnets), I am severely unimpressed if this is your proof that molecules can 'self assemble' into man: First you completely ignored the fact that Darwinists have yet to demonstrate the origination of a single non-trivial functional protein by purely material processes (Axe, Sauer), Second that model and test tube for virus 'self assembly', in the video you cited, is a gross oversimplification for what is actually happening in the assembly of a virus. And though the following video is still not close to showing the complexity involved, it is much better than the willful distortion you have presented in that video:

The Virus - Assembly Of A Molecular "Lunar Landing" Machine - video http://www.metacafe.com/watch/4023122 Virus caught in the act of infecting a cell (w/ video) - January 10, 2013 Excerpt: The researchers show that when searching for its prey, the virus briefly extends—like feelers—one or two of six ultra-thin fibers it normally keeps folded at the base of its head. Once a suitable host has been located, the virus behaves a bit like a planetary rover, extending these fibers to walk randomly across the surface of the cell and find an optimal site for infection. http://phys.org/news/2013-01-virus-caught-infecting-cell-video.html

bornagain77

DK: Please, observe the full context, all together:

Did you bother to read above in the thread where the case of the magnetic blocks shaken in a tube and clicking together as designed was discussed? What are the problems with it, and why does it seem to you to be anything but an intelligently designed system doing what it was made to do, reflecting the power of FSCO/I coming from such design? What does this say about the way the chance-necessity mindset is blinding people to see what SHOULD be obvious, is indeed blatant? (Do you see how frustrating it can be to have to go in circles to again explain what should have been obvious on a glance, then was stated in so many words already, a day ago; especially if there is now an argument on the case that is wholly unnecessary?)

The self assembling plastic mechanism with magnets aligned just so, was not ignored, the evidence instead is that you refused to simply scroll up and read, as was suggested. (I suggest you look here at 27 above before further replying.) Similarly, in the world of biological molecules, the issue is as you know that proteins are assembled in highly specific strings in ways that use codes to guide the AA sequences, which is what was to be explained. Just as, that on shaking the plastic fitted parts with embedded magnets fit together is not what is to be explained, it is how they come to be in that shape with those aligned magnets. As was pointed out almost 24 hrs ago above. What I find significant is that when confronted with something as obvious as this, there is a typical latching on that almost predictably fails to notice the obvious. The special shaping and the magnets involved are not exactly hidden. And, this is a carefully aligned, interfaced, with fit made just so, item. This is nothing more or less than a demonstration of how an intelligent designer can make something and use available random forces to assemble a designed object. As a way to get back on track, I suggest that the following, from a certain Michael Denton, will be helpful:

To grasp the reality of life as it has been revealed by molecular biology, we must magnify a cell a thousand million times until it is twenty kilometers in diameter [[so each atom in it would be “the size of a tennis ball”] and resembles a giant airship large enough to cover a great city like London or New York. What we would then see would be an object of unparalleled complexity and adaptive design. On the surface of the cell we would see millions of openings, like the port holes of a vast space ship, opening and closing to allow a continual stream of materials to flow in and out. If we were to enter one of these openings we would find ourselves in a world of supreme technology and bewildering complexity. We would see endless highly organized corridors and conduits branching in every direction away from the perimeter of the cell, some leading to the central memory bank in the nucleus and others to assembly plants and processing units. The nucleus itself would be a vast spherical chamber more than a kilometer in diameter, resembling a geodesic dome inside of which we would see, all neatly stacked together in ordered arrays, the miles of coiled chains of the DNA molecules. A huge range of products and raw materials would shuttle along all the manifold conduits in a highly ordered fashion to and from all the various assembly plants in the outer regions of the cell. We would wonder at the level of control implicit in the movement of so many objects down so many seemingly endless conduits, all in perfect unison. We would see all around us, in every direction we looked, all sorts of robot-like machines . . . . We would see that nearly every feature of our own advanced machines had its analogue in the cell: artificial languages and their decoding systems, memory banks for information storage and retrieval, elegant control systems regulating the automated assembly of components, error fail-safe and proof-reading devices used for quality control, assembly processes involving the principle of prefabrication and modular construction . . . . However, it would be a factory which would have one capacity not equaled in any of our own most advanced machines, for it would be capable of replicating its entire structure within a matter of a few hours . . . . Unlike our own pseudo-automated assembly plants, where external controls are being continually applied, the cell's manufacturing capability is entirely self-regulated . . . . [[Denton, Michael, Evolution: A Theory in Crisis, Adler, 1986, pp. 327 – 331. This work is a classic that is still well worth reading. Emphases added. (NB: The 2009 work by Stephen Meyer of Discovery Institute, Signature in the Cell, brings this classic argument up to date. The main thesis of the book is that: "The universe is comprised of matter, energy, and the information that gives order [[better: functional organisation] to matter and energy, thereby bringing life into being. In the cell, information is carried by DNA, which functions like a software program. The signature in the cell is that of the master programmer of life." Given the sharp response that has provoked, the onward e-book responses to attempted rebuttals, Signature of Controversy, would also be excellent, but sobering and sometimes saddening, reading.) ]

KF kairosfocus

Given that you’ve already inferred design, then please explain what that “more then” consists of.

I have, in a response to you, just minutes ago. Joe

When you came to the conclusion that there is more to life then matter and energy, could you describe how you eliminated chance and necessity in that process? You guys helped- by not being able to provide a testable hypothesis nor any positive evidence for teh claim. Thank you. And I ahve explained why I am an ID supporter. OTOH no one seems to be able to explain why they support evolutionism.

Joe

Joe, please watch tone. KF kairosfocus

“Therefor to refute ID and any given design inference all one has to do is step up and demonstrate that blind and undirected processes can account for it.” And Patrick disMay chimes in

So they’ve given up on even pretending that ID is anything other than a god of the gaps argument over there?

What a jerk. That is how one falsifies all given design inferences, Pat. Those are the rules. However to infer design more than eliminating blind and undirected processes are required. Again it is all based on our knowledge of cause and effect relationships- unlike your position. Joe

By your “logic” we cannot say that the Antikythera mechanism was designed.

We know humans made it.

LoL! That is NEITHER how nor when. Thank you for continuing to prove my point- you are a waste of time and skin. Joe

Therefor to refute ID and any given design inference all one has to do is step up and demonstrate that blind and undirected processes can account for it.

I’m afraid you lose out on the bonus points Joe. If you cannot talk about ID without bringing in Darwinism you are not providing positive evidence for your position.

Again with your ignorance. It wouldn't matter if darwinism never existed. The design inference mandates that necessity and chance be eliminated first. Ya see OM, it is as I said- you are scientifically illiterate and proud of it. Good luck with your ignorance and belligerence. You must be very happy... Joe

So you’ve done my work for me JoeG, you’ve shown that ID does not have answers to the questions that it claims to answer.

Strange, I didn't do any such thing. Again your ignorance is not a refutation. Joe

Yet you don’t know when or how the design happened, so on what basis are you inferring anything at all?

Please explain why it is relevant to know the how and when before determing design. By your "logic" we cannot say that the Antikythera mechanism was designed. So let's have that explanation or admit that you are not only a waste of time but also a waste of skin. Joe

And more lies:

Joe tends to attack the messenger and not the message and that is the most powerful weapon in the ID movement.

I attack people who just attack me, IDists and ignorantly swipe at ID. Your ilk's "mesage" is very clear- set up and destroy strawman after strawman, all the while ignoring the fact that your position has nothing. And buy a vowel- all you chumps do is attack the messengers. Joe

Yes, Intelligent Design is both testable and falsifiable. Intelligent Design relies on Newton's First Rule, meaning agencies are only added when REQUIRED. Therefor to refute ID and any given design inference all one has to do is step up and demonstrate that blind and undirected processes can account for it. IOW all evotards have to do to stop ID cold is to actually step up and A) produce a tyestable hypothesis for their position and B) produce positive, supporting evidence. How is ID tested? As in positive evidence? 1- See above as the way to the design inference is THROUGH the blind watchmaker 2- The criteria for inferring design in biology is, as Michael J. Behe, Professor of Biochemistry at Leheigh University, puts it in his book Darwin ' s Black Box: "Our ability to be confident of the design of the cilium or intracellular transport rests on the same principles to be confident of the design of anything: the ordering of separate components to achieve an identifiable function that depends sharply on the components.” So if nature, operating freely cannot account for it AND it meets that criteria, some agency is required and we infer design (or at least agency involvement). And again for the scientifically illiterate: Reality dictates that in the absence of direct observation or designer input, the only possible way to make any scientific determination about the designer(s) or the specific process(es) used, is by studying the design and all relevant evidence. OM has been told that countless times and yet it is so dense it just doesn't get through. Joe

So you don’t know when or how design happened, but you know it did happen and can study it? Is that about right?

That is how it works in archaelogy, forensic science and with SETI. We don't know how Stonehenge was designed and only via rigorous study have we determined a when- but that is tentative. And Stonehenge is something we are capable of constructing. The design of living organisms is above our design level. So it will take longer and more resources.

Yet it seems to me that if you don’t know when or how “intelligent design” events happen you can’t test those particular claims.

Really? Well it's obvious to me that you are a scientifically illiterate punk. The design inference is made based on our knowledge of cause and effect relationships. Period. And if you don't like it all you have to do is demonstrate that your position can account for what we say required a designer. But you can't, so you are forced into belligerent whining. Nice job Joe

Daniel, you are welcome. I take it that you are much more of an expert on molecular biology than Stephen L. Talbott. But the holistic view on life he tries to convey may be of interest to you. Do let me know what you think. Box

OM is proud to be ignorant:

Q: When do “intelligent design” events happen? Q: How do “intelligent design” events happen? Q: What have you learnt from studying the design?

Don't have to know when or how in order to determine design and study it. What have I learned? That there is more to living organisms than just matter and energy. I have also learned taht evos are cowardly losers. Unlike darwinism, ID can be tested and possibly falsified.

Please explain how.

I already have, several times. Others have also. Again your ignorance means nothing to us. Although I am sure that you are proud of your ignorance- it shows. Joe

KF,

What does this say about the way the chance-necessity mindset is blinding people to see what SHOULD be obvious, is indeed blatant?

What may be obvious to you is not obvious to me, based on my 30+ years of work in molecular biology. Of course I may be mistaken, but you might entertain the possibility that you are mistaken. Humility was a virtue extolled by St Francis of Assisi, I recall.

(Do you see how frustrating it can be to have to go in circles to again explain what should have been obvious on a glance, then was stated in so many words already, a day ago; especially if there is now an argument on the case that is wholly unnecessary?)

KF, I sympathize. But do you see how frustrating it can be to point out an example of spontaneous virus assembly (TMV) and have it ignored? Surely, we can reason together. Daniel King

And if OM ever demonstrates how his questions are relevant to ID, perhaps someone may attempt to answer them. However it is obvious that OM is ignorant of science, ignorant of ID and just plain ole ignorant. Joe

After all, Darwinism has a mechanism it can call upon.

Yes and it has failed to explain anything. Nice job. Joe

LoL!

My side “Darwinism” is the established accepted explanation for the observed fact of evolution.

It sure as hell wasn't established via positive evidence. And your questions don't have anything to do with ID. Unlike darwinism, ID can be tested and possibly falsified. I am very OK with that fact. Joe

Box, Thanks for the links to the essays by Stephen Talbott. There's a lot of material there and it may take me a while to read and digest it. I'm looking forward to learning a lot. Daniel King

OM sez:

Yes, I have asked Upright many times at what point his “information” is transferred into the universe, how that was done and so on.

And we have asked you many questions that you refuse to answer. I take it that makes you afraid. Joe

DK: Let me first note to you, again from yesterday as actually excepted above, that there is in fact a lab model for the behaviour on Saturn, which shows that the case is likely one of order stemming from mechanical necessity, of low contingency and to be contrasted with high information organisation. Second, the key distinction you need to reckon with is on contingency. When an outcome is driven by the forces acting in a mechanical way such that similar circumstances yield similar results what is at work is mechanical, lawlike necessity giving rise to order. That is, the compressibility of the description of the outcome on its antecedents is high. This is similar to something like F = m*a. A dropped heavy object reliably falls at 9.8N/kg on earth. This, of course, has been pointed out any number of times, over and over again literally for years on end, so we are back to the smart people acting like verrrry slow students problem. This points to induced blindness and blocks to seeing what should be obvious. Please think about this. Next, there are cases of high contingency, where under similar initial conditions, we have highly variable and divergent possible outcomes. If our dropped object is a fair die, its outcome will come from {1, 2, . . . 6} essentially by chance. But if we load it so say 6 comes up 1/2 the time, we have something else acting, design. This very case has been highlighted any number of times. For years. Highly contingent outcomes, as any decision tree analysis will highlight, come from two main alternatives, choice or chance. If you see 200 dice set up in a line to read all 1s, you are unlikely to ascribe that to chance. Likewise, if you were privy to a code and the dice are laid out in a code that spells the opening words of this post, that too is utterly unlikely by chance but very likely on design by comparison. We can go from this to the per aspect design inference filter -- and yes, the link is two years ago at UD -- that looks at various aspects of a phenomenon, process or object and infers from an extended form of the above analysis, grounds to see what is likely from necessity, what from chance, what from choice. Now, you seem to have a problem with messages vs information. If you equate information to the Shannon metric of information carrying capacity, you are very likely to confuse yourself, especially at the hands of design skeptics who should know better. But, in normal usage we are concerned with functional, configuration-specific information that is explicit in a string or implicit in an organised functional entity built in accordance with some sort of wiring diagram or blueprint. This is in fact the normal meaning of "information" in the context of IT etc. In that setting, messages are blocks of information transferred from a source to a sink in accord with various conventions. And, I assure you, as one with a relevant technical background to see for myself and understand [in short I am pointing out that you ate making presumptions and/or are indulging in Alinskyite personalise and polarise ad hominem attacks], that in D/RNA, the chemistry of chaining has little or nothing to do with the informational content stored in effect in prong height due to side-branches of the monomers. Rather like a Yale lock. Next, proteins in some cases do fold spontaneously to functional forms. Those forms are local energy minima specified by the van der Waals forces, interaction with water [a polar molecule], H bonds and the like. But what makes that happen is the sequence specified by the code in mRNA, transcribed form DNA. In short, proteins are informational macromolecules and they are also so uphill e4nergetically that it is unlikely indeed that hey would form in plausible prelife circumstances. There is evidence that just to get to folding, we are looking at 1 in 10^65 of AA sequence space, for typical proteins. That is a ratio of about 1 atom to a galaxy. And BTW, in many critical cases, chaperoning is used to assure that the protein folds to the desired shape. Misfolded, lower minima states are possible in significant cases, giving rise to prions, which have the nasty habit of propagating in a cascade. Hence, mad cow disease, and possibly Alzheimer's. Functional proteins are dependent on a string structure that is made in the ribosome under algorithmic, step by step control of mRNA. This in turn is made form DNA by unzipping and transcribing then editing and possibly rearranging. It is the case that the only observed source of FSCO/I is design, and it is further the case that on needle in the haystack analysis, chance processes and/or mechanical necessity are maximally unlikely to be able to create FSCO/I rich structures, due to the scope of time and atoms available in the solar system or the observed cosmos, relative to the space of possible configurations. I underscore again: self assembly is yet another red herring led away to a strawman. Including the video that is okay for a limited purpose but when used to beg the question of the source of FSCO/I befcomes a fallacy. KF kairosfocus

DK: Did you bother to read above in the thread where the case of the magnetic blocks shaken in a tube and clicking together as designed was discussed? What are the problems with it, and why does it seem to you to be anything but an intelligently designed system doing what it was made to do, reflecting the power of FSCO/I coming from such design? What does this say about the way the chance-necessity mindset is blinding people to see what SHOULD be obvious, is indeed blatant? (Do you see how frustrating it can be to have to go in circles to again explain what should have been obvious on a glance, then was stated in so many words already, a day ago; especially if there is now an argument on the case that is wholly unnecessary?) KF kairosfocus

Ha, I see that Box already linked to that video showing a model of virus assembly. Eric, it really is germane, because the self-assembly of viruses can be observed in the test tube. Google "tobacco mosaic virus self assembly" Daniel King

DK:

What does a “message” have to do with “information”?

Everything. In it's normal/ standard use, information, message and meaning all go hand-in-hand. DK, do you think that the fact that the hexagon is self-organising that means living organisms can arise from non-living matter via blind and undirected chemical processes? Joe

Daniel King @34:

I think it does relate to complex machines. I focused on DNA because that is the most obvious and easy case for most people to understand. Also, because the principle I have stated is most clearly seen in the digital information context (as kf has also noted @23).

The principle may apply to digital information, but it may not apply to chemical information.

In the context of physical machinery a similar principle holds, and I think we can still refer to the specific assembly of parts as the “information” that is used in constructing the system (think of any instruction manual you’ve seen to put together a piece of equipment).

Reasoning by analogy may have heuristic value, but this seems a stretch too far. What is the "instruction manual" analog in the chemical assembly of protein structures?

At a very basic, everyday, obvious level, we know that complex functional structure don’t just regularly come about through the natural processes of chemistry and physics.

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.

Incidentally, I don’t have an issue with the idea that some proteins might spontaneously fold into the right structure. The idea of spontaneous protein folding is a misunderstanding in most cases, because specific folding requirements exist and there is cellular machinery that helps to ensure the correct folding; but there might be cases in which spontaneous folding actually occurs.

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.

Regardless, the key point we need to focus on is the specific sequence arrangement of the amino acids – that is where the information lies, in this case being the result of a transcription and translation process from the information contained in the corresponding DNA sequence.

That looks like a change of subject. We were discussing self-assembly and self-organization. Here's a video on the subject of self-assembly: http://www.youtube.com/watch?v=X-8MP7g8XOE Daniel King

Eric Anderson commenting on a statement by Mike Elzinga about the hexagon on Saturn:

That is pretty funny. I wonder what information he imagines he sees in Saturn’s hexagonal cloud structure? Is there a message conveyed in the hexagon that only he is privy to? Sounds like he may need to study up a bit on the concepts we’re discussing.

What does a "message" have to do with "information"? Does all information have meaning? If you measure the atomic coordinates of a crystal, you have acquired information about the structure. What message have you acquired? Daniel King

Lizzie, still flailing away:

Well, yes it does, because DNA is information rich (the sequence is complex) and it is self-organising in the sense that it is part of a self-replicating system.

LoL! No Lizzie, the cell organizes the DNA. The DNA doesn't do anything that the cell doesn't tell it to do.

I am more than capable of being mistaken, but I do not intentionally post things I do not believe to be true.

Well when you keep making the same mistakes after you ahve been corrected, either you are dishonest or very stupid. Eiither way you don't belong in any discussion. And Lizzie there isn't any chemistry that makes a molecule self- replicating and self-organising. You just made that up, as usual. Joe

Optimus: Your link to Luskin's summary from Abel's 2009 work is timely. I of course cannot tell whether Abel is tongue in cheek or serious in his line of argument, but it is certainly in the peer reviewed literature. Let me clip:

while the author [Abel] notes that much effort has been spent "arguing to the lay community that we have proved the current biological paradigm," he concludes that the actual evidence for self-organization is "sorely lacking" and has been "inflated." The author emphasizes a distinction between "order" and "organization," arguing that self-ordered structures like whirlpools are readily constructed by natural processes, but "have never been observed to achieve 1) programming, 2) computational halting, 3) creative engineering, 4) symbol systems, 5) language, or 6) bona fide organization"--all hallmarks of living organisms. In contrast, living organisms are built upon programming and are highly organized, but "physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration." His solution suggests that a positive argument for design could be feasible: "No known natural process exists that spontaneously writes meaningful or functional syntax. Only agents have been known to write meaningful and pragmatic syntax." He notes that the kind of "sophisticated formal function" found in life "consistently requires regulation and control," but "[c]ontrol always emanates from choice contingency and intentionality, not from spontaneous molecular chaos."

Food for thought. KF kairosfocus

Folks: A useful onward discussion, though Joe -- kindly note -- needs to watch his language and should refrain from vulgar insults in future. Time to get back up on the wagon. Next, I had forgotten the old string length code game. JDH, thanks for the reminder. If the code can be reduced to a matrix, and a vector co-ordinate can be used, the string length can be reduced. For instance if we have an array of n * m to given the number of possibilities in the alphabet, with the (n,m) protocol adopted, we can reduce the string length to n + m [with a pause to separate strings]. This is what was done in North Vietnamese prisons by USAF and USN prisoners, who devised a 5 * 5 tapping code [I think they suppressed "c" or "k"], then later on a code based on more natural noises such as coughs etc. What this shows, again, is that a code does not exist on its own, it is embedded in an irreducibly complex system, and uses implied protocols for communication. AF has repeatedly been referred to a 101, but has evidently refused to go there. (If you want to see how he has been arguing and the evident gaps in it, cf here from Mar 19th.) Similarly, last evening, he put up an attempted counter example that in fact shows how intelligently designed chemical processes are what we can see producing DNA, and that such uses materials that come from living organisms as necessary ingredients. The evidence is that he is not here for serious interaction, nor does he acknowledge that he has duties of care to truth, accuracy and fairness. That is, he is here only to push talking points in order to try to derail serious discussion. That is sad and sadly revealing. Currently, apart from a claimed counter-example on self replication that his own link shows is not that, he has been pushing two talking points. First, that there is no such thing as design theory (which presumably implies absence of a research programme), and of course unsurprisingly, he refuses to acknowledge that there is a school of researchers on both sides of design theory work, cosmological [the likes of Gonzalez, expelled on ideological interventions precisely to hamper his research] and Scott Minnich et al on the bio side. The Marks and Dembski collaboration is very important, and of course we have the Biologic Institute. Discovery Institute is a thinktank with libertarian leanings, but it does have a list of fellows that is a pointer. Indeed, Durston is now a definite person to hold a PhD for ID related research, the first that I am aware of. That he did the work in Canada speaks volumes on the toxic environment in the US. On the life sciences side, there are now dozens of papers in the peer reviewed literature, regardless of attempts to suppress. On the Cosmological side, there is much more. His second talking point of note, is his attempt to pretend that by attacking alleged source and dismissing as of no account, he can refuse to address objective evidence regarding FSCO/I. But the problem here is first that the phenomenon obviously exists as the underlying reason why we so easily see the difference between (a) textual information, (b) repetition on constraint: XXXXXXXXXXXX, and (c) typical random strings: tgi823sqgigeofvh. Second, as a matter of fact, as the person who first used the summary descriptive abbreviation, the root of the term is two descriptions in the literature by Wicken and Orgel in the 1970's, which together point to the distinctive phenomenon of functionally specific complex organisation and associated information [FSCO/I], which may be implicit or explicitly coded. In short, AF is plainly being unreasonable and willfully mulish. This points to an attempt to push an agenda without respect to duties of care to accuracy, fairness and truth, not enter into serious dialogue. However, we should not reward such misbehaviour by allowing it to derail discussion. The focal point of this thread has been, EA's summary that when a medium is constrained by self-ordering forces, its capacity for information storage falls. This should be obvious, as the degree of flexibility [bearing in mind the need to resist noise also! one reason why digital comms can be better than analogue . . . ] allows for increased storage in the medium. DNA has 4 possible states per character, and potentially stores two bits. Proteins have 20 states per character as a rule and potentially store 4.32 bits. That is obviously more capability than we would see in a unary string that is only storing in the length, whether naive or array based. That objectors to design theory have taken something that is so simple and well substantiated, to make occasion to try to object, speaks volumes. Of course the onward issue is that it has been hoped that self-organising systems will explain origin of code based algorithm-implementing systems in life forms that unite metabolic automata and von Neumann self replicator code using facilities. To be a properly scientific assertion, such needs to be empirically warranted. That is a long way off, and there is a world of difference between vortices and geometric patterns that crop up in fluid dynamics [this weekend I was looking at jet or rocket exhaust diamond standing waves as another . . . ], and the like on the one hand and the sort of aperiodic, wiring diagram specific functional organisation of life forms and the more familiar textual and technological systems on the other. Perhaps, AF's citation from EL, is emblematic:

self-replicating molecule is both self-organising, or part of a self-organising system, and information-rich, and when that information is duplicated, it is transferred. Therefore it is a dense information storage system. Therefore DNA itself violates Eric’s rule.

DNA is in no way self-replicating, and the PolymerASE [--> enzyme, i.e. protein produced using DNA and the Ribosome system, so chicken-egg cycle . . . ] chain reaction shows no case of self replication. The assertion -- which seems to be a new talking point over at TSZ -- collapses. That is before we get to the issue that what is to be explained is the function of DNA in life forms, in which DNA stores a digital code, indeed several layers of code, and is a part of an information processing system that is embedded in the gated, encapsulated, metabolic automaton with code based self replication that we term the living cell. It is that cell that is self-replicating and pointing to its existence as though that answers the question of how such comes to be on the presumption that it "must" be by blind chance and mechanical necessity is little better than outright blatantly begging the question. The system is FSCO/I rich, and that becomes highly relevant, as such FSCO/I has but one observationally warranted -- this is inference based on what we know, having established a reliable sign -- cause, intelligent design. Given such, perhaps then it is little wonder that the pro darwinism free shot at goal challenge and invitation I issued, has now sat unanswered for six months this past weekend. What appears to me, is that we have a situation where there is a view, evolutionary materialism as ideology, that seems to be systematically blinding adherents to evidence that is there for all to inspect. The denial and dismissal stunts we are seeing, speak volumes, sad volumes. But that reductio to "eyes wide shut" and "don't confuse me with facts, my mind is made up" on the part of objectors tells us just where the balance of evidence is and what the trends are. Design theory is on the rise and ideological a priori materialism is collapsing, bit by bit. But just like the Marxists, Freudians and Behaviourists of a generation past, there will be ever so many bitter enders clinging to the sinking ship as it goes down. KF kairosfocus

Greetings, EA et al. This old ENV article from a few years back may prove helpful. http://www.evolutionnews.org/2011/01/peer-reviewed_pro-intelligent_042251.html Here's the link to the paper that's discussed http://www.mdpi.com/1422-0067/10/1/247/pdf Enjoying your comments as usual, EA! Optimus

Let me offer an olive branch in the hopes that it might help remove any possible confusion about what I stated, as quoted in the OP. In a discussion context about whether self-organizing processes in nature could account for complex biological systems, I wrote the following in a quick comment to KN:

. . . 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.

I think it is clear in this context that I am talking about an information-rich medium like DNA. I think it is also clear that we are talking about self-organization scenarios and whether such scenarios can produce something like DNA. I trust it is also clear to a reasonable reader that I am not questioning the existence of DNA. However, I realize that -- if taken out of context -- my last sentence might cause some confusion. I am obviously not trying to argue that DNA doesn't exist, but am arguing about the possible origin of an information-rich medium like DNA under self-organization scenarios. So let me restate my last sentence just so everyone is clear about the context and we are on the same page: "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 apologize if there was any confusion and hope that this helps clarify things in case there was any doubt. Thanks again to everyone for a very interesting discussion. Eric Anderson

Lizzie via Alan Fox @98:

I think what Eric might mean is that if a system is highly deterministic (given state A, it must attain state B) it can’t store additional information, because A already contains all you need to get to B.

No. What I mean is that if a medium (nucleotides, amino acids, letters in a language, etc.) has a tendency to self order, then that tendency will proportionally reduce the information carrying capacity of the medium. What this means is that we cannot rely on self-ordering scenarios to produce the information, because the self-ordering process works against the medium's information carrying capacity, as I have described in detail earlier. This does not mean that a self-replicating system cannot carry information (obviously it can). This does not mean that reproducing organisms cannot carry information (obviously they do). This does not mean that a guided/designed process cannot counteract the self-ordering tendency of a medium and nevertheless store information in the medium; but if so, it will be in spite of, not because of, the self-ordering tendency. The takeaway is that self-ordering ideas (or self-organization scenarios, as they are often called) about the formation of information-rich molecules like DNA/RNA, the formation of life, and the formation of other information-rich systems are non-starters. Such law-like processes cannot produce the kinds of information-rich systems we see. This does not mean that it didn't happen by purely natural and material processes. Remember, we still have that all-important materialist explanation for the origin of biological information: chance. Or that third possibility: design. But some are loathe to consider that option. Eric Anderson

Here is what leaves me dumbfounded: AF@34

…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.

I’m not the only one to think you are incorrect in your assertion, Eric.

You have to understand Alan that for you to say this sounds exactly like someone saying "I don't understand why you say 1 + 1 = 2, I have found a lot of people who don't believe that". If you can't get this from the very lucid explantation by EA and UpBd up above, then I begin to understand how you maintain your beliefs. You just really do not understand enough about probability, information theory, and/or signal processing to comprehend why your position is so unclear. Do you not understand the fact that a medium with only two states ( 1, 0 ), but with the additional self-orgnizing constraint that a '0' must follow a '1' and a '1' must follow a '0' carries exactly only twice as much information as a medium with only 1 character. Let's look at a practical example. If you wanted to craft a language with such a binary alphabet. The only thing you have available to you to carry information is length of string. So to create a vocabulary of 10000 unique words you need to allow for strings of 5000 characters. From each string you get only two types of information. ( 1. Which binary bir ('0' or '1') the string starts with ( after that the structure of the string is set ) 2. The the total number of characters in the string. ) So it takes strings of up to 5000 bits just to have a vocabulary of 10000 "words". OTOH - let's keep the same binary alphabet ( strings made of only '0' and '1' ) and take off the self-organizing constraint. To simplify the math ( for you ) let's add the constraint that all strings have the same length. To have a vocabulary of over 10000 words we only need strings of length 14 ( 2^14 = 16384 ). Do you not understand that removal of the self-organizing constraint allowed the information carried by 5000 bits to be carried by only 14. ( Even adding the constraint that all the strings in the second example were 14 bits long - which is only added to simplify the calculation. ) This is just not that difficult to explain. Stating that you found some people who don't believe it does not make it so. It just boggles my mind that you don't comrehend this. JDH

keiths has assured us that the existence of self-replicating molecules completely demolishes Upright BiPed's "Semiotic Argument." Mung

Elizabeth Liddle is allowed to lie all she wants to on her own blog. Mung

Lizzie via Joe @61:

Thirdly, a self-replicating molecule is both self-organising, or part of a self-organising system, and information-rich, and when that information is duplicated, it is transferred. Therefore it is a dense information storage system. Therefore DNA itself violates Eric’s rule.

DNA is most certainly not self-organizing. (BTW, I'm still looking for someone to point me to that alleged "self-replicating molecule" people keep referring to :) ). Furthermore, the existence of biological systems, including DNA and the replication machinery, is the very issue in question. So one cannot point to its existence and say, in effect, "See. There it is. That proves it can come about." The whole question is how it could come about in the first place. The existence of a self-reproducing system or a self-reproducing organism (that itself operates on the basis of information) is a red herring and is most certainly not a violation of the rule I stated. Let me say this again to make sure everyone is on the same page: the principle I outlined relates to the self-ordering tendency of an information carrying medium. What is the self-ordering tendency of the DNA bases? That's right. In the way DNA is organized the bases don't have any significant self-ordering tendency, which makes them ideal for information storage. If they did have a self-ordering chemical tendency, the information carrying capacity would be reduced, as I have already explained in detail (as has kf). This is basic. Eric Anderson

Anyone who thinks that DNA is a self-replicating molecule needs to get an education before they can join the discussion. Just sayin' Joe

Alan Fox:

I guess you didn’t follow my link. Let me quote Elizabeth Liddle:

And we have been laughing at that ever since she posted it. What was your point, Alan? It sure as hell doesn't contain any specific examples that counter what Eric said. Joe

I am open to specific examples that would counter what I stated. But general complaints without addressing the issues don’t concern me too much.

I guess you didn't follow my link. Let me quote Elizabeth Liddle:

I think what Eric might mean is that if a system is highly deterministic (given state A, it must attain state B) it can’t store additional information, because A already contains all you need to get to B. Which seems to me to be wrong for a number of reasons. Firstly, we can have self-organising systems that are highly non-deterministic – in which State A+1 depends not only on A but on other events. The result can be a highly “organised” State B, but now State B may well encode the events that resulted in State B, and not any other of the large numbers of states (also organised) that might have resulted had those events been different. Secondly, we can have self organising systems that result in highly ordered results, but which are non-reversable – A inevitably leads to B, but so do other initial states, and so A cannot be inferred from B – in which information is lost between A and B, but we can also have reversable systems in which A inevitably leads to B, but in which B is highly complex, and, while A can be inferred from it, can only be inferred from it by reversing the series of sequential steps that took it from A to B in the first place. Thus a simple pattern A could store a large amount of information, but that information is only revealed if A was allowed to “self-organise” itself into B. Thirdly, a self-replicating molecule is both self-organising, or part of a self-organising system, and information-rich, and when that information is duplicated, it is transferred. Therefore it is a dense information storage system. Therefore DNA itself violates Eric’s rule. Lastly, none of this tells you whether the thing was designed or not.>/blockquote>

Alan Fox

Thanks everyone for the comments. I’ve got a window for a few minutes so I’ll try to respond to a couple of items now. Box @25:

Do we need to distinguish between multiple kinds of self-ordering?

That is an interesting question and one worth exploring. For now, though, I think it is sufficient to distinguish between (i) something that is self-ordering in a purely natural way (which is obviously what we are talking about) and (ii) something that is self-ordering pursuant to a set of procedures and processes that have been put in place beforehand (i.e., something that comes about through a set of protocols geared toward that end). We are interested in the former in terms of some kind of naturalistic or self-organization theories of origins. BTW, the movie you linked to is interesting, but perhaps not really germane. The parts of the “virus” are of course carefully designed to fit together in a particular pattern (I can’t tell from the video, but it even looks like the parts are interchangeable). They are neatly contained in a bottle, conveniently isolated from other parts or potential cross-interference from other structures. There is no evidence that the final structure performs any function and no information content is apparent in the structure or the sequential arrangement of parts. Looks like an interesting toy, but not much beyond that. ----- Joe @26:

Mikey Elzinga“refutes” you by saying the hexagon we see on saturn is self-organising.

That is pretty funny. I wonder what information he imagines he sees in Saturn’s hexagonal cloud structure? Is there a message conveyed in the hexagon that only he is privy to? :) Sounds like he may need to study up a bit on the concepts we’re discussing.

They don’t undersatnd that DNA is not self-organising and if it were it wouldn’t be good for storing information.

Oh boy. I hope no-one is suggesting that DNA is self organizing. ----- Joe @30:

Every step of the process flows downhill, entropically, but somehow the existence of multiple alternative possibilities, and modern complexity, means that someone must have chosen this one.

I hope he isn’t suggesting that every process in DNA transcription and translation is entropically downhill. That would surely show a misunderstanding of the biology involved. In addition to misunderstanding the broader point about the mapping of nucleotides to amino acids, which is not determined by simple chemical tendencies. ----- Alan Fox @33: I am open to specific examples that would counter what I stated. But general complaints without addressing the issues don’t concern me too much. ----- Daniel King @34: I think it does relate to complex machines. I focused on DNA because that is the most obvious and easy case for most people to understand. Also, because the principle I have stated is most clearly seen in the digital information context (as kf has also noted @23). In the context of physical machinery a similar principle holds, and I think we can still refer to the specific assembly of parts as the "information" that is used in constructing the system (think of any instruction manual you've seen to put together a piece of equipment). At a very basic, everyday, obvious level, we know that complex functional structure don’t just regularly come about through the natural processes of chemistry and physics. Of course this is the realm Behe has focused on – irreducible complexity. I view irreducible complexity as something of a subset of the broader concept of complex specified information. Incidentally, I don’t have an issue with the idea that some proteins might spontaneously fold into the right structure. The idea of spontaneous protein folding is a misunderstanding in most cases, because specific folding requirements exist and there is cellular machinery that helps to ensure the correct folding; but there might be cases in which spontaneous folding actually occurs. Regardless, the key point we need to focus on is the specific sequence arrangement of the amino acids – that is where the information lies, in this case being the result of a transcription and translation process from the information contained in the corresponding DNA sequence. Eric Anderson

OK DNA is NOT a self-replicator. It gets replicated, either as part of the cellular process or via human technology and human involvement. And there isn't any theory of evolution, just a bunch of people who say there is. Joe

Evolutionary theory? Anyone? Joe

ID theory? Anyone? Alan Fox

Alan Fox:

What the people of the US decide to do in their own backyard is up to them.

By teaching evolutionism, we are crapping all over it. Joe

Am I?

Yup!

Wrong again. Have another drink and try again. Joe

Alan Fox

But baraminology? YOU summarized it Alan. YOU did.

I have to ask other commenters if they agree that baraminology is actually ID theory.

I never said it was. All I said was that YOU summarized baraminology. Why are you being such a dishonest [SNIP -- expulsion level word, warning! Time to get back up on the wagon] ?

Joe

Am I?

Yup! Alan Fox

...we should be able to teach baraminology in public schools...

Not my business, Joe. What the people of the US decide to do in their own backyard is up to them. But baraminology? I have to ask other commenters if they agree that baraminology is actually ID theory. I thought the current line is that ID is not creationism? Alan Fox

Look in the same journal that published the alleged theory of evolution. Just a couple articles after it.

Apparently you are!

Am I? Joe

Alan While I have your attention, your summary is meaningless because you cannot link to the actual thing. IOW your summary could be totally contrived. Not only that it summarizes BARAMINOLOGY. YOU have COMPLETELY dodged the question. You whiffed. Try again or admit that you are just a poseur. That said, iIs there a theory of forensic science? Is there a theory of archaeology? ID can be tested and possibly falsified. Your position cannot say the same. Joe

Look in the same journal that published the alleged theory of evolution. Just a couple articles after it.

Apparently you are! Alan Fox

By Alan's actions we can tell that there ain't no theory of evolution- one that is in a peer-reviewed journal anyway. And by the way he summarized his understanding of it, we should be able to teach baraminology in public schools as it is no diiferent from what Alan said. Joe

Joe While I have your attention, I gave you my summary of evolutionary theory. Are you now going to provide your version of "ID" theory? Is there an ID theory? You're not dodging the question, are you? Alan Fox

Alan Fox:

Presumably you mean by this there is a scientific theory of “Intelligent Design” So where is it, then?

Look in the same journal that published the alleged theory of evolution. Just a couple articles after it. Joe

Dear kairosfocus, As you can see, the word "imbecile" applies. Either that or perhaps just pathological. Should we take a vote? Joe

You now stand clearly revealed as willfully flying in the face of evident and accessible facts. KF

Presumably you mean by this there is a scientific theory of "Intelligent Design" So where is it, then? Alan Fox

Geez Alan, that-> PCR, was pathetic, even for you. Joe

Dear Alan, PCR is NOT an example of DNA self-replication. Why the dishonesty? Would DNA replicate without the technology? No. You lose, again, as usual.

“FSC-whatever” is your personal reification, G. Sorry that the Discovery Institute is not sponsoring you for further development of your “idea” but that’s life!

Dear Alan, We don't give a rat's butt what YOU call it. The fact is it exists as DEFINED. And it needs to be explained, again, regardless of what you call it. And guess what? Your position can't explain it, scientifically. Joe

...the underlying facts...

Hmm! Is someone doing field or lab work to get some underlying facts to support ID theory? But then one is driven to ask what is ID theory? I keep asking but... _______ You now stand clearly revealed as willfully flying in the face of evident and accessible facts. KF Alan Fox

You need to read the evolutionary literature, from Darwin on, which is full of the same sort of claimed dysteleological reasoning. The Panda’s thumb argument is a notorious case in point, and in fact is the name of one of the Darwin advocacy sites. That is how far wrong your confident manner assertions are. Again this evening, it seems you have not even paused to reflect on your gross error regarding the POLYMERASE Chain reaction. KF

Oh please! The Davescot speaker-in-the-ceiling is really irritating. How on Earth have I managed to make a "gross error" merely by pointing out PCR as in vitro DNA replication? Are you denying reality again? ________ AF, simply read above on how PCR works, as clipped from the opening words of the article you linked. The very name POLYMERASE Chain Rxn, is a clue, enzymes are proteins made by using DNA stored info, in this case, extracted originally from a thermophilic bacterium. The diagram and steps described will further show that this is not simple autocatalysis, you imagine and wish to pretend does the rhetorical work you claim or imply. In short, you have failed to do basic homework and have made a gross error that you seem unwilling to face. That tells us all we need to know. And the attempt to twist about the facts to pretend that I am wrong, is itself further revealing. That is now an outright propaganda tactic, one with a heritage you would not like to hear. KF. Alan Fox

...the known source of FSCO/I...

"FSC-whatever" is your personal reification, G. Sorry that the Discovery Institute is not sponsoring you for further development of your "idea" but that's life! _________ You here simply show that you are unwilling to face the underlying facts [already pointed out to you repeatedly, cf here for a recent example], starting with the concepts and terms used by Orgel, Wicken and Hoyle across the 70s and into the 80s. KF Alan Fox

In short this intended knock-down fails...

In vitro DNA replication is routine. Sorry if that causes you distress. _______ You obviously did not even bother to read the facts on PCR from the opening paragraphs of the very source you used. If this is a representation of the level of commentary at TSZ, the site you link, that speaks volumes, and not to your collective credit. KF Alan Fox

AF: One final note. At this point, when in the teeth of repeated correction, explanation and evidence -- onlookers cf here on in context for a 101 -- you insist on speaking of the empirically warranted inference from e.g. FSCO/I as sign to design as process -- your very posts are examples! -- given that you are obviously not delusional, you are willfully setting up and knocking over a strawman you have every reason to know is false. Perhaps you get some comfort from telling yourself that the vast body of evidence you add to with every post as to the known source of FSCO/I is not real evidence, but this is by now willful misrepresentation in pursuit of hoped for rhetorical advantage. We have every right to draw the conclusion on fair comment that your behaviour is not merely unfair and in default of duties of care to the truth, but outright decieitful. KF kairosfocus

Is there a theory of "Intelligent Design"? Is is a secret? ________ You know or should know that there is such a theory or more properly, a research programme. One that, on the bio side, in the teeth of unrelenting hostility has now published several dozens of articles in the professional literature. On the cosmological side, there has been much more. It is no accident that one of the precursors on that side was a holder of a Nobel Equivalent prize and that he was a lifelong agnostic. In short, your commentary this evening has been all too revealing and not to your credit. KF Alan Fox

How is this any different from the Darwinist claim that “God wouldn't have done it that way,” therefore evolution did it?

Unravelling your "when did you stop beating your wife" assumption: Point one: Darwin never suggested "god wouldn't have done it that way". Point two: Evolutionary theory attempts to explain the diversity of life found on Earth. It does not address alternative explanations. It stands on its own merits. _______ You need to read the evolutionary literature, from Darwin on, which is full of the same sort of claimed dysteleological reasoning. The Panda's thumb argument is a notorious case in point, and in fact is the name of one of the Darwin advocacy sites. That is how far wrong your confident manner assertions are. Again this evening, it seems you have not even paused to reflect on your gross error regarding the POLYMERASE Chain reaction. KF Alan Fox

AF: The world of life is one in which Joe's summary is precisely correct. You are correct that where you have a first DNA chain molecule and appropriate concentrations of monomers, we can have chain reactions where one DNA molecule templates its complement and so forth. However, just using the Wikipedia link that you so triumphantly trotted out, it will be evident that this is yet another chicken-egg cycle (once we bear in mind that enzymes are proteins dependent on a DNA based synthesis system):

The method relies on thermal cycling, consisting of cycles of repeated heating and cooling of the reaction for DNA melting and enzymatic replication of the DNA. Primers (short DNA fragments) containing sequences complementary to the target region along with a DNA polymerase [--> an enzyme . . . ] (after which the method is named) are key components to enable selective and repeated amplification. As PCR progresses, the DNA generated is itself used as a template for replication, setting in motion a chain reaction in which the DNA template is exponentially amplified. PCR can be extensively modified to perform a wide array of genetic manipulations. Almost all PCR applications employ a heat-stable DNA polymerase, such as Taq polymerase, an enzyme originally isolated from the bacterium Thermus aquaticus. This DNA polymerase enzymatically assembles a new DNA strand from DNA building-blocks, the nucleotides, by using single-stranded DNA as a template and DNA oligonucleotides (also called DNA primers), which are required for initiation of DNA synthesis. The vast majority of PCR methods use thermal cycling, i.e., alternately heating and cooling the PCR sample to a defined series of temperature steps. These thermal cycling steps are necessary first to physically separate the two strands in a DNA double helix at a high temperature in a process called DNA melting. At a lower temperature, each strand is then used as the template in DNA synthesis by the DNA polymerase to selectively amplify the target DNA. The selectivity of PCR results from the use of primers that are complementary to the DNA region targeted for amplification under specific thermal cycling conditions.

As the highlights show, this is precisely NOT self replication, and is obviously a laboratory method dependent on skilled and intelligent investigators who design, set up and effect the process. In short this intended knock-down fails, fails from the first few paragraphs of the link you so gleefully provided. KF kairosfocus

@Alan Fox How is this any different from the Darwinist claim that "God wouldn't have done it that way," therefore evolution did it?

In reality, all we can say is, in the absence of a reasonable working hypothesis, that we don’t yet have an explanation.

Indeed. And this humble approach is the same one employed by most high school textbooks, right? Right? Phinehas

Dear Ms. Lizzie, DNA is NOT a self-replicating molecule. DNA gets replicated as part of the cellular replication process. The cell is the replicator.

Has nobody here heard of PCR? Alan Fox

Dear Ms. Lizzie, DNA is NOT a self-replicating molecule. DNA gets replicated as part of the cellular replication process. The cell is the replicator. Has nobody here heard of PCR? Alan Fox

Kairosfocus (63), just the other day I stumbled upon the puzzling biological phenomenon 'chimera'. A single organism or person (Lydia Fairchild) who is composed of two or more different populations of genetically distinct cells. Chimeras are formed from at least four parent cells (two fertilized eggs or early embryos fused together). This also illustrates my point that the parts cannot account for the whole. And of course it illustrates the improvising skills of the whole. What do you think? Box

vjtorley

If a living thing can’t order itself, and if unintelligent things can’t order it, and if its order isn't due to blind chance, then the only option left is that intelligent things order it.

Vincent, your statement is no different from all ID arguments that I have so far seen. You claim that in the absence of a scientific explanation for some phenomenon, you are entitled to invoke the shibboleth of "Intelligent Design" as a default position. In reality, all we can say is, in the absence of a reasonable working hypothesis, that we don't yet have an explanation. "Intelligent Design" explains nothing at all. Alan Fox

If the memory on the server that hosts this blog were seC0Crdering, W0C0dn't p0Cts Ctart l0Cking liC0 thC0C0C0C0C0C0? Phinehas

Dr Liddle, Joe is right to point to the cell as the unit of self replication, as we should all remember at elementary level from school biology; let's not forget that viruses hijack cells. Likewise while we have heard of self replicating molecules and RNA world hyps, these have little or no empirical warrant. Even if there were such, what needs to be explained is the self-replicating cell that codes for and effects both the genetic and replication side and the metabolic automaton side. For that, it seems the very existence of such speculations is an index of how little empirical warrant there is for the OOL scenarios. KF kairosfocus

Box: I am not at all sure that an organism, by intent directs the elaboration of its body plan. During growth and development from embryonic or equivalent stages, there is evidence of algorithmic development in steps, that is partly genetic and partly epigenetic. Of course, if you eat too much and don't do enough physically, you will get fat. Conversely, we have body builders etc. But I doubt that is what you seem to be saying. KF kairosfocus

DK:

I suppose one can argue that an organism is organized from above by a mysterious authority, but how can that be tested?

I suppose one can argue that an organism is organized from the bottom up by a mysterious materialistic process, but how can that be tested? We test the design inference wrt biology pretty much we test the design inference wrt archaeology and forensic science (SETI too). That is we eliminate necessity and chance (to the best of our abilities, science doesn't require absolutes) and then see if it meets the design criteria. Joe

Lizzie sez:

Thirdly, a self-replicating molecule is both self-organising, or part of a self-organising system, and information-rich, and when that information is duplicated, it is transferred. Therefore it is a dense information storage system. Therefore DNA itself violates Eric’s rule.

Dear Ms. Lizzie, DNA is NOT a self-replicating molecule. DNA gets replicated as part of the cellular replication process. The cell is the replicator. Therefor your argument is total nonsense. Nice job. :razz: Joe

KF, I agree that FSCO/I points to a top-down process, namely designing. But I'm arguing that organisms are 'agents' - forms - capable of organizing their own parts. I believe that at one point in time the Designer created the parts - and probably the whole organism -, but I believe that after that creation the organism is granted control of itself. IOW an organism is not designed like a computer. Daniel King asks me if I can proof that the organism - on the level of the whole - is in control of its parts. I'm not sure if FSCO/I is helpful in answering this question. Box

Box, what can be tested, and is very well supported, is that FSCO/I is a reliable sign of design. Design is inherently about purpose and contrivance to achieve purpose, which makes it as top down as you get. Matters not if you start the specifics with components and networks, or system to blocks to components, or most likely a blend of the two. (A good place to begin is often the main plant that you want, to characterise its dynamics, then go to the supporting players to help it do its thing.) KF kairosfocus

Daniel King, Stephen L. Talbott wrote several essays about organisms. In ‘Getting Over the Code Delusion’ he writes about DNA not being able to account for a bottom-up explanation for the organism. Exerpt:

SLT: “If genes determine the form and substance of the organism, how is it that such radically different cellular architectures result from the same genes? What directs genes to produce the intricately sculpted and differentiated form of a complex organism, and how can this directing agency be governed by the very genes that it directs?”

I can also recommend e.g. ‘The Unbearable Wholeness of Beings’. I hope you will find it interesting. Box

Petrushka: Is this a case of attempted burden of proof shifting? I find the terms a bit ambiguous, as evolution is so shifty in meaning. As to "possible," that opens up a trivial answer: Last thursday evening, the world was created in an instant, by a creator who enjoys pranking. So the past we all think we experienced never happened, much less that we hear about on TV or in museums etc. Logically possible and empirically indistinguishable from the world we may think we inhabit, whether you are a 4.6 BY person or a 6,000 Y person. Trivial. Now, what is material, is that design theory is consistent with Last Thursdayism, with 6,000 Y YEC views, with progressive creation views, and with universal common descent views. Indeed, it would be compatible with a view where God ran the sims in his mind and picked the world to instantiate that beat the odds on chance-necessity processes all the way from hydrogen to humans. (Selection like that is a species of design.) That's because in all cases, we would be able to detect design from FSCO/I as a reliable sign. What design of life is not compatible with is a priori materialism with its before the facts can speak insertion of the criterion: no design. Similarly, design of the cosmos -- the money shot issue for design thought as this side points to a designer powerful and smart enough to build a cosmos [and is essentially independent of the question of biological design] -- is incompatible with materialist worldviews that declare before evidence is allowed to speak, in crude summary terms, that all that is is matter and derivatives thereof. Such materialism is self refuting, so it isn't even a tenable philosophy, as it decisively undercuts the knowing, cogently reasoning mind. As in what is needed to have good reasons to be a materialist. J B S Haldane summarises that, in simple terms:

"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. ]

Back on track, yesterday marked six full months in which the objectors to design have not taken up the free kick at goal challenge to provide an essay making a cogent, empirically backed up summary case for evo mat OOL and OO body plans, that I would host here at UD. KF kairosfocus

Box: I suppose it cannot be tested. One can infer that an organism is top-down organized by eliminating all mechanical – bottom-up – candidates one by one. So it is not DNA, not epigenome, not information … et cetera that can account for the organization of the whole organism. One can infer a lot of things, but as I understand science, one has to go beyond the inference by testing that inference, or it hangs there in the conceptual space as a "mere" inference. Daniel King

Thanks, Box, but as I said, I don't see your link to Talbott dealing with these issues. I am unfamiliar with his work. Do you have a more pertinent link? Daniel King

Daniel King, I suppose it cannot be tested. One can infer that an organism is top-down organized by eliminating all mechanical - bottom-up - candidates one by one. So it is not DNA, not epigenome, not information ... et cetera that can account for the organization of the whole organism. An assenting argument is that we - humans - experience ourselves as agents. We control our limbs, speech etc. top-down instead of the other way around - bottom up. The parts are functional for the whole and subjugated by the whole. And again I recommend reading S.L.Talbott about these issues. Box

F/N: A lab analogue to Saturn's hexagon, here: ____________ >> Though not as famous as Jupiter’s Great Red Spot, Saturn's Hexagon is equally mysterious. Now researchers have recreated this formation in the lab using little more than water and a spinning table—an important first step, experts say, in finally deciphering this cosmic mystery. Saturn’s striped appearance comes from jet streams that fly east to west through its atmosphere at different latitudes. Most jets form circular bands, but the Voyager spacecraft snapped pictures of an enormous hexagonally shaped one (each side rivals Earth's diameter) when it passed over the planet's north pole in 1988 . . . . Physicists Ana Claudia Barbosa Aguiar and Peter Read of the University of Oxford in the United Kingdom wanted to see if they could recreate the hexagon in the lab. They placed a 30-liter cylinder of water on a slowly spinning table; the water represented Saturn’s atmosphere spinning with the planet’s rotation. Inside this tank, they placed a small ring that whirled more rapidly than the cylinder. This created a miniature artificial "jet stream" that the researchers tracked with a green dye. Spinning 'round. Green fluorescent dye reveals eddies in an artificial jet stream created in the lab. Credit: Ana Claudia Barbosa Aguiar The faster the ring rotated, the less circular the green jet stream became. Small eddies formed along its edges, which slowly became larger and stronger and forced the fluid within the ring into the shape of a polygon. By altering the rate at which the ring spun, the scientists could generate various shapes. “We could create ovals, triangles, squares, almost anything you like,” says Read. The bigger the difference in the rotation between the planet and the jet steam—that is the cylinder and the ring—the fewer sides the polygon had, the team reports in this month's issue of Icarus. Barbosa Aguiar and Read suggest that Saturn’s north polar jet stream spins at a rate relative to the rest of the atmosphere that favors a six-sided figure, hence the hexagon. Such polygonal formations have been observed in the center of major hurricanes on Earth, says Barbosa Aguiar, though they quickly dissipate. “Most planetary scientists are not aware of how ubiquitous these sorts of patterns are in fluid dynamics.” >> _____________ Now, that's a case of observational support for a theoretical claim. And, here we have low contingency mechanical necessity giving rise to a natural regularity, one that seems to have a parallel in down to earth hurricanes. However, the mode-locking is suggestive: if we can figure out a way to control the speed of jet streams and are willing to tolerate atrocious bit rates, here is a system that can be modified to implement a code, through intelligent intervention. In principle. KF kairosfocus

petrushka sez:

have log been asking ID advocated to demonstrate that biological design is possible without evolution. I’d like to see a proof of concept.

Umm biological design refers to origins and we are told evolution doesn't tread there. Also Intelligent Design Evolution is, well, evolution by design. Joe

I suppose one can argue that an organism is organized from above by a mysterious authority, but how can that be tested? Daniel King

Box: I argued against a mechanistic bottom-up explanation from DNA, RNA, proteins or information. An organism is not a computer. In order to illustrate my point I cited Stephen L. Talbott. So an organism is organized top-down – a hierarchical organization from above. Not a mechanistic explanation from its parts, but instead a top down organization from a mysterious authority – form / agency. I must be missing something, but I don't see anything in your link to Talbott that supports your claim. Could you clarify? I suppose one can argue that an organism is organized from above a mysterious authority, but how can that be tested? And doesn't that assume the consequent? Daniel King

My summarization of the argument leading to EA’s statement: I argued that the organization of an organism cannot be explained from its parts. So I argued against a mechanistic bottom-up explanation from DNA, RNA, proteins or information. An organism is not a computer. In order to illustrate my point I cited Stephen L. Talbott. So an organism is organized top-down - a hierarchical organization from above. Not a mechanistic explanation from its parts, but instead a top down organization from a mysterious authority – form / agency. If one holds this concept of an organism the materialistic model of life is out. The mysterious authority – on the level of the whole organism- which operates from above towards the parts (DNA, proteins, cells, tissues, etc.) must be immaterial. At least according to my logic. At this very moment KN introduced an alternative explanation: (material) self-organizing processes. So the mysterious authority from above (form / agency) could also be self-ordering matter. I found KN’s attempt so absurd, so illogical that I was totally flabbergasted. At that moment Eric Anderson chimed in with his now famous statement. Box

Joe F: Strawman. The issue is not the chaining chemistry of the sugar-phosphate backbone, but the information content stored at "right angles" to it. That a long chain molecule is chemically possible [albeit massively uphill chemically speaking] and that it should have complementarity across interlocked chains is one thing. That it should hold a specific code-bearing sequence, should be unzipped by molecular machines, to be transcribed to mRNA, which is then transferred to complex ribosomes to serve as a control tape for a NC machine that builds proteins per the code is a wholly different other. As well, that the DNA should contain regulatory information is yet another. Chemistry of chaining monomers does nothing to explain digitally coded information stored at right angles to the sequence. Nor the systems that use the info. So, it is a strawman to twist the one into the other. And, with all due respect Joe F, that you would stoop to such tactics -- you MUST know better -- speaks volumes about your want of a case on the merits. KF kairosfocus

And Felsenstein notes:

which seems not to be saying that the evolution of a DNA genome is impossible. Instead it seems to be saying that DNA itself is impossible.

Bingo! Given materialism, DNA itself is impossible. IOW given only blind and undirected processes, DNA would not be here.

I guess the only reason we would see DNA is that leprechauns are constantly holding each DNA molecule together, because otherwise (according to UD) DNA molecules are impossible.

Nope. I guess you had too many donuts today, Felsy. Do you think that leprechauns are holding computers and computer programs together? Joe

Great, another moron chimed in:

If it’s not random, and it’s not “fixed by internal forces” when did your designer do it and how Upright? KF?

We can only answer those questions by studying the design and all relevant evidence- ie via science. We sure as heck don't have to know those answers to determine design is present and to study it, which is what ID is about. Joe

How can you summarize what doesn’t exist?

Out of the mouths of babes…

From the mouth of an imbecile... ======== Joe, please watch terms: im·be·cile (mb-sl, -sl) n. 1. A stupid or silly person; a dolt. 2. A person whose mental acumen is well below par. 3. A person of moderate to severe mental retardation having a mental age of from three to seven years and generally being capable of some degree of communication and performance of simple tasks under supervision. The term belongs to a classification system no longer in use and is now considered offensive. Joe

Box: Self ordering/organising -- the last is probably not apt -- systems have internal structures and forces that under certain circumstances will give rise to ordered structures, like condensation, crystallisation, convection loops, vortices and the like. Normally, this implies a symmetry that leads to things fitting together like the tumbling parts with magnetic couplers that can form a ball. The difference from organisation as Wicken and others have used it, is that the latter speaks to an aperiodic pattern that specifies a wiring diagram that then has to be effected in a fairly precise way for the composite entity to work. Much like an electronic circuit. Assembly per instructions is a paradigm for effecting such, from a factory building cars to a cell building proteins. KF kairosfocus

Alan Fox, choker:

I summarized my own understanding of evolutionary theory. This is an explanation for the diversity of life found on Earth, not its origin..

LoL! Unfortunately what you summarized doesn't explain the diversity of anything. Let alone life. Diffeential reproduction within a population cannot explain the diversity of life. [SNIP -- language deteriorating, Joe]. Joe

AF: It so happens that the ROOT of the darwinist tree[s] of life is necessary for there to be a tree. This brings up front centre, the hypotesised common, unicellular ancestor sitting at OOL, which has to explain a metabolising automaton with an integral self replicating facility, which per the onward observations and the von Neumann analysis, will require codes and systems for reading and processing same to effect replication. For argument, to preserve a stable internal environment, encapsulation and selective gating as well as disposal of wastes, should probably be present but are not as pivotal. This is not the strawman you erected to dismiss, a demand to explain everything. It is saying that until the root -- which happens to be BEFORE variation and differential reproductive success can properly be appealed to -- is cogently addressed on evidence, there is a root-level begged question. It so happens that such an entity will involve codes and communication and info processing systems, functionally specific complex organisation and information well beyond the solar system and observed cosmos thresholds. For instance, on simplest observed forms, the stored information is credibly of order 100 k - 1 mn bits. As you know but will not acknowledge, the only, routinely observed source of FSCO/I is design. (onlookers, cf. here on for a 101. AF dismisses such, but you may find there something that he is brushing aside unexamined.) Which also blows up your whole cascade. And, as an attempted turnabout is likely, let me save the onlooker a loop of further strawmen. I do not need to do more than show that per induction on widespread experience and the implications of blind chance + necessity search of huge config spaces, that FSCO/I is a credible, reliable sign of design. So, in cases where we have not had opportunity to see the actual origin but notice FSCO/I, that is itself evidence that points to design. Whether or not we have historical or scientific observations that allow us to identify the designers. That I may not know whodunit does not mean that I cannot credibly know that Fire X was arson, on signs. KF kairosfocus

Mr. Fox, It might surprise you to know that Plantinga's evolutionary argument against naturalism works from another angle. Let's suppose that naturalism were able to supply trustworthy cognitive faculties through evolutionary processes (instead of undermining them). Is we were to presuppose that then the argument would work this way:

Anthropic Principle - God Created The Universe - Michael Strauss PhD. - video http://www.metacafe.com/watch/4323661 This preceding video, at the 6:49 mark, has a very interesting quote: "So what are the theological implications of all this? Well Barrow and Tipler wrote this book, The Anthropic Cosmological Principle, and they saw the design of the universe. But they're atheists basically, there's no God. And they go through some long arguments to describe why humans are the only intelligent life in the universe. That's what they believe. So they got a problem. If the universe is clearly the product of design, but humans are the only intelligent life in the universe, who creates the universe? So you know what Barrow and Tipler's solution is? It makes perfect sense. Humans evolve to a point some day where they reach back in time and create the universe for themselves. (Audience laughs) Hey these guys are respected scientists. So what brings them to that conclusion? It is because the evidence for design is so overwhelming that if you don't have God you have humans creating the universe back in time for themselves." - Michael Strauss PhD. - Particle Physics

i.e. if evolutionary Naturalism were able to supply trustworthy cognitive faculties (instead of undermining them) then there is no parameter within evolutionary naturalism for Darwinists to appeal to prevent some creature to evolve to the point of being a godlike being with practically infinite heights of knowledge and power. Moreover the multiverse conjecture only compounds this problem for Darwinists like you Mr. Fox. If an infinite number of other possible universes must exist in order to explain the fine tuning of this one, then why is it not also infinitely possible for a infinitely powerful and transcendent Creator to exist? Using the materialist same line of reasoning for an infinity of multiverses to 'explain away' the extreme fine-tuning of this one we can thusly surmise; If it is infinitely possible for God to exist then He, of 100% certainty, must exist no matter how small the probability is of His existence in one of these other infinity of universes, and since He certainly must exist in some possible world then he must exist in all possible worlds since all possibilities in all universes automatically become subject to Him since He is, by definition, transcendent and infinitely Powerful.,,, i.e. The materialistic conjecture of an infinity of universes (the multiverse) to ‘explain away’ the fine tuning of this universe also insures, through the ontological argument, the 100% probability of the existence of God:

God Is Not Dead Yet – William Lane Craig – Page 4 The ontological argument. Anselm’s famous argument has been reformulated and defended by Alvin Plantinga, Robert Maydole, Brian Leftow, and others. God, Anselm observes, is by definition the greatest being conceivable. If you could conceive of anything greater than God, then that would be God. Thus, God is the greatest conceivable being, a maximally great being. So what would such a being be like? He would be all-powerful, all-knowing, and all-good, and he would exist in every logically possible world. But then we can argue: 1. It is possible that a maximally great being (God) exists. 2. If it is possible that a maximally great being exists, then a maximally great being exists in some possible world. 3. If a maximally great being exists in some possible world, then it exists in every possible world. 4. If a maximally great being exists in every possible world, then it exists in the actual world. 5. Therefore, a maximally great being exists in the actual world. 6. Therefore, a maximally great being exists. 7. Therefore, God exists. Now it might be a surprise to learn that steps 2–7 of this argument are relatively uncontroversial. Most philosophers would agree that if God’s existence is even possible, then he must exist. So the whole question is: Is God’s existence possible? The atheist has to maintain that it’s impossible that God exists. He has to say that the concept of God is incoherent, like the concept of a married bachelor or a round square. But the problem is that the concept of God just doesn’t appear to be incoherent in that way. The idea of a being which is all-powerful, all knowing, and all-good in every possible world seems perfectly coherent. And so long as God’s existence is even possible, it follows that God must exist. http://www.christianitytoday.com/ct/2008/july/13.22.html?start=4

But Mr. Fox there is a caveat, I did'nt tell you about, to this 'growing to infinite knowledge and power' conjecture I granted you if evolutionary naturalism were able to provide trustworthy cognitive faculties,

The End Of Christianity - Finding a Good God in an Evil World - Pg.31 William Dembski PhD. Mathematics Excerpt: "In mathematics there are two ways to go to infinity. One is to grow large without measure. The other is to form a fraction in which the denominator goes to zero. The Cross is a path of humility in which the infinite God becomes finite and then contracts to zero, only to resurrect and thereby unite a finite humanity within a newfound infinity." http://www.designinference.com/documents/2009.05.end_of_xty.pdf ,,I hold 'growing large without measure' to be a lesser quality infinity than a fraction in which the denominator goes to zero. The reason why I hold it to be a 'lesser quality infinity' is stated at the 4:30 minute mark of the following video: Can A "Beginning-less Universe" Exist? - William Lane Craig - video http://www.youtube.com/watch?v=K8YN0fwo5J4 As well, the reason why 'growing large without measure' would be a lesser quality infinity than 'a fraction in which the denominator goes to zero' can also be grasped in this following video: Georg Cantor – The Mathematics Of Infinity – video http://www.metacafe.com/watch/4572335

Music:

Steven Curtis Chapman - God is God (Original Version) - http://www.youtube.com/watch?v=qz94NQ5HRyk

bornagain77

How can you summarize what doesn’t exist?

Out of the mouths of babes... Alan Fox

You are not given, you have to find at OOl, on blind chance and necessity, which has not been done.

I did not offer an explanation of life, the universe and everything. I summarized my own understanding of evolutionary theory. This is an explanation for the diversity of life found on Earth, not its origin. You know, or should know, this. It has been pointed out enough times.

Next, you have to similarly account for increments of FSCO/I, again not done.

Of course I don't. I don't need to account for invisible pink unicorns, either. You come up with a credible definition of FSC whatever and then it may need considering. Alan Fox

WJM "One might posit there is “a priori bias” that blinds them to the obvious"

This is exactly what I suspect. I have often been amazed at the conceptual blindness at these folks. C.S. Lewis was too and wrote about it. There is obviously something different about them. CentralScrutinizer

Alan Fox links to a blog of clueless individuals and thinks he has refuted Eric. Priceless. Joe

Alan Fox:

I’ll summarize it in my own words.

How can you summarize what doesn't exist?

Given a population of self-sustaining self-replicators, where where the the replication process is not perfect and where there is competition for resources, differential survival may lead to change over time in that population.

LoL! Sounds like baraminology. Nice job Alan. And no one can say why Eric is wrong. Joe

AF 1: Given a population of self-sustaining self-replicators, where where the the replication process is not perfect and where there is competition for resources, differential survival may lead to change over time in that population. You are not given, you have to find at OOl, on blind chance and necessity, which has not been done. Next, you have to similarly account for increments of FSCO/I, again not done. 2: I’m not the only one to think you are incorrect in your assertion, Eric It's very simple, something that has a fixed structure and internal state set by internal forces cannot serve as an effective storage medium or unit. Now, where you have a set of internal states and triggers that can change state, that is a very different story. Basic digital electronics, think about flip flops. But then, DNA is much like ROM. It is not meant to be variable from moment to moment. The processing of templated mRNA with extrons and introns offers possibilities, that are exploited to give another level of FSCO/I: interwoven codes. That is very high art for digital design I can tell you, I just gave thanks for enough memory and never even tried. KF kairosfocus

Box (24): Thanks Eric Anderson (20) & Kairosfocus (23) for clarifying. I am also grateful to Eric and Kairos, but like Box I'm still unclear about the meaning of the term self-ordering. I also wonder, Do we need to distinguish between multiple kinds of self-ordering? Eric, your clarification was most helpful. You are applying the term self-ordering to a constraint on the freedom of a chain of molecules or of symbols to vary. I see that such a constraint is an example of order, and that a perfectly orderly system can't be varied to convey different messages, and that DNA is not similarly constrained. But why call that situation self-ordering? Where does the self come in? Was your claim (and the focus on DNA) relevant to the kinds of self-ordering to which Kantian Naturalist was referring? He didn't say so, but I assume that he was referring to such things as the self-assembly of proteins into complex machines like microtubules or viruses, or the spontaneous folding of a variety of proteins. I think you need to address those kinds of self-ordering. Daniel King

…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.

I'm not the only one to think you are incorrect in your assertion, Eric. Alan Fox

...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.

Alan Fox

What evolutionary theory? Can you please link to it.

I'll summarize it in my own words. Given a population of self-sustaining self-replicators, where where the the replication process is not perfect and where there is competition for resources, differential survival may lead to change over time in that population. I like to think of it as a process of environmental design. Now show me yours, Joe! :) Alan Fox

Allan Miller continues his strawman spewage:

The physicochemical thinking at UD is typically limited to short chains of cause-and-effect. Water flows downhill, that’s ‘natural law’. So when they think of a chemical system, they tend to think simply of one molecular configuration turning into another. Since the codon does not turn into the amino acid, they somehow think this is not governed by physical law – ‘necessity’. In order to get such a more complicated interaction, it must have been designed, because ‘everybody knows’ that the acids are ‘materially arbitrary’. Every step of the process flows downhill, entropically, but somehow the existence of multiple alternative possibilities, and modern complexity, means that someone must have chosen this one.

As I keep saying Allan, if you don't like ID then just start finding and presenting positive evidence for your position. The next time you do so will be the first. The point being is there isn't any physical law governing the genetic code. Just as there isn't any physical law governing a computer program. Joe

Which brings us to another point- why are these chumps, who are obvioulsy oblivious to ID claims, think they can rail against ID?

Programmed biological automatons cannot properly respond to concepts; they can only respond to words and phrases in accordance with their basic directives. What comes out of TSZ and most anti-ID advocates makes much more sense when examined in this light.

Yes I know they accuse of of doing the same to evolutionism, but they never provide any evidence to support that accusation.

Let's look at this from the perspective that the people at TMZ are what they claim to be - programmed biological automatons. Let's say that they are programmed to interpret all evidence and argument about evolution from a framework that materialism is true. Now, keep in mind that "materialism" isn't really even specifically termed in the coding; it's not a root folder full of materialist values and concepts that is protected; instead, materialism is just the assumption of the coding itself. Anti-ID advocates do no better a job at defending or arguing "materialism" than they do against ID, because they are not programmed to defend it. Their programming simply assumes it at a very fundamental level. So, when one of them reads any scientifically gathered biological or stratiographic data that has to do with evolutionary claims, they have no coding that questions whether or not materialism is a sufficient explanation; their coding assumes it. So, when we say "that is just an assumption", they point to the evidence as if it is evidence of what is being questioned. This is why no matter how many times you correct them that the "evidence" they point to has nothing whatsoever to do with what is being challenged, they simply don't get it and present the same irrelevant objections over and over. They are programmed to do so. No matter how many times Behe, Meyer, Dembski, etc. have said that ID makes no claim about any "god"; no matter how may sites explain that same thing; no matter that there is a FAQ here that explains it; the programmed automaton known as Elizabeth Liddle can still make a comment that "ID has failed to "prove" the existence of god." Here we have several perfectly understandable - even blatantly obvious - arguments about how materialism fails to account for the information in DNA, and perfectly understandable, obvious arguments why intelligence is the best explanation available, and yet they fail to understand such arguments even at their most basic level (under the charitable reading defense, and taking them at their word as to what they are). Why? Because they interpret all such arguments from the perspective that materialism is true; they do not know this is what they are doing because their conceptual framework, materialism, doesn't actually occupy specific code, it is the blind-spot assumption from which all their coding ensues. They are incapable of understanding concepts; they are self-proclaimed Turing machines. This is why they constantly take terms and phrases out of context and then reiterate already-addressed objections or invent new ones that have nothing to do with the concept that is being used. Under a charitable reading paradigm - assuming they aren't being deliberately evil - they obviously don't even understand the concepts they do employ or defend, because when they are shown the obvious failings, self-referential absurdity, or self-defeating consequences of those concepts, they are incapable of understanding it at the conceptual level - because they roll merrily along utilizing and defending the same concept - such as, the concept that the LNC is not necessarily binding, or the concept that materialism can produce a reliable mind. Since materialism is not a specifically coded concept, but rather the blind-spot source of programming, if they have a rational mind, then obviously - to them - materialism can produce it. If something exists, obviously materialism can produce it, even if they cannot rationally defend that notion, and even if they have no means of supporting that view, and even flying in the face of the obvious. This is how they can make the claim that "there is no evidence for design" even when everyone - including those testifying against personal interest - have admitted that it all looks precisely and overwhelmingly like it has been designed. How can any sane, intelligent entity with free will make such a series of inane statements? If we assume they are of good will and have the same free will faculty as we do to arbit true statements from an exterior perspective (true self-reflection at the conceptual level), there is no explanation for it. How is there a free will, sound mind explanation for anyone that disagrees with the LNC? One might posit there is "a priori bias" that blinds them to the obvious, but if they are incapable of overcoming bias that runs so counter to the obvious, so overpowering that it produces inane, self-defeating, self-denying, incomprehensible output as if they were making sense, is this not the same as, for all intents and purposes, being a Turing-machine automaton? William J Murray

Joe (and ME): Kindly see the just above. KF kairosfocus

Box: Something like a vortex is self-organising, so is a crystal. A snowflake -- esp star form -- is a crystal. In a case like this, the complex branches reflect rapid chance variations in local conditions as the crystal forms. The hex shape is necessity, the complex branches are highly contingent. That gives complexity but it is not specified functionally. Break a star snowflake and it is still a flake. Break a protein chain and it usually will not fold and work right. None of this is new, it is stuff that has been explained over and over, but the objectors are not attending to inconvenient facts. The slightly hexagonal cloud pattern at Saturn's north pole is an obviously fairly symmetrical vortex-linked feature. The red spot on Jupiter is apparently much the same and we are familiar with hurricanes and bathtub swirls. These do not have the highly contingent, information rich asymmetrical wiring diagram patterns associated with FSCO/I. Similarly, if you look at the movie, you will see little pairs of [obviously very strong) magnets and a specific curved tiling shape. That is, the system was intelligently designed and made to assemble on shaking in a tube. The smarts is in what gets you to that point. And in fact, this is yet another example of FSCO/I tracing to design. Unacknowledged, as usual. Observe the blurb:

This video shot in real time with no tricks shows the process of self-assembly driven by random motion [--> and, unacknowledged, by design of the component parts to fit in the right way and stick together when that happens, so that step by step the ball will be built] . It demonstrates how viruses and other complex biological organisms put themselves together without direction from the outside, except random motion from heat. [--> and dodges the highly information-driven organisation of the components to fit together.] Patent has been applied for. This model can now be purchased from sciencewithinreach.com .

See the trick in what has been left out of the narrative? See why FSCO/I is such a major blind spot? They are red herring and strawman arguments distractive from the inconvenient facts of a code based digital info storage and processing system in the heart of the living cell. And to store codes you need flexibility in the storage medium. KF kairosfocus

Eric Anderson- Nice job. You have Lizzie and the septic zone ilk all in a tither. Mikey Elzinga "refutes" you by saying the hexagon we see on saturn is self-organising. Therefor living organisms! It's funny that they disagree with you yet cannot provide any evidence that refutes what you say. Neil Rickert is his usual clueless self. They don't undersatnd that DNA is not self-organising and if it were it wouldn't be good for storing information. And if it were self-organising then we wouldn't see the diversity in DNA that we observe. DNA does NOT have a fixed chain of A's, C's, G's and T's. Geez Meyer has gone over and over why this is important. Which brings us to another point- why are these chumps, who are obvioulsy oblivious to ID claims, think they can rail against ID? Yes I know they accuse of of doing the same to evolutionism, but they never provide any evidence to support that accusation. But anyway, nice job Eric and kairosfocus... Joe

Thanks Eric Anderson (20) & Kairosfocus (23) for clarifying. Do we need to distinguish between multiple kinds of self-ordering? Are all kinds subject to E.A.'s law? This movie provides an example of self-ordering based on shape. Box

KF posted this:

Going beyond, you know protein chains then fold to form functional ones, which is yet another metastable state. Sometimes it has to be chaperoned, and as you know the existence of misfolded lower energy states — prions — is a notorious problem per Mad Cow disease and is suspected of involvement in Alzheimers.

Can you provide a citation showing that prions are at a lower energy state than a protein's "properly" folded form (presumably, you mean the form in which the protein does its "proper" job)? timothya

Box: Let's start with click-together beads, similar to Lego bricks. Say, they come in four colours, R, Y, B, P -- red, yellow, blue, purple. Now, in the normal case we have a universal coupler, the click together so any colour can follow any. We could devise a code and freely store messages in this string of beads: R-R-Y-B-P . . . Now, let us change things up a bit, so that R must now be followed by Y and B by P (and Y and P must be preceded by R and B), i.e. there is a peculiarity in the couplers that forces a certain degree of internal organisation. We now have been reduced to two units, not four: -RY-, -BP- This means the code-carrying capacity has been significantly reduced, because the number of choices in each available position is now 2 not 4. That reduces the carrying capacity of the positions, here from 2 bits per position to 1. (The usual measure of info carrying capacity is a log measure of the number of choices and likelihood of the alternatives at each point in the message, cf here on for a 101. If the base of the logs is 2, the measure is in bits. A flatly distributed, 20-state per position system holds 4.32 bits per position. In praxis, there is some tendency of proteins to have certain AA's more common and certain ones less so, and this reduces the average info carrying capacity per AA. As a rule, even when there are no physical constraints like in our beads example, codes do not have an even distribution of the possible states, e.g. in English about 1/8 of text is the letter e, and x is rather rarer except in Algebra books or the like. Similarly, unless one is dealing with QANTAS or Iraq or the like, q is almost certain to be followed by u. So, if you saw the following text: "qween" you would most likely infer a typo for "queen," unless something odd was going on. This means that u provides some redundancy that helps us pick up errors, but it carries little additional info, as there is a self organising tendency in the code we call textual English.) Now, try some Lego bricks with a twist, they have four lock points, maybe we can imagine them as pointing at the 4 arms of a cross, like in a + sign. This would allow us to make up some pretty complicated 2-d structures. Especially if we can lock to tools or components, or have a sort of end cap. Now, switch to 3-d, by making the four arms point to the four vertices of a tetrahedron, a pyramid with a triangular base. With the +-block now in 3-d, we can see how we could organise some very complex structures, and by adding the right tool-tips and end caps, we can put together all sorts of things. I have just given you a rough, initial model of Carbon chemistry for organic molecules, the context of the chemistry of life. The issue is that this great flexibility allows for complex functionally specific organisation, which is information-rich. If we did not have that flexibility, we could not construct things so easily. Which is information-poor. Indeed, in the ultimate case, we have the sort of lock up that makes for crystal arrays that have a uniform composition, like say NaCl in a 3-d array. Does this help make matters clearer? KF kairosfocus

Groov: The two electrical states of a light switch are metastable (with the intermediate one being a higher energy state), so they latch. But, that is by no means a ground state, as can be seen by leaving a light switch be for long enough. Just so, the state of the chain in D/RNA or protein is metastable, but it is by no means a ground state. It is downhill from the higher state just before bonding, but it is by no means the only bonded state or even compositional state possible. That is why there is such an elaborate system to control and force the chemistry using Le Chetalier's principle. Going beyond, you know protein chains then fold to form functional ones, which is yet another metastable state. Sometimes it has to be chaperoned, and as you know the existence of misfolded lower energy states -- prions -- is a notorious problem per Mad Cow disease and is suspected of involvement in Alzheimers. Apparently the misfold propagates and the increased stability is such that that leads to accumulation and a fatal progression. So, we should focus the contingency and the way this can be used to load and store information. KF kairosfocus

Alan Fox @1: You probably know you are putting up a red herring, but in case you care to review the matter, here is a brief summary of the design position: https://uncommondescent.com/evolution/why-on-earth-would-a-layman-accept-darwinistic-claims/#comment-450195 Eric Anderson

Daniel King @11:

That’s an exciting concept. Is there any evidence for it?

Thanks, Daniel. Good question. Not only is there evidence for it, it is a fundamental aspect of information storage and transmission. Just a couple of quick examples: 1. Take the sequence of nucleotides in DNA. Let's assume that there is an absolute chemical affinity between, say, A and T, such that every time A shows up in a chain, T (by force of chemistry) always follows. This would be an example of a "self ordering tendency of the medium." This would mean that, in effect, there is no individual character 'A' available for use in the code. Instead, you would have AT, T, C and G. At first glance, this might not look like an issue, because you still have 4 "characters." But in fact, we have reduced the storage capacity of the medium. Note that AT actually occupies two positions ('AT') to convey the same thing that was initially conveyed by one position ('A'). As a result, every time we want to convey A: (i) we have to bring along a T even though its inclusion does not convey any additional information, and (ii) we have to increase the length of the string required to convey the same amount of information. If we had a further chemical affinity between, say T and G, such that G always followed T, the situation would be even worse. Or if G and C always came together, we have a similar problem. Indeed, when early efforts were underway to explain the DNA code, one of the very first things that was studied was whether there was any particular chemical affinity or chemical necessity that would cause one nucleotide base to follow another. It was discovered that there isn't (due to the overall structure of the DNA helix), and at the same time it was appreciated that if there were such a chemical affinity, it would reduce the information carrying capacity of DNA. The primary problem with self-organization theories as they relate to the origin of information-rich systems like DNA (or RNA or any other information-bearing system), is that the very process called upon to produce the system in question is anathema to that system's capacity to carry information. Self-organization of information-rich systems is therefore a dead end from the get-go. It is not simply a question of needing more time or needing to discover some as-yet-unknown law of chemistry or physics. The very process of self organization is a destroyer of information. 2. Imagine we want to store some information in a computer memory, using conventional 1's and 0's. But the memory we are using is a bit strange in that a 1 must always be followed by a 0. In this two-bit system it is obvious (perhaps even moreso than it is with a 4-bit DNA system) that this self-ordering tendency reduces information carrying capacity. Now every time I want a 1, I get a 1 followed by a 0. So, for example, a string that would be 10110101 becomes 1001010010010. We've gone from 8 positions to 13 positions in this example, and on average across the board we'll need to add about 50% more positions to convey the same amount of information. 3. At the most extreme end of the self-ordering spectrum (complete self-ordering) would be a situation in which, for example, 1 is always followed by 0 and 0 is always followed by 1 or 0 (or in DNA, if each nucleotide is always followed by a specific nucleotide). In such cases, the medium completely loses its ability to convey information. Occasionally naturalistic OOL proponents will speculate about the information for life starting out with some kind of self-ordering crystals. Here we see why that is simply unworkable. ----- Self-organization is a dead end for explaining the origin of information rich systems in biology. The only remaining games in town are (i) blind chance, or (ii) purposeful design. ----- Now two quick final thoughts: - Someone might be tempted to say, "Yes, but in these examples you have assumed complete affinity." True, for simplicity in these examples I have used complete affinity, but the same issue holds if there is a tendency without complete affinity -- for example, if T had a 50% likelihood of following A due to some chemical affinity. In some ways the problem becomes even messier with a stochastic tendency rather than an absolute tendency, but it is essentially the same problem: the information carrying capacity of the medium is lessened proportionally. - At the risk of derailing the discussion with a topic that many people sorely misunderstand (present company, I trust, excluded), I cautiously bring up the so-called Shannon Information. Shannon Information, as I've mentioned previously, is not really about measuring the information in a particular string, but rather about measuring the information carrying capacity of the string (or the particular medium in question). So in answer to the initial question, yes, there is evidence for my statement in the OP and it can be empirically measured under Shannon's approach. Indeed, that is really what Shannon's measurement is all about: measuring the information carrying capacity of a medium, and it very much depends on the self-ordering tendency (rather, the lack thereof) of the medium in question. ------ Well, that is longer than I intended to take tonight. I hope that helps lay it out in a bit more detail. Eric Anderson

kf: Thanks for the kind post. This issue is critical to understand, particularly as it relates to any "natural law" or "self-organization" type of origins theories that are sometimes put forward. I've only got a few minutes tonight, but hopefully can respond to some of the comments in more detail tomorrow evening. Eric Anderson

SteRusJon, Thank You for your kind thoughts. You say: "I have to figure out how “assumes its lowest potential energy state,” relates to it all. I’ll have to think it all over a bit more." 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. You might think of it in general terms as an object seeking a balance of all the physical forces acting upon it. See here - - - - - - - - - - - groovamos, You say "As for information storage: A wall light switch for example has a spring which, in either position stores a lower potential energy than it does at the peak of the energy “hill” which must be traversed to change state." 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. Upright BiPed

I have to admit it: I don't understand any of it. Maybe it is simply my lack of understanding of the English language. The explanation given by Kairosfocus in the OP doesn't ring a bell whatsoever. Furthermore I cannot connect UB's talk about potential energy states to the subject at hand. Please explain the idea step by step in plain simple English so that even I can understand. BTW it would also be very much appreciated if one or two (simple) examples are included. Box

Is it my imagination, or is that Quote of the Day somewhat elliptical? Ironic, even? Axel

As for information storage: A wall light switch for example has a spring which, in either position stores a lower potential energy than it does at the peak of the energy "hill" which must be traversed to change state. Either state is stable. Unless the temperature goes very high, or after decades enough go by to rust the spring. Now I would like it if Biped would explain how this is "limited in its capacity" compared to the writing of the word apple on a piece of paper. Also how many types of information are there as for reference to the "type of information they can contain" phrase? Can the "types" be named? Is there another way, in which a structure can effect information storage without regard to potential energy in the analysis? For example can there be a system which dissipates the least amount of power in a stable state? What about a system that stores information in a maximum potential energy state? Or a system that stores information which can be analysed with energy states but that can store just as much information in a predetermined minimum energy state as in a predetermined maximum? Just curious why Biped is presenting only two generalities of how information is stored. I mean is there some scientific reasoning behind it all? groovamos

We are still waiting for the link Joe asked for, M Renard, mon pauvre vieux. I think M Renard means, 'conjecture'; it would seem, of a layman, a theologian manque, not someone with a scientific background; indeed, someone who did perhaps earn the designation of a 'stamp-collector', in accordance with Kelvin's rather mordant quote. I wonder if Darwin did collect stamps. British colonials. I did. Train-spotting, angling, too. Though anoraks didn't seem to exist in the fifties. But I didn't have badges on my jacket or lots of different pens and pencils in my top pocket; a very conservative geek, I suppose. Axel

Upright BiPed, Congratulations to your wife. I pray the fruit of her efforts was well received. Thanks for your reply. I have to figure out how "assumes its lowest potential energy state," relates to it all. I'll have to think it all over a bit more. Stephen SteRusJon

DK: The matter pivots on openness to highly contingent patterns vs lack of such. If something is self-ordering, its behaviour is largely controlled by built in forces, which make for ORDER, not ORGANISATION, just as a crystal or a single-monomer polymer like nylon or polyethylene, will be different from a D/RNA chain or a protein. The sequencing of the last two is independent of the chaining chemistry. The sequencing is not random and it is not fixed by internal forces. That is why we can write a different sequence, just as we do so with electronic memory or ASCII text sequences. KF kairosfocus

...the ability of a medium to store information is inversely proportional to the self-ordering tendency of the medium. That's an exciting concept. Is there any evidence for it? Daniel King

Hello SteRusJon, Sure. A pheromone, for instance, assumes its lowest potential energy state, and as a result of that state, it is an arrangement of matter that contains information by virtue of operating within a system that recognizes that specific state. On the other hand, the word "apple" written in ink on a piece of paper is also an arrangement of matter that assumes its lowest potential energy state. However, what makes the word "apple" recognizable within the system has nothing to do with the lowest potential energy state of ink on paper. It is the arrangement of the ink on paper that is functional within the system, and that exist independent of its lowest potential energy state. In other words, the ink on paper can be re-arranged, again assuming its lowest potential energy state, and result in something else entirely. By the way, the nucleic sequencing in DNA falls into this latter group. - - - - - I hope that helps. I am off for now, a gallery is unveiling my wife's latest artwork this afternoon. I'll check back later this evening. Cheers. Upright BiPed

Upright BiPed,

There are mediums that store information as a result of the medium physically assuming its lowest potential energy state, and there are others that store information in a way that is entirely independent of that energy state.

Would you do me a favor and give me a couple examples to help me understand the distinction you have in mind? Stephen SteRusJon

...and by the way, both medium types are entirely dependent upon the systems that actualize them. FSCI does not exist without FSCO. Upright BiPed

Just a note: There are mediums that store information as a result of the medium physically assuming its lowest potential energy state, and there are others that store information in a way that is entirely independent of that energy state. A practical distiction between these two isn't their ability to contain information, but in the type of information they can contain. The former is limited in its capacity, while the latter can potentially store any type at all. Upright BiPed

Dr Torley: Where, we have abundant evidence -- even the comments in this thread add to the body of evidence [a case of self referential warrant if there ever was one!] -- that FSCO/I is routinely produced by design. We know design to be capable of Wicken wiring diagram type organisation to achieve specific function, and the alternative candidates, nature acting under the forces, constraints and chance circumstances that may obtain, have not only not been shown capable, but face serious needle in the haystack challenges. KF kairosfocus

Kairosfocus, Thanks very much for this post. That single comment by Eric Anderson makes a lot of sense, on a profound metaphysical level. Eric Anderson, "The ability of a medium to store information is inversely proportional to the self-ordering tendency of the medium." Well said. A lot of things clicked into place in my head when I read that comment of yours. Thank you. Alan Fox, If a living thing can't order itself, and if unintelligent things can't order it, and if its order isn't due to blind chance, then the only option left is that intelligent things order it. vjtorley

Alan Fox:

Discount evolutionary theory in some spurious way and then default to “design”!

What evolutionary theory? Can you please link to it. Also I see you still don't understand the word "default". Darwinism was actively considered, and it failed. Joe

Alan, I will go with expressed thought. buffalo

AF: At this stage you full well know or -- almost worse -- should know that the "default to design" talking point you are now repeating like a drumbeat as if that could make it true is a willful falsehood. (Onlookers, cf. here for a 101.) Perhaps, you hope to indoctrinate those on "your" side with it, but that speaks loud volumes. KF kairosfocus

The only game left, as you say, is design. Unless, of course, we want to appeal to blind chance . . .

Don't ID proponents get tired of this refrain? Discount evolutionary theory in some spurious way and then default to "design"! By whom, when, how? We're not sayin'; it's just "design", duh! Alan Fox