Codes, Evolution, and Intelligent Design

It wouldn't self-replicate without the information contained within it. The primary information is 'copy me'. Any information that gets added to that either increases the replicative success of the DNA, decreases it or nothing. The information that increases the success gets to replicate more (by definition).When it boils down to it, one could simply ask 'how can a self-replicating agent naturally start and how can that agent store more information?'. We have no reason to assume that that some conscious entity kicked off the first basic replicator (whether it was DNA or some other nucleic acid, or perhaps something else entirely) - since there is no evidence of a conscious entity that existed at that time. Take care - I may not be around till tomorrow, so fare well till then!

At heart it comes down to whether you believe DNA contains information. I'm guessing you do not, because for DNA's information to pass from parent to child some form of communication would have to take place, and I believe you reject that possibility.I still view your argument as deconstructionist, like arguing that music is only in the notes and that higher levels of abstraction for viewing music like phrases, themes and sonatas are just helpful analogies. Sorry you think it's an insult, it's not intended that way.Another way of looking at it is that you're trying to take the easy route to countering the Dembski et. al. arguments by simply denying there's any communication of information going on. This is probably insulting, too, so I'll apologize in advance. --Percy

Let me say once again that I think the discussion will remain at an impasse until we agree on a definition of code. I won't type in the links again, but I suggest you respond to the definition at Wikipedia that I keep pointing you to, and to Shannon's point in the seminal paper on information theory that meaning is not part of information.--Percy

Yes, that's precisely what evolutionary principles applied to computer programs can do, allow them to fly where the original program couldn't. Genetic algorithms have proven capable of producing both novelty and innovation.--Percy

Not really. "At heart", it comes down to which theoretical framework you're using to understand what's going on in the cell. In other words, which analogy you think is a closer approximation of reality. Under the communications/information theory framework, of COURSE DNA contains "information" - almost by definition. It has to, otherwise the framework makes no sense whatsoever. I have stated that the framework is quite useful in context. I have also indicated that as an approximation of reality it falls short - cells aren't computers or radios or any other form of communications device - natural or artificial. IOW, communications/information theory is a highly abstract way of looking at what happens. Looking at it in light of an algorithm is also an abstraction, but is more closely related to reality than is information theory. Shannon, Schneider, et al's conceptual framework bears the same resemblance to what actually occurs inside a cell as chess does to midieval warfare - highly stylized and highly abstract - even though that's precisely what chess is based on. I'm still a bit surprised that a computer wiz like you can't see the similarities between DNA operation and an algorithm you program into a computer. Admittedly DNA is quarternary vice binary, but the concept of software "do loops" (do they still have those?) is very similar to what happens with DNA transcription.OTOH, your "deconstructing music" analogy falls flat in relation to what I am advocating here. If I were to proclaim that atomic phyisics is all that happens in the cell, then I think you'd have a case. However, unless you're prepared to deny that cellular chemistry is, well, chemistry (which I'm sure you aren't), then describing chemistry in chemical terms would seem to me anyway to be not "deconstructionist". It's simply a different framework for describing what happens. No, I don't think that's the case - at least not entirely. Yes, I would like to provide a different framework than the one they've mangled beyond recognition. However, I truly believe the algorithm framework is a less abstract representation of what is actually occurring than the communication/information framework. Again, I want to stress that communications theory provides a neat, abstract theoretical framework that allows us to easily manipulate and "mathematicize" (I just made that word up - all future users must pay royalties) DNA mechanics (see, for instance, Schneider's Sequence Logos, Machine/Channel Capacity, Maxwell's Demon, and Molecular Machines). It doesn't mean that it is a good representation of reality.In some respects you're right - I want to short stop Dembski and company. However, I think that providing a different framework that is less abstract and closer to reality that many people may be able to grasp more easily - although it'd still require work - is a better way to go than spending endless hours arguing over the definition of "information". Especially if the "new" framework is actually a better description of what is happening in the first place.

Maybe there's a misunderstanding. That there's a higher level of abstraction than cellular chemistry available in no way denies the critical importance of microbiology, at least not to me. I think systems can frequently be interpreted at more than one level of abstraction, and saying that the insights provided by one level of abstraction are valuable in no way diminishes the insights provided by other levels of abstraction.--Percy

Of course there are multiple levels of abstraction - all useful in context. That was the point I've been defending. I just think MY abstraction is better than YOUR abstraction. Nyah, nyah.

I have no objection to someone believing their abstraction is better than mine. I thought that when you called it an analogy that you were denying it status as a useful level of abstraction.--Percy

A code can't be created by nature. We need three things for a code.Start-> Middle-> End (same as start)The Start for any code is the information that you want to encode in it. In the case of DNA, there IS information, and it's true that we cannot "read" that information as it is. However, we know that information was not first; the DNA was first. A regular code would see the following steps:Information -> Encoded form -> InformationBut in DNA we do not see that (if we did, it would certainly be good evidence of a Designer). In DNA we have:"Encoded" form -> InformationIs English a code to you? It really is, but you wouldn't think of it as one because you understand it. If we were really able to "read" DNA 100%, we would understand it, and it would not appear as a code to us. There is an appearance of a code, but there is not an actual code because there was never anything encoded. It is our lack of understanding that leads to us viewing DNA sequences as codes.A code needs a creator, it cannot arise on its own. If it does, then it's just information, and just because we cannot read the information in its natural form doesn't make it a code. Structures (dams, cars, etc.) are defined by their structure. If that structure exists, then we can call it as it is. The structure does not require that it be built from something else. A code, on the other hand, requires the initial encoding process (a process clearly not seen in DNA--at least not the first strand).Jon

But that is not true. It is not infromation being represented in that orderly fashion. Sure, it looks orderly when we know what information we want, but if we looked for different information, we might find it scattered all over the place.Information is not being represented by the DNA sequence (for that to happen, we would need to START with information), instead, the sequence is defining the information. The sequence (or "encoded" form) starts first, and the information is created second. There is no encoding process, and without an encoding process, there can really be no code. My post above explains this a little better.Jon

Explain start and stop condons.

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Aslan is not a Tame Lion

You're again just finding arbitrary differences between DNA and what you think a code is. Start/Middle/End is not part of the definition of a code. I again refer you to the definition at Wikipedia: To say it another way, a code is a set of rules for converting information from one form to another. So this sequence that you provided is incorrect: To correctly express the transformation from one representation to another you would say this: Moving on: I refer you back to the Wikipedia definition, which doesn't mention a creator.The correct way to look at codes is that information in whatever representational form needs a set of transformation rules, a code, to convert it to another representational form.I think a lot of the misunderstanding is the sloppiness with which the word code is being used. A code is not, for example, a sequence of symbols. I know we use the word code in this way all the time, for example, looking at a sequence like "qeud fjdl jejc wpqx" and saying "Ah, this is a code," but it's not a code. A code is the set of rules used to create the sequence from the original representational form.This means that a sequence of symbols is one form of representation of information. A code can transform that sequence of symbols into some other representational form of information.Like I keep saying, this discussion is going nowhere as long as we all use different definitions of "code". The word "code" as used in communications *does* have a formal definition, as does "information".--PercyEdited by Percy, : Tighten up the usage of the the word code to be more precise.

As I explained in my previous message, we've been using the word "code" in a very sloppy way. DNA is *not* a code, not in the formal sense anyway. A code is a set of rules for transforming the representational form of information, and DNA is not, by that standard, a code. We refer to it as a code when we're not trying to be precise, but I think this discussion requires more precision.So by the formal definition of code, DNA is not a code, but it is encoded information. The encoding process occurs during reproduction when the DNA helix splits into two halves and each half acquires an opposite nucleotide. This is the encoding table:

• A => T
• T => A
• C => G
• G => C

Sometimes mistakes are made in the encoding process - these mistakes are referred to as mutations.--Percy

The nucleotides A, U, and G in that order, at the active site of a ribosome, cause it to be energetically advantageous for methianone-aminoacylated tRNA to hydrogen-bond its anti-codon to the codon of the mRNA. That leaves an open carboxyl terminus on the residue for additional residues to form peptide bonds with.The nucleotides sequences UAA, UGA, and UAG make it advantageous for nothing but release factors to bind to the ribosome's P site, releasing the polypeptide and decoupling the ribosomal subunits.

First: Been driving me nuts!!!The current topic being discussed here is not "Percy". :mad.Second:
Personally I find that very interesting that it is understood at that level of detail. However, perhaps you could explain it at a somewhat less jargon loaded level.