coded information in DNA

This topic requires some precise definitions, most importantly for information. Science already has a formal definition for information, but I have a feeling that isn't the definition you're using. So how are you defining information?A definition of code would also be helpful.Agreement on definition of terms is a prerequisite for this discussion.--PercyEdited by Percy, : Grammar.

Hi WordBeLogos,Sorry to reply to an old message, but I think this thread may have gotten off to a bad start due to some unfortunate definitions and incorrect interpretations. This one is probably the most fundamentally misleading definition: This definition looks like it comes from information theory, and it is taylored for its explanatory power in communicating the concepts of information theory in a digital world. It is not a general definition of coded information, but it's okay as long as it is not interpreted too strictly. For example, if a military sentry is supposed to make the sound of a bird if he sees an enemy force using increasing volume and pitch according to its size, then that is coded information. Your definition of "a system of symbols" might be used to exclude such codes if interpreted to mean only sets of symbols you can write on paper like (C A G T) or (0 1) and so forth.And so we have to correct and extend what you say next: But except for DNA your examples are all human constructs that we know can't arise naturally, and so this is begging the question. But you included radio signals in your list, and the natural world has no trouble producing radio signals, so allow me to focus on that.If you're using a wireless router to connect to the Internet, then your computer's network card is using radio signals to exchange coded information with the router in the form of 0's and 1's. Clearly this fits your definition of a code, but that definition is taylored for the information age that at heart communicates in binary.But now turn on your AM radio, where sound is modulated into the amplitude of a radio signal. No symbols here, but somehow information is being encoded, communicated, and decoded. See the inherent inadequacy of your definition?Now imagine that instead of turning on your AM radio that you turn on your radio telescope and point it at the Large Magellanic Cloud, a satellite galaxy of the Milky Way. Now you're receiving and attempting to decode the information encoded in the radio signals from that galaxy. Where did the information come from? What did the encoding? Where did the encoding system come from? Whatever answers you come up with, unless your answers are all "God did it" then they will be natural answers based upon our understanding of the laws of the natural world. In the context of information theory, this is clearly false. Ideas, concepts, plans, these all have meaning. Meaning is a human construct and is completely separate from coding systems. Let me quote Shannon himself from his landmark paper A Mathematical System of Communication: The fundamental reality is that the natural world is full of codes that communicate information, and DNA is probably the most complex and interesting example we've found so far.--PercyEdited by Percy, : Improve clarity of wireless router para.Edited by Percy, : Grammar in last para.Edited by Percy, : Fix typo.

I think we probably all agree about this. Evolution is about the origin of species, not the origin of life. You've misunderstood what people have been saying. No one has been saying that DNA isn't a code. What they've been telling you is that nearly everything is a code. Please see my Message 40. I just rebutted this in my Message 40. The crux of the matter is that your definition is crafted for the digital information age, and it can be misinterpreted to exclude non-symbolic codes. Symbols are not required for a code. Symbols are just an easy way to describe a code. As I point out in Message 40, your wireless router codes information into 0's and 1's, but AM radio codes information though continuous and non-symbolic amplitude modulation, and anything that emits or reflects light is communicating information about itself in codes. The deciphering of these natural codes to derive general laws is called science. Now you're getting confused about just what comprises a code. A code is not something that "contains instructions," although some codes do. A code is simply a systematic representation of information. When scientists point their telescopes at distant galaxies they translate the information in the detected radio signals into some other form, maybe notations in a lab book or, more likely today, digital bits on a spinning disk. Those radio signals contain coded information. The scientists certainly didn't create the information. Without the information encoded in those radio signals they'd just be making it up. Long ago in cave man days a witch doctor said, "Naturalism can't tell us where lightning comes from." Og spoke up and said, "Just because we don't know where lightning comes from today doesn't mean we'll never figure it out. Maybe the gods don't cause lightning, similar to other things we've figured out the gods didn't do." That night the witch doctor had Og for dinner in his cave.In other words, claims of what naturalism can't explain have been in constant retreat since the beginning of time. Regarding the origin of the DNA code, maybe we'll figure it out, maybe we won't. Certainly there's not much evidence left after several billion years, so even if we figure out a way it might have happened, that won't mean we've found the way that it actually did happen. But your argument has not had a single success so far. Not a single scientific mystery has ever been resolved in favor of the supernatural. Have you considered the possibility that Perry Marshall might be making overinflated and self-serving statements about his own successes? His thread over at the Free Thought and Rationalism discussion board ( Proof of god via DNA and evolution) doesn't reveal any greater success than you're experiencing here with the same arguments. In fact, the core of his strategy seems to be the same as your own: misdefine code, then insist the definition is correct no matter how often it is successfully rebutted.--Percy

You're repeating yourself. This here comes verbatim from your Message 18: By the way, Yockey is not "the foremost living specialist in bioinformatics." I don't know who, if anyone, would actually deserve that title, but it definitely is not Yockey. This isn't from Wikipedia. It's hard to tell where it actually originates, it appears verbatim at 10 different websites. If you check out the version at Fact-Archive you'll see that what you quote begins in the section Information as a message, and then without any hint that any text is missing picks up with the second sentence of the section Information as a pattern.And there are three more sections describing information as sensory input, an influence, and as a property in physics that you completely ignored. Who do you think you're fooling? Making matters worse you make no attempt to indicate where the part you're quoting ends and your own words resume.You need to pick a single definition of information rather than picking portions of different definitions that you happen to like. The only definition that makes sense in this context is Shannon information, because it is quantifiable. I've rebutted this bit about symbols being a required part of codes twice now, and this would be the third time except that I'm going to instead refer you to Message 40. You need to respond to the rebuttal and stop repeating yourself. They contained information before you arranged them in your driveway. Pick up one of the pebbles and look at it. The pebble has a color, a shape, a texture, a weight. Where did the information about these qualities come from? It didn't come from you, it came from the pebble. The color and shape were encoded as electromagnetic information reflected from the pebble to your eyes. The texture and weight came from its surface impinging directly on your fingers and hand. I've done this a number of times at this very website. See for example Message 81. This couldn't be more wrong. All information ultimately originates in nature. I suggest you stop mixing and matching your definitions and instead begin with Shannon information. Then, consistently sticking with this one definition, try to make your case.--Percy

You were corrected on far more than a mere misattribution. Might we at some point expect a response about a) your picking and choosing of different parts of different definitions of information; b) your incorrect definition of codes; c) your misconceived example involving pebbles; d) my explanation of a natural origin for information in DNA; e) how nature is the ultimate source of all information.--Percy

You're quoting Perry Marshall quoting a bunch of other sources. This is from the Forum Guidelines:

6. Avoid lengthy cut-n-pastes. Introduce the point in your own words and provide a link to your source as a reference. If your source is not on-line you may contact the Site Administrator to have it made available on-line.

--Percy

You need to be more attentive in your participation in this thread, because you seem unaware that you're ignoring most arguments and just repeating yourself. The purpose of debate is not so you can write essays but to have a back and forth.Here's what happened:You didn't respond to any of the significant points in my Message 52, then when I called your attention to this fact in Message 59 you responded to it and still ignored the actual arguments in Message 52. Message 59 was just a very brief list of the points you ignored. And you've been ignoring Message 40 for more than 20 posts now.To make this easy for you, I'll cut-n-paste the significant points from Message 52 here.

1. If you check out the version at Fact-Archive you'll see that what you quote begins in the section Information as a message, and then without any hint that any text is missing picks up with the second sentence of the section Information as a pattern.
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   And there are three more sections describing information as sensory input, an influence, and as a property in physics that you completely ignored. Who do you think you're fooling? Making matters worse you make no attempt to indicate where the part you're quoting ends and your own words resume.
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   You need to pick a single definition of information rather than picking portions of different definitions that you happen to like. The only definition that makes sense in this context is Shannon information, because it is quantifiable.
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2.  
   What's important here is 1) information always involves a sender and a receiver; 2) an encoding / decoding mechanism; 3) a convention of symbols ("code") which represent something distinct from what those symbols are made of.
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   I've rebutted this bit about symbols being a required part of codes twice now, and this would be the third time except that I'm going to instead refer you to Message 40. You need to respond to the rebuttal and stop repeating yourself.
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3.  
   If I arrange pebbles on the driveway to spell your name, those pebbles represent you. As such they now encode information, and possess a property they did not possess before I spelled your name with them. They now contain information.
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   They contained information before you arranged them in your driveway. Pick up one of the pebbles and look at it. The pebble has a color, a shape, a texture, a weight. Where did the information about these qualities come from? It didn't come from you, it came from the pebble. The color and shape were encoded as electromagnetic information reflected from the pebble to your eyes. The texture and weight came from its surface impinging directly on your fingers and hand.
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4. Having quoted Dawkins here, it's interesting to note that neither he, nor any materialist has ever provided any scientific (i.e. empirical, testable, falsifiable) explanation for the origin of information.
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   I've done this a number of times at this very website. See for example Message 81.
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5.  
   No naturally occuring molcule possesses the properties of information. Nature does not produce any kind of code, encoding/decoding mechanism or symbolic relationships at all; everything in nature represents only itself.
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   This couldn't be more wrong. All information ultimately originates in nature. As I've explained several times now, ask yourself where the information comes from that scientists record in their notebooks. Since they're not making it up, it must come from nature. I suggest you stop mixing and matching your definitions and instead begin with Shannon information. Then, consistently sticking with this one definition, try to make your case.

--Percy

WordBeLogos, other people's messages are not just another opportunity to restate your position. You're ignoring or misinterpreting many points. Just look at this prime example, the very first thing you say in your post: I described precisely how you were inconsistent in your definition of information, and you respond about how consistent you've been in your definition of codes. Now I have to repeat myself all over again. Could you *please* in the future make a greater effort to comprehend a point after just a few repetitions, preferably the first one? It would be nice if I could have some confidence that years from now as I lie on my deathbed I won't be typing a message to you explaining the same thing yet again for the 12,657th time.So once, again, there were five definitions of information at Fact Archive's definition of information. You combined part of the first definition of Information as a message, part of the second definition of Information as a pattern, and completely ignored other parts of these definitions as well as all of the three other definitions.Is this clear now?I then urged you to use the Shannon definition of information, which is the definition of information as a message, because it is quantifiable.Now let me *YET AGAIN* repeat my criticism of your definition of a code. First, here's your full paragraph: You have been very consistent in your definition of a code, but all you do is repeat how consistent you're being and how sufficient your definition is, ignoring the criticism, which I repeat yet again:

• You've chosen the definition of human created codes intended for a digital age and are in effect claiming, without justification, that there can be no other types of codes, and that therefore only human created codes can be codes.
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• Information can be encoded in ways that are not symbolic. With a finite set of symbols, how are you going to define a symbolic representation of the infinite range of pitch and volume used by our military sentry? How are you going to represent the continuous changes in amplitude of the human voice modulated onto an AM radio signal? You can, of course, approximate them through analog-to-digital conversion, which is how music is encoded onto CD's, but this is an approximation that while adequate for human hearing does not actually reproduce the original signal.

A few examples. A volcano makes a soft rumbling sound, and a nearby sentry assigned to watch the volcano journeys back to his tribe and when asked the status imitates the rumbling sound of the volcano. How is the rumbling sound coded information when made by a human, but not when made by the volcano?Or consider a rather strange arborist who decides to communicate the pattern of 60 growth rings in a recently deceased tree by growing another tree. For a thick growth ring in the old tree he richly waters and fertilizes his new tree for a year. For a thin growth ring he only waters and fertilizes his new tree sufficient to keep it alive for that year. For an average growth ring he gives it a normal amount of water and fertilizer. After 60 years his new tree contains a record in its pattern of rings of both its growth and the growth of the old tree. How can the tree rings of the new tree be information, while the tree rings of the old tree are not?Or consider Alphabits cereal. You select three letters and spell the word "yes". That's human encoded information. Now let's say you jostle the box of Alphabits, and three of the bits pop out and fall together to form the word "yes". How would someone arriving later determine whether the word "yes" was formed by an intelligence or not, and therefore whether it represented information or not?The reason your definition doesn't work is because it is artificially restrictive. You want codes to be something that only an intelligence can create. You've introduced this restriction because it allows you to reach the conclusion that is important to you. Unfortunately, by insisting on this restriction you've produced a definition that doesn't accurately describe the real world, as the contradictions indicated by my examples clearly tell us.Addressing the rest of the specifics in your message would just cause me to repeat the same basic points, so I'll skip ahead to address your last paragraph: Again, you're trying to draw a distinction that doesn't exist, and you're insisting on a restricted definition of code that was crafted for the specific context of communications in a digital age. The information that there's a large mass nearby in the form of a star is communicated in the form of electromagnetic radiation and gravity that takes about eight minutes to arrive. Clearly information is being communicated from the star to us, else we couldn't know it was there. Until you have an inclusive definition of information and codes, your ideas won't be representative of the real world.--PercyEdited by Percy, : Grammar.Edited by Percy, : Improve clarity slightly.

We can't derive geological principles from the laws of physics and chemistry, either, they're too complex. Are you therefore willing to conclude that only an intelligence could design sedimentary, erosive and tectonic processes, among many others. Yockey is essentially making the "complexity requires an intelligence" argument, just as does Dembski.Life is indeed complex and unique chemically in its sequenced reactions and processes, but when we examine life in detail what we observe is completely consistent with the laws of physics and chemistry. And the changing pattern of life over time is described by the theory of evolution, which is also consistent with the laws of physics and chemistry.You can point to things we don't yet understand about the origins of the genetic code, but this would only mean that you somehow don't comprehend that there will always be things we don't yet understand. That's why the religious who require their myths to be consistent with science always focus on the frontiers of science where knowledge is most uncertain. That's why intelligent design focuses so much energy on the tiniest processes of life at the nuclear level, and on the tiniest components of reality at the quantum level. Religion has had to retreat from claims of everyday experience like "God controls the weather" and "God controls the dance of the planets" to the far more esoteric and remote "God controls DNA" and "God controls quantum fluctuations."About the rest of your post, repeating your definition of codes in different ways over and over and over again doesn't make your particular choice of definition correct. Being right doesn't derive from repetition. I again encourage you to participate in a back and forth instead of just more repetitions of your definitions.--Percy

You're right about this, and I think that's why he said, for example, that matter contains only its "personal" information. But obviously he's wrong there, too, such as in geology where a rock layer contains not only information about itself specifically, but also about the context and environment in which it formed, such as limestone layers that formed in warm shallow seas. And of course the examples go on and on, like a spectrum light from a distant galaxy passing through a gas cloud and picking up hydrogen absorption lines. I don't think WordBeLogos's definition of communication requires an intelligent sender and receiver. I think his claim is that the origin of the code requires an intelligence. Of course there's a complex process built around the code, and I think WordBeLogos believes that that requires an intelligence, too.--Percy

What information are you referring to? The text you cut-n-pasted and mix-n-matched from different definitions of information to make it seem like the Fact Archive was saying something they weren't? The definitions of information you ignored? The introductory paragraph to the quote of Yockey that you keep repeating and that you evidently hoisted without attribution? Your refusal to engage in discussion, instead continually repeating the same points over and over again like a parrot or a broken record?And in this very message you've quoted Perry Marshall without attribution. Your next to the last paragraph is Perry Marshall's words, not your own.When you can't express arguments in your own words, it must be really difficult to find relevant cut-n-pastes from people who can. I can see now why you're having so much trouble responding to the points people actually make. This explains why all you do is keep repeating the same things over and over again.This also explains why you not only didn't respond to any argument I made in my last few posts, you didn't even respond to any argument I've ever made. Your quote from Perry Marshall was when he was rebutting someone who had claimed DNA isn't a code. But I've never claimed DNA isn't a code. So why are you arguing to me that DNA is too a code? Evidently because you screwed up and cut-n-pasted the wrong text.Whenever you're ready to respond to the arguments and rebuttals that people are actually making in their replies to you then we're ready to listen. But if you're not going to do that then just please stop posting.--PercyEdited by Percy, : Grammar.

Omigod, your last paragraph is an unattributed cut-n-paste, too. The first part is from the Cosmicfingerprints website. Go to Skeptic's Objection to Information Theory #1: "DNA is Not a Code" and search for "take that up".How many of the words in your messages are actually your own?--Percy

As long as you continue evading, misrepresenting, plagiarizing, ignoring, and violating the Forum Guidelines, I'll keep criticizing.But if you'd like to respond to what people have actually been saying, then it would be a welcome change.By the way, this is from the Forum Guidelines:

6. Avoid lengthy cut-n-pastes. Introduce the point in your own words and provide a link to your source as a reference. If your source is not on-line you may contact the Site Administrator to have it made available on-line.

The reason for the part about putting things in your own words is that in this board's early days we discovered that some people would cite arguments they didn't understand, thereby wasting a lot of people's time. Gee, just like what you're doing here! That's why we require people to describe and support their position in their own words. Which, to dwell on the obvious only because you seem reluctant to own up to anything, you haven't been doing as of yet.In other words, we're not here to rebut what someone else said on some other discussion board. We're here to debate other members. Give poor Perry a rest and start constructing your own arguments.--Percy

Hi WordBeLogos,Well, this is an improvement. Nice job! This is what you want to be doing: quoting what people say, then responding to it. Unfortunately in this case I still have to repeat my argument since you seem to have forgotten the context. What you originally posted back in Message 67 was this: What I challenged was Yockey's statement about not being able to derive the principles of biology from the laws of physics and chemistry. I didn't say anything about codes or plans.Yockey's statement is a non sequitur that cannot support his conclusions because there are many complex natural processes outside of biology whose principles can't be derived from the laws of physics and chemistry. And it has nothing to do with relative information content. "F=ma" is an extremely simple law of physics, and all matter in the universe follows this law (or its relativistic equivalent when necessary), yet even the tiniest grain of sand contains more information than "F=ma".Since Yockey's starting premise is false, the rest of his paragraph about the genetic code must necessarily fall apart. It didn't follow from his premise anyway, it was just another unsupported assertion. The genetic code is not what separates life from non-life, because there are the additional requirements of metabolism and reproduction. I think we all agree with Yockey when he makes the observation that the processes surrounding DNA are unique "in the physico-chemical world", but only in that they're the most intricate and complex that we know of. How can you offer as argument the very conclusion you're trying to prove? Same question. How can you offer as argument the very conclusion you're trying to prove? People have given you many examples of natural codes. Your rebuttal consists of, "No they're not." We're all waiting for you to elaborate. You're misconstruing the argument. The argument is not that I know the level at which God would provide compelling evidence. The argument is that the history of those trying to reconcile religion with science is to turn to the frontiers of knowledge where things are most uncertain. At one point the origin of lightning was on the fringe of science. At another point the planetary orbits were on the fringe of science. Now the complex microbiological and quantum processes are on the fringes of science. The history of these kinds of religious apologetics is to focus on areas we know least and to conclude, "Here be God." So far they've been wrong every time, and as science pushes the frontiers out ever further they have to pull up stakes and find new arguments. If we were debating 20 years ago, you'd be the guy pushing vapor canopies.Your quote from Perry is confusing meaning with information when he says, "Just like the molecular motion that we interpret as temperature, alpha particle radiation is not coded information until meaning is assigned to it." As Shannon says, and I've quoted this to you before, "Frequently the messages have meaning; that is they refer to or are correlated according to some system with certain physical or conceptual entities. These semantic aspects of communication are irrelevant to the engineering problem."In other words, Perry's confusing semantics with information. You're again stating as argument the conclusion you're trying to prove. Repetition isn't going to help you make your case.People here, including myself, have provided you a number of examples of natural codes and sources of information. I suggest you try to explain how they are not codes. Please try to remember this time that "This is not a code" is not an explanation, it's a statement.Why don't you address this one simple example: Let's say you're a scientist studying the sun and you're making notations in a notebook. Where does the information about the sun come from? Is it coming from the scientist? If it's coming from the scientist then he should be able to make the same notations without the sun. But he can't, right? Therefore the information he's writing down must come from the sun, because he can't just make up the information himself and have a prayer of any of it being correct. You've already conceded that matter contains information about itself, so it must be true that information was communicated from the sun to the scientist.Now we know you're insisting that the information from the sun is not *encoded information*, but it is. For example, the elements in the sun's outer atmosphere are encoded in the sun's absorption spectrum. Every black line in the spectrum represents an energy change in the electron shells of the isotope of a specific element. Here's an example of such a spectrum: And here's a table of some of the more significant absorption lines: Now explain to us how this correspondence between black lines at a frequency (symbols, since you're so insistent about them) and elements is not a code.--Percy

Of course gravity isn't a code like DNA, but DNA is not the standard for what constitutes a code. There must be uncountable numbers of types of codes, and the vast majority are not like DNA, and also not like other types of codes. Of course gravity is a code. It just isn't a code like DNA. The music encoded on CD's isn't like DNA, either. The ASCII code used by computers to encode alphabetic letters and symbols also isn't like DNA. If your requirement for something to be a code is that it be like DNA, then by your definition DNA is the only code in existence.Let's put things in context, WordBeLogos. You saw a horse in a race and you thought it looked beautiful, so without even caring whether it won that race (it lost miserably, by the way) you borrowed the horse to enter in this race only to find that it's running a distant last again.Beauty is in the eye of the beholder, and likely because of your religious predilictions Perry's arguments are most beautiful to you. Unfortunately for you, beauty is not an objective quality, and beauty doesn't win the race.--PercyEdited by Percy, : Provide elaboration in my 2nd paragraph.