A code or not a code?



  • A non-programmer friend and I had an interesting discussion today. He stated that besides DNA, there is no known naturally occurring code. The exact quote is "all codes are created by a conscious mind; there is no natural process known to science that creates coded information."

    I think that tree growth rings are encoded age and climate data and sedimentary layers are encoded geological data, but my friend does not agree because the data derived from those sources is a scientific conclusion based on observation of phenomenon. To him a code is like a language and can be decoded, not a pattern like tree growth rings.

    I'm wondering what perspective a larger programmer audience has on this matter. In programming we see codes (or encoding) like SHA-1 that does not carry the original information at all and we see ASCII codes that are certainly not a language. As an abstract concept I think things like tree rings can be codes, but that obviously doesn't work if you think of codes as precise instruments of information transfer. Does my perspective as a programmer agree with that of other programmers? If so, do programmers have a better grasp of the world of abstract codes than other people, or a warped sense of codes that doesn't make any sense?

    For those who haven't yet seen it, this article ( http://ds9a.nl/amazing-dna/ ) called DNA Seen Through The Eyes Of A Coder is an interesting read. Are programming languages the key to life?

     



  • I think your friend might be right. I don't think of "code" as a product of nature, but rather a crude imitation. The way I look at it, to "code" something is to examine a problem, system, or sequence of events in it's entirety, then abstract it out into it's smallest parts of logic and functionality. Then from that we "create" our own versions of those little building blocks(probably leaving some out, though this might be done at the initial step.). I would assume that "useful" code could only be created by a conscious mind.



  • useful codes are found everywhere in nature.  The code of the day/night and season cycles drives plant growth.  Organs in your body use a "code" to communicate to tell each other when to function.  The code medium might be the blood stream and hormones, or it might be the nervous system sending codes to the muscles to constrict.  Ants do not possess a conscious mind, yet they use scents to communicate to each other where food is.



  • @shakin said:

    A non-programmer friend and I had an interesting discussion today. He stated that besides DNA, there is no known naturally occurring code. The exact quote is "all codes are created by a conscious mind; there is no natural process known to science that creates coded information."

    I think that tree growth rings are encoded age and climate data and sedimentary layers are encoded geological data, but my friend does not agree because the data derived from those sources is a scientific conclusion based on observation of phenomenon. To him a code is like a language and can be decoded, not a pattern like tree growth rings.

    So he's overliteralizing the phrase "genetic code" to infer the existence of a genetic programmer, or just relying on wordplay to make a vein rhetorical point. There are lots of misleading expressions in science, for example its not uncommon for someone to assume that the phrase "Big Bang" actually refers to an explosion, or that "mitochondrial Eve" is a reference to Biblical character in Genesis.

    I personally don't see how tree rings don't contain intrinsic information the former tree, or how stepping in clay doesn't encode a lot of data about the object which left the impression.. But since your friends argument is entirely verbal and depends on whatever arbitrary definitions he chooses, so it might not be worth to time to dwell on.

    At any rate, DNA is governed by the same laws of physics that operate on the rest of the universe, its a product of matter and natural phenomena like everything else. Every year, first semester biochemistry students recreate some classic experiments by Stanley MIller and Harold Urey which attempt to simulate early conditions on earth; the experiments demonstrate that many important amino acids and simple proteins will form spontaneously from mixtures of inorganic compounds like water, methane, nitrogen, ammonia, and hydrogen. These things form readily without any intelligent coordination at all.

    For those who haven't yet seen it, this article ( http://ds9a.nl/amazing-dna/ ) called DNA Seen Through The Eyes Of A Coder is an interesting read. Are programming languages the key to life?

    Without much effort, a person could write up an article explaining how DNA and the entire universe seems to operate according to the laws of supply-side economics, or that the formation of DNA mirrors the relationships in a romance novel. At that point, the "genetic code / genetic programmer / genetic economist / genetic novelist" analogy is taken so far that it looses all meaning.



  • The exact quote is "all codes are created by a conscious mind; there is
    no natural process known to science that creates coded information."

     

    The fundamental flaw in this idea is that it doesn't go anywhere. What does it matter whether a coding system is "natural" or "created", for whatever arbitrary definitions of those words?

    Classifying things is pointless if you don't intend to do anything with the classifications.

    In programming we see codes (or encoding) like SHA-1 that does not carry the original information at all and we see ASCII codes that are certainly not a language. As an abstract concept I think things like tree rings can be codes, but that obviously doesn't work if you think of codes as precise instruments of information transfer. Does my perspective as a programmer agree with that of other programmers?

    This question is about information and coding theory, not programming. You're skirting around the edges of some of the fundamentals without really reaching them. People who have studied the subject will get it, others won't. The seminal paper on the subject is Shannon's "A Mathematical Theory of Communication", which founded the field.

    Are programming languages the key to life?

    No. That's pop-science gibberish. 



  • -- If a tree falls in the woods and there's nobody around, does it make a sound?

    -- Define 'sound'.



  • @Yahweh said:

    At any rate, DNA is governed by the same laws of physics that operate on the rest of the universe, its a product of matter and natural phenomena like everything else. Every year, first semester biochemistry students recreate some classic experiments by Stanley MIller and Harold Urey which attempt to simulate early conditions on earth; the experiments demonstrate that many important amino acids and simple proteins will form spontaneously from mixtures of inorganic compounds like water, methane, nitrogen, ammonia, and hydrogen. These things form readily without any intelligent coordination at all.

    I agree that Miller and Urey demonstrated they could form amino acids and simple proteins by adding energy to mixtures of organic and inorganic chemicals.  No question about that.

    The experiment which I've not seen, is this:  does the presence of a protein in a certain chemical environment increase the probability of the construction of other molecular structures which, in turn, increase the probability of creating another copy of that protein?

    Here's the starting point in my mind: What is the smallest cyclically-reproducing system involving D/RNA and proteins?  That is, what is the smallest string of D/RNA in the presence of certain other chemicals which will produce proteins that will in turn generate a new copy of that D/RNA.  Then, is that combination something that can occur at a high enough probability to be sustainable?

    Basically, take a glob or nucleic acid and throw it in some amino acids or whatever and see what amino acids "stick" to the RNA and form some structure.  Then blow the nucleic acid out of that structure, leaving just the protein, and stick the protein back in a vat of nucleic acid components and see if the same strand of nucleic acid forms.

    Of course, that doesn't matter at all - because the Intelligent Design folks that know what they are talking about always invoke Godel's Incompleteness Theorem: The physical laws of the universe which give rise to the natural occurrence of life could have been developed by an intelligent being. Because the universe is a sufficiently powerful system, certain truths and untruths are not provable within that system. When it comes to creation, it's not possible to determine the "why" of it - we can only, at best, understand the "how" of it.  (Personally, this is why I don't think Intelligent Design and Evolution are in opposition - Evolution talks about the "how" and Intelligent Design talks about the "why").  



  • @tster said:

    useful codes are found everywhere in nature.  The code of the day/night and season cycles drives plant growth.  Organs in your body use a "code" to communicate to tell each other when to function.  The code medium might be the blood stream and hormones, or it might be the nervous system sending codes to the muscles to constrict.  Ants do not possess a conscious mind, yet they use scents to communicate to each other where food is.

    I completely aggree with tster here. Codes are nearly as old and common as life itself. 



  • @too_many_usernames said:

    Of course, that doesn't matter at all - because the Intelligent Design folks that know what they are talking about always invoke Godel's Incompleteness Theorem: The physical laws of the universe which give rise to the natural occurrence of life could have been developed by an intelligent being. Because the universe is a sufficiently powerful system, certain truths and untruths are not provable within that system.

    This is complete nonsense. Godel's incompleteness theorems are about specific mathematical systems, and no proof has been offered that the universe is one of these systems (and there is considerable reason in quantum theory to think that it is not). Furthermore, the things which cannot be proven under the incompleteness theorems are, for the most part, not particularly interesting things. They mostly have to do with whether or not the system itself is a sane system. Even if the universe were one of these systems, there is no reason to think that the statements in question should be undecidable.

    This kind of pseudo-mathematical gibberish will only convince people who have no comprehension of the subject. They might as well say "Every partially ordered set, in which every chain has an upper bound, contains at least one maximal element, therefore God is a lettuce".



  • @dhromed said:

    -- If a tree falls in the woods and there's nobody around, does it make a sound?

    -- Define 'sound'.

    The real question is "If a tree falls on a mime in the woods, does anyone care?" 



  • @too_many_usernames said:

    Here's the starting point in my mind: What is the smallest cyclically-reproducing system involving D/RNA and proteins?  That is, what is the smallest string of D/RNA in the presence of certain other chemicals which will produce proteins that will in turn generate a new copy of that D/RNA.  Then, is that combination something that can occur at a high enough probability to be sustainable?

    If you can stretch "certain other chemicals" to include humans, then viruses would fit the bill. i.e.: The common cold, influenza, etc... They're certainly not a complete strand of DNA that can produce a living being, but they do reproduce in the presence of "other chemicals".



  • @asuffield said:

    This is complete nonsense. Godel's incompleteness theorems are about specific mathematical systems, and no proof has been offered that the universe is one of these systems (and there is considerable reason in quantum theory to think that it is not). Furthermore, the things which cannot be proven under the incompleteness theorems are, for the most part, not particularly interesting things. They mostly have to do with whether or not the system itself is a sane system. Even if the universe were one of these systems, there is no reason to think that the statements in question should be undecidable.

    This kind of pseudo-mathematical gibberish will only convince people who have no comprehension of the subject. They might as well say "Every partially ordered set, in which every chain has an upper bound, contains at least one maximal element, therefore God is a lettuce".

    The universe is so full of de-facto unprovable truths that Godel's theorem is completely unnecessary to make irrelevant statements. For example, (ignoring the uncertainity principle from quantum mechanics), one of the following statements is true but de-facto unprovable:

    The total number of atoms in the universe, as of July 31., 1822, 17:39:15 GMT, was even. 

    The total number of atoms in the universe, as of July 31., 1822, 17:39:15 GMT, was odd.

    Or, just a highly likely but nor 100% sure guess: 

    The total number of atoms in the universe, as of July 31., 1822, 17:39:15 GMT, was not prime.

     



  • @too_many_usernames said:

    Here's the starting point in my mind: What is the smallest cyclically-reproducing system involving D/RNA and proteins?  That is, what is the smallest string of D/RNA in the presence of certain other chemicals which will produce proteins that will in turn generate a new copy of that D/RNA.  Then, is that combination something that can occur at a high enough probability to be sustainable?

    That comes a little close to that "irreducible complexity" folly of the Behe-ists.



  • @ammoQ said:

    For example, (ignoring the uncertainity principle from quantum mechanics), one of the following statements is true but de-facto unprovable:

    The total number of atoms in the universe, as of July 31., 1822, 17:39:15 GMT, was even. 

    The total number of atoms in the universe, as of July 31., 1822, 17:39:15 GMT, was odd.

    Ironically enough, there's one theory about the formation of the universe that, if validated, could prove that the number of atoms in the universe is always even (it's something about matched pairs - no particular evidence for it, but no particular evidence against it either).

    In general, the term you're looking for is "unverifiable" rather than "de-facto unprovable" (which is something of a contradiction in terms).



  • @asuffield said:

    Ironically enough, there's one theory about the formation of the universe that, if validated, could prove that the number of atoms in the universe is always even (it's something about matched pairs - no particular evidence for it, but no particular evidence against it either).

    What about fusion and fission? Hard to believe that this happens in pairs, too.

     

    In general, the term you're looking for is "unverifiable" rather than "de-facto unprovable" (which is something of a contradiction in terms).

    ESL ;-) 



  • @ammoQ said:

    @asuffield said:

    Ironically enough, there's one theory about the formation of the universe that, if validated, could prove that the number of atoms in the universe is always even (it's something about matched pairs - no particular evidence for it, but no particular evidence against it either).

    What about fusion and fission? Hard to believe that this happens in pairs, too.

    A surprisingly large number of the nuclear interactions do, if you count free neutrons to be atoms (they decay into regular hydrogen atoms after a few minutes). A few don't appear to, but we don't have any evidence that they don't, since it's not possible to measure these things on the level of individual atoms. We probably won't find out for sure until quantum theory develops to the level where we can explain the behaviour of nuclear chemistry. Most physicists would consider it unlikely, but stranger things have been found to be correct (like quantum theory itself).



  • OK. I'm already conviced. From now on, I believe that the number of atoms in the universe is even.



  • @ammoQ said:

    OK. I'm already conviced. From now on, I believe that the number of atoms in the universe is even.

    Could I interest you in purchasing some real estate? 



  • @asuffield said:

    @ammoQ said:

    OK. I'm already conviced. From now on, I believe that the number of atoms in the universe is even.

    Could I interest you in purchasing some real estate? 

    Only timesharing models. Owning 1/50th of a small appartment somewhere in Spain makes me feel rich and famous.



  • @Yahweh said:

    ...or that "mitochondrial Eve" is a reference to Biblical character in Genesis.

     

    That's ridiculous. Everybody (even Yahweh) knows that Mitochondrial Eve is the day before the ancient pagan festival of Mitochondrial.

     



  • @Hatshepsut said:

    @Yahweh said:

    ...or that "mitochondrial Eve" is a reference to Biblical character in Genesis.

     

    That's ridiculous. Everybody (even Yahweh) knows that Mitochondrial Eve is the day before the ancient pagan festival of Mitochondrial.

     

     

    And, of course, that the only things biblical in Genesis are the proportions of Mike Rutherford's ego.

     



  • @shakin said:

    A non-programmer friend and I had an interesting discussion today. He stated that besides DNA, there is no known naturally occurring code. The exact quote is "all codes are created by a conscious mind; there is no natural process known to science that creates coded information."

    I think that tree growth rings are encoded age and climate data and sedimentary layers are encoded geological data, but my friend does not agree because the data derived from those sources is a scientific conclusion based on observation of phenomenon. To him a code is like a language and can be decoded, not a pattern like tree growth rings.

    I'm wondering what perspective a larger programmer audience has on this matter. In programming we see codes (or encoding) like SHA-1 that does not carry the original information at all and we see ASCII codes that are certainly not a language. As an abstract concept I think things like tree rings can be codes, but that obviously doesn't work if you think of codes as precise instruments of information transfer. Does my perspective as a programmer agree with that of other programmers? If so, do programmers have a better grasp of the world of abstract codes than other people, or a warped sense of codes that doesn't make any sense?

    For those who haven't yet seen it, this article ( http://ds9a.nl/amazing-dna/ ) called DNA Seen Through The Eyes Of A Coder is an interesting read. Are programming languages the key to life?

    An interesting problem. If code is defined as the product of a conscious mind, how do you define consciousness?  IS DNA a code? It is essentially a "million-monkey-typewriter" product. If a million monkeys wrote Windows Vista (which may or may not have already happened :P ) would this program then be code? But if a million neurons in our brains exchange impulses that result in a real program being written by our fingers, does that somehow have more intention behind it than the stuff the monkeys produced? The only actual difference is in how well the neural network is trained...


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