coded information in DNA

pmarshall writes:Unfortunately, it is not possible for us to have a productive discussion without a proper definition of terms. Since the extensive papers, dictionaries and mathematical definitions I have cited thus far have not been sufficient to persuade some in this forum that DNA is literally a code, I am happy to provide you with further support for my thesis, and more textbook definitions so that all can agree:Quote:
The genetic code is a set of 64 base triplets (nucleotide bases, read in blocks of three). A codon is a base triplet in mRNA. Different combinations of codons specify the amino acid sequence of different polypeptide chains, start to finish.
-Cell Biology and Genetics, Starr and Taggart, Wadsworth Publishing, 1995Genetic Code: The sequence of nucleotides, coded in triplets (codons) along the messenger RNA, that determines the sequence of amino acids in protein synthesis. The DNA sequence of a gene can be used to predict the mRNA sequence, and the genetic code can in turn be used to predict the amino acid sequence.
-50 years of DNA, Clayton and Dennis, Nature Publishing, 2003The problem of how a sequence of four things (nucleotides) can determine a sequence of twenty things (amino acids) is known as the ‘coding’ problem.��? —Francis CrickThe unique mark of a living organism, shared with no other known entity, is its possession of a genetic program that specifies that organism’s chemical makeup. The program has two essential and related features: first, it is ‘read’ by the organism, and the instructions embodied therein expressed, second, it is replicated with high fidelity whenever the organism reproduces.DNA carries genetic specificity. This structure immediately suggests that genetic specificity, the information��? that distinguishes one gene from another, resides in the sequence of nucleotides.Genetic information flows in linear fashion from the sequence of bases in DNA to that of amino acids in proteins. The parallel with letters and words is inescapable the quantity of information transmitted can be estimated with the aid of algorithms derived from wartime researches on the fidelity of communications.��?The most compelling instance of biochemical unity is, of course, the genetic code. Not only is DNA the all but universal carrier of genetic information (with RNA viruses the sole exception), the table of correspondences that relates a particular triplet of nucleotides to a particular amino acid is universal. There are exceptions, but they are rare and do not challenge the rule.��?-The Way of the Cell, Franklin M. Harold, Oxford University Press, 2001A code is a set of rules governing the order of symbols in communication. This defines a code, regardless of the nature of the symbols, be they alphabetic letters, voice sounds, dots and dashes, DNA bases, amino acids, nerve impulses, or what have you. Codes are generally expressed as binary relations or as geometric correspondences between a domain and a counterdomain; one speaks of mapping in the latter case. Thus, in the International Morse Code, 52 symbols consisting of sequences of dots and dashes map on 52 symbols of the alphabet, numbers and punctuation marks; or in the genetic code, 61 of the possible symbol triplets of the RNA domain map on a set of 20 symbols of the polypeptide counterdomain.In intercellular communication the domains and counterdomains are the signal molecules and their receptors, and the code is like the base-pair rules of the first-tier code of the DNA, a simple rule between pairs of molecules of matching surfaces.Why There are no Double-Entendres in Biological Communication: The basic information for the encoding in intercellular communication (a high-class encoding complying with Shannon’s Second Theorem) is all concentrated in the interacting molecular surfaces. And this information is what makes the communications unambiguous. We can now define an unambiguous communication: a communication in which each incoming message or signal at a receiver (or retransmitter) stage is encoded in only one way; or, stated in terms of mapping, a communication in which there is a strict one to one mapping of domains, so that for every element in the signal domain there is only one element in the counterdomain.The table in Figure 7.9 tells us at a glance that a given amino acid may have more than one coding triplet: UUA, UUG, CUU, CUC, CUA, CUG, for instance, are all synonyms for leucine. A code of this sort is said to be degenerate.��? That is OK despite the epithet, so long as the information flow goes in the convergent direction, as it normally does. The counterdomain here consists of only one element, and so a given triplet codes for no more than one amino acid. Thus, there is synonymity, but no ambiguity in the communications ruled by the genetic code.��?-The Touchstone of Life: Molecular Information, Cell Communication and the Foundations of Life, by Werner R. Loewenstein, Oxford University Press, 1999(George) Gamow devised a scheme, illustrated by means of playing cards, that involved sets of three adjacent nucleotides per amino acide unit (triplet��? code) in a sequence of overlapping triplets. That proposal spurred Francis Crick and his colleagues to examine the coding problem more critically and to use knowledge gained from genetic experiments to test the possible validity of Gamow’s scheme and its variants. By 1961 they had concluded that the nucleotides of each triplet did not belong to any other triplet (nonoverlapping��? code); that sets of triplets are arranged in continuous linear sequence starting at a fixed point on a polynucleotide chain, without breaks (commaless��? code), thus determining how a long sequence is to be read off as triplets; and that more than one triplet can code for a particular amino acid (degenerate��? code).-Proteins, Enzymes, Genes: The Interplay of Chemistry and Biology, Joseph S. Fruton, Yale University Press 1999The genome of any organism could from then on be understood in a detailed way undreamt of 20 years earlier. It had been revealed as the full complement of instructions embodied in a series of sets of three DNA nitrogenous bases. The totality of these long sequences were the instructions for the construction, maintenance, and functioning of every living cell. The genome was a dictionary of code words, now translated, that determined what the organism could do. It was the control center of the cell. Differences among organisms were the result of differences among parts of these genome sequences.��?-The Human Genome Project: Cracking the Genetic Code of Life, by Thomas F. Lee, Plenum Press, 1991The three-nucleotide, or triplet code, was widely adopted as a working hypothesis. Its existence, however, was not actually demonstrated until the code was finally brokenWith a knowledge of the genetic code, we can turn our attention to the question of how the information encoded in the DNA and transcribed into mRNA is subsequently translated into a specific sequence of amino acids in a polypeptide chain. The answer to this question is now understood in great detail instructions for protein synthesis are encoded in sequences of nucleotides in the DNA molecule.��?-Biology, 5th Edition, by Curtis & Barnes, Worth Publishers, 1989If there’s still anyone who asserts that DNA is not a code, take up this issue with the authors and publishers of these books — Oxford University Press, Yale University Press, Francis Crick, George Gamow, etc. I have presented not only volumes of material evidence that DNA is a code, I have also provided proof based on formal mathematical definitions.

Living things do occur naturally. There's nothing more natural than biology.

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.

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 (Thread Evolving New Information).

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.

Michamus writes:Negative. The definition you have provided is insufficient, as it does not include known means of communication which do not rely on symbols. Percy has called you out on this 3 or 4 times now.

Michamus writes:I maybe nitpicking here, but it does seem like your definition has evolved (oh the irony).

Michamus writes:ROFL! Oh wow! Now sounds are symbols? You are certainly playing the "I make up my own definitions of words on the spot" game.

Michamus writes:"quote:
--------------------------------------------------------------------------------Source - Dictionary.com
symbol
-noun
1. something used for or regarded as representing something else; a material object representing something, often something immaterial; emblem, token, or sign.
2. a letter, figure, or other character or mark or a combination of letters or the like used to designate something: the algebraic symbol x; the chemical symbol Au.--------------------------------------------------------------------------------"

Michamus writes:BZZZTTT! Wrong again. You are arbitrarily making "Life" different because you want it to be. Life is a series of chemical reactions that occur no differently than any other chemical reactions.DNA is composed of molecules that contain no more "coded information" than the sum of their parts. If I were to present you with the chemical composition of that same pebble, and then compare it to the chemical composition of DNA, the only difference that you would see would be that they are composed of slightly different elements, as well as different amounts of the same elements.

Michamus writes:Yes. It is utterly ridiculous to think that Evolution is solely based on random mutation and natural selection.

Michamus writes:It is quite obvious why you want to insert the distinction though. You want life to be different. You want DNA to be something special that can't be accounted for in science.

pmarshall writes:My own lexical definition of information is as follows:Code is defined as communication between an encoder (a writer or speaker) and a decoder (a reader or listener) using agreed upon symbols.In this discussion, information and code are interchangeable terms.The above definition is analytic a priori because it IS just as clear as all bachelors are unmarried.According to Shannon’s model, for communication to take place, an encoder, decoder and transmitted code must be in place. We can look at any system and see if it has an encoder, decoder and a message - or not. DNA is a communication system. A snowflake is not. The definitions are black and white.I see no difference between the way bachelors are defined and the way information is defined.Any particular example of an observed communication system is posteriori synthetic because the components can be observed and labeled. DNA unambiguously fits this definition because as Yockey showed (see diagram at Is DNA a Code? ) it matches Shannon’s 1948 model exactly.Therefore DNA is a communication system based on the above definition and observations, and my argument is on solid ground so far.

Every instance of biological life that we observe is indeed the result of a mindless natural process, namely biological reproduction

We have no examples of DNA occurring in defiance of the laws of nature.

Every example of DNA we have was produced by well-understood processes that conform to the laws of nature.

Let me ask you again. Do you deny that my DNA was produced by the entirely natural process of my father and mother reproducing sexually?

Is this clear now?

Thus a message in English writing can be in the form of a book, words produced by an LCD screen, or dots and dashes of Morse code and still have the same "symbolic meaning". The message (information) is independent of the carrier. I think that is a requirement he has but I'm not sure.

Of course, if the above is true, then DNA is not a code meeting this definition. It can not be conveyed in any other way and still "work". It is pure chemistry and the "sender" and "receiver" are chemical reactions which have to have it in it's chemical form

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.

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."

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.

Q: The distances of alpha particles from a speck of radium provide coded information about the time of decay of each nucleus. Perry, you are just presenting assertions by simple fiat.A: If we say the temperature in the room is 70 degrees F, we have used a convention of symbols to describe a very real characteristic of air. However "70 degrees F" is the symbolic representation of a man-made encoding / decoding system; the air itself is just molecules in motion.Now if mercury is sitting in a tube (a naturally occurring thermometer, let's say) and it rises when the temperature rises, we still do not yet have an encoding / decoding system. However, if we take a red pen and mark degree marks on the tube so that the rising of the mercury corresponds to a specific temperature, now we do have an encoding / decoding system, and when we read the thermometer, we have coded information.This is consistent with my definition of "coded information" as "a system of symbols used by an encoding and decoding mechanism, which transmits a message that is independent of the communication medium."Just like the molecular motion that we interpret as temperature, alpha particle radiation is not coded information until meaning is assigned to it. Alpha particles are being radiated, but what message do they symbolize that is independent of the particles themselves? Did the count go up because the speck of radium moved closer to the sensor, or because we added more radium? The alpha particles have no symbolic relationship until we assign a meaning to their arrival, just like we do with temperature.

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.

The genetic code is itself subject to mutation, e.g. the observable evolution of "amber-suppressor" strains. Such mtations produce new codes.

Which laws of physics, chemistry, etc are contravened by its existence?

I have invented several codes. Which laws of nature was I breaking when I did so?

Can you give me one observable example of a code coming into existence in defiance of the laws of nature?

The problem is that when you say "the definition of coded information", you presume that there is only one -- "the" definition. There is not.

It seems that the posters to that thread have refuted his argument. And he has not returned to defend his position.

If you disagree, perhaps you could tell us -- in your own words -- why you disagree.

Even taking out the quotes from other people his latest post is still over 2000 words long. If we consider that a representative post length you are asking people to read over 50,000 words.

The problem with #2 is that the "codes we know the origin of" are the ones WE (humans) made. The fact that we made some codes and know that we made them doesn't itself tell us squat about the origin of codes we *didn't* make...

and (allegedly) don't know the origin of (such as DNA).

Even the way he words it, he *admits* that we don't know the origin of non-manmade codes (by contrasting them with the codes we *do* know origination stories for).

All #2 really says is that we know that men made manmade codes. Big whoop-de-do. That's pretty much a tautology. That really doesn't tell us anything about codes found in nature, the ones we know *we* didn't make, the ones he admits we *don't* know origins for.

Actually, he's speaking for himself -- *he* may know nothing about the origin of natural codes, but lots of people *do* know quite a bit about the origins of natural codes, even if we don't yet know every detail.

Somehow, he makes an unsupported, fallacious leap from #2 to his #3 which out of nowhere "concludes" that DNA was the result of a mind and that information is "proof of the action of a Superintelligence". Say what? How did he get from #2 to #3?

Of course we do. We have The Gravity Code. But it's okay, I know you're just ignoring it because you don't want to accept that The Gravity Code is a better code than DNA.

It seems to me that central to your argument is the assertion that the functionality of DNA is seperable from its form. But this is not so.

Chemistry and physics do not work without the same type of code found in DNA. Those codes can be found in the spin, charge, and mass of particles and the orbitals of electrons. For example, the code for neon is: 1s^2 2s^2 2p^6 The code for a W boson is: Charge -1, Spin 1, Mass 80.4 These are as much a code as DNA.

..The Gravity Code is also a code.

pmarshall writes:This definition is Shannon’s, and Shannon’s accurately describes all communication systems. Years after Shannon wrote his paper, we also discovered that DNA matches his model 100%. Shannon’s definition has been working just fine for 61 years.All definitions are restrictive, otherwise we couldn’t have meaningful communication about anything at all.There are no contradictions. DNA fits Shannon’s model. As does everything on the Internet, and human languages.Snowflakes, rocks, volcanos and hurricanes do not fit Shannon’s model.

pmarshall writes:If you press the button on your garage door opener and the garage door opens, this happens because a code has been successfully transmitted and received.The opening of the garage door is real.Therefore the information that was passed between the transmitter and the receiver was also real.Communication is real. It’s physically measurable.Communication systems are real. They are also physically measurable.We can make a judgment as to whether the code was successfully transmitted and received. If you push the button and the garage door doesn’t open, then transmission was unsuccessful.It could be unsuccessful because the battery was dead. It could be unsuccessful because the I set the DIP switches wrong in the transmitter and it was transmitting the wrong code or using the wrong frequency.It could be unsuccessful because you were too far away or because there was interference from electrical noise.In any case there is an implicit definition of success or failure based on the INTENT of the code - and the intended consequences of pushing the button. The fact that the right transmitter is supposed to open my garage (notice the teleology here) and that all other transmitters in the neighborhood are not supposed to open my garage door.We can describe this in terms of the OSI 7-layer model - physical layer, data link layer, transport layer, application layer, etc.In the garage example there are only a few of layers in use. There’s the radio transmission (physical layer), and there is a code that is transmitted (transport layer). Then there is the application layer, which is the command to open the garage door (i.e. pushing the button).In any communication system, there is ALWAYS at least one additional implied layer, on top of the ones that are physically present. In this example it’s the INTENT to open the garage; and also the INTENT to build a system that performs this task in the first place. All communication systems imply intent. DNA implies intent to convert GGG triplets to Glycine.This implied intent is posteriori analytic. We can infer that this system existed as a thought experiment before it existed as a physical system. We make this inference from our observation that the system uses agreed-upon symbols. Symbols are abstract.In DNA, the tables that map triplets to mRNA to proteins are not physical but the tables describe ideas that accurately describe the rules of a real coding system.I think you are trying to ask the question, are symbols real? Are the rules of a communication system real?(BTW I recognize the distinction between a physical object and the labels we attach to it. Glycine is a label we attach to a certain amino acid. As the Neuro Linguistic Programming people say, the territory is not the map.)The rules of a communication system are not physically real. You cannot weigh them on a scale.However the fact that we can MEASURE whether the rules were followed or not; whether the symbols were properly decoded or not; proves that they are still real. We could not talk sensibly about them if they were not.We can measure whether the rules of a communication were followed or not just as accurately as we can measure a tree.Correct programming of a garage door opener is real because the garage door opens. A measurable event.Incorrect programming of a garage door opener is real because the garage door does not open. Also a measurable event.Therefore communication is real; communication systems are real; the information in those systems is real; and the rules that govern them are real.The fact that these words on this blog have appeared on your screen, properly decoded by your PC and in turn properly decoded by you, is proof of the reality of multiple layers information. And intent. Even on a purely mechanical level, ie your Wi-Fi sending this information to your computer.Our judgment of proper or improper decoding is not a physical object. But the judgment exists and it is still measurably true or false.This is proof that Norbert Weiner was right: Information is information, neither matter nor energy.So information is on solid footing on priori analytic, posteriori synthetic, and posteriori analytic grounds.This brings us to the priori synthetic - my metaphysical proposition of God.Communication systems are built using rules that are arbitrary. The choice of 1000001 meaning the letter A in ASCII is arbitrary. The choice of GGG coding for Glycine in DNA is arbitrary.Neither the rules of ASCII nor the rules of the genetic code can be derived from the laws of physics (Yockey, 2005). The rules of any particular coding system are not properties of pure matter and energy. Rather, these rules organize the movement of matter and energy.In the OSI model, these rules operate in the upper layers, not at the physical layer. The physical layer simply obeys the instructions of the layers above it.Since physical laws can never be disobeyed, the rules of codes are fundamentally different from the laws of physics. Why? Because they can fail. The intended outcome can fail to occur. The decoder can fail to properly decode.The only place that rules of this kind originate, so far as we have ever observed, is from conscious intelligent minds. We have 100% inference from millions of codes supporting this statement and 0% inference to the contrary.Rocks do not talk. Therefore the rules of communication systems come from consciousness and not from matter or energy.Information is a separate entity from matter and energy and therefore has a separate source.Since information exists and does not come from unconscious material sources, it must come from an immaterial conscious source that exists.Therefore an immaterial conscious source exists, and information has a metaphysical origin.Therefore God exists.I have not formally proven this; such a thing is inherently unprovable in the formal mathematical sense. As Gdel said, all knowledge rests on axioms that you know are true but cannot be proven.I have shown that all human knowledge provides 100% inference to this. Based on current knowledge and the scientific method of induction, we can be just as certain that God exists as we are certain about the laws of thermodynamics.

Depending on the context, there's always a different way to express an idea in order to be better understood. You can either simplify the idea, use analogies or detail the idea more, detail some parts more while simplfying other parts if you want to highlight the parts revelant to the discussion, etc.....