quote:
DNA isn't really a code though, it is just convenient to speak of it as one for preliminary study.
Take a look at a these.
“Information, transcription, translation, code, redundancy, synonymous, messenger, editing, and proofreading are all appropriate terms in biology. They take their meaning from information theory (Shannon, 1948) and are not synonyms, metaphors, or analogies.”
(From Hubert Yockey, Information Theory, Evolution, and the Origin of Life, Cambridge University Press, 2005).
The book Information Theory, Evolution and the Origin of Life is written by Hubert Yockey, the foremost living specialist in bioinformatics. The publisher is Cambridge University press. Yockey rigorously demonstrates that the coding process in DNA is identical to the coding process and mathematical definitions used in Electrical Engineering. This is not subjective, it is not debatable or even controversial. It is a brute fact:
“Information, transcription, translation, code, redundancy, synonymous, messenger, editing, and proofreading are all appropriate terms in biology. They take their meaning from information theory (Shannon, 1948) and are not synonyms, metaphors, or analogies.” (Hubert P. Yockey, Information Theory, Evolution, and the Origin of Life, Cambridge University Press, 2005)
The encoding / decoding process in DNA happens without the intervention of intelligence, just like your computer getting automatic virus updates. Water flows and hailstones and sand dunes do not encode and decode information in this way. Only intelligently designed systems map 1:1 to Shannon's model. (From The Mathematical Theory of Communication, University of Illinois Press, 1998).
Yockey describes the encoding, transmission and decoding within the cell and its analogue to a recording tape. (Quoting Yockey): “Figure 5.2 describes the DNA-mRNA-proteome communication system to show its isomorphism with the standard communication system of the communication engineer. The genome, or the ensemble of genetic messages, is generated by a stationary Markov process and recorded in the DNA sequence, which is isomorphic with the tape in a tape-recording machine (Turing, 1936).
“The idea of encoding, of the accurate representation of one thing by another, occurs in other contexts as well. Geneticists believe that the whole plan for a human body is written out in the chromosomes of the germ cell. Some assert that the ”text' consists of an orderly linear arrangement of four different units, or ”bases' in the DNA forming the chromosome. This text in turn produces an equivalent text in RNA, and by means of this RNA text proteins made up of sequences of 20 amino acids are synthesized. Some cryptanalytic effort has been spent in an effort to determine how the 4 character message of RNA is re-encoded into the 20 character code of the protein. Actually, geneticists have been led to such considerations by the existence of information theory. The study of the transmission of information has brought about a new general understanding of the problems of encoding, an understanding which is important to any sort of encoding, whether it be the encoding of cryptography or the encoding of genetic information.”
(John R. Pierce, An Introduction to Information Theory: Symbols, Signals and Noise, 2nd edition, 1980)
(Hubert Yockey): “The genetic code has many of the properties of codes in general, specifically the Morse Code, the Universal Product Bar Code, ASCII, and the US Postal Code. I shall explain the relation of these codes to the genetic code in the following discussion. Every code, as the term is used in this book, can be regarded as a channel with an input alphabet A and an output alphabet B.”
Here is the formal definition of a code: Given a source with probability space [Omega, A, p(A)] and a receiver with probability space [Omega, B, p(B)], then a unique mapping of the letters of alphabet A onto letters of alphabet B is called a code.
Here p(A) is the probability vector of the elements of alphabet A and p (B) is the probability vector of the elements of alphabet B. (Perlwitz, Burks and Waterman, 1988)
Nature has extended the primary four-letter alphabet to the six-bit, 64 member alphabet of the genetic code. Each amino acid except Trytophan and Methionine has more than one codon. Thus, the genetic code is redundant (not degenerate). The sloppy terminology designating the genetic code as degenerate is responsible for most of the misunderstanding of the genetic information processing system.
“The genetic code is distinct and uniquely decodable, because the single Methionine codon AUG, and sometimes the Leucine codons UUG and CUG, serve as a starting signal for the protein sequence and performs the same function as the long frame bars at the beginning of the postal message in the ZIP+4 code and the Universal Product Code. The codons UGA, UAA and UAG function usually as non-sense and stop the translation of the protein from the mRNA and initiate the release of the protein sequence from the mRNA (Maeshiro and Kimura, 1998). They perform the same function as the long frame bar at the end of the postal bar code message (Bertram, 2001). Remember that non-sense does not mean nonsense or foolishness. Code letters are called non-sense because they have been given no sense or meaning assignment in the receiving alphabet.”(From Hubert Yockey, Information Theory, Evolution, and the Origin of Life, Cambridge University Press, 2005)
“The decoding of the genetic message from the DNA alphabet to the mRNA alphabet is called transcription in molecular biology. mRNA plays the role of the channel, which communicates the genetic message to the ribosomes, which serve as the decoder. The genetic message is decoded by the ribosomes from the 64 letter mRNA alphabet to the 20 letter alphabet of the proteome. This decoding process is called translation in molecular biology . (Ribosomes) act like the reading head on a tape machine (Turing, 1936). The protein molecule, which is the destination, is also a tape. Thus, the one-dimensional genetic message is recorded in a sequence of amino acids, which folds up to become a 3-dimensional active protein molecule. One is reminded of the linear signals that fold up to show a 2-dimensional picture on the television screen.”
(From Hubert Yockey, Information Theory, Evolution, and the Origin of Life, Cambridge University Press, 2005)
“The 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 Crick)
Genetic 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, 2003)
“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, 2001)
“A 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 1999)
“The 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, 1991)
“The three-nucleotide, or triplet code, was widely adopted as a working hypothesis. Its existence, however, was not actually demonstrated until the code was finally broken .
“With 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, 1989)
™ Version 4.2