You have not shown that DNA qualifies as a code under definition 3. Your mere assertion won't cut it. The chemical interactions in DNA are not a message in any conventional sense. No communication has taken place. Nothing there is in any way symbolic. Our descriptions may be symbolic but the chemistry is not.
“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.”
Mr. Marshall is uninformed about evo-devo and epigenetics . The environment always affects growth so there is no 1:1 mapping from DNA to phenotype. DNA is not a code, it's a recipe. Since there is no 1:1 mapping, the metaphor breaks down.
From 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)
If, as you have already inferred, DNA uniquely determines any phenotype characteristic at all, then it does qualify as a code. As Yockey states in this one example (and there are others), it does.
Your point 1 (“DNA is a code”
is wrong. You are not familiar with DNA and its' function. Saying that DNA is a code or a language, etc, is a misinterpretation. Scientists and biologists use these terms in an analogous way to explain to non scientific people what DNA does. DNA of itself does nothing but act something like a template, but not exactly like a template. It does not code, nor does it encode, nor does it decode. mRNA , in RNA and other proteins do "communication like" activities.
These words are communication LIKE. This is not really communication but something similar. I won't attempt to explain this since it takes a number of book sized documents to describe the process adequately.
“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 word 'code' is misleading because DNA is actually a template – not just to copy itself, but to make proteins. “The genome is sometimes called a ‘blueprint' by people who have never seen a blueprint. Blueprints, no longer used, were two-dimensional, a poor metaphor indeed, for the linear and digital sequence of nucleotides in the genome. The linear structure of DNA and mRNA is often referred to as a template. A template is two-dimensional, it is not subject to mutations, nor can it reproduce itself. This is a poor metaphor as anyone who has used a jigsaw will be aware. One must be careful not to make a play on words.”
(From Hubert Yockey , Information Theory, Evolution, and the Origin of Life, Cambridge University Press, 2005).
Perry unfortunately has been mislead by the word code (and probably by anti-evolutionary material about Information Theory).
Yockey's work is far from being anti-evolutionary material about information theory; Yockey is in fact an evolutionist.
DNA is not communicating with anything else, it's just making copies of itself and controlling the cell. There is no receiver and no message.
“Figure 5.2 [see top of this web page - Perry Marshall] 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 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)
DNA's communication is no symbolic, it's pure chemistry. There's no higher level code. If I create a self replicating machine that makes copies of itself using the resources around it, that doesn't require a code.
Instructions, by definition, require a mapping from probability space A to probability space B. Therefore any set of specific instructions is necessarily a code.
My self replicating machine would not be in communication with any other machines or any people.
Parts of the machine must still communicate with other parts, to read and carry out the instructions. Therefore, communication is taking place.
DNA does not specify the geometry of a plant, or the shape of the optical centers of a cat, and it cannot control the events leading to the death of an organism.
DNA uniquely specifies what kind of plant it is, and that it a cat is a cat. A sequence of symbols only has to uniquely determine one thing in order to qualify as a code.
Perry, you have completely missed the point. All the texts you quote are allegorical or else analogies. From John R. Pierce to the end you are using texts that are making a comparison, not expressing the actual idea. Yes, DNA can be compared to a code but these are just analogies for uneducated lay people.
This objection has already been answered. Please carefully re-read my previous post, quoting Yockey : “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.”
There are thousands of cats, thousands of oak trees, and DNA doesn't uniquely determine any particular cat or oak tree.
The DNA for a particular cat uniquely determines that one cat in the exact same sense that a crime scene investigator uses DNA to uniquely identify one criminal. Any particular strand of DNA, by itself, uniquely specifies many characteristics. This is well-established. Gravity, by itself uniquely specifies nothing in advance, and by all formal definitions in information theory, cannot be defined as a code . To say otherwise is to conflate two completely different things. Gravity is not a code. It's a force.
You literalist, don't you know that when biology textbooks use words like “code”, they're just dumbing down complex ideas for unsophisticated people?
I went through a literal stack of biology textbooks at the Oak Park IL library yesterday, just to make 100% sure my terminology is consistent with scientific convention. The words “code” and “symbol” are not used metaphorically in any of them. Science textbooks and papers are written very literally, and the word
genetic code in biology is just as literal as the word
protein. When you look up these definitions in biology textbooks, they don't say DNA is a "code" with quotation marks, or that it contains "information" with quotation marks, or that it is
like a code, or that it contains something
like information. They say that DNA is the basis for genetic code, and that it contains real, measurable information, and that the code uniquely determines real proteins.
“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
A review of the literature quickly shows that this terminology has been standard for over 40 years. See Yockey's earlier statement about this. This is not a matter of opinion, this is a matter of rigorous definitions from information theory. (HRG, I should also point out that you have been insisting that DNA is not literally a code, while at the very same time arguing that gravity is literally a code.)
DNA is a set of instructions only in the same sense that chemistry itself is a set of instructions. All molecules know or decode is the laws of physics.
The bits and bytes on your hard drive don't “know” anything either, they simply obey the laws of physics. It's a purely electro-mechanical process. But they still have to be programmed to do what they do. Computer programs don't emerge naturally, they are designed. The information on your computer cannot be reduced to so many pounds of magnetic material or silicon. Similarly, you and I cannot be reduced to so many pounds of carbon atoms. A book cannot be reduced to paper and ink.
