Wednesday, April 2, 2014

Bio-Semiotics - The Intelligent Design of Life Revealed

There is growing scientific evidence that intelligence is necessary for the development of life. This evidence is leading into the development of a new field, bio-semiotics. A growing number of biologists have realized that the laws of physics and chemistry alone cannot account for the behavior of DNA and other macro-molecules, because that same chemical composition and electrical affinities can produce many different kinds of molecules depending on the physical arrangement of the atoms in the molecule. These different physical shapes are important, as they determine what an organism is biologically. Biologist have developed models that account for semantic information in DNA that is not reducible to physical and chemical laws.

The Significance of the Existence of Semantic Information
Semantic information is the smoking gun for Intelligent Design. Semantic information is information that has logical and linguistic properties that are not causally connected to physical processes. Semantic information would include things like alphabetical, logical and mathematical symbols, and grammar.

Semantic information is used in both human language and computer programming. In human language, it includes how we use alphabets and words. In programming, it involves how both data and programming instruction are encoded. To help better explain the nature of semantic information, I shall include a couple of examples from human language and computer programming.

 Semantics in language involves constructs that cannot be reduced to physical causes. These involves potential many to many correspondences that can only be logically mapped by arbitrary conventions. There are many words, for example, that represent what is meant by the color green. Green  in English is expressed as 'verde' in Spanish, 'зеленый' in Russian, 'grün' in German, and 'ירוק'in Hebrew.  Additionally, the same word can mean different things in different languages. These are sometimes called false friends. Linguists believes that this sometimes happens because of common etymology (word origins) and other times it is a separate evolution of different words. For example, the word 'bra' means good in Swedish; The same word is an abbreviation of the French word 'brassierre' in English and refers to an undergarment designed to cover a woman's breast. There is no physical reason for a given word to signify a given object.

If a word can have many different objects and an object  can have many words, then there is a many to many correspondence of words to objects. From a physical perspective, there is no possibility of a causal relationship between any physical phenomena and linguistic symbols. Language involves a logical mapping of symbols and language constructs to reality. This logical mapping requires a mind to perform the operation; it cannot be explained totally in terms of physical or chemical causation.

In computer programming, semantic meaning is attached to any of a number of logical layers of abstraction that go on. The windows or graphic interfaces that exist in a Windows, Mac, Linux, Android, and iOS are not really inside the computer. They are graphics generated for  the purpose of making them user-friendly. The computer does not think in terms of windows or graphic user interfaces.

When user clicks on a graphic interface, programming code is executed. This code is often written in a high level language like PHP (my favorite), C++, or Javascript. The computer cannot think in terms of these languages. These languages have been created to make programming more user friendly to human programmers; they are compiled or interpreted by a compiler or interpreter that logically maps these languages with the language that the computer understands. There is no physical cause for any given mapping. A computer engineer builds a compiler that is designed to  map the source code of the high level language to  the language of the processor; The engineer uses his knowledge of how the computer actually thinks and his knowledge of how a given high level language works to design a method of mapping these two in a logical way. This can be done in multiple ways, and is done in different way in different computer architecture. Compiling for Linux or Android does this mapping in a different way than compiling for Windows. Higher level instructions will be translated into smaller steps that are done step by step in the processor. These steps are then encoded as binary code instruction set.

When programmers type code, they will generally type using  characters that are defined in an encoding standard. One such encoding system is called  American Standard Code for Information Interchange (ASCII). ASCII maps character to binary code. The ASCII code for the letter 'A' is 01000001 (65 in decimal). The 01000001 is binary code.  There is no physical reason for 01000001 to be 'A.' It could have been anything.

Binary code is the place where characters and instructions can be mapped to physical hardware. The digits of binary code represent electrical states. On is represented as 1, and off is represented as 0. binary code is read sequentially in time with a processor clock cycles. Using these clock cycles, the processor can differentiate discretely between on and off signals. Compilers will present these signals in a format that will allows the processor to receive both instructions and data and know which signals are instructions and which are data. There are multiple way of doing this mapping. There is no physical causal relationship that locks in any one method. The logical to physical mapping only works if there is a mind to map a meaningful relationship between the logical and the physical.

The existence of arbitrary mappings between logical and physical structures is irrefutable proof of intelligent design. Evidence of such in DNA and biologic processes is, then, proof of intelligent design of life.

The Existence of Semantic Information in DNA
Biologists are beginning to realize that purely physical models are not sufficient to explain the structure and function of DNA. Semantic and linguistic models are emerging as better explanations of the structure and function of DNA

Sungjul Ji, a researcher  at the Department of Pharmacology and Toxicology at Rutgers University, wrote the following in an article that appeared in Volume 870 of the Annals of the New York Academy of Sciences
There are theoretical reasons to believe that biologic systems cannot be fully accounted for in terms of the principles and laws of physics and chemistry alone, but they require in addition the principles of semiotics - the science of symbols and signs, including linguistics.1-3 for convenience, we may refer to the belief, common among contemporary biologists, that the laws of physics and chemistry are necessary and sufficient as the PC (physics and chemistry) paradigm, while  the alternative view that the principles of semiotics are additionally absolutely required for a complete understanding of living systems and processes as the PCS(physics, chemistry, and semiotics) paradigm.(1, 2)
Ji develops two ideas in his article. He identifies six markers of language in DNA*, and he  develops a hypothesis that there are two functional types of genetic code: Syntactic and Semantic genetic code. According to Ji, the non-coding DNA - the so-called junk DNA- is actually DNA that carries semantic meaning that controls the expression of the coding genes hypothesis. Think of them as advanced control structures in a high level language.

According to Ji, interactions in the DNA show evidence of double articulation. In Linguistic analysis, double articulation (sometimes called duality) is where meaningless symbols like letters can be combined to form meaningful symbols. This duality is played out in the biochemistry of the DNA, this plays because molecules in DNA can use Out of a macro-molecule that has the same combination of atoms, the same co-valencies, and the same ionic affinities can form different products based on the geometry of the molecule. Another way of putting this is that from the same chemical differing proteins can be made because the molecule can geometrically fold into different shapes.  The different shapes matter because which shapes protein fold into determines whether life continues and determine whether the organism is an ameoba, a dog, or a human.

Because of these multiple possibilities, this process cannot be determined solely in terms of physical causation. Ji proposes that the final products of genes are not statically fixed by physical laws but "dynamic processes collectively called intracellular dissipative structures whose generation is catalyzed by enzymes encoded in structural gene." In what Ji calls the "DNA-polypeptide-IDS hypothesis,"Structural genes operate "under the control of spatio-temporal genes," which are really semantic DNA.

Ji study relies heavily on the work of von Neumann and Patte, who developed a theory of Matter-symbol complementarity.

We easily agree with Einstein that a Beethoven symphony cannot be appreciated as only “agraph of air pressures,” although in principle it has such a physical description. In the same waywe understand Bohr that, “You don’t explain a tea party by quantum mechanics.” On the other hand, it is not so easy to understand why you cannot adequately explain genetics with biochemistry or enzyme catalysis with quantum mechanics. Because we believe no events at tea parties, in genes, or in enzymes violate any physical laws we might assume that their descriptions differ only in their degrees of complexity. What biosemiotics illustrates is that symbolic controls are categorically different from laws and that they are irreducible to physical laws even though their material vehicles obey the laws and have a correct physical description.

What we need to understand is that physical laws are universal and must apply to all conceivable systems. Therefore laws are empirically moot with respect to any particular system until its particular initial conditions are specified. This requires information, and physical laws cannot specify this information. In physics jargon symbol systems are special types of initial condition called boundary conditions or constraints (Polanyi, 1968; Pattee, 1972). Consequentlyan adequate explanation of any living organism requires more than a detailed lawful physicald escription or merely the confirmation that the laws of nature are always inerrantly followed. One must explain how informational constraint structures locally control the universal physicallaws so as to propagate and evolve. (3)

Symbolic controls are not reducible to physical laws. Physical laws can only have universal effects and they cannot specify initial conditions. Information is required to specify initial condition. Information must be front-loaded into a biological system as the initial condition in a process that is not determine by physical law. While physical laws can set boundaries to linguistic systems, the linguistic are determined by non-physical causes.

The Max Planck Institute has created a slide presentation of describing semantic information in DNA sequences. This information includes using "non-sense codons" to create "formatting" so that the code can be properly read (slide 10). According slide 17 "DNA translation similar to Turing machine." A Turing machine is any machine  that can compute a task according to a set of instructions or algorithm The probability of  semantic information to have entered DNA by accident is astronomically low. For even a small protein, it is 1 in 10120(Slides 25-26). (4)

The study of biosemiotics is a growing field. The wikipedia article on it describes biosemiotics as "a paradigmatic shift in the scientific view of life."
Because bio-semiotics is not reducible to physical and chemical processes, it represents a logical layer embedded in the physical world of life. Biosemiotics demonstrates that biological systems  carry semantic meaning that can only be established by minds.

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