The four interdependent requirements to have an information transmission system

The four interdependent requirements to have an information transmission system

https://reasonandscience.catsboard.com/t3030-the-four-interdependent-requirements-to-have-an-information-transmission-system

Information is what is conveyed or represented by a particular arrangement or sequence of things. To have an information transmission system, following things are indispensable, essential, and required ( if any of those is missing, information transmission cannot be established - all have to be precisely defined in advance before any form of communication can be possible at all): 

1. A language, 2. the information (message) produced upon that language,  the 3 .information storage mechanism ( a hard disk, paper etc.), 4. an information transmission system, that is: encoding - sending and decoding) and eventually fifth, sixth, and seventh ( not essential): translation, conversion, and transduction

1. The rules or protocol of any informational communication and information system  must be preestablished and agreed in advance between those that communicate with each other, through establishing in common agreement of the meaning where a symbol, letters, words, waves or frequency variations, sounds, pulses, or a combination of those are assigned to something else,  otherwise the transmission of information is not possible. A message can only be created once a language has been established.  A code is an abstract, immaterial, nonphysical set of rules. Statistics, Semantics, Synthax, and Pragmatics are used according to combinatorial, context-dependent, and content-coherent rules. 
2. This set of rule, code, or language, permits to produce a blueprint, which contains instructional complex information, that permits to produce goods for specific purposes, control or maintain the operation of factories.  
3. Then there has to be a device, that is the harddisk, a paper, or any hardware upon which the information can be recorded.
4. And there has to be a system to encode, send, and decode the message. 
5. Eventually, during the transmission of information, it can be translated from one language to another. That requires a system of translation/cipher.  It’s like when you visit a Russian website and your browser has the language plug-in for Russian. Conveying meaning of the Russian and english language must be established in advance, that is the alphabet (symbols), syntax (grammar), and semantics (meaning) before any translation can take place. Otherwise, it would never be certain that what the transmitter is communicating is the same as what the receiver is understanding.
6. Eventually signal conversion ( digital-analog conversion, modulators, amplifiers)
7. Eventually signal transduction converting the nonelectrical signals into electrical signals

In Cells, we see all these things.


1. The language of  DNA: 
https://upload.wikimedia.org/wikipedia/commons/1/17/Cell_Biology.pdf
In the alphabet of the three letter word found in cell biology are the organic bases, which are adenine (A), guanine (G), cytosine (C) and thymine (T). It is the triplet recipe of these
bases that make up the ‘dictionary’ we call in molecular biology genetic code. The codal system enables the transmission of genetic information to be codified, which at molecular level, is conveyed through genes.

http://ds9a.nl/amazing-dna/
The language of DNA is digital, but not binary. Where binary encoding has 0 and 1 to work with (2 - hence the 'bi'nary), DNA has 4 positions, T, C, G and A.

Rutgers University professor Sungchul Ji’s :
“Biologic systems and processes 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.”
Ji identifies 13 characteristics of human language. DNA shares 10 of them.

The genetic language: grammar, semantics, evolution
http://www.ncbi.nlm.nih.gov/pubmed/8335231
The genetic language is a collection of rules and regularities of genetic information coding for genetic texts. It is defined by alphabet, grammar, collection of punctuation marks and regulatory sites, semantics.

Experts in Information Theory define 5 LEVELS of Information:
statistics ( transmitting the signal ) 
syntax (transmission, using a code. The rules according to which words are sequenced to sentences, signs that appear, etc.  )
semantics (expressin an idea, meaning. The relationship between a sign or a word to what it is pointing to in reality), 
pragmatics ( understand the command and perform action. Rules for applying words and signs in written or verbal conversations and broader social situations frame meaning. ), 


The code in DNA completely conforms to all four of these levels of information

2. The information (message) produced upon the DNA language
The DNA alphabet can be used to write a message, a recipe, or a blueprint, it can be copied, edited, read, transmitted, replicated, transcribed, or translated. In cells, DNA contains the instructions for making complicated living beings 52

3. Information stored in DNA
Chance of intelligence to set up the first blueprint for life: 
Mycoplasma  is one of the smallest self-replicating cells, and its genome has about 500 thousand base-pairs. It is, however, a pathogen, which has to be hosted by other organisms to survive.  It does not produce the twenty amino acids used in life. In order to know the threshold or minimal organismal complexity to sustain life, Pelagibacter ubique is a good candidate, since it is one the smallest self-replicating free-living cells, and produces all 20 amino acids used in life.  It has a genome size of 1,3 million base pairs which codes for about 1,300 proteins. That would be the size of a book with 400 pages, each page with 3000 characters. The chance to sequence each of the 1,3 million characters in the right order by unguided means, to get the precise instructional complex information to have a working self replicating cell is is 10^700,000. This is in the realm of the absolutely impossible.
The likelyhood of intelligence to set up an information system essential for life is  100% We KNOW by repeated experience that intelligence does elaborate blueprints, instructional information and constructs complex machines, production lines, transistors and computers and factories with specific purposes.

DNA has Ultra-High-Density Data Storage and Compression
Our cells contain at least 92 strands of DNA and 46 double-helical chromosomes. In total, they stretch 6 feet (1.8 meters) end to end. Every human DNA strand contains as much data as a CD. Every DNA strand in our body stretched end to end would reach from Earth to the sun and back 600 times. Cells store data at millions of times more density than hard drives. Not only that, they use that data to store instructions vastly more effectively than human-made programs; consider that Windows takes 20 times as much space (bits) as our genome. The genome is unfathomably more elegant, more sophisticated, and more efficient in its use of data than anything we have ever designed.  A single gene can be used a hundred times by different aspects of the genetic program, expressed in a hundred different ways.

4. An information transmission system
David F. Coppedge (2007): Most signal-relay stations we know about were intelligently designed. Signal without recognition is meaningless.  Communication implies a signaling convention (a “coming together” or agreement in advance) that a given signal means or represents something: e.g., that S-O-S means “Send Help!”   The transmitter and receiver can be made of non-sentient materials, but the functional purpose of the system always comes from a mind.  The mind uses the material substances to perform an algorithm that is not itself a product of the materials or the blind forces acting on them.  Signal sequences may be composed of mindless matter, but they are marks of a mind behind intelligent design.

In living cells, information is encoded through at least 30 genetic, and almost 50 epigenetic codes that form various sets of rules and languages. They are transmitted through a variety of means, that is the cell cilia as the center of communication, microRNA's influencing cell function, the nervous system, the system synaptic transmission, neuromuscular transmission, transmission b/w nerves & body cells, axons as wires, the transmission of electrical impulses by nerves between brain & receptor/target cells, vesicles, exosomes, platelets, hormones, biophotons, biomagnetism, cytokines and chemokines, elaborate communication channels related to the defense of microbe attacks, nuclei as modulators-amplifiers. These information transmission systems are essential for keeping all biological functions, that is organismal growth and development, metabolism, regulating nutrition demands, controlling reproduction, homeostasis, constructing biological architecture, complexity, form, controlling organismal adaptation, change,  regeneration/repair, and promoting survival.

Besides the information transmission system of DNA to make proteins, there is the most amazing and advanced information transmission system in operation in each of our cells, which works through light.  The more sophisticated and fast an Information transmission system is, the more intelligence is required to project and implement it. Light-fidelity, or Li-Fi, is a 5th generation cutting edge technology, the fastest information transmission system so far invented by man. Life uses not only light, but quantum entanglement to transmit information, which occurs basically instantly. It is logical, therefore, to infer a super-intelligent agency created life's awesome high-speed internet on a molecular level.

The origin of such complex communication systems is best explained by an intelligent designer. Since no humans were involved in creating these complex computing systems, a suprahuman super intelligent agency must have been the creator. 

5. An information translation system
The translation of a word in one language, to another language, is always of mental origin. For example the assignment of the word chair, in English, to xizi, in Chinese, can only be made by intelligence upon common agreement of meaning.
In biology the genetic code is the assignment ( a cipher) of 64 triplet codons to 20 amino acids.

Origin and evolution of the genetic code: the universal enigma
In our opinion, despite extensive and, in many cases, elaborate attempts to model code optimization, ingenious theorizing along the lines of the coevolution theory, and considerable experimentation, very little definitive progress has been made. Summarizing the state of the art in the study of the code evolution, we cannot escape considerable skepticism. It seems that the two-pronged fundamental question: “why is the genetic code the way it is and how did it come to be?”, that was asked over 50 years ago, at the dawn of molecular biology, might remain pertinent even in another 50 years. Our consolation is that we cannot think of a more fundamental problem in biology.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3293468/


1. The assignment of a word to represent something, like the word chair to an object to sit down, is always of mental origin.
2. The translation of a word in one language, to another language, is always of mental origin. For example the assignment of the word chair, in English, to xizi, in Chinese, can only be made by intelligence upon common agreement of meaning.
3. In biology the genetic code is the assignment ( a cipher) of 64 triplet codons to 20 amino acids.
4. Since we know only of intelligence to be able to do so, this assignment is best explained by the deliberate, arbitrary action of a non-human intelligent agency.


Quantum mechanic communication in cells: A paradigm shift in biology
https://reasonandscience.catsboard.com/t3021-awe-inspiring-biophoton-cell-cell-communication-points-to-design#7981

Cell internet: Cells have their own internet communication channels and cargo delivery service, all in one
https://reasonandscience.catsboard.com/t2760-cell-internet-cells-have-their-own-internet-communication-channels-and-cargo-delivery-service-all-in-one

Cell-Cell Communication in Bacteria
https://reasonandscience.catsboard.com/t2334-cell-cell-communication-in-bacteria

Cell Communication and signaling, evidence of design
https://reasonandscience.catsboard.com/t2181-cell-communication-and-signaling-evidence-of-design

Complexity of the cell's transport and communication system
https://reasonandscience.catsboard.com/t2118-complexity-of-the-cell-s-transport-and-communication-system

Arbitrariness, and the semantic meaning of the genetic code point to a designed set-up

https://reasonandscience.catsboard.com/t3030-the-four-interdependent-requirements-to-have-an-information-transmission-system#8666

The semantic argument
1. 64 Triplet codons ( three-letter words ) stored in DNA have meaning ( semantics). Arbitrarily, they are assigned to 20 amino acids, the building blocks of proteins. ( The codon UUA ( uracil/uracil/adenine = leucine)
2. Codons are therefore information-bearing molecules. They inform the translation machinery, which amino acid has to be added in the nascent polypeptide chain to make functional proteins.
3. Information is a disembodied abstract entity independent of its physical carrier.  Information is neither classical nor quantum, it is independent of the properties of physical systems used to its processing.
4. The set-up of an information system, based on semiotic information is always traced back to an intelligent source that sets it up it for purposeful, specific goals. 
5. The origin of the genetic code, based on semiotics, is therefore, best explained by intelligent design.
https://arxiv.org/pdf/1402.2414.pdf

V A Ratner: The genetic language: grammar, semantics, evolution  1993 May;29
The genetic language is a collection of rules and regularities of genetic information coding for genetic texts. It is defined by alphabet, grammar, collection of punctuation marks and regulatory sites, semantics. 1

Georgi Muskhelishvili: Integration of syntactic and semantic properties of the DNA code reveals chromosomes as thermodynamic machines converting energy into information  2013 Dec;7 2
Compelling evidence suggests that the DNA, in addition to the digital information of the linear genetic code (the semantics), encodes equally important continuous, or analog, information that specifies the structural dynamics and configuration (the syntax) of the polymer.

Syntax determines the structure of the rules of language and, thus, the way in which the words are assembled in sentences, whereas semantics determine the meaning of the words and so the available vocabulary. However, the structural rules of language cannot determine the meanings of the words, and nor is the vocabulary determinative for the structural rules of the language (we do not concern ourselves with any generative mechanisms relevant to the formal language theory here). Therefore, viewed as a coding system composed of two non-convertible types of information, natural language is not self-referential. By the same token, the Jacob–Monod paradigm separating the gene regulatory context from the genetic information is at variance with the self-referential organization. Notably, we do not use this term in the sense of elaborated mathematical concepts of distinction, circulation, feedback, re-entry, recursion, etc. Self-referential organization, as we put it here implies inter-conversion of information between logically distinct coding systems specifying each other reciprocally. Thus, the holistic approach assumes self-referentiality (completeness of the contained information and full consistency of the different codes) as an irreducible organizational complexity of the genetic regulation system of any cell.

It appears that for both the bacterial and eukaryotic chromosomes, the genetic and chromatin organization are inseparable and coming to light as one integrated whole. This device inherent in the primary sequence organization of the chiral DNA polymer is sufficient to specify a self-referential organization and explain the coordination of the genetic programs in space and time. On this view, the DNA architectural proteins acting according to the cellular physiological state, such as NAPs in bacteria and remodeling complexes in eukaryotes, serve as auxiliary factors optimizing the delivery of the integrated DNA information.


Miao Yu: The Three-Dimensional Organization of Mammalian Genomes 2018 Jun 6 3
Animal development depends on not only the linear genome sequence that embeds millions of cis-regulatory elements, but also the three-dimensional (3D) chromatin architecture that orchestrates the interplay between cis-regulatory elements and their target genes.

My comment: An interdependent system where all particular and discrete parts do only bear function, integrated into the whole cannot be the product of sequential step-up evolutionary development. The interdependences between the chromosome-structuring, chromosome-reading, and metabolic–enzymatic components of the genetic regulation system, is an all or nothing business and had therefore to emerge all at once. Complex interdependent communication networks that act on a structural level in an integrated interlocked fashion require planning and foresight. That points to design, rather than evolution as a causal principle in play. 

The Genetic Code in Operation for Protein Construction
The use of a formal code to accomplish a purpose requires the receiver of the code to understand the rules and the meaning of the symbols, and be able to use the information received to accomplish a task. In the language of information science, the code must have a syntax and semantics. For the communication of information, the receiver must be in possession of that syntax and semantics, and possibly also a cipher to be able to decode the information. The receiver must also be able to carry out the task communicated.

Meaning is given to combinations of symbols, like a language
Three-letter combinations from the four-letter alphabet of bases form the genetic code. These base triplets act as codons to specify one of the letters of the 20 letter alphabet of amino acids.

My comment: The three-letter "words", the codons, bear meaning, that the translation machinery is able to interpret, and translate in order to add the right amino-acids to the nascent polypeptide chain in the ribosome.

Ulrich E. Stegmann:  The arbitrariness of the genetic code March 2004 5
The genetic code has been regarded as arbitrary in the sense that the codon-amino acid assignments could be different than they actually are. This general idea has been spelled out differently by previous, often rather implicit accounts of arbitrariness. They have drawn on the frozen accident theory, on evolutionary contingency, on alternative causal pathways, and on the absence of direct stereochemical interactions between codons and amino acids.
A particular codon specifies one particular amino acid rather than a different one. It has also been suggested that the arbitrariness of the genetic code justifies attributing semantic information to macromolecules, notably to DNA.

My comment: The proposal of a "frozen accident" is not a theory, but an ad-hoc assertion that is not backed up by evidence. Arbitrarily selecting, assigning, specifying, and attributing meaning is always the product of a mind.  And that's precisely the function of the genetic code. The genetic code summarises which codons specify which amino acids during protein synthesis.

Linguistic arbitrariness expresses the fact that the linguistic properties of a word are usually not naturally related to its meaning. The phonetic form of ‘dog’ does not reflect a property of dogs. In Peircean terms, the relation between a word and its meaning is symbolic. Similarly, the genetic code’s arbitrariness is understood as the absence of a natural connection between codons and amino acids. Chemical arbitrariness arguably establishes a language-like symbolic relation between codons and amino acids. It is then thought legitimate to attribute meaning and semantic information to genes or their components.

Some of the processes expected to involve semantic information are certainly not chemically arbitrary and, therefore, chemical arbitrariness is not a necessary condition for a semantic relation.

My comment: If there is no physical (chemical) necessity to generate the arbitrariness, then what is it? The only rational alternative is a mind with foresight and a goal to generate a specific outcome.

Information is immaterial
https://reasonandscience.catsboard.com/t3028-information-is-immaterial

Information is not physical   https://arxiv.org/pdf/1402.2414.pdf
Information  is a disembodied abstract entity independent of its physical carrier. ”Information is always tied to a physical representation. It is represented by engraving on a stone tablet, a spin, a charge, a hole in a punched card, a mark on paper, or some other equivalent. This ties the handling of information to all the possibilities and restrictions of our real physical word, its laws of physics and its storehouse”. However, the legitimate questions concern the physical properties of information carriers like ”stone tablet, a spin, a charge, a hole in a punched card, a mark on paper”, but not the information itself.  Information is neither classical nor quantum, it is independent of the properties of physical systems used to its processing.

The algorithmic origins of life
https://reasonandscience.catsboard.com/t3061-the-algorithmic-origins-of-life

In addition to algorithm execution, there needs to be an assembly algorithm. Any manufacturing engineer knows that nothing (in production) is built without plans that precisely define orders of operations to properly and economically assemble components to build a machine or product. There must be by necessity, an order of operations to construct biological machines. This is because biological machines are neither chaotic nor random, but are functionally coherent assemblies of proteins/RNA elements. A set of operations that govern the construction of such assemblies may exist as an algorithm which we need to discover. It details real biological processes that are operated upon by a set of rules that define the construction of biological elements both in a temporal and physical assembly sequence manner.


1. https://pubmed.ncbi.nlm.nih.gov/8335231/
2. https://sci-hub.ren/10.1007/s00018-013-1394-1
3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5837811/
4. http://hyperphysics.phy-astr.gsu.edu/hbase/Organic/gencode.html
5. https://sci-hub.ren/10.1023/b:biph.0000024412.82219.a6