The word chair is written through the alphabet. The letters c, h, a, i, r, are characters of the alphabet. They are symbols to which we with reasoning abilities give meaning. They represent the phonemes of certain spoken languages. To outline here is the word "representation". When I write the letters, and someone else reads them, the writer and the reader can understand them both, when a common agreement of its meaning is established previously. There is no other mechanism besides intelligent agents with intellectual abilities that can do this assignment. If rather than chair, I write the word hirca, using the same letters, but in a random order, and there is no common agreement between us of what hirca means, then communication fails. The receiver cannot understand the meaning. There must be a right sequence, the right order of the letters to get a word, which has an assigned meaning. We can go a step further and translate the word chair in the English language to the Chinese language, using both, a different language, and a different alphabet. The assignment of the word chair to the word 椅子 ( Yǐzi )can as well exclusively be done by minds with intellectual abilities.
Codes are a system of rules to convert information—such as letters or words into another form, for communication through a communication channel. Keep in mind, as said previously, a system of rules is ALWAYS established by intelligent agents with intellectual abilities.
Let's go a step further. Mechanical engineering and design are some of the important steps in manufacturing things for specific goals. One part of a car is for example the gearbox of the car. The gearbox comprises a group of gears that are subjected to not only motion but also the load of the vehicle. For the gears to run at desired speeds and take desired loads it must be developed, tested. Etc. During development, various calculations are performed considering desired speeds and loads and finally, the gear of particular material and specific dimensions that can take all loads and that can be manufactured at least possible cost giving an optimum performance is designed, in order to be able to be sent to the factory and be manufactured. In a similar fashion, all the components of the car, including the engine, have to be projected, developed, so that they optimally meet all the functional requirements at the lowest possible cost, and finally designed for production.
It is this process by which first the engineering team develops the car, and each individual component, invest their intelligence and intellectual abilities and foresight to project it in the desired form as per the needs of human beings. And the machine designer has the job to design the car upon the instructions from the engineering team, making a blueprint, that is at the end sent to the factory for production. The gearbox has to be designed to meet all the requirements in order to obtain its functionality, capable of performing the highly specialized tasks as individual part, operating in an integrated manner with other parts. The car as the higher system becomes only functional if the individual systems work together in an integrated, interdependent manner. So, the engineering team has to foresee and envision both, the complex structure of the individual parts individually, and how they convey function to the higher end and system, once integrated and working synchronized as a complex whole. The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’. If the designer fails to foresee the necessity just of one component, of the gearbox for example and projects the entire car without that part, the care becomes non-functional.
The designer must consider in his project the availability of the raw materials to make the individual parts. Organize to buy parts from suppliers, coordinate that they are all at disposal once the build process begins. Once this is done, manufacturing can begin.
In what I described above, there is a functional relationship and interdependence. An organizational structure between the domain of invention, project elaboration, producing the instructional complex information and computation to make the car, and the mechanistic domain, where the car is made based on the information provided by the engineering and the machine design team and department.
In this entire trajectory, the keyword is prescribed information through blueprints as an essential requirement. This is what we see analogously in the molecular world, in biological cells.
“If the analogy of two phenomena be very close and striking, while, at the same time, the cause of one is very obvious, it becomes scarcely possible to refuse to admit the action of an analogous cause in the other, though not so obvious in itself.”
A metaphor (“A biological cell is like a production system”) demonstrates that similar behaviors are driven by similar causal mechanisms.
The Genetic Code
The sequence of bases in DNA operates as a true code.
DNA is represented in these abstract terms, as information comprising a sequence of arbitrary symbols. Changes in the DNA sequence of an organism's genome translate in a regular causative way into biological changes in the concrete physical world. There is a causative connection between DNA sequence information, which is an arbitrary abstraction of material property, and the reality of events in the physical world of molecules embodying the sequence.
Genes contain complex functional instructional specifying information. The information is necessary to build a protein expressed in a four-letter alphabet of bases which is transcribed to mRNA and then translated to the twenty-amino-acid alphabet necessary to build the protein. It defines a feature of living systems that calls for an explanation every bit as much as the beforementioned blueprints to make the gearbox and the car. Saying that the genetic code is a true code involves the idea that the code is free and unconstrained; any of the four bases can be placed in any of the positions in the sequence of bases. Their sequence is not determined by the chemical bonding. The bases occur in the complementary base pairs A-T and G-C, but along the sequence on one side, the bases can occur in any order, like the letters of a language used to compose words and sentences. The DNA nucleobase sequence prescribes, specifies, instructs how to build and join correctly amino acids, resulting in complex polymer macromolecules that fold into correct 3D folds, that bear machine-like functions.
To further illustrate what is meant by a true code, consider the magnetic letters fixed to a magnetic board. The letters are held to the board by the magnetic forces, but those forces do not impose any specific ordering of the letters. The letters can be arranged to spell out a meaningful message in the English language (code) or to form a meaningless sequence like the one at the bottom.
The genetic code defines how a three-nucleotide codon specifies a single amino acid which will be added next during protein synthesis. Most genes are encoded with a single scheme, which is the RNA codon table, often referred to as the canonical or standard genetic code. It is what determines a protein's amino acid sequence. Codons consist of three DNA bases. If amino acids were randomly assigned to triplet codons, there would be 1.5 × 10^84 possible genetic codes. The origin of this assignment coding principle is a scientific mystery, if the only plausible, possible, and probable mechanism capable to do the assignment, a mind, is excluded a priory by modern science as a permissible explanation.
Origin and evolution of the genetic code: the universal enigma
Let us suppose that assignment was a frozen accident, and we had in a miraculous manner a genetic code, assigning tri-nucleotide sequences for amino acids. How would there suddenly appear millions of sequences frozen in codon sequences, hypothetically assigned to a selected set of 20 amino acids? Consider, that there was no machinery to transcribe nor translate the code into amino acid sequences.
But let us go further, and suppose all the machinery was set and prepared to go, and do its job.
With four possible bases, the three nucleotides can give 4^3 = 64 different possibilities, 61 coding codons, and 3 start and stop signs, and these combinations are used to specify the 20 different amino acids used by living organisms. Now let us suppose, using an illustration and analogy, we had millions of 3 digit master locks, 64 different ones, each with a correct combination set useful to assign an amino acid, already locked up, for each of the 61 to specify one of the 20 amino acids used in life.
For an enzyme to be functional, it must fold in a precise three-dimensional pattern. A small chain of 150 amino acids making up an enzyme must be tested within the cell for 10^12 different possible configurations per second, taking 10^26 ( 1,000,000,000,000,000,000,000,000,000) years to find the right one. This example comprises a very, very, very small degree of the chemical complexity of a human cell.
To specify a protein with 400 amino acids having a sequence which would be functional, and permit the sequence to fold into a 3D form, we would need to line up 400 3 digit master locks in the right sequence. In EACH of the 400 positions, there would be 64 different 3 digit master locks to select from.
That would give us the combinatorial possibilities of one chance in 64^400 or one chance in 10^153. If we posit that a minimal free-living cell had a proteome consisting of 1300 proteins, then the chance to get that right would be one chance in 10^700,000. A clearly astronomical number, in the realm of the absolutely impossible.
There are multiple problems here. Starting first with the set up of the genetic code, secondly, freeze it to have triplets that assign to amino acids, and then join triplet combinations to have a functional sequence that would translate into sequencing amino acids, that would fold into functional 3D form. Not considering the fact, that the hardware would somehow also be required to emerge. We can safely say, that this scenario is too unlikely to happen purely by blind chemical forces. They could never have accomplished this challenging task. Intelligent design by a designer with foresight is absolutely necessary to come up with this exquisitely engineered marvelous molecular arrangement
Cells are cybernetic, ingeniously crafted cities full of factories, the most sophisticated self-replicating factory of the universe - containing an informational code system and programming languages like our alphabet or computer code, more versatile than C, Visual Basic, or PHP, and more robust and error-free than any other code system out of 1 million alternatives - using a communication protocol which wastes far less space than human-made ones - using furthermore a collection of rules and regularities of information coding for instructional complex texts - defined by alphabet, grammar, a collection of punctuation marks and regulatory sites, and semantics, and then uses that code system to create a blueprint for a self-replicating factory, which requires about 1500 books, each with 300 pages, 300.000,00 characters per book, each containing the precise complex instructions and information to create this factory, and stored in the smallest storage device possible and known, a trillion times denser than a CD, used to prescribe, drive, direct, operate and control interlinked compartmentalized self-replicating cell factory parks that perpetuate and thrive life. Large high-tech multimolecular robotlike machines ( proteins ) and factory assembly lines of striking complexity ( fatty acid synthase, non-ribosomal peptide synthase ) are interconnected into functional large metabolic networks. All this, of course, requires energy. Responsible for energy generation are high-efficiency power turbines ( ATP synthase )- superb power generating plants ( mitochondria ) and electric circuits ( highly intricate metabolic networks ).
Coded information obeys fundamental laws of nature which, in summarized form, can be expressed as follows:
It is impossible to set up, store, or transmit information without using a code.
It is impossible to have a code apart from a free and deliberate convention.
It is impossible to have information without a sender.
It is impossible that information can exist without having had a mental source.
It is impossible for information to exist without having been established voluntarily by a free will.
It is impossible for information to exist without all five hierarchical levels: statistics, syntax, semantics, pragmatics, and apobetics [the purpose for which the information is intended, from the Greek apobeinon = result, success, conclusion].
It is impossible that information can originate in statistical processes.