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Intelligent Design, the best explanation of Origins » Intelligent Design » Information Theory, Coded Information in the cell » The origin of the genetic cipher, the most perplexing problem in biology

The origin of the genetic cipher, the most perplexing problem in biology

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The origin of the genetic cipher, the most perplexing problem in biology

http://reasonandscience.heavenforum.org/t2267-the-origin-of-the-genetic-cipher-the-most-perplexing-problem-in-biology

On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1894784/
The origin of the translation system is, arguably, the central and the hardest problem in the study of the origin of life, and one of the hardest in all evolutionary biology. The problem has a clear catch-22 aspect: high translation fidelity hardly can be achieved without a complex, highly evolved set of RNAs and proteins but an elaborate protein machinery could not evolve without an accurate translation system. The origin of the genetic code and whether it evolved on the basis of a stereochemical correspondence between amino acids and their cognate codons (or anticodons), through selectional optimization of the code vocabulary, as a "frozen accident" or via a combination of all these routes is another wide open problem despite extensive theoretical and experimental studies.

DNA is transcribed (sort of copied) to RNA which is translated to(codes for) Protein. DNA>>RNA>>>Protein. He is referring to the mechanism by which this occurs today.
Imagine a recording tape made of RNA.  It passes through a structure (a machine) called a Ribosome. The tape has a sequence of nucleotides (a chain of sugars each connected to a phosphate and a nitrogen containing chemical). Every 3 nucleotides codes for an amino acid.  Somehow the sequence (the chain) of RNA has to result in a chain of amino acids. This sequence of RNA is called messenger-RNA (M-RNA)  The chain of amino acids is an entirely different substance than the M-RNA.  Like imagining cassette recording tape going through a machine and on the other side of the machine a chain of “metal charms” is made that corresponds to the musical notes coded for by the magnetic recording tape.
So this is accomplished in a structure called a ribosome and another molecule of RNA physically attached to an amino acid.  This other molecule of RNA is called Transfer-RNA (T-RNA).

So anyway, one end of the T-RNA mirrors the code on the M-RNA and the other end is attached to the amino acid that that is coded for.  the correct amino acid is attached to the correct T-RNA by an enzymne called aminoacid T-RNA Synthase.. When Prof Bio uses the cryptic abbreviation aars he is referring to Alanyl-TRNA Synthetase.  This enzyme attaches the amino alanine to the T-RNA that codes for Alanine. There are T-RNA synthetases for each amino acid.







A review of Paul Davies book, the fifth miracle, about the genetic code. Starting at page 105:

I have described life as a deal struck between nucleic acids and proteins. However, these molecules inhabit very different chemical realms; indeed, they are barely on speaking terms. This is most clearly reflected in the arithmetic of information transfer. The data needed to assemble proteins are stored in DNA using the four-letter alphabet A, G, C, T. On the other hand, proteins are made out of twenty different sorts of amino acids. Obviously twenty into four won’t go. So how do nucleic acids and proteins communicate?
Earthlife has discovered a neat solution to this numerical mismatch by packaging the bases in triplets.

How could earthlife have discoverd a mechanism upon which life depends ? 

Four bases can be arranged in sixty-four different permutations of three, and twenty will go into sixty-four, with some room left over for redundancy and punctuation. The sequence of rungs of the DNA ladder thus determines, three by three, the exact sequence of amino acids in the proteins. To translate from the sixty-four triplets into the twenty amino acids means assigning each triplet (termed a codon) a corresponding amino acid. This assignment is called the genetic code. The idea that life uses a cipher was first suggested in the early 1950s by George Gamow, the same physicist who proposed the modern big-bang theory of the universe. As in all translations, there must be someone, or something, that is bilingual, in this case to turn the coded instructions written in nucleicacid language into a result written in amino-acid language. From what I have explained, it should be apparent that this crucial translation step occurs in living organisms when the appropriate amino acids are attached to the respective molecules of tRNA prior to the protein-assembly process.  This attachment is carried out by a group of clever enzymes  


cleverness is something we do usually assign to someone that is intelligent

that recognize both RNA sequences and the different amino acids, and marry them up accordingly with the right designation. 

The recognition must be PRE-PROGRAMMED. In the same manner, as a translator must learn two languages, in order to be able to assign one written word in english,  for example, to the written symbol in chinese with the same significance. There must be a previous common agreement of meaning before the translation process can begin. As for example, the word  translator, is written 翻譯者 in traditional chinese. Ask someone that does not speak chinese, to translate the word translator  into chinese . He has around 3500 different symbols to chose from. In the " amino acid language", there are 20 different amino acids to chose from.  The translator must know both, the word translator in english and in chinese, and know both written alphabets, previous to make the assignment. Only mental processes are able to do this. Chance is simply a impotent cause. 


William Dembsky:
http://www.discovery.org/a/1256
The problem is that nature has too many options and without design couldn’t sort through all those options. The problem is that natural mechanisms are too unspecific to determine any particular outcome. Natural processes could theoretically form a protein, but also compatible with the formation of a plethora of other molecular assemblages, most of which have no biological significance. Nature allows them full freedom of arrangement. Yet it’s precisely that freedom that makes nature unable to account for specified outcomes of small probability.Nature, in this case, rather than being intent on doing only one thing, is open to doing any number of things. Yet when one of those things is a highly improbable specified event, design becomes the more compelling, better  inference. Occam's razor also boils down to an argument from ignorance: in the absence of better information, you use a heuristic to accept one hypothesis over the other.



The genetic code, with a few recently discovered minor variations, is common to all known forms of life. That the code is universal is extremely significant, for it suggests it was used by the common ancestor of all life, and is robust enough to have survived through billions of years of evolution. Without it, the production of proteins would be a hopelessly hit-or-miss affair. Questions abound. How did such a complicated and specific system as the genetic code arise in the first place? Why, out of the 10 possible codes based on triplets, has nature chosen the one in universal use? Could a different code work as well? If there is life on Mars, will it have the same genetic code as Earthlife? Can we imagine uncoded life, in which interdependent molecules deal directly with each other on the basis of their chemical affinities alone? Or is the origin of the genetic code itself (or at least a genetic code) the key to the origin of life? The British biologist John Maynard Smith has described the origin of the code as the most perplexing problem in evolutionary biology. With collaborator Eörs Szathmáry he writes: “The existing translational machinery is at the same time so complex, so universal, and so essential that it is hard to see how it could have come into existence, or how life could have existed without it.” To get some idea of why the code is such an enigma, consider whether there is anything special about the numbers involved. Why does life use twenty amino acids and four nucleotide bases? It would be far simpler to employ, say, sixteen amino acids and package the four bases into doublets rather than triplets. Easier still would be to have just two bases and use a binary code, like a computer. If a simpler system had evolved, it is hard to see how the more complicated triplet code would ever take over. The answer could be a case of “It was a good idea at the time.” A good idea of whom ?  If the code evolved at a very early stage in the history of life, perhaps even during its prebiotic phase, the numbers four and twenty may have been the best way to go for chemical reasons relevant at that stage. Life simply got stuck with these numbers thereafter, their original purpose lost. Or perhaps the use of four and twenty is the optimum way to do it. There is an advantage in life’s employing many varieties of amino acid, because they can be strung together in more ways to offer a wider selection of proteins. But there is also a price: with increasing numbers of amino acids, the risk of translation errors grows. With too many amino acids around, there would be a greater likelihood that the wrong one would be hooked onto the protein chain. So maybe twenty is a good compromise. Do random chemical reactions have knowledge to arrive at a optimal conclusion, or a " good compromise" ?  

An even tougher problem concerns the coding assignments—i.e., which triplets code for which amino acids. How did these designations come about? Because nucleic-acid bases and amino acids don’t recognize each other directly, but have to deal via chemical intermediaries, there is no obvious reason why particular triplets should go with particular amino acids. Other translations are conceivable. Coded instructions are a good idea, but the actual code seems to be pretty arbitrary. Perhaps it is simply a frozen accident, a random choice that just locked itself in, with no deeper significance. 

That frozen accident means, that good old luck would have  hit the jackpot  trough trial and error amongst 1.5 × 1084 possible genetic codes . That is the number of atoms in the whole universe. That puts any real possibility of chance providing the feat out of question. Its , using  Borel's law, in the realm of impossibility.  The maximum time available for it to originate was estimated at 6.3 x 10^15 seconds. Natural selection would have to evaluate roughly 10^55 codes per second to find the one that's universal. Put simply, natural selection lacks the time necessary to find the universal genetic code. 

Paul Hayden  The fundamental question is how these regularities of the standard code came into being, considering that there are more than 10 ^ 84 possible alternative code tables if each of the 20 amino acids and the stop signal are to be assigned to at least one codon. More specifically, the question is, what kind of interplay of chemical constraints, historical accidents, and evolutionary forces could have produced the standard amino acid assignment, which displays many remarkable properties.

And how could that make sense ? THINK !! 

On the other hand, there may be some subtle reason why this particular code works best. If one code had the edge over another, reliability-wise, then evolution would favor it

The problem once more is, that evolution could not be in play at this time and stage of affairs, since evolution only works upon replication. Replication depends on the machinery in question. Catch22.... 

, and, by a process of successive refinement, an optimal code would be reached. It seems reasonable.

DOES IT SEEM REASONABLE ? TO ME IT SEEMS UTMOST IRRATIONAL. IRRATIONAL TO THE EXTREME. So did random , unguided, non-intelligent chemicals have a pre-established goal to reach a optimal code? And even if that were the case, what good would it be without the translation machinery, the ribosome, fully set up aind in place, and doing its job ? 

But this theory is not without problems either. Darwinian evolution works in incremental steps, accumulating small advantages over many generations. In the case of the code, this won’t do. Changing even a single assignment would normally prove lethal, because it alters not merely one but a whole set of proteins. Among these are the proteins that activate and facilitate the translation process itself. So a change in the code risks feeding back into the very translation machinery that implements it, leading to a catastrophic feedback of errors that would wreck the whole process. To have accurate translation, the cell must first translate accurately. This conclusion seems paradoxical. A possible resolution has been suggested by Carl Woese. He thinks the code assignments and the translation mechanism evolved together. Initially there was only a rough-and-ready code, and the translation process was very sloppy. At this early stage, which is likely to have involved less than the present complement of twenty amino acids, organisms had to make do with very inefficient enzymes: the highly specific and refined enzymes life uses today had not yet evolved. Obviously some coding assignments would prove better than others, and any organism that employed the least error-prone assignments to code for its most important enzymes would be on to a winner.

Since when does dead matter have the intrinsic desire to get alive, and to win ? 

It would replicate more accurately, and in the process its coding arrangements would predominate among daughter cells. In this context, a “better” coding assignment would mean a robust one, so that, if there was a translation error, the same amino acid would nevertheless be made—i.e., there would be enough ambiguity for the error to make no difference. Or, in case the error did cause a different amino acid to be made, it would be a close cousin of the intended one, and the resulting protein would do the job almost as well. Successive refinements of this process might then lead to the universal code seen today—like a picture gradually coming into focus.

Now THAT was a great lecture of how to do pseudo-science, and assign to chance creative power that it does not have. 

The code may have an altogether deeper explanation. If a table of coding assignments is drawn up, it can be analyzed mathematically to see if there are any hidden patterns. Peter Jarvis and his colleagues at the University of Tasmania claim that the universal code conceals abstract sequences similar to the energy levels of atomic nuclei, and might even involve a subtle property of subatomic particles called supersymmetry. These mathematical correspondences may be purely coincidental, or they may point to some underlying connection between the physics of the molecules involved and the organization of the code. I have subjected the reader to the technicalities of the genetic code to make a general conceptual point that goes right to the heart of the mystery of life. Any coded input is merely a jumble of useless data unless an interpreter or a key is available. A coded message is only as good as the context in which it is put to use. That is to say, it has to mean something. In chapter 2, I drew the distinction between syntactic and semantic information. On their own, genetic data are mere syntax. The striking utility of encoded genetic information stems from the fact that amino acids “understand” it. The information distributed along a strand of DNA is biologically relevant. In computerspeak, genetic data are semantic data. For a clear perspective on this point, consider the way in which the four bases A, G, C, and T are arranged in DNA. As explained, these sequences are like letters in an alphabet, and the letters may spell out, in code, the instructions for making proteins. A different sequence of letters would almost certainly be biologically useless. Only a very tiny fraction of all possible sequences spells out a biologically meaningful message, in the same way that only certain very special sequences of letters and words constitute a meaningful book. Another way of expressing this is to say that genes and proteins require exceedingly high degrees of specificity in their structure. As I stated in my list of properties in chapter 1, living organisms are mysterious not for their complexity per se, but for their tightly specified complexity. To comprehend fully how life arose from nonlife, we need to know not only how biological information was concentrated, but also how biologically useful information came to be specified, given that the milieu from which the first organism emerged was presumably just a random mix of molecular building blocks. In short, how did meaningful information emerge spontaneously from incoherent junk?

I began this section by stressing the dual nature of biomolecules: they can be both hardware— particular three-dimensional forms—and software. The genetic code shows just how important the informational aspect of biomolecules is. The job of explaining the origin of life goes beyond finding a plausible chemical pathway out of a primordial soup. We need to know, conceptually, how mere hardware can give rise to software.

The genetic code, with a few recently discovered minor variations, is common to all known forms of life. That the code is universal is extremely significant, for it suggests it was used by the common ancestor of all life, and is robust enough to have survived through billions of years of evolution. Without it, the production of proteins would be a hopelessly hit-or-miss affair. Questions abound. How did such a complicated and specific system as the genetic code arise in the first place? Why, out of the 10^84 possible codes based on triplets, has nature chosen the one in universal use? Could a different code work as well? If there is life on Mars, will it have the same genetic code as Earthlife? Can we imagine uncoded life, in which interdependent molecules deal directly with each other on the basis of their chemical affinities alone? Or is the origin of the genetic code itself (or at least a genetic code) the key to the origin of life? The British biologist John Maynard Smith has described the origin of the code as the most perplexing problem in evolutionary biology. With collaborator Eörs Szathmáry he writes: “The existing translational machinery is at the same time so complex, so universal, and so essential that it is hard to see how it could have come into existence, or how life could have existed without it.” To get some idea of why the code is such an enigma, consider whether there is anything special about the numbers involved. Why does life use twenty amino acids and four nucleotide bases? It would be far simpler to employ, say, sixteen amino acids and package the four bases into doublets rather than triplets. Easier still would be to have just two bases and use a binary code, like a computer. If a simpler system had evolved, it is hard to see how the more complicated triplet code would ever take over. The answer could be a case of “It was a good idea at the time.” A good idea of whom ? If the code evolved at a very early stage in the history of life, perhaps even during its prebiotic phase, the numbers four and twenty may have been the best way to go for chemical reasons relevant at that stage. Life simply got stuck with these numbers thereafter, their original purpose lost. Or perhaps the use of four and twenty is the optimum way to do it. There is an advantage in life’s employing many varieties of amino acid, because they can be strung together in more ways to offer a wider selection of proteins. But there is also a price: with increasing numbers of amino acids, the risk of translation errors grows. With too many amino acids around, there would be a greater likelihood that the wrong one would be hooked onto the protein chain. So maybe twenty is a good compromise.

Do random chemical reactions have knowledge to arrive at a optimal conclusion, or a " good compromise" ?

An even tougher problem concerns the coding assignments—i.e., which triplets code for which amino acids. How did these designations come about? Because nucleic-acid bases and amino acids don’t recognize each other directly, but have to deal via chemical intermediaries, there is no obvious reason why particular triplets should go with particular amino acids. Other translations are conceivable. Coded instructions are a good idea, but the actual code seems to be pretty arbitrary. Perhaps it is simply a frozen accident, a random choice that just locked itself in, with no deeper significance.

That frozen accident means, that good old luck would have hit the jackpot trough trial and error amongst 1.5 × 1084 possible genetic codes . That is the number of atoms in the whole universe. That puts any real possibility of chance providing the feat out of question. Its , using Borel's law, in the realm of impossibility. The maximum time available for it to originate was estimated at 6.3 x 10^15 seconds. Natural selection would have to evaluate roughly 10^55 codes per second to find the one that's universal. Put simply, natural selection lacks the time necessary to find the universal genetic code.


1) https://en.wikipedia.org/wiki/Genetic_code
2) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3293468/



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Biophysicist Hubert Yockey - author of "Information theory, evolution, and the origin of life"

Hubert Yockey has determined that natural selection would have to explore 1.40 x 10^70 different genetic codes to discover the optimal universal genetic code that is found in nature. He states that the maximum amount of time available for it to originate is 6.3 x 10^15 seconds, and that Natural Selection would have to evaluate roughly 10^55 codes per second to find the one that is optimal, which amount to one trillion times the 15 billion years of the imagined age of the universe for natural Selection to have created the genetic code, and therefore, the genetic code cannot have been produced by evolutionary processes. He states also that the genetic code posesses characteristics which could only have been a product of intelligence.


HOW DID THE GENETIC CODE HAPPEN TO BE SO OPTIMIZED, if it couldnt evolve, if it was a frozen event, - and it appears so suddenly at the first emergence of LIFE ..?

1) The OP quotes exactly what Yockey wrote in his book , 
it DOES NOT MISRESPRESENT what he actually said in anyway

and then on page 96 (which is Dudleys quote above) , but under the heading
"7. 1. 2 Did the genetic code reach its present form by trying many codes and
selecting the best?" 

"Thus these rk-tuple subpopulations may be arranged in 6!, 4!, 3!, and 2! different ways without replacement. Substituting these numbers in Equation 7.2, we have:

(64!) /(6!)3(4!)5(3!)(2!)9 x 1 x 1 = 1.40 x 10^70 combinations.

Any other arrangement in which all but three codons are assigned to at least one of the twenty amino acids also results in a very large number of this order of magnitude. Clearly, this is an implausibly large number of genetic codes from which the modern standard genetic code is presumed to have been selected by evolution in the 6.3 x 1015 seconds of the Earth's early history during which the origin of life events occurred."

//
One must presume that the modern genetic code did not originate from among 1.40 x 10 ^70
codes awaiting assignment.
//

------------------------------------------------------
2) However, previously on page 93, Yockey conceeds that the ORIGIN of the genetic code is UNKNOWNABLE.

//
Many papers have been published with titles indicating that their subject is the origin of the genetic code, but actually the content deals only with its evolution. Authors asswne that the origin of the genetic code is inevitable once they have created a scenario that provides the components of an informational molecule.
//

//
The paradox is seldom mentioned that enzymes are required to define or generate the reaction network, and the network is required to synthesize the enzymes and their component amino acids. There is no trace in physics or chemistry ofthe control of chemical reactions by a sequence of any sort or of a code between sequences. Thus, when we make the distinction between the origin of the genetic code and its evolution we find the origin of the genetic code is unknowable (Chapter 11).
//

------------------------------------------------------
3) Further from point 1) above , on page 97, Yockey then proceeds to explain AN EVOLUTION OF GENETIC CODE FROM A PREVIOUS UNKNOWNABLE ORIGIN under the heading :

"7.2 Did the genetic code evolve from a first extension of a four-letter alphabet?"

and then he moves onto jukes proposal under the heading :
"7.2.2 Jukes ' proposal that the genetic code evolved from a doublet code" 
and then 
"7.2.5 Expansion of the genetic vocabulary and decreasing the number of possible genetic codes"

we Yockey then proceeds to postulate that this could have been a markov process involved in the EVOLUTION 
(not the origin , which as hes clearly stated on p93 is unknownable)

------------------------------------------------------
4) in Chapter 11 he addresses again the origin of the genetic code

"1 1. 2. 2 The unknowable origin of the genetic code"
//
In Chapter 7 we found that the genetic code is much like all codes usedin communication. Looking backward in time, through a glass darkly, hownear to the origin of the genetic code can we see? It is often speculated thatthe genetic code began as a binary alphabet. This is not a fruitful speculationas DNA and RNA are composed of four compounds that form a primary four letter alphabet. Even with some imagination we may consider a sixteen member code composed of the doublets of UCAG. The origin of the genetic code is unknowable. I have no doubt that if the historic process leading to the origin of life were knowable it would be a process of physics and chemistry. Thus, the process of the origin of life is possible but unknowable.
//

folks, stop for a second and Think about what he is saying here for a minute:
//the process of the origin of life is possible but unknowable.//
a)
Its possible because we are here, buts its unknownable
b)

" I have no doubt that if the historic process leading to the origin of life were knowable it would be a process of physics and chemistry."

JOCKEY DOESNT KNOW - HE SAYS ITS UNKNOWNABLE, **BUT** THEN HES INSISTING AND ASSERTING THAT IF WE DID KNOW THEN IT WOULD BE A PROCESS OF PHYSICS AND CHEMISTRY.

SO HES ASSERTING IT IS A SOLELY NATURALISTIC PROCESS

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3 Genetic code optimisation: Part 1 on Wed Jan 20, 2016 2:41 pm

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Genetic code optimisation: Part 1

The genetic code as we find it in nature—the canonical code—has been shown to be highly optimal according to various criteria. It is commonly believed the genetic code was optimised during the course of an evolutionaryprocess (for various purposes). We evaluate this claim and find it wanting. We identify difficulties related to the three families of explanations found in the literature as to how the current 64 x 21 convention may have arisen through natural processes

The order of amino acids in proteins is determined by information coded on genes. There are over 1.51 x 10^84 possible  genetic codes based on mapping 64 codons to 20 amino acids and a ‘stop’ signal  (i.e. 64 => 21). The origin of code-based genetics is for proponents of evolution an utter mystery, since this requires a large number of irreducibly complex machines: ribosomes, RNA and DNA polymerases, aminoacyl-tRNA synthetases (aaRS), release factors, etc. These machines consist for the most part of proteins, which poses a paradox:

dozens of unrelated proteins are needed (plus several special RNA polymers) to process the encoded information. Without them the genetic code won’t work, but generating such proteins requires that the code already be functional. This is one of many examples of ‘chicken-and-egg’ dilemmas faced by materialists.

Another is the need for a reliable source of ATP for amino acids to polymerise to proteins: without the necessary proteins and genes already in place such ATP molecules won’t be produced. In addition, any genetic replicator needs a reliable ‘feed stock’ of nucleotides and amino acids, but several of the metabolic processes used by cells are interlinked. For example, until various amino acid biosynthetic networks are functional, the nucleotides can’t be metabolised. These are some of the reasons we believe natural processes did not produce the genetic code step-wise.  The literature is full of papers which claim the universal code has evolved over time and is in some sense now far better than earlier, perhaps even near optimal.  These claims are ‘flights of fantasy’. No real workable mechanism has yet been offered as to how a simpler genetic system could have increased dramatically in complexity and in robustness towards mutations. If a primitive replicator had gotten started, contra all chemical logic, would it be possible according to various evolutionary scenarios to refine the system to generate the 64 codon => 20 amino acid + ‘stop’ signal convention used by the standard genetic code?

In the standard genetic code, 64 codons map to 20 amino acids and a stop signal. The particular assignments show clear evidence that the coding convention used protects against the deleterious effects of mutations. Naturalists believe the standard code went through multiple refining stages preceding the Last Universal Common Ancestor (LUCA). Variant genetic codes are usually found in mitochondria and are caused by post-transcriptional chemical modifications of the nucleotides of tRNAs and mRNAs. These are complex biochemical processes unlikely to arise naturally. During code modification, ambiguous codon translations lead to a multitude of protein variants present concurrently in a cell. Natural selection therefore would be faced with an ever-varying set of inconsistent goals. Two algorithms programmed with Java show that there are over 1.5 x 10^84 genetic codes based on a {64 : 21} mapping, most of which are far less robust to mutations than the standard code. In the face of such a huge number of coding possibilities, and an internal and external cellular environment which is changing constantly, natural selection cannot focus on exploring one code after the other in searching for better versions. We suggest that some variants of the standard code may be degenerations, but believe alternatives may have been designed from the beginning, optimal for specific organisms.

The origin of the genetic code is a mystery to the materialist. With but one notable exception,1 the details and complexity of the genetic machinery are glossed over in various ad hoc hypotheses to the point of retaining no chemical or biological relevance. It is not our purpose to analyse here the origin of genetic code theories themselves. Instead we critically examine the common assumption that the code has evolved over time, leading to an increase in sophistication and robustness. A large number of interpretative frameworks have been published, proposing naturalistic reasons for the particular assignment of 64 codons to 20 amino acids and a stop signal. We have summarized these frameworks  in three categories: (I) chemical/stereochemical theories, (II) coevolution of biosynthetically related amino acid pathways, and (III) evolution and optimisation to prevent errors. they lack explanatory substance. We extend the arguments here and introduce new aspects, showing that code modification and improvement is more difficult than generally conceded.

Only an infinitesimal minority of polypeptides fold into stable structures, which is comparable to selecting a single kernel of sand from among all the beaches on Earth. A protein cannot be built using amorphic, randomly folded polypeptides. And the instructions to produce useful proteins, based on suitable orders of amino acids, have nothing to do with the physics of codon-anticodon (tRNAmRNA) interactions. This information-theoretic fact is important, since it means that the messages which need to be generated (here proteins) can be freely encoded genetically. And once encoded, a lack of bias is necessary to permit the intended messages to remain constant over multiple generations. Furthermore, if thermodynamically stronger binding were to be favoured by nature, then more than three nucleotides would be yet stronger. Triplet codes would not have evolved if thermodynamic stability was a major driving force in creating a genetic code. There are incomprehensibly many kinds of interactions between polymers constructed from sugar monomers which are much stronger than the triplet nucleotide hydrogen-bonds used by the genetic code. Nature would have had to ignore all these, and concentrated on a minuscule subset involving weaker interactions using only three nucleotides. But the thermodynamic argument claims the opposite, that the stronger interactions determine the original structure of the genetic code

https://creation.com/images/pdfs/tj/j21_2/j21_2_90-100.pdf
https://creation.com/images/pdfs/tj/j21_3/j21_3_84-92.pdf



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Materialism Cannot Explain the Origin of the Genetic Code. Intelligent Design is a More Reasonable Explanation. 1

Materialism cannot explain the origin of the genetic code. The probability that the necessary chemical reactions could occur through the unguided working of physical laws is too low. No one who has investigated the problem believes there is a satisfactory explanation of how life or the genetic code could arise through natural means.
For the genetic code to work, there has to be a semiotic system to use DNA or RNA to represent the sequence of amino acids in each protein and 




there has to be a cybernetic system to produce the machinery that uses the genetic code to produce proteins. This requires:

http://ncu9nc.blogspot.com.br/2013/04/materialism-cannot-explain-origin-of.html

The development of the code whereby each possible triplet of nucleotides represents an amino acid.
The determination of the sequence of amino acids for each protein that is to be produced.
The creation of the specific genes (molecules of DNA or maybe RNA) that use the triplet code to specify the proteins.
The many tRNAs, one for each triplet, and the amino acids and enzymes that combine amino acids and tRNA.
Ribosomes.

All of this has to come into existence at the same time because:

The parts are not useful individually.
But paradoxically, according to materialism these parts are the information and machinery that is needed to produce itself.
The genetic code is finely tuned to reduce the effects of point mutations and there is no explanation as to how the genetic code could evolve from something simpler, something less finely tuned. Any change in the genetic code would be catastrophic because it would effect every gene. It would be like changing every letter "n" to the letter "p" in an entire book. It would create so many "misspellings" for an organism that it is impossible that it could survive.
Evolving from a double code to a triplet code would require simultaneous changes in every codon in every gene and in all the tRNAs and the mechanism that moves the mRNA with respect to the ribosome during protein synthesis.

All these parts have to be produced in the correct numbers and arranged in a configuration where they will work together.

These factors all contribute to the impossibly low probability of the genetic code arising through the unguided action of natural forces, chance, self assembly, and/or evolution.
However, we know there is a phenomenon that can create semiotic and cybernetic systems that would otherwise have no chance of arising through natural processes. This phenomenon is intelligence. Therefore it is reasonable to suppose that the genetic code was created by an intelligence. This is not a "god of the gaps" argument. It is the same mode of logic, "like phenomena have like causes", whereby the measurement of gravity on earth leads to the conclusion that gravity causes the planets to orbit the sun.



 It is the same mode of logic used by many early naturalists, such as geologist Charles Lyell, to explain phenomena that occurred in the remote past by identifying causes known to be effective in the present time. Additionally, you don't need evidence of who the intelligence was to make this supposition. If a NASA space craft found machinery on Mars, we would not think that the machinery arose naturally just because there were no Martians around who could have made it. The existence of machinery that could not arise naturally is sufficient to conclude the existence of an intelligent maker.
However, the belief that naturalism can explain something that current science says is impossible is a "god of the gaps" argument. Our current understanding of chemistry and the conditions on the early earth says there is no good natural explanation for the origin of life and the genetic code.1 To disregard science and maintain faith in naturalism is a "god of the gaps" argument. To paraphrase the Nobel prize winning neurophysiologist Sir John Eccles: Promissory materialism is superstition.

Sources


1) http://ncu9nc.blogspot.com.br/2013/04/materialism-cannot-explain-origin-of.html

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