Intelligent Design, the best explanation of Origins

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Intelligent Design, the best explanation of Origins » Intelligent Design » Information Theory, Coded Information in the cell » The genetic code, insurmountable problem for non-intelligent origin

The genetic code, insurmountable problem for non-intelligent origin

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The genetic code, insurmountable problem for non-intelligent origin

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/

The genetic code is one in a million
if we employ weightings to allow for biases in translation, then only 1 in every million random alternative codes generated is more efficient than the natural code. We thus conclude not only that the natural genetic code is extremely efficient at minimizing the effects of errors, but also that its structure reflects biases in these errors, as might be expected were the code the product of selection.
http://www.ncbi.nlm.nih.gov/pubmed/9732450

The genetic code is nearly optimal for allowing additional information within protein-coding sequences
DNA sequences that code for proteins need to convey, in addition to the protein-coding information, several different signals at the same time. These “parallel codes” include binding sequences for regulatory and structural proteins, signals for splicing, and RNA secondary structure. Here, we show that the universal genetic code can efficiently carry arbitrary parallel codes much better than the vast majority of other possible genetic codes. This property is related to the identity of the stop codons. We find that the ability to support parallel codes is strongly tied to another useful property of the genetic code—minimization of the effects of frame-shift translation errors. Whereas many of the known regulatory codes reside in nontranslated regions of the genome, the present findings suggest that protein-coding regions can readily carry abundant additional information.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1832087/?report=classic

Determination of the Core of a Minimal Bacterial Gene Set
Based on the conjoint analysis of several computational and experimental strategies designed to define the minimal set of protein-coding genes that are necessary to maintain a functional bacterial cell, we propose a minimal gene set composed of 206 genes ( which code for 13 protein complexes ) Such a gene set will be able to sustain the main vital functions of a hypothetical simplest bacterial cell with the following features. These protein complexes could not emerge through evolution ( muations and natural selection ) , because evolution depends on the dna replication, which requires precisely these original genes and proteins ( chicken and egg prolem ). So the only mechanism left is chance, and physical necessity.
http://mmbr.asm.org/content/68/3/518.full.pdf

On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization
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.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1894784/

Literature from those who posture in favor of creation abounds with examples of the tremendous odds against chance producing a meaningful code. For instance, the estimated number of elementary particles in the universe is 10^80. The most rapid events occur at an amazing 10^45 per second. Thirty billion years contains only 10^18 seconds. By totaling those, we find that the maximum elementary particle events in 30 billion years could only be 10^143. Yet, the simplest known free-living organism, Mycoplasma genitalium, has 470 genes that code for 470 proteins that average 347 amino acids in length. The odds against just one specified protein of that length are 1:10^451.







The genetic code, insurmountable problem for non-intelligent origin Sdfsds12

Problem no.1
The genetic code system ( language ) must be created, and the universal code is nearly optimal and maximally efficient

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.

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/

The genetic code is one in a million
if we employ weightings to allow for biases in translation, then only 1 in every million random alternative codes generated is more efficient than the natural code. We thus conclude not only that the natural genetic code is extremely efficient at minimizing the effects of errors, but also that its structure reflects biases in these errors, as might be expected were the code the product of selection.
http://www.ncbi.nlm.nih.gov/pubmed/9732450

The genetic code is nearly optimal for allowing additional information within protein-coding sequences
DNA sequences that code for proteins need to convey, in addition to the protein-coding information, several different signals at the same time. These “parallel codes” include binding sequences for regulatory and structural proteins, signals for splicing, and RNA secondary structure. Here, we show that the universal genetic code can efficiently carry arbitrary parallel codes much better than the vast majority of other possible genetic codes. This property is related to the identity of the stop codons. We find that the ability to support parallel codes is strongly tied to another useful property of the genetic code—minimization of the effects of frame-shift translation errors. Whereas many of the known regulatory codes reside in nontranslated regions of the genome, the present findings suggest that protein-coding regions can readily carry abundant additional information.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1832087/?report=classic

Problem no.2
The origin of the information to make the first living cells must be explained.

Determination of the Core of a Minimal Bacterial Gene Set
Based on the conjoint analysis of several computational and experimental strategies designed to define the minimal set of protein-coding genes that are necessary to maintain a functional bacterial cell, we propose a minimal gene set composed of 206 genes ( which code for 13 protein complexes ) Such a gene set will be able to sustain the main vital functions of a hypothetical simplest bacterial cell with the following features. These protein complexes could not emerge through evolution ( muations and natural selection ) , because evolution depends on the dna replication, which requires precisely these original genes and proteins ( chicken and egg prolem ). So the only mechanism left is chance, and physical necessity.
http://mmbr.asm.org/content/68/3/518.full.pdf

Literature from those who posture in favor of creation abounds with examples of the tremendous odds against chance producing a meaningful code. For instance, the estimated number of elementary particles in the universe is 10^80. The most rapid events occur at an amazing 10^45 per second. Thirty billion years contains only 10^18 seconds. By totaling those, we find that the maximum elementary particle events in 30 billion years could only be 10^143. Yet, the simplest known free-living organism, Mycoplasma genitalium, has 470 genes that code for 470 proteins that average 347 amino acids in length. The odds against just one specified protein of that length are 1:10^451.

Paul Davies once said;
How did stupid atoms spontaneously write their own software … ? Nobody knows … … there is no known law of physics able to create information from nothing.

Problem no.3
The genetic cipher

On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization
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.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1894784/

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.

Put it in other words : The task compares to invent two languages, two alphabets, and a translation system, and the information content of a book ( for example hamlet)  being written in english translated  to chinese  in a extremely sophisticared hardware system. The conclusion that a intelligent designer had to setup the system follows not based on missing knowledge ( argument from ignorance ). We know that minds do invent languages, codes, translation systems, ciphers, and complex, specified information all the time.  The genetic code and its translation system is best explained through the action of a intelligent designer.

Bill Faint:  The attribution of the design has to be to God or purely materialistic mechanisms. The gigantic pull to swallow in the second case is the fact that the output is the product of code, and that the molecular machinery needed to replicate the code (for inheritance/perpetuation), transcribe it, translate it into protein with many intermediate steps requiring highly specific operations, and to repair it in the foreseen event that it is damaged (to preserve/protect it) or destroy it in the event that it suffers irreparable damage (to forestall cancer) is just too big to swallow. DNA had an intentional purpose. That's the only reasonable conclusion I can come to.

Origin and evolution of the genetic code: the universal enigma
http://reasonandscience.catsboard.com/t2001-origin-and-evolution-of-the-genetic-code-the-universal-enigma

The genetic code is nearly optimal for allowing additional information within protein-coding sequences
http://reasonandscience.catsboard.com/t1404-the-genetic-code-is-nearly-optimal-for-allowing-additional-information-within-protein-coding-sequences

The genetic code cannot arise through natural selection
http://reasonandscience.catsboard.com/t1405-the-genetic-code-cannot-arise-through-natural-selection

The origin of the genetic cipher, the most perplexing problem in biology
http://reasonandscience.catsboard.com/t2267-the-origin-of-the-genetic-cipher-the-most-perplexing-problem-in-biology



Last edited by Admin on Thu Feb 20, 2020 3:51 am; edited 4 times in total

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Evolution of the Genetic Code: The Ribosome-Oriented Model

Large numbers of exceptions to the canonical genetic code

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The hardware & software to make proteins, what mechanism explains best its origin?

http://reasonandscience.catsboard.com/t2363-the-genetic-code-insurmountable-problem-for-non-intelligent-origin#7010

What commonly is discussed in Theism x Atheism debates, is where the information stored in DNA come from. That is an enigma, which biological sciences never addressed in a convincing manner. And science generally doesn't go further than hypothetical guesswork.

But far more than just the origin of the message, the instructions must be explained.

Shakespeares Hamlet cam undoubtedly from Shakespeare's mind.
But the alphabet he used to convey his story, was pre-existent. He learned it and used to write down his romance.

But where the alphabet came from, is an entirely different issue.
So it is in genetics. DNA uses a genetic code, which is composed of 64 entries, composed of codons, three letters of nucleotides, which form together one genetic "letter". Each of these is ascribed to one of the twenty amino acids.  Since there are only twenty amino acids used to make proteins, several different codons can mean the same amino acids, so there is a redundancy, which is very useful since it permits the system to be more robust and error-prone. During the transcription and translation process, errors are minimized.

Science has discovered, that the genetic code is best suited for its task amongst at least one million other possible codes.

And the amino acid selection is as well the best suited for the purpose of constructing molecular machines, enzymes and proteins.

Now that is another not resolved question: How did the genetic code " alphabet " emerge on prebiotic earth?

How were the 64 genetic codons ascribed to 20 amino acids?

These questions belong to the most enigmatic in biological sciences, without good answers.

Besides the above-mentioned problems, which can be considered software problems, there is also the question of how the hardware emerged.

In order for the translation of messenger RNA to amino acids can occur, there are adapter molecules, transfer RNA's (tRNAs)

Transfer RNA, and its biogenesis
http://reasonandscience.catsboard.com/t2058-transfer-rna-and-its-biogenesis

tRNA's are very specific and complex molecules, and the " made of " follows several steps, requiring a significant number of proteins and enzymes, which are by themselves also enormously complex, not only in their structure but as well in their " made of ". So the question in the end arises: did natural processes have the foresight of the end product, tRNA, to make this highly specific nanorobot - like molecular machines which remove, add and modify the nucleotides? If not, how could they have arisen, since, without end goal, there would be no function for them? these enzymes are all specifically made for the production of tRNAs. And tRNA is essential for life

Another essential central player, that workes in an interdependent manner:

Aminoacyl-tRNA synthetases.
http://reasonandscience.catsboard.com/t2280-aminoacyl-trna-synthetases

The synthetases have several active sites that enable them to:

(1) recognize a specific amino acid,
(2) recognize a specific corresponding tRNA(with a specific anticodon),
(3) react the amino acid with ATP (adenosine triphosphate) to form an AMP (adenosine monophosphate) derivative, and then, finally,
(4) link the specific tRNA molecule in question to its corresponding amino acid. Current research suggests that the synthetases recognize particular three-dimensional or chemical features (such as methylated bases) of the tRNA molecule. In virtue of the specificity of the features they must recognize, individual synthetases have highly distinctive shapes that
derive from specifically arranged amino-acid sequences. In other words, the synthetases are themselves marvels of specificity.

And there is, of course, the Ribosome, a veritable ultracomplex factory making proteins:

Ribosomes amazing nanomachines
http://reasonandscience.catsboard.com/t1661-translation-through-ribosomes-amazing-nano-machines

* Each cell contains around 10 million ribosomes, i.e. 7000 ribosomes are produced in the nucleolus each minute.
* Each ribosome contains around 80 proteins, i.e. more than 0.5 million ribosomal proteins are synthesized in the cytoplasm per minute.
* The nuclear membrane contains approximately 5000 pores. Thus, more than 100 ribosomal proteins are imported from the cytoplasm to the nucleus per pore and minute. At the same time 3 ribosomal subunits are exported from the nucleus to the cytoplasm per pore and minute.

But these are just a few of the many players essential to make proteins:

The interdependent and irreducible structures required to make proteins
http://reasonandscience.catsboard.com/t2039-the-interdependent-and-irreducible-structures-required-to-make-proteins

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