On origin of genetic code and tRNA before translation

On origin of genetic code and tRNA before translation

Common language talks about DNA as 'information' or 'a code'. For a very long time, scientists suspected that something—some kind of plan, specificity or driving force—resided within the sperm and/or egg, such that a snake developed from a snake egg and humans created human offspring. But it was only in the late 1940s and 1950s, when cyberneticists, physicists and mathematicians entered the field of molecular biology, that scientists came to interpret this 'something' as information. The physicist Erwin Schrödinger probably coined the term 'code' when he described living organisms in terms of their molecular and atomic structure, in his influential book What is Life (Schrödinger, 1944). The complete pattern of the future development of an organism and its function when mature, Schrödinger wrote, is contained in the chromosomes in the form of a 'code'. His writings had a strong influence on both Francis Crick and James Watson and their later discovery of the structure of DNA. “Schrödinger probably wasn't the first, but he was the first one I'd read to say that there must be a code of some kind that allowed molecules in cells to carry information,” Watson said in an interview with Scientific American (Watson, 2003). Indeed, Watson and Crick, in a paper on the implications of their DNA structure, picked up Schrödinger's metaphor when they wrote that “it therefore seems likely that the precise sequence of the bases is the code which carries the genetical information.” 4

Just five nucleobases, also termed the genetic alphabet, are known to dominate the composition of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)



The quest of the origin of the coded information stored in DNA is a unresolved problem .

Lee Strobel writes:

“The six feet of DNA coiled inside every one of our body's one hundred trillion cells contains a four-letter chemical alphabet that spells out precise assembly instructions for all the proteins from which our bodies are made … No hypothesis has come close to explaining how information got into biological matter by naturalistic means” (Strobel, p. 282).

However, not only must the specified complex arrangement of the nucleotides stored in DNA be explained, which are the information required to make proteins, but also the origin of the basepairs  itself and why only four bases, aka letters were selected, that is,  the narrow selection of restricted variety of organic molecules upon which life is based. That is, in the same manner as not only  the origin of the poem written through a alphabet might have to be figured out, but the origin of the alphabet itself, that is in our case, why 4, and not more or less nucleobases, but also why these four types, that is, why not different nucleobases since there are miridas from which the code  could be chosen from. But also, why the assignment at all, rather than none ? Why arised a code, rather than none ?   That is not a trivial question, but a fundamental one, which hardly can find good explanations through naturalism, however if a mind is involved, it makes perfect sense, since we know of minds inventing various kinds of alphabets all the time,  there are european, asian, russian , japanese, chinese etc. types of alphabets.



In the paper : 

On the Origin of the Canonical Nucleobases: An Assessment of Selection Pressures across Chemical and Early Biological Evolution 5

The native bases of RNA and DNA are prominent examples of the narrow selection of organic molecules upon which life is based. How did nature “decide” upon these specific heterocycles? Evidence suggests that many types of heterocycles could have been present on the early Earth. It is therefore likely that the contemporary composition of nucleobases is a result of multiple selection pressures that operated during early chemical and biological evolution. The persistence of the fittest heterocycles in the prebiotic environment towards, for example, hydrolytic and photochemical assaults, may have given some nucleobases a selective advantage for incorporation into the first informational polymers. 

The prebiotic formation of polymeric nucleic acids employing the native bases remains, however, a challenging problem to reconcile.

Hypotheses have proposed that the emerging RNA world may have included many types of nucleobases. This is supported by the extensive utilization of non-canonical nucleobases in extant RNA and the resemblance of many of the modified bases to heterocycles generated in simulated prebiotic chemistry experiments.

The prebiotic formation of polymeric nucleic acids employing the native bases remains, however, a challenging problem to reconcile. Hypotheses have proposed that the emerging RNA world may have included many types of nucleobases. This is supported by the extensive utilization of non-canonical nucleobases in extant RNA and the resemblance of many of the modified bases to heterocycles generated in simulated prebiotic chemistry experiments. Selection pressures in the RNA world could have therefore narrowed the composition of the nucleic acid bases. Two such selection pressures may have been related to genetic fidelity and duplex stability. Considering these possible selection criteria, the native bases along with other related heterocycles seem to exhibit a certain level of fitness. We end by discussing the strength of the N-glycosidic bond as a potential fitness parameter in the early DNA world, which may have played a part in the refinement of the alphabetic bases.

So basically, there is no reason why the four extant nucleobases are selected. Any other could be assigned. But then there could be 4, 6, 10 or eventually even more nucleobases. This remains a challenging problem for naturalism, not however for intelligent design, where the creator selected arbitrarly the four bases to create life.
Since when did a prebiotic environment establish " selection pressures ", and why and how should there have been a goal to reach genetic fidelity and duplex stability ? There is triple stranded DNA, and it has nice stability

The alphabetic composition is the product of a continual process of refinement that evolved to its current state. 


There is no evolution prior DNA replication.....

Not only the native bases were likely present on the early Earth, but so were many others. One of the more enigmatic and difficult problems confronting the prebiotic chemistry community is identifying how the monomers of RNA, or pre-RNA, or even non-related polymeric components selectively formed and self-assembled out of the presumed random prebiotic mixtures. Focusing on just a narrow view of RNA precursors, the linking of a nucleo-base to a ribose sugar is one such pressure. There are multiple ways in which a nucleobase can be attached to ribose via an N-glycosidic bond, but only one is found in contemporary nucleic acids (via the N9 of purines and N1 of pyrimidines). Achieving regio- and stereochemical selectivity of glycosylation reactions under simulated prebiotic conditions has plagued the community ever since Orgel and others began working on this problem.

We have found that a short stretch (30mer or larger) of triple-stranded DNA structure formed at the terminus (or very near) of linear DNA molecules is unusually stable, withstanding heat treatment at as high as 95 degrees C.  6



And the base pairs are also different :

The Hoogsteen base pair, consisting of a syn adenine base paired with an anti thymine base, is found in the 2.1 Å resolution structure of the MATα2 homeodomain bound to DNA in a region where a specifically and a non‐specifically bound homeodomain contact overlapping sites. 7

The paper then continues :


the alphabetic composition is the product of a continual process of refinement that evolved to its current state.

The only problem with this assertion is that they make things up. How do they know the state of affairs was due to evolution ? Answer : they don't know !! Atheists however will immediately conclude, because the paper says so, it must be true.......

Results from simulated prebiotic chemistry experiments conducted over the past fifty years and the ongoing analysis of meteorites provide evidence that not only the native bases were likely present on the early Earth, but so were many others.

So that means, life had many options, but choose to select just the extant four bases. See below



It would seem reasonable to hypothesize that the bases used by nature would have been selected to exhibit some of the highest stabilities against these spontaneous deamination reactions in comparison to alternative nucleobases.

Here applies the same as said above: Since when did a prebiotic environment establish " selection pressures ", and why and how should there have been a goal to reach highest stability  against these spontaneous deamination reactions in comparison to alternative nucleobases ? It seems almost as if nature had the goal to create life ?

Greater persistence in this environment would have given the native bases an advantage over others, possibility facilitating their selective incorporation into the first primitive genetic polymers.

Again : nature has no mind, and no goals. And so it really does not matter at all, primitive genetic polymers are produced, or not.





1) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3050877/
4) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1298980/
5) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4181368/
6) http://www.ncbi.nlm.nih.gov/pubmed/16769700
7) http://nar.oxfordjournals.org/content/30/23/5244
8 ) Bruce Alberts : Molecular biology of the cell , pg.367
9 ) file:///E:/Downloads/43-308-1-PB%20(1).pdf


http://www.ncbi.nlm.nih.gov/pubmed/3381099

Wow! Great presentation. It must have taken an enormous commitment. Let me see if I've got this equation right. (1) Start with emotionally motivated presuppositions, (2) exclude any alternative views you don't want to be true, (3) add extensive discussion of scientific discoveries that are not actually at issue, (4) interpret the facts in light of your unsubstantiated presuppositions, (5) speculate at length about causalities that cannot be directly observed or indirectly tested without circular reasoning, (6) then conclude that the evidence supports your presupposed parameters.

We could call that Science After Darwin and use the acronym SAD. Kind of like what I feel when I observe truth being obscured by faulty, blind faith rationalizations. But there is consensus science in a nutshell today. And we must learn the lesson well or we won't get funding, career opportunities or advancement, and we will be persecuted for questioning ... payback is a bitch when you offend the dark side of the Force.

Sorry. This was more tongue-in-cheek than it might appear to be, but I see this kind of propaganda passed off as real science far too often. Half truths and desperate wishful thinking can never make irrational presuppositions reasonable. If 50 million "scientists" believe a foolish thing it is still a foolish thing. It's your life, and the results may be forever, follow the Truth not the rhetoric.

How the codon arrangement and arbitrary selection of the genetic code points to design 1

https://reasonandscience.catsboard.com/t2055-on-origin-of-genetic-code-and-trna-before-translation#5101

Marcello Barbieri Code Biology A New Science of Life : 



A messenger RNA is certainly a unique and objective chain of nucleotides but in no way it is a unique sequence of codons because different codemakers could scan it in different ways. If the nucleotides were scanned two-by-two, for example, the sequence of codons would be totally different. The same chain of nucleotides, in other words, can give origin to many sequences of codons, and it is always the codemaker that determines the sequence because it is the codemaker that defines the codons. 

The logical question is : who or what defined or determined that the sequence had to be 3 nucleotides to form a codon. Why not 4, or 2 ? Why a code at all ? Who or what is the codemaker ? How could the rules of the genetic code emerge without intelligent agent involved ?  There is no necessary connections between nucleotides and amino acids, that would oblige the two to relate to each other in the way they do to produce life essential molecular machines. 

Life  does not only transcribe and translate  genetic information to produce proteins, but it is also replicates its DNA  through DNA polymerase to produce a complementary copy of its sequence. DNA replication is a ESSENTIAL process in order for  perpetuation of life  on earth, irreducible and enormously complex, using in the simplest life forms at least 20 essential protein complexes, proof reading and error correction mechanisms.  
Question: WHY would lifeless chemical reactions and molecules emerge with such a extraordinarly process AT ALL ? Did chemistry have the inherent drive to become alive and self replicating in order to not get extinct again ?

Life  is based on copying and coding,  transcribing, translating, and replicating. How and why could  these concepts have emerged  and be implemented at all by chemical unguided reactions  ? There is no satisfactory answer outside of the realm of a intelligent agent conceptualizing these processes with a end goal in mind to create life.  

A linear sequence of codons, in short, does not exist without a codemaker and outside a codemaking process. It is totally dependent on codemaking and is therefore a codemaker-dependent entity, which is precisely what a sign is. In the same way, the linear sequence of amino acids that is produced by the translation apparatus is also a codemaker-dependent entity, because only a codemaker can produce it. Any spontaneous assembly of amino acids would not make linear chains, and above all it would not arrange the amino acids in a specific order. Specific linear sequences of amino acids can be produced only by codemakers, but different codemakers would arrange the amino acids in different ways, which shows that the sequence of a protein is only one of the many possible ‘meanings’ that could be given to a string of nucleotides.

The question is : Can there be meaning without intelligence giving meaning to things ? Is that not  a mental process ?  

The sequence of a gene and the sequence of a protein, in conclusion, are not objective properties of those molecules. They are codemaker-dependent properties because they do not exist without a codemaking process, and because they would be different if the codemaker had different properties. The sequences of genes and proteins, in short, have precisely the characteristics that define signs and meanings. They are codemaker-dependent entities made of organic molecules and are therefore organic signs and organic meanings. All we need to keep in mind is that signs and meanings are mental entities when the codemaker is the mind, but they are organic entities when the codemaker is an organic system (Barbieri 2003).

"When the codemaker is a organic system". When.... but when can a non-mental process  produce instructional complex information, and a information bearing code system and  per se ? At the day of saint never ?!  

Every living cell contains all four components of semiosis (signs, meanings, code and codemaker) and is therefore a real semiotic system. Signs and meanings require mental entities. That entity is God. 

The evidence, in other words, tells us that codes consist of arbitrary rules not only in the cultural world but also at the molecular level. There are various important differences between organic codes and
cultural codes, but arbitrariness is not one of them. On the contrary, it is the property that best reveals the existence of coding rules and represents a defining feature in all codes.

And that of course once again raises the question, how this arbitrariness was established, and why. There was no physical necessity to establish such a code in the first place.  

This allows us to say that a code is a set of rules that establish a mapping between two independent worlds, where two worlds are said to be independent when there is no necessary connection between them and a mapping can be established in countless different ways by arbitrary rules. This in turn means that a specific mapping between the two worlds can only be achieved by selecting a fixed number of coding rules.

This is undoubtly a process that for obvious reason can only be established by intelligence. For what reason would chemical reactions establish such a connection by arbitrary rules ? Makes no sense at all. 

Stereochemistry and Arbitrariness

In 1954, George Gamow proposed the stereochemical hypothesis, the idea that the genetic code is the result of direct interactions in space between nucleotides and amino acids. More precisely, he proposed that the amino acids fit with a lock-andkey mechanism into ‘holes’ formed by four nucleotides, a reaction that he called stereochemical because he assumed that it is the three-dimensional shape of each hole that determines which amino acid can bind to it. He added that two of the four nucleotides in every hole are complementary, which implies that each amino acid is effectively identified by a triplet.
This diamond code proposed by Gamow (1954) was soon found in disagreement with the evidence, but the stereochemical hypothesis was reproposed in many other ways, even when it became clear that there are molecular intermediaries between codons and amino acids (Pelc and Weldon 1966; Melcher 1974; Shimizu 1982). Today it is known that codons are recognized by anticodons carried by transfer-RNAs, and that the transfer-RNAs receive amino acids from molecules called aminoacyl-tRNA-synthetases.

In order for the translation process from messengerRNA to proteins being sucessful, a number of physical parts are essential, basically 

mRNA, 
tRNA's, 
aminoacyl-tRNA-synthetases, 
left handed amino acids,
the ribosome
error check and repair mechanisms during translation 

There are 20 different synthetases, one per amino acid, and each synthetase donates its amino acid to one or more transfer-RNAs that are recognized by a small number of loci, or identity marks, that are distributed in various places on the surface of the tRNAs. The crucial point is that the recognition of the amino acids is independent from the anticodons because it has been shown that in many cases the synthetases have no access at all to the anticodons (Schimmel 1987; Schimmel et al. 1993).

So the assigning was arbitrary. How could and would it emerge by natural, unguided, random chemical reactions ? And why should it do so ? If it were by trial and error, then we would have non functional proteins during the trial and error process all along.  

The synthetases, in other words, are true adaptors because they perform two independent recognition processes, and establish connections that could have been realized in many other different ways.

That is PRECISELY the problem.

As Dembski writes :

We also know from broad and repeated experience that intelligent agents can and do produce information-rich systems: we have positive experience-based knowledge of a cause that is sufficient to generate new instructing complex information, namely, intelligence.  the design inference  does not constitute an argument from ignorance. Instead, it constitutes an "inference to the best explanation" based upon our best available knowledge.  It asserts the superior explanatory power of a proposed cause based upon its proven—its known—causal adequacy and  based upon a lack of demonstrated efficacy among the competing proposed causes.  The problem is that nature has too many options and without design couldn’t sort them all out. Natural mechanisms are too unspecific to determine any particular outcome. 

Natural chemical unguided, random reactions could theoretically form a new complex morphological feature like tRNA or a ribosome with the right size and form , and arrange to find out the right loci to insert a amino acid,  but it could  also select all kind of unfavourable locis , or non at all, most of which have no biological advantage or are most probably deleterious to the cell. Natural mechanisms have no constraints, they could produce any kind of novelty. Its however that kind of freedom that makes it extremely unlikely that mere natural developments provide new specific  arrangements that are advantageous to the cell.  Nature would have to arrange almost a infinite number of trials and errors until getting a new positive  arrangement. Since that would become a highly  unlikely event, design is a better explanation. This situation becomes even more acentuated when natural selection is not a possible constrainer, since evolution depends on replication, which did not exist prior dna replication

Today, Darwinists level the same charge against the contemporary theory of intelligent design (ID). They insist that ID is just an argument from ignorance—plugging God into the gaps of our current scientific understanding. Proponents of naturalism have made many thoughtful arguments over the years, but this isn’t one of them. The theory of intelligent design holds that many things in nature carry a clear signature of design. The theory isn’t based on what scientists don’t know about nature but on what they do know. It’s built on a host of scientific discoveries in everything from biology to astronomy, and some of them are very recent discoveries.

What Dembski writes, finds confirmation by the fact that  the rules of the genetic code can be changed in countless different ways, because they are the result of interactions between synthetases and tRNAs that can be modified virtually at will by adding or subtracting a few molecules. This means that the number of adaptors between codons and amino acids is potentially unlimited, and only the selection of a fixed number of them can ensure a specific link. It also means that the rules of the genetic code are not dictated by stereochemistry and in this sense they are arbitrary.