My articles

Explaining the origin of the triplet code, its translation, and the machinery to make proteins

https://reasonandscience.catsboard.com/t2057-origin-of-translation-of-the-4-nucleic-acid-bases-and-the-20-amino-acids-and-the-universal-assignment-of-codons-to-amino-acids

In order to explain the origin of manufacturing of proteins, the origin of the hardware, that is the numerous enzymes and proteins, especially the enormously complex  RNA polymerases, transcription factors, repair enzymes, ribosome, as well as the DNA double helix and mRNA's, amino acids  involved must be explained, but specially and also  the origin of the code itself, and how the translation of the triplet anticodon to amino acids, and its assignment, arose. There is no physical affinity between the anticodon and the amino acids. What must be explained, is the arrangement of the codons in the standard codon table which is highly non-random, redundant and optimal, and serves to translate the information into the amino acid sequence to make proteins,  the origin of the assignment of the 64 triplet codons to the 20 amino acids. That is the origin of its translation. The origin of an alphabet through the triplet codons is one thing, but on top, it has to be translated to another " alphabet " constituted through the 20 amino acid sequence.

 That is as to explain the origin of capability to translate the English language into Chinese. We have to constitute the English and Chinese language and symbols first, in order to know its equivalence. That is a mental process. On top of that, the machinery itself to promote the process has also to be explained, that is the hardware. When humans translate English to Chinese, we recognize the English word, and the translator knows the equivalent Chinese symbol and writes it down to form the sentence. In the cell, Aminoacyl tRNA synthetase, special enzymes, of which each one is assigned to a specific amino acid, recognize the triplet anticodon of the tRNA and attach the equivalent amino acid to the tRNA, which afterward bonds it to the next amino acid.  How could random chemical reactions produce this recognition? Some theories try to explain the mechanism, but they all remain unsatisfactory. Obviously. Furthermore, Aminoacyl tRNA synthetase is complex enzymes. For what reason would they arise, if the final function could only be employed after the whole translation process would be set in place, with a fully functional ribosome being able to do its job? Remembering the catch22 situation, since they are by themselves made through the very own process in question? Why is it not rational to conclude that the code itself, the software, as well as the hardware, are best explained through the creative act of a highly intelligent creator, rather than random chemical affinities and reactions?

Question: what good would the ribosome be for without tRNAs? without amino acids, which are the product of enormously complex chemical processes and pathways? What good would the machinery be good for, if the code was not established, and neither the assignment of each codon to the respective amino acid? had the software and the hardware not have to be in place at the same time? Were all the parts not only fully functional if fully developed, interlocked, set-up, and tuned to do its job with precision, far better and more advanced than a human-made motor? And even it lets say, the whole thing was fully working and in place, what good would it be for without all the other parts required, that is, the DNA double helix, its compactation through histones and chromatins and chromosomes, its highly complex mechanism of information extraction and transcription into mRNA? Had the whole process, that is INITIATION OF TRANSCRIPTION, CAPPING, ELONGATION, SPLICING, CLEAVAGE,POLYADENYLATION AND TERMINATION, EXPORT FROM THE NUCLEUS TO THE CYTOSOL, INITIATION OF PROTEIN SYNTHESIS (TRANSLATION), COMPLETION OF PROTEIN SYNTHESIS AND PROTEIN FOLDING, and its respective machinery not have to be all in place? Does that not constitute an interdependent and irreducibly complex system?

Reducibility of "irreducible" systems

http://evidenceofgodarationalbelief.blogspot.com.br/

Its interesting that Wiki provides as argument for macro change the fact that a research published in the peer-reviewed journal Nature  showed that computer simulations of evolution demonstrated that it is possible for complex features to evolve naturally..This paper describes a computer simulation and thus contains no actual biology. So rather than provide evidence in the natural world, they resort to computer simulations.

following is the paper :

The evolutionary origin of complex features

http://myxo.css.msu.edu/papers/nature2003/Nature03_Complex.pdf

A long-standing challenge to evolutionary theory has been whether it can explain the origin of complex organismal features. We examined this issue using digital organisms—computer programs that self-replicate, mutate, compete and evolve. Populations of digital organisms often evolved the ability to perform complex logic functions requiring the coordinated execution of many genomic instructions. Complex functions evolved by building on simpler functions that had evolved earlier, provided that these were also selectively favoured. However, no particular intermediate stage was essential for evolving complex functions. The first genotypes able to perform complex functions differed from their non-performing parents by only one or two mutations, but differed from the ancestor by many mutations that were also crucial to the new functions. In some cases, mutations that were deleterious when they appeared served as stepping-stones in the evolution of complex features. These findings show how complex functions can originate by random mutation and natural selection.

In the discussion section, we read: "Some readers might suggest that we 'stacked the deck' by studying the evolution of a complex feature that will be built on simpler features that were also useful. However, that is precisely what evolutionary theory requires..."

Well, no. The Lenski simulation requires that complex systems exhibiting complex functions can always be built up from  simpler systems exhibiting simpler function . Macro change needs to explain many de novo features, like the arise of wings, legs, body organs etc, starting from biological systems which did not have such features at all.  

http://www.ideacenter.org/contentmgr/showdetails.php/id/1319#critique

"The simulation by Lenski et al. assumes that all functioning biological systems are evolutionary kludges of subsystems that presently have function or previously had function. But there's no evidence that real-life irreducibly complex biological machines, for instance, can be decomposed in this way. If there were, the Lenski et al. computer simulation would be unnecessary. Without it, their demonstration is an exercise in irrelevance.

Following are the main critique points :

1.Stacking the Deck: It was pre-ordained that the complex function can be created from the less complex functions (they hand-coded a solution before even running the simulation)--but there is no such guarantee in biology that subsystems can be so easily combined to produce anything useful! The complexity gap between the smaller functions (NAND, etc.) and the target functions (EQU) is not very big. In fact, they were able to create EQU using only 5 of the more primitive logic operation subsystems. This means that as far as logic is concerned, only 5 of the basic logic functions used in the programs are needed to evolve EQU. They created a simulation which they knew could evolve the target function through the subsystems. (This is why I have titled this critique "Evolution by Intelligent Design.")

2.Too Much Selective Advantage: Selective advantage was given to literally every single addition of logic functions in the organisms which evolved EQU. Additionally, every mutation which added code, always added functional line(s) of code, while in nature mutations are never guaranteed to have any meaning or functionality in the environment. This makes the evolution of EQU essentially inevitable, and it does not test irreducible complexity. In a true irreducibly complex system, there will be no selective advantage along an evolutionary pathway. In real world, there is no guarantee that the subsystems you need will necessarily give you a selective advantage along your evolutionary pathway.

3.Illustrating that Irreducible Complexity is Unevolvable: When the aforementioned "selective advantage" was taken away, and fitness only increased when the target function EQU appeared, EQU NEVER EVOLVED in their simulations! This is very significant because it shows that they modeled true irreducible complexity, and that when they did, irreducible complexity could not evolve!

Modeling Irreducible Complexity

The paper made one profound finding when it accurately modeled true irreducible complexity (first full paragraph, pg. 143). Michael Behe has defined irreducible complexity as:
"An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations). The degree of irreducible complexity is the number of unselected steps in the pathway." (A Response to Critics of Darwin’s Black Box, by Michael Behe, PCID, Volume 1.1, January February March, 2002; iscid.org/)

When Lenski et al. created a simulation with high irreducible complexity, i.e. there was no selective advantage until the target function arose, EQU never evolved! Consider this quote from the Lenski paper:

"At the other extreme, 50 populations evolved in an environment where only EQU was rewarded, and no simpler function yielded energy. We expected that EQU would evolve much less often because selection would not preserve the simpler functions that provide foundations to build more complex features. Indeed, none of these populations evolved EQU, a highly significant difference from the fraction that did so in the reward-all environment (P ~= 4.3 x 10-9, Fisher's exact test)."

In other words, when there is no selective advantage until you get the final function, the final function doesn't evolve. In this case, their simulation probably DID model biological reality because irreducible complexity claims that there is no advantage until you get the final function. In fact in such a scenario, it found that the evolution of such a structure was impossible. In other words, they just proved that irreducible complexity is unevolvable.

The Lenski paper can only be seen as a scientific response to the claims of ID proponents, published in a high profile journal such as Nature. Despite the fact that the authors of the Lenski paper would likely deny this fact, there are many clues which show that the article is intended as a rebuttal to the claims of ID proponents. Not only does this validate the work of ID proponents as posing a legitimate challenge to Darwin's theory, but it also indicates that the claims of ID proponents are eminently testable, falsifiable (though as discussed above, not yet falsified), and therefore also scientific in nature.

The article even attempts to address irreducible complexity without using the term. "Thus, although more than two dozen mutations were used to build EQU, undoing any one of them destroyed this function." They are stating that EQU was irreducibly complex, but yet it evolved. Thus, Exhibit C is as follows: the article directly purports to test the evolution of irreducible complexity but yet never uses the phrase. (Note: It is arguable that their stated conclusions about the evolution of irreducible complexity do not match the findings of their simulations. When EQU evolved, the study did not truly model irreducible complexity because it employed a "reward-all" environment where some function could be gained by adding parts which could also contribute to the final function. When the article properly modeled irreducible complexity, where only EQU was rewarded, EQU never evolved!)

While the author Carl Zimmer quotes co-author Christopher Adami to sing an over-inflated victory song, one important point should not be lost: this study implicitly proves that the claims of ID proponents, such the claim that some biological features are irreducible complexity, are eminently testable via the methods of science. Apparently Nature saw the claim of irreducible complexity as such a threat to evolution that it saw fit to publish a study which attempted to model the evolution of irreducible complexity.

https://reasonandscience.catsboard.com/t2056-reducibility-of-irreducible-systems

On origin of genetic code and tRNA before translation

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 four, and not more or less nucleobases, but also why these four types, that is, why not different nucleobases since there are miriads 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, the author asks :   How did nature “decide” upon these specific heterocycles? ( A heterocyclic compound or ring structure is a cyclic compound that has atoms of at least two different elements as members of its ring(s) )  Evidence suggests that many types of heterocycles could have been present on the early Earth.

the paper continues : 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.

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 to form the language with  alphabet, grammar, collection of punctuation marks and regulatory sites, semantics.  . This remains a challenging problem for naturalism, not however for intelligent design, where a intelligent designer selected arbitrarly the four bases to create life.

The authors try to answer the question, stating following : Two such selection pressures may have been related to genetic fidelity and duplex stability ( of the DNA double helix ). Clearly, the considerations applicable to potential prebiotic synthetic pathways do not appear to provide much insight into the selection of the bases of interest. We have not taken into account, however, stability, which is considered by many to be the more important factor regarding prebiotic abundance.

Since when did a prebiotic environment establish " selection pressures ", and why and how should there have been such goal to reach genetic fidelity and duplex stability ? There is triple stranded DNA, and it has nice stability........ In the paper:

Stable triple-stranded DNA formation and its application to the SNP detection, the authors state :

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.  

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.  

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 ? 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. The authors continue :  

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 ?  

The authors go on:

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 mental forsight, and no goals. And so it really does not matter at all, if primitive genetic polymers would have been  produced, or not.

http://evidenceofgodarationalbelief.blogspot.com.br/2015/06/on-origin-of-genetic-code-and-trna.html

Why RNA cannot emerge prior to DNA. ( the RNA world hypothesis is bunk )

https://reasonandscience.catsboard.com/t2028-origin-of-the-dna-double-helix#3436

1. Biosynthesis DNA is made from RNA. The deoxynucleotides are made from nucleotides with ribonucleotide reductases (RNR's), producing uracil-DNA or u-DNA. The uracil is then converted to thymine by adding a methyl group, making thymine-DNA or t-DNA, the kind that is actually used. 4)

The reaction catalyzed by RNR is strictly conserved in all living organisms. Furthermore, RNR plays a critical role in regulating the total rate of DNA synthesis so that DNA to cell mass is maintained at a constant ratio during cell division and DNA repair. A somewhat unusual feature of the RNR enzyme is that it catalyzes a reaction that proceeds via a free radical mechanism of action.The substrates for RNR are ADP, GDP, CDP, and UDP. dTDP (deoxythymidine diphosphate) is synthesized by another enzyme (thymidylate kinase) from dTMP (deoxythymidine monophosphate). 1

The iron-dependent enzyme, ribonucleotide reductase (RNR), is essential for DNA synthesis.

The structures of a class III ribonucleotide reductase (RNR) and pyruvate formate lyase exhibit striking homology within their active site domains with respect to each other and to the previously published structure of class I RNR. The common structures and the common complex-radical-based chemistry of these systems, as well as of the class II RNRs, suggest that RNRs evolved by divergent evolution and provide an essential link between the RNA and DNA world. 2

RNR is a complex of two dimeric proteins termed R1 and R2. 8

That brings us to the classic chicken and egg, catch22 situation. RNR enzymes are required to make DNA. DNA is however required to make RNR enzymes. What came first ?? We can conclude with high certainty that this enzyme buries any RNA world fantasies and any possibility of transition from RNA to DNA world scenarios.

and

2. Prebiotic thymine synthesis

Thymidylate synthases (Thy) are key enzymes in the synthesis of deoxythymidylate, 1 of the 4 building blocks of DNA. As such, they are essential for all DNA-based forms of life and therefore implicated in the hypothesized transition from RNA genomes to DNA genomes. Two unrelated Thy enzymes, ThyA and ThyX, are known to catalyze the same biochemical reaction. 7

Thymidylate synthase (Thy) is a fundamental enzyme in DNA synthesis because it catalyzes the formation of deoxythymidine 5′-monophosphate (dTMP) from deoxyuridine 5′-monophosphate (dUMP). For decades, only one family of thymidylate synthase enzymes was known, and its presence was considered necessary to maintain all DNA-based forms of life. Then, a gene encoding an alternative enzyme was discovered and characterized (Dynes and Firtel 1989; Myllykallio et al. 2002), and the novel enzyme was named ThyX, whereas the other enzyme was renamed ThyA. Even though both reactions accomplish the same key step, the reaction mechanisms or steps, catalyzed by the FDTS and TS enzymes are structurally different.The 2 enzymes, ThyA and ThyX, were found to have distinctly different sequences and structures, thus alluding to independent origins.

That's interesting, as we find two distinct enzymes with two different sequences and structures synthesizing the same reaction, thus being an example of convergence right in the beginning. How remote was the chance for this to happen by natural means, considering, that convergence does not favor naturalistic explanations?

as Stephen J.Gould wrote: “…No finale can be specified at the start, none would ever occur a second time in the same way, because any pathway proceeds through thousands of improbable stages. Alter any early event, ever so slightly, and without apparent importance at the time, and evolution cascades into a radically different channel.1

Stephen J. Gould, Wonderful Life: The Burgess Shale and the Nature of History (New York, NY: W.W. Norton & Company, 1989), 51.

By virtue of their function and phyletic distribution, Thys are ancient enzymes, implying 1) the likely participation of one or both enzymes during the transition from an RNA world to a DNA world (based on protein catalysts: Joyce 2002) and 2) the probable presence of a gene encoding Thy in the genome of the common ancestors of eukaryotes, bacteria, and archaea (Penny and Poole 1999; Woese 2002; Koonin 2003; Kurland et al. 2006). Thus, tracing back the pathway of genes encoding ThyA and ThyX may shed light on the actively debated wider issue regarding the origins of viral and cellular DNA

This brings us to the same problem as with Ribonucleotide Reductase enzymes (RNR), which is the classic chicken and egg, catch22 situation. ThyA and ThyX enzymes are required to make DNA. DNA is however required to make these enzymes. What came first ?? We can conclude with high certainty that this enzyme buries any RNA world fantasies, and any possibility of transition from RNA to DNA world scenarios, since both had to come into existence at the same time.

3. A new chicken-and-egg paradox relating to the origin of life

Cells could not have evolved without viruses, as they need reverse transcriptase (which is found only in viruses) in order to move from RNA to DNA.

In other words, instead of helping to solve the problem of the origin of life on Earth, recent research has only served to highlight one of its central paradoxes. And yet the science media reports the latest discoveries as if the solution is just around the corner. Don’t you find that just a little strange?

“In order to move from RNA to DNA, you need an enzyme called reverse transcriptase,” Dolja said. “It’s only found in viruses like HIV, not in cells. So how could cells begin to use DNA without the help of a virus?”

Creation of double-stranded DNA occurs in the cytosol as a series of these steps:

A specific cellular tRNA acts as a primer and hybridizes to a complementary part of the virus RNA genome called the primer binding site or PBS
Complementary DNA then binds to the U5 (non-coding region) and R region (a direct repeat found at both ends of the RNA molecule) of the viral RNA
A domain on the reverse transcriptase enzyme called RNAse H degrades the 5’ end of the RNA which removes the U5 and R region
The primer then ‘jumps’ to the 3’ end of the viral genome and the newly synthesized DNA strands hybridize to the complementary R region on the RNA
The first strand of complementary DNA (cDNA) is extended and the majority of viral RNA is degraded by RNase H
Once the strand is completed, second strand synthesis is initiated from the viral RNA
There is then another ‘jump’ where the PBS from the second strand hybridizes with the complementary PBS on the first strand

Nucleosomes and irreducible complexity

A nucleosome is a basic unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound in sequence around eight  histone protein cores. This structure is often compared to thread wrapped around a spool. The basic level of DNA compaction is the nucleosome, where the double helix is wrapped around the histone octamer containing two copies of each histone H2A, H2B, H3 and H4. Linker histone H1 binds the DNA between nucleosomes and facilitates packaging of the 10 nm "beads on the string" nucleosomal chain into a more condensed 30 nm fiber.

Histones are among the most highly conserved eucaryotic proteins. For example, the amino acid sequence of histone H4 from a pea and from a cow differ at only 2 of the 102 positions. This strong evolutionary conservation suggests that the functions of histones involve nearly all of their amino acids, so that a change in any position is deleterious to the cell. This suggestion has been tested directly in yeast cells, in which it is possible to mutate a given histone gene in uitro andintroduce it into the yeast genome in place of the
normal gene. As might be expected, most changes in histone sequences are lethal; the few that are not lethal cause changes in the normal pattern of gene expression, as well as other abnormalities.

If a change in histone sequences are lethal, how could it probably come to be in gradual steps, or trial and error ? As long as the correct sequence is not reached, no function.....

Nucleosome assembly following DNA replication, DNA repair and gene transcription is critical for the maintenance of genome stability and epigenetic information.

In assembling a nucleosome, the histone folds first bind to each other to form H3-H4 and H2A-H2B dimers, and the H3-H4 dimers combine to form tetramers. An H3-H4 tetramer then further combines with two HZA-H2B dimers to form the compact octamer core, around which the DNA is wound

The  assembly is a sequential  multistep process, requiring several  folds and steps in a highly organized, regulated and precise manner, and must have been programmed and functional right from the beginning. Histone chaperones play important roles in regulating the intricate steps involved in folding of histones together with DNA to form correctly assembled nucleosomes, furthermore  assembly, disassembly and histone exchange to facilitate DNA replication, repair and transcription. There is a need for histone chaperones to guide the process and each step along the assembly pathway is carefully controlled and regulated by these histone chaperones. It is evident that a stepwise evolutionary fashion of development of histone chaperones to guide the process would result in a disaster. They had to be there fully working and programmed to do their job right from the start.  
Furthermore, to add to the already amazing machine like performance,  (linker histones) have to participate at each step in the processes of nucleosome assembly, disassembly and histone exchange during different genomic processes.   Linker histone H1 is an essential component of chromatin structure ( so its irreducible ).  H1 links nucleosomes into higher order structures.

Nucleosome formation is dependent on the positive charges of the H4 histones and the negative charge on the surface of H2A histone fold domains. Acetylation of the histone tails disrupts this association, leading to weaker binding of the nucleosomal components. Histone acetyltransferases (HATs) and Histone deacetylase ( HDAC ) are also essential enzymes, that  remove through acetylation the  positive charge on the histones, and as a consequence, the condensed chromatin is transformed into a more relaxed structure that is associated with greater levels of gene transcription. This relaxation can be reversed by HDAC activity.

So we can conclude that all these parts, DNA,  Linker histone H1, histones H2A, H2B, H3 and H4,and acetyltransferases (HATs) and Histone deacetylase ( HDAC ) form a  set of well-matched, mutually interacting, nonarbitrarily individuated parts such that each part in the set is indispensable to maintaining the system's basic, and therefore original, function.  The set of these indispensable parts is known as the irreducible core of the system, while Histone chaperones are also essential to build the since they guide the process and each step along the assembly pathway.

A new chicken-and-egg paradox relating to the origin of life

http://www.uncommondescent.com/intelligent-design/do-viruses-help-explain-the-origin-of-life/

Cells could not have evolved without viruses, as they need reverse transcriptase (which is found only in viruses) in order to move from RNA to DNA.

In other words, instead of helping to solve the problem of the origin of life on Earth, recent research has only served to highlight one of its central paradoxes. And yet the science media reports the latest discoveries as if the solution is just around the corner. Don’t you find that just a little strange?

“In order to move from RNA to DNA, you need an enzyme called reverse transcriptase,” Dolja said. “It’s only found in viruses like HIV, not in cells. So how could cells begin to use DNA without the help of a virus?”

https://en.wikipedia.org/wiki/Reverse_transcriptase#In_eukaryotes

Creation of double-stranded DNA occurs in the cytosol as a series of these steps:

A specific cellular tRNA acts as a primer and hybridizes to a complementary part of the virus RNA genome called the primer binding site or PBS
Complementary DNA then binds to the U5 (non-coding region) and R region (a direct repeat found at both ends of the RNA molecule) of the viral RNA
A domain on the reverse transcriptase enzyme called RNAse H degrades the 5’ end of the RNA which removes the U5 and R region
The primer then ‘jumps’ to the 3’ end of the viral genome and the newly synthesised DNA strands hybridizes to the complementary R region on the RNA
The first strand of complementary DNA (cDNA) is extended and the majority of viral RNA is degraded by RNAse H
Once the strand is completed, second strand synthesis is initiated from the viral RNA
There is then another ‘jump’ where the PBS from the second strand hybridizes with the complementary PBS on the first strand
Both strands are extended further and can be incorporated into the hosts genome by the enzyme integrase

Creation of double-stranded DNA also involves strand transfer, in which there is a translocation of short DNA product from initial RNA dependent DNA synthesis to acceptor template regions at the other end of the genome, which are later reached and processed by the reverse transcriptase for its DNA-dependent DNA activity

http://evidenceofgodarationalbelief.blogspot.com.br/2015/06/a-new-chicken-and-egg-paradox-relating.html

The amazing organisation and design  of DNA, genomes, histones, nucleosomes and chromosomes

DNA, as a very stable nano-molecule. It is an formidable, ideal massive storage device for long-term data archive. 22 The organisation of this higher order structure of chromosomes and respective substructures is awe inspiring when looking closer at its features and functionality. DNA nanotechnology tries to mimic its capabilities since this type of storage system is more compact than current magnetic tape or hard drive storage systems due to the data density of the DNA. For example, DNA stores the information to make over 100.000 different types of proteins in the human body, each with a unique function. We think that we have done very well with human technology, packing information very densely on to computer hard drives, chips and CD-ROM disks. However, these all store information on the surface, whereas DNA stores it in three dimensions. It is by far the densest information storage mechanism known in the universe.

Let's look at the amount of information that could be contained in a pinhead volume of DNA. If all this information were written into paperback books, it would make a pile of such books 500 times higher than from here to the moon! The design of such an incredible system of information storage indicates a vastly intelligent Designer. A paper , published in Nature, reports that "existing technologies for copying DNA are highly efficient," this makes DNA an "excellent medium for the creation of copies of any archive for transportation, sharing or security." The authors conclude that "DNA-based storage has potential as a practical solution to the digital archiving problem and may become a cost-effective solution for rarely accessed archives." 1

In Alberts book molecular biology of the Cell, we read : The structure and chemical properties of DNA make it ideally suited as the raw material of genes. The packing has to be done in an orderly fashion so that the chromosomes can be replicated and apportioned correctly between the two daughter cells at each cell division. We also confront the serious challenge of DNA packaging. Each human cell contains approximately 2 meters of DNA if stretched end-to-end; yet the nucleus of a human cell, which contains the DNA, is only about 6 μm in diameter. This is geometrically equivalent to packing 40 km (24 miles) of extremely fine thread into a tennis ball! The complex task of packaging DNA is accomplished by specialized proteins that bind to and fold the DNA, generating a series of coils and loops that provide increasingly higher levels of organization, preventing the DNA from becoming an unmanageable tangle. Amazingly, although the DNA is very tightly folded, it is compacted in a way that allows it to easily become available to the many enzymes in the cell that replicate it, repair it, and use its genes to produce proteins.

Packing ratio - the length of DNA divided by the length into which it is packaged

For example, the shortest human chromosome contains 4.6 x 107 bp of DNA (about 10 times the genome size of E. coli). This is equivalent to 14,000 µm of extended DNA. In its most condensed state during mitosis, the chromosome is about 2 µm long. This gives a packing ratio of 7000 (14,000/2).

To achieve the overall packing ratio, DNA is not packaged directly into final structure of chromatin. Instead, it contains several hierarchies of organization. The first level of packing is achieved by the winding of DNA around a protein core to produce a "bead-like" structure called a nucleosome. This gives a packing ratio of about 6. This structure is invariant in both the euchromatin and heterochromatin of all chromosomes. The second level of packing is the coiling of beads in a helical structure called the 30 nm fiber that is found in both interphase chromatin and mitotic chromosomes. This structure increases the packing ratio to about 40. The final packaging occurs when the fiber is organized in loops, scaffolds and domains that give a final packing ratio of about 1000 in interphase chromosomes and about 10,000 in mitotic chromosomes.

In Wikipedia we read in this regard : DNA has a striking property to pack itself in the appropriate solution conditions with the help of ions and other molecules. Usually, DNA condensation is defined as "the collapse of extended DNA chains into compact, orderly particles containing only one or a few molecules" 4

Furthermore: Without histones, the unwound DNA in chromosomes would be very long (a length to width ratio of more than 10 million to 1 in human DNA). For example, each human cell has about 1.8 meters of DNA, (~6 ft) but wound on the histones it has about 90 micrometers (0.09 mm) of chromatin, which, when duplicated and condensed during mitosis, result in about 120 micrometers of chromosomes

This is a amazing example of extraordinary design, unparalleled by human intelligence. Question: Is it not unlikely that natural processes could achieve this feat to condense DNA into such a enormously tiny , highly regulated and functional structure ? Why at all should it happen ?

Dr. Stephen C. Meyer in his 1996 essay The Origin of Life and the Death of Materialism, wrote that
"the information storage density of DNA, thanks in part to nucleosome spooling, is several trillion times that of our most advanced computer chips

How could undirected natural processes have produced the most advanced storage system known in the universe ? Evolution is not not a explanation, since its depends on this very own storage system in order for natural selection to occur.

Eukaryotic chromosomes consist of a DNA-protein complex that is organized in a compact manner which permits the large amount of DNA to be stored in the nucleus of the cell. The subunit designation of the chromosome is chromatin. The fundamental unit of chromatin is the nucleosome.

Everything in the cell is organized and in its expected place and function. Nothing in the cell is left to chance. The nucleus is no exception. In fact, in some ways, the nucleus is more organized and complex than the rest of the cell. One aspect of the complexity and organization of the nucleus is the chromatin. 3

Furthermore, in following paper, Integration of syntactic and semantic properties of the DNA code reveals chromosomes as thermodynamic machines converting energy into information, we find a true mind blower, showing the irreducible organizational complexity (author’s description) of DNA analog and digital information, that genes are not arbitrarily positioned on the chromosome etc. 5

The paper argues that cellular mechanisms involved in processing genetic information make up an irreducibly complex system. The system requires genetic information, genetic machinery keyed to read that genetic information, as well as specific chromosomal organization. All of these components are necessary for what the paper calls "the organisational complexity of the genetic regulation system."

To be precise, the paper uses the term "irreducible organization" but it amounts to the same thing as biochemist Michael Behe's "irreducible complexity," and points implicitly to the same challenge to Darwinian accounts of origins.

1) the authors are “serious” scientists, not fringe people
2) They are using “irreducible complexity” in the same sense as Behe. This is not a case of accidental use of the same phrase to mean something different. Their term “holistic” is another way of saying the same thing, that the system requires all of its parts to work.
3) This “holistic” approach is one that is becoming common in systems biology.

1) http://www.nature.com/nature/journal/v494/n7435/full/nature11875.html
2) http://www.ndsu.edu/pubweb/~mcclean/plsc431/eukarychrom/eukaryo3.htm
3) http://creationrevolution.com/chromatin-%E2%80%93-simple-cell-part-18/
4) https://en.wikipedia.org/wiki/DNA_condensation
5) http://www.evolutionnews.org/2013/10/paper_irreducib077761.html

more: http://reasonandscience.heavenforum.org/t2017-the-amazing-organisation-and-design-of-dna-genomes-histones-nucleosomes-chromosomes#3392

DNA repair mechanisms, designed with special care in order to provide integrity of DNA, and  essential for living organisms of all domains.

Maintaining the genetic stability that an organism needs for its survival requires not only an extremely accurate mechanism for replicating DNA, but also mechanisms for repairing the many accidental lesions that occur continually in DNA.

DNA damage is an alteration in the chemical structure of DNA, such as a break in a strand of DNA, a base missing from the backbone of DNA, or a chemically changed base.  Naturally occurring DNA damages arise more than 60,000 times per day per mammalian cell.   DNA damage appears to be a fundamental problem for life. DNA damages are a major primary cause of cancer. DNA damages give rise to mutations and epimutations. The mutations, if not corrected,  would be propagated throughout subsequent cell generations. Such a high rate of random changes in the DNA sequence would have disastrous consequences for an organism

Different pathways for DNA repair exists, Nucleotide excision repair (NER),  Base excision repair (BER),  DNA mismatch repair (MMR),  Repair through alkyltransferase-like proteins (ATLs) amongst others.

Its evident that the repair mechanism is essential for the cell to survive. It could not have evolved after life arose, but must have come into existence before. The mechanism is highly complex and elaborated, as consequence, the design inference is justified and seems to be the best way to explain its existence.

Base excision repair (BER)  involves a category of enzymes  known as  DNA-N-glycosylases.

One example of DNA's  automatic error-correction utilities are enough to stagger the imagination.  There are dozens of repair mechanisms to shield our genetic code from damage; one of them was portrayed in Nature  in terms that should inspire awe.

From Nature's article :
Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA 11

How DNA repair proteins distinguish between the rare sites of damage and the vast expanse of normal DNA is poorly understood. Recognizing the mutagenic lesion 8-oxoguanine (oxoG) represents an especially formidable challenge, because this oxidized nucleobase differs by only two atoms from its normal counterpart, guanine (G).  The X-ray structure of the trapped complex features a target G nucleobase extruded from the DNA helix but denied insertion into the lesion recognition pocket of the enzyme. Free energy difference calculations show that both attractive and repulsive interactions have an important role in the preferential binding of oxoG compared with G to the active site. The structure reveals a remarkably effective gate-keeping strategy for lesion discrimination and suggests a mechanism for oxoG insertion into the hOGG1 active site.

Of the four bases in DNA (C, G, A, and T) cytosine or C is always supposed to pair with guanine, G, and adenine, A, is always supposed to pair with thymine, T.  The enzyme studied by Banerjee et al. in Nature is one of a host of molecular machines called BER glycosylases; this one is called human oxoG glycosylase repair enzyme (hOGG1), and it is specialized for finding a particular type of error: an oxidized G base (guanine).  Oxidation damage can be caused by exposure to ionizing radiation (like sunburn) or free radicals roaming around in the cell nucleus.  The normal G becomes oxoG, making it very slightly out of shape.  There might be one in a million of these on a DNA strand.  While it seems like a minor typo, it can actually cause the translation machinery to insert the wrong amino acid into a protein, with disastrous results, such as colorectal cancer.  12

The machine latches onto the DNA double helix and works its way down the strand, feeling every base on the way.  As it proceeds, it kinks the DNA strand into a sharp angle.  It is built to ignore the T and A bases, but whenever it feels a C, it knows there is supposed to be a G attached.  The machine has precision contact points for C and G.  When the C engages, the base paired to it is flipped up out of the helix into a slot inside the enzyme that is finely crafted to mate with a pure, clean G.  If all is well, it flips the G back into the DNA helix and moves on.  If the base is an oxoG, however, that base gets flipped into another slot further inside, where powerful forces yank the errant base out of the strand so that other machines can insert the correct one.

Now this is all wonderful stuff so far, but as with many things in living cells, the true wonder is in the details.  The thermodynamic energy differences between G and oxoG are extremely slight – oxoG contains only one extra atom of oxygen – and yet this machine is able to discriminate between them to high levels of accuracy.

The author, David, says in the Nature article :

Structural biology:  DNA search and rescue

DNA-repair enzymes amaze us with their ability to search through vast tracts of DNA to find subtle anomalies in the structure. The human repair enzyme 8-oxoguanine glycosylase (hOGG1) is particularly impressive in this regard because it efficiently removes 8-oxoguanine (oxoG), a damaged guanine (G) base containing an extra oxygen atom, and ignores undamaged bases.

Natural selection cannot act without accurate replication, yet the protein machinery for the level of accuracy required is itself built by the very genetic code it is designed to protect.  Thats a catch22 situation.  It would have been challenging enough to explain accurate transcription and translation alone by natural means, but as consequence of UV radiation, it  would have quickly been destroyed through accumulation of errors.  So accurate replication and proofreading are required for the origin of life. How on earth could proofreading enzymes emerge, especially with this degree of fidelity, when they depend on the very information that they are designed to protect?  Think about it....  This is one more prima facie example of chicken and egg situation. What is the alternative explanation to design ? Proofreading DNA by chance ?  And a complex suite of translation machinery without a designer?

I  enjoy to learn about  the wonder of these incredible mechanisms.  If the apostle Paul could understand that creation demands a Creator as he wrote in Romans chapter one 18, how much more we today with all the revelations about cell biology and molecular machines?  

http://reasonandscience.heavenforum.org/t2043-dna-repair#3475

The complexity of  transcription through RNA polymerase enzymes  and general transcription factors in eukaryotes

Transcription is the process of making RNA from a DNA template. Several key factors are involved in this process. Including, DNA, transcription factors, RNA polymerase, and ATP.

Many proteins (well over 100 individual subunits) must assemble at the start point of transcription to initiate transcription in a eucaryotic cell.

This is a irreducible complex system. DNA, transcription factors, RNA polymerase, and ATP must be present, otherwise transcription cannot occur.

Transcription begins with a strand of DNA. It is divided into several important regions. The largest of these is the transcription unit. This portion of the DNA will be used to produce RNA. Upstream of the transcription unit is the TATA box. An enhancer region may also be involved.

Several complexes, known as transcription factors, are required for successful transcription. The first is TFIID, the largest of the general factors. A component of this factor, TBP, binds to the DNA using the TATA box to position TFIID near the transcription initiation site. Other transcription factors, including TFIIA and TFIIB, then attach.

These complexes prepare the DNA for the successful binding of RNA polymerase. One RNA polymerase is bound, other transcription factors complete the mature transcription complex.

Now, energy must be added to the system for transcription to begin. This energy is provided by the reduction of ATP into ADP and Pi.

RNA polymerase then synthesizes an RNA template from the strand of DNA. Most factors are released after transcription begins. When the end of the transcription unit is reached, the RNA polymerase dissociates, and the newly formed strand of RNA is released.

All the parts must come into existence at the same time, one has no function without the others. Also the whole sequence of events must be coordinated, and all parts must fit precisely together. There is no feasable mechanism producing this complex system randomly and in a stepwise fashion. Evolution is not a option, since transcription is required to make proteins, which are required to make replication work, which is essential upon which evolution works.

more :

http://reasonandscience.heavenforum.org/t2036-the-complexity-of-transcription-through-rna-polymerase-enzymes-and-general-transcription-factors-in-eukaryotes#3451

Origin of the cell membrane

A simple primitive cell, or protocell, would consist of two key components: a protocell membrane that defines a spatially localized compartment, and an informational polymer that allows for the replication and inheritance of functional information.  1

The emergence of the first cells on the early Earth was the culmination of a long history of prior chemical and geophysical processes.

Question: How do they know that ? They don't know. Thats just one of the typical baseless assertions without a shred of evidence.

Modern cell membranes are composed of complex mixtures of amphiphilic molecules such as phospholipids, sterols, and many other lipids as well as diverse proteins that perform transport and enzymatic functions. Phospholipid membranes are stable under a wide range of temperature, pH, and salt concentration conditions. Such membranes are extremely good permeability barriers, so that modern cells have complete control over the uptake of nutrients and the export of wastes through the specialized channel, pump and pore proteins embedded in their membranes. A great deal of complex biochemical machinery is also required to mediate the growth and division of the cell membrane during the cell cycle.

Question: Had this complex machinery for growth and division not have to be fully functional with the first cell, otherwise replication would not be able to occur, and life would not continue  ??

Fatty acids are attractive as the fundamental building block of prebiotic membranes in that they are chemically simpler than phospholipids. Fatty acids with a saturated acyl chain are extremely stable compounds and therefore might have accumulated to significant levels, even given a relatively slow or episodic synthesis.

An early RNA replicase probably would not have a built-in way of differentiating between a replicase or non-replicase sequence, and as a result, will make a copy of any RNA that happens to be close by.  Without some means of separating the replicases from the non-replicases, the population of replicases is unlikely to grow and prosper.  This issue can be resolved if the replicases are placed within a compartment, such as a vesicle, which can physically separate the replicases from other RNAs. 2

In addition, a membrane may have played an important role in the early cell's ability to store energy in the form of a chemical gradient. In modern eukaryotic cells, the mitochondria, often called the "cellular powerhouse" uses an internal chemical gradient to create energy-storing molecules known as ATP.

FORMING FATTY ACIDS ON THE EARLY EARTH

How might fatty acids have formed on the early Earth? Some scientists have proposed that hydrothermal vents may have been sites where prebiotically important molecules, including fatty acids, were formed.  Research has shown that some minerals can catalyze the stepwise formation of hydrocarbon tails of fatty acids from hydrogen and carbon monoxide gases -- gases that may have been released from hydrothermal vents. Fatty acids of various lengths are eventually released into the surrounding water.

It seems likely that primitive cells incorporated lipid-like molecules from the environment as a nutrient, rather than undertaking the much more complex process of synthesizing complex lipids by an enzyme-catalyzed process.

Based on what that scenario seems likely is a mistery to me......

http://www.csj.jp/journals/bcsj/bc-cont/b12may/85_20110349.html

Submarine hydrothermal systems (SHSs) have been thought of as a suitable environment for the origin of life subsequent to the abiotic synthesis of organic molecules. However, it has been pointed out that bioorganic molecules, such as amino acids, are easily degraded at a high temperature, and thus not likely to survive for the next step of chemical evolution in a SHS environment.

http://physwww.mcmaster.ca/~higgsp/3D03/MillerHighTemp.pdf

The problem with monomers is bad enough,but it is worse with polymers,e.g.,RNA and DNA (Lindahl1993),whose stability in the absence of efficient repair enzymes is too low to maintain genetic integrity iyperthermophiles. RNA and DNA are clearly too unstable to exist in a hot prebiotic environment.The existence of an RNA world with ribose appears to be incompatible with the idea of a hot origin of life.

Although such materials might have been synthesized near hydrothermal vents in the early seas, the assembly of such materials is quite problematic. Conditions requiring high concentrations, exact pH and temperature, plus the absence of high sodium and small amounts of certain metal ions, prevents the assembly of such components within the earth's early oceans. Conditions that might concentrate fatty acids to sufficient levels to form membranes would also concentrate solutes that disrupt the formation of those membranes. Encapsulation of a proto-cell replicator and metabolic system would be quite problematic, since the conditions that would encourage such activity would likely lead to conditions that would disrupt the primitive membrane completely. Primitive membranes must be able to transport nutrients and wastes, although passive transport systems would readily reach equilibrium and active transport systems would not be expected to be produced immediately upon encapsulation. Energy acquisition is problematic, since fatty acids membranes cannot generate a proton gradient. Membranes composed of unsaturated fatty acids or phospholipids can generate proton gradients, but would not be expected to have existed in early earth environments. Virtually all studies that have examined membrane growth and division have used unsaturated fatty acid membranes, which would not have been present on the early earth. Because of this problem, these studies have questionable relevance to the origin of life on earth. 4)

While a wide range of amphiphilic compounds that could serve as lipid components for primitive biological membranes self-assemble into bilayers, this self-assembly process requires “just right” conditions and “just right” molecular components. It is unlikely that such conditions would exist or persist for long time frames on early Earth. 5

1) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2926753/
2) http://exploringorigins.org/fattyacids.html
3) http://www.ucmp.berkeley.edu/education/events/deamer1.html
4) http://www.godandscience.org/evolution/origin_membranes.html#n07
5) http://www.reasons.org/articles/biotic-borders-cell-membranes-under-scrutiny

Origin of the DNA deoxyribonucleic acid  double helix : Only design provides compelling explanations

https://www.youtube.com/watch?v=t09Pzg9MSZ8

the origin of following must be explained :

the nucleotides :  

adenine (A) - a purine
cytosine(C) - a pyrimidine
guanine (G) - a purine
thymine (T) - a pyrimidine

- the formation of the double-helix spiral staircase-like structure
- why they are  running in opposite directions
- the backbone made up of (deoxy-ribose) sugar molecules
- the phosphate groups which links it together. ( also called 3'-5' phosphodiester linkage )
- the assembly and synthesis of the first structure

Scientists have long known that a myriad of sugars and numerous other nucleobases could have conceivably become part of the cell’s information storage medium (DNA). But why do the nucleotide subunits of DNA and RNA consist of those particular components? Phosphates can form bonds with two sugars simultaneously (called phosphodiester bonds) to bridge two nucleotides, while retaining a negative charge. This makes this chemical group perfectly suited to form a stable backbone for the DNA molecule. 2

How is that better explained ? Through natural processes, or intentional design ?

Other compounds can form bonds between two sugars but are not able to retain a negative charge. The negative charge on the phosphate group imparts the DNA backbone with stability, thus giving it protection from cleavage by reactive water molecules. Furthermore, the intrinsic nature of the phosphodiester bonds is also finely-tuned. For instance, the phophodiester linkage that bridges the ribose sugar of RNA could involve the 5’ OH of one ribose molecule with either the 2’ OH or 3’ OH of the adjacent ribose molecule. RNA exclusively makes use of 5’ to 3’ bonding. As it turns out, the 5’ to 3’ linkages impart far greater stability to the RNA molecule than does the 5’ to 2’ bonds.

That seems to be powerful evidence for design.

Why do deoxyribose and ribose serve as the backbone constituents of DNA and RNA respectively? Both are five-carbon sugars which form five-membered rings. It is possible to make DNA analogues using a wide range of different sugars that contain four, five and six carbons that can form five- and six-membered rings. But these DNA variants possess undesirable properties as compared to DNA and RNA. For instance, some DNA analogues do not form double helices. Others do, but the nucleotide strands either interact too tightly or too weakly, or they display inappropriate selectivity in their associations. Furthermore, DNA analogues made from sugars that form 6-membered rings adopt too many structural conformations. In this event, it becomes exceptionally difficult for the cell’s machinery to properly execute DNA replication and transcription. Other research shows that deoxyribose uniquely provides the necessary space within the backbone region of the double helix of DNA to accommodate the large nucleobases. No other sugar fulfils this requirement.

The right properties of deoxyribose and ribose are in my view far better explained through a designer, than random natural processes.

The molecular constituents of the DNA structure appear to have optimized chemical properties to produce a stable helical structure capable of storing the information required for the cell’s operation. Detailed accounts of how such an optimized structure for the cell’s most fundamental information storage medium could have arisen naturally have not been produced. To suppose that such extensive optimization could have come into being by blind chance is a far greater leap of faith than design.

In molecular biology, DNA ligase is a specific type of enzyme, a ligase, (EC 6.5.1.1) that facilitates the joining of DNA strands together by catalyzing the formation of a phosphodiester bond.

one of the most important ones is DNA ligase which joins DNA fragments via phosphodiester bonds and is used in processes such as DNA replication where Okazaki fragments need to be annealed in order to complete the formation of the lagging strand.

DNA ligase is a crucial element in recombinant technology 3

No DNA ligase enzymes, no formation of DNA strands, no life. Observe the nomenclature : " recombinant technology".....  

"Adenine synthesis is perhaps the best example of an irreducibly complex system that can be found in life ..."
the process doesn't work unless all 11 enzymes are present.

Adenine synthesis requires unreasonable HCN concentrations. Adenine deaminates with a half-life of 80 years (at 37°C, pH 7). Therefore, adenine would never accumulate in any kind of "prebiotic soup." The adenine-uracil interaction is weak and nonspecific, and, therefore, would never be expected to function in any specific recognition scheme under the chaotic conditions of a "prebiotic soup."

Cytosine  has not been reported in analyses of meteorites nor is it among the products of electric spark discharge experiments. The reported prebiotic syntheses of cytosine involve the reaction of cyanoacetylene (or its hydrolysis product, cyanoacetaldehyde), with cyanate, cyanogen, or urea. These substances undergo side reactions with common nucleophiles that appear to proceed more rapidly than cytosine formation. To favor cytosine formation, reactant concentrations are required that are implausible in a natural setting. Furthermore, cytosine is consumed by deamination (the half-life for deamination at 25°C is ≈340 yr) and other reactions. No reactions have been described thus far that would produce cytosine, even in a specialized local setting, at a rate sufficient to compensate for its decomposition. 1

The evidence that is available at the present time does not support the idea that RNA, or an alternative replicator that uses the current set of RNA bases, was present at the start of life.

guanine -- the G in the four-letter code of life -- has proven to be a particular challenge. While the other three bases of RNA -- adenine (A), cytosine (C) and uracil (U) -- could be created by heating a simple precursor compound in the presence of certain naturally occurring catalysts, guanine had not been observed as a product of the same reactions.

Prebiotic ribose synthesis: A critical analysis

The evidence that is currently available does not support the availability of ribose on the prebiotic earth, except perhaps for brief periods of time, in low concentration as part of a complex mixture, and under conditions unsuitable for nucleoside synthesis.

read more :

http://reasonandscience.heavenforum.org/t2028-origin-of-the-dna-double-helix#3425

Ribonucleotide reductase, one of the most essential enzymes of life, and how it buries the RNA world scenarios

This is one of the most essential enzymes of life

Ribonucleotide reduction is the only pathway for de novo synthesis of deoxyribonucleotides ( DNA )  in extant organisms. This chemically demanding reaction, which proceeds via a carbon-centered free radical, is catalyzed by ribonucleotide reductase (RNR). The mechanism has been deemed unlikely to be catalyzed by a ribozyme, creating an enigma regarding how the building blocks for DNA were synthesized at the transition from RNA to DNA-encoded genomes.

read more:

http://reasonandscience.heavenforum.org/t2029-ribonucleotide-reductase-one-of-the-most-essential-enzymes-of-life-and-how-it-buries-the-rna-world#3428

DNA is the genetic material in all cellular organisms plus many viruses. DNA’s building blocks, deoxyribonucleotides (dNTPs), are always synthesized by reduction of ribonucleotides (either NTPs or NDPs), the building blocks of RNA.

Origin of Ribonucleotide Reduction

How and when ribonucleotide reduction evolved is a question that is intimately associated with the transition from the RNA world to the modern RNA + protein + DNA world, since it is the only known de novo mechanism for dNTP synthesis.

The maintenance of life on Earth depends on the ability to reproduce. Reproduction requires an accurate and stable storage system for the genetic information in all organisms, including viruses. It has been recently suggested that the RNA molecule, with autoreplicative capacity, is the primary primitive molecule for the genetic information storage. Despite the wide acceptance of this idea, there are arguments against the concept of an RNA world that cannot be underestimated. 7

Today, three different RNR classes have been described, with little apparent similarity between them in terms of primary protein sequence (approximately 10–20% similarity). Thus, it could be assumed that each RNR class appeared independently from each other over time.

Three main classes of ribonucleotide reductases (RNR) have been discovered that depend on different metal cofactors for the catalytic activity:

class I enzymes contain a diiron-oxygen cluster,
class II a cobalt containing cobalamin cofactor (vitamin B12), and
class III an 4Fe-4S iron-sulfur cluster coupled to S-adenosylmethionine (SAM)

But, surprisingly, there is a great similarity the reaction mechanism, allosteric regulation and three-dimensional structure (tertiary structure) of these enzymes, suggesting a potential common origin.

The enzymatic activation of class III RNR requires Sadenosylmethionine (SAM), one of the most ancestral molecules, with few steps required for its biosynthesis

Biosynthesis DNA is made from RNA. The deoxynucleotides are made from nucleotides with ribonucleotide reductases (RNR's), producing uracil-DNA or u-DNA. The uracil is then converted to thymine by adding a methyl group, making thymine-DNA or t-DNA, the kind that is actually used.

The reaction catalyzed by RNR is strictly conserved in all living organisms.  Furthermore RNR plays a critical role in regulating the total rate of DNA synthesis so that DNA to cell mass is maintained at a constant ratio during cell division and DNA repair. A somewhat unusual feature of the RNR enzyme is that it catalyzes a reaction that proceeds via a free radical mechanism of action.The substrates for RNR are ADP, GDP, CDP and UDP. dTDP (deoxythymidine diphosphate) is synthesized by another enzyme (thymidylate kinase) from dTMP (deoxythymidine monophosphate).

The iron-dependent enzyme, ribonucleotide reductase (RNR), is essential for DNA synthesis.

The structures of a class III ribonucleotide reductase (RNR) and pyruvate formate lyase exhibit striking homology within their active site domains with respect to each other and to the previously published structure of a class I RNR. The common structures and the common complex-radical-based chemistry of these systems, as well as of the class II RNRs, suggest that RNRs evolved by divergent evolution and provide an essential link between the RNA and DNA world.

Genetic information can be stored stably only because a battery of DNA repair enzymes scan the DNA and replace the damaged nucleotides. Without these enzymes it would be inconceivable how primitive cells kept abreast of the constant high-level damage by the environment and by endogenous reactions. If unrepaired, cell death would result.

RNR is a complex of two dimeric proteins termed R1 and R2.

That brings us to the classic chicken and egg, catch22 situation.  RNR enzymes are required to make DNA. DNA is however required to make RNR enzymes. What came first ??
We can conclude with high certainty that this enzyme buries any RNA world fantasies, and any possibility of transition from  RNA to DNA world scenarios.

Problematic Chemical Postulates of the RNA World Scenario

http://www.arn.org/docs/odesign/od171/rnaworld171.htm#text9

Postulate 1: There was a prebiotic pool of beta-D-ribonucleotides.

Beta-D-ribonucleotides (see Figure 2) are compounds made up of a purine (adenine or guanine) or a pyrimidine (uracil or cytosine) linked to the 1'-position of ribose in the beta-configuration.

There is, in addition, a phosphate group attached to the 5'-position of the ribose. For the four different ribonucleotides in this prebiotic scenario, there would be hundreds of other possible isomers.

But each of these four ribonucleotides is built up of three components: a purine or pyrimidine, a sugar (ribose), and phosphate. It is highly unlikely that any of the necessary subunits would have accumulated in any more than trace amounts on the primitive Earth. Consider ribose. The proposed prebiotic pathway leading to this sugar, the formose reaction, is especially problematic.

The improbability of prebiotic nucleic acid synthesis.

Many accounts of the origin of life assume that the spontaneous synthesis of a self-replicating nucleic acid could take place readily. Serious chemical obstacles exist, however, which make such an event extremely improbable. Prebiotic syntheses of adenine from HCN, of D,L-ribose from adenosine, and of adenosine from adenine and D-ribose have in fact been demonstrated. However these procedures use pure starting materials, afford poor yields, and are run under conditions which are not compatible with one another. Any nucleic acid components which were formed on the primitive earth would tend to hydrolyze by a number of pathways. Their polymerization would be inhibited by the presence of vast numbers of related substances which would react preferentially with them. It appears likely that nucleic acids were not formed by prebiotic routes

The nitrogenous substances react with formaldehyde, the intermediates in the pathways to sugars, and with sugars themselves to form non-biological materials10. Furthermore, as Stanley Miller and his colleagues recently reported, "ribose and other sugars have suprisingly short half-lives for decomposition at neutral pH, making it very unlikely that sugars were available as prebiotic reagents."

Or consider adenine. Reaction pathways proposed for the prebiotic synthesis of this building block start with HCN in alkaline (pH 9.2) solutions of NH4OH.12 These reactions give small yields of adenine (e.g., 0.04%) and other nitrogenous bases provided the HCN concentration is greater than 0.01 M. However, the reaction mixtures contain a great variety of nitrogenous substances that would interfere with the formose reaction. Therefore, the conditions proposed for the prebiotic synthesis of purines and pyrimidines are clearly incompatible with those proposed for the synthesis of ribose. Moreover, adenine is susceptible to deamination and ring-opening reactions (with half-lives of about 80 years and 200 years respectively at 37º C and neutral pH), making its prebiotic accumulation highly improbable. This makes it difficult to see how any appreciable quantities of nucleosides and nucleotides could have accumulated on the primitive Earth. If the key components of nucleotides (the correct purines and pyrimidines, ribose, and phosphate) were not present, the possibility of obtaining a pool of the four beta-D-ribonucleotides with correct linkages would be remote indeed.

If this postulate, the first and most crucial assumption, is not valid, however, then the entire hypothesis of an RNA World formed by natural processes becomes meaningless.

Postulate 2: Beta-D ribonucleotides spontaneously form polymers linked together by 3', 5'-phosphodiester linkages (i.e., they link to form molecules of RNA

nucleotides do not link unless there is some type of activation of the phosphate group. The only effective activating groups for the nucleotide phosphate group (imidazolides, etc.), however, are those that are totally implausible in any prebiotic scenario. In living organisms today, adenosine-5'-triphosphate (ATP) is used for activation of nucleoside phosphate groups, but ATP would not be available for prebiotic syntheses. Joyce and Orgel note the possible use of minerals for polymerization reactions, but then express their doubts about this possibility

Joyce and Orgel then note that if there were activation of the phosphate group, the primary polymer product would have 5', 5'-pyrophosphate linkages; secondarily 2', 5'-phosphodiester linkages -- while the desired 3',5'-phosphodiester linkages would be much less abundant. However, all RNA known today has only 3',5'-phosphodiester linkages, and any other linkages would alter the three-dimensional structure and possibilities for function as a template or a catalyst.

Even waiving these obstacles, and allowing for minute amounts of oligoribonucleotides, these molecules would have been rendered ineffective at various stages in their growth by adding incorrect nucleotides, or by reacting with the myriads of other substances likely to have been present. Moreover, the RNA molecules would have been continuously degraded by spontaneous hydrolysis and other destructive processes operating on the primitive Earth.

THE RNA WORLD, PEPTIDE BOND SYNTHESIS,  AND THE ORIGINS OF LIFE

read the whole post at my personal virtual library:

http://reasonandscience.heavenforum.org/t2024-the-rna-world-peptide-bond-synthesis-and-the-origins-of-life#3414

Lets have a closer look at RNA world  - origin of life proposals : Here from the book of bruce alberts :  The Evolution of the Cell

Simple organic molecules such as amino acids and nucleotides can associate to form polymers. One amino acid can join with another by forming a peptide bond,

In modern biology, the condensation reactions necessary in the formation of peptide bonds are facilitated catalytically by the large subunit of the ribosome.

Peptide bond synthesis occurs in the 50S subunit ( of the ribosome ) at the peptidyl transferase center, (PTC) 4

The crucial peptide bond formation of protein synthesis is catalyzed by the ribosome in all organisms. 5

Question: How could simple organic molecules such as amino acids and nucleotides  associate to form polymers,  one amino acid  joining with another by forming a  peptide bond, if peptide bonds are sinthesized in the probably most complex protein complex known, the ribosome ?

Prebiotic peptide synthesis was likely initiated in a simple way, yet must have evolved into the contemporary complexity of the ribosome.

( Of course. There is no other explanation, since a Intelligent designer is excluded a priori. )

In order to know how the current ribosome-catalyzed reaction evolved from a primitive system, model systems based on the RNA world hypothesis with the molecules like the minihelix and tRNA were postulated. Elucidation of the evolutionary route from the simple system to the present complex ribosome is a big challenge in modern science; this gap may be filled by the concept of the proto-ribosome, which is composed of a symmetrical tRNA-like dimer. 5

The peptide synthesis hypotheses must jump over a large gap to attain ribosome-based peptide synthesis. 5

We have right at the beginning of naturalistic proposals of the origin of life the typical guess work which extends all over the key issues of origin of life, transition to the 3 domains of cells, from unicellular to multicellular , and biodiversity on earth. That seems to be a RED LINE extending through all scientific papers, which deal with key issues in biology. Naturalism is simply not tenable, the explanations all end at a dead end, where guesswork is common, and evolution of the gaps arguments.  

The origin of life requires that in an assortment of such molecules there must have been some possessing, if only to a small extent, a crucial property: the ability to catalyze reactions that lead, directly or indirectly, to production of more molecules of the catalyst itself. Production of catalysts with this special self-promoting property would be favored, and the molecules most efficient in aiding their own production would divert raw materials from the production of other substances. In this way one can envisage the gradual development of an increasingly complex chemical system of organic monomers and polymers that function together to generate more molecules of the same types, fueled by a supply of simple raw materials in the environment. Such an autocatalytic system would have some of the properties we think of as characteristic of living matter: it would comprise a far from random selection of interacting molecules; it would tend to reproduce itself; it would compete with other systems dependent on the same feedstocks; and if deprived of its feedstocks or maintained at a wrong temperature that upsets the balance of reaction rates, it would decay toward chemical equilibrium and "die."

What we see here, is a typical fairy tale story, based on no evidence, just fantasy without a shred data to back up the story. Why should someone be credule towards such a scenario ? Words like must have been, would be, one can envisage, would, would have, we think of, it would do not invoke much credibility.....

Templating mechanisms require additional catalysts to promote polymerization; without these the process is slow and inefficient and other, competing reactions prevent the formation of accurate replicas. Today, the catalytic functions that polymerize nucleotides are provided by highly specialized catalytic proteins that is, by enzymes. In the "prebiotic soup" primitive polypeptides might perhaps have provided some catalytic help. But molecules with the appropriate catalytic specificity would have remained rare unless the RNA itself were able somehow to reciprocate and favor their production. We shall come back to the reciprocal relationship between RNA synthesis and protein synthesis, which is crucially important in all living cells. But let us first consider what could be done with RNA itself, for RNA molecules can have a variety of catalytic properties, besides serving as templates for their own replication. In particular, an RNA molecule with an appropriate nucleotide sequence can act as catalyst for the accurate replication of another RNA molecule - the template - whose sequence can be arbitrary.

The special versatility of RNA molecules is thought to have enabled them to play a central role in the origin of life.

We have however to ignore what is stated above, namely that without catalysts the process is slow and inefficient which makes this hypothesis remotely possible. That makes the scenario very unlikely. And so far, the sequence would be completely random, no coded information to form life permitting proteins.

The expression of hereditary information requires extraordinarily complex machinery and proceeds from DNA to protein through an RNA intermediate. This machinery presents a central paradox: if nucleic acids are required to synthesize proteins and proteins are required, in turn, to synthesize nucleic acids, how did such a system of interdependent components ever arise? One view is that an RNA world existed on Earth before modern cells arose. According to this hypothesis, RNA both stored genetic information and catalyzed the chemical reactions in primitive cells. Only later in evolutionary time did DNA take over as the genetic material and proteins become the major catalyst and structural component of cells. Heredity is perhaps the central feature of life. Not only must a cell use raw materials to create a network of catalyzed reactions, it must do so according to an elaborate set of instructions encoded in the hereditary information. The replication of this information ensures that the complex metabolism of cells can accurately reproduce itself.  6

The emergence of life requires a way to store information, a way to duplicate it, a way to change it, and a way to convert the information through catalysis into favorable chemical reactions. But how could such a system begin to be formed?

In present-day cells the most versatile catalysts are polypeptides, composed of many different amino acids with chemically diverse side chains and, consequently, able to adopt diverse three-dimensional forms that bristle with reactive chemical groups. Polypeptides also carry information, in the order of their amino acid subunits. But there is no known way in which a polypeptide can reproduce itself by directly specifying the formation of another of precisely the same sequence.

1) http://www.bioon.com/book/biology/mboc/mboc.cgi@action=figure&fig=1-4.htm
2)http://www.bioon.com/book/biology/mboc/mboc.cgi@code=010103174953651.htm
3) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465415/
4) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2926754/
5) http://journalofcosmology.com/Abiogenesis130.html
6) Alberts, molecular biology of the cell, pg.401
7)http://www.bioon.com/book/biology/mboc/mboc.cgi@code=010102442543328.htm

DNA is a nucleic acid containing the genetic instructions to develop all living organisms. DNA is made of two anti-parallel “columns” that hold together a sequence of pairs of four available options called nucleobases. This is what God used to embed information in every system.
DNA works very similar to computers, except DNA is way more complex.
Computer binary code has only two possible elements which is only half of DNA. Now let’s apply simple math to this:
Binary code: A chain of 50 bits contains exactly (2 ^ '50') possible combinations.
That is: 1,125,899,906,842,624.
DNA code: A chain of 50 nucleobases contains exactly (4 ^ '50') possible combinations.
That is: 1,267,650,600,228,229,401,496,703,205,376
Using DNA, you can embed 1,125,899,906,842,624 times more information than binary can at only (4 ^ 50). Ask any Information Technology engineer what we could do with computers if we could use DNA encoding instead of binary.
These large numbers also tell you the probability a specific sequence has in forming by random chance.
Example:
The binary code for the number “25” is: 00011001. The probability of getting this exact sequence is:
1/256 or (1 / 2 ^ '8') or 0.00390625.
The complete human code is about 2.9 billion pairs. Now let’s calculate the probability for this sequence length:
(4 ^ 5,800,000,000) = “Unable to compute”
This number is so large, that you would need multiple pages to write it down. The probability is impossible to happen in only 4.5 billion years.

It has been calculated that it would be statistically impossible to randomly type even the first 100 characters in Shakespeare's "Hamlet". If the monkeys typed only in lower case, including the 27 spaces in the first 100 characters, the chances are 27100 (ie. one chance in 10143).
Extrapolating the amount of information in
human genome is contained in pocket books (each with 160
Pages) in order, then this corresponds toalmost 12 000
Copies.
Did you know that a scientific programmer in the
Average developes about 40 sign design program codes per day? Assuming only one of the
Amount of characters in the human genome from, then for
This programming task needs an army of over 8000 programmers
to work their entire career only to develope
this project

3'-end Cleavage and Polyadenylation.

Introduction

Most of the RNA found in our cells is built using our DNA genome as a template. In special cases, however, our cells also build RNA strands without a template. For instance, the end of (almost) every messenger RNA strand is composed of a long string of repeated adenosine nucleotides. These long poly(A) tails are not encoded in the genome. Instead, they are added after RNA polymerase finishes its normal process of transcription.

Its evident that this process and the instructions in order for this to happen after RNA polymerase finished its job,  had to be pre-programmed in DNA.

After RNA polymerase releases the RNA strand, other enzymes add the finishing touches, editing out introns, adding a cap to the front end, and building the long poly(A) tail at the other end.

Add the finishing touches, editing, adding , building the long poly (A) tail at the other end are highly ordered and precise processes. They could not have arisen without a intelligence actually instructing these sequenced and ordered proceedings, just by natural random processes.  

The Tail End

A complex of over a dozen enzymes oversees the creation of a poly(A) tail on messenger RNA molecules.

Had these enzymes not have to be fully operational right from the start ? Unless they were fully working right from the start, the process could not happen.

Several special sequences at the end of the RNA recruit this complex to the proper place. Then the RNA strand is cleaved, and about 250 adenosine nucleotides are added to the new end. The enzyme poly(A) polymerase (PAP)  is responsible for the creation of the poly(A) tail. With the help of two magnesium ions, it binds to the messenger RNA and adds adenosine nucleotides one at a time to the end of the strand.

Recruit to the proper place, cleaving, adding...... are all organized precise processes like in a regular manufacturing process in factories. How did natural process find out that magnesium ions would be required for a binding process ??

Heads and Tails

The poly(A) tail plays several important roles in the function of messenger RNA molecules. With the help of poly(A)-binding protein , it protects the end of the RNA strand, shielding it from RNA-cutting nucleases. It also assists with the transport of the messenger RNA out of the nucleus through nuclear pores. Surprisingly, the poly(A) tail, which is at the end the messenger RNA, also stimulates the start of protein synthesis by helping to recruit translation initiation factors at the front end of the RNA. Some researchers actually think that poly(A)-binding protein links the RNA strand into a big circle. This could have a very useful consequence: since the beginning of the messenger RNA is so close to the end, ribosomes that have just finished making a protein could jump immediately to the beginning and start again.  

The process of mRNA begins with transcription. Soon after RNA polymerase begins with transcription, a methylated cap is added to the 5" end. Transcription then ends to completion. Following completion, RNA polymerase releases the cap strand of mRNA. Specific nucleotide sequences in the mRNA are boung by  CstF: cleavage stimulation factor enzymes. The 3" end of the mRNA is then next moved into the right configuration for cleavage. Stabilizing factors are then added to the complex. Poly (A) polymerase now binds to the mRNA and cleaves the 3" end. The complex begins to disassociate, and the cleaved 3" end quickly degrades. Poly (A) polymerase now synthesizes the polyadenylated tail adenine to the tal. Additional proteins then add to the tail, increasing the rate at which it grows. When the tail reaches its full length, the poly (A) polymerase is signalled to stop , and the process is concluded. The processed mRNA is ready now to undergo splicing in preparation for translation.

Genetic studies in yeast indicate that virtually every subunit of the core complex is essential – for viability and for pre-mRNA processing and polyadenylation in vitro and in vivo.  

Although polyadenylation is seen in almost all organisms, it is not universal. However, the wide distribution of this modification and the fact that it is present in organisms from all three domains of life implies that the last universal common ancestor of all living organisms, it is presumed, had some form of polyadenylation system

Question: how could this extraordinarly machine like , highly precise and coordenated process  and its highly specific amazingly complex enzymes  come into existence,  considering that evolution was not a option, since it was present before the first self replicating cell existed ? Unless it was fully working with the core parts of the mechanism in place, it could not function, and the individual parts would have only function, after fully assembled , and the whole process coordenated and programmed, and all individual parts available ? My inference of the scientific evidence is, that only design is a rational explanation. Chance, or physical necessity, would be absolutely unable to encode all the information correctly, to make this mechanism work.

references, and further reading :

http://reasonandscience.heavenforum.org/t2022-3-end-cleavage-and-polyadenylation

Sir Isaac had an accomplished artisan fashion for him a small scale model of our solar system, which was to be put in a room in Newton's home when completed. The assignment was finished and installed on a large table. The workman had done a very commendable job, simulating not only the various sizes of the planets and their relative proximities, but also so constructing the model that everything rotated and orbited when a crank was turned. It was an interesting, even fascinating work, as you can imagine, particularly to anyone schooled in the sciences.
Newton's atheist-scientist friend came by for a visit. Seeing the model, he was naturally intrigued, and proceeded to examine it with undisguised admiration for the high quality of the workmanship. "My, what an exquisite thing this is!" he exclaimed. "Who made it?"
Paying little attention to him, Sir Isaac answered, "Nobody." Stopping his inspection, the visitor turned and said, "Evidently you did not understand my question. I asked who made this." Newton, enjoying himself immensely no doubt, replied in a still more serious tone, "Nobody. What you see just happened to assume the form it now has." "You must think I am a fool!" the visitor retorted heatedly, "Of course somebody made it, and he is a genius, and I would like to know who he is!" Newton then spoke to his friend in a polite yet firm way: "This thing is but a puny imitation of a much grander system whose laws you know, and I am not able to convince you that this mere toy is without a designer or maker; yet you profess to believe that the great original from which the design is taken has come into being without either designer or maker! Now tell me by what sort of reasoning do you reach such an incongruous conclusion?"

Origin of  translation of the 4 nucleic acid bases and the 20 amino acids, and the universal assignment of codons to amino acids

The cell converts the information carried in an mRNA molecule into a protein molecule. This feat of translation was a focus of attention of biologists in the late 1950s, when it was posed as the “coding problem”: how is the information in a linear sequence of nucleotides in RNA translated into the linear sequence of a chemically quite different set of units—the amino acids in proteins?

The first scientist after Watson and Crick to find a solution of the coding problem, that is the relationship between the DNA structure and protein synthesis was Russian  physicist George Gamow. Gamow published  in the October 1953 issue of Nature  a solution called the “diamond code”, an overlapping triplet code based on a combinatorial scheme in which 4 nucleotides arranged 3-at-a-time would specify 20 amino acids.  Somewhat like a language, this highly restrictive code was primarily hypothetical, based on then-current knowledge of the behavior of nucleic acids and proteins.

The concept of coding applied to genetic specificity was somewhat misleading, as translation between the four nucleic acid bases and the 20 amino acids would obey the rules of a cipher instead of a code. As Crick acknowledged years later, in linguistic analysis, ciphers generally operate on units of regular length (as in the triplet DNA scheme), whereas codes operate on units of variable length (e.g., words, phrases). But the code metaphor worked well, even though it was literally inaccurate, and in Crick’s words, “‘Genetic code’ sounds a lot more intriguing than ‘genetic cipher’.”

An mRNA Sequence Is decoded in sets of three nucleotides

Once an mRNA has been produced by transcription and processing, the information present in its nucleotide sequence is used to synthesize a protein. Transcription is simple to understand as a means of information transfer: since DNA and RNA are chemically and structurally similar, the DNA can act as a direct template for the synthesis of RNA by complementary base-pairing. As the term transcription signifies, it is as if a message written out by hand is being converted, say, into a typewritten text. The language itself and the form of the message do not change, and the symbols used are closely related.

In contrast, the conversion of the information in RNA into protein represents a translation of the information into another language that uses quite different symbols. Moreover, since there are only 4 different nucleotides in mRNA and 20 different types of amino acids in a protein, this translation cannot be accounted for by a direct one-to-one correspondence between a nucleotide in RNA and an amino acid in protein. The nucleotide sequence of a gene, through the intermediary of mRNA, is translated into the amino acid sequence of a protein. This code was deciphered in the early 1960s.

Each group of three consecutive nucleotides in RNA is called a codon, and each codon specifies either one amino acid or a stop to the translation process.

AUG is the Universal Start Codon. Nearly every organism (and every gene) that has been studied uses the three ribonucleotide sequence AUG to indicate the "START" of protein synthesis (Start Point of Translation).

Why and how should natural processes have " chosen " to insert a punctuation signal, a Universal Start Codon in order for the Ribosome to " know " where to start translation ? This is essential in order for the machinery to start translating at the correct place.

tRNA Molecules match Amino Acids to codons in mRNA

The codons in an mRNA molecule do not directly recognize the amino acids they specify: the group of three nucleotides does not, for example, bind directly to the amino acid. Rather, the translation of mRNA into protein depends on adaptor molecules that can recognize and bind both to the codon and, at another site on their surface, to the amino acid. These adaptors consist of a set of small RNA molecules known as transfer RNAs (tRNAs), each about 80 nucleotides in length.

RNA molecules can fold into precise three-dimensional structures, and the tRNA molecules provide a striking example. Four short segments of the folded tRNA are double-helical, producing a molecule that looks like a cloverleaf when drawn schematically.

Two regions of unpaired nucleotides situated at either end of the L-shaped molecule are crucial to the function of tRNA in protein synthesis. One of these regions forms the anticodon, a set of three consecutive nucleotides that pairs with the complementary codon in an mRNA molecule. The other is a short single- stranded region at the 3" end of the molecule; this is the site where the amino acid that matches the codon is attached to the tRNA. The genetic code is redundant; that is, several different codons can specify a single amino acid . This redundancy implies either that there is more than one tRNA for many of the amino acids or that some tRNA molecules can base-pair with more than one codon. In fact, both situations occur. Some amino acids have more than one tRNA and some tRNAs are constructed so that they require accurate base-pairing only at the first two positions of the codon and can tolerate a mismatch (or wobble) at the third position . See below

Question: how did the tranlation of the triplet anti codon to amino acids translation, and its assignment, arise ?  There is no physical affinity between the anti codon and the amino acids. What must be explained, is the arrangement of the codon " words " in the standard codon table which is highly non-random, redundant and optimal, and serves to translate the information into the amino acid sequence to make proteins, and the origin of the assignment of the 64 triplet codons to the 20 amino acids. That is, the origin of its translation. The origin of a alphabet through the triplet codons is one thing, but on top, it has to be translated to a other " alphabet " constituted through the 20 amino acids. That is as to explain the origin of capability to translate the english language into chinese. We have to constitute the english and chinese language and symbols first, in order to know its equivalence. That is a mental process.

Specific enzymes couple each Amino Acid to its appropriate tRNA Molecule

We now consider how each tRNA molecule becomes linked to the one amino acid in 20 that is its appropriate partner. Recognition and attachment of the correct amino acid depends on enzymes called aminoacyl-tRNA synthetases, which covalently couple each amino acid to its appropriate set of tRNA molecules

Most cells have a different synthetase enzyme for each amino acid (that is, 20 synthetases in all); one attaches glycine to all tRNAs that recognize codons for glycine, another attaches alanine to all tRNAs that recognize codons for alanine, and so on. Many bacteria, however, have fewer than 20 synthetases, and the same synthetase enzyme is responsible for coupling more than one amino acid to the appropriate tRNAs. In these cases, a single synthetase places the identical amino acid on two different types of tRNAs, only one of which has an anticodon that matches the amino acid. A second enzyme then chemically modifies each “incorrectly” attached amino acid so that it now corresponds to the anticodon displayed by its covalently linked tRNA. The synthetase-catalyzed reaction that attaches the amino acid to the 3" end of the tRNA is one of many reactions coupled to the energy-releasing hydrolysis of ATP , and it produces a high-energy bond between the tRNA and the amino acid. The energy of this bond is used at a later stage in protein
synthesis to link the amino acid covalently to the growing polypeptide chain. The aminoacyl-tRNA synthetase enzymes and the tRNAs are equally important in the decoding process

These enzymes are not gentle with tRNA molecules. The structure of glutaminyl-tRNA synthetase with its tRNA (entry 1gtr) is a good example ( see above ) The enzyme firmly grips the anticodon, spreading the three bases widely apart for better recognition. At the other end, the enzyme unpairs one base at the beginning of the chain, seen curving upward here, and kinks the long acceptor end of the chain into a tight hairpin, seen here curving downward. This places the 2' hydroxyl on the last nucleotide in the active site, where ATP and the amino acid (not present in this structure) are bound.

The tRNA and ATP fits precisely in the active site of the enzyme, and the structure is configured and designed to function in a finely tuned manner. How could such a functional device be the result of random unguided forces and chemical reactions without a end goal ?

Editing by tRNA Synthetases Ensures Accuracy

Several mechanisms working together ensure that the tRNA synthetase links the correct amino acid to each tRNA. The synthetase must first select the correct amino acid, and most synthetases do so by a two-step mechanism. First, the correct amino acid has the highest affinity for the active-site pocket of its synthetase and is therefore favored over the other 19. In particular, amino acids larger than the correct one are effectively excluded from the active site. However, accurate discrimination between two similar amino acids, such as isoleucine and valine (which differ by only a methyl group), is very difficult to achieve by a one-step recognition mechanism. A second discrimination step occurs after the amino acid has been covalently linked to AMP. When tRNA binds the synthetase, it tries to force the amino acid into a second pocket in the synthetase, the precise dimensions of which exclude the correct amino acid but allow access by closely related amino acids. Once an amino acid enters this editing pocket, it is hydrolyzed from the AMP (or from the tRNA itself if the aminoacyl-tRNA bond has already formed), and is released from the enzyme. This hydrolytic editing, which is analogous to the exonucleolytic proofreading by DNA polymerases , raises the overall accuracy of tRNA charging to approximately one mistake in 40,000 couplings.

This is a amazing error proofreading technique, which adds to other repair mechanisms in the cell. Once again the question arises : How could these precise molecular machines have arisen by natural means, without intelligence involved ? This seems to me one more amazing example of highly sophisticated nano molecular machinery designed to fullfill its task with high degree of fidelity and error minimization, which can arise only by the forsight of a incredibly intelligent creator.

http://reasonandscience.heavenforum.org/t2057-origin-of-translation-of-the-4-nucleic-acid-bases-and-the-20-amino-acids-and-the-universal-assignment-of-codons-to-amino-acids#3528

Proteins: striking evidence of design

Paper Reports that Amino Acids Used by Life Are Finely Tuned to Explore "Chemistry Space"

A recent paper in Nature's journal Scientific Reports, "Extraordinarily Adaptive Properties of the Genetically Encoded Amino Acids," 3  has found that the twenty amino acids used by life are finely tuned to explore "chemistry space" and allow for maximal chemical reactions. Considering that this is a technical paper, they give an uncommonly lucid and concise explanation of what they did:

We drew 108 random sets of 20 amino acids from our library of 1913 structures and compared their coverage of three chemical properties: size, charge, and hydrophobicity, to the standard amino acid alphabet. We measured how often the random sets demonstrated better coverage of chemistry space in one or more, two or more, or all three properties. In doing so, we found that better sets were extremely rare. In fact, when examining all three properties simultaneously, we detected only six sets with better coverage out of the 108 possibilities tested. That's quite striking: out of 100 million different sets of twenty amino acids that they measured, only six are better able to explore "chemistry space" than the twenty amino acids that life uses. That suggests that life's set of amino acids is finely tuned to one part in 16 million. Of course they only looked at three factors -- size, charge, and hydrophobicity. When we consider other properties of amino acids, perhaps our set will turn out to be the best:

Bruce Alberts writes in Molecular biology of the cell :

Since each of the 20 amino acids is chemically distinct and each can, in principle, occur at any position in a protein chain, there are 20 x 20 x 20 x 20 = 160,000 different possible polypeptide chains four amino acids long, or 20n different possible polypeptide chains n amino acids long. For a typical protein length of about 300 amino acids, a cell could theoretically make more than 10^390  different pollpeptide chains. This is such an enormous number that to produce just one molecule of each kind would require many more atoms than exist in the universe. Only a very small fraction of this vast set of conceivable polypeptide chains would adopt a single, stable three-dimensional conformation-by some estimates, less than one in a billion. And yet the vast majority of proteins present in cells adopt unique and stable conformations. How is this possible?

The complexity of living organisms is staggering, and it is quite sobering to note that we currently lack even the tiniest hint of what the function might be for more than 10,000 of the proteins that have thus far been identified in the human genome. There are certainly enormous challenges ahead for the next generation of cell biologists, with no shortage of fascinating mysteries to solve.

Now comes Alberts  striking explanation of how the right sequence arised :

The answer Iies in natural selection. A protein with an unpredictably variable structure and biochemical activity is unlikely to help the survival of a cell that contains it. Such
proteins would therefore have been eliminated by natural selection through the enormously long trial-and-error process that underlies biological evolution. Because evolution has selected for protein function in living organisms, the amino acid sequence of most present-day proteins is such that a single conformation is extremely stable. In addition, this conformation has its chemical properties finely tuned to enable the protein to perform a particular catalltic or structural function in the cell. Proteins are so precisely built that the change of even a few atoms in one amino acid can sometimes disrupt the structure of the whole molecule so severelv that all function is lost.

Proteins are not rigid lumps of material. They often have precisely engineered moving parts whose mechanical actions are coupled to chemical events. It is this coupling of chemistry and movement that gives proteins the extraordinary capabilities that underlie the dynamic processes in living cells

Now think for a moment . It seems that natural selection ( does that not sound soooo scientific and trustworthy ?! ) is the key answer to any phenomena in biology, where there is no scientific evidence to make a empricial claim. Much has been written about the fact that natural selection cannot produce coded information. Alberts short explanation is a prima facie example about how main stream sciencists  make without hesitation " just so "  claims without being able to provide a shred of evidence, just in order to mantain a paradigm on which the scientific establishment relies, where evolution is THE answer to almost every biochemical phenomena. Fact is that precision, coded information, stability, interdependence and irreducible complexity etc. are products of intelligent minds. The author seems also to forget that natural selection cannot occur before the first living cell replicates. Several hundred proteins had to be already in place and fully operating in order to make even the simplest life possible  

Amino acids link together when the amino group of one amino acid bonds to the carboxyl group of another. Notice that water is a by-product of the reaction (called a condensation reaction).

Stephen Meyer writes  in Signature of the cell:

Consider the way this combinatorial problem might play itself out in the case of proteins in a hypothetical prebiotic soup. To construct even one short protein molecule of 150 amino acids by chance within the prebiotic soup there are several combinatorial problems—probabilistic hurdles—to overcome. First, all amino acids must form a chemical bond known as a peptide bond when joining with other amino acids in the protein chain

How rare, or common, are the functional sequences of amino acids  among all the possible sequences of amino acids in a chain of any given length?

Douglas Axe answered this question in 2004 3 , and  Axe was able to make a careful estimate of the ratio of (a) the number of 150-amino-acid sequences that can perform that particular function to (b) the whole set of possible amino-acid sequences of this length. Axe estimated this ratio to be 1 to 10^77.

This was a staggering number, and it suggested that a random process would have great difficulty generating a protein with that particular function by chance. But I didn't want to know just the likelihood of finding a protein with a particular function within a space of combinatorial possibilities. I wanted to know the odds of finding any functional protein whatsoever within such a space. That number would make it possible to evaluate chance-based origin-of-life scenarios, to assess the probability that a single protein—any working protein—would have arisen by chance on the early earth.

Fortunately, Axe's work provided this number as well.17 Axe knew that in nature  proteins perform many specific functions. He also knew that in order to perform these functions their amino-acid chains must first fold into stable three-dimensional structures. Thus, before he estimated the frequency of sequences performing a specific (beta-lactamase) function, he first performed experiments that enabled him to estimate the frequency of sequences that will produce stable folds. On the basis of his experimental results, he calculated the ratio of (a) the number of 150-amino-acid sequences capable of folding into stable "function-ready" structures to (b) the whole set of possible amino-acid sequences of that length. He determined that ratio to be 1 to 10^74.

In other words, a random process producing amino-acid chains of this length would stumble onto a functional protein only about once in every 10^74 attempts.

When one considers that Robert Sauer was working on a shorter protein of 100 amino acids, Axe's number might seem a bit less prohibitively improbable. Nevertheless, it still represents a startlingly small probability. In conversations with me, Axe has compared the odds of producing a functional protein sequence of modest (150-amino-acid) length at random to the odds of finding a single marked atom out of all the atoms in our galaxy via a blind and undirected search. Believe it or not, the odds of finding the marked atom in our galaxy are markedly better (about a billion times better) than those of finding a functional protein among all the sequences of corresponding length.

more:

http://evidenceofgodarationalbelief.blogspot.com.br/2015/06/proteins-striking-evidence-of-design.html

There is no selective advantage until you get the final function

Lenksy et al published a article in Nature 8 to which Luskin of the Discovery institute replied upon which Richard B. Hoppe at  the Panda's thumb in his article desperately dissing Avida  replied again.   The debate is interesting as it touches some core questions of the evolution x intelligent design controversy.

Hoppe writes following as reply to Luskin:

Co-option and modification of existing structures is a ubiquitous phenomenon in evolution at levels ranging from molecular mechanisms to high-level structures like wings.

this is a confortable way to avoid the relevant  questions, and Hoppe keeps avoiding them despite Luskin  pointed  out that its not only about modification and co-option of existing parts, but  how  de-novo genes evolved to start the make of new features. How did new structures and new kind of cells begin to evolve ?

Biological structures are well organized , structured, and build up like human made factories and machines. The process takes place fully automated inside the cell. The process of protein production ,starting from the genes, is extremely complex, and several steps are required.  Bruce Alberts writes in "The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists,"  :

But, as it turns out, we can walk and we can talk because the chemistry that makes life possible is much more elaborate and sophisticated than anything we  had ever considered. We now know that nearly every major process in a cell is carried out by assemblies of 10 or more protein molecules. And, as it carries out its biological functions, each of these protein assemblies interacts with several other large complexes of proteins. Indeed, the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines.

Ordered Movements Drive Protein Machines
Why do we call the large protein assemblies that underlie cell function protein machines? Precisely because, like the machines invented by humans to deal efficiently with the macroscopic world, these protein assemblies contain highly coordinated moving parts. Within each protein assembly, intermolecular collisions are not only restricted to a small set of possibilities, but reaction C depends on reaction B, which in turn depends on reaction A—just as it would in a machine of our common experience.

Underlying this highly organized activity are ordered conformational changes in one or more proteins driven by nucleoside triphosphate hydrolysis (or by other sources of energy, such as an ion gradient).the nearly ubiquitous use of energy-driven conformational changes to promote the local assembly of protein complexes, thereby creating a high degree of order in the cell, has become universally recognized.

Many different types of chemical reactions are required to produce a properly folded protein from the information contained in a gene

The journey from gene to protein is complex and tightly controlled within each cell. It consists of two major steps: transcription and translation. Together, transcription and translation are known as gene expression.

The cell sends activator proteins to the site of the gene that needs to be switched on, which then jump-starts the RNA polymerase machine by removing a plug which blocks the DNA's entrance to the machine.  The DNA strands do shift position so that the DNA lines up with the entrance to the RNA polymerase. Once these two movements have occurred and the DNA strands are in position, the RNA polymerase machine gets to work melting them out, so that the information they contain can be processed to produce mRNA 2 The process follows then after INITIATION OF TRANSCRIPTION through RNA polymerase enzyme complexes, the mRNA is  capped through Post-transcriptional modifications by several different enzymes ,  ELONGATION provides the main transcription process from DNA to mRNA, furthermore  SPLICING and CLEAVAGE ,  polyadenylation where a long string of repeated adenosine nucleotides is added,  AND TERMINATION through over a dozen different enzymes,    EXPORT FROM THE NUCLEUS TO THE CYTOSOL ( must be actively transported through the Nuclear Pore Complex channel in a controlled process that is selective and energy dependent 3 )  INITIATION OF PROTEIN SYNTHESIS (TRANSLATION) in the Ribosome in a enormously complex process,  COMPLETION OF PROTEIN SYNTHESIS AND PROTEIN FOLDING through chaperone enzymes. From there the proteins are transported by specialized proteins to the end destination. Most of these processes require ATP, the energy fuel inside the cell.  

Each of these steps requires extremely complex proteins and enzymes, the working horses of the cell, which work like robots in a assembly line in  highly regulated precise steps, and  these machines are by themself encoded in the genome. Not only is the information to make them stored in the genome. But these machines require further , different proteins and enzymes in order to be prepared and assembled. And the information for these processes taking place is also recorded in the genome. And a few genes contain the information to produce  molecules that help the cell assemble proteins, that is, the build up of the whole machinery must also be pre-programmed, and happen in a sequencial special, ordered manner. Many different processes need to happen at the same time, driven by ATP, which means, the ATPase powerhouse and proton gradient and membranes must be extant since the beginning. In the same way, that we build a machine, each part must be mounted at the right place, at the right time, in the right sequence and order, and the parts must fit together in a functional and precise way. And the right materials are needed. In a car engine, the pistons must be made by the right temperature resistant metals, and so it is also inside the cells. Most enzymes have reaction centers , where special substrates and reacton factors are required to exercise their specific reactions, and many enzymes require the presence of other compounds - cofactors - before their catalytic activity can be exerted. 5 How could natural mechnisms " figure out " what special materials, like metal-ion-activators, are required to produce given reaction ? Trial and error ? Furthermore, following is required:

C1: Availability. Among the parts available for recruitment to form a biological system consisting of multiple parts, there would need to be ones capable of performing the highly specialized tasks of the specific system, even though all of the items serve some other function or no function in another system where they were recruited from.
C2: Synchronization. The availability of these parts would have to be synchronized so that at some point, either individually or in combination, they are all available at the same time.
C3: Localization. The selected parts must all be made available at the same ‘construction site,’ perhaps not simultaneously but certainly at the time they are needed.
C4: Coordination.The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if the subunits  are put together in the right order, they also need to interface correctly. The parts must be coordinated in just the right way: even if all of the parts of a ribosome are available at the right time, it is clear that the majority of ways of assembling them will be non-functional or irrelevant.
C5: Interface compatibility. The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if the subunits  are put together in the right order, they also need to interface correctly.

So these further questions arise :

For what reason would natural processes produce the machines like for example Ribonuclease P, which processes pre-tRNA, which contains additional tRNA sequences at both the 5’ and 3’-ends and need to be removed ? For what reason would natural processes produce tRNA which are required inside the Ribosome , the central molecule in the translation process ?
P Ribonuclease P would have no function by its own. tRNA has no function by its own. The Ribosome has no function by its own. These individual parts exercise only their function, if interlocked and working in a interdependent way together. Supposing everything would start through natural processes, how could these machines arise separately, in a stepwise fashion, if they do not have any use by their own ? Its not that we can argue that we simply don't know yet. What we do know, permits us rationally to infer, that naturalistic explanations are entirely inadequate to explain the phenomena in question.  A initial blueprint is required, where the whole process is pre-programmed, which is the case in the genome, where all the information to build a cell is stored, and the whole process has to start all at once. That seems to be best explained through a intelligent designer.  

As uncommondescent  puts it:

ID is not proposing “God” to paper over a gap in current scientific explanation. Instead ID theorists start from empirically observed, reliable, known facts and generally accepted principles of scientific reasoning:
(a) Intelligent designers exist and act in the world.
(b) When they do so, as a rule, they leave reliable signs of such intelligent action behind.
(c) Indeed, for many of the signs in question such as CSI and IC, intelligent agents are the only observed cause of such effects, and chance + necessity (the alternative) is not a plausible source, because the islands of function are far too sparse in the space of possible relevant configurations.
(d) On the general principle of science, that “like causes like,” we are therefore entitled to infer from sign to the signified: intelligent action.
(e) This conclusion is, of course, subject to falsification if it can be shown that undirected chance + mechanical forces do give rise to CSI or IC. Thus, ID is falsifiable in principle but well supported in fact.

In sum, ID is indeed a legitimate scientific endeavor: the science that studies signs of intelligence.

read more:

http://evidenceofgodarationalbelief.blogspot.com.br/2015/07/there-is-no-selective-advantage-until.html

The proposal of intelligent design in nature is a littlebit older than most might expect:

[Cicero, THE NATURE OF THE GODS BK II Ch XXXVII, C1 BC, as trans Yonge (Harper & Bros., 1877), pp. 289 - 90.]

. . . Is it possible for any man to behold these things, and yet imagine that certain solid and individual bodies move by their natural force and gravitation, and that a world so beautifully adorned was made by their fortuitous concourse? He who believes this may as well believe that if a great quantity of the one-and-twenty letters, composed either of gold or any other matter, were thrown upon the ground, they would fall into such order as legibly to form the Annals of Ennius. I doubt whether fortune could make a single verse of them. How, therefore, can these people assert that the world was made by the fortuitous concourse of atoms, which have no color, no quality—which the Greeks call [poiotes], no sense?

http://evidenceofgodarationalbelief.blogspot.com.br/2015/07/the-proposal-of-intelligent-design-in.html#sthash.4RDlRW5m.dpuf

Transfer RNA, and its biogenesis, best explained through design

http://reasonandscience.heavenforum.org/t2070-transfer-rna-and-its-biogenesis?highlight=Transfer+RNA

Transfer RNA is an ancient molecule, central to every task a cell performs and thus essential to all life. The enzyme is one of only two ribozymes which can be found in all kingdoms of life (Bacteria, Archaea, and Eukarya) The three major RNAs involved in the flow of genetic information are messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). All these RNAs participate in the protein-synthesizing pathway in cells. tRNA has two distinct characteristics. It carries an anticodon corresponding to the mRNA codon and it binds to the corresponding amino acid in a reaction catalyzed by a specific aminoacyl-tRNA synthetase.  tRNA's are therefore essential components in the sequential information flow process from DNA to mRNA to proteins. No tRNA, no proteins, no advanced life.  tRNA's are transcribed and processed in a extremely complex manner by several holoenzymes and proteins. tRNA is a key bridging molecule between ribonucleotide information (RNA world) and peptide information (protein world). Therefore, tracing the  origin of tRNA molecules is likely to cast light on the processes that led to the establishment of the central processes of life.



tRNA's are very specific molecules, and the " made of " follows several steps, requiring a significant number of proteins and enzymes, which are often made of several subunits and ainded by essential co-factors and metals.

The challenge for evolution to the fact, that biological systems incorporate several essential parts, that cannot be eliminated without losing the core function of the  system in question, and that these parts have no function of their own and could therefore not be product of natural mechanisms, of gradual evolutionary steps,  is in my view more severe than most philosophers of science  and scientists like Behe exemplify. In systems of enormous biological complexity like the cell,  thousands of parts are essential , many more parts, than the well known examples like the flagellum. Irreducibility is found from the highest level of biological organisation and systems, to  a single DNA deoxyribonucleotide, which loses  function if reduced to its single components, the bases, phosphate or sugar. Just take off one, and the molecule loses its function. Same goes for the cell. Take off one building block, like the spindle apparatus, and mitosis and cell division is not possible, and life could not reproduce itself.

The make of proteins is similar to the make of cars in a car factory. If the grinder machine to make the motor pistons  has a mal function,  the pistons cannot be finished,  the car's motor block cannot be  assembled with all parts, and the motor would not function without that essential part. Amongst thousands of parts, just a tiny one will compromise the function of the whole system. In biological nano-factories, the solutions to overcome problems like damage must all be pre-programmed, and the repair "working horses" to resolve the problem must be ready in place and "know" what to do how, and when. If a roboter in a factory assembly line fails, employees are ready to detect the error and make the repair . In the cell, the mal function of any  part even as tiny and irrelevant as it might seem, can be fatal, and if the repair mechanisms are not functioning correctly and fully in place right from the start, the repair can't be done, and life ceases.  These repair enzymes which cleave, join, add, replace etc. must be programmed in order to function properly right from the start. Aberrantly processed pre-tRNAs for example are eliminated through a nuclear surveillance pathway by degradation of their 3′ ends, whereas mature tRNAs lacking modifications are degraded from their 5′ends in the cytosol.  

B.Alberts writes:  Eucaryotic tRNAs are transcribed from DNA by RNA Polymerase III. Afterwards, tRNA's are covalently modified before they are allowed to exit from the nucleus. Both bacterial and eucaryotic tRNAs are typically synthesized as larger precursor tRNAs, which are then trimmed to produce the mature tRNA. In addition, some tRNA precursors (from both bacteria and eucaryotes) contain introns that must be spliced out.  tRNA splicing uses a cut-and-paste mechanism that is catalyzed by proteins.  Trimming and splicing both require the precursor tRNA to be correctly folded in its cloverleaf configuration. Because misfolded tRNA precursors will not be processed properly, the trimming and splicing reactions are thought to act as quality- control steps in the generation of tRNA's. All tRNA's are modified chemically—nearly 1 in 10 nucleotides in each mature tRNA molecule is an altered version of a standard G, U, C, or A ribonucleotide. Over 50 different types of tRNA modifications are known. Some of the modified nucleotides—most notably inosine, produced by the deamination of adenosine—affect the conformation and basepairing of the anticodon and thereby facilitate the recognition of the appropriate mRNA codon by the tRNA molecule.  This means, if the basepairing of the codons of mRNA with the anticodons of tRNA does not fit and match correctly,it will affect the accuracy with which the correct amino acid is attached to the tRNA , or it is eventually not even capable of identifiyng the right tRNA. In other words, its like the key that must fit in the door lock. It it does not fit, the door will not open. If the match of the codons do not fit precisely into the anticodon's of the mRNA, the precise assignment of the amino acid is compromised, or not possible, and proteic amino acid chains cannot be sinthesized successfully. So that is another keystep.

The processing into mature tRNA  happens through  the removal, addition and chemical modification of nucleotides. Processing for some tRNA involves

1) removal of the leader sequence at the 5 prime end
2) replacement of two nucleotides at the 3 prime end by the sequence CCA (with which all mature tRNA molecules terminate)
3) chemical modification of certain bases and  
4) excision of  introns. The mature tRNA is often diagrammed as a flattened cloverleaf which clearly shows the base pairing between self-complementary stretches in the molecule.

Each of these steps is a essential requirement for the synthesis of tRNA, if one doesn't do its job properly, tRNA cannot be made. The biosynthesis of tRNA is a irreducible complex process.



To give a example in tRNA maturation in Homo sapiens, following Enzymatic  complexes are involved in the process:

Proteins:

CCA tRNA nucleotidyltransferase 1 ,
Zinc phosphodiesterase ELAC protein 2

and  Enzymatic  complexes:

Ribonuclease P
tRNA ligase complex
tRNA-splicing endonuclease

CCA tRNA nucleotidyltransferase 1 uses a Magnesium co-factor, Zinc phosphodiesterase ELAC protein 2 uses zinc as co-factor,  Human nuclear RNase P consists of 10 Protein subunits and one RNA subunit, the tRNA ligase complex uses 6 protein components, and tRNA-splicing endonuclease uses 4 protein subunits. In total 20 proteins subunits, one RNA subunit, and 2 different co-factors.

Each of these protein complexes exercises very precise coordinated tasks, which all have to be pre-programmed in the genome. Lets have a look at the special capabilities:

Ribonuclease P has the function  to cleave off an extra, or precursor, sequence of RNA on tRNA molecules. For ( supposedly )  billions of years and still to this day, the function of RNase P -- found in nearly all organisms, from bacteria to humans -- has been to cleave transfer tRNA. If the tRNA is not cleaved, it is not useful to the cell.

Once RNase P recognizes tRNA, it docks and, assisted by metal ions, cuts one chemical bond.

This happens in  a stepwise, orderly process, where the enzyme " knows " exactly where to cleave with a precise target. How could such a function have arisen ? trial and error ? coding the genetic instructions until the right sequence permitted to cleave off the right nucleotides ? why at all would some unknown mechanism do this  trial and error ? Or had chemicals a end goal ? or the goal of " survival of the fittest " ( despite the fact that they are not alive ) ? if the enzyme cleaved too much or too less, tRNA could not be used properly, so its function had to be programmed correctly in the genome right from the start, otherwise, well, no life.... Not only the cleavage at the right place has to be explained, but also the arise of this sophisticated mechanism, which follows precise , complex steps in a machinelike manner.

In the paper The enigma of ribonuclease P evolution, the authors,  Enno  Roland K. Hartmann write :

The simplest interpretation is that RNase P has an ‘RNA-alone’ origin and progenitors of Bacteria and Archaea diverged very early in evolution and then pursued completely different strategies in the recruitment of protein subunits during the transition from the ‘RNA-alone’ to the ‘RNA-protein’ state of the enzyme.’


The authors write about recruitment and strategies. Its interesting that they atribute  mental and conscient activities to chemical processes and reactions. But as such, they have no end goal, so how does it make sense to write in these terms ? Furthermore, recruitment of what ? of extant subunits ? were they readily available to choose from in the surrounding ?  how could RNase know which ones to select  and  how to incorporate them correctly in its system ? Is that not one more nice example of pseudo science ?

As Luskin of the discovery institute writes : When certain biologists discuss the early stages of life there is a tendency to think too vaguely. They see a biological wonder before them and they tell a story about how it might have come to be. They may even draw a picture to explain what they mean. Indeed, the story seems plausible enough, until you zoom in to look at the details. I don't mean to demean the intelligence of these biologists. It's just that it appears they haven't considered things as completely as they should. Like a cartoon drawing, the basic idea is portrayed, but there is nothing but blank space where the profound detail of biological processes should be.

Would these five conditions not have to be met in order to recruit and insert the subunits into the system ?


C1: Availability. Among the parts available for recruitment to form the system, there would need to be ones capable of performing the highly specialized tasks of individual parts, even though all of these items serve some other function or no function.

C2: Synchronization. The availability of these parts would have to be synchronized so that at some point, either individually or in combination, they are all available at the same time.

C3: Localization. The selected parts must all be made available at the same ‘construction site,’ perhaps not simultaneously but certainly at the time they are needed.

C4: Coordination. The parts must be coordinated in just the right way: even if all of the parts of a system are available at the right time, it is clear that the majority of ways of assembling them will be non-functional or irrelevant.

C5: Interface compatibility. The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if sub systems or parts are put together in the right order, they also need to interface correctly.

( Agents Under Fire: Materialism and the Rationality of Science, pgs. 104-105 (Rowman & Littlefield, 2004). HT: ENV.)

In the paper tRNA-nucleotidyltransferases: Highly unusual RNA polymerases with vital functions, the authors Stefan Vörtler, and Mario Mörl write:

tRNA-nucleotidyltransferases are fascinating and unusual RNA polymerases responsible for the synthesis of the nucleotide triplet CCA at the 3′-terminus of tRNAs. As this CCA end represents an essential functional element for aminoacylation and translation, these polymerases (CCA-adding enzymes) are of vital importance in all organisms. Elucidation of the role of the CCA enzyme in the cellular network of tRNA quality control and the identities of the RNases accompanying the CCA enzyme constitute new questions that warrant active investigation.

CCA-adding enzymes obviously can count until three: after the addition of three nucleotides, the polymerization reaction is efficiently stopped.  Additionally, and most interestingly, the CCA-adding enzymes recognize if nucleotides are previously added to a tRNA primer and incorporate then only the missing ones, completing thereby the CCA triplet. A tRNA that carries already the first C residue of the CCA terminus is elongated only by one C and one A, while on a tRNA ending with CC, only the terminal A residue is added. This feature shows that CCA-adding enzymes are not only responsible for the de novo synthesis of CCA ends but have an important maintenance and repair function for tRNA ends. This stringent sequence and length control of the tRNA CCA end reflects the recognition requirements for aminoacylation and translation.

( This is amazing. How did it " learn "  that feat ? trial and error ?  )

Furthermore, positioning in the ribosome during translation and even peptide release from the ribosome depend on an intact CCA end, which is critical for water coordination and efficient hydrolysis of the ester bound translation product.

These facts indicate that an accurate CCA end participates, beyond simple recognition and binding, as an integral part in several reaction mechanisms and is therefore of vital importance for the cell.

Surprisingly, these polymerases with such unusual features evolved twice in evolution, leading to classes 1 and 2 CCA-adding enzymes

Convergence is evidence against evolution, and the author supposes evolution prior the existence of a replicating cell.......

While class 1 is exclusively found in archaea, class 2 tRNA-nucleotidyltransferases are present in eukaryotes and bacteria, where they fulfill identical functions. Structural organization of classes 1 and 2 CCA-adding enzymes. While both enzyme versions have a hook-like shape of similar size, the allocation of secondary structure elements in neck, body and tail domains are quite different. In class 1 enzymes, these regions contain alpha-helical as well as beta-sheet elements. Class 2, on the other hand, has exclusively alpha-helical structures in these domains. The catalytic cores, located in head and neck domains of both enzyme versions, are indicated by the grey arrows. The rainbow color bar represents the consecutive protein regions from N- (blue) to C-terminus (red).

One of the most fascinating aspects of both classes of tRNA-nucleotidyltransferases is the fact that CCA-addition does not require an external nucleic acid as a template – somehow these enzymes “know” when to incorporate which nucleotide.

Indeed. Or maybe the intelligent designer programmed them in order for them to know ?? what makes more sense, inanimated matter to know something, or a intelligent creator programming these enzymes to exercise special tasks and functions upon pre-programming ?

Crystal structures of both classes 1 and 2 enzymes revealed a set of highly conserved amino acid residues located in the single nucleotide binding pocket that interact with the incoming nucleotide by forming Watson/Crick-like hydrogen bonds.

So these enzymes do not only " know " when to incorporate which nucleotide, but also " know " how to bind each nucleotide to the next through hydrogen bonds..... amazing.

Structural organization of classes 1 and 2 CCA-adding enzymes. While both enzyme versions have a hook-like shape of similar size, the allocation of secondary structure elements in neck, body and tail domains are quite different. In class 1 enzymes, these regions contain alpha-helical as well as beta-sheet elements. Class 2, on the other hand, has exclusively alpha-helical structures in these domains. The catalytic cores, located in head and neck domains of both enzyme versions, are indicated by the grey arrows. The rainbow color bar represents the consecutive protein regions from N- (blue) to C-terminus (red).

One of the most fascinating aspects of both classes of tRNA-nucleotidyltransferases is the fact that CCA-addition does not require an external nucleic acid as a template – somehow these enzymes “know” when to incorporate which nucleotide.

Indeed. Isn't that a magnificient example and evidence of design ?

Crystal structures of both classes 1 and 2 enzymes revealed a set of highly conserved amino acid residues located in the single nucleotide binding pocket that interact with the incoming nucleotide by forming Watson/Crick-like hydrogen bonds

So these enzymes do not only " know " when to incorporate which nucleotide, but also " know " how to bind each nucleotide to the next through hydrogen bonds..... amazing.

So the question  arises : Did natural processes have foresight of the end product, tRNA, to make these highly specific nano robot - like molecular machines which  remove, add and  modify  the nucleotides of tRNA? If not, how could they have emerged, since without end goal, there would be no function for them ? neither could they have been co-opted because of their high specificity and uniqueness, required only in these molecular machines? They are specifically made for the production and make of tRNA's. Isnt the make of tRNA not another prime example of intelligent design ?

My contemption is once more that naturalistic explanations are  inadequate to explain this sophisticated mechanism in question. While a designer, which had the intention to make life, could have well invented the process, and set it up.

Chromosome condensation, amazing evidence of design

Imagine trying to stuff about 10,000 miles of spaghetti inside a basketball.  Then, if that was not difficult enough, attempt to find a unique one inch segment of pasta from the middle of this mess, or try to duplicate, untangle and separate individual strings to opposite ends.  This simple analogy illustrates some of the daunting tasks associated with the transcription, repair and replication of the nearly 2 meters of DNA that is packaged into the confines of a tiny eukaryotic nucleus.  The solution to each of these problems lies in the assembly of the eukaryotic genome into chromatin, a structural polymer that not only solves the basic packaging problem, but also provides a dynamic platform that controls all DNA-mediated processes within the nucleus.

Every second, the cells constituting our bodies are replaced through cell division.An adult human consists of about 50,000 billion cells, 1% of which die and are replaced by cell division every day. In order to ensure cell survival and controlled growth of these new cells, the genetic information, stored in DNA molecules, must first be correctly copied and then accurately distributed during cell division. Moreover, to fully ascertain that the new cells will contain the same genetic information as the parental cells, any damage to the DNA, which is organised into several chromosomes, must be repaired.

Quite a bit is known about two of these complexes. One of them, cohesin, keeps the DNA copies together such that they do not separate too early; while the other, condensin, makes the chromosomes more compact, making the separation easier.

Packing ratio - the length of DNA divided by the length into which it is packaged

The shortest human chromosome contains 4.6 x 107 bp of DNA (about 10 times the genome size of E. coli). This is equivalent to 14,000 µm of extended DNA, or about 2 meters. In its most condensed state during mitosis, the chromosome is about 2 µm long. This gives a packing ratio of 7000 (14,000/2).

To achieve the overall packing ratio, DNA is not packaged directly into final structure of chromatin. Instead, it contains several hierarchies of organization.

The first level of packing is achieved by the winding of DNA around a protein core to produce a "bead-like" structure called a nucleosome. This gives a packing ratio of about 6. This structure is invariant in both the euchromatin and heterochromatin of all chromosomes.

The second level of packing is the coiling of beads in a helical structure called the 30 nm fiber that is found in both interphase chromatin and mitotic chromosomes. This structure increases the packing ratio to about 40.

The final packaging occurs when the fiber is organized in loops, scaffolds and domains that give a final packing ratio of about 1000 in interphase chromosomes and about 7,000 in mitotic chromosomes.

Thats a amazing change , from a ratio of 6, to 7.000 !!

To fit 2 meters of DNA into a tiny nucleus is a monumental engineering feat. DNA is highly compacted yet has to be instantly available to rapidly make proteins in neurons with a momentary change of thought. This regulation is different in each type of cell. . It has been known for some time that the shape of proteins determines their function and the folding is very complex involving four levels of folding .

Condensins: universal organizers of chromosomes with diverse functions

Condensins are multisubunit protein complexes that play a fundamental role in the structural and functional organization of chromosomes in the three domains of life.   It is a molecular machine that helps to condense and package chromosomes for cell replication. It is a five subunit complex, and is “the key molecular machine of chromosome condensation.

Condensin produces “supercoils” of DNA, one of many steps in packing the delicate DNA strands into a hierarchy of coils that results in a densely-packed chromosome.  “It is not entirely clear how the DNA is held in this supercoiled state,” , “but several studies suggest that the V-shaped arms of the condensin complex may loop and clamp the DNA in place.”  This clamping is “rapid and reversible.”  Scientists watching the process in both bacteria and humans are “showing that both vertebrate and bacterial condensins drive DNA compaction in an ATP-dependent fashion with a surprising level of co-operativity that was not fully appreciated.” The condensin molecules work as a team; if not enough condensin is around, nothing happens.      condensin is just one of many enzymes involved in chromosome formation.  

The chromosomal condensin complex is a major molecular effector of chromosome condensation and segregation in diverse organisms ranging from bacteria to humans. Condensin is a large, evolutionarily conserved, multisubunit protein assembly composed of dimers of the structural maintenance of chromosomes (SMC) family of ATPases, clasped into topologically closed rings by accessory subunits.

At the end of S phase, the immensely long DNA molecules of the sister chromatids are tangled in a mass of partially catenated DNA and proteins. Any attempt to pull the sisters apart in this state would undoubtedly lead to breaks in the chromosomes. To avoid this disaster, the cell devotes a great deal of energy in early mitosis to gradually reorganizing the sister chromatids into relatively short, distinct structures that can be pulled apart more easily in anaphase. These chromosomal changes involve two processes: chromosome condensation, in which the chromatids are dramatically compacted; and sister-chromatid resolution, whereby the two sisters are resolved into distinct, separable units

How could these nano machines arise by natural means, in a gradual stepwise manner ? These molecular machines had to be in place when life began, since they are essential. Mutation and natural selection is not a conceivable mechanism at this stage.  Unless someone can demonstrate a series of small steps to climb mount unprobable (as Richard Dawkins calls the challenge of evolving complex, information-rich, functional biological structures), this is wishful thinking.  The mountain is not a series of small steps, but a  cliff with slippery vertical walls.  And why would a mindless molecule even want to go climb uphill against its natural inclinations? The discoveries in biochemistry are making evolution increasingly untenable.  Here we see highly complex molecules, made up of building blocks (amino acids) arranged in precise sequences to build functioning machines.  The complexity is mind-boggling, and it exists all the way down in the very simplest single-celled life forms, with no precursors.  Without these machines, the cell could not divide. Proposing intelligent design is not a argument of ignorance. We know that intelligent minds are capable of projecting complex machines where ideas of problem solutions are required. Intelligent minds are able to store large quantities of information into small spaces, computer chips are a good example. As conclusion, Intelligent design constitutes the best, most causally adequate, explanation for the existence of these highly complex, essential nano machines in the cell.

http://reasonandscience.heavenforum.org/t2086-chromosome-condensation-amazing-evidence-of-design#3646

Evolve me a Cilium

The flagellum is a prima facie example of intelligent design, which has become well known since Behe's book Darwins Blackbox. In his following book, The edge of evolution, Behe describes in detail the Cilia, the non motile sister of the flagellum. It is less known.  What science has discovered  in recent years, is  a serious challenge for proponents of naturalistic origins.  Jon Lieff describes the amazing capabilities of the cilia:

Given the sophistication of the cilium’s function it is not surprising the cilium is one of the most structurally complex organelles in the cell.  More recently it has been found to be critical for cellular communication and signaling in fetal development of all cells.

Cilia are composed of multiple interacting parts, all of which must be present for the cilium to work. A single cilium is made up of some 600 protein pieces—more than many other cellular structures. 2  Removal or damage to a single part destroys the cilium and results in serious disease to the organism

With no center microtubules, the primary cilium is a unique environment 1/10,000th the size of the cell. Because it is a circumscribed small area with a very specific diameter, unusual neuron cilium autismproteins can anchor there and perform unique functions. There are many different sensory receptors in the membrane responding to the environment, tracking mechanical and chemical forces and sending signals to the organism. Some properties of the membrane are unique in the primary cilium. Because it is separate from the rest of the cell, special proteins can accumulate 100 times more than other places and make the signaling much more efficient.

The single, non-beating primary cilia has many different receptors and very important functions. In the kidneys the primary cilium responds to the flow of the liquid through tubules. Bending from the pressure triggers calcium signaling and is part of critical kidney regulation.

In the nose the olfactory receptors are in primary cilium.  In the eye the light sensing receptor is an outpouching at the tip of the primary cilium. The PI ( primary cilium )senses light wavelengths in eye cells, pressure in cartilage, and blood flow in heart cells.In the ear, cilia sense vibrations.

PI has also been shown to be critical for fetal brain development.When receptors in the PI respond to the external environment of the cell, receptors activate cascades that communicate to the cell nucleus using special transport motors. Without the PI in neurons during development, several brain diseases occur.

The transport system uses motors that travel along microtubules to get the important material to the tip of the primary cilium  from the base. Special motors are built at the base of the primary cilium and they pull many different types of material into the primary cilium—receptor proteins and building blocks for microtubules.Once at the tip of the PI, the motors deposit the cargo. At the tip the motor is altered and becomes a different machine to bring signaling material down the PI to the base. At the based messages are created and sent to the nucleus.

Once at the base of the primary cilium, the motor rearranges itself and becomes the train that drives cargo up into the primary cilium. The train that pulls this material to the tip of the primary cilium is made of at least four motors, one type active at a time. These motors are not just motors; they also interact with the membrane to regulate other functions including sensing extracellular situations and influencing decisions during fetal development. These motors are also able to connect through the membrane to objects outside of the cell to stimulate different types of cell movement. In this situation the motor is anchored to a particular spot, but the entire cell moves when the motor is turned on.

This very complex motor system is critical for the elaborate function of the primary cilium by transporting all receptors and signaling materials that are used for the antenna function.

Johns Hopkins researchers say they have figured out how human and all animal cells tune in to a key signal, one that literally transmits the instructions that shape their final bodies.  It turns out the cells assemble their own little radio antenna on their surfaces to help them relay the proper signal to the developmental proteins “listening” on the inside of the cell.     The transmitters are primary cilia, relatively rigid, hairlike “tails” that respond to specialized signals from a host of proteins, including a key family of proteins known as Wnts.  The Wnts in turn trigger a cascade of shape-making decisions that guide cells to take specific shapes, like curved eyelid cells or vibrating hair cells in the ear, and even make sure that arms and legs emerge at the right spots.

The case for Intelligent Design gets stronger with  new findings like this. And the cilia is truly a mind blowing example.   Imagine: a radio antenna on each cell, signalling the inside world about the outside world.  Most signal-relay stations we know about were intelligently designed.     Signal without recognition is meaningless.  Communication implies a signalling convention (a “coming together” or agreement in advance) that a given signal means or represents something: e.g., that S-O-S means “Send Help!” or, in this case, that Wnt proteins mean “put this arm here.”  The transmitter and receiver can be made of non-sentient materials, but the functional purpose of the system always comes from a mind.  The mind uses the material substances to perform an algorithm that is not itself a product of the materials or the blind forces acting on them.  Thus the analogy in the press release: cilia are just like radio antennas.  Antennas may be composed of mindless matter, but they are marks of a mind behind the intelligent design.

http://reasonandscience.heavenforum.org/t2089-primary-cilium-a-cells-antenna-or-its-brain#3655