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Theory of Intelligent Design, the best explanation of Origins » Origin of life » The RNA & DNA World » Origin of the DNA double helix

Origin of the DNA double helix

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1 Origin of the DNA double helix on Sun May 24, 2015 12:12 pm

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Origin of the DNA double helix, evidence of design

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

DNA is the “blueprint of life” and stores within the necessary instructions for living cells to grow and to function. The existence of DNA has been known since 1869. It took, however, almost a century to discern DNA structure and its role in the storage of genetic information. Cellular DNA undergoes harmful modifications every day as a result of exposure to UV light, environmental stress, and toxic chemicals. DNA damage can also result from errors during DNA synthesis. Damaged DNA must be repaired promptly and efficiently; otherwise, the replication machinery can incorporate the wrong nitrogenous base, leave nicks and gaps, and stall or disengage during subsequent rounds of DNA synthesis, resulting in deleterious mutations and chromosomal instability. The cell utilizes a number of repair pathways to prevent the loss of genetic information. The enzymes that are involved in the repair process are specific to the type of DNA damage encountered and depend on the stage of the cell cycle. Not surprisingly, defects in key components of these systems in humans are associated with a broad spectrum of disorders, usually characterized by premature aging, susceptibility to cancers, and other diseases bearing hallmarks of aging, immunodeficiency, or mental retardation.

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

DNA is something like a computer tape that stores many programs for a large computer to run. If we would scale up the linear dimension of DNA by a factor of 1 000 000 or 10^6. When we do so, the relative sizes and proportions of objects remain the same. Note that the length of DNA from a typical chromosome on this expanded scale is about 30 km, while its diameter is just 2 mm. Very few objects in the physical world are so long and so narrow.

Following the unresolved issues of nucleotide biogenesis:

(1) Laboratory experiments show that DNA spontaneously and progressively disintegrates over time. Estimates indicate that DNA should completely break down within 10,000 years. Any fossil DNA remaining after this period (especially more than say 100,000 years) must of necessity indicate that the method of dating the fossil is in error. Nature, Vol. 352, August 1, 1991 p:381

(2) The classic evolutionary problem of 'which came first, protein or DNA' has not been solved by the 'self-reproducing' RNA theory as many textbooks imply. The theory is not credible as it was based on laboratory simulations which were highly artificial, and was carried out with a 'great deal of help from the scientists'. Scientific American, February, 1991 p:100-109

(3) DNA can only be replicated in the presence of specific enzymes which can only be manufactured by the already existing DNA. Each is absolutely essential for the other, and both must be present for the DNA to multiply. Therefore, DNA has to have been in existence in the beginning of life to be controlled by DNA. Scott M. Huse, "The Collapse of Evolution", Baker Book House: Grand Rapids (Michigan), 1983 p:93-94

(4) There is no natural chemical tendency for the series of base chemicals in the DNA molecule to line up a series of R-groups in the orderly way required for life to begin. Therefore being contrary to natural chemical laws, the base-R group relationship and the structure of DNA could not have formed by random chemical action. Scott M. Huse, "The Collapse of Evolution", Baker Book House: Grand Rapids (Michigan), 1983 p:94

(5) "The origin of the genetic code is the most baffling aspect of the problem of the origins of life and a major conceptual or experimental breakthrough may be needed before we can make any substantial progress." Written by biochemist Dr. Leslie Orgel (Salk Institute, California) in the article "Darwinism at the Very Beginning of Life" in New Scientist, April 15, 1982 p:151

(6) Computer scientists have demonstrated that information does not, and cannot arise spontaneously. Information only results from the input of energy, under the all-important direction of intelligence. Therefore, as DNA is information, it cannot have been formed by natural chemical means. P. Moorhead & M. Kaplan (eds.), "Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution", Wistar Institute: Philadelphia (Pennsylvania), 1967

(7) The transformation of one species into another by viruses transferring small sections of the DNA of another species could not cause evolution for three reasons:- (1) if genes for a particular feature or action were transmitted as a small piece of DNA, the animal would not be able to utilize the code unless it had all the other structures present to support that feature, (2) there is no guarantee that without the rest of the supporting DNA code, that the feature would appear in the right place, and (3) the information transmitted would already be in existence and would not lead to the formation of a species with totally new features. Reader's Digest, March 1980

(8 "A scientist who won the Nobel Prize for his discovery of the DNA technique that inspired (the film) Jurassic Park was asked how likely it was that in the future, a dinosaur could be re-created from ancient DNA trapped in amber, as in the movie. Dr. Kary Mullis replied in essence that it would be more realistic to start working on a time machine to go back and catch one." From Creation Ex Nihilo, Vol. 16, No. 2, March 1994, p:8, summarizing The Salt Lake Tribune, December 5, 1993


Molecular Biology: Principles of Genome Function page 61


Identifying conditions that lead to the robust synthesis of nucleic acids has been much more difficult. First, there are several chemically distinct components that are needed:
the nucleotide bases, the sugar moieties, and the phosphate backbone. Although adenine is synthesized efficiently from mixtures of hydrogen cyanide and ammonia, the other bases (G, C, and U) are much less readily synthesized. Prebiotic synthesis of the sugar ring, ribose, presents another significant chemical challenge, as does formation of the glycosidic bond between the bases and the sugars.

the basics :

http://pt.slideshare.net/JDIngram/jingram-200743868-emerging-topics-dr-chen-paper-seminar-17878200?next_slideshow=1

evidence from biochemistry does not provide many clues to explain the evolution of pyrimidine and purine synthesis. 4

http://www.godandscience.org/evolution/all_about_dna.html

Evolution 1

It is unclear how long in the 4-billion-year history of life DNA has performed this function, as it has been proposed that the earliest forms of life may have used RNA as their genetic material. RNA may have acted as the central part of early cell metabolism as it can both transmit genetic information and carry out catalysis as part of ribozymes. This ancient RNA world where nucleic acid would have been used for both catalysis and genetics may have influenced the evolution of the current genetic code based on four nucleotide bases. This would occur, since the number of different bases in such an organism is a trade-off between a small number of bases increasing replication accuracy and a large number of bases increasing the catalytic efficiency of ribozymes.
However, there is no direct evidence of ancient genetic systems, as recovery of DNA from most fossils is impossible. This is because DNA survives in the environment for less than one million years, and slowly degrades into short fragments in solution. Claims for older DNA have been made, most notably a report of the isolation of a viable bacterium from a salt crystal 250 million years old,but these claims are controversial.
Building blocks of DNA (adenine, guanine and related organic molecules) may have been formed extraterrestrially in outer space. Complex DNA and RNA organic compounds of life, including uracil, cytosine and thymine, have also been formed in the laboratory under conditions mimicking those found in outer space, using starting chemicals, such as pyrimidine, found in meteorites. Pyrimidine, like polycyclic aromatic hydrocarbons (PAHs), the most carbon-rich chemical found in the universe, may have been formed in red giants or in interstellar dust and gas clouds.

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



The individual macromolecules are complex

But the complex interaction of biological macromolecules is only one aspect of the problem facing the origin of life. What compounds the enigma is that the individual macromolecular components are themselves complex, in the sense that their sequences - of ribonucleotides in the case of RNA, or amino acids for proteins - are very specific.
The linear amino acid sequence of a protein is specific because it must (a) be able to fold into a discrete 3-dimensional structure, and (b) have the right amino acids in the right positions in the linear sequence so that, when folded, they are in exactly the right positions in relation to each other to form the active site(s) of the protein. (And similar considerations apply to RNAs.)
Sequences which meet these criteria are exceedingly rare compared with the astronomical number of possible sequences of a suitable length. For example Douglas Axe has estimated that only 1 in about 10^74 possible sequences will have biological function (Axe). So it is totally unrealistic to think that such sequences could have arisen by chance. How much less a suite of mutually dependent macromolecules?
If the components themselves were not so improbable then it might be realistic to think that a complex combination of components could arise by chance; but the extreme improbability of the individual components is such that they are very unlikely to arise individually, and hence there is no chance whatever of an interdependent system.

Where even just two macromolecules are required to perform a function, then it would be necessary for both components to arise together: Because natural selection does not have foresight: if one component arises alone it will not be retained for potential future usefulness (when the second component is available), but will almost certainly degrade by mutation. And, it should be noted, if the probability of getting one component is 1 in 10^74 then the probability of getting two together is 1 in 10^148 (not 1 in 2x10^74); and so on for multi-component systems. This is why the obligatory mutual dependence of many macromolecules in even basic biological systems completely defies any hope of an evolutionary origin.
So, in summary, the crux of the problem is that even a basic biological replicating system requires (a) several macromolecules with complementary functions with (b) each having a highly improbable sequence. And this combination of complexities presents an insurmountable challenge to a naturalistic origin of life. 3

However, just as there are severe problems with an abiotic origin of polypeptides, similar issues apply to the production of polynucleotides, except that chemical considerations make the situation even worse.

Example of a ribonucleotide- guanonsine monophosphate





This is because the nucleotides themselves each comprise a base, sugar, and phosphate (Figure 4) which need to be joined together correctly - involving two endothermic condensation reactions (with all the problems that means) to make a nucleotide in addition to the endothermic condensation reaction involved in joining the nucleotides. In other words, compared with polypeptides, nucleotides are even harder to synthesise and easier to destroy; in fact, to date, there are no reports of nucleotides arising from inorganic compounds in primeval soup experiments.


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.
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.


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If there is no salt in the surrounding medium, there is a strong repulsion between the two strands and they will fall apart. Therefore counter-ions are essential for the double-helical structure.

- the origin of the counter-ions




1) http://en.wikipedia.org/wiki/DNA#Evolution
2) http://www.allaboutscience.org/dna-structure.htm
3) https://www.c4id.org.uk/index.php?option=com_content&view=article&id=211:the-problem-of-the-origin-of-life&catid=50:genetics&Itemid=43
4) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4390864/



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Following the unresolved issues of nucleotide biogenesis :

http://reasonandscience.heavenforum.org/t2028-origin-of-the-dna-double-helix#3426

DNA: Destroys the theory of Evolution. Unmasking the lies

(1) Laboratory experiments show that DNA spontaneously and progressively disintegrates over time. Estimates indicate that DNA should completely break down within 10,000 years. Any fossil DNA remaining after this period (especially more than say 100,000 years) must of necessity indicate that the method of dating the fossil is in error. Nature, Vol. 352, August 1, 1991 p:381

(2) The classic evolutionary problem of 'which came first, protein or DNA' has not been solved by the 'self-reproducing' RNA theory as many textbooks imply. The theory is not credible as it was based on laboratory simulations which were highly artificial, and were carried out with a 'great deal of help from the scientists'. Scientific American, February, 1991 p:100-109

(3) DNA can only be replicated in the presence of  specific enzymes which can only be manufactured by the already existing DNA. Each is absolutely essential for the other, and both must be present for the DNA to multiply. Therefore, DNA has to have been in existence in the beginning for life to be controlled by DNA. Scott M. Huse, "The Collapse of Evolution", Baker Book House: Grand Rapids (Michigan), 1983 p:93-94

(4) There is no natural chemical tendency for the series of base chemicals in the DNA molecule to line up a series of R-groups in the orderly way required for life to begin. Therefore being contrary to natural chemical laws, the base-R group relationship and the structure of DNA could not have formed by random chemical action. Scott M. Huse, "The Collapse of Evolution", Baker Book House: Grand Rapids (Michigan), 1983 p:94

(5) "The origin of the genetic code is the most baffling aspect of the problem of the origins of life and a major conceptual or experimental breakthrough may be needed before we can make any substantial progress." Written by biochemist Dr Leslie Orgel (Salk Institute, California) in the article "Darwinism at the Very Beginning of Life" in New Scientist, April 15, 1982 p:151

(6) Computer scientists have demonstrated that information does not, and cannot arise spontaneously. Information only results from the input of energy, under the all-important direction of intelligence. Therefore, as DNA is information, it cannot have been formed by natural chemical means. P. Moorhead & M. Kaplan (eds.), "Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution", Wistar Institute: Philadelphia (Pennsylvania), 1967

(7) The transformation of one species into another by viruses transferring small sections of the DNA of another species could not cause evolution for three reasons:- (1) if genes for a particular feature or action were transmitted as a small piece of DNA, the animal would not be able to utilize the code unless it had all the other structures present to support that feature, (2) there is no guarantee that without the rest of the supporting DNA code, that the feature would appear in the right place, and (3) the information transmitted would already be in existence and would not lead to the formation of a species with totally new features. Reader's Digest, March 1980

(8  "A scientist who won the Nobel Prize for his discovery of the DNA technique that inspired (the film) Jurassic Park was asked how likely it was that in the future, a dinosaur could be re-created from ancient DNA trapped in amber, as in the movie. Dr Kary Mullis replied in essence that it would be more realistic to start working on a time machine to go back and catch one." From Creation Ex Nihilo, Vol. 16, No. 2, March 1994, p:8, summarizing The Salt Lake Tribune, December 5, 1993

Adenine

Adenine is one of the most important organic molecules for life as we know it today.

Adenine is an integral part of DNA, RNA, and ATP. DNA, as you might know, is the genetic code used for cellular life on earth. It is through the precise inheritance of on organism's DNA from its parent that the traits of an organism are passed on. Here is the partial structure of DNA with an Adenine group attached. Adenine is a purine. Purines are six-membered rings attached to five membered rings. When Adenine is attached to DNA, it forms a bond with another molecule called Thymine, a pyrimidine, on the other side of the DNA strand. It is these bonds which give DNA its double-helix structure. The sequence of DNA, or the order in which nucleotides are placed, allows for the diversity among all living organisms. The importance of Adenine to RNA is similar to that of DNA.

Besides DNA and RNA, Adenine is also an important part of adenosine triphosphate, or ATP. Adenosine triphosphate is the nitrogenous base adenine bonded to a five carbon sugar. This molecule is important because it has the ability to phosphorylize, or add a phosphate group to, other molecules. This transfer of a phosphate group allows energy to be released. It is this energy which is used by cells in living organisms. This is why the molecules ATP, and its nitrogenous base Adenine, are so important.

"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. ( So we have a chicken/egg problem here )

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

Cytosine  is one of the four main bases found in DNA and RNA, along with adenine, guanine, and thymine (uracil in RNA).

To date, scientists have failed to produce cytosine in a spark-discharge experiment, nor has cytosine been recovered from meteorites or extraterrestrial sources. Because meteorites (and other extraterrestrial materials) serve as a proxy for early Earth’s chemistry, the absence of cytosine in these sources would seem to affirm Shapiro’s conclusion. Shapiro also critically analyzed prebiotic simulation experiments that produced the DNA and RNA component adenine. As with cytosine, he showed that adenine formation on early Earth (by currently recognized prebiotic routes) could not reasonably have occurred, for many of the same reasons. Recent work by James Cleaves and Stanley Miller uncovers an additional problem. Nucleobases readily react with formaldehyde and acetaldehyde, compounds most certainly present on early Earth, to form both small molecule derivatives and large intractable molecules. Even under mild conditions, these reactions take place so rapidly that they would preferentially occur at the expense of reactions that could lead to RNA. Thus, if nucleobases could form, competing reactions would likely consume them.

Prebiotic cytosine synthesis: A critical analysis and implications for the origin of life 4

The deamination of cytosine and its destruction by other processes such as photochemical reactions place severe constraints on prebiotic cytosine syntheses. If cytosine concentrations are to be maintained on a worldwide basis, then synthesis must be sufficient to replace depletion. The syntheses described thus far do not possess the necessary speed and selectivity to meet this requirement. The use of drying lagoons as a site for prebiotic synthesis has been suggested as a remedy: synthetic rates would be enhanced by greatly increasing the concentration of the reagents. The lagoon suggestion appears geologically implausible, however. All schemes in which cytosine is synthesized locally and distributed globally also are handicapped in that the enormous dilution that takes place when cytosine is released into a global sea offsets any gain in synthetic efficiency.

Guanine 

Guanine is one of the four main nucleobases found in the nucleic acids DNA and RNA. 

For scientists attempting to understand how the building blocks of RNA originated on Earth, 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.

Thymine 

DNA can only be replicated in the presence of  specific enzymes (described below )  which can only be manufactured by the already existing DNA. Each is absolutely essential for the other, and both must be present for the DNA to multiply. Therefore, DNA has to have been in existence in the beginning for life to be controlled by DNA. Scott M. Huse, "The Collapse of Evolution", Baker Book House: Grand Rapids (Michigan), 1983 p:93-94

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 , 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.

Thats interesting, as we find two distinct enzymes with two different sequences and structures synthesizing the same reaction, thus being a example of convergence right in the beginning. How remote was the chance for this to happen by natural means , considering, that convergence does not favour 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 . 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. 
Ribonucleotide reductase

This is one of the most essential enzymes of life 

Ribonucleotide reduction is the only pathway for de novo synthesis of deoxyribonucleotides in extant organisms. This chemically demanding reaction  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.

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.

RNRs  provide an essential link between the RNA and DNA world

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.

We have been able to make significant advances towards solving the long-standing problem of nucleotide abiogenesis, but our results highlight a number of issues that demand further investigation. First, what chemistry could have furnished the necessary chemical precursors, most importantly enantiomerically enriched glyceraldehyde? 2

The origins of homochirality and nucleotides seem to be inherently linked at the level of glyceraldehyde. As a racemizable molecule with one stereogenic center, glyceraldehyde
would appear to be the ideal molecule through which to provide at least enantiomeric enrichment or, ideally, dynamic kinetic resolution. Elucidating the origin of chiral glyceraldehyde and demonstrating the sequential sequestration of glycolaldehyde and glyceraldehyde or the separation/sanitization of ribonucleotide precursors may lead to the discovery of the chemical transformations that led to homochiral nucleotides.

Nucleotides must be oligomerized to generate RNA, and assuming that RNA must be 5′-3′-linked,28 a significant issue of regioselectivity must be overcome. Though, as a result of ringstrain, and  are activated relative to NMP’s, they are not specifically activated to 5′-3′-oligomerization.

DNA components (the deoxyribonucleotides dADP, dCDP, dGDP and dUDP) are synthesised from their corresponding ribonucleotides by the reduction of the C2' position. The enzymes that do this are named ribonucleotide reductases.

When DNA is randomly polymerized in pre-biotic type experiments, you end up get a mix dominated by 2′-5′ over 3′-5′ links, whereas for DNA to be readable it has to be uniformly 3′-5′. Without the homogeneity of homochirality, identical kinds of links, etc., even if life could have miraculously formed without all this, it would quickly self destruct for the next generation. 3

The canonical nucleotides must be: 1. aldose not ketose; 2. pentose not tetrose, hexose, etc; 3. ribo, not arabino, lyxo, or xylo; 4. furanosyl not pyranosyl; 5. b not a; 6. D not L; 7. regiospecifically glycosylated; 8. regiospecifically phosphorylated; 9. activated (or activatable) toward regiospecific oligomerization. Each of these requirements must ultimately be satisfied by the inherent chemoselectvity and predisposed reactivity of abiotic chemical space, without requiring enzymatic control 1

“Equally disappointing, we can induce copying of the original template only when we run our experiments with nucleotides having a right-handed configuration; All nucleotides synthesized biologically today are right-handed. Yet on the primitive earth, equal numbers of right- and left-handed nucleotides would have been present.”

Leslie E. Orgel, “The Origin of Life on the Earth,” Scientific American, Vol. 271, October 1994, p. 82.

The incorporation of even a single L-ribose or L-deoxyribose residue into a nucleic acid, if it should ever occur in the course of cellular syntheses, could seriously interfere with vital structure-function relationships. The well-known double helical DNA structure does not allow the presence of L-deoxyribose; the replication and transcription mechanisms generally require that any wrong sugar such as L-deoxyribose has to be eliminated, that is, the optical purity of the D-sugars units has to be 100%.” Dose, p. 352.

Complex molecules such as DNA and proteins are built by adding one building block at a time onto an ever-growing chain. In a "primordial soup" made up of equal proportions of right and left-handed building blocks, there is an equal probability at each step of adding either a right or left-handed building block. Consequently, it is a mathematical absurdity to propose that only right-handed nucleotides would be added time after time without a single left-handed one being added to a growing DNA molecule. Sooner or later an incorrect, left-handed nucleotide will be added. 4

The formation and accumulation of a certain length of polymers of nucleic acids and peptides are essential process toward the emergence of life-like system. 2

http://www.sciencedaily.com/releases/2016/01/160112125415.htm
DNA supply chain explained - January 12, 2016
Excerpt: A new study from MIT chemists sheds light on a longstanding puzzle: how a single enzyme known as ribonucleotide reductase (RNR) generates all four of these building blocks (of DNA) and maintains the correct balance among them.
Unlike RNR, most enzymes specialize in converting just one type of molecule to another,, "Ribonucleotide reductase is very unusual. I've been fascinated with this question of how it actually works and how this enzyme's active site can be molded into four different shapes."
They found that the enzyme's active site -- the region that binds the substrate -- changes shape depending on which effector molecule is bound to a distant site on the enzyme.,,,
"It's exquisitely designed so that if you have the wrong substrate in there, you can't close up the active site," Drennan says. "It's a really elegant set of movements that allows for this kind of molecular screening process."


The “Wow! signal” of the terrestrial genetic code
Genomic DNA is already used on Earth to store non-biological information. Though smaller in capacity, but stronger in noise immunity is the genetic code. The code is a flexible mapping between codons and amino acids, and this flexibility allows modifying the code artificially. But once fixed, the code might stay unchanged over cosmological timescales; in fact, it is the most durable construct known. Therefore it represents an exceptionally reliable storage for an intelligent signature, if that conforms to biological and thermodynamic requirements. As the actual scenario for the origin of terrestrial life is far from being settled, the proposal that it might have been seeded intentionally cannot be ruled out.
http://www.sciencedirect.com/science/article/pii/S0019103513000791?np=y

1)http://www.chtf.stuba.sk/~szolcsanyi/education/files/Organicka%20chemia%20II/Prednaska%2010_Nukleozidy/Doplnkove%20studijne%20materialy/The%20Origins%20of%20Nucleotides.pdf
2) http://cdn.intechopen.com/pdfs-wm/46508.pdf
3. http://www.uncommondescent.com/chemistry/relevance-of-coin-analogies-to-homochirality-and-symbolic-organization-in-biology/
4) http://xwalk.ca/origin.html#fn20

further readings:

http://reasonandscience.heavenforum.org/t1474-nucleotide-biosynthesis?highlight=nucleotide
http://www.godandscience.org/evolution/chemlife.html#n02
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC16343/



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3 Ribonucleotide reductase on Sun May 24, 2015 5:42 pm

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Ribonucleotide reductase

This is one of the most essential enzymes of life 5

Ribonucleotide reduction is the only pathway for de novo synthesis of deoxyribonucleotides 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. 10


1. An electron is transferred from a cysteine residue on R1 to a tyrosine radical on R2, generating a highly reactive cysteine thiyl radical. 2. This radical abstracts a hydrogen atom from C-3′ of the ribose unit. 3. The radical at C-3′ causes the removal of the hydroxide ion from the C-2′ carbon atom. Combined with a hydrogen atom from a second cysteine residue, the hydroxide ion is eliminated as water. 4. A hydroxide ion is transferred from a third cysteine residue. 5. The C-3′ radical recaptures the originally abstracted hydrogen atom. 6. An electron is transferred from R2 to reduce the thiyl radical. The deoxyribonucleotide is free to leave R1. The disulfide formed in the active site must be reduced to begin another reaction cycle.



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. 6


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) [PMID: 15158709].

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. 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 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. 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.




 9



Biosynthesis or RNR enzymes

In this study, we report our findings for two temperature-conditional Chl-deficient rice mutants, v3 and st1, which harbor mutations in the open reading frames (ORFs) of the V3 and St1 genes that encode the large and small subunits of ribonucleotide reductase (RNR), respectively. RNR is an essential enzyme for DNA replication and damage repair in all living organisms, because it provides the DNA precursors by catalyzing the de novo synthesis of deoxyribonucleotide diphosphates from their corresponding ribonucleotide diphosphates 10

Ribonucleotide reductases and thymidylate synthases are encoded in all cellular genomes and in the genomes of many DNA viruses. 11

The first ribonucleotide reductases and thymidylate synthases were thus made by ancestral ribosomes containing both RNA and proteins and that were capable to perform already accurate translation. The RNA to DNA transition thus should have occurred in a complex cellular environment suitable for the production of these enzymes. This environment had to be elaborated enough to support the entire metabolism for the production of RNA precursors (rNTPs), including mechanisms for energy production. Hence, the cellular environment in which DNA finally emerged was not as “simple” as sometimes imagined, but was certainly populated by elaborated cells and viruses with an already complex metabolic network and well-organized membrane systems.

That means: It takes a complex DNA world to make DNA.....





Cell survival depends on having a plentiful and balanced pool of the four chemical building blocks that make up DNA. However, if too many of these components pile up, or if their usual ratio is disrupted, that can be deadly for the cell. Chemists have discovered how a single enzyme maintains a cell's pool of DNA building blocks. 12


1) http://en.wikipedia.org/wiki/Ribonucleotide_reductase
2) http://journal.frontiersin.org/article/10.3389/fcimb.2014.00052/abstract
3) http://www.ncbi.nlm.nih.gov/pubmed/11114511
4) http://evolutionwiki.org/wiki/RNA_world
5) http://www.nature.com/nsmb/journal/v18/n3/full/nsmb0311-251.html
6) file:///E:/Downloads/life-05-00604-v2.pdf
7) file:///E:/Downloads/fcimb-04-00052.pdf
8 ) http://ac.els-cdn.com/S0969212696001128/1-s2.0-S0969212696001128-main.pdf?_tid=c961a940-0289-11e5-82eb-00000aacb35f&acdnat=1432522831_8571d89fe458862e512f4f821993f918
9 ) http://www.mdpi.com/2075-1729/5/1/604/htm
10) http://www.plantphysiol.org/content/150/1/388.full
11) http://www.ncbi.nlm.nih.gov/books/NBK6338/
12) http://www.sciencedaily.com/releases/2016/01/160112125415.htm



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4 Phosphodiester bonds on Wed May 27, 2015 1:27 am

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Phosphodiester bonds

Activated monomers are essential because polymerization reactions occur in an aqueous medium and are therefore energetically uphill in the absence of activation. 4
A central problem therefore concerns mechanisms by which prebiotic monomers could have been activated to assemble into polymers.

In life today, the removal of water is performed upstream of the actual bond formation. This process involves the energetically downhill transfer of electrons, which is coupled to either substrate-level oxidation or generation of a proton gradient that in turn is the energy source for the synthesis of anhydride pyrophosphate bonds in ATP. The energy stored in the pyrophosphate bond is then distributed throughout the cell to drive most other energy‐dependent reactions. This is a complex and highly evolved process, so here we consider simpler ways in which energy could have been captured from the environment and made available for primitive versions of metabolism and polymer synthesis. Because the atmosphere of the primitive Earth did not contain appreciable oxygen, this review of primitive bioenergetics is limited to anaerobic sources of energy.

a plausible energy source for polymerization remains an open question. Condensation reactions driven by cycles of anhydrous conditions and hydration would seem to be one obvious possibility, but seem limited by the lack of specificity of the chemical bonds that are formed.


Initial studies established that some montmorillonite clays catalyze condensation of activated mononucleotides to oligomers which contain about ten monomer units. For example, the self-condensation of the 5'-phosphorimidazolide of adenosine (ImpA) in pH 8 aqueous solution in the presence of montmorillonite results in the formation of 2-10 mers in which 66% of the phosphodiester bonds are 3',5'-linked.  5

Take the clay used in the Ferris et al. experiments, for instance. Montmorillonite (often used in cat litter) is a layered clay "rich in silicate and aluminum oxide bonds" (Shapiro 2006, 108). But the montmorillonite employed in the Ferris et al. experiments is not a naturally-occuring material, as Ertem (2004) explains in detail. Natural or native clays don't work, because they contain metal cations that interfere with phosphorylation reactions:

(Shapiro 2006, 108)

This handicap was overcome in the synthetic experiments by titrating the clays to a monoionic form, generally sodium, before they were used. Even after this step, the activity of the montmorillionite depended strongly on its physical source, with samples from Wyoming yielding the best results....Eventually the experimenters settled on Volclay, a commercially processed Wyoming montmorillonite provided by the American Colloid Company. Further purification steps were applied to obtain the catalyst used for the "prebiotic" formation of RNA.


Phosphodiester bonds are central to most life on Earth, as they make up the backbone of the strands of DNA. In DNA and RNA, the phosphodiester bond is the linkage between the 3' carbon atom of one sugar molecule and the 5' carbon atom of another, deoxyribose in DNA and ribose in RNA. Strong covalent bonds form between the phosphate group and two 5-carbon ring carbohydrates (pentoses) over two ester bonds. 1

In order for the phosphodiester bond to be formed and the nucleotides to be joined, the tri-phosphate or di-phosphate forms of the nucleotide building blocks are broken apart to give off energy required to drive the enzyme-catalyzed reaction. When a single phosphate or two phosphates known as pyrophosphates break away and catalyze the reaction, the phosphodiester bond is formed.

Hydrolysis of phosphodiester bonds can be catalyzed by the action of phosphodiesterases which play an important role in repairing DNA sequences.

A phosphodiester bond occurs when exactly two of the hydroxyl groups in phosphoric acid react with hydroxyl groups on other molecules to form two ester bonds. An example is found in the linking of two pentose (5 carbon sugar) rings to a phosphate group by strong, covalent ester bonds. Each ester bond is formed by a condensation reaction in which water is lost. This bond is a key structural feature of the backbone of DNA and RNA and links the 3’ carbon of one nucleotide to the 5’ carbon of another to produce the strands of DNA and RNA.  2


gif hosting

Ligase is a type of enzyme that forms a link between carbon and either: carbon, sulphur, oxygen, or nitrogen; using the hydrolysis of ATP and its high energy bond to drive formation of the new covelant bond [1]. There are various types of ligases; 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".....  

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. It plays a role in repairing single-strand breaks in duplex DNA in living organisms, but some forms (such as DNA ligase IV) may specifically repair double-strand breaks (i.e. a break in both complementary strands of DNA). Single-strand breaks are repaired by DNA ligase using the complementary strand of the double helix as a template,[1] with DNA ligase creating the final phosphodiester bond to fully repair the DNA.

DNA ligase has applications in both DNA repair and DNA replication


 6


1) http://en.wikipedia.org/wiki/Phosphodiester_bond
2) https://teaching.ncl.ac.uk/bms/wiki/index.php/Phosphodiester_bond
3) https://teaching.ncl.ac.uk/bms/wiki/index.php/DNA_ligase#cite_note-0
4) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2828274/
5) http://homepages.rpi.edu/~whittd/COOL/chem.html
6) file:///E:/Downloads/challenges-05-00193%20(3).pdf



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5 Adenine synthesis in life on Fri May 29, 2015 3:27 pm

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Adenine synthesis in life

Adenine is one of the most important organic molecules for life as we know it today.

Adenine is an integral part of DNA, RNA, and ATP. DNA, as you might know, is the genetic code used for cellular life on earth. It is through the precise inheritance of on organism's DNA from its parent that the traits of an organism are passed on. Here is the partial structure of DNA with an Adenine group attached. Adenine is a purine. Purines are six-membered rings attached to five membered rings. When Adenine is attached to DNA, it forms a bond with another molecule called Thymine, a pyrimidine, on the other side of the DNA strand. It is these bonds which give DNA its double-helix structure. The sequence of DNA, or the order in which nucleotides are placed, allows for the diversity among all living organisms. The importance of Adenine to RNA is similar to that of DNA.

Besides DNA and RNA, Adenine is also an important part of adenosine triphosphate, or ATP. Adenosine triphosphate is the nitrogenous base adenine bonded to a five carbon sugar. This molecule is important because it has the ability to phosphorylize, or add a phosphate group to, other molecules. This transfer of a phosphate group allows energy to be released. It is this energy which is used by cells in living organisms. This is why the molecules ATP, and its nitrogenous base Adenine, are so important.

"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." 1


Shapiro also critically analyzed prebiotic simulation experiments that produced the DNA and RNA component adenine. As with cytosine, he showed that adenine formation on early Earth (by currently recognized prebiotic routes) could not reasonably have occurred, for many of the same reasons. 2






Adenine biosynthesis pathway :



https://books.google.com.br/books?id=5ZGUD49fMcAC&pg=PA206&lpg=PA206&dq=Metabolic+pathways,+irreducible+complexity&source=bl&ots=FdagRE2T-M&sig=pVeMIrlHluDJSkL2Bp3Si4M4Xh4&hl=pt-BR&sa=X&ei=s1pNVZPQAcmpNsb8gbAH&ved=0CFsQ6AEwBzge#v=onepage&q=Metabolic%20pathways%2C%20irreducible%20complexity&f=false



1) http://www.ncbi.nlm.nih.gov/pubmed/11536683?dopt=Abstract
2) Hugh Ross & Fazale Rana, Origins of life pg.79



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6 Prebiotic cytosine synthesis on Fri May 29, 2015 3:38 pm

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Prebiotic cytosine synthesis

Cytosine  is one of the four main bases found in DNA and RNA, along with adenine, guanine, and thymine (uracil in RNA).

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.

The RNA/DNA base cytosine is not produced in spark discharge experiments. The proposed prebiotic productions are chemically unrealistic because the alleged precursors are unlikely to be concentrated enough, and they would undergo side reactions with other organic compounds, or hydrolyse.  Cytosine itself is too unstable to accumulate over alleged geological ‘deep time’, as its half life for deamination is 340 years at 25 °C.  2

For a long time the synthesis of RNA monomers under prebiotic conditions appeared to be a fundamental problem since the condensation of sugar (ribose) and nucleobase (purines and pyrimidines) does not work (Orgel, 2004). The prebiotic synthesis of purine ribonucleotides is still unclear, yet recently a breakthrough has been made with regard to the synthesis of pyrimidine ribonucleotide monomers (which incorporate cytosine and uracil). It now appears in principle to be solved, in a completely unexpected manner. The study by the group of John Sutherland (Powner et al. 2009)  shows how nature could have spontaneously assembled pyrimidine ribonucleotide monomers from prebiotically plausible molecules through intermediates that contribute atoms to both the sugar and base portions of the ribonucleotides, thus avoiding a condensation step of sugar and base altogether 3

Sutherland's research produced only 2 of the 4 RNA nucleobases, and Dr. Garner also explained why, as is often the case, the basic chemistry itself also required the hand of an intelligent chemist:

As far as being relevant to OOL, the chemistry has all of the usual problems. The starting materials are "plausibly" obtainable by abiotic means, but need to be kept isolated from one another until the right step, as Sutherland admits. One of the starting materials is a single mirror image for which there is no plausible way to get it that way abiotically. Then Sutherland ran these reactions as any organic chemist would, with pure materials under carefully controlled conditions. In general, he purified the desired products after each step, and adjusted the conditions (pH, temperature, etc.) to maximum advantage along the way. Not at all what one would expect from a lagoon of organic soup. He recognized that making of a lot of biologically problematic side products was inevitable, but found that UV light applied at the right time and for the right duration could destroy much (?) of the junk without too much damage to the desired material. Meaning, of course, that without great care little of the desired chemistry would plausibly occur. But it is more than enough for true believers in OOL to rejoice over, and, predictably, to way overstate in the press. 4

Robert Shapiro, professor emeritus of chemistry at New York University disagrees.

'Although as an exercise in chemistry this represents some very elegant work, this has nothing to do with the origin of life on Earth whatsoever,' he says. According to Shapiro, it is hard to imagine RNA forming in a prebiotic world along the lines of Sutherland's synthesis.
'The chances that blind, undirected, inanimate chemistry would go out of its way in multiple steps and use of reagents in just the right sequence to form RNA is highly unlikely,' argues Shapiro.
5

In the book origins of life, Hugh Ross writes at  page 79 :

Cytosine is one of the molecular components of nucleic acids (DNA and RNA), cytosine assumes an important place in both RNA-world and pre-RNA-world origin-of-life models (this posits that RNA or some RNA precursor chemically evolved before proteins and DNA). Cytosine, a pyrimidine, is a six-membered ring composed of four carbon atoms and two nitrogen atoms. Along with other ring compounds, such as adenine, guanine, thymine, and uracil, cytosine repeatedly extends from the chainlike backbone of DNA and RNA. The nitrogen-containing rings sequenced along DNA or RNA provide the chemical information that determines biochemical function. Chemists have discovered two possible pathways that produce cytosine. One route involves a reaction between cyanoacetylene and cyanate, and the other reaction begins with cyanoacetaldehyde and urea.6 These four compounds represent essential ingredients of early Earth’s supposed prebiotic soup. Chemist Robert Shapiro demonstrated, however, that the two chemical routes lack any relevance.7 He points out the unlikelihood that cyanoacetylene, cyanate, cyanoacetaldehyde, and urea existed at sufficient levels on primordial Earth to effect the production of cytosine. Even if they had occurred at appropriate levels, interfering chemical reactions would have quickly consumed these compounds before cytosine could form. Cyanoacetylene rapidly reacts with ammonia, amines, thiols, and hydrogen cyanide. Cyanate undergoes rapid reaction with water. In the presence of water, cyanoacetaldehyde decomposes into acetonitrile and formate. When cytosine does form, it rapidly decomposes. At room temperature and with a neutral pH, cytosine breaks down, losing half its molecules in 340 years. At 32 °F (0 °C), its half-life is 17,000 years—still too short a time for cytosine to be part of the supposed first self-replicator. To date, scientists have failed to produce cytosine in a spark-discharge experiment, nor has cytosine been recovered from meteorites or extraterrestrial sources. Because meteorites (and other extraterrestrial materials) serve as a proxy for early Earth’s chemistry, the absence of cytosine in these sources would seem to affirm Shapiro’s conclusion. Shapiro also critically analyzed prebiotic simulation experiments that produced the DNA and RNA component adenine. As with cytosine, he showed that adenine formation on early Earth (by currently recognized prebiotic routes) could not reasonably have occurred, for many of the same reasons. Recent work by James Cleaves and Stanley Miller uncovers an additional problem.11 Nucleobases readily react with formaldehyde and acetaldehyde, compounds most certainly present on early Earth, to form both small molecule derivatives and large intractable molecules. Even under mild conditions, these reactions take place so rapidly that they would preferentially occur at the expense of reactions that could lead to RNA. Thus, if nucleobases could form, competing reactions would likely consume them.


Prebiotic cytosine synthesis: A critical analysis and implications for the origin of life
1

The deamination of cytosine and its destruction by other processes such as photochemical reactions place severe constraints on prebiotic cytosine syntheses. If cytosine concentrations are to be maintained on a worldwide basis, then synthesis must be sufficient to replace depletion. The syntheses described thus far do not possess the necessary speed and selectivity to meet this requirement. The use of drying lagoons as a site for prebiotic synthesis has been suggested as a remedy: synthetic rates would be enhanced by greatly increasing the concentration of the reagents. The lagoon suggestion appears geologically implausible, however. All schemes in which cytosine is synthesized locally and distributed globally also are handicapped in that the enormous dilution that takes place when cytosine is released into a global sea offsets any gain in synthetic efficiency.

Prebiotic guanine synthesis

Guanine is one of the four main nucleobases found in the nucleic acids DNA and RNA.

For scientists attempting to understand how the building blocks of RNA originated on Earth, 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. 1



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The backbone made up of (deoxy-ribose) sugar molecules

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. 1

Sugars are very unstable, and easily decompose or react with other chemicals. This counts against any proposed mechanism to concentrate them to useable proportions. 2


Asphalt, Water, and the Prebiotic Synthesis of Ribose, Ribonucleosides, and RNA  3

RNA has been called a “prebiotic chemist’s nightmare” because of its combination of large size, carbohydrate building blocks, bonds that are thermodynamically unstable in water, and overall intrinsic instability.

However, a discontinuous synthesis model is well-supported by experimental work that might produce RNA from atmospheric CO2, H2O, and N2. For example, electrical discharge in such atmospheres gives formaldehyde (HCHO) in large amounts and glycolaldehyde (HOCH2CHO) in small amounts. When rained into alkaline aquifers generated by serpentinizing rocks, these substances were undoubtedly converted to carbohydrates including ribose. Likewise, atmospherically generated HCN was undoubtedly converted in these aquifers to formamide and ammonium formate, precursors for RNA nucleobases. Finally, high reduction potentials maintained by mantle-derived rocks and minerals would allow phosphite to be present in equilibrium with phosphate, mobilizing otherwise insoluble phosphorus for the prebiotic synthesis of phosphite and phosphate esters after oxidation.

So why does the community not view this discontinuous synthesis model as compelling evidence for the RNA-first hypothesis for the origin of life? In part, the model is deficient because no experiments have joined together those steps without human intervention. Further, many steps in the model have problems. Some are successful only if reactive compounds are presented in a specific order in large amounts. Failing controlled addition, the result produces complex mixtures that are inauspicious precursors for biology, a situation described as the “asphalt problem”. Many bonds in RNA are thermodynamically unstable with respect to hydrolysis in water, creating a “water problem”. Finally, some bonds in RNA appear to be “impossible” to form under any conditions considered plausible for early Earth.



1) http://www.ncbi.nlm.nih.gov/pubmed/2453009
2) http://creationwiki.org/Origin_of_life
3) http://pubs.acs.org/doi/abs/10.1021/ar200332w

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8 Re: Origin of the DNA double helix on Sun Jun 21, 2015 10:07 am

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



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9 Re: Origin of the DNA double helix on Sun Jun 21, 2015 9:11 pm

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https://books.google.com.br/books?id=rlIyVJ9dpzkC&pg=PA149&lpg=PA149&dq=thymidylate+synthase+origin+of+life&source=bl&ots=cocJIaoVZg&sig=VtlcxunaYAkxx4DZwpEjvHnh_-0&hl=en&sa=X&ei=AnyHVYyRA8qy-AG1v4HYBw&ved=0CDAQ6AEwAw#v=onepage&q=thymidylate%20synthase%20origin%20of%20life&f=false




further readings :

https://www.c4id.org.uk/index.php?option=com_content&view=article&id=211:the-problem-of-the-origin-of-life&catid=50:genetics&Itemid=43

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10 Re: Origin of the DNA double helix on Tue Aug 04, 2015 6:54 am

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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.

Thats interesting, as we find two distinct enzymes with two different sequences and structures synthesizing the same reaction, thus being a example of convergence right in the beginning. How remote was the chance for this to happen by natural means , considering, that convergence does not favour 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.

Further implications :  There is a third enzyme doing doing the same reaction:

New Chemical Reaction For DNA Production In Bacteria And Viruses Discovered 6

Scientists have discovered a new chemical reaction for producing one of the four nucleotides, or building blocks, needed to build DNA. The reaction includes an unusual first step, or mechanism, and unlike other known reactions that produce the DNA building block, uses an enzyme that speeds up, or catalyzes, the reaction without bonding to any of the compounds, or substrates, in the reaction.

The chemical reaction discovered by the researchers uses an enzyme called flavin-dependent thymidylate synthase, or FDTS. The enzyme is coded by the thyX gene and has been found primarily in bacteria and viruses, including several human pathogens and biological warfare agents.

Both the new and classical enzymatic reactions complete a key step in producing the DNA building block by adding a methyl group--one carbon atom attached to three hydrogen atoms--to the building block's precursor molecule called deoxy-uridine monophosphate, or dUMP.





1) http://www.pnas.org/content/96/8/4396.full
2) http://www.trueorigin.org/originoflife.php
3) http://www.talkorigins.org/faqs/abioprob/originoflife.html
4) http://www.evolutionnews.org/2009/07/scientists_say_intelligent_des022621.html
5) http://www.rsc.org/chemistryworld/News/2009/May/13050902.asp
6) http://www.sciencedaily.com/releases/2009/04/090416161133.htm
7) http://www.ncbi.nlm.nih.gov/pubmed/20525631

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11 Re: Origin of the DNA double helix on Fri Aug 07, 2015 11:15 am

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http://www.ncbi.nlm.nih.gov/books/NBK6360/figure/A43731/?report=objectonly

Metabolic pathways for RNA and DNA precursors biosynthesis: a palimpsest from the RNA to DNA world transition? The biosynthetic pathways for purine and pyrimidine nucleotides both start with ribose 5-monophosphate. The formation of the four bases requires several amino-acids, formate and carbamyl-phosphate. Nucleotide monophosphates (NMP) are converted into RNA precursors (NTP) by NMP kinases (k) and NDP kinases (K). These reactions probably are relics of the RNA-protein world. DNA precursors are produced from NDP and/or NTP by ribonucleotide reductases (RNR), except for dTTP, which results from methylation of dUMP. dTMP is produced from dUMP by Thymidylate synthases (ThyA or ThyX) and converted into dTTP by the same kinases that convert NMP into NTP. dUMP can be produced either by dUTPAse or by dCTP deaminase. In the U-DNA world, it could have been also produced by degradation of U-DNA. The mode of dTMP production clearly suggests that U-DNA was an evolutionary intermediate between RNA and T-DNA. Some viruses contain U-DNA, whereas others contain HMC-DNA (HMC= hydroxymethyl-cytosine). Transformation of C into HMC occurs at the level of dCMP, and conversion of dCMP into dHMCMP is catalyzed by a dCMP hydroxy-methyl transferase (dCMP HM transferase), which is homologue to ThyA (See refs. 11, 14, and 19 for more details).

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12 Re: Origin of the DNA double helix on Fri Sep 18, 2015 5:24 am

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DNA: Destroys the theory of Evolution. Unmasking the lies

(1) Laboratory experiments show that DNA spontaneously and progressively disintegrates over time. Estimates indicate that DNA should completely break down within 10,000 years. Any fossil DNA remaining after this period (especially more than say 100,000 years) must of necessity indicate that the method of dating the fossil is in error. Nature, Vol. 352, August 1, 1991 p:381
(2) The classic evolutionary problem of 'which came first, protein or DNA' has not been solved by the 'self-reproducing' RNA theory as many textbooks imply. The theory is not credible as it was based on laboratory simulations which were highly artificial, and were carried out with a 'great deal of help from the scientists'. Scientific American, February, 1991 p:100-109
(3) DNA can only be replicated in the presence of a specific enzyme which can only be manufactured by the already existing DNA. Each is absolutely essential for the other, and both must be present for the DNA to multiply. Therefore, DNA has to have been in existence in the beginning for life to be controlled by DNA. Scott M. Huse, "The Collapse of Evolution", Baker Book House: Grand Rapids (Michigan), 1983 p:93-94
(4) There is no natural chemical tendency for the series of base chemicals in the DNA molecule to line up a series of R-groups in the orderly way required for life to begin. Therefore being contrary to natural chemical laws, the base-R group relationship and the structure of DNA could not have formed by random chemical action. Scott M. Huse, "The Collapse of Evolution", Baker Book House: Grand Rapids (Michigan), 1983 p:94
(5) "The origin of the genetic code is the most baffling aspect of the problem of the origins of life and a major conceptual or experimental breakthrough may be needed before we can make any substantial progress." Written by biochemist Dr Leslie Orgel (Salk Institute, California) in the article "Darwinism at the Very Beginning of Life" in New Scientist, April 15, 1982 p:151
(6) Computer scientists have demonstrated that information does not, and cannot arise spontaneously. Information only results from the input of energy, under the all-important direction of intelligence. Therefore, as DNA is information, it cannot have been formed by natural chemical means. P. Moorhead & M. Kaplan (eds.), "Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution", Wistar Institute: Philadelphia (Pennsylvania), 1967
(7) The transformation of one species into another by viruses transferring small sections of the DNA of another species could not cause evolution for three reasons:- (1) if genes for a particular feature or action were transmitted as a small piece of DNA, the animal would not be able to utilize the code unless it had all the other structures present to support that feature, (2) there is no guarantee that without the rest of the supporting DNA code, that the feature would appear in the right place, and (3) the information transmitted would already be in existence and would not lead to the formation of a species with totally new features. Reader's Digest, March 1980
(8 ) "A scientist who won the Nobel Prize for his discovery of the DNA technique that inspired [the film] Jurassic Park was asked how likely it was that in the future, a dinosaur could be re-created from ancient DNA trapped in amber, as in the movie. Dr Kary Mullis replied in essence that it would be more realistic to start working on a time machine to go back and catch one." From Creation Ex Nihilo, Vol. 16, No. 2, March 1994, p:8, summarizing The Salt Lake Tribune, December 5, 1993



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13 Re: Origin of the DNA double helix on Fri Sep 18, 2015 5:25 am

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DNA is irreducible complex

http://reasonandscience.heavenforum.org/t2093-dna-is-irreducible-complex

Individual bases : take away the sugar in the DNA backbone = no function
Take away the phosphate in the backbone = no function
Take away the nucleic acid bases = no function
Evolution is not a driving force at this stage, since replication of the cell depends on DNA.
So the individual DNA molecules are irreducible complex
DNA in general ( the double helix )
Unless the two types, purines, and pyrimidines are present, and so the individual four bases = no function, and no hability of information storage
The enzymes and proteins for assembly and synthesis of the DNA structure must also be present, otherwise, no DNA double helix......

Origin of the DNA deoxyribonucleic acid  double helix

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

Self-organizing biochemical cycles 1

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC18793/

How were ribonucleotides first formed on the primitive earth? This is a very difficult problem. Stanley Miller's synthesis of the amino acids by sparking a reducing atmosphere (2) was the paradigm for prebiotic synthesis for many years, so at first, it was natural to suppose that similar methods would meet with equal success in the nucleotide field. However, nucleotides are intrinsically more complicated than amino acids, and it is by no means obvious that they can be obtained in a few simple steps under prebiotic conditions. A remarkable synthesis of adenine (3) and more or less plausible syntheses of the pyrimidine nucleoside bases (4) have been reported, but the synthesis of ribose and the regiospecific combination of the bases, ribose, and phosphate to give β-nucleotides remain problematical.

1) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC18793/

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14 Re: Origin of the DNA double helix on Fri Jan 29, 2016 3:28 am

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The DNA story



Like RNA, deoxyribonucleic acid (DNA) is a linear polymer of nucleotides. Each nucleotide consists of a pentose sugar, a nitrogenous base and a phosphate group. The sugar–phosphate linkages form an external backbone with the bases sticking in and hydrogen-bonding with complementary bases of the opposite sugar–phosphate backbone, zipper-fashion, producing the famous double helix structure of DNA. The helix can take on alternate forms in which it twists to alter the compactness of its spiral and bends to change its overall shape. The packing of DNA in a microscopically visible chromosome represents a 10,000-fold shortening of its actual length. Little is known of the structure of DNA in the natural state within the cell. Clearly it is dynamic, and by assuming different forms DNA controls various biological processes such as replication, transcription and recombination. This is a fruitful area for research.


The Synthesis of β-d-Ribose



The abiotic origin of DNA is beset with problems similar to those seen with RNA.48 The synthesis of deoxyribose forms the nub. We have already mentioned the difficult synthesis of even small amounts of β-d-ribose for the in vitroproduction of RNA. Furthermore, we might have expected deoxyribonucleotides to be biosynthesised de novo from deoxyribose precursors. In real life, however, DNA components (the deoxyribonucleotides dADP, dCDP, dGDP and dUDP) are synthesised from their corresponding ribonucleotides by the reduction of the C2' position. The enzymes that do this are named ribonucleotide reductases. There are three main classes of reductases. All replace the 2'-OH group of ribose via some elegant free radical mechanisms.49,50 The class III anaerobic Escherichia coli reductase is thought to be the most closely related to the common reductase ancestor from which the three main classes are presumed to have evolved. It has been proposed that the pristine reductase enzyme, similar to present-day class III enzymes, arose before the advent of photosynthesis and therefore before the appearance of oxygen. Now the E. coli class III enzyme mentioned above can be induced by culturing the bacteria under anaerobic conditions. This enzyme is an Fe-S protein that in its active form contains an oxygen-sensitive glycyl free radical.51


This poses a conundrum: the survival and continual evolution of an oxygen-sensitive enzyme when oxygen appeared. On the other hand, the class I reductases require oxygen for free radical generation. Surely they could not have evolved and operated in the anaerobic first cell in an oxygen-free environment.52 Moreover, one of the most remarkable aspects of this E. coli ribonucleotide class I reductase is its ability to maintain its highly reactive free radical state for a long period. Interestingly, this is achieved in vivo by internally generated oxygen. Four proteins have to be in place:

Flavin oxidoreductase, which releases superoxide ion (O2–),
Superoxide dismutase, to rapidly convert this destructive radical to H2O2 and O2,
A catalase, to disproportionate H2O2 to H2O and O2, and
A fourth protein, thioredoxin, that functions as a reductant.

The oxygen oxidises Fe II and a deeply buried tyrosyl residue (Tyr122). Herein lies a difficulty. The reductases are complex protein reaction centres acting in tandem on each other and on the 2'-OH group of ribose. These must all have co-evolved before DNA and along with RNA. Could this be seriously contemplated for a metabolically naive RNA “progenote”?
The origins of deoxyribose and of DNA therefore remain unsolved mysteries.


Even if the DNA molecule were assembled abiotically, there is the instability and decay of the polymer by hydrolysis of the glycosyl bonds and the hydrolytic deamination of the bases.53 Each human cell turns over 2,000–10,000 DNA purine bases every day owing to hydrolytic depurination and subsequent repair. 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. Indeed, the spontaneous errors resulting from intrinsic DNA instability are usually many times more dangerous than chance injuries from environmental causes.54 The enzymes of the DNA repair system are a marvel in themselves and have been rightfully recognised as such.55 Reports of the culture of Bacillus sphaericus from spores preserved in amber for over “25 million years” does not tally with what is known of the physico-chemical properties of DNA.56

Several DNA Paradoxes


The total amount of DNA in the haploid genome is its C-value. Intuitively we would expect that there should be a relationship between the complexity of an organism and the amount of its DNA. The failure to consistently correlate the total amount of DNA in a genome with the genetic and morphological complexity of the organism is called the C-value paradox.57 This paradox manifests itself in three ways. Many plant species have from two to ten times more DNA per cell than the human cell. Among the vertebrates with the greatest amount of DNA are the amphibians. Salamander cells contain 10–100 times more DNA than mammalian cells. It is hard to make sense of the existence of such major redundancies in organisms evolutionarily less complex than man.There is also considerable intragroup variation in DNA content where morphology does not vary much. For example, the broad bean contains about three to four times as much DNA per cell as the kidney bean. Variations of up to 100 times are found among insects and among amphibians. In other words, cellular DNA content does not correlate with phylogeny.Large stretches of DNA in the genome, say, of humans, appear to have no demonstrable function. This will be discussed later.


http://creation.com/origin-of-life-critique

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Scientists discover new clue to chemical origins of life

"We are trying to understand the chemical origins of life. One of the interesting questions is where carbohydrates come from because they are the building blocks of DNA and RNA. What we have achieved is the first step on that pathway to show how simple sugars -- threose and erythrose -- originated. We generated these sugars from a very simple set of materials that most scientists believe were around at the time that life began."

1.https://www.sciencedaily.com/releases/2012/01/120124092930.htm

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