No evidence that RNA molecules ever had the broad range of catalytic activities

No evidence that RNA molecules ever had the broad range of catalytic activities

https://reasonandscience.catsboard.com/t2243-no-evidence-that-rna-molecules-ever-had-the-broad-range-of-catalytic-activities

Paul Davies The Algorithmic Origins of Life 
Despite the conceptual elegance of the RNA world, the hypothesis faces problems, primarily due to the immense challenge of synthesizing RNA nucleotides under plausible prebiotic conditions and the susceptibility of RNA oligomers to degradation via hydrolysis 21 Due to the organizational structure of systems capable of processing algorithmic (instructional) information, it is not at all clear that a monomolecular system – where a single polymer plays the role of catalyst and informational carrier – is even logically consistent with the organization of information flow in living systems, because there is no possibility of separating information storage from information processing (that being such a distinctive feature of modern life). As such, digital–first systems (as currently posed) represent a rather trivial form of information processing that fails to capture the logical structure of life as we know it. 

We need to explain the origin of both the hardware and software aspects of life, or the job is only half finished. Explaining the chemical substrate of life and claiming it as a solution to life’s origin is like pointing to silicon and copper as an explanation for the goings-on inside a computer. It is this transition where one should expect to see a chemical system literally take-on “a life of its own”, characterized by informational dynamics which become decoupled from the dictates of local chemistry alone (while of course remaining fully consistent with those dictates). Thus the famed chicken-or-egg problem (a solely hardware issue) is not the true sticking point. Rather, the puzzle lies with something fundamentally different, a problem of causal organization having to do with the separation of informational and mechanical aspects into parallel causal narratives. The real challenge of life’s origin is thus to explain how instructional information control systems emerge naturally and spontaneously from mere molecular dynamics.

Systems of interconnected software and hardware like in the cell are irreducibly complex and  interdependent. There is no reason for information processing machinery to exist without the software, and vice versa.

Perry Marshall, Evolution 2.0, page 151:
There are problems with the RNA world hypothesis: Many scientists believe RNA is too complex to have arisen without the presence of the very same life forms it is believed to have created;  RNA is inherently unstable, so even if it did arise, it wouldn’t last long without a cell to protect it; catalysis of chemical reactions is seldom observed to occur in long RNA sequences only; and the catalytic abilities of RNA are limited. The RNA world hypothesis doesn’t actually solve the chicken-and-egg problem of RNA and proteins: You need RNA to produce proteins, but you need proteins to build the machinery to read the RNA in the first place. As a communication engineer, my objection to the RNA hypothesis is that to evolve any kind of cell, RNA would have to self-replicate. But the RNA strand formation you read about in the literature is not codebased self-replication. It’s similar to crystal growth, which does not use codes at all! RNA strand formation in a chemical lab is not in any way, shape, or form the same as DNA transcription and translation. In DNA transcription and translation, in order to convert code to proteins, you need a ribosome to transcribe the message. But in order to have a ribosome you have to have a plan for building a ribosome first. A ribosome is partly made from RNA. So before that, you have to have a code in the RNA. Many books and papers on the Origin of Life only discuss the assembly of the chemicals themselves. Nothing we know about chemicals tells us where codes come from. Saying you can get real DNA by stringing chemicals together is like telling your kid that TVs come from a glass factory

Without code there can be no self-replication. Without self-replication you can’t have reproduction. Without reproduction you can’t have evolution or natural selection.


from the book: The Logic of Chance: The Nature and Origin of Biological Evolution
By Eugene V. Koonin

https://reasonandscience.catsboard.com/t2234-the-origin-of-replication-and-translation-and-the-rna-world

The origin of replication and translation and the RNA World

The primary incentive behind the theory of self-replicating systems that Manfred Eigen outlined was to develop a simple model explaining the origin of biological information and, hence, of life itself. Eigen’s theory revealed the existence of the fundamental limit on the fidelity of replication (the Eigen threshold): If the product of the error (mutation) rate and the information capacity (genome size) is below the Eigen threshold, there will be stable inheritance and hence evolution; however, if it is above the threshold, the mutational meltdown and extinction become inevitable (Eigen, 1971). The Eigen threshold lies somewhere between 1 and 10 mutations per round of replication (Tejero, et al., 2011); regardless of the exact value, staying above the threshold fidelity is required for sustainable replication and so is a prerequisite for the start of biological evolution

Indeed, the very origin of the first organisms presents at least an appearance of a paradox because a certain minimum level of complexity is required to make self-replication possible at all; high-fidelity replication requires additional functionalities that need even more information to be encoded (Penny, 2005). However, the replication fidelity at a given point in time limits the amount of information that can be encoded in the genome. What turns this seemingly vicious circle into the (seemingly) unending spiral of increasing complexity—the Darwin-Eigen cycle, following the terminology introduced by David Penny (Penny, 2005)—is a combination of natural selection with genetic drift. Even small gains in replication fidelity are advantageous to the system, if only because of the decrease of the reproduction cost as a result of the increasing yield of viable copies of the genome. In itself, a larger genome is more of a liability than an advantage because of higher replication costs. However, moderate genome increase, such as by duplication of parts of the genome or by recombination, can be fixed via genetic drift in small populations. Replicators with a sufficiently high fidelity can take advantage of such randomly fixed and initially useless genetic material by evolving new functions, without falling off the “Eigen cliff” (see Figure 12-1B). Among such newly evolved, fitness-increasing functions will be those that increase replication fidelity, which, in turn, allows a further increase in the amount of encoded information. And so the Darwin- Eigen cycle recapitulates itself in a spiral progression, leading to a steady increase in genome complexity (see Figure 12-1A). The crucial question in the study of the origin of life is how the Darwin-Eigen cycle started—how was the minimum complexity that is required to achieve the minimally acceptable replication fidelity attained? In even the simplest modern systems, such as RNA viruses with the replication fidelity of only about 10^3 and viroids that replicate with the lowest fidelity among the known replicons (about 10^2; Gago, et al., 2009), replication is catalyzed by complex protein polymerases. The replicase itself is produced by translation of the respective mRNA(s), which is mediated by the immensely complex ribosomal apparatus. Hence, the dramatic paradox of the origin of life is that, to attain the minimum complexity required for a biological system to start on the Darwin-Eigen spiral, a system of a far greater complexity appears to be required. How such a system could evolve is a  puzzle that defeats conventional evolutionary thinking, all of which is about biological systems moving along the spiral; the solution is bound to be unusual. 
 
Or the solution might be outside the realm of philosophical naturalism, that is, intelligent design ?!!  




A protein must be able to fold into a specific 3-dimensional shape in order to have biological activity. But the forces holding the folded protein in shape are so weak that many amino acids need to be involved - imposing a minimum length on their sequence of about 70 (Kyte), and maybe 50 for nucleic acids. So trying to improve the odds of finding a biologically active macromolecule by starting with short ones, just will not work.

A similar misperception is that the first replicator need only have had poor replicating ability, which could gradually have improved (by mutation and selection of improved versions). But it is important to note that a poor replicator is more likely to degrade through miscopying than to improve its performance, and this poses a dilemma for the production of a primitive replicator. Although the common presumption is that a crude replicator can gradually improve its performance through a natural selection sort of process, in fact there is a threshold before that could take place. That is, a replicator must already have a reasonably good performance in order to be able to improve on that performance. 

In other words, natural selection cannot take place until there is a reasonably reliable replicating system. So the first replicating system would need to have arisen exclusively by chance.


The "RNA World" is essentially a hypothetical stage of life between the first replicating molecule and the highly complicated DNA-protein-based life. The chief problem facing an RNA world is that RNA cannot perform all of the functions of DNA adequately to allow for replication and transcription of proteins.

New findings challenge assumptions about origins of life
https://reasonandscience.catsboard.com/t1428-replicator-first-and-metabolism-first-scenarios
There is currently no known chemical pathway for an "RNA world" to transform into a "DNA/protein world."

http://phys.org/news/2013-09-assumptions-life.html#jCp
But for the hypothesis to be correct, ancient RNA catalysts would have had to copy multiple sets of RNA blueprints nearly as accurately as do modern-day enzymes. That's a hard sell; scientists calculate that it would take much longer than the age of the universe for randomly generated RNA molecules to evolve sufficiently to achieve the modern level of sophistication. Given Earth's age of 4.5 billion years, living systems run entirely by RNA could not have reproduced and evolved either fast or accurately enough to give rise to the vast biological complexity on Earth today.

OOL theorist Leslie Orgel notes that an "RNA World" could only form the basis for life, "if prebiotic RNA had two properties not evident today: a capacity to replicate without the help of proteins and an ability to catalyze every step of protein synthesis." The RNA world is thus a hypothetical system behind which there is little positive evidence, and much materialist philosophy: "The precise events giving rise to the RNA world remain unclear … investigators have proposed many hypotheses, but evidence in favor of each of them is fragmentary at best. The full details of how the RNA world, and life, emerged may not be revealed in the near future. 

http://www.ncbi.nlm.nih.gov/pubmed/22793875
(i) RNA is too complex a molecule to have arisen prebiotically;
(ii) RNA is inherently unstable;
(iii) catalysis is a relatively rare property of long RNA sequences only; and
(iv) the catalytic repertoire of RNA is too limited.

The best claimed evidence of an "RNA World" includes the fact that there are RNA enzymes and genomes, and that cells use RNA to convert the DNA code into proteins. However, RNA plays only a supporting role in the cell, and there is no known biochemical system completely composed of RNA.

RNA experts have created a variety of RNA molecules which can perform biochemical functions through what is commonly termed "test tube evolution." However, "test tube evolution" is just a description for what is in reality nothing more than chemical engineering in the laboratory employing Darwinian principles; that does not imply that there is some known pathway through which these molecules could arise naturally.

In order a molecule to be a self replicator , it has to be a homopolymer, of which the backbone must have the same repetitive units; they must be identical. On the prebiotic world, the generation of a homopolymer was however impossible.

Steven A. Benner, Ph.D. Chemistry, Harvard, prominent origin-of-life researcher and creator of the Foundation for Applied Molecular Evolution, was posted on Huffington Post on December 6, 2013.  In it he said,

"We have failed in any continuous way to provide a recipe that gets from the simple molecules that we know were present on early Earth to RNA." 

That lead Leslie Orgel to say :
It would take a miracle if a strand of RNA ever appeared on the primitive Earth.

(Dover, 1999, p. 218).
I would have thought it relevant to point out for biologists in general that not one self-replicating RNA has emerged to date from quadrillions (1024) of artificially synthesized, random RNA sequences 

How  could the first living cells with DNA-based molecular biology have originated by spontaneous chemical processes on the prebiotic Earth? Primordial DNA synthesis would have required the presence of specific enzymes, but how could these enzymes be synthesized without the genetic information in DNA and without RNA for translating that information into the amino acid sequence of the protein enzymes? In other words, proteins are required for DNA synthesis and DNA is required for protein synthesis.

This classic "chicken-and-egg" problem made it immensely difficult to conceive of any plausible prebiotic chemical pathway to the molecular biological system. Certainly no such chemical pathway had been demonstrated  2

Joyce and Orgel note, it seems unlikely that a structure with fewer than 40 nucleotides would be sufficient. Suppose, then, that "there is some 50-mer [RNA molecule of 50 nucleotides length]," Joyce and Orgel speculate, that "replicates with 90% fidelity. ... Would such a molecule be expected to occur within a population of random RNAs?"

Perhaps: but one such self-replicating molecule will not suffice.

"Unless the molecule can literally copy itself," Joyce and Orgel note, "that is, act simultaneously as both template and catalyst, it must encounter another copy of itself that it can use as a template." Copying any given RNA in its vicinity will lead to an error catastrophe, as the population of RNAs will decay into a collection of random sequences. But to find another copy of itself, the self-replicating RNA would need (Joyce and Orgel calculate) a library of RNA that "far exceeds the mass of the earth."18

In the face of these difficulties, they advise, one must reject the myth of a self-replicating RNA molecule that arose de novo from a soup of random polynucleotides. Not only is such a notion unrealistic in light of our current understanding of prebiotic chemistry, but it should strain the credulity of even an optimist's view of RNA's catalytic potential. If you doubt this, ask yourself whether you believe that a replicase ribozyme would arise in a solution containing nucleoside 5'-diphosphates and polynucleotide phosphorylase!

G. F. Joyce, L. E. Orgel, "Prospects for Understanding the Origin of the RNA World," In the RNA World, Cold Spring Harbor Laboratory Press, New York, 1993, p. 13.

This discussion… has, in a sense, focused on a straw man: the myth of a self-replicating RNA molecule that arose de novo from a soup of random polynucleotides. Not only is such a notion unrealistic in light of our current understanding of prebiotic chemistry, but it would strain the credulity of even an optimist's view of RNA's catalytic potential
Even if we suppose that there was self-replicating RNA in the primordial world, that numerous amino acids of every type ready to be used by RNA were available, and that all of these impossibilities somehow took place, the situation still does not lead to the formation of even one single protein. For RNA only includes information concerning the structure of proteins. Amino acids, on the other hand, are raw materials. Nevertheless, there is no mechanism for the production of proteins. To consider the existence of RNA sufficient for protein production is as nonsensical as expecting a car to assemble itself by simply throwing the blueprint onto a heap of parts piled up on top of each other. A blueprint cannot produce a car all by itself without a factory and workers to assemble the parts according to the instructions contained in the blueprint; in the same way, the blueprint contained in RNA cannot produce proteins by itself without the cooperation of other cellular components which follow the instructions contained in the RNA.

The problem of the origin of the RNA World is far from being solved. One can sketch out a logical order of events, beginning with prebiotic chemistry and ending with DNA/protein-based life. However, it must be said that the details of this process remain obscure and are not likely to be known in the near future.   3

1) http://reasonandscience.heavenforum.org/t2043-dna-and-rna-error-checking-and-repair-amazing-evidence-of-design#4671

The Logic of Chance: The Nature and Origin of Biological Evolution, Eugene V. Koonin, page 365:  
The RNA World hypothesis faces grave difficulties. First, despite all invested effort, the in vitro evolved ribozymes remain (relatively) poor catalysts for most reactions; the lack of efficient, processive ribozyme polymerases seems particularly troubling, but there is also a serious shortage of other activities, such as those required for the synthesis of nucleotides. Admittedly, it might be unrealistic to expect that experiments on in vitro evolution of ribozymes could easily mimic the actual complexity of the primordial RNA World. Although these experiments harness the power of selection, they are obviously performed on a totally different time scale and under conditions that cannot accurately reproduce the (unknown) conditions at the origin of life

The overall situation in the origin of life field appears rather grim. Even under the (highly nontrivial) assumption that monomers such as NTP are readily available, the problem of the synthesis of sufficiently stable, structurally regular polymers (RNA) is formidable, and the origin of replication and translation from such primordial RNA molecules could be an even harder problem. As emphasized repeatedly in this book, evolution by natural selection
and drift can begin only after replication with sufficient fidelity is established. Even at that stage, the evolution of translation remains highly problematic.

Origin of Life Researchers: Intelligent Design of Self-Replicating RNA Molecules Refutes Intelligent Design

A recent Nature news article remarks about the production of the first self-replicating RNA molecules capable of catalyzing their own replication. Origin of life researchers are excited about this because they think it shows one possible step in their story about how life might have arisen via natural processes, without intelligent design (ID).


 One big problem with their story: under no uncertain terms did natural processes produce this molecule. One line from the Nature article says it all: "Joyce and his colleague Tracey Lincoln made paired RNA catalysts." (emphasis added) One pro-ID chemist explained to me privately the precise design parameters that were required to produce the self-replicating enzymes and to use it to produce life:

The system is completely contrived consisting ONLY of catalysts and substrates. No competing materials or reactions were allowed. No natural analog is possible.There is a vast gulf between their reaction mixtures and anything that might possibly come from a Stanley Miller type electric discharge experiment. This requires explanation.The 5'-end of the oligonucleotides were primed for the condensation reaction by prior synthesis of the high energy triphosphate form. Simple phosphates fail to react or react at rates orders of magnitude slower. Clearly the reaction only does what the chemist intended.
Reactions were carried out at 42 deg C. --> fine-tuning --> fine-tuner!

Only one bond is formed by either of the paired enzymes. The rest of the molecule was pre-assembled by Joyce and his colleagues. What this experiment shows is that some clever chemists have spent ten years of their lives re-engineering a pair of RNA-zymes to catalyze ONE reaction. And without a constant supply of pre-fabricated component parts, nothing happens. Indeed, if anything, the road to self-assembly just got longer.

[size=13][size=13]The take-home point here is that origin-of-life experiments--while fascinating in their chemical accomplishments--demonstrate little if they do not mimic natural conditions. When intelligent agents intervene to create conditions that would never exist in the real-world, the experiments instead show the need for intelligent design to insert information to form life, not the power of material causes.
William Dembski and Jonathan Wells, in The Design of Life, likewise discuss how similar experiments generating functional ribozymes require the intelligent insertion of information at each step:

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Do SELEX experiments therefore demonstrate the power of purely materialistic forces to evolve biologically significant RNA structures under realistic prebiotic conditions? Not at all. Intelligent intervention by the experimenter is indispensable. In SELEX experiments, large pools of randomized RNA molecules are formed by intelligent synthesis and not by chance--there is no natural route to RNA (in fact, the chemical processes in nature that facilitate the formation of nucleotide bases undercut the formation of RNA's sugar-phosphate backbone and vice versa). The artificially synthesized molecules are then sifted chemically by various means to select for catalytic function. What's more, the catalytic function is specified by the investigator. Those molecules showing some activity are isolated and become templates for the next round of selection. And so on, round after round. At every step in SELEX and ribozyme (catalytic RNA) engineering experiments, the investigator is carefully arranging the outcome, even if he or she does not know the specific sequence that will emerge. It is simply irrelevant that the investigator learns the identity or structure of the evolved ribozyme only after the experiment is over. The investigator first had to specify a precise catalytic function. Next, the investigator had to specify a fitness measure gauging degree of catalytic function for a given polynucleotide. And finally, the investigator had to run an experiment to optimize the fitness measure. Only then does the investigator obtain a polynucleotide exhibiting the catalytic function of interest. In all such experiments the investigator is inserting crucial information at every step. Ribozyme engineering is engineering. Indeed, there is no evidence that natural processes as found in nature can do their own ribozyme engineering without the aid of human intelligence.
(William Dembski & Jonathan Wells, The Design of Life: Discovering Sign of Intelligence in Biological Systems, General Notes, pg. 59)

Incredibly, the Nature news article about these newly constructed RNA molecules offers the following punchline:

"Ellington says that the observation that different winning enzymes emerge in different conditions is crucial because it further undermines the intelligent-design idea that life is too complex to have arisen without the intervention of a supernatural being."

Ignoring the fact that Ellington wrongly mischaracterizes ID as a necessary appeal to the "supernatural," it's amazing to believe that intelligent agency is now being cited as a refutation of intelligent agency. For some materialists, it seems that no form of evidence can count against their viewpoint.

http://www.evolutionnews.org/2009/02/origin_of_life_researchers_int016441.html

No evidence that RNA molecules ever had the broad range of catalytic activities

in the early 1980s, the discovery of self-splicing, catalytic RNA molecules (in the ciliated protozoan Tetrahymena thermophila), put molecular flesh on the speculative bones of the idea of an early evolutionary stage dominated by RNA. These catalytic RNA molecules have subsequently been termed "ribozymes." "One can contemplate an RNA World," wrote Walter Gilbert in 1986, "containing only RNA molecules that serve to catalyze the synthesis of themselves." 2

The primordial...conundrum -- which came first, informational polynucleotides or functional polypeptides -- was obviated by the simple but elegant compaction of both genetic information and catalytic function into the same molecule

RNA molecules are not just strings of symbols that carry information in an abstract way. They also have chemical personalities that affect their behavior. In particular, the specific sequence of nucleotides governs how the molecule folds up in solution. Just as the nucleotides in a polynucleotide can pair with free complementary nucleotides in their environment to form a new polymer, so they can pair with complementary nucleotide residues within the polymer itself. A sequence GGGG in one part of a polynucleotide chain can form a relatively strong association with a CCCC sequence in another region of the same molecule. Such associations produce complex three-dimensional patterns of folding, and the molecule as a whole takes on a specific shape that depends entirely on the sequence of its nucleotides


upload pic

Conformation of an RNA molecule.Nucleotide pairing between different regions of the same polynucleotide (RNA) chain causes the molecule to adopt a distinctive shape.

The three-dimensional folded structure of a polynucleotide affects its stability, its actions on other molecules, and its ability to replicate, so that not all polynucleotide shapes will be equally successful in a replicating mixture.

An RNA molecule therefore has two special characteristics: it carries information encoded in its nucleotide sequence that it can pass on by the process of replication, and it has a specific folded structure that enables it to interact selectively with other molecules and determines how it will respond to the ambient conditions.

The only problem is that random sequences are not information.....

The odds of suddenly having a self-replicating RNA pop out of a prebiotic soup are vanishingly low," says evolutionary biochemist Niles Lehman of Portland State University in Oregon.


Moreover, errors inevitably occur in any copying process, and imperfect copies of the originals will be propagated. With repeated replication, therefore, new variant sequences of nucleotides will be continually generated. Thus, in laboratory studies, replicating systems of RNA molecules have been shown to undergo a form of natural selection in which different favorable sequences eventually predominate, depending on the exact conditions.

"Polymerization" thus requires "dehydration synthesis." Many have proposed alternatives to get around this stumbling block. Since polymerization reactions also require an input of energy, heating and drying has been theorized to input energy, and remove the water. However, this heating and drying has to take place in such a way as to not wipeout the created polymers. Some theorized locations for this reaction have been intertidal pools or volcanic ridges where repeated cycles of heating and drying can take place. The problem is that all the water must be removed, but you don’t want to over-cook the polymers you are creating. Organic molecules tend to break down rapidly (i.e. cook) in the presence of heat. This would have to be a very fine balancing act that would also requires rapid input of organic material to overcome the rate at which the heat would destroy the molecules. A successful scenario is very difficult to imagine. Even under ideal laboratory conditions using pure monomers and carefully measured heating and drying cycles, only small amounts of polymers have been created. 1


OOL theorist Leslie Orgel notes that an "RNA World" could only form the basis for life, "if prebiotic RNA had two properties not evident today: a capacity to replicate without the help of proteins and an ability to catalyze every step of protein synthesis." The RNA world is thus a hypothetical system behind which there is little positive evidence, and much materialist philosophy:
"The precise events giving rise to the RNA world remain unclear … investigators have proposed many hypotheses, but evidence in favor of each of them is fragmentary at best. The full details of how the RNA world, and life, emerged may not be revealed in the near future.

The best claimed evidence of an "RNA World" includes the fact that there are RNA enzymes and genomes, and that cells use RNA to convert the DNA code into proteins.42 However, RNA plays only a supporting role in the cell, and there is no known biochemical system completely composed of RNA.42

RNA experts have created a variety of RNA molecules which can perform biochemical functions through what is commonly termed "test tube evolution." However, "test tube evolution" is just a description for what is in reality nothing more than chemical engineering in the laboratory employing Darwinian principles; that does not imply that there is some known pathway through which these molecules could arise naturally.

The most interesting RNA molecule synthesized is perhaps an RNA "polymerase" which can replicate 14 base pairs of RNA.42 Yet, the polymerase itself is 200 pairs long.42 As Gerald Joyce noted, OOL theorists are thus 14 / 200 towards achieving a possible model molecule for the RNA World. $2 However, Joyce also noted that the replication accuracy of this molecule is too poor to allow for it to persist as a functional form of life.42

These purely speculative scenarios aren't bad on their own merits, but they are just another reminder of the philosophical presupposition driving this research in the first place: naturalism. Only when scientists assume there must be a natural explanation do they turn to completely unfalsifiable unverifiable and incomplete speculatory hypotheses.

The theory then says that some unknown precursor of RNA turned into RNA through an unknown process. This "RNA-world hypothesis" states that life then arose from a population of self-replicating RNA molecules. RNA is a sister molecule to DNA, used when DNA breaks up to create proteins or replicate. Like a copy from the library, RNA has a complementary code to DNA and goes out to do the dirty work. A few types of RNA have been known to have auto-catalytic self-replicating abilities, however this scenario inevitably encounters a chicken and egg problem18.

But these molecules must be encapsulated within a "cell wall structure" or a small protective enclosure from the outside world. But, the protective cell requires replicating genetic machinery to be created. Thus, we now have a "chicken and egg scenario"--which came first? the self-replicating machinery (which needs a cell to operate), or the cell itself, which protects (and is created by) the cellular machinery? The answer is neither came first for both are required for self-replication. How could self-replicating RNA arise naturally when it essentially is an irreducibly complex system that cannot functionally replicate without other distinct components.



free photo upload

Three successive steps in the evolution of a self-replicating system of RNA molecules capable of directing protein synthesis.

How  could the first living cells with DNA-based molecular biology have originated by spontaneous chemical processes on the prebiotic Earth? Primordial DNA synthesis would have required the presence of specific enzymes, but how could these enzymes be synthesized without the genetic information in DNA and without RNA for translating that information into the amino acid sequence of the protein enzymes? In other words, proteins are required for DNA synthesis and DNA is required for protein synthesis.

This classic "chicken-and-egg" problem made it immensely difficult to conceive of any plausible prebiotic chemical pathway to the molecular biological system. Certainly no such chemical pathway had been demonstrated  2

Joyce and Orgel note, it seems unlikely that a structure with fewer than 40 nucleotides would be sufficient. Suppose, then, that "there is some 50-mer [RNA molecule of 50 nucleotides length]," Joyce and Orgel speculate, that "replicates with 90% fidelity. ... Would such a molecule be expected to occur within a population of random RNAs?"

Perhaps: but one such self-replicating molecule will not suffice.

"Unless the molecule can literally copy itself," Joyce and Orgel note, "that is, act simultaneously as both template and catalyst, it must encounter another copy of itself that it can use as a template." Copying any given RNA in its vicinity will lead to an error catastrophe, as the population of RNAs will decay into a collection of random sequences. But to find another copy of itself, the self-replicating RNA would need (Joyce and Orgel calculate) a library of RNA that "far exceeds the mass of the earth."

In the face of these difficulties, they advise, one must reject

the myth of a self-replicating RNA molecule that arose de novo from a soup of random polynucleotides. Not only is such a notion unrealistic in light of our current understanding of prebiotic chemistry, but it should strain the credulity of even an optimist's view of RNA's catalytic potential. If you doubt this, ask yourself whether you believe that a replicase ribozyme would arise in a solution containing nucleoside 5'-diphosphates and polynucleotide phosphorylase!

Stephen Meyer :

The (historical) question that must be asked about biological origins is not "Which materialistic scenario will prove adequate?" but "How did life as we know it actually arise on earth?" Since one of the logically appropriate answers to this latter question is that "Life was designed by an intelligent agent that existed before the advent of humans," I believe it is anti-intellectual to exclude the "design hypothesis" without consideration of all the evidence, including the most current evidence, that would support it


1) http://www.ideacenter.org/contentmgr/showdetails.php/id/838
2) http://www.arn.org/docs/odesign/od171/rnaworld171.htm

No evidence that RNA molecules ever had the broad range of catalytic activities

Paul Davies The Algorithmic Origins of Life 
Despite the conceptual elegance of the RNA world, the hypothesis faces problems, primarily due to the immense challenge of synthesizing RNA nucleotides under plausible prebiotic conditions and the susceptibility of RNA oligomers to degradation via hydrolysis 21 Due to the organizational structure of systems capable of processing algorithmic (instructional) information, it is not at all clear that a monomolecular system – where a single polymer plays the role of catalyst and informational carrier – is even logically consistent with the organization of information flow in living systems, because there is no possibility of separating information storage from information processing (that being such a distinctive feature of modern life). As such, digital–first systems (as currently posed) represent a rather trivial form of information processing that fails to capture the logical structure of life as we know it. 

We need to explain the origin of both the hardware and software aspects of life, or the job is only half finished. Explaining the chemical substrate of life and claiming it as a solution to life’s origin is like pointing to silicon and copper as an explanation for the goings-on inside a computer. It is this transition where one should expect to see a chemical system literally take-on “a life of its own”, characterized by informational dynamics which become decoupled from the dictates of local chemistry alone (while of course remaining fully consistent with those dictates). Thus the famed chicken-or-egg problem (a solely hardware issue) is not the true sticking point. Rather, the puzzle lies with something fundamentally different, a problem of causal organization having to do with the separation of informational and mechanical aspects into parallel causal narratives. The real challenge of life’s origin is thus to explain how instructional information control systems emerge naturally and spontaneously from mere molecular dynamics.

Systems of interconnected software and hardware like in the cell are irreducibly complex and  interdependent. There is no reason for information processing machinery to exist without the software, and vice versa.

Perry Marshall, Evolution 2.0, page 151:
There are problems with the RNA world hypothesis: Many scientists believe RNA is too complex to have arisen without the presence of the very same life forms it is believed to have created;  RNA is inherently unstable, so even if it did arise, it wouldn’t last long without a cell to protect it; catalysis of chemical reactions is seldom observed to occur in long RNA sequences only; and the catalytic abilities of RNA are limited. The RNA world hypothesis doesn’t actually solve the chicken-and-egg problem of RNA and proteins: You need RNA to produce proteins, but you need proteins to build the machinery to read the RNA in the first place. As a communication engineer, my objection to the RNA hypothesis is that to evolve any kind of cell, RNA would have to self-replicate. But the RNA strand formation you read about in the literature is not codebased self-replication. It’s similar to crystal growth, which does not use codes at all! RNA strand formation in a chemical lab is not in any way, shape, or form the same as DNA transcription and translation. In DNA transcription and translation, in order to convert code to proteins, you need a ribosome to transcribe the message. But in order to have a ribosome you have to have a plan for building a ribosome first. A ribosome is partly made from RNA. So before that, you have to have a code in the RNA. Many books and papers on the Origin of Life only discuss the assembly of the chemicals themselves. Nothing we know about chemicals tells us where codes come from. Saying you can get real DNA by stringing chemicals together is like telling your kid that TVs come from a glass factory

Without code, there can be no self-replication. Without self-replication, you can’t have reproduction. Without reproduction, you can’t have evolution or natural selection.


from the book: The Logic of Chance: The Nature and Origin of Biological Evolution
By Eugene V. Koonin

The primary incentive behind the theory of self-replicating systems that Manfred Eigen outlined was to develop a simple model explaining the origin of biological information and, hence, of life itself. Eigen’s theory revealed the existence of the fundamental limit on the fidelity of replication (the Eigen threshold): If the product of the error (mutation) rate and the information capacity (genome size) is below the Eigen threshold, there will be stable inheritance and hence evolution; however, if it is above the threshold, the mutational meltdown and extinction become inevitable (Eigen, 1971). The Eigen threshold lies somewhere between 1 and 10 mutations per round of replication (Tejero, et al., 2011); regardless of the exact value, staying above the threshold fidelity is required for sustainable replication and so is a prerequisite for the start of biological evolution

Indeed, the very origin of the first organisms presents at least an appearance of a paradox because a certain minimum level of complexity is required to make self-replication possible at all; high-fidelity replication requires additional functionalities that need even more information to be encoded (Penny, 2005). However, the replication fidelity at a given point in time limits the amount of information that can be encoded in the genome. What turns this seemingly vicious circle into the (seemingly) unending spiral of increasing complexity—the Darwin-Eigen cycle, following the terminology introduced by David Penny (Penny, 2005)—is a combination of natural selection with genetic drift. Even small gains in replication fidelity are advantageous to the system, if only because of the decrease of the reproduction cost as a result of the increasing yield of viable copies of the genome. In itself, a larger genome is more of a liability than an advantage because of higher replication costs. However, moderate genome increase, such as by duplication of parts of the genome or by recombination, can be fixed via genetic drift in small populations. Replicators with a sufficiently high fidelity can take advantage of such randomly fixed and initially useless genetic material by evolving new functions, without falling off the “Eigen cliff” (see Figure 12-1B). Among such newly evolved, fitness-increasing functions will be those that increase replication fidelity, which, in turn, allows a further increase in the amount of encoded information. And so the Darwin- Eigen cycle recapitulates itself in a spiral progression, leading to a steady increase in genome complexity (see Figure 12-1A). The crucial question in the study of the origin of life is how the Darwin-Eigen cycle started—how was the minimum complexity that is required to achieve the minimally acceptable replication fidelity attained? In even the simplest modern systems, such as RNA viruses with the replication fidelity of only about 10^3 and viroids that replicate with the lowest fidelity among the known replicons (about 10^2; Gago, et al., 2009), replication is catalyzed by complex protein polymerases. The replicase itself is produced by translation of the respective mRNA(s), which is mediated by the immensely complex ribosomal apparatus. Hence, the dramatic paradox of the origin of life is that, to attain the minimum complexity required for a biological system to start on the Darwin-Eigen spiral, a system of a far greater complexity appears to be required. How such a system could evolve is a  puzzle that defeats conventional evolutionary thinking, all of which is about biological systems moving along the spiral; the solution is bound to be unusual. 
 
Or the solution might be outside the realm of philosophical naturalism, that is, intelligent design ?!!