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This is my personal virtual library, where i collect information, which leads in my view to Intelligent Design as the best explanation of the origin of the physical Universe, life, and biodiversity


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Intelligent Design, the best explanation of Origins » Origin of life » The RNA & DNA World » RNA & DNA: It's prebiotic synthesis: Impossible !!

RNA & DNA: It's prebiotic synthesis: Impossible !!

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Otangelo


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RNA & DNA: It's prebiotic synthesis: Impossible !! Part 1
https://www.youtube.com/watch?v=-ZFlmL_BsXE

RNA & DNA: It's prebiotic synthesis: Impossible !! Part 2
https://www.youtube.com/watch?v=dv4mUjmuRRU

Main points addressed in the video
Synthesis of nitrogenous bases in prebiotic environments
- High-energy precursors to produce purines and pyrimidines would have had to be produced in a sufficiently concentrated form. There is no known prebiotic route to this.  
- Scientists have failed to produce cytosine in spark-discharge experiments, nor has cytosine been recovered from meteorites or extraterrestrial sources. The deamination of cytosine and its destruction by other processes such as photochemical reactions place severe constraints on prebiotic cytosine syntheses.
- The origin of guanine bases has proven to be a particular challenge. While the other three bases of RNA  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.
- Adenine synthesis requires unreasonable Hydrogen cyanide concentrations. Adenine deaminates 37°C with a half-life of 80 years. 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."
- Uracil has also a half-life of only 12 years at 100◦C. For nucleobases to accumulate in prebiotic environments, they must be synthesized at rates that exceed their decomposition.
Ribose: Synthesis problems of the Pentose 5 carbon sugar ring
The best-studied mechanism relevant to the prebiotic synthesis of ribose is the formose reaction. Several problems have been recognized for the ribose synthesis via the formose reaction. The formose reaction is very complex. It depends on the presence of a suitable inorganic catalyst. Ribose is merely an intermediate product among a broad suite of compounds including sugars with more or fewer carbons.
The phosphate group

On prebiotic earth, however, there would have been no way to activate phosphate somehow, in order to promote the energy dispendious reaction.

Prebiotic RNA and DNA synthesis
1. No prebiotic mechanism is known to select:
- Right-handed configurations of RNA and DNA
- The right backbone sugar
- How to get size complementarity of the nucleotide bases to form a DNA strand and strands of the DNA molecule running in the opposite directions
2. Bringing all the parts together and joining them in the right position
- Attach the nucleic bases to the ribose and in a repetitive manner at the same, correct place, and the backbone being a repetitive homopolymer
- Prebiotic glycosidic bond formation between nucleosides and the base
- Prebiotic phosphodiester bond formation
- Fine-tuning of the strength of the hydrogen base pairing forces
3. The instability, degradation, and asphalt problem
- Bonds that are thermodynamically unstable in water, and overall intrinsic instability. RNA’s nucleotide building blocks degrade at warm temperatures in time periods ranging from nineteen days to twelve years. These extremely short survival rates for the four RNA nucleotide building blocks suggest why life’s origin would have to be virtually instantaneous—all the necessary RNA molecules would have to be assembled before any of the nucleotide building blocks decayed.
4. The energy problem
- Doing things costs energy. There has to be a ready source of energy to produce RNA. In modern cells, energy is consumed to make RNA.
5. The minimal nucleotide quantity problem.
- The prebiotic conditions would have had to be right for reactions to give perceptible yields of bases that could pair with each other.
6. The Water Paradox  
- The hydrolytic deamination of DNA and RNA nucleobases is rapid and irreversible, as is the base-catalyzed cleavage of RNA in water. This leads to a paradox: RNA requires water to do its job, but RNA cannot emerge in water and cannot replicate with sufficient fidelity in water without sophisticated repair mechanisms in place.
7.The transition problem from prebiotic to biochemical synthesis
- Even if all this in a freaky accident occurred by random events, that still says nothing about the huge gap and enormous transition that would be still ahead to arrive at a fully functional interlocked and interdependent metabolic network, where complex biosynthesis pathways produce nucleotides in modern cells.
Unguided prebiotic synthesis of RNA and DNA: an unsolved riddle!

The origin of the RNA and DNA molecule is an origin of life problem, not evolution.

Steve Benner, one of the world’s leading authorities on abiogenesis:  The “origins problem” CANNOT be solved.
Graham Cairns-Smith: The odds against a successful unguided synthesis of a batch of primed nucleotide on the primitive Earth would be a huge number, represented approximately by a 1 followed by 109 zeros ( 10^109). 'The odds are enormous against its being coincidence. No figures could express them.'







RNA & DNA: It's prebiotic synthesis: Impossible !!  

https://reasonandscience.catsboard.com/t2865-rna-dna-it-s-prebiotic-synthesis-impossible

RNA & DNA: It's prebiotic synthesis: Impossible !! Part 1
https://www.youtube.com/watch?v=-ZFlmL_BsXE

RNA & DNA: It's prebiotic synthesis: Impossible !! Part 2
https://www.youtube.com/watch?v=dv4mUjmuRRU

Main points addressed in the video

Synthesis of nitrogenous bases in prebiotic environments
- High-energy precursors to produce purines and pyrimidines would have had to be produced in a sufficiently concentrated form. There is no known prebiotic route to this.  
- Scientists have failed to produce cytosine in spark-discharge experiments, nor has cytosine been recovered from meteorites or extraterrestrial sources. The deamination of cytosine and its destruction by other processes such as photochemical reactions place severe constraints on prebiotic cytosine syntheses.
- The origin of guanine bases has proven to be a particular challenge. While the other three bases of RNA  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.
- Adenine synthesis requires unreasonable Hydrogen cyanide concentrations. Adenine deaminates 37°C with a half-life of 80 years. 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."
- Uracil has also a half-life of only 12 years at 100◦C. For nucleobases to accumulate in prebiotic environments, they must be synthesized at rates that exceed their decomposition.

Ribose: Synthesis problems of the Pentose 5 carbon sugar ring
The best-studied mechanism relevant to the prebiotic synthesis of ribose is the formose reaction. Several problems have been recognized for the ribose synthesis via the formose reaction. The formose reaction is very complex. It depends on the presence of a suitable inorganic catalyst. Ribose is merely an intermediate product among a broad suite of compounds including sugars with more or fewer carbons.

The phosphate group
On prebiotic earth, however, there would have been no way to activate phosphate somehow, in order to promote the energy dispendious reaction.

Prebiotic RNA and DNA synthesis

1. No prebiotic mechanism is known to select: 
- Right-handed configurations of RNA and DNA
- The right backbone sugar
- How to get size complementarity of the nucleotide bases to form a DNA strand and strands of the DNA molecule running in the opposite directions

2. Bringing all the parts together and joining them in the right position 
- Attach the nucleic bases to the ribose and in a repetitive manner at the same, correct place, and the backbone being a repetitive homopolymer
- Prebiotic glycosidic bond formation between nucleosides and the base
- Prebiotic phosphodiester bond formation
- Fine-tuning of the strength of the hydrogen base pairing forces

3. The instability, degradation, and asphalt problem 
- Bonds that are thermodynamically unstable in water, and overall intrinsic instability. RNA’s nucleotide building blocks degrade at warm temperatures in time periods ranging from nineteen days to twelve years. These extremely short survival rates for the four RNA nucleotide building blocks suggest why life’s origin would have to be virtually instantaneous—all the necessary RNA molecules would have to be assembled before any of the nucleotide building blocks decayed.

4. The energy problem
- Doing things costs energy. There has to be a ready source of energy to produce RNA. In modern cells, energy is consumed to make RNA.

5. The minimal nucleotide quantity problem.
- The prebiotic conditions would have had to be right for reactions to give perceptible yields of bases that could pair with each other.

6. The Water Paradox  
- The hydrolytic deamination of DNA and RNA nucleobases is rapid and irreversible, as is the base-catalyzed cleavage of RNA in water. This leads to a paradox: RNA requires water to do its job, but RNA cannot emerge in water and cannot replicate with sufficient fidelity in water without sophisticated repair mechanisms in place.

7.The transition problem from prebiotic to biochemical synthesis 
- Even if all this in a freaky accident occurred by random events, that still says nothing about the huge gap and enormous transition that would be still ahead to arrive at a fully functional interlocked and interdependent metabolic network, where complex biosynthesis pathways produce nucleotides in modern cells.

Unguided prebiotic synthesis of RNA and DNA: an unsolved riddle!

The origin of the RNA and DNA molecule is an origin of life problem, not evolution.
Steve Benner, one of the world’s leading authorities on abiogenesis:  The “origins problem” CANNOT be solved.
Graham Cairns-Smith: The odds against a successful unguided synthesis of a batch of primed nucleotide on the primitive Earth would be a huge number, represented approximately by a 1 followed by 109 zeros ( 10^109). 'The odds are enormous against its being coincidence. No figures could express them.'


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James Watson at left and Francis Crick discovered the structure of the DNA (deoxyribonucleic acid) molecule in 1953.  DNA are the molecules which make up the “alphabet” which specifies biological heredity.  DNA are the molecules which store the blueprint of life, and as such, hold a central indispensable position.

The RNA polymerase machine complex transcribes the instructional information stored in DNA into RNA. RNA is built of (almost) the same four-letter alphabet as DNA. It is more fragile, and as such, it could also be an information carrier, but less adequate long term.

Who wants to find answers about how life started, needs to find compelling explanations about how RNA and DNA first emerged on earth. In all known living beings, genetic information flows from DNA to RNA to proteins

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Their work on the structure of DNA was performed with some access to the X-ray crystallography of Maurice Wilkins and Rosalind Franklin at King's College London. Combining all of this work led to the deduction that DNA exists as a double helix. This information was critical for their further progress. They obtained this information as part of a report by Franklin to the Medical Research Council. 

The report was by no means secret, but it put the critical data on the parameters of the helix (base spacing, helical repeat, number of units per turn of the helix, and diameter of the helix) in the hands of two who had contributed none of those data. 

With this information, they could begin to build realistic models. The big problem was where to put the purine and pyrimidine bases. Details of the diffraction pattern indicated two strands, and indicated that the relatively massive phosphate ribose backbones must be on the outside, leaving the bases in the center of the double helix.

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Crick, Watson and Wilkins shared the 1962 Nobel Prize for Physiology or Medicine, Franklin having died of cancer in 1958.

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Four major classes of organic molecules are found in living cells. All forms of life have organic molecules and macromolecules that fall into these four broad categories, based on their chemical and biological properties: carbohydrates, lipids, proteins, and nucleic acids. 

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Nucleotides are essential to cellular metabolism, and nucleic acids are the molecules of genetic information storage and expression.

General description of the structure of the RNA and DNA molecule


DNA is the molecule of life, which contains the blueprint, or instructions to make for example proteins that perform most life functions. 

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Nucleotides are building blocks for DNA and RNA. The two classes of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA molecules store genetic information coded in the sequence of their building blocks.  

DNA can be considered as a modified form of RNA since the ribose sugar in RNA is transformed into deoxyribose in DNA at the 5 prime positions ( see the red circle in the picture above ), and the uracil base is methylated into thymidine ( More about this, later). The structural difference between these sugars is that ribonucleic acid contains a hydroxyl (-OH) group, whereas deoxyribonucleic acid contains only a hydrogen atom in the place of this hydroxyl group.

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Nucleotides which contain deoxyribonucleic acid are known as deoxyribonucleotides.  Those containing ribonucleic acid are known as ribonucleotides. Thus, the sugar molecule determines whether a nucleotide forms part of a DNA molecule or a RNA molecule. 

These molecules consist of three components: a phosphate, a ribose sugar, and a nitrogenous (nitrogen-containing) ring compound that behaves as a base.  The nucleotide is the repeating structural unit of both DNA and RNA. 

The picture shows the repeating unit of nucleotides found in DNA and RNA. DNA and RNA contain deoxyribose and ribose respectively as its sugar and the bases attached. The locations of the attachment sites of the base and phosphate to the sugar molecule are important to the nucleotide’s function, and how prebiotic events supposedly came up with the right configuration is one of the unsolved riddles. 

The nitrogenous base
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Nucleotide bases appear in two forms: A single-ring nitrogenous base, called a pyrimidine, and a double-ringed base, called a purine.


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High-energy precursors to produce purines and pyrimidines would have had to be produced in a sufficiently concentrated form. There is no known prebiotic route to this.  

Scientists have failed to produce cytosine in spark-discharge experiments, nor has cytosine been recovered from meteorites or extraterrestrial sources. The deamination of cytosine and its destruction by other processes such as photochemical reactions place severe constraints on prebiotic cytosine syntheses. 

The origin of guanine bases has proven to be a particular challenge. While the other three bases of RNA  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.

Adenine synthesis requires unreasonable Hydrogen cyanide concentrations. Adenine deaminates 37°C with a half-life of 80 years. 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."

Uracil has also a half-life of only 12 years at 100◦C. For nucleobases to accumulate in prebiotic environments, they must be synthesized at rates that exceed their decomposition.

Ribose: The Pentose 5 carbon sugar ring of RNA and DNA

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DNA has the ribose sugar in RNA transformed into deoxyribose in DNA at the 2 prime positions. A base is attached to the 1 prime carbon atom, and a phosphate group is attached at the 5 prime positions. Compared with ribose, deoxyribose lacks a single oxygen atom at the 2 prime positions; the prefix deoxy- (meaning without oxygen) refers to this missing atom.

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The pentose sugar is a 5-carbon monosaccharide. These form two groups: aldopentoses and ketopentoses. The pentose sugars found in nucleotides are aldopentoses. Deoxyribose and ribose are two of these sugars. A DNA strand is formed when the nitrogenous bases are joined by hydrogen bonds, and the phosphates of one group are joined to the pentose sugars of the next group with a phosphodiester bond.

Ribose is a monosaccharide containing five carbon atoms. d-ribose is present as the six different forms. The β-d-furanose form is extensively used in biological systems as a component of RNA. The best-studied mechanism relevant to the prebiotic synthesis of ribose is the formose reaction.

Several problems have been recognized for the ribose synthesis via the formose reaction. The formose reaction is very complex. It depends on the presence of a suitable inorganic catalyst. Ribose is merely an intermediate product among a broad suite of compounds including sugars with more or fewer carbons.

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The reality of the formose reaction is that it descends into an inextricable mixture. The vast array of sugars produced is overwhelming and the intrinsic lack of selectivity for ribose is its undoing. Ultimately, the formose reaction produces a disastrously complex mixture of linear and branched aldo and keto-sugars in the racemic forms.

The consequences of such uncontrolled reactivity is that ribose is formed in less than 1% yield among a plethora of isomers and homologs. The instability of ribose prevents its accumulation and requires it to undergo extremely rapid onward conversion to ribonucleosides before the free sugar is lost to rapid degradation. 

There are no further alternatives: Either chance "choose" by lucky random events the five-membered ring ribofuranose backbone for DNA and RNA, or it was a choice by intelligence with specific purposes. What makes more sense?

This reaction requires a high concentration of  Formaldehyde, which, however, readily undergoes a variety of reactions in aqueous solutions. Another problem is that ribose is unstable and rapidly decomposes in water. 

Furthermore, as Stanley Miller and his colleagues recently reported, "ribose and other sugars have surprisingly short half-lives for decomposition at neutral pH, making it very unlikely that sugars were available as prebiotic reagents."

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Leslie Orgel concludes: Some progress has been made in the search for an efficient and specific prebiotic synthesis of ribose and its phosphates. However, in every scenario, there are still a number of obstacles to the completion of a synthesis that yields significant amounts of sufficiently pure ribose in a form that could readily be incorporated into nucleotides.

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There have been a wide variety of attempts and proposals to try to solve the riddle, but up to date, without success. The article in Science magazine from 2016 admits: Ribose is the central molecular subunit in RNA, but the prebiotic origin of ribose remains unknown.

And a recent research paper from 2018 reports: Even if some progress has been made to understand the ribose formation under prebiotic conditions, each suggested route presents obstacles, limiting ribose yield and purity necessary to form nucleotides. A selective pathway has yet to be elucidated.

The third component of a nucleotide is a phosphate group

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Phosphorus is the third essential element making part of the structures of DNA and RNA. It is perfect to form a stable backbone for the DNA molecule. Phosphates can form two phosphodiester bonds with two sugars at the same time and connect two nucleotides. Phosphorus is difficult to dissolve, and that would be a problem both in an aquatic as-as well on a terrestrial environment.

Phosphoesters form the backbone of DNA molecules. 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.

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Phosphodiester bonds are central to all life on Earth as they make up the backbone of the strands of nucleic acid. 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 ribose 5-carbon rings over two ester bonds. 

On prebiotic earth, however, there would have been no way to activate phosphate somehow, in order to promote the energy dispendious reaction. 

That adds up to the fact that concentrations on earth are very low.  So far, no geochemical process that led to abiotic production of polyphosphates in high yield on the Earth has been discovered. 

The phosphate is connected to ribose which is connected to the nitrogenous base. Each of the 3 parts of nucleotides must be just right in size, form, and must fit together. The bonds must have the right forces in order to form the spiral form DNA molecule. And there would have to be enough units concentrated at the same place on prebiotic earth of the four bases in order to be able to form a self-replicating RNA molecule if the RNA world is supposed to be true.

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A nucleotide is differentiated from a nucleoside by one phosphate group. Accordingly, a nucleotide can also be a nucleoside monophosphate. If more phosphates bond to the nucleotide (nucleoside monophosphate) it can become a nucleoside diphosphate (if two phosphates bond), or a nucleoside triphosphate (if three phosphates bond), such as adenosine triphosphate (ATP). 

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Adenosine triphosphate, or ATP, is the energy currency in the cell, a crucial component of respiration and photosynthesis, amongst other processes.

The base, sugar, and phosphate need to be joined together correctly - involving two endothermic condensation reactions involved in joining the nucleotides, which means it has to absorb energy from its surroundings. In other words, compared with polymerization to make proteins, nucleotides are even harder to synthesize and easier to destroy; in fact, to date, there are no reports of nucleotides arising from inorganic compounds in primaeval soup experiments. 



Prebiotic RNA and DNA synthesis


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What must be explained, is the origin and prebiotic making of nucleotides, that is adenine, guanine, cytosine,  uracil and thymine and the transition to enzymatic biosynthesis of these. 

The emergence in the 1980s of the RNA world as a major theory for the origin of life led to increased attention on the prebiotic synthesis of simple RNA and RNA-like molecules. RNA is a complex, polymeric structure. But its prebiotic synthesis faces many problems, of which we will give a closer look just to a few. 

1. Selecting the right components
1a. Selecting right-handed configurations of RNA and DNA
1b. Selecting the right backbone sugar
1c. Size Complementarity of the nucleotide bases to form a DNA strand and strands of the DNA molecule running in the opposite directions

2. Bringing all the parts together and joining them in the right position Attach the nucleic bases to the ribose and in a repetitive manner at the same, correct place, and the backbone being a repetitive homopolymer
2a. Glycosidic bond formation between nucleosides and the base
2b. Prebiotic phosphodiester bond formation
2c. Fine-tuning of the strength of the hydrogen base pairing forces

3. The instability, degradation, and asphalt problem Bonds that are thermodynamically unstable in water, and overall intrinsic instability. RNA’s nucleotide building blocks degrade at warm temperatures in time periods ranging from nineteen days to twelve years. These extremely short survival rates for the four RNA nucleotide building blocks suggest why life’s origin would have to be virtually instantaneous—all the necessary RNA molecules would have to be assembled before any of the nucleotide building blocks decayed.

4. The energy problem: Doing things costs energy. There has to be a ready source of energy to produce RNA. In modern cells, energy is consumed to make RNA. 

5. The minimal nucleotide quantity problem.  The prebiotic conditions would have had to be right for reactions to give perceptible yields of bases that could pair with each other.

6. The Water Paradox:  The hydrolytic deamination of DNA and RNA nucleobases is rapid and irreversible, as is the base-catalyzed cleavage of RNA in water. This leads to a paradox: RNA requires water to do its job, but RNA cannot emerge in water and cannot replicate with sufficient fidelity in water without sophisticated repair mechanisms in place.

7 .The transition problem from prebiotic to biochemical synthesis Even if all this in a freaky accident occurred by random events, that still says nothing about the huge gap and enormous transition that would be still ahead to arrive at a fully functional interlocked and interdependent metabolic network, where  complex biosynthesis pathways produce nucleotides in modern cells.


1. Selecting the right components

1a. Selecting right-handed configurations of RNA and DNA
Once the three components would have been synthesized prebiotically, they would have had to be separated from the confusing jumble of similar molecules nearby, and they would have had to become sufficiently concentrated in order to move to the next steps, to join them to form nucleosides, and nucleotides. 

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At a chemical level, a deep bias permeates all of biology. The molecules that make up DNA and other nucleic acids such as RNA have an inherent “handedness.” These molecules can exist in two mirror-image forms, but only the right-handed version is found in living organisms. Handedness serves an essential function in living beings; many of the chemical reactions that drive our cells only work with molecules of the correct handedness.

DNA takes on this form for a variety of reasons, all of which have to do with intermolecular forces. The phosphate/ribose backbone of DNA is hydrophilic (water-loving), so it orients itself outward toward the solvent, while the relatively hydrophobic bases bury themselves inside.

Additionally, the geometry of the deoxyribose-phosphate linkage allows for just the right pitch, or distance between strands in the helix, a pitch that nicely accommodates base pairing. Lots of things come together to create the beautiful right-handed double-helix structure.

Production of a mixture of d- and l-sugars produces nucelotides that do not fit together properly, producing a very open, weak structure that cannot survive to replicate, catalyze, or synthesize other biological molecules.

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In DNA the atoms C1', C3', and C4' of the sugar moiety are chiral, while in RNA the presence of an additional OH group renders also C2' of the ribose chiral

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A biological system exclusively uses d-ribose, whereas abiotic experiments synthesize both right- and lefthanded-ribose in equal amounts. But the pre-biological building blocks of life didn’t exhibit such an overwhelming bias. Some were left-handed and some right. So how did right-handed RNA emerge from a mix of molecules? 

Some kind of symmetry-breaking process leading to enantioenriched biomonomers would have had to exist. But none is known. 

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Gerald Joyce wrote a science paper which was published in Nature magazine, in 1984. His findings, published in Nature in 1984, suggested that in order for life to emerge, something first had to crack the symmetry between left-handed and right-handed molecules, an event biochemists call “breaking the mirror.”

Since then, scientists have largely focused their search for the origin of life’s handedness in the prebiotic worlds of physics and chemistry, not biology - but with no success. So what is the cop-out ? 

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Pure chance !! Luck did the job. That is the only thinkable explanation. How could that be a satisfying answer in face of the immense odds? 

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But then, the same author, Christian de Duve, Nobel prize winner in physiology or medicine, dismisses instant creation as " heuristically sterile". A sterile discovery ?? in other words, a discovery lacking evidence? 

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In his following book, Genetics of Original Sin, he then extended a bit further, and exposed what he meant by "heuristically sterile". 

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It is conceivable that the molecules were short enough for all possible sequences, or almost, to be realized (by way of their genes) and submitted to natural selection. So, this is the way de Duve thought that Intelligent Design could be dismissed. This coming from a Nobel prize winner in medicine is nothing short than shocking, to say the least. 

De Duve dismissed intelligent design and replaced it with natural selection. Without providing a shred of evidence. But based on pure guesswork and speculation.



Last edited by Admin on Thu Jul 02, 2020 11:47 am; edited 143 times in total

https://reasonandscience.catsboard.com

Otangelo


Admin
1b. Selecting the right backbone ribose sugar
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Another interesting observation is that RNA and DNA use a five-membered ribose ring structure as a backbone element. It is found that six-membered ring with backbones containing six carbons per sugar unit instead of five carbons and six-membered pyranose rings instead of five-membered furanose rings do not possess the capability of efficient informational Watson–Crick base-pairing. 

Therefore, these systems could not have acted as functional competitors of RNA of a genetic system, even though these six-carbon alternatives of RNA should have had a comparable chance of being formed under the conditions that formed RNA. The reason for their failure revealed itself in chemical model studies: six-carbon-six-membered-ring sugars are found to be too bulky to adapt to the requirements of Watson–Crick base-pairing within oligonucleotide duplexes.

In sharp contrast, an entire family of nucleic acid alternatives in which each member comprises repeating units of one of the four possible five-carbon sugars (ribose being one of them) turns out to be highly efficient informational base-pairing system.

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But why and how would natural unguided events on early earth select what works? Observe the authors end note of above science paper: Optimization, not maximization, of base-pairing strength, was a determinant of RNA's selection. But why would unguided events select something, that by its own has no function? The five-membered furanose or six-membered pyranose ring would simply lay around and then disintegrate without any function whatsoever. 

The smuggling in of evolutionary jargon is evident, and so the fact that the authors do omit these relevant questions that should be asked in order to keep the naturalistic paradigm alive. But its also evident how nonsensical such inferences are. 

1c. Size Complementarity of the nucleotide bases to form a DNA strand
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DNA molecules are asymmetrical, such property is essential in the processes of DNA replication and transcription. Above picture demonstrates why bases need to be paired between pyrimidines and purines. In molecular biology, complementarity describes a relationship between two structures each following the lock-and-key principle.

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The formation of the double-helix spiral staircase-like structure, how did it arise? 

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Complementarity is the base principle of DNA replication and transcription as it is a property shared between two DNA or RNA sequences, such that when they are aligned antiparallel to each other, the nucleotide bases at each position in the sequences will be complementary, much like looking in the mirror and seeing the reverse of things. This complementary base pairing is essential for cells to copy information from one generation to another.






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There is no reason why these structures could or would have emerged in this functional complex configuration by random trial and error processes. Above paper from Nature magazine, from 2016, demonstrates the complete lack of explanations despite of decades of attempts to solve the riddle. 

2. Bringing all the parts together and joining them in the right position

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Once all the parts would have been available, they would have had to be joined together to the same assembly site,  and sorted out from non-functional molecules.  Joining all three components together involves two difficult reactions: formation of a glycosidic bond, with the right stereochemistry linking the nucleobase and ribose, and phosphorylation of the resulting nucleoside.



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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, for what reason would the generation of a homopolymer be useful? Consider that only random unguided events could account for the generation, which seems rationally extremely unlikely, if not impossible. The chance for that alone occurring randomly is extremely remote

2a. Glycosidic bond formation between nucleosides and the base
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Whatever the mode of joining base and sugar was, it had to be between the correct nitrogen atom of the base and the correct carbon atom of the sugar.

The prebiotic synthesis of simple RNA molecules would, therefore, require an inventory of ribose and the nucleobases. Assembly of these components into proto-RNA would further require a mechanism to link the ribose and nucleobase together in  the proper configuration to form polymers, 

and then to activate the combined molecule (called a nucleoside) with a pyrophosphate or some other functional component that would promote formation of a bond between the nucleoside and the growing polymer.

Nucleosides are formed by linking an organic base ( guanine, adenine, uracil or cytosine) to a sugar (here D-ribose). This reaction looks simple, but how it could have occurred by an enzyme-free prebiotic synthesis, in particular involving pyrimidine bases, is an open question. There have been many imaginative ideas and attempts for its solution, all unsuccessful.  

In most cases the nucleoside components generated in the experiments, attempting to join the bases to the Ribose backbone represent only a minor fraction of a full suite of compounds produced, so that synthesis of a nucleoside would require either that the components be further purified or that some mechanism exist to selectively bring the components together out of a complex mixture.

How would non-guided random events be able to attach the nucleic bases to the ribose and in a repetitive manner at the same, correct place?  The coupling of ribose with a base is the first step to form RNA, and even those engrossed in prebiotic research have difficulty envisioning that process, especially for purines and pyrimidines.”

The emergence and existence of catalytic polymers are fundamental. Postulates of how polymerisation could have occurred on prebiotic earth are, therefore, another essential question that has not been elucidated.

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There are no known ways of bringing about this thermodynamically uphill reaction in aqueous solution: purine nucleosides have been made by dry-phase synthesis, but not even this method has been successful for condensing pyrimidine bases and ribose to give nucleosides.

Laboratory-based chemical syntheses of ribonucleotides do most, if not all, require manipulation of sugars and nucleobases with protecting group strategies to overcome the thermodynamic and kinetic pitfalls that prevent their fusion. 

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In a research paper from 2010, John D. Sutherland reported: Under plausible prebiotic conditions, condensation of nucleobases with ribose to give β-ribonucleosides is fraught with difficulties. The reaction with purine nucleobases is low-yielding and the reaction with the canonical pyrimidine nucleobases does not work at all.  Fitting the new synthesis to a plausible geochemical scenario is a remaining challenge.

2b. The prebiotic phosphodiester bond formation problem

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Another major problem that origin of life research faces is how to explain the transition from monomer ribonucleotides to polynucleotides. Phosphodiester bonds are central to all life on Earth as they make up the backbone of the strands of nucleic acid. 

In DNA and RNA, the phosphodiester bond is the linkage between the 3' prime carbon atom of one sugar molecule and the 5' prime carbon atom of another, deoxyribose in DNA and ribose in RNA.

In modern cells, 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.

Once a single phosphate or two phosphates (pyrophosphates) break apart and participate in a catalytic reaction, the phosphodiester bond is formed.

The general problem regarding the condensation of small organic molecules to form macromolecules in an aqueous environment is the thermodynamically unfavorable process of water removal. In the current biosphere, these types of reactions are catalyzed by enzymes and energetically driven by pyrophosphate hydrolysis.

Obviously, biocatalysts and energy-rich inorganic phosphorus species were not extant on the Earth before life began. In all cases, the starting problem in a prebiotic synthesis would be the fact that materials would consist of an enormous amount of disparate molecules lying around unordered, and would have had to be separated and sorted out.

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The intrinsic nature of the phosphodiester bonds is also finely-tuned. For instance, the phosphodiester 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. There are no explanations of how the right position could have been selected abiotically in a repeated manner in order to produce functional polynucleotide chains. 

As it turns out, the 5’ to 3’ linkages impart far greater stability to the RNA molecule than does the 5’ to 2’ bonds. Nucleotides can polymerize via condensation reactions.. Ribonucleotides are shown above, but the same reaction occurs between deoxyribonucleotides.

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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 extremely unlikely, if not impossible.

The activated nucleotides (or the nucleotides with coupling agent) now had to be polymerised. Initially, this could not have happened with a pre-existing polynucleotide template.

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In the case of RNA, not only must phosphodiester links be repeatedly forged, but they must ultimately connect the 5 prime‑oxygen of one nucleotide to the 3 prime‑oxygen, and not the 2 prime‑oxygen, of the next nucleotide. .  

How could and would random events attach a phosphate group to the right position of a ribose molecule to provide the necessary chemical activity? 
 

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Above science paper admits: "A fundamental requirement of the RNA world hypothesis is a plausible nonenzymatic polymerisation of ribonucleotides that could occur in the prebiotic environment, but the nature of this process is still an open issue."


In present-day cells, polymerisation is carried out by enzymes with high efficiency and specificity. Enzymes are genetically encoded polymers requiring a complex, protein-based synthetic machinery

Observe what they write at the conclusion: " Selection toward highly efficient catalytic peptides, which eventually resulted in present-day enzymes, could have started at a very early stage of chemical evolution." 


This is an entirely unsupported claim. Readers without training in biochemistry will simply believe it, without further questioning. And that is what goes in basically the entire scientific literature that deals with origins. Nothing besides just so stories based on evolutionary guesswork !!

In living organisms today, adenosine-5'-triphosphate (ATP) is used for activation of nucleoside phosphate groups, but ATP would not be available for prebiotic syntheses. Joyce and Orgel note the possible use of minerals for polymerization reactions, but then express their doubts about this possibility

2c. Fine-tuning of the strength of the hydrogen base pairing forces 

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Hydrogen bond base pairing forces are essential for the mechanisms associated with DNA stability.

[size=12]DNA  has by its own no function. Its purpose is to be used as "letters", storing codified instructional complex information based on their specific sequences arranged in the DNA molecules.[/size]

[size=12]It is sufficiently striking already to know that the universe, its initial conditions, cosmic constants, physical laws, and conditions on earth must be finely tuned for the emergence and flourishing of life.  What is less known however is, that fine-tuning is also extending and required in biochemistry.[/size]

Fine-tuning in biochemistry is represented by the strength of the chemical bonds that makes the universal genetic code possible. Neither transcription nor translation of the messages encoded in RNA and DNA would be possible if the strength of the bonds had different values. Hence, life, as we understand it today, would not have arisen.

As it happens, the average bond energy of a carbon-oxygen double bond is about 30 kilocalories per mol higher than that of a carbon-carbon or carbon-nitrogen double bond, a difference that is life essential. If it were not so, Watson–Crick base-pairing would not exist – nor would the kind of life we know.


3. The instability, degradation, and asphalt problem 
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The chemical instability of RNA is explained by the presence of a hydroxyl group in position 2’, which results in an easy strand cleavage through an intramolecular reaction. Such a cleavage is impossible in DNA, where the hydroxyl group at 2’ is absent.


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“An enormous amount of empirical data have established, as a rule, that organic systems, given energy and left to themselves, devolve to give uselessly complex mixtures, ‘asphalts’ .” In summary, the asphalt problem, also known as the tar problem, is the typical, expected outcome of prebiotic processes. 

Randomly joined assemblies of random molecules of either covalent or hydrogen bonds should plausibly form random, chaotic mixtures not linear polymers. This has been repeatedly, consistently observed experimentally.

Furthermore, RNA typically degrades in a matter of days and there is no known mechanism to remove the products of degradation from the setting. Eventually, accumulated degradation products should present yet another layer of contamination. 

Natural processes tend to make many more wrong products than usable ones and the ratio is plausibly large enough to prove fatal to abiogenesis.

Stanley L. Miller concluded that the instability of ribose stemming from its carbonyl group “preclude[s] the use of ribose and other sugars as prebiotic reagents. . . . It follows that ribose and other sugars were not components of the first genetic material.”

4. The energy problem


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Prebiotic processes are similar in character to dumping a tank of gasoline on a car and igniting it.  By contrast, living cells have machinery which converts energy appearing in a specified form into ATP, the energy currency of the cell, which is useful for biotic processes. 

The form of energy to be converted into ATP varies among cellular types, such as UV light, visible light, methane, metallic ion flow, or digestible nutrients. 

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Without machinery matched to the form of energy, energy tends either to have no effect or to act as a tank of gas dumped on a car.

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How an ordered energy supply got " off the hook" is a serious enigma and conundrum. It is as if a rock chose a road to roll upwards, 


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or a rusty nail "figuring out" how to spontaneously rust and add layers of galvanizing zinc on itself to fight corrosion. 



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Unintelligent simple chemicals can't self-organize into instructions for building solar farms (photosystem 1 and 2 in photosynthesis), hydroelectric dams (ATP synthase), propulsion (motor proteins) , self repair (p53 tumor suppressor proteins) or self-destruct (caspases) in the event that these instructions become too damaged by the way the universe USUALLY operates.


 Abiogenesis is not an issue that scientists simply need more time to figure out but a fundamental problem with materialism

5. The minimal nucleotide quantity problem 
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The prebiotic conditions would have had to be right for reactions to give perceptible yields of bases that could pair with each other. Even if prebiotic events would have been able to make RNA prebiotically, not only a few nucleotides would have been required, but trillions.  A minimal cell requires a genome of at least 541,000  nucleotides. 

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Proposing that unguided random chemical reaction events would have produced trillions of repetitive units of each type of nucleotides, all right sized and complementary to form a double helix structure stretches far beyond what is plausible of what chance can do. Regardless of whether the actual minimum is 100,000  or 500,000 nucleotides, this is far beyond the possible range of a prebiotic nucleic acid generating mechanism.

It would eventually be able to generate a polymer with 200 nucleotides, which however soon would fall apart. Current understanding of information can give many explanations of the difficulties of creating it. It cannot explain where it comes from. 

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The prebiotic appearance of nucleotides and long polymers is more difficult than the appearance of amino acids and proteins. Hence, it should take longer than 10^100.000  years to for the appearance of a gene with 780 nucleotides able to code for a specifically required protein. Yet, a 200  ribonucleic acid degrades in a matter of days.

It is implausible that a googol of googol years would be enough time. On a practical basis this discussion is nonsense. These numbers are so extreme that the human mind cannot comprehend their significance.

What is required here is not some wild one-off freak of an event: it is not true to say ‘it only had to happen once’. Trillions of attempts would have had to occur to start the role of  RNA's both, as a catalyst and informational carrier.
Prebiotic processes inherently function as random product generators, producing non-functional random substrates.

6. The Water Paradox 
Water is commonly viewed as essential for life, and theories of water are well known to support this as a requirement. So are RNA, DNA, and proteins. However, these biopolymers are corroded by water. For example, the hydrolytic deamination of DNA and RNA nucleobases is rapid and irreversible, as is the base-catalyzed cleavage of RNA in water.

This leads to a paradox: RNA requires water to do its job, but RNA cannot emerge in water and cannot replicate with sufficient fidelity in water without sophisticated repair mechanisms in place. There are no solutions in sight to solve this paradox; life needs water that is inherently toxic to RNA necessary for life.

7. The transition problem from prebiotic to biochemical synthesis
Even if all this in a freaky accident occurred by random events, that still says nothing about the huge gap and enormous transition that would be still ahead to arrive at a fully functional interlocked and interdependent metabolic network and information system, where complex biosynthesis pathways produce nucleotides and all basic building blocks in modern cells. 

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The huge gap cannot be outlined enough, leading straight to the famous chicken & egg situation. Chicken and egg scenarios in cellular function can be discovered at will. The essential components of a minimal cell cooperate with each other, such that when all work together life appears and missing any one of them prevents its appearance.

The gap between prebiotic chemistry and biochemistry is one of the biggest problems of abiogenesis research.  Prebiotic chemistry does not resemble extant biochemistry in terms of substrates, reaction pathways, catalysts or energy coupling.


The difficult condensation reactions to form nucleotides and polymers including RNA, DNA and polypeptides are accomplished in water, using energy in the form of ATP. None of this bears any resemblance to prebiotic chemistry proposals.

The difficulty is extrapolating backwards from the supposed so-called last universal common ancestor (LUCA) to prebiotic chemistry. LUCA certainly had genes and proteins, and that level of complexity is undeniably a long way from prebiotic chemistry.


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How could chemical evolution define a proper genetic structure to instruct the make of a protein so that the protein could provide a step in the production of an essential product before all of the other proteins required in the biosynthesis pathway had appeared? There is a long list of products essential to the appearance of the first cell. 

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Biological systems work as factories or machines. Cells host a big number of the most various molecular machines equal to factory production lines. DNA is trascribed to RNA, which is translated into proteins. But proteins are required to make DNA and RNA. This creates an endless loop, which is only solved when we posit that all three were created at the same time. 


Pick any one of the products, and try to explain how this product could appear apart from single-step, the sudden first appearance of all enzymes and proteins required in the production-line-like metabolic process, where several proteins work in a joint venture in a holistic manner to produce all basic building blocks, essential for life?

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The scenarios of prebiotic production of the basic building blocks of life are far distant from the extremely complex metabolic pathways used in even the smallest known cells, like mycoplasma genitalum. The pathway to make pyrimidines, namely cytosine and uracil which yields RNA, and the further transformation of uracil to thymine, the base used in DNA, is extremely complex.

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The pathway to make purines is even more complex, as can be seen in the picture above.  The pathway consists of 11 enzymatic steps.

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The transition from RNA to DNA is extremely complex, and one enzyme deserves to be mentioned in special: Ribonucleotide Reductase. which converts Ribonucleotides to Deoxyribonucleotides used in DNA. 

Ribonucleotide Reductase are essential enzymes to sustain life in all free-living cells, providing the only known de novo pathway for the biosynthesis of deoxyribonucleotides, the immediate precursors for DNA synthesis and repair.

Consider that the making of DNA and all these extremely complex enzymes had to emerge prior when life began and without evolution. 

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And that brings us again to the catch-22 situation as mentioned before:

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essential basically means, irreducible....

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This exposure here had not dealt with the problem of information, the fact that self-replication would only have been possible after the Eigen treshold would have been reached, and the fact that the make of proteins is an irreducibly complex process, involving besides DNA and RNA many other ingredients, as listed above. 

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Unguided prebiotic synthesis of RNA and DNA: an unsolved riddle!

One of the more enigmatic and difficult problems confronting the prebiotic chemistry community is identifying how the monomers of RNA, or pre-RNA, or even non-related polymeric components selectively formed and self-assembled out of the presumed random prebiotic mixtures. 


It is in this assembly into informational polymers  where significant selection processes must have occurred not only for the base composition but also for the other components of nucleic acids (or nucleic acid alternatives and precursors). 

Nucleotide metabolism is central to all biological systems, due to their essential role in genetic information and energy transfer, which in turn suggests its possible presence in the supposed last universal common ancestor (LUCA) from which all life forms originate, that is  Bacteria, Archaea and Eukaryotic cells.

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A vast number of books and scientific literature exists on this subject.  For several decades, the best chemists in the world have vigorously addressed the problem of the prebiotic synthesis of RNA. Their efforts however determined and imaginative their approaches, have not been encouraging.

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First of all, the origin of the RNA and DNA molecule is an origin of life problem, not evolution. Evolution depends on DNA replication, therefore, DNA must have preceded evolution. And therefore, its origin cannot be explained by evolutionary mechanisms. DNA  had to emerge together with the machinery of replication and transcription as a pre-requisite for kick-starting life. 

 The supposed abiotic synthesis of RNA and thus the abiotic assembly of its components, including nucleobases, as precursors, is, therefore, a central issue in understanding the origins of life. 

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This observation is highly relevant because it outlines that the origin of ribonucleotides, the building blocks of DNA, could not have emerged prior to life started, but are a pre-requisite.

 The above paper confirms this when they write: The highly conserved ribonucleotide biosynthetic pathway very likely appeared prior to the divergence of the three major lineages.  

RNA and ribonucleotides are ubiquitous and play key catalytic, structural and regulatory roles in biological processes. It is remarkable how the authors then proceed by making several claims, and inferences which are a non-sequitur based on the evidence at hand. Also, when they claim that polyribonucleotides interacted with other compounds. 

Well, before even starting about interactions of what polyribonucleotides supposedly did, it has to be explained how they came to be, which the authors confess:

 We still do not know how the RNA World first appeared. This is a remarkable admission. But then rather than elucidating why they don't know they move forward with further assertions lacking support entirely, despite they claim otherwise. 

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Above is another paper which outlines that RNA and DNA had to be fully setup when life began. The authors write: Thermally stable RNA is restricted to a narrow sequence space that is incompatible with the freedom of sequence information required for an RNA genome. Therefore, LUCA must have exhibited the extant DNA/RNA dichotomy. DNA has a half-life on geologic time scales, while catalytic mRNA has a half-life on metabolic time scales.

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This paper is worth mentioning for several reasons. As usual, it starts with the unsupported claim that nucleotides of RNA appear to be products of evolution.

Then, soon after, they admit that the origin of RNA is an open question. The blatant contradiction could not be more evident. In the end, outlined in red, the authors point out that there is a vast chemical space from where the possible molecules had to be separated. 

Again, it is obvious, that there is no reason whatsoever why natural causes without foresight nor goals would start such a selection process.

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The book: Biological science admits:
The production of nucleotides remains a serious challenge for the theory of chemical evolution. At this time, experiments that attempt to simulate early Earth environments have yet to synthesize complete nucleotides.

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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.



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The inevitable conclusion of this survey of nucleotide synthesis is that there is at present no convincing, prebiotic total synthesis of any of the nucleotides.

Many individual steps that might have contributed to the formation of nucleotides on the primitive Earth have been demonstrated, but few of the reactions give high yields of products, and those that do tend to produce complex mixtures of products.

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Steve Benner is the founder and president of the Westheimer Corporation, a private research organization, and a prior Harvard University professor. He is one of the world’s leading authorities on abiogenesis. This is his evaluation of what he has observed: We are now 60 years into the modern era of prebiotic chemistry. 

That era has produced tens of thousands of papers attempting to define processes by which “molecules that look like biology” might arise from “molecules that do not look like biology” …. For the most part, these papers report “success” in the sense that those papers define the term…. And yet, the problem remains unsolved

Steven Benner has been remarkably courageous by admitting openly and categorically:  The “origins problem” cannot be solved. Long periods of time do not make life inevitable. Molecules rather disintegrate based on the second law of thermodynamics. and randomization turns more complete.

Since prebiotic processes are natural randomizers and abiogenesis requires specific products, it does not appear that prebiotic processes have inherent capability to meet the requirements necessitated for successful abiogenesis. This plausibly characterizes every hypothetical step of abiogenesis and explains why none have succeeded.  

Claude Shannon showed that randomization is the fundamental behavior and entropy is simply a mathematical expression of certain of its aspects

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2017, english Chemist John Sutherland formed nucleotides, amongst all of the basic building blocks—lipids for compartments, amino acids for metabolism, starting with cyanide as a common initial substrate.

 However, this ended up requiring six separate ponds with their own unique geochemical conditions and whose products then needed to be mixed together in a specific sequence.

Even this degree of complexity did not supply required products, but only precursors.  The requirement of so many unique ponds and associated chemistries in such close proximity to each other, of coure, stretches plausibility.


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I think, to say that on average the 14 hurdles that it would take to make primed nucleotides would each take 10 unit operations - that at least 140 little events would have to be appropriately sequenced. Unguided, the appropriate thing happened at each point on one occasion in six. 

The odds against a successful unguided synthesis of a batch of primed nucleotide on the primitive Earth would be a huge number, represented approximately by a 1 followed by 109 zeros ( 10^109).

How did Nature start to play this game? At the very least a maintained supply of primed nucleotides would be required for any kind of organism using our kind of message tapes. A nucleotide making factory would be needed.
 
'The odds are enormous against its being coincidence. No figures could express them.'



Last edited by Admin on Sat Jun 15, 2019 9:43 am; edited 62 times in total

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Otangelo


Admin
Biochemical fine-tuning - essential for life
https://reasonandscience.catsboard.com/t2591-biochemical-fine-tuning-essential-for-life

Chemical Etiology of Nucleic Acid Structure
http://sci-hub.tw/https://science.sciencemag.org/content/284/5423/2118

Formation of RNA Phosphodiester Bond by HistidineContaining Dipeptides 
http://sci-hub.tw/https://onlinelibrary.wiley.com/doi/full/10.1002/cbic.201200643

Non-enzymatic Polymerization of Nucleic Acids from Monomers: Monomer SelfCondensation and Template-Directed Reactions
http://sci-hub.tw/https://www.eurekaselect.com/104564/article

New Twist Found in the Story of Life’s Start
https://www.quantamagazine.org/chiral-key-found-to-origin-of-life-20141126/

Chiral selection in poly(C)-directed synthesis of oligo(G)
http://sci-hub.tw/https://www.nature.com/articles/310602a0

Origins of building blocks of life: A review
https://www.sciencedirect.com/science/article/pii/S1674987117301305

Spontaneous formation and base pairing of plausible prebiotic nucleotides in water
https://www.nature.com/articles/ncomms11328

Ribose and related sugars from ultraviolet irradiation of interstellar ice analogs
http://sci-hub.tw/https://science.sciencemag.org/content/352/6282/208

Phosphodiester bond
https://en.wikipedia.org/wiki/Phosphodiester_bond

DNA & RNA: The foundation of life on Earth
http://xaktly.com/NucleicAcids.html

Life as a guide to prebiotic nucleotide synthesis
https://www.nature.com/articles/s41467-018-07220-y

The Quote Mine Project
http://www.talkorigins.org/faqs/quotes/mine/part2.html

Studies on the origin of life — the end of the beginning
http://sci-hub.tw/https://www.nature.com/articles/s41570-016-0012

The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1892545/

Prebiotic Systems Chemistry: Complexity Overcoming Clutter
https://www.cell.com/chem/fulltext/S2451-9294(17)30087-6?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2451929417300876%3Fshowall%3Dtrue

Miller-Urey and Beyond: What Have We Learned About Prebiotic Organic Synthesis Reactions in the Past 60 Years?
http://sci-hub.tw/https://www.annualreviews.org/doi/abs/10.1146/annurev-earth-040610-133457

A Natural Origin-of-Life: Every Hypothetical Step Appears Thwarted by Abiogenetic Randomization
This is truly a top notch research paper on abiogenesis, where the authors deal with honesty about the problems, without sugar coat  it with evolutionary nonsense vocabulary. They go straight to the facts, expose the problems, and provide a honest conclusion.
https://osf.io/p5nw3/

Paradoxes in the origin of life
http://sci-hub.tw/https://www.ncbi.nlm.nih.gov/pubmed/25608919

Studies on the origin of life  the end of the beginning
http://sci-hub.tw/https://www.nature.com/articles/s41570-016-0012

Ring Structure for Ribose:
http://chemistry.elmhurst.edu/vchembook/543ribose.html
https://chem.libretexts.org/Bookshelves/Biological_Chemistry/Supplemental_Modules_(Biological_Chemistry)/Carbohydrates/Monosaccharides/Ribose

Ribonucleotides
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2845210/

Exploring the Emergence of RNA Nucleosides and Nucleotides on the Early Earth
https://www.mdpi.com/2075-1729/8/4/57/htm

Evolutionist criticisms of the RNA World conjecture
https://creation.com/cairns-smith-detailed-criticisms-of-the-rna-world-hypothesis

Prebiotic chemistry and the origin of the RNA world.
http://sci-hub.tw/https://www.ncbi.nlm.nih.gov/pubmed/15217990



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4RNA & DNA: It's prebiotic synthesis: Impossible !!  Empty Main points addressed in the video Sat Jun 15, 2019 1:17 pm

Otangelo


Admin
Main points addressed in the video

Synthesis of nitrogenous bases in prebiotic environments
- High-energy precursors to produce purines and pyrimidines would have had to be produced in a sufficiently concentrated form. There is no known prebiotic route to this.  
- Scientists have failed to produce cytosine in spark-discharge experiments, nor has cytosine been recovered from meteorites or extraterrestrial sources. The deamination of cytosine and its destruction by other processes such as photochemical reactions place severe constraints on prebiotic cytosine syntheses.
- The origin of guanine bases has proven to be a particular challenge. While the other three bases of RNA  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.
- Adenine synthesis requires unreasonable Hydrogen cyanide concentrations. Adenine deaminates 37°C with a half-life of 80 years. 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."
- Uracil has also a half-life of only 12 years at 100◦C. For nucleobases to accumulate in prebiotic environments, they must be synthesized at rates that exceed their decomposition.

Ribose: Synthesis problems of the Pentose 5 carbon sugar ring
The best-studied mechanism relevant to the prebiotic synthesis of ribose is the formose reaction. Several problems have been recognized for the ribose synthesis via the formose reaction. The formose reaction is very complex. It depends on the presence of a suitable inorganic catalyst. Ribose is merely an intermediate product among a broad suite of compounds including sugars with more or fewer carbons.

The phosphate group
On prebiotic earth, however, there would have been no way to activate phosphate somehow, in order to promote the energy dispendious reaction.

Prebiotic RNA and DNA synthesis

1. No prebiotic mechanism is known to select: 
- Right-handed configurations of RNA and DNA
- The right backbone sugar
- How to get size complementarity of the nucleotide bases to form a DNA strand and strands of the DNA molecule running in the opposite directions

2. Bringing all the parts together and joining them in the right position 
- Attach the nucleic bases to the ribose and in a repetitive manner at the same, correct place, and the backbone being a repetitive homopolymer
- Prebiotic glycosidic bond formation between nucleosides and the base
- Prebiotic phosphodiester bond formation
- Fine-tuning of the strength of the hydrogen base pairing forces

3. The instability, degradation, and asphalt problem 
- Bonds that are thermodynamically unstable in water, and overall intrinsic instability. RNA’s nucleotide building blocks degrade at warm temperatures in time periods ranging from nineteen days to twelve years. These extremely short survival rates for the four RNA nucleotide building blocks suggest why life’s origin would have to be virtually instantaneous—all the necessary RNA molecules would have to be assembled before any of the nucleotide building blocks decayed.

4. The energy problem
- Doing things costs energy. There has to be a ready source of energy to produce RNA. In modern cells, energy is consumed to make RNA.

5. The minimal nucleotide quantity problem.
- The prebiotic conditions would have had to be right for reactions to give perceptible yields of bases that could pair with each other.

6. The Water Paradox  
- The hydrolytic deamination of DNA and RNA nucleobases is rapid and irreversible, as is the base-catalyzed cleavage of RNA in water. This leads to a paradox: RNA requires water to do its job, but RNA cannot emerge in water and cannot replicate with sufficient fidelity in water without sophisticated repair mechanisms in place.

7.The transition problem from prebiotic to biochemical synthesis 
- Even if all this in a freaky accident occurred by random events, that still says nothing about the huge gap and enormous transition that would be still ahead to arrive at a fully functional interlocked and interdependent metabolic network, where complex biosynthesis pathways produce nucleotides in modern cells.

Unguided prebiotic synthesis of RNA and DNA: an unsolved riddle!

The origin of the RNA and DNA molecule is an origin of life problem, not evolution.
Steve Benner, one of the world’s leading authorities on abiogenesis:  The “origins problem” CANNOT be solved.
Graham Cairns-Smith: The odds against a successful unguided synthesis of a batch of primed nucleotide on the primitive Earth would be a huge number, represented approximately by a 1 followed by 109 zeros ( 10^109). 'The odds are enormous against its being coincidence. No figures could express them.'

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RNA & DNA: It's prebiotic synthesis: Impossible !! Part 1
https://www.youtube.com/watch?v=-ZFlmL_BsXE

RNA & DNA: It's prebiotic synthesis: Impossible !! Part 2
https://www.youtube.com/watch?v=dv4mUjmuRRU

Despite remarkable work in viable DNA design, we have not yet been able to synthesize even a small functional peptide from basic components, and are still a long way from understanding exactly what distinguishes a collection of molecules from the collection of molecules that make up a living system
https://royalsocietypublishing.org/doi/10.1098/rsif.2018.0640?fbclid=IwAR0ZbSkdiPrAekSAgeEi17VX5HJX6N2f2JIG6sLeL2Je7zuk0mpxwimgTNY

Main points addressed in the video
Synthesis of nitrogenous bases in prebiotic environments
- High-energy precursors to produce purines and pyrimidines would have had to be produced in a sufficiently concentrated form. There is no known prebiotic route to this.  
- Scientists have failed to produce cytosine in spark-discharge experiments, nor has cytosine been recovered from meteorites or extraterrestrial sources. The deamination of cytosine and its destruction by other processes such as photochemical reactions place severe constraints on prebiotic cytosine syntheses.
- The origin of guanine bases has proven to be a particular challenge. While the other three bases of RNA  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.
- Adenine synthesis requires unreasonable Hydrogen cyanide concentrations. Adenine deaminates 37°C with a half-life of 80 years. 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."
- Uracil has also a half-life of only 12 years at 100◦C. For nucleobases to accumulate in prebiotic environments, they must be synthesized at rates that exceed their decomposition.
Ribose: Synthesis problems of the Pentose 5 carbon sugar ring
The best-studied mechanism relevant to the prebiotic synthesis of ribose is the formose reaction. Several problems have been recognized for the ribose synthesis via the formose reaction. The formose reaction is very complex. It depends on the presence of a suitable inorganic catalyst. Ribose is merely an intermediate product among a broad suite of compounds including sugars with more or fewer carbons.
The phosphate group

On prebiotic earth, however, there would have been no way to activate phosphate somehow, in order to promote the energy dispendious reaction.

Prebiotic RNA and DNA synthesis
1. No prebiotic mechanism is known to select:
- Right-handed configurations of RNA and DNA
- The right backbone sugar
- How to get size complementarity of the nucleotide bases to form a DNA strand and strands of the DNA molecule running in the opposite directions
2. Bringing all the parts together and joining them in the right position
- Attach the nucleic bases to the ribose and in a repetitive manner at the same, correct place, and the backbone being a repetitive homopolymer
- Prebiotic glycosidic bond formation between nucleosides and the base
- Prebiotic phosphodiester bond formation
- Fine-tuning of the strength of the hydrogen base pairing forces
3. The instability, degradation, and asphalt problem
- Bonds that are thermodynamically unstable in water, and overall intrinsic instability. RNA’s nucleotide building blocks degrade at warm temperatures in time periods ranging from nineteen days to twelve years. These extremely short survival rates for the four RNA nucleotide building blocks suggest why life’s origin would have to be virtually instantaneous—all the necessary RNA molecules would have to be assembled before any of the nucleotide building blocks decayed.
4. The energy problem
- Doing things costs energy. There has to be a ready source of energy to produce RNA. In modern cells, energy is consumed to make RNA.
5. The minimal nucleotide quantity problem.
- The prebiotic conditions would have had to be right for reactions to give perceptible yields of bases that could pair with each other.
6. The Water Paradox  
- The hydrolytic deamination of DNA and RNA nucleobases is rapid and irreversible, as is the base-catalyzed cleavage of RNA in water. This leads to a paradox: RNA requires water to do its job, but RNA cannot emerge in water and cannot replicate with sufficient fidelity in water without sophisticated repair mechanisms in place.
7.The transition problem from prebiotic to biochemical synthesis
- Even if all this in a freaky accident occurred by random events, that still says nothing about the huge gap and enormous transition that would be still ahead to arrive at a fully functional interlocked and interdependent metabolic network, where complex biosynthesis pathways produce nucleotides in modern cells.
Unguided prebiotic synthesis of RNA and DNA: an unsolved riddle!

The origin of the RNA and DNA molecule is an origin of life problem, not evolution.

Steve Benner, one of the world’s leading authorities on abiogenesis:  The “origins problem” CANNOT be solved.
Graham Cairns-Smith: The odds against a successful unguided synthesis of a batch of primed nucleotide on the primitive Earth would be a huge number, represented approximately by a 1 followed by 109 zeros ( 10^109). 'The odds are enormous against its being coincidence. No figures could express them.'



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When I say that abiogenesis is impossible, I say it by all means. Even to make one of the essential building blocks, DNA, is the matter of so huge odds, that it is in the realm of the utter impossible by natural unguided forces & events.

Cairns-Smith: I think, to say that on average the 14 hurdles that it would take to make primed nucleotides would each take 10 unit operations - that at least 140 little events would have to be appropriately sequenced. Unguided, the appropriate thing happened at each point on one occasion in six.

The odds against a successful unguided synthesis of a batch of primed nucleotide on the primitive Earth would be a huge number, represented approximately by a 1 followed by 109 zeros ( 10^109).

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The implausibility of prevital nucleic acid

Genetic takeover, Cairns Smith, page 66:
Now you may say that there are alternative ways of building up nucleotides, and perhaps there was some geochemical way on the early Earth. But what we know of the experimental difficulties in nucleotide synthesis speaks strongly against any such supposition. However it is to be put together, a nucleotide is too complex and metastable a molecule for there to be any reason to expect an easy synthesis.

If you were to consider in more detail a process such as the purification of an intermediate ( to form amide bonds between amino acids and nucleotides ) you would find many subsidiary operations — washings, pH changes and so on. (Remember Merrifield’s machine: for one overall reaction, making one peptide bond, there were about 90 distinct operations required.)

Chemistry and the Missing Era of Evolution A. Graham Cairns-Smith
What is missing from this story of the evolution of life on earth is the original means of producing such sophisticated materials as RNA. The main problem is that the replication of RNA depends on a clean supply of rather complicated monomers—activated nucleotides. What was required to set the scene for an RNA world was a highly competent, long-term means of production of at least two nucleotides. In practice the discrimination required to make nucleotide parts cleanly, or to assemble them correctly, still seems insufficient.

Claim: Your argument is based on ignorance, gaps, and incredulity.
Reply:
1. if there is no money in the wallet
2. It's an argument of knowledge to say: There is no money in the wallet after you check.
3. The same happens in molecular biochemistry. We checked, and scientists discovered that DNA stores specified complex information, which is a blueprint, instructing the precise sequence of amino acids to make proteins. Such information has never been observed to emerge by chance, and therefore, we have evidence that something is extremely unlikely (e.g., that chance could inform the correct instructions to make proteins). Indeed, scientists will often debate whether an experiment's result should be considered evidence of absence. Something has proven not to be the result of X ( as chance, for example )
4. Intelligence can act towards achieving specific goals, and knows how to create codified language, and use that language to create blueprints, used to make complex machines, production lines, and factories. It can finely tune and arrange things to work in a precise fashion. it can shape and form parts that perform tasks by interacting like lock and key. None of all this has been observed to be achieved by any alternative non-intelligent mechanism. if anyone wants to propose an alternative to replace intelligence, it should meet the burden of proof, and falsify the claim based on empirical testing and falsification.
5. Hence, the argument of Intelligent Design as best explanation of origins is based on experiments and observation, gained knowledge and experience. Not from ignorance.

Eliminative inductions argue for the truth of a proposition by arguing that competitors to that proposition are false. ( Contrast this with Popperian falsification, where propositions are corroborated to the degree that they successfully withstand attempts to falsify them ) When the available option form a dichotomy, just to option, A, or not A, they form a mutually exclusive and exhaustive class, eliminating all the competitors entails that the proposition is true. As Sherlock Holmes famous dictum says: when you have eliminated the impossible, whatever remains, however improbable, must be the truth. In this case, eliminative inductions, in fact, become deductions.

While theists hear the claim that inferring God is a gaps argument in almost every debate, are atheists not themselves actually guilty of using it?

We don't know:
- if the universe is eternal, there might be multiverses
- how the Big bang started, maybe virtual particles
- why the universe is finely tuned - maybe bubble universes
- how life started, but the Urey Miller experiment showed that amino acids can emerge in the lab, and what science not yet knows, one day it will find out - and it won't be a God
- how exactly evolution works to produce biodiversity, but its a theory, and there is consensus in science, therefore it must be true.
- how the brain can produce thoughts and conscience, but we don't know of a mind being able to exist outside the brain, therefore, monism must be true.

Let us consider some of the difficulties.
1. as we have seen, it is not even clear that the primitive Earth would have generated and maintained organic molecules. All that we can say is that there might have been prevital organic chemistry going on, at least in special locations. 
2. highenergy precursors of purines and pyrimidines had to be produced in a sufficiently concentrated form (for example at least 0.01 M HCN). 
3. the conditions must now have been right for reactions to give perceptible yields of at least two bases that could pair with each other. 
4. these bases must then have been separated from the confusing jumble of similar molecules that would also have been made, and the solutions must have been sufficiently concentrated. 
5. in some other location a formaldehyde concentration of above 0.01 M must have built up. 
6. this accumulated formaldehyde had to oligomerise to sugars. 
7. somehow the sugars must have been separated and resolved, so as to give a moderately good concentration of, for example, D-ribose. 
8. bases and sugars must now have come together. 
9. Ninth, they must have been induced to react to make nucleosides. (There are no known ways of bringing about this thermo dynamically uphill reaction in aqueous solution: purine nucleosides have been made by dry phase synthesis, but not even this method has been successful for condensing pyrimidine bases and ribose to give nucleosides
10. Whatever the mode of joining base and sugar it had to be between the correct nitrogen atom of the base and the correct carbon atom of the sugar. This junction will fix the pentose sugar as either the a- or fl-anomer of either the furanose or pyranose forms. For nucleic acids it has to be the fl-furanose. (In the dry-phase purine nucleoside syntheses referred to above, all four of these isomers were present with never more than 8 ‘Z, of the correct structure.) 
11. phosphate must have been, or must now come to have been, present at reasonable concentrations. (The concentrations in the oceans would have been very low, so we must think about special situations—evaporating lagoons and such things  
12. the phosphate must be activated in some way — for example as a linear or cyclic polyphosphate — so that (energetically uphill) phosphorylation of the nucleoside is possible. 
13. to make standard nucleotides only the 5’- hydroxyl of the ribose should be phosphorylated. (In solid-state reactions with urea and inorganic phosphates as a phosphorylating agent, this was the dominant species to begin with. Longer heating gave the nucleoside cyclic 2’,3’-phosphate as the major product although various dinucleotide derivatives and nucleoside polyphosphates are also formed 
14. if not already activated — for example as the cyclic 2’,3’-phosphate — the nucleotides must now be activated (for example with polyphosphate) and a reasonably pure solution of these species created of reasonable concentration. Alternatively, a suitable coupling agent must now have been fed into the system. 
15. the activated nucleotides (or the nucleotides with coupling agent) must now have polymerised. Initially this must have happened without a pre-existing polynucleotide template (this has proved very difficult to simulate ; but more important, it must have come to take place on pre-existing polynucleotides if the key function of transmitting information to daughter molecules was to be achieved by abiotic means. This has proved difficult too. Orgel & Lohrmann give three main classes of problem. 
(i) While it has been shown that adenosine derivatives form stable helical structures with poly(U) — they are in fact triple helixes — and while this enhances the condensation of adenylic acid with either adenosine or another adenylic acid — mainly to di(A) - stable helical structures were not formed when either poly(A) or poly(G) Were used as templates. 
(ii) It was difficult to find a suitable means of making the internucleotide bonds. Specially designed water-soluble carbodiimides were used in the experiments described above, but the obvious pre-activated nucleotides — ATP or cyclic 2’,3’-phosphates — were unsatisfactory. Nucleoside 5'-phosphorimidazolides, for example: N/\ n K/N/P-r’o%OHN/\N were more successful, but these now involve further steps and a supply of imidazole, for their synthesis. 
(iii) Internucleotide bonds formed on a template are usually a mixture of 2’—5’ and the normal 3’—5’ types. Often the 2’—5’ bonds predominate although it has been found that Zn“, as well as acting as an eflicient catalyst for the templatedirected oligomerisation of guanosine 5’-phosphorimidazolide also leads to a preference for the 3’—5’ bonds. 
16. the physical and chemical environment must at all times have been suitable — for example the pH, the temperature, the M2+ concentrations. 
17. all reactions must have taken place well out of the ultraviolet sunlight; that is, not only away from its direct, highly destructive effects on nucleic acid-like molecules, but away too from the radicals produced by the sunlight, and from the various longer lived reactive species produced by these radicals. 
18. unlike polypeptides, where you can easily imagine functions for imprecisely made products (for capsules, ionexchange materials, etc), a genetic material must work rather well to be any use at all — otherwise it will quickly let slip any information that it has managed to accumulate. 
19. what is required here is not some wild one-off freak of an event: it is not true to say ‘it only had to happen once’. A whole set-up had to be maintained for perhaps millions of years: a reliable means of production of activated nucleotides at the least.




As the difficulties accumulate the stakes get higher: success would be all the more resounding, but it becomes less likely. Sooner or later it becomes wiser to put your money elsewhere.






RNA & DNA: It's prebiotic synthesis: Impossible !!  Adfasf10



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I think, to say that on average the 14 hurdles that I referred to in the making of primed nucleotides would each take 10 unit operations - that at least 140 little events would have to be appropriately sequenced. (If you doubt this, go and watch an organic chemist at work; look at all the things he actually does in bringing about what he would describe as 'one step' in an organic synthesis.) And it is surely on the optimistic side to suppose that, unguided, the appropriate thing happened at each point on one
occasion in six. But if we take this as the kind of chance that we are
talking about, then we can say that the odds against a successful
unguided synthesis of a batch of primed nucleotide on the primitive
Earth are similar to the odds against a six coming up every time with
140 throws of a dice. Is that sort of thing too much of a coincidence
or not?
There are 6 possible outcomes from throwing a dice once; 6 x 6
from a double throw; 6 x 6 x 6 from a triple throw; and 6 multiplied
by itself 140 times from 140 throws. This is a huge number,
represented approximately by a 1 followed by 109 zeros (i.e. ~ 101 0 9 ).
This is the sort of number of trials that you would have to make to
have a reasonable chance of hitting on the one outcome that
represents success. Throwing one dice once a second for the period
of the Earth's history would only let you get through about 1015 trials:
so you would need about 109 4 dice. That is far more than the number
of electrons in the observed Universe (estimated at around 108 0).
Of course you might argue that in practice a synthesis might be
carried through in different ways, and that is true, but remember
what generous allowances we made in cutting down the actual
amount of sheer skill that organic synthesis requires. And remember

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the number of wrong reactions possible for adenine, thymine, cytosine, and guanine, phosphate, and deoxyribose sugar in generating a proper DNA dinucleotide.Beautiful snowflakes are the product of natural chemistry. Amino acids can be the product of natural chemistry. DNA or proteins, on the other hand, emphatically cannot be the product of natural chemistry.
This is the conclusion of a long and detailed calculation of the number of possible isomers of the same molecular weight as two properly joined nitrogenous bases of a single DNA strand, and then extrapolated out
"The total isomers of both strands of our desired genome is the product of the numbers of isomers of the first strand and those of the second strand: isomers of the first strand (AT) X isomers of the second strand (CG) = 16200 x 9000 = 145,800,000.
145,800,000 isomers for a genome of only two base pairs!"
However, the smallest known genome of a free-living cell (Mycoplasma genitalium) is 580,070 base pairs, the genome of our familiar Escherichia coli is 4.6 million base pairs, and the human genome is three billion base pairs."
This is telling us that for the two sides of one DNA strand, the number of possible ways of joining of the sugar, phosphate, and nitrogenous base is one hundred forty-five million eight hundred forty five thousand that the proper bonds will be formed for a single dinucleotide.
At every single step of the joining of sugars, nitrogenous bases, and phosphate groups, that is the absolute possibility of getting the sugar, the phosphate group, and the nitrogenous base arranged correctly.
Now can you calculate how many tries it might take to get about 900 nitrogenous bases in a proper sequence to form an average small gene?

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RNA world easier to make

Although Sutherland has shown that it is possible to build one part of RNA from small molecules, objectors to the RNA-world theory say the RNA molecule as a whole is too complex to be created using early-Earth geochemistry. "The flaw with this kind of research is not in the chemistry. The flaw is in the logic — that this experimental control by researchers in a modern laboratory could have been available on the early Earth," says Robert Shapiro

Shapiro sides with supporters of another theory of life's origins – that because RNA is too complex to emerge from small molecules, simpler metabolic processes, which eventually catalysed the formation of RNA and DNA, were the first stirrings of life on Earth.

Sutherland, though, hopes that ingenious organic chemistry might provide an RNA synthesis so convincing that it effectively serves as proof. "We might come up with something so coincidental that one would have to believe it," he says. "That is the goal of my career."

https://www.nature.com/news/2009/090513/full/news.2009.471.html?fbclid=IwAR3yzRX1QJX5qE9elEBvq1lY4jQvlOsELIZLm4r1C-4UuP_UyecapjCqCLQ

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A Simpler Origin for Life
The sudden appearance of a large self-copying molecule such as RNA was exceedingly improbable. Energy-driven networks of small molecules afford better odds as the initiators of life.

https://www.scientificamerican.com/article/a-simpler-origin-for-life/?fbclid=IwAR0oMG32MWATWqtqg96hC-V4MEDAQAbW6oBcg_c_FNLxAUsmX8szZja5Mo8

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All of these path‐hypotheses involve relatively reduced organic molecules that serve as the precursors of the four standard RNA nucleobases (guanine, adenine, cytosine, and uracil) or “grandfather′s axe” heterocycles (not shown). Thus, all assume the production of substantial amounts of reduced primary precursors, likely in the Hadean atmosphere (before 4 billion years ago). These primary precursors include hydrogen cyanide (HCN), cyanamide (H2NCN), cyanoacetylene (HCCCN), cyanogen (NCCN), ammonia (NH3), and cyanic acid (HCNO). Further, they all assume that these (or their downstream products) avoided dilution into a global ocean, perhaps by adsorbing on solids, or by delivery to sub‐aerial land with a constrained aquifer.

Most chemical path‐hypotheses to create RNA prebiologically all but require an atmosphere that is more reducing than what planetary accretion models suggest was the norm above the Hadean Earth.

https://onlinelibrary.wiley.com/doi/full/10.1002/syst.201900035

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On the Origin of the Canonical Nucleobases: An Assessment of Selection Pressures across Chemical and Early Biological Evolution
2013 Jun
Evidence suggests that many types of heterocycles ( nucleobases) could have been present on the early Earth.
The native bases of RNA and DNA are prominent examples of the narrow selection of organic molecules upon which life is based.

Question: How were the four nucleobases selected, if there was no evolutionary natural selection extant prior to when life began?

How did nature “decide” upon these specific heterocycles?

Non-mental matter does not have the ability to make decisions.

It is therefore likely that the contemporary composition of nucleobases is a result of multiple selection pressures that operated during early chemical and biological evolution.

Why is that likely? Is that not a just so, an ad-hoc assertion without evidence? a red herring? 

The persistence of the fittest heterocycles in the prebiotic environment towards, for example, hydrolytic and photochemical assaults, may have given some nucleobases a selective advantage for incorporation into the first informational polymers.

It is observable, how evolutionary vocabulary is smuggled in into abiogenesis research. There was no evolutionary fitness prior when life began. 

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

There is no problem if we permit the inference of intelligent design, though.

Two such selection pressures may have been related to genetic fidelity and duplex stability. 

There was no need for monomers to form DNA duplex forms.

The amino groups of the nucleobases in the native alphabet are absolutely essential to maintaining the fidelity of genetic information. Spontaneous deamination reactions are thus highly deleterious

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14RNA & DNA: It's prebiotic synthesis: Impossible !!  Empty Do natural clays catalyze this reaction? Thu Mar 19, 2020 7:44 pm

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Do natural clays catalyze this reaction?
June 2006 Robert Shapiro
The attractiveness of this oligonucleotide synthesis rests in part in the ready availability of the catalyst. Montmorillonite is a layered clay mineral-rich in silicate and aluminum oxide bonds. It is widely distributed in deposits on the contemporary Earth. If the polymerization of RNA subunits was a common property of this native mineral, the case for RNA at the start of life would be greatly enhanced.
However, the “[c]atalytic activity of native montmorillonites before being converted to their homoionic forms is very poor” (Ertem 2004:567). The native clays contain bound polyvalent cations, such as Cu2, Fe3, and Zn2, that interfere with phosphorylation reactions. 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 montmorillonite depended strongly on its physical source, with samples from Wyoming yielding the best results (Ferris et al. 1989; Ertem 2004). 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.
https://sci-hub.tw/https://www.jstor.org/stable/10.1086/506024?seq=1

RNA world easier to make
Although Sutherland has shown that it is possible to build one part of RNA from small molecules, objectors to the RNA-world theory say the RNA molecule as a whole is too complex to be created using early-Earth geochemistry. "The flaw with this kind of research is not in the chemistry. The flaw is in the logic — that this experimental control by researchers in a modern laboratory could have been available on the early Earth," says Robert Shapiro
https://www.nature.com/news/2009/090513/full/news.2009.471.html?fbclid=IwAR3yzRX1QJX5qE9elEBvq1lY4jQvlOsELIZLm4r1C-4UuP_UyecapjCqCLQ


RNA & DNA: It's prebiotic synthesis: Impossible !!  Shapir10



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15RNA & DNA: It's prebiotic synthesis: Impossible !!  Empty The problem of making Ribose prebiotically Mon Mar 23, 2020 11:14 am

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What is Benner's solution to explain how the right-handedness of ribose was selected amongst a mixed pool of enantiomeric right and left-handed ribose? In life, only right-handed ribose is viable, and biological systems exclusively use d-ribose, whereas abiotic experiments synthesize both right- and lefthanded-ribose in equal amounts. But the pre-biological building blocks of life didn’t exhibit such an overwhelming bias. Some were left-handed and some right. So how did right-handed RNA emerge from a mix of molecules?

Some kind of symmetry-breaking process leading to enantioenriched biomonomers would have had to exist. But none is known.

You resort to Benner's YouTube videos. Shall we see what he says about this issue?

https://www.youtube.com/watch?v=v5HQB3JFIZg
We've not said a word about chirality here and that's a big problem
That's all. What else did he say about it? Nothing.

RNA and DNA use a five-membered ribose ring structure as a backbone element. It is found that six-membered ring with backbones containing six carbons per sugar unit instead of five carbons and six-membered pyranose rings instead of five-membered furanose rings do not possess the capability of efficient informational Watson–Crick base-pairing.

Therefore, these systems could not have acted as functional competitors of RNA of a genetic system, even though these six-carbon alternatives of RNA should have had a comparable chance of being formed under the conditions that formed RNA. The reason for their failure revealed itself in chemical model studies: six-carbon-six-membered-ring sugars are found to be too bulky to adapt to the requirements of Watson–Crick base-pairing within oligonucleotide duplexes.

In sharp contrast, an entire family of nucleic acid alternatives in which each member comprises repeating units of one of the four possible five-carbon sugars (ribose being one of them) turns out to be highly efficient informational base-pairing system.

Stanley L. Miller concluded that the instability of ribose stemming from its carbonyl group “preclude[s] the use of ribose and other sugars as prebiotic reagents. . . . It follows that ribose and other sugars were not components of the first genetic material.”

As Shapiro has pointed out, the formose reaction which makes ribose  will not produce sugars in the presence of nitrogenous substances. These include peptides, amino acids, and amines, a category of molecules that includes the nucleotide bases. This obviously poses difficulties. First, it creates a dilemma for scenarios that envision proteins and nucleic acids arising out of a prebiotic soup rich in amino acids. Either the prebiotic environment contained amino acids, which would have prevented sugars (and thus DNA and RNA) from forming, or the prebiotic soup contained no amino acids, making protein synthesis impossible. Of course, RNA-first advocates might try to circumvent this difficulty by proposing that proteins arose well after RNA. Yet since the RNA-world hypothesis envisions RNA molecules coming into contact with amino acids early on within the first protocellular membranes, choreographing the origin of RNA and amino acids to ensure that the two events occur separately becomes a considerable problem.

James Tour:
“The coupling of a ribose with a nucleotide is the first step [in abiogenesis], and even those engrossed in prebiotic research have difficulty envisioning that process, especially for purines and pyrimidines.”

A further problem lies in the synthesis and preservation of ribose, with the right chirality. ribose is not particularly preferred over other sugars nor is it stable. Hence, an autocatalytic cycle designed to produce large amounts of carbohydrates from formaldehyde will not preferentially make ribose nor preserve it. One then faces the question of how ribose molecules were maintained against chemical processes that tend to decompose them quickly into a nondescript assemblage of polymeric mixtures. The ribose produced must have the correct handedness or chirality; on Earth, d-sugars are exclusively involved in living processes. Production of a mixture of d- and l-sugars produces nucelotides that do not fit together properly, producing a very open, weak structure that cannot survive to replicate, catalyze, or synthesize other biological molecules. In fact, the synthesis of the RNA molecule itself is interrupted by mixing nucleotides of different chirality; only in a controlled laboratory experiment or theoretical model can such an assemblage be realized.
To create a properly functioning RNA molecule out of a batch of heterochiral l- and d-sugars is a daunting challenge. The genetic template that sustains a particular kind of chemistry and set of structures is quickly lost after just one generation.

Has Benner solved all these issues? No.
Has any other scientist solved these issues? No.
Can we conclude that these issues will not be solved? Yes. The evidence points to this direction.

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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.

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RNA & DNA: It's prebiotic synthesis: Impossible !!  Inorga10

The synthesis of ribonucleotides RNA requires the following steps:

- synthesis of the bases
- synthesis of ribose
- bonding the bases to ribose
- bonding phosphate to the nucleosides
- activation of nucleotides
- polymerization to make oligonucleotides

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The problem of the origin of life is much bigger than most people imagine, or believe. I often hear: We have not yet found a way to re-create life in the lab, but science is working on it. When someone makes that claim, i immediately know, that person doesn't know the problem. I will give just one example. Deoxyribonucleotides, DNA, the information carrier in life, uses
four nucleobases. They are divided in two types of bases, Pyrimidines, and Purines. Pyrimidines use a one ring structure, composed of six members. Each member uses four carbon atoms, and two nitrogen atoms. Purins use a nine ring structure, composed of two rings, five carbons, and four nitrogens. The first problem is to answer, where did Carbon and Nitrogen come from on prebiotic earth? In modern organisms, extraordinarily complex machinery is employed to generate carbon and nitrogen in useful form. That machinery was not extant on early earth. But let us suppose that this problem was somehow overcome. Secondly, there are millions of different forms how carbon and nitrogen could be joined to make these rings. Usually, nature takes the simplest and fastest routes, and forms simple rather than complex molecules. The four bases however are rather complex, and there is no physical constraint, why nature should form that specific composition.

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The origin of life is widely regarded as one of the most difficult open problems in science.  ‘Bottom-up’ approaches in the laboratory have not generated anything nearly as complex as a living cell. And what has been achieved, is a far cry from the complexity of anything living. The total lack of any kind of experimental evidence leading to the re-creation of life; not to mention the spontaneous emergence of life…  undermines the worldview of who wants materialism to be true. But of course, there is always an excuse: Science is working on it. But is it really justified to put hope that one day a materialistic explanation will be found?

David Denton stated:
We now know not only of the existence of a break between the living and non-living world but also that it represents the most dramatic and fundamental of all the discontinuities of nature. Between a living cell and the most highly ordered non-biological systems, such as a crystal or a snowflake, there is a chasm as vast and absolute as it is possible to conceive.

And Lynn Margulis stated: To go from a bacterium to people is less of a step than to go from a mixture of amino acids to a bacterium.

And Eugene Koonin advisory editorial board of Trends in Genetics stated:
A succession of exceedingly unlikely steps is essential for the origin of life, from the synthesis and accumulation of nucleotides to the origin of translation; through the multiplication of probabilities, these make the final outcome seem almost like a miracle. The difficulties remain formidable. For all the effort, we do not currently have coherent and plausible models for the path from simple organic molecules to the first life forms. Most damningly, the powerful mechanisms of biological evolution were not available for all the stages preceding the emergence of replicator systems. Given all these major difficulties, it appears prudent to seriously consider radical alternatives for the origin of life. "

And in fact, there are basically just two options to consider: Either life emerged by a lucky accident, spontaneously through self-organization by unguided natural events, or through the direct intervention, creative force, and activity of an intelligent designer. Evolution is not a possible explanation, because evolution depends on DNA replication. Many have claimed that physical necessity could have promoted chemical reactions, which eventually resulted in the emergence of life. The problem here however is, that the genetic sequence that specifies the arrangement of proteins can be of any order, there is no constraint by physical needs.


Michael Polanyi wrote in an article titled, “Life’s Irreducible Structure,” published in the journal Science in 1968:

“Suppose that the actual structure of a DNA molecule were due to the fact that the bindings of its bases were much stronger than the bindings would be for any other distribution of bases, then such a DNA molecule would have no information content. Its code-like character would be effaced by an overwhelming redundancy. […] Whatever may be the origin of a DNA configuration, it can function as a code only if its order is not due to the forces of potential energy. It must be as physically indeterminate as the sequence of words is on a printed page.”
https://sci-hub.ren/10.1126/science.160.3834.1308

To understand why random events are not a good explanation, we best have a look at the deepest level, on an atomic scale. Life uses just five nucleobases to make DNA and RNA. Two purines, and three pyrimidines. Purines use two rings with nine atoms, pyrimidines use just one ring with six atoms. Hydrogen bonding between purine and pyrimidine bases is fundamental to the biological functions of nucleic acids, as in the formation of the double-helix structure of DNA. This bonding depends on the selection of the right atoms in the ring structure. Pyrimidine rings consist of six atoms: 4 carbon atoms and 2 nitrogen atoms. Purines have nine atoms forming the ring: 5 carbon atoms and 4 nitrogen atoms.

Remarkably, it is the composition of these atoms that permit that the strength of the hydrogen bond that permits to join the two DNA strands and form Watson–Crick base-pairing, and well-known DNA ladder.  Neither transcription nor translation of the messages encoded in RNA and DNA would be possible if the strength of the bonds had different values. Hence, life, as we understand it today, would not have arisen.

Now, someone could say, that there could be no different composition, and physical constraints and necessity could eventually permit only this specific order and arrangement of the atoms. Now, in a recent science paper from 2019, Scientists explored how many different chemical arrangements of the atoms to make these nucleobases would be possible. Surprisingly, they found well over a million variants.   The remarkable thing is, among the incredible variety of organisms on Earth, these two molecules are essentially the only ones used in life. Why? Are these the only nucleotides that could perform the function of information storage? If not, are they perhaps the best? One might expect that molecules with smaller connected Carbon components should be easier for abiotic chemistry to explore.

According to their scientific analysis, the natural ribosides and deoxyribosides inhabit a fairly redundant ( in other words, superfluous, unnecessary, needless, and nonminimal region of this space.  This is a remarkable find and implicitly leads to design. There would be no reason why random events would generate complex, rather than simple, and minimal carbon arrangements. Nor is there physical necessity that says that the composition should be so. This is evidence that a directing intelligent agency is the most plausible explanation. The chemistry space is far too vast to select by chance the right finely-tuned functional life-bearing arrangement.

In the mentioned paper, the investigators asked if other, perhaps equally good, or even better genetic systems would be possible.  Their chemical experimentations and studies concluded that the answer is no. Many nearly as good, some equally good, and a few stronger base-pairing analog systems are known. There is no reason why these structures could or would have emerged in this functional complex configuration by random trial and error. There is a complete lack of scientific-materialistic explanations despite decades of attempts to solve the riddle.

What we can see is, that direct intervention, a creative force, the activity of an intelligent agency, a powerful creator, is capable to have the intention and implement the right arrangement of every single atom into functional structures and molecules in a repetitive manner, in the case of DNA, at least 500 thousand nucleotides to store the information to kick-start life, exclusively with four bases, to produce a storage device that uses a genetic code, to store functional, instructional, complex information, functional amino acids, and phospholipids to make membranes, and ultimately, life.  Lucky accidents, the spontaneous self-organization by unguided coincidental events, that drove atoms into self-organization in an orderly manner without external direction, chemical non-biological are incapable and unspecific to arrange atoms into the right order to produce the four classes of building blocks, used in all life forms.

One Among Millions: The Chemical Space of Nucleic Acid-like Molecules  September 13, 2019
Various types of nucleic acid-like molecules have been enumerated and synthesized, but this is the first systematic attempt to enumerate, quantify and describe this chemical space. This space is surprisingly large, though its size appears predictable by typical isomerism studies. It is remarkable, given the existence of this structure space, that biology found a solution to the need for information storage. Is the solution life found to genetic molecular information storage optimal? In one sense obviously yes: it works very well and has managed to robustly support biological evolution over 3.5-4 Ga of planetary change. In another sense, from the standpoint of xeno- and synthetic biology, could other, perhaps equally good, or even better genetic systems be devised? The answer to this question will require sophisticated and protracted chemical experimentation. Studies to date suggest that the answer could be no. Many nearly as good, some equally good, and a few stronger base-pairing analogue systems are known. 1

1. https://sci-hub.ren/10.1021/acs.jcim.9b00632



Last edited by Otangelo on Sun Jan 24, 2021 2:48 pm; edited 3 times in total

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Otangelo


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Linking to science papers of more recent publication, did not justify you of accusing me of lying.  You made that accusation, without considering that I might have come to my conclusion based on older scientific information, which would eventually have been overturned with more recent, and new scientific findings. That is not so. 

Selective prebiotic formation of RNA pyrimidine and DNA purine nucleosides

Selective prebiotic formation of RNA pyrimidine and DNA purine nucleosides
https://sci-hub.st/https://www.nature.com/articles/s41586-020-2330-9

Claim: In contrast to all previous attempts to synthesize purine nucleosides, our synthesis is both prebiotically plausible and strictly stereo-, regio- and furanosyl-selective for the only isomer of the deoxypurine nucleosides used in modern biology. The pathway proceeds mostly via simple hydrolysis or dry-state processes, with a key reduction step promoted by UV irradiation supported by distinct mechanisms.
Reply:  That does not solve the problem of the lack of a mechanism to select  carbon and nitrogen in the nucleobases, outlined below:

https://reasonandscience.catsboard.com/t2865-rna-dna-it-s-prebiotic-synthesis-impossible#7700

Life uses just five nucleobases to make DNA and RNA. Two purines, and three pyrimidines. Purines use two rings with nine atoms, pyrimidines use just one ring with six atoms. Hydrogen bonding between purine and pyrimidine bases is fundamental to the biological functions of nucleic acids, as in the formation of the double-helix structure of DNA. This bonding depends on the selection of the right atoms in the ring structure. Pyrimidine rings consist of six atoms: 4 carbon atoms and 2 nitrogen atoms. Purines have nine atoms forming the ring: 5 carbon atoms and 4 nitrogen atoms.

Remarkably, it is the composition of these atoms that permit that the strength of the hydrogen bond that permits to join the two DNA strands and form Watson–Crick base-pairing, and well-known DNA ladder. Neither transcription nor translation of the messages encoded in RNA and DNA would be possible if the strength of the bonds had different values. Hence, life, as we understand it today, would not have arisen.

Now, someone could say, that there could be no different composition, and physical constraints and necessity could eventually permit only this specific order and arrangement of the atoms. Now, in a recent science paper from 2019, Scientists explored how many different chemical arrangements of the atoms to make these nucleobases would be possible. Surprisingly, they found well over a million variants. The remarkable thing is, among the incredible variety of organisms on Earth, these two molecules are essentially the only ones used in life. Why? Are these the only nucleotides that could perform the function of information storage? If not, are they perhaps the best? One might expect that molecules with smaller connected Carbon components should be easier for abiotic chemistry to explore.

According to their scientific analysis, the natural ribosides and deoxyribosides inhabit a fairly redundant ( in other words, superfluous, unnecessary, needless, and nonminimal region of this space. This is a remarkable find and implicitly leads to design. There would be no reason why random events would generate complex, rather than simple, and minimal carbon arrangements. Nor is there physical necessity that says that the composition should be so. This is evidence that a directing intelligent agency is the most plausible explanation. The chemistry space is far too vast to select by chance the right finely-tuned functional life-bearing arrangement.

In the mentioned paper, the investigators asked if other, perhaps equally good, or even better genetic systems would be possible. Their chemical experimentations and studies concluded that the answer is no. Many nearly as good, some equally good, and a few stronger base-pairing analog systems are known. There is no reason why these structures could or would have emerged in this functional complex configuration by random trial and error. There is a complete lack of scientific-materialistic explanations despite decades of attempts to solve the riddle.

Claim: Evidence implies that life may have started with a heterogeneous nucleic acid genetic system that included both RNA and DNA.
Reply: Even IF a prebiotic route of DNA synthesis would be found, the transition to an enzymatic biosynthesis pathway is a huge gap. How do you go from one to the other?
The replacement of RNA as the repository of genetic information by its more stable cousin, DNA, provides a more reliable way of transmitting information. DNA uses thymine (T) as one of its four informational bases, whereas RNA uses uracil (U).  At the C2' position of ribose, an oxygen atom is removed. The remarkable enzymes that do this are named Ribonucleotide reductases (RNR) The iron-dependent enzyme is essential for DNA synthesis, and most essential enzymes of life 32 , and it has one of the most sophisticated allosteric regulations known today. 50  
The thymine-uracil exchange constitutes one of the major chemical differences between DNA and RNA. Before being incorporated into the chromosomes, this essential modification takes place. Uracil bases in RNA are transformed into thymine bases in DNA. The synthesis of thymine requires seven enzymesDe novo biosynthesis of thymine is an intricate and energetically expensive process. 
All in all, not considering the metabolic pathways and enzymes required to make the precursors to start RNA and DNA synthesis requires at least 26  enzymes.

So, you need 26 enzymes to make DNA. But you need enzymes to make DNA. What came first?

Origin of prebiotic nucleotides - a viable hypothesis?
https://reasonandscience.catsboard.com/t2964-origin-of-prebiotic-nucleotides-a-viable-hypothesis

DNA: Destroys the theory of Evolution. Unmasking the lies
https://reasonandscience.catsboard.com/t2719-dna-origin-of-life-scenarios#6124

Prevital unguided origin of the four basic building blocks of life: Impossible !!
https://reasonandscience.catsboard.com/t2894-prevital-unguided-origin-of-the-four-basic-building-blocks-of-life-impossible

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Admin
Dimiter,

thanks for your reply. 

in order to start a plausible narrative of how life could have emerged from nonlife, one has to start from the beginning. You have not answered in regards to the ( in my opinion ) unbridgeable problem to synthesize RNA prebiotically, without enzymes. The papers which you quoted, did not provide a solution to the problems exposed. But we can go even a bit further.

One major problem is that there was NO prebiotic selection process of the functional nucleobases for Watson-Crick basepairing amongst myriads of possible configurations. THIS ALONE is a check-mate situation for the unguided abiotic origin of life hypotheses. 

https://reasonandscience.catsboard.com/t2865-rna-dna-it-s-prebiotic-synthesis-impossible#7700

As following paper reports:

Prebiotic Syntheses of Noncanonical Nucleosides and Nucleotides May 18, 2020
https://sci-hub.st/https://pubs.acs.org/doi/10.1021/acs.chemrev.0c00069

Even if the noncanonical nucleotides present on the prebiotic Earth were not able to achieve the functions that would have allowed for the action of evolution to push these molecules along the path to the extant nucleotides, the work reviewed earlier on possible prebiotic syntheses of the canonical nucleotides, primarily by the groups of Carell, Sutherland, and Powner, also raises the possibility that the prebiotic importance of noncanonical nucleosides was simply their mechanistic intermediacy en route to canonical nucleosides. 

Question: Why should that be the case? Did noncanonical nucleosides have the anthropomorphic "urge" or goal to become complex semantophoretic macromolecules that carry genetic information ? 

An enormous amount of effort has been put into finding the prebiotic origins of the extant nucleotides and our opinion that the journey is not yet complete.

My comment: And upon my understanding, the simple fact that there was no SELECTION MECHANISM of the dearly needed basic building blocks of life, and the fact that Systems, given energy and left to themselves, DEVOLVE to give uselessly complex mixtures, “asphalts”.  ( Steven A. Benner  https://sci-hub.st/https://www.ncbi.nlm.nih.gov/pubmed/25608919 ) makes ANY unguided abiogenesis hypothesis untenable and unlikely to the extreme. Using my pharising, i keep saying, impossible !! 

The trajectory from a prebiotic synthesis of the basic building blocks of life, to the sophisticated synthesis by cell factories: an unsolved riddle
https://reasonandscience.catsboard.com/t2894-prevital-unguided-origin-of-the-four-basic-building-blocks-of-life-impossible#7650

Nucleotides are building blocks for DNA and RNA. Three Pyrimidines and Two Purines Are Commonly Found in Cells.
The pyrimidine synthesis pathway requires six regulated steps, seven enzymes, and energy in the form of ATP.
The starting material for purine biosynthesis is Ribose 5-phosphate, a product of the highly complex pentose phosphate pathway, which uses 12 enzymes1 
De novo purine synthesis pathway requires ten regulated steps, eleven enzymes, and energy in the form of ATP. 

Question:  How would you go from a prebiotic synthesis of RNA, to enzymatic synthesis, required all the enzymes mentioned above?

The DNA double helix, evidence of design
https://reasonandscience.catsboard.com/t2028-biosynthesis-of-the-dna-double-helix-evidence-of-design

Enzyme expert Dr Richard Wolfenden, of the University of North Carolina, showed in 1998 that a reaction ‘“absolutely essential” in creating the building blocks of DNA and RNA would take 78 million years in water’, but was speeded up 10^18 times by an enzyme.1 This was orotidine 5′-monophosphate decarboxylase, responsible for de novo synthesis of uridine 5′-phosphate, an essential precursor of RNA and DNA, by decarboxylating orotidine 5′-monophosphate (OMP).

Wolfenden said,
‘Without catalysts, there would be no life at all, from microbes to humans. It makes you wonder how natural selection operated in such a way as to produce a protein that got off the ground as a primitive catalyst for such an extraordinarily slow reaction.’

Question:  In order to make RNA and DNA, prebiotic earth without this enzyme would have needed to wait 78 million years to yield Uridine monophosphate to make RNA. by natural processes......

The problems do not end here. In order to make nucleobases, carbon and nitrogen

DK: RNA-peptide hypothesis for the origin of life is based on well-known facts like Watson/Crick base pair interactions
Reply: As previously elucidated, Watson-Crick base-pairing depends on the very specific isomeric arrangement of nucleobases, in special carbon and nitrogen.

But carbon and nitrogen were not ready available on early earth. That is another huge, unsolved problem. 

Availability of nitrogen and ammonia on early earth
https://reasonandscience.catsboard.com/t2689-availability-of-nitrogen-and-ammonia-on-early-earth

Where did Glucose come from in a prebiotic world ?
https://reasonandscience.catsboard.com/t2419-where-did-glucose-come-from-in-a-prebiotic-world#8116

DK: Let me give you an example of fantasy: Assembly of the complicated organism “out of blue” due to some unknown force of intelligent designer. No previous scientific data, no physico-chemical interaction no laws allowing this. The explanation that comes from irreducible complexity or  “I believe so” is not a scientific explanation, therefore we are talking about fantasy.  
Having this in mind to criticize that something IS JUST HYPOTHESIS is unfair, especially if you have an alternative fantasy.
Reply: Chance of intelligence to set up life: 
100% We KNOW by repeated experience that intelligence produces all the things, as follows:
factory portals  ( membrane proteins ) factory compartments ( organelles ) a library index ( chromosomes, and the gene regulatory network ) molecular computers, hardware ( DNA ) software, a language using signs and codes like the alphabet, an instructional blueprint, ( the genetic and over a dozen epigenetic codes ) information retrieval ( RNA polymerase ) transmission ( messenger RNA ) translation ( Ribosome ) signaling ( hormones ) complex machines ( proteins ) taxis ( dynein, kinesin, transport vesicles ) molecular highways ( tubulins ) tagging programs ( each protein has a tag, which is an amino acid sequence  informing other molecular transport machines were to transport them.) factory assembly lines ( fatty acid synthase ) error check and repair systems  ( exonucleolytic proofreading ) recycling methods ( endocytic recycling ) waste grinders and management  ( Proteasome Garbage Grinders )   power generating plants ( mitochondria ) power turbines ( ATP synthase ) electric circuits ( the metabolic network ) computers ( neurons ) computer networks ( brain ) all with specific purposes.

Chance of unguided random natural events producing just a minimal functional proteome, not considering all other essential things to get a first living self-replicating cell,is:

Let's suppose, we have a fully operational raw material, and the genetic language upon which to store genetic information. Only now, we can ask: Where did the information come from to make the first living organism? Various attempts have been made to lower the minimal information content to produce a fully working operational cell. Often, Mycoplasma is mentioned as a reference to the threshold of the living from the non-living. Mycoplasma genitalium is held as the smallest possible living self-replicating cell. It is, however, a pathogen, an endosymbiont that only lives and survives within the body or cells of another organism ( humans ).  As such, it IMPORTS many nutrients from the host organism. The host provides most of the nutrients such bacteria require, hence the bacteria do not need the genes for producing such compounds themselves. As such, it does not require the same complexity of biosynthesis pathways to manufacturing all nutrients as a free-living bacterium. 

The simplest free-living bacteria is Pelagibacter ubique. 13 It is known to be one of the smallest and simplest, self-replicating, and free-living cells.  It has complete biosynthetic pathways for all 20 amino acids.  These organisms get by with about 1,300 genes and 1,308,759 base pairs and code for 1,354 proteins.  14  That would be the size of a book with 400 pages, each page with 3000 characters.  They survive without any dependence on other life forms. Incidentally, these are also the most “successful” organisms on Earth. They make up about 25% of all microbial cells.   If a chain could link up, what is the probability that the code letters might by chance be in some order which would be a usable gene, usable somewhere—anywhere—in some potentially living thing? If we take a model size of 1,200,000 base pairs, the chance to get the sequence randomly would be 4^1,200,000 or 10^722,000. This probability is hard to imagine but an illustration may help.  

Imagine covering the whole of the USA with small coins, edge to edge. Now imagine piling other coins on each of these millions of coins. Now imagine continuing to pile coins on each coin until reaching the moon about 400,000 km away! If you were told that within this vast mountain of coins there was one coin different to all the others. The statistical chance of finding that one coin is about 1 in 10^55. 

DK: evolution of proto-aaRS is based on aaRS phylogenetic DATA.
Reply:  How can there be a phylogenetic tree about proteins that must be there all at once, and on top of that, prebiotically,  in order for the translation machinery to work? There is NO evidence that a smaller genetic code, as for example using two, rather three nucleotides, and a smaller set of amino acids would/could confer functional proteins. Also, how do you explain the selection of an optimal amino acid set?

Extraordinarily Adaptive Properties of the Genetically Encoded Amino Acids
https://www.nature.com/articles/srep09414
Additional factors beyond selection for the three properties principally considered in our test contributed to the adaptability of the coded set as a LUCA organism colonized habitable spaces on Earth. Given that each additional criterion greatly reduces the number of better sets, it would seem that adding functional criteria would only make the coded set even more unusual, and possibly reflect the truly limited set of possibilities that life has to choose from.

Not considering, that proteins by their own have no use, and no function, unless embedded and working in a joint venture with other proteins, as in metabolic pathways, productionline-like arrangements to make complex macromolecules, to generate energy etc.

Homology: A Concept in Crisis
https://reasonandscience.catsboard.com/t1454-homology-a-concept-in-crisis
Phylogenetic methods are philosophically grounded, and so can be philosophically biased in ways that limit explanatory power. This constitutes an important methodologic dimension not often taken into account.

Structural similarities among automobiles, even similarities between older and newer models are due to construction according to pre-existing patterns, i.e., to design. Ironically, even striking similarities are not sufficient to exclude design-based explanations. In order to demonstrate naturalistic evolution, it is necessary to show that the mechanism by which organisms are constructed (unlike the mechanism by which automobiles are constructed) does not involve design.

DK: PREBIOTICALLY nothing complicated can come to be. The complication comes AFTER the formation of Darwinian evolution. There is an initial function of short peptides (not fully formed aaRS) to stabilized RNA-peptide complex (experimentally proven fact). After that, the short peptides EVOLVED into longer peptides accepting step by step more functions in a step by step more complicated life system until you have a fully developed translation system.
Reply: You keep ASSERTING that. Please give me good reasons why I should take your claim at face value. 

Proteins and Protein synthesis
https://reasonandscience.catsboard.com/t2706-main-topics-on-proteins-and-protein-synthesis

How Did Protein Synthesis Evolve?
The molecular processes underlying protein synthesis in present-day cells seem inextricably complex. Although we understand most of them, they do not make conceptual sense in the way that DNA transcription, DNA repair, and DNA replication do. It is especially difficult to imagine how protein synthesis evolved because it is now performed by a complex interlocking system of protein and RNA molecules; obviously the proteins could not have existed until an early version of the translation apparatus was already in place. As attractive as the RNA world idea is for envisioning early life, it does not explain how the modern-day system of protein synthesis arose.
Molecular biology of the cell, 6th ed. pg. 365

Kind regards

Otangelo

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Otangelo


Admin
Open questions in prebiotic chemistry to explain the origin of the four basic building blocks of life

https://reasonandscience.catsboard.com/t1279p75-abiogenesis-is-mathematically-impossible#7759

One of the few biologists, Eugene Koonin, Senior Investigator at the National Center for Biotechnology Information, a recognized expert in the field of evolutionary and computational biology, is honest enough to recognize that abiogenesis research has failed. He wrote in his book: The Logic of Chance page 351:
" Despite many interesting results to its credit, when judged by the straightforward criterion of reaching (or even approaching) the ultimate goal, the origin of life field is a failure—we still do not have even a plausible coherent model, let alone a validated scenario, for the emergence of life on Earth. Certainly, this is due not to a lack of experimental and theoretical effort, but to the extraordinary intrinsic difficulty and complexity of the problem. A succession of exceedingly unlikely steps is essential for the origin of life, from the synthesis and accumulation of nucleotides to the origin of translation; through the multiplication of probabilities, these make the final outcome seem almost like a miracle.

Eliminative inductions argue for the truth of a proposition by demonstrating that competitors to that proposition are false. Either the origin of the basic building blocks of life and self-replicating cells are the result of the creative act by an intelligent designer, or the result of unguided random chemical reactions on the early earth. Science, rather than coming closer to demonstrate how life could have started, has not advanced and is further away to generating living cells starting with small molecules. Therefore, most likely, cells were created by an intelligent designer.

I have listed 27 open questions in regard to the origin of RNA and DNA on the early earth, 27 unsolved problems in regard to the origin of amino acids on the early earth, 12 in regard to phospholipid synthesis, and also unsolved problems in regard to carbohydrate production. The open problems are in reality far greater. This is just a small list. It is not just an issue of things that have not yet been figured out by abiogenesis research, but deep conceptual problems, like the fact that there were no natural selection mechanisms in place on the early earth.

The implausibility of prevital RNA and DNA synthesis

RNA & DNA: It's prebiotic synthesis: Impossible !! Part 1
https://www.youtube.com/watch?v=-ZFlmL_BsXE

RNA & DNA: It's prebiotic synthesis: Impossible !! Part 2
https://www.youtube.com/watch?v=dv4mUjmuRRU

How would prebiotic processes have purified the starting molecules to make RNA and DNA which were grossly impure? They would have been present in complex mixtures that contained a great variety of reactive molecules.
How did the Synthesis of the nitrogenic nucleobases in prebiotic environments occur?
How did fortuitous accidents select the five just-right nucleobases to make DNA and RNA, Two purines, and three pyrimidines?
How did unguided random events select purines with two rings, with nine atoms, forming the two rings: 5 carbon atoms and 4 nitrogen atoms, amongst almost unlimited possible configurations?
How did stochastic coincidence select pyrimidines with one ring, with six atoms, forming its ring: 4 carbon atoms and 2 nitrogen atoms, amongst an unfathomable number of possible configurations?
How did random trial and error foresee that this specific atomic arrangement of the nucleobases is required to get the right strength of the hydrogen bond to join the two DNA strands and form Watson–Crick base-pairing?
How did mechanisms without external direction foresee that this specific atomic arrangement would convey one of, if not the best possible genetic system to store information?
How would these functional bases have been separated from the confusing jumble of similar molecules that would also have been made?
How were high-energy precursors to produce purines and pyrimidines produced in a sufficiently concentrated form and joined to the assembly site?
How could the adenine-uracil interaction function in any specific recognition scheme under the chaotic conditions of a "prebiotic soup" considering that its interaction is weak and nonspecific?
How could sufficient uracil nucleobases accumulate in prebiotic environments in sufficient quantities, if it has a half-life of only 12 years at 100◦C ?
How could the ribose 5 carbon sugar rings which form the RNA and DNA backbone have been selected, if 6 or 4 carbon rings, or even more or less, are equally possible but non-functional?
How would the functional ribose molecules have been separated from the non-functional sugars?
How were the correct nitrogen atom of the base and the correct carbon atom of the sugar selected to be joined together?
How could right-handed configurations of RNA and DNA have been selected in a racemic pool of right and left-handed molecules? Ribose must have been in its D form to adopt functional structures ( The homochirality problem )
How could random events have brought all the 3 parts together and bonded them in the right position ( probably over one million nucleotides would have been required ?)
How could prebiotic reactions have produced functional nucleosides? (There are no known ways of bringing about this thermodynamically uphill reaction in aqueous solution)
How could prebiotic glycosidic bond formation between nucleosides and the base have occurred if they are thermodynamically unstable in water, and overall intrinsically unstable?
How could RNA nucleotides have accumulated, if they degrade at warm temperatures in time periods ranging from nineteen days to twelve years? These are extremely short survival rates for the four RNA nucleotide building blocks.
How was phosphate, the third element, concentrated at reasonable concentrations?. (The concentrations in the oceans or lakes would have been very low)
How would prebiotic mechanisms phosphorylate the nucleosides at the correct site (the 5' position) if, in laboratory experiments, the 2' and 3' positions were also phosphorylated?
How could phosphate have been activated somehow? In order to promote the energy dispendious nucleotide polymerization reaction, and (energetically uphill) phosphorylation of the nucleoside had to be possible.
How was the energy supply accomplished to make RNA? In modern cells, energy is consumed to make RNA.
How could a transition from prebiotic to biochemical synthesis have occurred? There are a huge gap and enormous transition that would be still ahead to arrive at a fully functional interlocked and interdependent metabolic network.
How could RNA have formed, if it requires water to make them, but RNA cannot emerge in water and cannot replicate with sufficient fidelity in water without sophisticated repair mechanisms in place?
How would the prebiotic synthesis transition of RNA to the highly regulated cellular metabolic synthesis have occurred? The pyrimidine synthesis pathway requires six regulated steps, seven enzymes, and energy in the form of ATP.
The starting material for purine biosynthesis is Ribose 5-phosphate, a product of the highly complex pentose phosphate pathway, which uses 12 enzymes. De novo purine synthesis pathway requires ten regulated steps, eleven enzymes, and energy in the form of ATP.

DNA is more stable than RNA. uracil (U) is replaced in DNA by thymine (T)
At the C2' position of ribose, an oxygen atom is removed by hypercomplex RNR molecular machines. The thymine-uracil exchange is the major chemical difference between DNA and RNA. Before being incorporated into the chromosomes, this essential modification takes place. The synthesis of thymine requires seven enzymes. De novo biosynthesis of thymine is an intricate and energetically expensive process.
All in all, not considering the metabolic pathways and enzymes required to make the precursors to start RNA and DNA synthesis, at least 26 enzymes are required. How did these enzymes emerge, if DNA is required to make them?

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Life: What A Concept!
https://jsomers.net/life.pdf

SHAPIRO: Great advance for RNA world because if you put nucleotides in, they'll be concentrated enough to form RNA; and if you put RNA in, the RNA will come together and form aggregates, giving you much more chance of forming a ribosome or whatever. I looked at the paper and thought, How did nucleotides come in? How did RNA come in? How did anything come in? The point is, you would take whatever mess prebiotic chemistry gives you and you would concentrate that mess so it's relevant to RNA or the origin of life — it's all in the eye of the beholder. And almost all of prebiotic chemistry is like this; they take chemicals of their own selection.

People were talking about Steve Benner and his borate paper where he selected, of his own free will, the chemical formaldehyde, the chemical acid-aldehyde, and the mineral borate, and he decided to mix them together and got a product that he himself said was significant in leading to the origin of RNA world, and I, looking at the same thing, see only the hands of Steve Benner reaching to the shelf of organic chemicals, picking formaldehyde, and from another shelf, picking acidaldehyde, etc. Excluding them carefully. Picking a mineral which occurs only in selective places on the Earth and putting it in in heavy doses. And at the end getting a complex of ribose and borate, which by itself would be of no use for making RNA, because the borate loves to hold onto the ribose, and as long as it holds onto the ribose it can't be used to make RNA. If it lets go of the ribose, then the ribose becomes vulnerable to destruction by all the other environmental agents. The half-life of pure ribose in solution, a different experiment and a very good one, by Stanley Miller is of the order of one or two hours, and all of the other sugars prominent in Earth biology have similar instability.

I was publishing papers like this and I got the reputation, or the nickname in the laboratory of the prebiotic chemist, of 'Dr. No'. If someone wanted a paper murdered, send it to me as a referee. And so on. At some point, someone said, Shapiro, you've got to be positive somewhere. So how did life start? And do we have any examples of authentic abiotic chemistry, not subject to investigator interference? The only true samples we have are those meteorites, which are scooped up quickly and often fallen in an unspoiled place — there was a famous meteorite that fell in France in a sheep field in the 1840s and led to dreadful chemistry of people seeing all sorts of bio molecules in it, not surprisingly. But if you took pristine meteorites and look inside, what you see are a predominance of simple organic compounds. The smaller the organic compound, the more likely it is to be present. The larger it is, the less likely it is to be present. Amino acids, yes, but the simplest ones. Over a hundred of them. All the simplest ones, some of which, coincidentally, overlap the unique set of 20 that coincide with Earth life, but not
containing the larger amino acids that overlap with Earth life. And no sample of a nucleotide, the building block of RNA or DNA, has ever been discovered in a natural source apart from Earth life. Or even take off the phosphate, one of the three parts, and no nucleoside has ever been put together. Nature has no inclination whatsoever to build nucleosides or nucleotides that we can detect, and the pharmaceutical industry has discovered this.

Life had to start with the mess — a miscellaneous mixture of organic chemistry to begin with. How do you organize this? You have to have a preponderance of some chemicals or lacking others would be against the second law of thermo-dynamics — it violates a concept that as a non-physicist that I barely grasp called 'entropy'.

In the simplest case, and there may be many more elaborate cases, they found that the energy wouldn't be released unless some chemical transformations took place. If the chemical transformations took place then the energy was released, a lot of it is heat. If this just went on continuously, all you do is use up the energy. Release all of it and you've converted one chemical to another. Big deal. To get things interesting, you have to close the cycle where the chemicals can be recycled by processes of their own, and then go through it again, releasing more energy. And once you have that, you can then develop nodes — because organic chemistry is very robust, there are reaction pathways leading everywhere, which is why it's such a mess.

One doesn't need a freak set of perhaps a hundred consecutive reactions that will be needed to make an RNA, and life becomes a probable thing that can be generated through the action of the laws of chemistry and physics, provided certain conditions are met. You must have the energy. It's good to have some container or compartment, because if your products just diffuse away from each other and get lost and cease to react with one another you'll eventually extinguish the cycle. You need a compartment, you need a source of energy, you need to couple the energy to the chemistry involved, and you need a sufficiently rich chemistry to allow for this network of pathways to establish itself. Having been given this, you can then start to get evolution.

RNA & DNA: It's prebiotic synthesis: Impossible !!  Robert10



Last edited by Otangelo on Sat Jan 30, 2021 12:21 am; edited 1 time in total

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But RNA is also incredibly complex and sensitive, and some experts are skeptical that it could have arisen spontaneously under the harsh conditions of the prebiotic world.
https://www.quantamagazine.org/lifes-first-molecule-was-protein-not-rna-new-model-suggests-20171102/

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Tan, Change; Stadler, Rob. The Stairway To Life
The longest chains (up to fifty monomers) and the highest production of molecules with the correct bonds have been achieved in the presence of montmorillonite clay. With purine nucleotides (adenosine and guanine), the percentage of correct phosphodiester bonds actually exceeded that of the incorrect bonds. However, the addition of each monomer to the chain comes with a probability of incorrect bonding, and one incorrect bond irreversibly destroys the homolinkage of the growing polymer, just as a train with one derailed boxcar can destroy the entire train. Therefore, the synthetic yield of biopolymers with the desired homolinkage decreases exponentially as the length of the biopolymer increases—even when starting only with pure building blocks.

In the presence of montmorillonite, polymerization of purine nucleotides (i.e., adenine and guanine) is favored over pyrimidine nucleotides (i.e., cytosine, thymine, and uracil) . This would constrain the potential information-carrying capacity of the resulting polymers, somewhat like requiring an author to have the letters A through M appear in their writing twice as often as the letters N through Z.

Another issue with the montmorillonite-catalyzed reaction is that the most successful polymerization occurred with an inosine nitrogenous base, which is not used to synthesize natural DNA or RNA. Also, the resulting oligomers decompose in the presence of water and the clay accelerates this decomposition.

Production of DNA with perfect homolinkage throughout the length of a genome (for example, there are approximately 500,000 nucleotides in the simplest known free-living organism’s genome) is impossible without the molecular machinery that is available only in living organisms.

Tan, Change; Stadler, Rob. The Stairway To Life:
An E. coli cell is about two micrometers long (two millionths of a meter) and one micrometer in diameter, and it contains a circular DNA molecule with 4.6 million base pairs. If fully extended, the DNA molecule would measure about 1.4 millimeters, or about 700 times longer than the E. coli cell. Picture your car, representing an E. coli, containing a rope that represents the DNA. Scaling up the E. coli to become the size of your car (about five meters or sixteen feet in length), the DNA would correspondingly scale up to approximately 3.5 kilometers or 2.2 miles of rope with a diameter of six millimeters or ¼ inch, contained in your car. Indeed, all of that DNA has to be compressed to fit within each bacterial cell. Now, imagine the E. coli cell duplicating this DNA before replication and needing to separate the two interlinked copies before cell division. Genomic DNAs are so long that they cannot fit into any cells without being highly compacted with the help of multiple proteins. Also, such a length of rope cannot be manipulated without kinking and supercoiling, especially when DNA is unwound for reproduction. Additional topoisomerase enzymes and structural maintenance of chromosome (SMC) proteins are essential for this purpose.





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