Scientific advances in abiogenesis

[shunyadragon]

This got taken more seriously than I had intended, few years ago something strange happened and I said "what are the chances of that?" My friend replied "since it just happened... 100%". Similarly the odds of someone who currently exists, existing is 1:1 or 100%... No?

Concerning God, No.

 

[tas8831]

Deep sea vents are the worst possible place. Water is a solvent. RNA, DNA, proteins, sugars, etc dissolve in water without a functioning cell to protect it.

The latest experiments in water only lasted a few hours before the chains were broken down and dissolved. Long before anything useful would have time to arise....

Water is only useful to life with fully functioning cells to protect it from the solvent effects of water....

Interesting.

What is the most abundant compound in the cytosol?

Are you sure "dissolve" is the word you wanted to use?

What is your background in chemistry?

I ask because as written, your post makes little sense.

 

[shunyadragon]

Deep sea vents are the worst possible place. Water is a solvent. RNA, DNA, proteins, sugars, etc dissolve in water without a functioning cell to protect it.

The latest experiments in water only lasted a few hours before the chains were broken down and dissolved. Long before anything useful would have time to arise....

Water is only useful to life with fully functioning cells to protect it from the solvent effects of water....

Terrible lack of knowledge of the proposed origin of life in the region of sea vents based on a religious agenda as usual.

You need scientific references, and NOT just opinions expressed out of the air.


Scientist DO NOT propose that life began in the sea vents, but in the region of sea vents.

 

[Subduction Zone]

Deep sea vents are the worst possible place. Water is a solvent. RNA, DNA, proteins, sugars, etc dissolve in water without a functioning cell to protect it.

The latest experiments in water only lasted a few hours before the chains were broken down and dissolved. Long before anything useful would have time to arise....

Water is only useful to life with fully functioning cells to protect it from the solvent effects of water....

I see that others have answered this, but let me chime in as well. Crude cell walls form naturally long before "life" does:

Szostak Lab: Research

They will grow and divide without being alive.

 

[OrtaYol]

Concerning God, No.

It wasn't concerning God, it was directed at another member.

 

[shunyadragon]

It wasn't concerning God, it was directed at another member.

What was it concerning?

 

[sayak83]

I see that others have answered this, but let me chime in as well. Crude cell walls form naturally long before "life" does:

Szostak Lab: Research

They will grow and divide without being alive.

Amino acid chains spontaneously build up in typical early earth conditions recreated in labs.
Could yesterday's Earth contain clues for making tomorrow's medicines?
Izabela Sibilska, Yu Feng, Lingjun Li, John Yin. Trimetaphosphate Activates Prebiotic Peptide Synthesis across a Wide Range of Temperature and pH. Origins of Life and Evolution of Biospheres, 2018; 48

Research abstract:-
The biochemical activation of amino acids by adenosine triphosphate (ATP) drives the synthesis of proteins that are essential for all life. On the early Earth, before the emergence of cellular life, the chemical condensation of amino acids to form prebiotic peptides or proteins may have been activated by inorganic polyphosphates, such as tri metaphosphate (TP). Plausible volcanic and other potential sources of TP are known, and TP readily activates amino acids for peptide synthesis. But de novo peptide synthesis also depends on pH, temperature, and processes of solvent drying, which together define a varied range of potential activating conditions. Although we cannot replay the tape of life on Earth, we can examine how activator, temperature, acidity and other conditions may have collectively shaped its prebiotic evolution. Here, reactions of two simple amino acids, glycine and alanine, were tested, with or without TP, over a wide range of temperature (0-100 °C) and acidity (pH 1-12), while open to the atmosphere. After 24 h, products were analyzed by HPLC and mass spectrometry. In the absence of TP, glycine and alanine readily formed peptides under harsh near-boiling temperatures, extremes of pH, and within dry solid residues. In the presence of TP, however, peptides arose over a much wider range of conditions, including ambient temperature, neutral pH, and in water. These results show how polyphosphates such as TP may have enabled the transition of peptide synthesis from harsh to mild early Earth environments, setting the stage for the emergence of more complex prebiotic chemistries.

 

[shunyadragon]

Amino acid chains spontaneously build up in typical early earth conditions recreated in labs.
Could yesterday's Earth contain clues for making tomorrow's medicines?
Izabela Sibilska, Yu Feng, Lingjun Li, John Yin. Trimetaphosphate Activates Prebiotic Peptide Synthesis across a Wide Range of Temperature and pH. Origins of Life and Evolution of Biospheres, 2018; 48

Research abstract:-
The biochemical activation of amino acids by adenosine triphosphate (ATP) drives the synthesis of proteins that are essential for all life. On the early Earth, before the emergence of cellular life, the chemical condensation of amino acids to form prebiotic peptides or proteins may have been activated by inorganic polyphosphates, such as tri metaphosphate (TP). Plausible volcanic and other potential sources of TP are known, and TP readily activates amino acids for peptide synthesis. But de novo peptide synthesis also depends on pH, temperature, and processes of solvent drying, which together define a varied range of potential activating conditions. Although we cannot replay the tape of life on Earth, we can examine how activator, temperature, acidity and other conditions may have collectively shaped its prebiotic evolution. Here, reactions of two simple amino acids, glycine and alanine, were tested, with or without TP, over a wide range of temperature (0-100 °C) and acidity (pH 1-12), while open to the atmosphere. After 24 h, products were analyzed by HPLC and mass spectrometry. In the absence of TP, glycine and alanine readily formed peptides under harsh near-boiling temperatures, extremes of pH, and within dry solid residues. In the presence of TP, however, peptides arose over a much wider range of conditions, including ambient temperature, neutral pH, and in water. These results show how polyphosphates such as TP may have enabled the transition of peptide synthesis from harsh to mild early Earth environments, setting the stage for the emergence of more complex prebiotic chemistries.

Good reference. Thanks!!!

 

[exchemist]

Amino acid chains spontaneously build up in typical early earth conditions recreated in labs.
Could yesterday's Earth contain clues for making tomorrow's medicines?
Izabela Sibilska, Yu Feng, Lingjun Li, John Yin. Trimetaphosphate Activates Prebiotic Peptide Synthesis across a Wide Range of Temperature and pH. Origins of Life and Evolution of Biospheres, 2018; 48

Research abstract:-
The biochemical activation of amino acids by adenosine triphosphate (ATP) drives the synthesis of proteins that are essential for all life. On the early Earth, before the emergence of cellular life, the chemical condensation of amino acids to form prebiotic peptides or proteins may have been activated by inorganic polyphosphates, such as tri metaphosphate (TP). Plausible volcanic and other potential sources of TP are known, and TP readily activates amino acids for peptide synthesis. But de novo peptide synthesis also depends on pH, temperature, and processes of solvent drying, which together define a varied range of potential activating conditions. Although we cannot replay the tape of life on Earth, we can examine how activator, temperature, acidity and other conditions may have collectively shaped its prebiotic evolution. Here, reactions of two simple amino acids, glycine and alanine, were tested, with or without TP, over a wide range of temperature (0-100 °C) and acidity (pH 1-12), while open to the atmosphere. After 24 h, products were analyzed by HPLC and mass spectrometry. In the absence of TP, glycine and alanine readily formed peptides under harsh near-boiling temperatures, extremes of pH, and within dry solid residues. In the presence of TP, however, peptides arose over a much wider range of conditions, including ambient temperature, neutral pH, and in water. These results show how polyphosphates such as TP may have enabled the transition of peptide synthesis from harsh to mild early Earth environments, setting the stage for the emergence of more complex prebiotic chemistries.

This is very interesting indeed. Is it saying TP acts as a catalyst, or is it providing an energy source to drive the reaction? I'm not sure of the thermodynamics of the peptide condensation.

If it takes part and is turned to DP in the process that would be even more suggestive, I imagine.

 

[sayak83]

Abiogenesis is appearing in a number of threads off topic There were many negative views of abiogensis. This is the inspiration for this thread.

This version actually proposes the 'warm pond' hypothesis,' but it could have taken place in several different environments.

First reference:

LIFE'S FIRST SPARK RE-CREATED IN THE LABORATORY

A fundamental but elusive step in the early evolution of life on Earth has been replicated in a laboratory.

Researchers synthesized the basic ingredients of RNA, a molecule from which the simplest self-replicating structures are made. Until now, they couldn't explain how these ingredients might have formed.

"It's like molecular choreography, where the molecules choreograph their own behavior," said organic chemist John Sutherland of the University of Manchester, co-author of a study in Nature Wednesday.

RNA is now found in living cells, where it carries information between genes and protein-manufacturing cellular components. Scientists think RNA existed early in Earth's history, providing a necessary intermediate platform between pre-biotic chemicals and DNA, its double-stranded, more-stable descendant.

However, though researchers have been able to show how RNA's component molecules, called ribonucleotides, could assemble into RNA, their many attempts to synthesize these ribonucleotides have failed. No matter how they combined the ingredients — a sugar, a phosphate, and one of four different nitrogenous molecules, or nucleobases — ribonucleotides just wouldn't form.

Sutherland's team took a different approach in what Harvard molecular biologist Jack Szostak called a "synthetic tour de force" in an accompanying commentary in Nature.

"By changing the way we mix the ingredients together, we managed to make ribonucleotides," said Sutherland. "The chemistry works very effectively from simple precursors, and the conditions required are not distinct from what one might imagine took place on the early Earth."

Like other would-be nucleotide synthesizers, Sutherland's team included phosphate in their mix, but rather than adding it to sugars and nucleobases, they started with an array of even simpler molecules that were probably also in Earth's primordial ooze.

They mixed the molecules in water, heated the solution, then allowed it to evaporate, leaving behind a residue of hybrid, half-sugar, half-nucleobase molecules. To this residue they again added water, heated it, allowed it evaporate, and then irradiated it.

At each stage of the cycle, the resulting molecules were more complex. At the final stage, Sutherland's team added phosphate. "Remarkably, it transformed into the ribonucleotide!" said Sutherland.

According to Sutherland, these laboratory conditions resembled those of the life-originating "warm little pond" hypothesized by Charles Darwin if the pond "evaporated, got heated, and then it rained and the sun shone."

Such conditions are plausible, and Szostak imagined the ongoing cycle of evaporation, heating and condensation providing "a kind of organic snow which could accumulate as a reservoir of material ready for the next step in RNA synthesis."

Intriguingly, the precursor molecules used by Sutherland's team have been identified in interstellar dust clouds and on meteorites.

"Ribonucleotides are simply an expression of the fundamental principles of organic chemistry," said Sutherland. "They're doing it unwittingly. The instructions for them to do it are inherent in the structure of the precursor materials. And if they can self-assemble so easily, perhaps they shouldn't be viewed as complicated."

Not so specified complexity

The key argument of creationists is that life systems are too specialized and interlinked to have it gradually emerge in a piecemeal fashion through evolution or generic laws of chemistry. One prime example often cited is the translating molecules (ribosomes) that translate the genetic information into protein sequences.

"Every living thing exists because the translational system receives messages from DNA delivered to it by RNA and translates the messages into proteins. The system centers on a cellular machine called the ribosome, which is made of multiple large molecules of RNA and protein and is ubiquitous in life as we know it."

The common core of the ribosome structure is universal to all existing life and Magnesium ions play the key part within these ribosome molecules in their translating functions. However, magnesium ions will not be available in the environment of ancient earth seas and lakes when life began. Thus the universal ribosome structure and the centrality of Magnesium in it was a problem for naturalistic explanations of evolution of these molecules.

"In living systems today, magnesium helps shape ribosomes by holding them together. Magnesium is also needed for some 20 additional enzymes of the translational system. It's one reason why dietary magnesium (Mg) is so important.
The number of different things magnesium does in the ribosome and in the translational system is just enormous," said Williams. "There are so many types of catalytic activities in translation, and magnesium is involved in almost all of them."

But since Magnesium ions were not available in early earth, the researchers wanted to look at what would happen if they were removed and the far more abundant Iron and Manganese ions were added in instead.

Bray incubated ribosomes in the presence of iron, or manganese inside a special chamber with an artificial atmosphere devoid of oxygen, like the Earth four billion years ago.
Amazingly, the atomic swaps barely changed the shape of the ribosome.

"It's totally unbelievable this would work because biology makes very specific use of things. Change one atom and it can wreck a whole protein," Williams said. "When we probed the structure, we saw that all three metals do essentially the same thing to the structure."When they tested the performance of the translational system with iron replacing magnesium, it was 50 to 80 percent as efficient as normal (with magnesium). "Manganese worked even better than iron," Bray said.
"I think these may be textbook-rewriting results since the whole field of ribosome research involves magnesium," Bray said. "Now, with what we've done, it's no longer the case that only magnesium works."

This is yet another example that demonstrates that the machinery of life, even those that are universal today, are not specified in such a manner that they cannot emerge from simpler alternatives in a piecemeal fashion. Many alternative structures can also deliver the same results, even if less efficiently, and the high functional specificity is an artifact of the evolutionary process itself as life systems continued to become more efficient and hence "fitter" through natural selection over the eons that followed.

Stripping the linchpins from the life-making machine reaffirms its seminal evolution: A daring experiment corroborates translational system's place at earliest foundations of life on Earth

Full text article
Multiple prebiotic metals mediate translation

Conclusion

We have shown that the translation system functions with mixtures of divalent cations, which are variable during long-term evolutionary history and during short-term changes in bioavailability and oxidative stress. When combined with previous results that DNA replication and transcription can be facilitated by Fe2+ and Mn2+ (18⇓–20, 22⇓⇓⇓–26, 39, 40), our findings that both Fe2+ and Mn2+ can mediate rRNA folding and translation of active protein has revealed that these prebiotic divalent metals can facilitate the entire central dogma of molecular biology (DNA→RNA→protein). These findings raise important questions about evolutionary and physiological roles for Fe2+ and Mn2+ in ancient and extant biological systems. Were Mg2+, Fe2+, and Mn2+ collaborators as cofactors on the ancient Earth, when Fe2+ and Mn2+ were more abundant (1⇓⇓⇓–5), and Mg2+ was less abundant (2), than today? What was the role of Fe2+ and Mn2+ in the origin and early evolution of the translational system? Finally, what are the implications for ribosome-bound Fe2+ in oxidative damage and disease

 

[sayak83]

This is very interesting indeed. Is it saying TP acts as a catalyst, or is it providing an energy source to drive the reaction? I'm not sure of the thermodynamics of the peptide condensation.

If it takes part and is turned to DP in the process that would be even more suggestive, I imagine.

I will check the paper in more detail when time permits.

 

[Polymath257]

This is very interesting indeed. Is it saying TP acts as a catalyst, or is it providing an energy source to drive the reaction? I'm not sure of the thermodynamics of the peptide condensation.

If it takes part and is turned to DP in the process that would be even more suggestive, I imagine.

My understanding is that peptide condensation typically requires an energy source, so I would bet that the TP is used and becomes DP. This would be analogous to ATP->ADP in modern biological systems.

 

[exchemist]

My understanding is that peptide condensation typically requires an energy source, so I would bet that the TP is used and becomes DP. This would be analogous to ATP->ADP in modern biological systems.

Yes indeed, that is what I was wondering. Let's see if sayak can confirm this. Having an inorganic precursor for ATP as the energy source for protein-building would be a really significant step forward.

 

[Polymath257]

This is a quote from the original article on the processes involved:

"In the alkaline environment activation of amino acids by TP occurs by a two-step mechanism (Rabinowitz
1970 ). First, nucleophilic attack of a free (deprotonated) amine moiety at the phosphorus
results in a formation of an N-triphosphoramidate with subsequent formation of a five-
membered cyclic mixed anhydride. Ring closing is possible by the attack of the carboxylate
on the phosphorus which is coupled to displacement of pyrophosphate. The second step
involves reaction of another monomer amine moiety with the activated carbon of the mixed
anhydride, followed by the hydrolysis of the phosphoramidate, yielding a dipeptide. In contrast
with the amino acid monomers, formation of a cyclic intermediate is not possible for longer
oligopeptides. In such cases, activation of the C -terminus proceeds intermolecularly, where
phosphate is transferred from another N-phosphoro-dipeptide, and upon formation of an active
acyl compound, polymerization can progress further. At and below pH 7, when the nucleo-
philic property of the amine drastically drops due to its protonation, and the carboxylate
remains deprotonated, attack of a phosphate proceeds directly on the carbonyl. As we move
from higher to lower pH, peptide bond formation is driven more by the electrophilicity of
phosphate than the nucleophilicity of the amine, and for pH 2 –3 the process fully depends on
electrophilic phosphate activation. Consequently, peptide bond formation in the presence of TP
proceeds at lower pH and at lower temperatures owing to activation effects of the phosphate
and mixed reaction mechanisms."

It looks like the TP is split in these reactions. The authors also make an explicit analogy to activation
via ATP in biological systems.

http://link-springer-com-443.webvpn.jxutcm.edu.cn/content/pdf/10.1007/s11084-018-9564-7.pdf

 

[sayak83]

This is a quote from the original article on the processes involved:

"In the alkaline environment activation of amino acids by TP occurs by a two-step mechanism (Rabinowitz
1970 ). First, nucleophilic attack of a free (deprotonated) amine moiety at the phosphorus
results in a formation of an N-triphosphoramidate with subsequent formation of a five-
membered cyclic mixed anhydride. Ring closing is possible by the attack of the carboxylate
on the phosphorus which is coupled to displacement of pyrophosphate. The second step
involves reaction of another monomer amine moiety with the activated carbon of the mixed
anhydride, followed by the hydrolysis of the phosphoramidate, yielding a dipeptide. In contrast
with the amino acid monomers, formation of a cyclic intermediate is not possible for longer
oligopeptides. In such cases, activation of the C -terminus proceeds intermolecularly, where
phosphate is transferred from another N-phosphoro-dipeptide, and upon formation of an active
acyl compound, polymerization can progress further. At and below pH 7, when the nucleo-
philic property of the amine drastically drops due to its protonation, and the carboxylate
remains deprotonated, attack of a phosphate proceeds directly on the carbonyl. As we move
from higher to lower pH, peptide bond formation is driven more by the electrophilicity of
phosphate than the nucleophilicity of the amine, and for pH 2 –3 the process fully depends on
electrophilic phosphate activation. Consequently, peptide bond formation in the presence of TP
proceeds at lower pH and at lower temperatures owing to activation effects of the phosphate
and mixed reaction mechanisms."

It looks like the TP is split in these reactions. The authors also make an explicit analogy to activation
via ATP in biological systems.

http://link-springer-com-443.webvpn.jxutcm.edu.cn/content/pdf/10.1007/s11084-018-9564-7.pdf

But I am not sure if TP gets converted to DP during the process. The specific reaction sequence is not drawn. Will have to look at references to check that.

 

[Polymath257]

But I am not sure if TP gets converted to DP during the process. The specific reaction sequence is not drawn. Will have to look at references to check that.

At the very least, it seems the TP is split up.

 

[OrtaYol]

What was it concerning?

Another member... you guys should read more carefully. It helps a lot when you are trying to sound clever.

The initial post that was quoted (#258) and I replied to was concerning a member here who it was claimed had a very small chance of existing. At no point in any of my posts was God(or any other supernatural being) mentioned, referenced or implied.

 

[shunyadragon]

Another member... you guys should read more carefully. It helps a lot when you are trying to sound clever.

The initial post that was quoted (#258) and I replied to was concerning a member here who it was claimed had a very small chance of existing. At no point in any of my posts was God(or any other supernatural being) mentioned, referenced or implied.

The problem with proposing the issue of probability in whether abiogenesis took place or 'small chance of happening' is that it is a theological/philosophical argument for the necessity of another 'source' than natural for the beginning of life. This argument for probability requires statistical assumptions that are not scientific. The scientific literature on abiogenesis deals dominantly with the mechanisms, chemistry, and environments for abiogenesis, and not hypothetical probabilities.