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ElShamah - Reason & Science: Defending ID and the Christian Worldview

Otangelo Grasso: This is my library, where I collect information and present arguments developed by myself that lead, in my view, to the Christian faith, creationism, and Intelligent Design as the best explanation for the origin of the physical world.

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The hydrothermal-vent hypothesis, and why it fails

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The hydrothermal-vent hypothesis , and why it fails


Dr. Stanley L. Miller, University of California San Diego  14
What about submarine vents as a source of prebiotic compounds?
I have a very simple response to that . Submarine vents don't make organic compounds, they decompose them. Indeed, these vents are one of the limiting factors on what organic compounds you are going to have in the primitive oceans. At the present time, the entire ocean goes through those vents in 10 million years. So all of the organic compounds get zapped every ten million years. That places a constraint on how much organic material you can get. Furthermore, it gives you a time scale for the origin of life. If all the polymers and other goodies that you make get destroyed, it means life has to start early and rapidly. If you look at the process in detail, it seems that long periods of time are detrimental, rather than helpful.


The high concentrations of water on the early Earth would have diluted reactants, diffused away products, AND inhibited condensation reactions 10

A lot of origin-of-life reactions involve getting rid of water
Kevin Zahnle, a planetary scientist at the NASA Ames Research Center at Moffett Field, Calif.

The formation of the monomers does not imply the formation of their polymers, which has its own unique set of challenges in a prebiotic context. All three types of biopolymers are formed via condensation polymerization, producing a single water molecule per bond formed. Water is the solvent of life, and geologists predict that a significant ocean volume existed on the prebiotic Earth. However, polymerization reactions in aqueous media drive the polymerization reaction toward the reactants, via hydrolysis, since water is a product of the reaction. In origins of life research, this is referred to as the “water problem”. Dilution is another challenge for prebiotic polymerization, due the large volume of the ocean and the relatively small amount of monomer that would have been present. 12

RNA has been called a “prebiotic chemist's nightmare” because of its combination of large size, carbohydrate building blocks, bonds that are thermodynamically unstable in water, and overall intrinsic instability. 13 Many bonds in RNA are thermodynamically unstable with respect to hydrolysis in water, creating a “water problem”. Finally, some bonds in RNA appear to be “impossible” to form under any conditions considered plausible for early Earth.

The argument follows, that perhaps life first originated in the ocean, then over time evolved enough to come up to the surface to photosynthesize without getting burned by UVR. But even this theory has its own problems. Namely the problem of hydrolysis or “water-splitting.” The US National Academy of Sciences explains, “In water, the assembly of nucleosides from component sugars and nucleobases, the assembly of nucleotides from nucleosides and phosphate, and the assembly of oligonucleotides from nucleotides are all thermodynamically uphill in water. Two amino acids do not spontaneously join in water. Rather, the opposite reaction is thermodynamically favored at any plausible concentrations: polypeptide chains spontaneously hydrolyze in water, yielding their constituent amino acids,”. Physicist Richard Morris concurs, “… water tends to break chains of amino acids. If any proteins had formed in the ocean 3.5 billion years ago, they would have quickly disintegrated,” (Morris, 167). Additionally, the cytoplasm of living cells contains essential minerals of potassium, zinc, manganese and phosphate ions. If cells manifested naturally, these minerals would need to be present nearby. But marine environments do not have widespread concentrations of these minerals (Switek). Thus, it is clear, life could not have formed in the ocean. 2

A requirement for ultraviolet irradiation to generate hydrated electrons would rule out deep sea environments. This, along with strong bioenergetic and structural arguments, suggests that the idea that life originated at vents should, like the vents themselves, remain ‘In the deep bosom of the ocean buried’. 11

If this hypothesis were true, we would have to be able to find the development of proto-cells at all stages at these vents. Even today. Why would the origin of life have happened only once? It the alkaline hydrothermal vents offer today the same environment as 3,5 bio years ago and favor the emergence of life, we should observe this being a process happening constantly, and see protocells in all stages of development, and fully formed cells nearby. There is no trace of it. Why ?!!


Given an ocean full of small molecules of the types likely to be produced on a pre biological earth with the types of processes postulated by the origin of life enthusiasts, we must next approach the question of polymerization. This question poses a two-edged sword: we must first demonstrate that macromolecule synthesis is possible under pre biological conditions, then we must construct a rationale for generating macromolecules rich in the information necessary for usefulness in a developing precell. 

The synthesis of proteins and nucleic acids from small molecule precursors represents one of the most difficult challenges to the model of prebiological evolution. There are many different problems confronted by any proposal. Polymerization is a reaction in which water is a product. Thus it will only be favored in the absence of water. The presence of precursors in an ocean of water favors depolymerization of any molecules that might be formed. Careful experiments done in an aqueous solution with very high concentrations of amino acids demonstrate the impossibility of significant polymerization in this environment.

Polymer formation in aqueous environments would most likely have been necessary on early Earth because the liquid ocean would have been the reservoir of amino acid precursors needed for protein synthesis. 3 

           Sidney Fox, an amino acid chemist, and one of my professors in graduate school, recognized the problem and set about constructing an alternative. Since water is unfavorable to peptide bond formation, the absence of water must favor the reaction. Fox attempted to melt pure crystalline amino acids in order to promote peptide bond formation by driving off water from the mix. He discovered to his dismay that most amino acids broke down to a tarry degradation product long before they melted. After many tries he discovered two of the 20 amino acids, aspartic and glutamic acid, would melt to a liquid at about 200oC. He further discovered that if he were to dissolve the other amino acids in the molten aspartic and glutamic acids, he could produce a melt containing up to 50% of the remaining 18 amino acids. It was no surprise then that the amber liquid, after cooking for a few hours , contained polymers of amino acids with some of the properties of proteins. He subsequently named the product proteinoids. The polymerized material can be poured into an aqueous solution, resulting in the formation of spherules of protein-like material which Fox has likened to cells. Fox has claimed nearly every conceivable property for his product, including that he had bridged the macromolecule to cell transition. He even went so far as to demonstrate a piece of lava rock could substitute for the test tube in proteinoid synthesis and claimed the process took place on the primitive earth on the flanks of volcanoes. However, his critics as well as his own students have stripped his credibility. 

“It’d be like trying to make life evolve from hot Coca-Cola.” Stanley Miller of Miller-Urey experiment fame told Discover Magazine in 1992 that overall, “The vent hypothesis is a real loser. I don’t understand why we even have to discuss it.” One difficulty is that the oldest known fossils are stromatolites, clumps of bacteria from 3.5 billion years ago, which suggests that life began in shallow seas, not deep ones.

"We  posit  that  the primordial   lipids   coating   the   inorganic   cells   were   synthesised by Fischer-Tropsch-type reactions in hydrothermal systems." 1

Submarine hydrothermal systems (SHSs) have been thought of as a suitable environment for the origin of life subsequent to the abiotic synthesis of organic molecules. However, it has been pointed out that bioorganic molecules, such as amino acids, are easily degraded at a high temperature, and thus not likely to survive for the next step of chemical evolution in a SHS environment. 3

The problem with monomers is bad enough,but it is worse with polymers,e.g.,RNA and DNA (Lindahl1993),whose stability in the absence of efficient repair enzymes is too low to maintain genetic integrity iyperthermophiles. RNA and DNA are clearly too unstable to exist in a hot prebiotic environment.The existence of an RNA world with ribose appears to be incompatible with the idea of a hot origin of life. 4

Hydrothermal vents are hot, inhospitable places and the DNA of microbes that live there is continually being damaged, such that the microbes must have sophisticated error-protecting and correcting systems to survive. They are not at all simple and do not provide any sort of viable model for explaining the origin of life 5

fatty acids are formed along the face of a geyser. Research has shown that some minerals can catalyze the stepwise formation of hydrocarbon tails of fatty acids from hydrogen and carbon monoxide gases -- gases that may have been released from hydrothermal vents. Fatty acids of various lengths are eventually released into the surrounding water. 6

Unfortunately for both warm-pond and hydrothermal-vent theorists, the extreme heat has proven to be a major downfall of their theories. This is because high temperatures would accelerate the breakdown of amino acids, just as cooking meat breaks down the bonds, causing meat to become more tender. 9

The discovery of hydrothermal vents at oceanic ridge crests has spawned several origin-of-life hypotheses. It seemed an attractive suggestion that, given the dissolved gases issuing from the vents, with hydrothermal mixing there would emerge peptides, nucleotides and even protocells of some sort. Miller and Bada, however, dispute the plausibility.1

“This proposal, however, is based on a number of misunderstandings concerning the organic chemistry involved. An example is the suggestion that organic compounds were destroyed on the surface of the early Earth by the impact of asteroids and comets, but at the same time assuming that organic syntheses can occur in hydrothermal vents. The high temperatures in the vents would not allow synthesis of organic compounds, but would decompose them, unless the exposure time at vent temperatures was short. Even if the essential organic molecules were available in the hot hydrothermal waters, the subsequent steps of polymerization and the conversion of these polymers into the first organisms would not occur as the vent waters were quenched to the colder temperatures of the primitive oceans.”

[E]xperiments simulating the conditions of hydrothermal vents have only succeeded in producing RNA chains a few monomers long.

"Therefore, unless the origin of life took place extremely rapidly (<100 yr), we conclude that a high-temperature origin of life may be possible, but it cannot involve adenine, uracil, guanine, or cytosine. The rates of hydrolysis at 100°C also suggest that an ocean-boiling asteroid impact would reset the prebiotic clock, requiring prebiotic synthetic processes to begin again."

1) http://creation.com/origin-of-life-critique   
Miller, S.L. and Bada, J.L., Submarine hot springs and the origin of life, Nature 334:609–611, 1988.
2) https://matthew2262.wordpress.com/category/biology-related/
3) http://www.csj.jp/journals/bcsj/bc-cont/b12may/85_20110349.html
4) http://physwww.mcmaster.ca/~higgsp/3D03/MillerHighTemp.pdf
5) http://creation.com/origin-of-life
6) http://exploringorigins.org/fattyacids.html
7) http://christiananswers.net/q-crs/abiogenesis.html
8  http://creation.com/why-the-miller-urey-research-argues-against-abiogenesis
9) Sarfati, J., Origin of life: the polymerization problem, TJ 12(3):281–284, 1998.
10) http://web.pdx.edu/~niles/Lehman_Lab_at_PSU/Chem_460_560_files/CH460_Sp12_slides_final.pdf
11) Opinion: Studies on the origin of life — the end of the beginning
12. http://www.mdpi.com/2227-9717/3/2/309/pdf.
13. http://pubs.acs.org.sci-hub.cc/doi/abs/10.1021/ar200332w
14. https://web.archive.org/web/20080518054852/http://www.accessexcellence.org/WN/NM/miller.php

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How life emerged from deep-sea rocks


ocks, water and hot alkaline fluid rich in hydrogen gas spewing out of deep-sea vents: this recipe for life has been championed for years by a small group of scientists.  Now two of them have fleshed out the detail on how the first cells might have evolved in these vents, and escaped their deep sea lair.

Nick Lane at University College London and Bill Martin at the University of Düsseldorf in Germany think the answer to how life emerged lies in the origin of cellular ion pumps, proteins that regulate the flow of ions across the cell's membrane, the barrier that separates it from the outside world.

Life in the rocks
In all cells today, an enzyme called ATP synthase uses the energy from the flow of ions across membranes to produce the universal energy-storage molecule ATP. This essential process depends in turn on ion-pumping proteins that generate these gradients. But this creates a chicken-and-egg problem: cells store energy by means of proteins that make ion gradients, but it takes energy to make the proteins in the first place.

Lane and Martin argue that hydrogen-saturated alkaline water meeting acidic oceanic water at underwater vents would produce a natural proton gradient across thin mineral 'walls' in rocks that are rich in catalytic iron–sulphur minerals.  1  

This set-up could create the right conditions for converting carbon dioxide and hydrogen into organic carbon-containing molecules, which can then react with each other to form the building blocks of life such as nucleotides and amino acids.

This is a simplistic explanation. See why:


The rocks of deep-sea thermal vents contain labyrinths of these tiny thin-walled pores, which could have acted as 'proto-cells', both producing a proton gradient and concentrating the simple organic molecules formed, thus enabling them eventually to generate complex proteins and the nucleic acid RNA.

Thats science fiction at its best.


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

These proto-cells were the first life-forms, claim Lane and Martin.

It is assumed that the rocky proto-cells would initially be lined with leaky organic membranes. If the cells were to escape the vents and become free-living in the ocean, these membranes would have to be sealed. But sealing the membrane would cut off natural proton gradients, because although an ATP synthase would let protons into the cell, there would be nothing to pump them out, and the concentration of protons on each side of the membrane would rapidly equalize. Without an ion gradient “they would lose power,” says Lane.

Proteins that pump protons out of the cell would solve the problem, but there would have been no pressure for such proteins to evolve until after the membranes were closed. In which case, “They would have had to evolve a proton pumping  system in no time, which is impossible,” says Lane.

Modern microbes
Lane and Martin think that proto-cells escaped this dilemma because they evolved a sodium-proton antiporter — a simple protein that uses the influx of protons to pump sodium ions out of the cell.

We hypothesize that a sodium-proton antiporter (SPAP) provided the first step towards modern membranes.

Sodium/proton (Na+/H+) antiporters, located at the plasma membrane in every cell, are vital for cell homeostasis 3
NhaA is made up of two distinct domains: a core domain and a dimerization domain. In the NhaA crystal structure a cavity is located between the two domains, providing access to the ion-binding site from the inward-facing surface of the protein

So there is actually nothing simple about this protein.

At any stage before the dna-protein world, the presence of a non-random protein, no matter how simple, is forbidden. 4

The hydrothermal-vent hypothesis, and why it fails Sodium10

 Of course they could not be there, because they depend on all the complex cell machinery that makes proteins, which was obviously not there at this stage.

As the proto-cell membranes started closing up, they became impermeable to the large sodium ions before the smaller protons. This would have provided advantages  to cells that evolved a sodium-pumping protein, while they could still rely on the vents’ natural proton gradients to generate energy. The antiporters created sodium gradients as well, and when the membrane closed up completely, the cells could run on the sodium gradient, and be free to leave the vent.

Lane and Martin drew inspiration for their hypothesis from bacteria and archaea that live in these extreme environments today. “Their biochemistry seems to emerge seamlessly from the conditions in vents,” says Lane. These microbes use iron–sulphur-containing proteins to convert hydrogen and carbon dioxide into organic molecules. They rely on sodium–proton antiporters to generate ion gradients, and their membrane proteins, such as the ATP synthase, are compatible with gradients of sodium ions or protons.

Wolfgang Nitschke, a biochemist at the French National Center for Scientific Research in Marseille, praises the duo for using knowledge of modern microbes to produce detailed scenarios for the origin of life. “In stark contrast to basically all other origin-of-life hypotheses, research in the framework of the alkaline-vent scenario is empirical,” he says. “It is an outstanding paper.”

1) http://www.ncbi.nlm.nih.gov/pubmed/23260134
2) http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001926
3) http://www.nature.com/nature/journal/v501/n7468/full/nature12484.html
4) http://korthof.blogspot.com.br/2012/12/new-origin-of-life-model-fatally.html

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The Origin of Membrane Bioenergetics


The Vital Question by Nick Lane – a game-changing book about the origins of life


The “Origin of Life” is a conundrum that could once be safely consigned to wistful armchair musing – we’ll never know so don’t take it too seriously. You will probably imagine that it’s still safe to leave the subject in this speculative limbo, without very much in the way of evidence.

You’d be very wrong, because in the last 20 years, and especially the last decade, a powerful new body of evidence has emerged from genomics, geology, biochemistry and molecular biology. Here is the book that presents all this hard evidence and tightly interlocking theory to a wider audience.

While most researchers have been bedazzled by DNA into focusing on how such replicating molecules have evolved, Nick Lane’s answer could be characterised as “it’s the energy, stupid”. Of all the definitions of life, the one that matters most concerns energy: the churn of metabolic chemistry in the cells and the constant intake of nutrients and expulsion of waste are the essence of life. Information without energy is useless (pull the plug on your computer); information could not have started the whole thing off but energy could.

It is widely recognised that the creation of a viable primitive living cell, capable of reproduction and Darwinian selection, has three requirements: a containing membrane, which acts as an interface between the organism and the environment; replicators able to store the genetic instructions for the organism and to synthesise its chemical apparatus; and a way of taking energy from the environment and putting it to work to run the cell’s processes. Lane shows how all the rest can follow if we put energy first.

The evidence now is highly detailed: the essential biochemical machinery of life is known down to the last atom; the remarkable large protein complexes that catalyse the cascade of energy reactions have been, thanks to x-ray crystallography, charted in atomic detail. What these precise structures reveal are clues such as the existence of mineral centres in the otherwise proteinaceous complexes of life’s vital enzymes: iron sulphide is found at the heart of the respiratory enzymes. Why is that significant?

Because the most plausible location for where life on Earth began is the alkaline hydrothermal vents near the Mid-Atlantic Ridge, on the deep ocean floor, and other such formations. These structures, discovered only in 2000 after being predicted by the pioneering geochemist Mike Russell at Nasa’s Jet Propulsion Laboratory, have the right credentials: masses of warm energetic minerals pour out of the ocean bed and form calcium carbonate chimneys full of micropores. In the conditions of the primitive world, they would also have contained the ingredients necessary to create organic chemicals, the precursors of life; the micropores would have contained and concentrated them and the hot chemicals that spewed forth, rich in iron and sulphur, would have created energy gradients.




The argument follows, that perhaps life first originated in the ocean, then overtime evolved enough to come up to the surface to photosynthesize without getting burned by UVR. But even this theory has its own problems. Namely the problem of hydrolosis or “water-splitting.” The US National Academy of Sciences explains, “In water, the assembly of nucleosides from component sugars and nucleobases, the assembly of nucleotides from nucleosides and phosphate, and the assembly of oligonucleotides from nucleotides are all thermodynamically uphill in water. Two amino acids do not spontaneously join in water. Rather, the opposite reaction is thermodynamically favored at any plausible concentrations: polypeptide chains spontaneously hydrolyze in water, yielding their constituent amino acids,” (Luskin). Physicist Richard Morris concurs, “… water tends to break chains of amino acids. If any proteins had formed in the ocean 3.5 billion years ago, they would have quickly disintegrated,” (Morris, 167). Additionally, the cytoplasm of living cells contain essential minerals of potassium, zinc, manganese and phosphate ions. If cells manifested naturally, these minerals would need to be present nearby. But marine environments do not have widespread concentrations of these minerals (Switek). Thus, it is clear, life could not have formed in the ocean.


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Although Russell, Martin and others [23-26] have argued that proton and thermal gradients between the outflow from hot alkaline (pH 9-11) under-sea hydrothermal vents and the surrounding cooler more acidic ocean may have constituted the first sources of energy at the origin of life, the lack of RNA stability at alkaline pH ( [5] and references within) would appear to make such vents an unlikely location for RNA world evolution.






The prebiotic formation of oligonucleotides could have occurred from activated monomers, which are considered on primitive Earth (Lohrmann and Orgel, 1973 ; Lohrmann, 1977 ) . The activated nucleotide monomers have been used for the formation of oligonucleotides with and without a polynucleotide template in the presence of metal ions and clay catalysts. From the viewpoint of hydrothermal origin-of-life hypothesis, we have carried out kinetic analyses of prebiotic formation models of RNA using the activated nucleotide monomers or water-soluble carbodiimide as a condensation reagent at temperatures up to 100°C. The following models have been successfully analyzed regarding

(1) the template-directed formation of oligoguanylate on a polycytidylate template (TD reaction) (Kawamura and Umehara, 2001 ) ,
(2) the cyclization of oligonucleotides (CY reaction) (Kawamura et al., 2003 ) ,
(3) the oligocytidylate formation in the presence of Pb 2+ (ME reaction) (Kawamura and Maeda, 2007 ) , and
(4) the oligocytidylate formation in the presence of montmorillonite clay (CL reaction) (Kawamura and Maeda, 2008 ) .

Here, it is noted that the accumulation of oligonucleotides is determined by the relative magnitude of the formation and degradation processes. The kinetic analyses of the four types of RNA formation models suggested that the low efficiency of oligonucleotide formation at high temperatures is mainly due to the weak association between an activated nucleotide monomer and an elongating oligonucleotide at high temperatures since hydrogen bonding and hydrophobic interaction decrease with increasing temperature. This trend was observed for all the four types of prebiotic reactions. For the cases of TD, ME, and CL reactions, it is generally found that the association between an activated monomer and a monomer (or another activated monomer) for the formation of 2-mer becomes weak and the relative rate of the formation of 2-mer decreases notably as compared
to 3-mer and 4-mer formations. According to these data, it was conclusively implied that the oligonucleotides could have formed at high temperatures if the association between the activated nucleotide monomer and the elongation oligonucleotide is facilitated by additives, such as protein-like molecules, mineral surfaces, and metal ions.

On the other hand, the formation of protein-like molecules is also possible under the hydrothermal conditions in the absence of condensation reagent (Imai et al., 1999 ) , while the efficiency is lower than that of the dry model. Actually, the formation of proteins from amino acids under hydrothermal conditions is not so easy, where the yield of oligopeptides formation is typically 0.1–1%. One reason is that the dehydration of amino acids is generally difficult in aqueous solution. By using the hydrothermal flow reactor, we have discovered the oligoalanine formation within 10–30 s at 250–330°C using 4-mer oligoalanine and longer (Kawamura et al., 2005 ) with 10% yield and the one-step formation of oligopeptides including 20 amino acid units from Asp and Glu within 3 min at 275°C (Kawamura and Shimahashi, 2008 ) . However, the oligopeptides could not have survived for a long time under hydrothermal conditions because they are thermodynamically unstable. Thus, it has been frequently assumed that oligopeptides could have accumulated in the surrounding cool ocean once the peptides are evacuated from the hydrothermal vent (Imai et al., 1999 ) .


According to our recent investigations regarding the interactions of biopolymers under hydrothermal conditions, double-stranded DNA becomes single-stranded DNA at temperatures below 100°C and single-stranded DNA becomes insoluble in aqueous medium at temperatures higher than 100°C. At above 200°C, DNA is decomposed to short oligonucleotides or monomeric nucleotides (Kawamura and Nagayoshi, 2007 ) . On the other hand, the stability of proteins and the interaction between proteins with chromogenic reagents have been investigated. It was concluded that 

(1) the solubility of proteins likely decreases with increasing temperature and 
(2) the association of a protein with chromogenic reagent becomes weak mainly due to the conformational change of the protein (Kawamura et al., 2010 ) .


Conclusively, prebiotic biopolymers could have kinetically accumulated under hydrothermal conditions, as shown in Fig. 4 . (Kawamura, 2004, 2009 ) .

The hydrothermal-vent hypothesis, and why it fails Hydrot10

In addition, although biological interactions become weak with increasing temperature, it seems not effective as compared to the increase of degradation rates of biomolecules. Furthermore, the solubility of biomolecules should be taken into account while this has not been focused for the evaluation of the hydrothermal origin-of-life hypothesis.

The RNA world hypothesis and the GADV protein world hypothesis have been independently constructed from different evidences. From the viewpoint of the assignment between information and function, RNA-based life-like system would possess an advantage since RNA preserves both informational and catalytic functions, while proteins are not capable to preserve information in modern organisms. However, if these hypotheses were evaluated from the viewpoint of hydrothermal conditions, protein-based life-like system would be suitable rather than the RNA-based system because of the stability of proteins. However, it is hardly determined which of nucleotides or proteins are more advantageous under such extreme conditions since 

(1) the stabilities of these biopolymers are much shorter than the geological time scale and 
(2) the temperature effect for weak interactions would act for both RNA and proteins. 

Thus, it is reasonable to assume such corporative cochemical evolution on primitive Earth. However, there are few investigations on the cooperative chemical evolution of RNA and proteins. Thus, we have investigated the TD reaction of RNA and the stability of RNA in the presence of protein-like molecules. It was found that the infl uence of protein-like molecules is very limited, and we found merely weak activities of protein-like molecules for the formation and degradation of RNA (Kawamura et al., 2004 ) . On contrary, the formation of oligonucleotides under hydrothermal conditions is not yet studied since the moieties of nucleotides are less stable than amino acids, peptides, and proteins.
The viewpoints to determine whether biopolymers are stable or not have been discussed in the previous investigations (Kawamura, 2004 ) . The following two views were applied to evaluate the possibility of the accumulation of biopolymers.

View I: The accumulation of prebiotic biopolymers should be evaluated from the viewpoint of kinetics of the accumulation of prebiotic polymers (Fig. 4 ). The accumulation of biopolymers in a cell is determined by the formation with inflow and the degradation with outflow.

View II: Since enzymes control reactions in modern organisms, the rate of reactions in primitive life-like systems should be evaluated from the standpoint of possible primitive enzymatic reaction rates.

On view I, our data regarding the prebiotic formation of oligonucleotides suggested that the phosphodiester bond formation could be faster than that of the decomposition even at high temperatures if potential prebiotic catalysts, such as protein-like molecules, clay minerals, and metal ions, could have facilitated the association of the monomer and the elongating oligomers for RNA and peptides.

On view II, enzymes control biological reactions in modern organisms. However, it is noted that the reactions can proceed even at very slow rates without enzymes as background reactions in organisms. According to the importance of this principle (Radzicka and Wolfenden, 1995 ; Kawamura, 2004 ) , we have deduced that this principle would provide a temperature limit for the primitive life-like system, where primitive enzymes could have facilitated the target reactions with faster rates than the background reactions (Fig. 5 ).

The hydrothermal-vent hypothesis, and why it fails Possib10

Even a small difference  between the rates with enzyme-like molecule and background rates could be considered as candidate primitive enzyme activity. The large difference between the enzymatic rates and the background rates even at very high temperatures might reflect that the primitive enzymatic activities would have emerged at high temperatures. 

Why does the author speculate about enzyme activity in a environment, where enzymes were not present yet, and which origin we actually try to explain ?!

Besides, it is well known that weak interactions for biomolecules, such as hydrogen bonding, become strong with decreasing of temperature. The fact that the strength of biologically important interactions becomes weak can be illustrated in Fig. 5 . These investigations imply that the chemical evolution of
primitive enzymes would have been synchronized with the decrease of temperature of primitive Earth. Furthermore, the evaluation from the viewpoint of hydrothermal origin-of-life hypothesis emphasizes the importance of stabilities of biopolymers. The importance of the stability should be applied to the evaluation of a life-like system to determine if the system could have survived under primitive Earth environments.

Hugh Ross, Fazale Rana,  Origins of Life, page 73
Underwater vents. Deep-sea hydrothermal vents are popularly considered the possible sites for prebiotic molecule synthesis and life’s origins. These vents are the only places on Earth with the necessary hydrogen-rich and (supposedly) oxygen-free chemical environments to facilitate the production of amino acid and/or nucleotide molecules (the building blocks of proteins, DNA, and RNA). Laboratory experiments simulating a hot, chemically harsh environment modeled after deepsea hydrothermal vents indicate that amino acids, peptides, and other biomoleculars can form under such conditions.41
However, a team led by Stanley Miller has found that at 660 °F (350 °C), a temperature that the vents can and do reach, the amino acid half-life in a water environment is only a few minutes. (In other words, half the amino acids break down in just a few minutes.) At 480 °F (250 °C) the half-life of sugars measures in seconds. For a nucleobase to function as a building block for DNA or RNA it must be joined to a sugar. For polypeptides (chains of amino acids linked together by peptide bonds but with much lower molecular weight than proteins) the half-life is anywhere from a few minutes to a few hours. RNA molecules themselves hydrolyze (render themselves useless) within minutes at 480 °F (250 °C) and within just seconds at 662 °F (350 °C). These results led Miller and his team to conclude that the same vent conditions that can produce amino acids and/or nucleotides also destroy them. In other words, molecular decomposition outstrips composition at hydrothermal vents, making vents more damaging than helpful.

It is possible that some biomolecules could survive after production in deep-sea hydrothermal vents. A fraction of biomolecules produced in superheated water would make their way to cold water only a few seconds after leaving the hydrothermal vent’s chimney. It remains unclear at this time if the amount of prebiotics formed could achieve levels significant for naturalistic origin-of-life scenarios. Researchers at Penn State and SUNY Stony Brook identified another problem with prebiotic formation at deep-sea hydrothermal vents: ammonia production.43 For prebiotic molecules to be synthesized at deep-sea hydrothermal vents, ammonia must be present. Ammonia serves as a key starting material in the synthesis of amino acids and other biologically important nitrogen-containing compounds. However, researchers recognize that ammonia did not exist at appreciable levels on early Earth. For prebiotic synthesis to occur, ammonia must form at the hydrothermal vents. In principle, ammonia could form there from nitrogen via a route that involves hydrogen sulfide or another route involving iron(2) sulfide. Laboratory experiments, however, show that the hydrogensulfide- mediated route yields too low a level of ammonia to sustain prebiotic compound formation, and the iron(2) sulfide reaction occurs too slowly. Deep-sea hydrothermal vents not only make poor candidates for life molecule synthesis but also serve to frustrate prebiotic synthesis anywhere in their vicinity. In fact, they eliminate that possibility anywhere in Earth’s oceans. As Miller’s team pointed out, the current density of hydrothermal vents is such that all the water in the oceans is destined to circulate through the vents over the course of 10 million years. When life originated on Earth 3.8 billion years ago, the density of hydrothermal vents would have been much higher than at present, reducing the circulation time to much less than 10 million years. Any possible success in the assembly of life molecules anywhere in Earth’s oceans would have been largely lost as those molecules passed through the vents. Deep-sea vents, then, just like volcanoes, Earth’s early atmosphere, and other suggested sources, appear inadequate to produce the hypothetical prebiotic soup. Of even greater significance is the fact that scientists now have direct ways of testing whether the prebiotic soup existed at all.

Direct Evidence
Geochemists have developed two powerful tools for measuring the quantity of prebiotics on ancient Earth. One uses carbon. The other uses nitrogen. Both lead to the same conclusion. 

Carbon ratio. Carbonaceous substances (the decay products of once-living organisms) manifest a distinctly lower ratio of carbon-13 to carbon-12 than do the same carbonaceous substances that chemically developed from inorganic compounds. Therefore, careful measurements of the carbon-13 to carbon-12 ratio in ancient deposits yield the quantity of prebiotics present on ancient Earth. The surprising result of carbon-13 to carbon-12 ratio measurements of carbonaceous deposits is that all such deposits formed from the remains of once-living organisms. None of the deposits formed from prebiotic material. The researchers who made some of the most extensive carbon-13 to carbon-12 ratio measurements concluded, “No known abiotic process can explain the data.” With this accumulation of data, the primordial-soup hypothesis evaporates. Given the measurable abundance of life on Earth 3.8 billion years ago, a primordial soup—if it existed—would be geochemically obvious. Origin-of-life researcher Hubert Yockey points out, “The significance of the isotopic enhancement of carbon-12 in the very old kerogen in the Isua rocks in Greenland is that there never was a primordial soup and that, nevertheless, living matter must have existed abundantly on Earth before 3.8 billion years ago.”

Nitrogen ratio. A second geochemical tool, nitrogen isotope ratios, now provides independent confirmation that no primordial soup ever existed on (or in) Earth. The first of these confirmations comes from nitrogen-15 to nitrogen-14 ratio analysis. The same ancient carbonaceous filamentous microstructures in which researchers read the carbon-13 to carbon-12 ratio signature for postbiotic decay (as opposed to prebiotic origin) also reveal a nitrogen-15 to nitrogen-14 ratio indicative of a biogenic origin. Another confirmation arises from calculations of ammonia abundances. For any kind of primordial soup or mineral substrate to yield a chemical pathway for the development of complex life molecules, significant quantities of ammonia must be present. Laboratory simulation experiments, lacking significant quantities of ammonia, consistently fail to produce any amino acids. Several studies of the nitrogen-15 to nitrogen-14 ratio in ancient kerogens (carbonaceous deposits) show that while there may have been some ammonia in Earth’s atmosphere at the time of life’s origins 3.8 to 3.5 billion years ago, the quantities would have been inadequate to sustain the prebiotic chemical pathways necessary for life’s spontaneous origin. The answer is in: There was no prebiotic soup on the menu billions of years ago when life began.

1. Cellular Origin, Life in Extreme Habitats and Astrobiology, page 131




An RNA-making reactor for the origin of life 1

Two concomitant hydrodynamic processes, namely, thermal convection and thermophoresis along the temperature gradient, are shown to result in a >1,000-fold accumulation of mononucleotides near the bottom of a plugged pore.

Of course, the results of Baaske et al. (4) by no means put away all of the severe difficulties associated with the origin of life. In particular, at the earliest stages of biogenesis, the formation of mononucleotides, in the first place, remains problematic, and when it comes to the more advanced stages, a ribozyme replicase still is a hypothetical entity (18), and the evolutionary path to the translation systems remains essentially uncharted (19). Nevertheless, the intermediate stage, the transition from a solution of small organic molecules to a population of RNAs, now appears much less mysterious than before. Moreover, the hard combinatorial search for the extremely rare RNA sequences capable of catalyzing complex reactions, such as RNA replication, would be substantially facilitated in this setting through ligation of RNA molecules. Best of all, perhaps, the model of Baaske et al. suggests a straightforward experimental design, and such experiments, if successful, could bring us closer to an actual laboratory reproduction of the origin of life than anything done previously.

1. http://www.pnas.org/content/104/22/9105.full


8The hydrothermal-vent hypothesis, and why it fails Empty The challenge to start harvesting energy Sun Sep 04, 2022 9:18 pm



The challenge to start harvesting energy


Geoffrey Zubay (2000):  Metabolism depends on factors that are external to the organism. The living system must extract nutrients from the environment and convert them to a biochemically useful form. In the next phase of the metabolism, which is internal, small molecules are synthesized and degraded. 19

Jeremy England (2020): EVERY LIFE IS ON FIRE How Thermodynamics Explains the Origins of Living Things: A spring has first to be brought to a compressed state, that is ready to burst apart, forcefully, when properly triggered. When glass and dishes are thrown to the ground, the stored energy is released, but they get smashed, broken, or damaged. Accordingly, people can eat sugar, but not dynamite; plants love sunlight,  but not intense gamma rays. Life needs access to energy, but it has to absorb it in specific ways that are conducive to activating “healthy” motions while avoiding “unhealthy” ones. To get a little bit more technical, it helps to remember that living things are in highly specialized, exceptionally rare configurations of their constituent parts that would not easily be discovered by a random and unbiased search of the space of their possible arrangements. 17

ADDY PROSS (2012) Organized complexity and one of the most fundamental laws of the universe—the Second Law of Thermodynamics—are inherently adversarial. Nature prefers chaos to order, so disorganization is the natural order. Within living systems, however, the highly organized state that is absolutely essential for viable biological function is somehow maintained with remarkable precision. : The living cell is able to maintain its structural integrity and its organization through the continual utilization of energy, which is in fact part of the cell’s modus operandi. . So there is no thermodynamic contradiction in life’s organized high-energy state, just as there is no contradiction in a car being able to drive uphill in opposition to the Earth’s gravitational pull, or a refrigerator in maintaining a cool interior despite the constant flow of heat into that interior from the warmer exterior. Both the car driving uphill and the refrigerator with its cold interior can maintain their energetically unstable state through the continual utilization of energy. In the car’s case the burning of gasoline in the car’s engine is the energy source, while in the case of the refrigerator, the energy source is the electricity supply that operates the refrigerator’s compressor. In an analogous manner, energetically speaking, the body can maintain its highly organized state through the continual utilization of energy from some external source—the chemical energy inherent within the foods we eat, or, in the case of plants, the solar energy that is captured by the chlorophyll pigment found in all plants. But how the initial organization associated with the simplest living system came about originally is a much tougher question. 15

ATP - the Miracle molecule
Geoffrey Zubay (2000): The compound adenosine triphosphate (ATP) is the main source of chemical energy used by living systems. Through hydrolysis, ATP is converted into adenosine diphosphate (ADP) and inorganic phosphate ion (Pi ), and in the process a great deal of free energy is made available to drive other reactions. 19

Daniel Zuckerman: ATP is the most important energized molecule in the cell. ATP is an activated carrier that stores free energy because it is maintained out of equilibrium with its hydrolysis products, ADP and Pi. There is a strong tendency for ATP to become hydrolyzed (split up) into ADP and Pi, and any process that couples to this reaction can be "powered" by ATP - even if that process would be unfavorable on its own. 14

Libretext: ATP is an unstable molecule that hydrolyzes to ADP and inorganic phosphate when it is in equilibrium with water. The high energy of this molecule comes from the two high-energy phosphate bonds. The bonds between phosphate molecules are called phosphoanhydride bonds. They are energy-rich and contain a ΔG of -30.5 kJ/mol. 12

Yijie Deng (2021): Adenosine triphosphate (ATP) is the key energy source for all living organisms, essential to fundamental processes in all cells from metabolism to DNA replication and protein synthesis.  Cellular power consumption varies significantly from approximately 0.8 and 0.2 million ATP/s for a tested strain during lag and stationary phases to 6.4 million ATP/s during exponential phase, indicating ~ 8–30-fold changes of metabolic rates among different growth phases. Bacteria turn over their cellular ATP pool a few times per second during the exponential phase and slow this rate by ~ 2–5-fold in lag and stationary phases. [url=https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-021-01023-2#:~:text=Our model also shows that,under physiological conditions in E.]3[/url]

ATP was not extant prebiotically. So there had to be a way, a trajectory from non-ATP, to ATP. Prebiotic energy sources were sunlight, chemical compounds, electric discharges, cosmic rays, radioactivity, volcanoes, steam vents, and hydrothermal vents.

Cell membranes, proton gradients, and the origin of life
Every factory needs energy to do its work, and fuel for its machines to operate. So does the living chemical cell factory. It was a long way for researchers to discover how cells tackle this problem and make their energy. It comes out, that the solution is unusual and unexpected. A masterpiece of sophisticated engineering.  

Leslie E. Orgel (1999): One day a young scientist unknown to me made an appointment to talk about a theoretical matter that he thought would interest me. He was Peter Mitchell, and he wanted to talk about his ideas on how living cells derive energy: his novel chemiosmotic hypothesis. According to Mitchell's ideas, metabolic energy was used to pump protons across a biological membrane thus establishing a concentration gradient. It was the return of protons down the gradient that led to the synthesis of ATP. Energy could, in principle, be obtained by transporting an ion across a membrane from a more concentrated to a less concentrated solution. His ideas seemed bizarre to most of his contemporaries. They might well have asked, “Are you serious, Dr. Mitchell?” Of course, he was and he was right. 13

Alicia Kowaltowski (2015): Peter Mitchell was awarded the 1978 Nobel Prize in Chemistry for his discovery of the chemiosmotic mechanism of ATP synthesis, a hypothesis he first published in 1961. All groups of lifeforms present today have the genes necessary to build ATP synthases. 18

Kevin Drum (2016): A proton gradient is a complex and highly unusual way of providing energy, but it’s also nearly universal in modern life, suggesting that it goes back to the very beginnings of life. But if it’s so unusual, how did it get its start? 4

Nick Lane (2017): Chemiosmotic coupling – the harnessing of electrochemical ion gradients across membranes to drive metabolism – is as universally conserved as the genetic code. It requires not only a rotor-stator ATP synthase but also (apparently) ion-tight lipid membranes and complex proton pumps to generate electrochemical ion gradients. The claim that the last universal common ancestor had chemiosmotic coupling is treated with reservation.  All that might seem too complex to be primitive, and so it is understandable that most researchers have put the vexed question of its origins aside until more is known. Nonetheless, the fact remains that the ATP synthase is as universally conserved across life as the ribosome itself, and shares the same deep split between the bacteria and archaea. Some form of chemiosmotic coupling probably evolved very early in the history of life, arguably before LUCA; the question is how, and why?   5

Nick Lane (2010): Proton gradients are strictly necessary to the origin of life. The proton gradients that power respiration are as universal as the genetic code itself, giving an insight into the origin of life and the singular origin of complexity. There is a proton gradient across a membrane. It works much like a hydroelectric dam. The energy released by the oxidation of food (via a series of steps) is used to pump protons across a membrane — the dam — creating, in effect, a proton reservoir on one side of the membrane. The flow of protons through amazing protein turbines embedded in this membrane powers the synthesis of ATP in much the same way that the flow of water through mechanized turbines generates electricity. The flow of protons through the membrane turbines rotates the stalk of the ATP synthase, and the conformational changes induced by this rotation catalyze ATP synthesis.  How do bacteria keep their insides different from the outside? Membrane proteins can create gradients across a membrane, and these gradients can in turn power work. Although cells can generate sodium, potassium, or calcium gradients, proton gradients rule supreme. Protons power respiration not only in mitochondria but also in bacteria and archaea. Proton gradients are equally central to all forms of photosynthesis, as well as to bacterial motility (via the famous flagellar motor, a rotary motor similar to the ATP synthase) and homeostasis (the import and export of many molecules in and out of the cell is coupled directly to the proton gradient). [url=https://www.nature.com/scitable/topicpage/why-are-cells-powered-by-proton-gradients-14373960/#:~:text=Recent research suggests that proton,as they do in cells.]1[/url]

Lane comes to the conclusion: The idea that LUCA was chemiosmotic is not actually particularly challenging, as LUCA certainly had genes and proteins, and the ATP synthase is no more complex than the ribosome. It is a product of natural selection, and presumably the recruitment of subunits with pre-existing functions. 5 He references Eugene Koonin's paper published in 2007, where Koonin writes: We propose that these ATPases originated from membrane protein translocases, which, themselves, evolved from RNA translocases. We suggest that in these ancestral translocases, the position of the central stalk was occupied by the translocated polymer. 6

Is it plausible to believe that RNA translocases would be the product of prebiotic non-designed processes?

Effrosyni Papanikou (2007) The Sec machinery is essential for life. All cells must traffic proteins across their membranes. This essential process is responsible for the biogenesis of membranes and cell walls, motility and nutrient scavenging and uptake. The translocase is an impressively dynamic nanomachine that is the central component that catalyzes transmembrane crossing. This complex, the multi-stage reaction involves a cascade of inter-and intramolecular interactions that select, sort and target polypeptides to the membrane, and use energy to promote the movement of these polypeptides across — or their lateral escape and integration into — the phospholipid bilayer, with high fidelity and efficiency. Metabolic energy in the form of both ATP and the proton motive force is used to power pre-protein movement through the translocase machine  10

ATP synthase, which makes ATP, is explained by the evolution from a translocase, which requires ATP in order to be made. That is a catch22 situation. 

Is a transition from a proton gradient in inorganic compartments in hydrothermal vents, to membrane-based proton gradients a plausible hypothesis? It doesn't seem so. Here is, why: 

Inorganic compartments versus membrane-bounded cells as the means for confining the LUCA 
Eugene V. Koonin (2005): It has been repeatedly argued that the complex molecular composition inferred for LUCA could not have been attained without prior evolution of biogenic-membrane-bounded cells, mainly because (i) compartmentalization is a prerequisite for the evolution of any complex system; and (ii) certain key membrane-associated enzymes, such as the signal recognition particle (SRP) and the proton ATPase, are conserved in eubacteria and archaebacteria. The model of a compartmentalized, but inorganically confined LUCA obviates the first problem. However, the second problem – the conservation of certain membrane-associated functions in all modern forms of life – is more challenging. The ubiquity of the SRP (with its notable RNA component) and the proton ATPase across genomes, together with the clear split between archaebacterial–eukaryotic and eubacterial versions, suggests that these complexes were present in LUCA. Because the SRP inserts proteins into hydrophobic layers and ATPase requires a hydrophobic layer to function, this would seem to imply the existence of membranes in LUCA, apparently in contradiction to arguments concerning the late and independent emergence of lipid biosynthetic pathways. The essential distinction to be made is between a ‘hydrophobic layer’ and a ‘biogenic membrane’. The latter requires elaborate suites of lineage-specific enzymes (given the unrelated isoprene ether versus fatty acid ester chemistries of the membrane lipids in archaebacteria and eubacteria, respectively). 9

J. Baz Jackson (2016):  The hypothesis that a natural pH gradient across inorganic membranes lying between the ocean and fluid issuing from hydrothermal alkali vents provided energy to drive chemical reactions during the origin of life has an attractive parallel with chemiosmotic ATP synthesis in present-day organisms. However, such natural pH gradients are unlikely to have played a part in life’s origin. There is as yet no evidence for thin inorganic membranes holding sharp pH gradients in modern hydrothermal alkali vents at Lost City near the Mid-Atlantic Ridge. Proposed models of non-protein forms of the H+-pyrophosphate synthase that could have functioned as a molecular machine utilizing the energy of a natural pH gradient are unsatisfactory. Some hypothetical designs of non-protein motors utilizing a natural pH gradient to drive redox reactions are plausible but complex, and such motors are deemed unlikely to have assembled by chance in prebiotic times. Small molecular motors comprising a few hundred atoms would have been unable to function in the relatively thick (>1 μm) inorganic membranes that have hitherto been used as descriptive models for the natural pH gradient hypothesis. 11

Tan, Change; Stadler, Rob: The Stairway To Life (2020): The cell uses the proton gradient to charge “batteries” such as adenosine triphosphate (ATP), hence the “coupling” part of chemiosmotic coupling. ATP is a nearly universal battery in life. Once charged, it can be “plugged into” a wide variety of molecular machines to perform a wide variety of functions: activating amino acids for protein synthesis, copying DNA, untangling DNA, breaking bonds, transporting molecules, or contracting muscles. Like rechargeable batteries, ATP cycles frequently between powering gadgets and recharging. Although a human body contains only about sixty grams of ATP at any given moment, it is estimated that humans regenerate approximately their own weight in molecules of ATP every day. Because chemiosmotic coupling is essential for life and is highly conserved across all of life, abiogenesis must include a purely natural means to arrive at chemiosmotic coupling. This requires a membrane, a mechanism for pumping protons across the membrane, and a mechanism for producing or “recharging” ATP. The challenge is particularly onerous because these three components are highly complex in all of life and are interdependent to provide energy for life. In other words, the pumping of protons is of no use unless the membrane is there to maintain a gradient of protons. The membrane has no function for energy generation unless there is a mechanism for pumping protons across it. Similarly, the method of ATP production is of no use without a proton gradient across a membrane. 2

Rob Stadler (2022): The energy density required by life is about 100,000,000 times that which can be produced by the pH gradients of the vents. The small compartments in the rock structure have “membranes” that are far too thick for energy harnessing. And they would still require complex molecular machinery to make use of the free pH gradient. Energy harnessing in even the simplest forms of life requires extreme complexity and exhibits circular causality. Advocates for abiogenesis desperately seek to sidestep this complexity, but their best approach thus far requires placing blind faith in the wonders of natural selection. 23

Michael Marshall (2020): The biggest problem for the alkaline vent hypothesis is its most unique element, which at first sight seems the most convincing: the idea that a natural proton gradient could supply the energy to kick-start metabolism. This idea is a brilliant intuitive leap, but there is no experimental evidence. All life does use proton gradients, but all life also uses ribosomes and nobody thinks ribosomes were present at the very beginning. The problem is twofold. First, we do not know that there are sharp proton gradients within alkaline vents like Lost City. Instead, alkali may slowly blend into acid over the length of each chimney, in which case the proton gradient will be too gentle to generate useful power. Second, the enzymes that life uses, including the one that makes ATP, are big and complex. So far, nobody has found a simpler version that works and could plausibly have formed. This absence is glaring, just as the lack of a self-replicating RNA has been a problem for the RNA World. In the last few years Russell has tried to solve this problem. It seems unlikely that the first life used ATP itself, as the adenosine part of the molecule is elaborate. However, the key part is the chain of phosphates, and these ‘polyphosphate’ chains may simply have formed on their own. Indeed, Harold Morowitz pointed out in 1992 that many microorganisms make polyphosphates and used them to store chemical energy. Russell now suspects that the first life used the simplest possible polyphosphate: pyrophosphate, which is simply two phosphates strung together. To integrate pyrophosphate into his scheme, he has abandoned the idea of iron sulfide bubbles. ‘There were a lot of people who loved that because it looked like a cell,’ he says. However, he now thinks the pores in the rocks of alkaline vents were lined with multiple thin layers of ‘green rust’. Most of us have seen green rust, for instance on old iron ships that have long been exposed to seawater. It is a compound of iron, hydrogen, oxygen, and other chemicals, and Russell found it often formed when he tried to simulate conditions in the vents. He posits that these layers of green rust within the rock pores were the first cell membranes. This may seem an odd addition – surely the pores themselves were suitable containers for proto-life? – but Russell thinks the film of green rust could have been how the first life harnessed proton gradients to make pyrophosphate, without an enzyme. His proposal is that the proton gradient over the green rust membrane pulled phosphates and protons into narrow gaps in the green rust crystals, where they fused to form pyrophosphate. This was then released into the gaps between green rust layers, where it drove the synthesis of other biological molecules. It is an ingenious idea, which he is now trying to test. ‘If we can’t show in three years that that works, then we’re in dead trouble,’ he says. However, Russell is facing a new obstacle. In 2019 he lost his long-standing position at NASA’s Jet Propulsion Laboratory, and he is now living in Italy. He’s trying to get the experiments done at European Universities. Meanwhile, genetics has yielded a startlingly powerful piece of evidence in favor of the alkaline vent hypothesis.

In 2016, Martin’s team published a detailed reconstruction of the Last Universal Common Ancestor (LUCA) from which all modern organisms are descended. They did so by examining the genes of 1930 microorganisms, searching for genes that they all shared – which probably existed in LUCA. This was not easy, because microbes sometimes take a gene from an unrelated species; a process called horizontal gene transfer. This can make a gene appear universal and ancestral, when it actually evolved later and then spread. After the team had cleaned up the data as best they could, they were left with 355 gene families that seemingly existed in LUCA. These suggested that LUCA lived somewhere hot – which is compatible with an alkaline vent but doesn’t prove it – and that it used the Wood–Ljungdahl pathway to make biological molecules, as Martin predicted. Furthermore, it seems LUCA had the equipment to harness a proton gradient, but not to generate one – which fits with the idea that it relied on a natural proton gradient in a vent. This latter finding is striking, but must be taken with a pinch of salt because of the horizontal gene transfer problem. The alkaline vent hypothesis is beautiful and detailed and lines up with microbiology. But that doesn’t make it true. Plenty of beautiful, plausible seeming ideas have turned out to be wrong. It is not at all clear that the hypothesis can surmount its many problems. However, several of its key elements are so compelling that the true theory must surely incorporate them, or find some other solution to the problems they address. A source of chemical energy to fuel metabolism is obviously crucial, but possibly so is the ability to harness, or even generate, a proton gradient. Finally, it is striking that the hypothesis attempts to make two of the components of life – a metabolic cycle and a compartment – at once. It is this more holistic approach that is arguably most significant. Rather than trying to do everything with RNA, or with proteins, Russell’s idea endeavors to build something that looks more like a complete cell. In this, if nothing else, it hints at a better explanation for life on Earth. In the twenty-first century, many researchers followed Russell’s example and stopped trying to do everything with one kind of chemical. Instead, they would find ways to create all of life’s components at once. Even if Russell’s hypothesis turns out to be wrong, his work clearly foreshadowed this new approach. 24

M. J. RUSSELL (2010): The alkaline nature of hydrothermal effluent in serpentinizing systems creates naturally formed pH and redox gradients across the precipitate at the vent-ocean interface, which could readily have served as the geochemical template upon which biological chemiosmotic harnessing evolved. More generally, hydrothermal vent precipitates provide natural three-dimensional microcompartments within which the products of serpentinization-driven organic synthesis could have been retained, so that the path to chemical complexity would not be faced with otherwise insurmountable problems of diffusion to the ocean. 26

Dr. Hideshi Ooka (2018): Deep-sea environments can harness thermal and chemical energy, and this may be used to drive specific chemical reactions such as CO2 reduction. This is possible due to the material properties of the chimney wall, namely their electrical conductivity and thermal insulation. These features allow the thermal and chemical gradients to be maintained, leading to variations in reaction environments which would likely create an environment suitable for the generation of a specific CO2 reduction product. In this way, hydrothermal vents occupy a large chemical reaction space, and may “search” for the optimum spatial and physicochemical environments for CO2 reduction. 27

D.Deamer (2019): Assumptions and conjectures not tested by experiments or observation: 

- The vent minerals can catalyze the reduction of CO2 by the dissolved hydrogen. 
- A substantial pH gradient develops between the alkaline fluid and relatively acidic seawater. 
- The porous minerals compartments can concentrate potential reactants and maintain products within their volume. 
- The reduced carbon compounds can act as a substrate to initiate a primitive version of metabolism. 
- A lipid film seals the otherwise porous mineral membranes so that pH gradients can be maintained. 
- The pH gradients can serve as a source of chemiosmotic energy coupled to pyrophosphate bond synthesis.

As is proper in scientific research, recent papers from other experts express skepticism about whether CO2 can actually be reduced under vent conditions, as well as the conclusions that follow from that assumption. For instance, Jackson (2016) makes the point that mineral membranes are much too thick to function as a chemiosmotic membrane because chemiosmosis requires a thin membrane to harvest the energy of a pH gradient. An analogy that may help clarify this point is to imagine a turbine and generator capturing the energy of a 10-meter waterfall over a cliff (a “sharp” gradient) and then putting the same generator into a river that falls the same distance—10 meters— but over a distance of one kilometer (analogous to a thick membrane). Virtually no energy can be captured from the slow-moving river. 25

Phosphate’s Role in Primitive Metabolism? 
ATP is an extraordinary molecule that has permeated all life as an energy currency, yet the origin of this particular molecule is a major gap in our understanding. Cells use ATP to gather energy from a source such as photosynthesis or respiration and then deliver it to energy-requiring reactions in the rest of the cytoplasm. The chemical-energy content of ATP is present in the pyrophosphate bond that links its second and third phosphate groups. This is called a high-energy bond because of its relatively large energy content, expressed as kilocalories per mole of ATP (kcal/ mol) or as kilojoules per mole (kJ/mol) in international units. To give a sense of the amount of energy available in the bond, the units were originally measured as calories, with units defined as the amount of heat that raises the temperature of a gram (approximately one cubic centimeter) of water by one degree Celsius. (This is simplified, but the technical definition is not necessary here.) A  kilocalorie will therefore raise the temperature of a liter of water (one thousand grams) by one degree C.  If one mole of ATP (507 grams) is dissolved in one liter of water and allowed to hydrolyze, the temperature of the water would increase by approximately 7 degrees C. This energy, by the way, is a chemist’s version which is measured under carefully defined conditions of temperature and concentration. In a living cell, the conditions are quite different and ATP makes a greater amount of energy available, closer to 10 kcal per mole. ATP hydrolysis is the primary source of the heat used by mammals and birds to maintain their body temperature at a fixed point above that of the environment. 


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