Molecules, when left alone, tend to break down and become less complex instead of evolving into components of a living system
https://reasonandscience.catsboard.com/t3384-molecules-when-left-alone-tend-to-break-down-and-become-less-complex-instead-of-evolving-into-components-of-a-living-system
Ilya Prigogine (1972): The probability that at ordinary temperatures a macroscopic number of molecules is assembled to give rise to the highly ordered structures and to the coordinated functions characterizing living organisms is vanishingly small. The idea of spontaneous genesis of life in its present form is therefore highly improbable, even on the scale of the billions of years during which prebiotic evolution occurred. 1
Prigogine, I. Thermodynamics of evolution https://pubs.aip.org/physicstoday/article-abstract/25/11/23/428444/Thermodynamics-of-evolutionThe-functional-order
Steven A. Benner (2014): The Asphalt Paradox: An enormous amount of empirical data have established, as a rule, that organic systems, given energy and left to themselves, devolve to give uselessly complex mixtures, “asphalts”. The literature reports (to our knowledge) exactly zero confirmed observations where “replication involving replicable imperfections” (RIRI) evolution emerged spontaneously from a devolving chemical system. Further, chemical theories, including the second law of thermodynamics, bonding theory that describes the “space” accessible to sets of atoms, and structure theory requiring that replication systems occupy only tiny fractions of that space, suggest that it is impossible for any non-living chemical system to escape devolution to enter into the Darwinian world of the “living”. Such statements of impossibility apply even to macromolecules not assumed to be necessary for RIRI evolution. Lipids that provide tidy compartments under the close supervision of a graduate student (supporting a protocell first model for origins) are quite non-robust with respect to small environmental perturbations, such as a change in the salt concentration, the introduction of organic solvents, or a change in temperature.
https://sci-hub.ren/10.1007/s11084-014-9379-0
David Deamer (2017):
It is clear that non-activated nucleotide monomers can be linked into polymers under certain laboratory conditions designed to simulate hydrothermal fields. However, both monomers and polymers can undergo a variety of decomposition reactions that must be taken into account because biologically relevant molecules would undergo similar decomposition processes in the prebiotic environment. Decomposition of Monomers, Polymers and Molecular Systems: An Unresolved Problem 2017 Jan 17 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5370405/
Luisi (2014): Attempts to obtain copolymers, for instance by a random polymerization of monomer mixtures, yield a difficult to characterize mixture of all different products. To the best of our knowledge, there is no clear approach to the question of the prebiotic synthesis of macromolecules with an ordered sequence of residues.
https://www.sciencedirect.com/science/article/pii/S2001037014600076
Rob Stadler ( 2020): Even in a very short DNA of just two nucleotides, there are dozens of incorrect possible arrangements of the components, and only one correct arrangement. The probability of consistent arrangement decreases exponentially as the DNA lengthens. If natural processes could polymerize these monomers, the result would be chaotic “asphalt,” not highly organized, perfectly consistent biopolymers. Think about it — if monomers spontaneously polymerized within cells, the cell would die because all monomers would be combined into useless random arrangements.
https://evolutionnews.org/2021/12/long-story-short-a-strikingly-unnatural-property-of-biopolymers/
A. W. Schwartz (2007): Whatever the exact nature of an RNA precursor which may have become the first selfreplicating molecule, how could the chemical homogeneity which seems necessary to permit this kind of mechanism to even come into existence have been achieved? What mechanism would have selected for the incorporation of only threose, or ribose, or any particular building block, into short oligomers which might later have undergone chemically selective oligomerization? Virtually all model prebiotic syntheses produce mixtures.
https://pubmed.ncbi.nlm.nih.gov/17443881/
Cairns-Smith, A. G.(1982): Suppose that by chance some particular coacervate droplet in a primordial ocean happened to have a set of catalysts, etc. that could convert carbon dioxide into D-glucose. Would this have been a major step forward towards life? Probably not. Sooner or later the droplet would have sunk to the bottom of the ocean and never have been heard of again. It would not have mattered how ingenious or life-like some early system was; if it lacked the ability to pass on to offspring the secret of its success then it might as well never have existed. So I do not see life as emerging as a matter of course from the general evolution of the cosmos, via chemical evolution, in one grand gradual process of complexification. Instead, following Muller (1929) and others, I would take a genetic View and see the origin of life as hinging on a rather precise technical puzzle. What would have been the easiest way that hereditary machinery could have formed on the primitive Earth? Genetic takeover, page 70 https://archive.org/details/genetictakeoverm01cair
Comment: The conundrum of life's origins, sometimes termed the “Asphalt Paradox,” centers on the observation that organic systems, when left to their own devices, invariably devolve into complex, unusable mixtures, or “asphalts,” rather than evolving towards order and complexity necessary for life. Steven A. Benner highlights the absence of any recorded instances where replication involving replicable imperfections (RIRI) evolution has emerged spontaneously from such a devolving chemical system, suggesting the impossibility of transitioning from non-living to living chemical systems. This challenge to the spontaneous origin of life is supported by empirical data and fundamental chemical theories including the second law of thermodynamics. David Deamer further underscores the difficulty facing the formation of biologically relevant molecules in the prebiotic environment. While laboratory conditions can simulate some aspects of the hypothesized prebiotic world, they often fail to account for the decomposition reactions that would have likely affected both monomers and polymers in real-world conditions. This raises questions about the stability and longevity of these molecules in a prebiotic setting, further complicating the puzzle of life’s origins. Pier Luigi Luisi adds to this discourse, noting the significant challenges in the prebiotic synthesis of macromolecules with ordered sequences of residues. The polymerization of monomer mixtures typically yields a vast array of different products, making the formation of specific, ordered macromolecules extraordinarily improbable. Rob Stadler reinforces this probability issue, observing that even a short DNA molecule has an astronomical number of possible arrangements, with only one being correct. The natural polymerization of monomers, if it could occur, would more likely result in chaotic and useless arrangements rather than the highly organized and consistent biopolymers necessary for life. A. W. Schwartz and A. G. Cairns-Smith further contribute to these objections. Schwartz highlights the problem of chemical homogeneity in RNA precursors, pointing out that model prebiotic syntheses typically produce mixtures, complicating the path to specific, functional biopolymers. Cairns-Smith, in turn, emphasizes the essential role of hereditary machinery in life’s emergence, a feature not likely to have originated spontaneously in the primitive Earth environment. These authors collectively illuminate multiple significant and perhaps insurmountable challenges to the hypothesis of life spontaneously emerging from non-life, emphasizing the issues of chemical devolution, the improbability of ordered macromolecule formation, and the difficulty in achieving the chemical homogeneity necessary for life’s origins.
The Water Paradox:
The hydrolytic deamination of DNA and RNA nucleobases is rapid and irreversible, as is the base-catalyzed cleavage of RNA in water. RNA requires water to function, but RNA CANNOT emerge in water and does not persist in water without repair. Life seems to need a substance (water) that is inherently toxic to RNA necessary for life.
The Information-Need Paradox.
Biopolymers that might plausibly support “replication involving replicable imperfections” RIRI evolution ARE TOO LONG TO HAVE ARISEN SPONTANEOUSLY from the amounts of building blocks that might plausibly (again by theory) have escaped asphaltic devolution in water.
The Single Biopolymer Paradox.
Even if we can make biopolymers prebiotically, it IS HARD TO IMAGINE making two or three (DNA, RNA, proteins) at the same time.
The Probability Paradox.
Experiments show that RNA molecules that catalyze the destruction of RNA are more likely to arise in a pool of random (with respect to fitness) sequences than RNA molecules that catalyze the replication of RNA, with or without imperfections. Thus, even if we solve the asphalt paradox, the water paradox, the information need paradox, and the single biopolymer paradox, we still must mitigate or set aside chemical theory that makes destruction, not biology, the natural outcome of are already magical chemical system.
(a) The Asphalt Paradox (Neveu et al. 2013).
An enormous amount of empirical data have established, as a rule, that organic systems, given energy and left to themselves, devolve to give uselessly complex mixtures, “asphalts”. Theory that enumerates small molecule space, as well as Structure Theory in chemistry, can be construed to regard this devolution a necessary consequence of theory. Conversely, the literature reports (to our knowledge) exactly zero confirmed observations where “replication involving replicable imperfections” (RIRI) evolution emerged spontaneously from a devolving chemical system. Further, chemical theories, including the second law of thermodynamics, bonding theory that describes the “space” accessible to sets of atoms, and structure theory requiring that replication systems occupy only tiny fractions of that space, suggest that it is impossible for any non-living chemical system to escape devolution to enter into the Darwinian world of the “living”. Such statements of impossibility apply even to macromolecules not assumed to be necessary for RIRI evolution. Again richly supported by empirical observation, material escapes from known metabolic cycles that might be viewed as models for a “metabolism first” origin of life, making such cycles short-lived. Lipids that provide tidy compartments under the close supervision of a graduate student (supporting a protocell first model for origins) are quite non-robust with respect to small environmental perturbations, such as a change in the salt concentration, the introduction of organic solvents, or a change in temperature.
b) The Water Paradox:
Water is commonly viewed as essential for life, and theories of water are well known to support this as a requirement. So are biopolymers, like RNA, DNA, and proteins. However, these biopolymers are corroded by water. For example, the hydrolytic deamination of DNA and RNA nucleobases is rapid and irreversible, as is the base-catalyzed cleavage of RNA in water. This allows us to construct a paradox: RNA requires water to function, but RNA cannot emerge in water, and does not persist in water without repair. Any solution to the “origins problem” must manage the paradox forced by pairing this theory and this observation; life seems to need a substance (water) that is inherently toxic to polymers (e.g. RNA) necessary for life.
(c) The Information-Need Paradox.
Theory can estimate the amount of information required for a chemical system to gain access to replication with imperfections that are themselves replicable. These estimates vary widely. However, by any current theory, biopolymers that might plausibly support RIRI evolution are too long to have arisen spontaneously from the amounts of building blocks that might plausibly (again by theory) have escaped asphaltic devolution in water. If a biopolymer is assumed to be necessary for RIRI evolution, we must resolve the paradox arising because implausibly high concentrations of building blocks generate biopolymers having inadequate amounts of information. These propositions from theory and observation also force the conclusion that the emergence of (in this case, biopolymer-based) life is impossible.
(d) The Single Biopolymer Paradox.
Even if we can make biopolymers prebiotically, it is hard to imagine making two or three (DNA, RNA, proteins) at the same time. For several decades, this simple observation has driven the search for a single biopolymer that “does” both genetics and catalysis. RNA might be such a biopolymer. However, genetics versus catalysis place very different demands on the behavior of a biopolymer. According to theory, catalytic biopolymers should fold; genetic biopolymers should not fold. Catalytic biopolymers should contain many building blocks; genetic biopolymers should contain few. Perhaps most importantly, catalytic biopolymers must be able to, catalyze reactions, while genetic biopolymers should not be able to catalyze reactions and, in particular, reactions that destroy the genetic biopolymer. Any “biopolymer first” model for origins must resolve these paradoxes, giving us a polymer that both folds and does not fold, has many building blocks at the same time as having few, and has the potential to catalyze hard-but-desired reactions without the potential to catalyze easy-but undesired reactions.
(e) The Probability Paradox.
Some biopolymers, like RNA, strike a reasonable compromise between the needs of genetics and the needs of catalysis. Further, no theory creates a paradox that excludes the possibility that some RNA might catalyze the replication of RNA, with imperfections, where the imperfections are replicable. However, experiments show that RNA molecules that catalyze the destruction of RNA are more likely to arise in a pool of random (with respect to fitness) sequences than RNA molecules that catalyze the replication of RNA, with or without imperfections. Chemical theory expects this to be the case, as the base-catalyzed cleavage of RNA is an “easy” reaction (stereoelectronically), while the SN2 reaction that synthesizes a phosphodiester bond is a “difficult” reaction. Thus, even if we solve the asphalt paradox, the water paradox, the information need paradox, and the single biopolymer paradox, we still must mitigate or set aside chemical theory that makes destruction, not biology, the natural outcome of are already magical chemical system.
Steven A. Benner Prebiotic plausibility and networks of paradox-resolving independent models 12 December 2018
Unfortunately, current theory holds that Earth’s native atmosphere was more oxidizing than the Miller atmosphere. Carbon was more likely present as carbon dioxide (CO2), not methane. Nitrogen was more likely present as dinitrogen (N2), not ammonia. This model is supported by detailed studies of rocks surviving from that time8. More unfortunately, such atmospheres are very bad sources of HCN, HCCCN, and the other reduced molecules on these lists of prebiotically plausible compounds, including those in popular models for the prebiotic synthesis of adenine. Thus, the prebiotic plausibility of HCN, the other molecules, and adenine long ago vanished as Earth-made species, even though literature too voluminous to cite here continues to assume otherwise.
This creates a paradox. If one premises that life originated via an RNA-First prebiotic process that used adenine as a precursor and that adenine was formed from HCN from a Hadean terran atmosphere, then the premises that view HCN as an impossible product of our early atmosphere force the conclusion that life could not have originated on Earth. An unacceptable conclusion follows by the force of logic from seemingly acceptable premises.
https://www.nature.com/articles/s41467-018-07274-y
Timothy R. Stout, George Matzko A Natural Origin-of-Life: Every Hypothetical Step Appears Thwarted by Abiogenetic Randomization May 5, 2019
Prebiotic processes naturally randomize their feedstock. This has resulted in the failure of every experimentally tested hypothetical step in abiogenesis beginning with the 1953 Miller-Urey Experiment and continuing to the present. Not a single step has been demonstrated that starts with appropriate supply chemicals, operates on the chemicals with a prebiotic process, and yields new chemicals that represent progress towards life and which can also be used in a subsequent step as produced. Instead, the products of thousands of experiments over more than six decades consistently exhibit either increased randomization over their initial composition or no change. We propose the following hypothesis of Abiogenetic Randomization as the root cause for most if not all of the failures: 1) prebiotic processes naturally form many different kinds of products; life requires a few very specific kinds. 2) The needs of abiogenesis spatially and temporally are not connected to and do not change the natural output of prebiotic processes. 3) Prebiotic processes naturally randomize feedstock. A lengthy passage of time only results in more complete randomization of the feedstock, not eventual provision of chemicals suitable for life. The Murchison meteorite provides a clear example of this. 4) At each hypothetical step of abiogenesis, the ratio of randomized to required products proves fatal for that step. 5. The statistical law of large numbers applies, causing incidental appearances of potentially useful products eventually to be overwhelmed by the overall, normal product distribution. 6) The principle of emergence magnifies the problems: the components used in the later steps of abiogenesis become so intertwined that a single-step first appearance of the entire set is required. Small molecules are not the answer. Dynamic self-organization requires from the beginning large proteins for replication, metabolism, and active transport. Many steps across the entire spectrum of abiogenesis are examined, showing how the hypothesis appears to predict the observed problems qualitatively. There is broad experimental support for the hypothesis at each observed step with no currently known exceptions.
Just as there are no betting schemes that allow a person to overcome randomness in a casino, there appear to be no schemes able to overcome randomness using prebiotic processes. We suggest that an unwillingness to acknowledge this has led to the sixty plus years of failure in the field. There is a large body of evidence—essentially all experiments in abiogenesis performed since its inception sixty plus years ago—that appear to be consistent with the hypothesis presented in this paper. Randomization prevails.
https://osf.io/p5nw3/?fbclid=IwAR0vAV5jVQR7Z-IT_S1fQzJQ_fMonIgUW9xvj0quKIOFdgWWwcnzPPStXIc
Muriel Gargaud: Young Sun, Early Earth and the Origins of Life 2012:
Every living being consists of a collection of molecules that are constantly renewed and which appear to coordinate their evolution. We are therefore dealing with organized systems, the emergence of which, perforce, implies a process of self-organization. However, the spontaneous formation of an ordered system from disorder contradicts our everyday experience. We all know that over time, the most beautiful building is inevitably reduced to ruins. In physical or chemical terms, this tendency is expressed as a quantity, entropy, which expresses the degree of disorder in a system. The second law of thermodynamics expresses the idea that the entropy of an isolated system increases, and thus that disorder tends to increase. An isolated chemical system must, therefore, evolve towards an equilibrium state in which the concentration of different chemical species will be determined by their individual energy levels and the laws of statistics. So how could a system that was as disordered as that of the primitive Earth, with an incredible diversity of forms and structures, give rise to life?
The answer lies in the fact that the process of self-organization, which is linked to the emergence and development of life, concerns only one part of the system. Hence, the formation of an ordered structure in a sub-system will be compensated by an increase in disorder in its environment, such that overall, the entropy does not decrease. That means then that exchanges of energy and matter are the basis of the dynamics of self-organization.
My comment: Since the authors apply methodological naturalism and exclude design a priori, they are left with the only alternative to design, which is self-organization. Mount Improbable is, however, higher to climb, to get life the first go, then keep it going. That implies a paradox: If the inorganic matter had the unbound drive to get self-organized and become alive, why do thermodynamic mechanisms, and evolution, permit life to die? Why does the cycle of self-replication, which had to be fully set up as well right from the beginning, perpetuate life for millennia, if not millions of years, but living organisms die? If the unbound drive of atoms is to self-organize and get alive, why not the unbound drive to KEEP alive? We know, for instance, that turtles live for centuries. If the struggle is for survival, why do not more species steal DNA from other species like bdelloids? why can Glass Sponges live for 15 thousand years, but evolution has not helped us to get so far? Turritopsis doohmii jellyfish has found a way to cheat death by actually reversing its aging process. If the jellyfish is injured or sick, it returns to its polyp stage over a three-day period, transforming its cells into a younger state that will eventually grow into adulthood all over again. If molecules drive for survival, why have not many more organisms evolved in a convergent manner, and adopted this extraordinary mechanism?
Moreover, the inescapable evolution towards disorder and the state of thermodynamic equilibrium does not predict in any way the duration of the chemical reactions involved, which may occur in a fraction of a second or, on the other hand, over a period that is reckoned in millions of years. The speed of this evolution depends on the dynamics of the reaction (the subject of chemical kinetics) and not on thermodynamics, which only predicts the sense in which it unfolds. In chemistry, it is difficult to envisage self-organization without having recourse to the heterogeneous nature of matter on a microscopic scale, that is to the fact that matter is not indefinitely divisible. If that were the case, how could it form complex structures? It was undoubtedly this type of reasoning that led, in antiquity, certain philosophers, the best known of which remains Democritus, to postulate the existence of atoms as being the basis of matter. The difficulty comes in passing from this microscopic heterogeneity to a single macroscopic entity that involves a coordination in the arrangement or the movement of a multiplicity of atoms or molecules (either within a three-dimensional structure or within an entire organism). The properties that molecules have of associating with one another may give rise to the formation of crystals or other macroscopic structures such as vesicles (such as those that form cellular membranes ) or the micelles of surfactants. Structures that have a dynamical character may also appear through amplification mechanisms that are highly efficient, such as replication or autocatalysis. These mechanisms are at work in what are known as oscillating reactions, which are often considered chemical curiosities, such as the Belousov-Zhabotinsky reaction . The concentration of certain intermediates then varies until the reagents are exhausted, in a cyclic or stochastic
https://reasonandscience.catsboard.com/t3384-molecules-when-left-alone-tend-to-break-down-and-become-less-complex-instead-of-evolving-into-components-of-a-living-system
Ilya Prigogine (1972): The probability that at ordinary temperatures a macroscopic number of molecules is assembled to give rise to the highly ordered structures and to the coordinated functions characterizing living organisms is vanishingly small. The idea of spontaneous genesis of life in its present form is therefore highly improbable, even on the scale of the billions of years during which prebiotic evolution occurred. 1
Prigogine, I. Thermodynamics of evolution https://pubs.aip.org/physicstoday/article-abstract/25/11/23/428444/Thermodynamics-of-evolutionThe-functional-order
Steven A. Benner (2014): The Asphalt Paradox: An enormous amount of empirical data have established, as a rule, that organic systems, given energy and left to themselves, devolve to give uselessly complex mixtures, “asphalts”. The literature reports (to our knowledge) exactly zero confirmed observations where “replication involving replicable imperfections” (RIRI) evolution emerged spontaneously from a devolving chemical system. Further, chemical theories, including the second law of thermodynamics, bonding theory that describes the “space” accessible to sets of atoms, and structure theory requiring that replication systems occupy only tiny fractions of that space, suggest that it is impossible for any non-living chemical system to escape devolution to enter into the Darwinian world of the “living”. Such statements of impossibility apply even to macromolecules not assumed to be necessary for RIRI evolution. Lipids that provide tidy compartments under the close supervision of a graduate student (supporting a protocell first model for origins) are quite non-robust with respect to small environmental perturbations, such as a change in the salt concentration, the introduction of organic solvents, or a change in temperature.
https://sci-hub.ren/10.1007/s11084-014-9379-0
David Deamer (2017):
It is clear that non-activated nucleotide monomers can be linked into polymers under certain laboratory conditions designed to simulate hydrothermal fields. However, both monomers and polymers can undergo a variety of decomposition reactions that must be taken into account because biologically relevant molecules would undergo similar decomposition processes in the prebiotic environment. Decomposition of Monomers, Polymers and Molecular Systems: An Unresolved Problem 2017 Jan 17 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5370405/
Luisi (2014): Attempts to obtain copolymers, for instance by a random polymerization of monomer mixtures, yield a difficult to characterize mixture of all different products. To the best of our knowledge, there is no clear approach to the question of the prebiotic synthesis of macromolecules with an ordered sequence of residues.
https://www.sciencedirect.com/science/article/pii/S2001037014600076
Rob Stadler ( 2020): Even in a very short DNA of just two nucleotides, there are dozens of incorrect possible arrangements of the components, and only one correct arrangement. The probability of consistent arrangement decreases exponentially as the DNA lengthens. If natural processes could polymerize these monomers, the result would be chaotic “asphalt,” not highly organized, perfectly consistent biopolymers. Think about it — if monomers spontaneously polymerized within cells, the cell would die because all monomers would be combined into useless random arrangements.
https://evolutionnews.org/2021/12/long-story-short-a-strikingly-unnatural-property-of-biopolymers/
A. W. Schwartz (2007): Whatever the exact nature of an RNA precursor which may have become the first selfreplicating molecule, how could the chemical homogeneity which seems necessary to permit this kind of mechanism to even come into existence have been achieved? What mechanism would have selected for the incorporation of only threose, or ribose, or any particular building block, into short oligomers which might later have undergone chemically selective oligomerization? Virtually all model prebiotic syntheses produce mixtures.
https://pubmed.ncbi.nlm.nih.gov/17443881/
Cairns-Smith, A. G.(1982): Suppose that by chance some particular coacervate droplet in a primordial ocean happened to have a set of catalysts, etc. that could convert carbon dioxide into D-glucose. Would this have been a major step forward towards life? Probably not. Sooner or later the droplet would have sunk to the bottom of the ocean and never have been heard of again. It would not have mattered how ingenious or life-like some early system was; if it lacked the ability to pass on to offspring the secret of its success then it might as well never have existed. So I do not see life as emerging as a matter of course from the general evolution of the cosmos, via chemical evolution, in one grand gradual process of complexification. Instead, following Muller (1929) and others, I would take a genetic View and see the origin of life as hinging on a rather precise technical puzzle. What would have been the easiest way that hereditary machinery could have formed on the primitive Earth? Genetic takeover, page 70 https://archive.org/details/genetictakeoverm01cair
Comment: The conundrum of life's origins, sometimes termed the “Asphalt Paradox,” centers on the observation that organic systems, when left to their own devices, invariably devolve into complex, unusable mixtures, or “asphalts,” rather than evolving towards order and complexity necessary for life. Steven A. Benner highlights the absence of any recorded instances where replication involving replicable imperfections (RIRI) evolution has emerged spontaneously from such a devolving chemical system, suggesting the impossibility of transitioning from non-living to living chemical systems. This challenge to the spontaneous origin of life is supported by empirical data and fundamental chemical theories including the second law of thermodynamics. David Deamer further underscores the difficulty facing the formation of biologically relevant molecules in the prebiotic environment. While laboratory conditions can simulate some aspects of the hypothesized prebiotic world, they often fail to account for the decomposition reactions that would have likely affected both monomers and polymers in real-world conditions. This raises questions about the stability and longevity of these molecules in a prebiotic setting, further complicating the puzzle of life’s origins. Pier Luigi Luisi adds to this discourse, noting the significant challenges in the prebiotic synthesis of macromolecules with ordered sequences of residues. The polymerization of monomer mixtures typically yields a vast array of different products, making the formation of specific, ordered macromolecules extraordinarily improbable. Rob Stadler reinforces this probability issue, observing that even a short DNA molecule has an astronomical number of possible arrangements, with only one being correct. The natural polymerization of monomers, if it could occur, would more likely result in chaotic and useless arrangements rather than the highly organized and consistent biopolymers necessary for life. A. W. Schwartz and A. G. Cairns-Smith further contribute to these objections. Schwartz highlights the problem of chemical homogeneity in RNA precursors, pointing out that model prebiotic syntheses typically produce mixtures, complicating the path to specific, functional biopolymers. Cairns-Smith, in turn, emphasizes the essential role of hereditary machinery in life’s emergence, a feature not likely to have originated spontaneously in the primitive Earth environment. These authors collectively illuminate multiple significant and perhaps insurmountable challenges to the hypothesis of life spontaneously emerging from non-life, emphasizing the issues of chemical devolution, the improbability of ordered macromolecule formation, and the difficulty in achieving the chemical homogeneity necessary for life’s origins.
The Water Paradox:
The hydrolytic deamination of DNA and RNA nucleobases is rapid and irreversible, as is the base-catalyzed cleavage of RNA in water. RNA requires water to function, but RNA CANNOT emerge in water and does not persist in water without repair. Life seems to need a substance (water) that is inherently toxic to RNA necessary for life.
The Information-Need Paradox.
Biopolymers that might plausibly support “replication involving replicable imperfections” RIRI evolution ARE TOO LONG TO HAVE ARISEN SPONTANEOUSLY from the amounts of building blocks that might plausibly (again by theory) have escaped asphaltic devolution in water.
The Single Biopolymer Paradox.
Even if we can make biopolymers prebiotically, it IS HARD TO IMAGINE making two or three (DNA, RNA, proteins) at the same time.
The Probability Paradox.
Experiments show that RNA molecules that catalyze the destruction of RNA are more likely to arise in a pool of random (with respect to fitness) sequences than RNA molecules that catalyze the replication of RNA, with or without imperfections. Thus, even if we solve the asphalt paradox, the water paradox, the information need paradox, and the single biopolymer paradox, we still must mitigate or set aside chemical theory that makes destruction, not biology, the natural outcome of are already magical chemical system.
(a) The Asphalt Paradox (Neveu et al. 2013).
An enormous amount of empirical data have established, as a rule, that organic systems, given energy and left to themselves, devolve to give uselessly complex mixtures, “asphalts”. Theory that enumerates small molecule space, as well as Structure Theory in chemistry, can be construed to regard this devolution a necessary consequence of theory. Conversely, the literature reports (to our knowledge) exactly zero confirmed observations where “replication involving replicable imperfections” (RIRI) evolution emerged spontaneously from a devolving chemical system. Further, chemical theories, including the second law of thermodynamics, bonding theory that describes the “space” accessible to sets of atoms, and structure theory requiring that replication systems occupy only tiny fractions of that space, suggest that it is impossible for any non-living chemical system to escape devolution to enter into the Darwinian world of the “living”. Such statements of impossibility apply even to macromolecules not assumed to be necessary for RIRI evolution. Again richly supported by empirical observation, material escapes from known metabolic cycles that might be viewed as models for a “metabolism first” origin of life, making such cycles short-lived. Lipids that provide tidy compartments under the close supervision of a graduate student (supporting a protocell first model for origins) are quite non-robust with respect to small environmental perturbations, such as a change in the salt concentration, the introduction of organic solvents, or a change in temperature.
b) The Water Paradox:
Water is commonly viewed as essential for life, and theories of water are well known to support this as a requirement. So are biopolymers, like RNA, DNA, and proteins. However, these biopolymers are corroded by water. For example, the hydrolytic deamination of DNA and RNA nucleobases is rapid and irreversible, as is the base-catalyzed cleavage of RNA in water. This allows us to construct a paradox: RNA requires water to function, but RNA cannot emerge in water, and does not persist in water without repair. Any solution to the “origins problem” must manage the paradox forced by pairing this theory and this observation; life seems to need a substance (water) that is inherently toxic to polymers (e.g. RNA) necessary for life.
(c) The Information-Need Paradox.
Theory can estimate the amount of information required for a chemical system to gain access to replication with imperfections that are themselves replicable. These estimates vary widely. However, by any current theory, biopolymers that might plausibly support RIRI evolution are too long to have arisen spontaneously from the amounts of building blocks that might plausibly (again by theory) have escaped asphaltic devolution in water. If a biopolymer is assumed to be necessary for RIRI evolution, we must resolve the paradox arising because implausibly high concentrations of building blocks generate biopolymers having inadequate amounts of information. These propositions from theory and observation also force the conclusion that the emergence of (in this case, biopolymer-based) life is impossible.
(d) The Single Biopolymer Paradox.
Even if we can make biopolymers prebiotically, it is hard to imagine making two or three (DNA, RNA, proteins) at the same time. For several decades, this simple observation has driven the search for a single biopolymer that “does” both genetics and catalysis. RNA might be such a biopolymer. However, genetics versus catalysis place very different demands on the behavior of a biopolymer. According to theory, catalytic biopolymers should fold; genetic biopolymers should not fold. Catalytic biopolymers should contain many building blocks; genetic biopolymers should contain few. Perhaps most importantly, catalytic biopolymers must be able to, catalyze reactions, while genetic biopolymers should not be able to catalyze reactions and, in particular, reactions that destroy the genetic biopolymer. Any “biopolymer first” model for origins must resolve these paradoxes, giving us a polymer that both folds and does not fold, has many building blocks at the same time as having few, and has the potential to catalyze hard-but-desired reactions without the potential to catalyze easy-but undesired reactions.
(e) The Probability Paradox.
Some biopolymers, like RNA, strike a reasonable compromise between the needs of genetics and the needs of catalysis. Further, no theory creates a paradox that excludes the possibility that some RNA might catalyze the replication of RNA, with imperfections, where the imperfections are replicable. However, experiments show that RNA molecules that catalyze the destruction of RNA are more likely to arise in a pool of random (with respect to fitness) sequences than RNA molecules that catalyze the replication of RNA, with or without imperfections. Chemical theory expects this to be the case, as the base-catalyzed cleavage of RNA is an “easy” reaction (stereoelectronically), while the SN2 reaction that synthesizes a phosphodiester bond is a “difficult” reaction. Thus, even if we solve the asphalt paradox, the water paradox, the information need paradox, and the single biopolymer paradox, we still must mitigate or set aside chemical theory that makes destruction, not biology, the natural outcome of are already magical chemical system.
Steven A. Benner Prebiotic plausibility and networks of paradox-resolving independent models 12 December 2018
Unfortunately, current theory holds that Earth’s native atmosphere was more oxidizing than the Miller atmosphere. Carbon was more likely present as carbon dioxide (CO2), not methane. Nitrogen was more likely present as dinitrogen (N2), not ammonia. This model is supported by detailed studies of rocks surviving from that time8. More unfortunately, such atmospheres are very bad sources of HCN, HCCCN, and the other reduced molecules on these lists of prebiotically plausible compounds, including those in popular models for the prebiotic synthesis of adenine. Thus, the prebiotic plausibility of HCN, the other molecules, and adenine long ago vanished as Earth-made species, even though literature too voluminous to cite here continues to assume otherwise.
This creates a paradox. If one premises that life originated via an RNA-First prebiotic process that used adenine as a precursor and that adenine was formed from HCN from a Hadean terran atmosphere, then the premises that view HCN as an impossible product of our early atmosphere force the conclusion that life could not have originated on Earth. An unacceptable conclusion follows by the force of logic from seemingly acceptable premises.
https://www.nature.com/articles/s41467-018-07274-y
Timothy R. Stout, George Matzko A Natural Origin-of-Life: Every Hypothetical Step Appears Thwarted by Abiogenetic Randomization May 5, 2019
Prebiotic processes naturally randomize their feedstock. This has resulted in the failure of every experimentally tested hypothetical step in abiogenesis beginning with the 1953 Miller-Urey Experiment and continuing to the present. Not a single step has been demonstrated that starts with appropriate supply chemicals, operates on the chemicals with a prebiotic process, and yields new chemicals that represent progress towards life and which can also be used in a subsequent step as produced. Instead, the products of thousands of experiments over more than six decades consistently exhibit either increased randomization over their initial composition or no change. We propose the following hypothesis of Abiogenetic Randomization as the root cause for most if not all of the failures: 1) prebiotic processes naturally form many different kinds of products; life requires a few very specific kinds. 2) The needs of abiogenesis spatially and temporally are not connected to and do not change the natural output of prebiotic processes. 3) Prebiotic processes naturally randomize feedstock. A lengthy passage of time only results in more complete randomization of the feedstock, not eventual provision of chemicals suitable for life. The Murchison meteorite provides a clear example of this. 4) At each hypothetical step of abiogenesis, the ratio of randomized to required products proves fatal for that step. 5. The statistical law of large numbers applies, causing incidental appearances of potentially useful products eventually to be overwhelmed by the overall, normal product distribution. 6) The principle of emergence magnifies the problems: the components used in the later steps of abiogenesis become so intertwined that a single-step first appearance of the entire set is required. Small molecules are not the answer. Dynamic self-organization requires from the beginning large proteins for replication, metabolism, and active transport. Many steps across the entire spectrum of abiogenesis are examined, showing how the hypothesis appears to predict the observed problems qualitatively. There is broad experimental support for the hypothesis at each observed step with no currently known exceptions.
Just as there are no betting schemes that allow a person to overcome randomness in a casino, there appear to be no schemes able to overcome randomness using prebiotic processes. We suggest that an unwillingness to acknowledge this has led to the sixty plus years of failure in the field. There is a large body of evidence—essentially all experiments in abiogenesis performed since its inception sixty plus years ago—that appear to be consistent with the hypothesis presented in this paper. Randomization prevails.
https://osf.io/p5nw3/?fbclid=IwAR0vAV5jVQR7Z-IT_S1fQzJQ_fMonIgUW9xvj0quKIOFdgWWwcnzPPStXIc
Muriel Gargaud: Young Sun, Early Earth and the Origins of Life 2012:
Every living being consists of a collection of molecules that are constantly renewed and which appear to coordinate their evolution. We are therefore dealing with organized systems, the emergence of which, perforce, implies a process of self-organization. However, the spontaneous formation of an ordered system from disorder contradicts our everyday experience. We all know that over time, the most beautiful building is inevitably reduced to ruins. In physical or chemical terms, this tendency is expressed as a quantity, entropy, which expresses the degree of disorder in a system. The second law of thermodynamics expresses the idea that the entropy of an isolated system increases, and thus that disorder tends to increase. An isolated chemical system must, therefore, evolve towards an equilibrium state in which the concentration of different chemical species will be determined by their individual energy levels and the laws of statistics. So how could a system that was as disordered as that of the primitive Earth, with an incredible diversity of forms and structures, give rise to life?
The answer lies in the fact that the process of self-organization, which is linked to the emergence and development of life, concerns only one part of the system. Hence, the formation of an ordered structure in a sub-system will be compensated by an increase in disorder in its environment, such that overall, the entropy does not decrease. That means then that exchanges of energy and matter are the basis of the dynamics of self-organization.
My comment: Since the authors apply methodological naturalism and exclude design a priori, they are left with the only alternative to design, which is self-organization. Mount Improbable is, however, higher to climb, to get life the first go, then keep it going. That implies a paradox: If the inorganic matter had the unbound drive to get self-organized and become alive, why do thermodynamic mechanisms, and evolution, permit life to die? Why does the cycle of self-replication, which had to be fully set up as well right from the beginning, perpetuate life for millennia, if not millions of years, but living organisms die? If the unbound drive of atoms is to self-organize and get alive, why not the unbound drive to KEEP alive? We know, for instance, that turtles live for centuries. If the struggle is for survival, why do not more species steal DNA from other species like bdelloids? why can Glass Sponges live for 15 thousand years, but evolution has not helped us to get so far? Turritopsis doohmii jellyfish has found a way to cheat death by actually reversing its aging process. If the jellyfish is injured or sick, it returns to its polyp stage over a three-day period, transforming its cells into a younger state that will eventually grow into adulthood all over again. If molecules drive for survival, why have not many more organisms evolved in a convergent manner, and adopted this extraordinary mechanism?
Moreover, the inescapable evolution towards disorder and the state of thermodynamic equilibrium does not predict in any way the duration of the chemical reactions involved, which may occur in a fraction of a second or, on the other hand, over a period that is reckoned in millions of years. The speed of this evolution depends on the dynamics of the reaction (the subject of chemical kinetics) and not on thermodynamics, which only predicts the sense in which it unfolds. In chemistry, it is difficult to envisage self-organization without having recourse to the heterogeneous nature of matter on a microscopic scale, that is to the fact that matter is not indefinitely divisible. If that were the case, how could it form complex structures? It was undoubtedly this type of reasoning that led, in antiquity, certain philosophers, the best known of which remains Democritus, to postulate the existence of atoms as being the basis of matter. The difficulty comes in passing from this microscopic heterogeneity to a single macroscopic entity that involves a coordination in the arrangement or the movement of a multiplicity of atoms or molecules (either within a three-dimensional structure or within an entire organism). The properties that molecules have of associating with one another may give rise to the formation of crystals or other macroscopic structures such as vesicles (such as those that form cellular membranes ) or the micelles of surfactants. Structures that have a dynamical character may also appear through amplification mechanisms that are highly efficient, such as replication or autocatalysis. These mechanisms are at work in what are known as oscillating reactions, which are often considered chemical curiosities, such as the Belousov-Zhabotinsky reaction . The concentration of certain intermediates then varies until the reagents are exhausted, in a cyclic or stochastic
