Abiogenesis: The possible mechanisms to explain the origin of life

The possible mechanisms to explain the origin of life

https://reasonandscience.catsboard.com/t2515-abiogenesis-the-possible-mechanisms-to-explain-the-origin-of-life

Either life just coalesced from atomic building blocks through a random fluke collision of disorderly pieces, emerging by  “dumb, blind” mechanical processes, a fortuitous accident, spontaneously through self-organization by unguided, non-designed, unintended stochastic coincidence, natural events that turned into self-organization in an orderly manner without external direction, chemical non-biological, purely physico-dynamic kinetic processes and reactions influenced by environmental parameters, or through the direct intervention, direction-giving creative force, and design activity of an intelligent cognitive agency, a powerful conscious creator with intentions, inventive power,  will, foreseeing goals and foresight, able to instantiate and create successful solutions in a planned manner.  

Rational Wiki: Often brought up in the origins debate is how evolution does not explain the origin of life. Let's get something abundantly clear: abiogenesis and evolution are two completely different things. The theory of evolution says absolutely nothing about the origin of life. It merely describes the processes that take place once life has started.
https://rationalwiki.org/wiki/Abiogenesis

Koonin, E. V. (2012): The emergence of the first replicator system, which represented the “Darwinian breakthrough,” was inevitably preceded by a succession of complex, difficult steps for which biological evolutionary mechanisms were not accessible.  The Logic of Chance: The Nature and Origin of Biological Evolution. Amazon.

ADDY PROSS (2012): Darwinian theory is a biological theory and therefore deals with biological systems, whereas the origin of life problem is a chemical problem, and chemical problems are best solved with chemical (and physical) theories. Attempting to explain chemical phenomena with biological concepts is methodologically problematic.
What is Life?: How Chemistry Becomes Biology 

Paul Davies (2021): I think in all honesty a lot of people even confuse it the people who aren't familiar with the area that oh I presume Darwinian evolution sort of accounts for the origin of life but of course, you don't get an evolutionary process until you've got a self-replicating molecule. ( Darwin )  gave us a theory of evolution about how life has evolved but he uh didn't want to tangle with how you go from non-life to life and for me, that's a much bigger step. Why Darwinian evolution does NOT explain the origin of life 

Fry, Iris. (2010): The Role of Natural Selection in the Origin of Life. Origins of Life and Evolution of Biospheres  Link.
Iris Fry analyzes various theories on the origin of life, including RNA-first, metabolism-first, and others. She concludes that while none of these paradigms have decisive experimental support, gene-first theories show potential. As of her writing, no functioning system of genetic replication had been achieved without the addition of an external protein enzyme.

Alan W. Schwartz (2007): A problem that is familiar to organic chemists is the production of unwanted byproducts in synthetic reactions. For prebiotic chemistry, where the goal is often the simulation of conditions on the prebiotic Earth and the modeling of a spontaneous reaction, it is not surprising – but nevertheless frustrating – that the unwanted products may consume most of the starting material and lead to nothing more than an intractable mixture, or -gunk.. The most well-known examples of the phenomenon can be summarized quickly: Although the Miller –Urey reaction produces an impressive set of amino acids and other biologically significant compounds, a large fraction of the starting material goes into a brown, tar-like residue that remains uncharacterized; i.e., gunk. While 15% of the carbon can be traced to specific organic molecules, the rest seems to be largely intractable  Even if we focus only on the soluble products, we still have to deal with an extremely complex mixture of compounds. The carbonaceous chondrites, which represent an alternative source of starting material for prebiotic chemistry on Earth, and must have added enormous quantities of organic material to the Earth at the end of the Late Heavy Bombardment (LHB), do not offer a solution to the problem just referred to. The organic material present in carbonaceous meteorites is a mixture of such complexity that much ingenuity has gone into the design of suitable extraction methods, to isolate the most important classes of soluble (or solubilized) components for analysis. 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. 2

A.G.Cairns-Smith (1985):  It is one of the most singular features of the unity of biochemistry that this mere convention is universal. Where did such agreement come from? You see non-biological processes do not as a rule show any bias one way or the other, and it has proved particularly difficult to see any realistic way in which any of the constituents of a 'prebiotic soup' would have had predominantly 'left-handed' or right-handed' molecules. It is thus particularly difficult to see this feature as having been imposed by initial conditions. 3

A.G.Cairns-Smith (1985): genetic takeover, page 70: 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 primitive Earth? 4

PROFESSOR DR KLAUS DOSE:  The Origin of Life:  More Questions Than Answers
Evolution, as used here, refers to any development or change influenced by the environment. The term "chemical evolution" specifically pertains to changes in chemical substances, indicating that fundamental transformations occur within molecules. Often, it is employed as a synonym for the "abiotic" or "prebiotic formation" of organic molecules in cosmic systems, particularly in the context of the early Earth. It is assumed that these organic molecules were produced from the constituents present in the primitive atmosphere, hydrosphere, and, to some extent, the lithosphere. On the other hand, "molecular evolution" encompasses a broader scope than chemical evolution. It encompasses self-assembly into more complex structures, such as membranes, protocells, cell-like systems, and protocellular organelles. Additionally, it involves the subsequent evolution of proto-cells or protobionts, leading to the emergence of the first modern cells, also known as "Urzellen" or progenotes. The transition from protobionts to progenotes has been referred to as proto-Darwinian evolution. In contrast, "Darwinian evolution" pertains to the evolution from progenotes to the vast array of contemporary cells and organisms.
https://sci-hub.ee/10.1179/isr.1988.13.4.348

Comment:  According to the description provided, "chemical evolution" primarily focuses on the changes in chemical substances and the fundamental transformations that occur within molecules. It is often used as a term synonymous with the "abiotic" or "prebiotic formation" of organic molecules in cosmic systems, particularly in the context of the early Earth. The key aspect of chemical evolution is the formation of organic molecules from inorganic precursors found in the primitive atmosphere, hydrosphere, and lithosphere. Notably, the concept of "chemical evolution" does not explicitly include natural selection, which is a fundamental mechanism of Darwinian evolution. Natural selection is a process that acts on existing life forms, favoring certain traits or characteristics that provide a reproductive advantage in a given environment. Over time, this leads to the accumulation of beneficial traits within a population, leading to the adaptation and diversification of organisms. While chemical evolution sets the stage by forming the necessary building blocks of life, such as amino acids and nucleotides, it does not inherently involve the process of natural selection. Instead, it provides the foundation upon which subsequent evolutionary processes, like "molecular evolution" and "Darwinian evolution," can take place. "Molecular evolution," as mentioned in the initial description, goes beyond chemical evolution by encompassing the self-assembly of complex structures and the subsequent evolution of proto-cells to modern cells. This process involves changes in the molecular and structural organization of early life forms, leading to the emergence of more advanced cellular systems. On the other hand, "Darwinian evolution" encompasses the evolution of progenotes (early simple cells) to the vast array of contemporary cells and organisms we observe today. Natural selection is a central driving force in this form of evolution, shaping the diversity of life through the differential survival and reproduction of individuals with advantageous traits.
Self-organization refers to the supposed and hypothesized spontaneous emergence of order and complexity without external direction or control and without the need for external instructions. While self-organization is a hypothesized concept, it has never been directly observed or reproduced in a laboratory setting.

Gennady Shkliarevsky: THE UNIVERSAL EVOLUTION AND THE ORIGIN OF LIFE 2021
Most current OOL perspectives invoke chance or coincidence in their explanations of the origin of life. Sean Carroll, a well-known evolutionary biologist, refers to the emergence of life as “the mother of all accidents” and “the accident of all mothers.” There are also additional problems that plague the dominant scenario on the origin of prokaryotic cells. Most, if not all of them, invoke chance or coincidence to explain the origin of major cell components. Not only that, but they also invoke chance or coincidence to explain why these components came together to form a cell. As has been explained earlier, invoking chance even once is highly problematic; invoking it twice to explain the same phenomenon makes an explanation very questionable. As has been repeatedly pointed out, the liberal use of chance and coincidence as an explanatory mode is also a source of concern in theories about the origin and evolution of early life. In order to explain the emergence of radical novelty, many current OOL perspectives invoke chance or coincidence.
https://arxiv.org/ftp/arxiv/papers/2104/2104.08076.pdf

Alexei A. Sharov: Coenzyme world model of the origin of life 2016 Mar 9
The probability of transferring the full set of coding molecules to descendants by pure chance may be problematic especially if droplets carry too many kinds of coding molecules and some of them are present in a small number of copies. This combinatorial problem can be partially meliorated by the “stochastic corrector” mechanism, which is a preferential propagation of systems with a full set of coding molecules (Szathmáry, 1999). Systems with an incomplete set of coding molecules are more likely to fail in surviving and reproduction because some of their functions appear missing. This kind of stochastic correction is a primordial version of the purifying selection; and like the purifying selection, it reduces the overall reproduction rate of the population.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4875852/

Horst Rauchfuss Chemical Evolution and the Origin of Life
An important, but as yet unsolved, problem is provided by the chirality of the amino acids. The main question is whether the enantiomeric selection of the amino acids took place before or after the evolution of life.
Others see the genetic code as being purely fortuitous, a system that was “frozen” at some time in history.

William Dembski (2002): The problem is that nature has too many options and without design couldn’t sort through all those options. The problem is that natural mechanisms are too unspecific to determine any particular outcome. Natural processes could theoretically form a protein, but also compatible with the formation of a plethora of other molecular assemblages, most of which have no biological significance. Nature allows them full freedom of arrangement. Yet it’s precisely that freedom that makes nature unable to account for specified outcomes of small probability. Nature, in this case, rather than being intent on doing only one thing, is open to doing any number of things. Yet when one of those things is a highly improbable specified event, design becomes the more compelling, better inference. Occam's razor also boils down to an argument from ignorance: in the absence of better information, you use a heuristic to accept one hypothesis over the other. 5

There's nothing about inert chemicals and physical forces that say we want to get life at the end of the abiogenesis process. Molecules do not have the "drive", they do not "want" to find ways to harness the energy and become more efficient

One cannot explain the origin of evolution, through evolution. It is widespread and very common to see the attempt to smuggle the Darwinian dynamic of replication with a heritable variation into the origin of life.  Biological evolution by natural selection does and cannot explain the origin of life. Natural selection only acts on the random variation of alleles based on DNA replication, but the origin of genes, and replication is among the origin of the entire self-replicating cell, what the origin of life research has to explain.  

1. When we see complexification, that is: Interconnecting parts, weaving together, aggregating subunits, wrapping around, encompassing, interlinking, interlocking, twisting, interlacing, fusing, assembling related things, intricately combining things, where the system is greater than the sum of their parts. then it is logical to attribute such actions to an intelligently acting mind with foresight and foreknowledge, and distant goals.
2. Making systems with the hallmark of complexity depends on the careful elaboration and design in detail of many elementary parts and interconnecting them in a meaningful way conferring a specific purpose or function. Not rarely, small changes in one part of the system can cause sudden and unexpected outputs in other parts of the system, system-wide reorganization, or breaking down of the higher function.
3. Why WOULD a molecule self-replicate apart from duplication performed by the DNA replication machinery? There was no prebiotic natural selection with the goal to survive and reproduction.  Why should be assumed that molecules - that are randomly assembled by chemical/physical forces/happenstance and just happened to stay in place - have the drive or goal to self-replicate, to become the complex macromolecular building blocks of living cells?  Or to have any goal at all? Why would/should molecules strive toward increasing complexity without any possible "psychological" basis for doing so? Random accidents are not the best case-adequate explanation for the origin of emerging properties of a complex system. Intelligent design is.

Exploring the Deep Mystery of Life's Origins Aug 8, 2022
Nick Lane: Our kind of cell arose once in four billion years of evolution. And it seems to have been something of a bit of a freak accident.
https://www.youtube.com/watch?v=ATubwpnVLAY

Wilhelm T. S. Huck Robustness, Entrainment, and Hybridization in Dissipative Molecular Networks, and the Origin of Life May 30, 2019
Life emerged spontaneously from the selfassembly, or spontaneous organization, of the organic products of reactions, occurring in complex mixtures of molecules formed abiotically from simple precursors and sequences of reactions.
https://robobees.seas.harvard.edu/files/gmwgroup/files/1320.pdf

Phillip E. Johnson,  DARWIN ON TRIAL:  Darwin persuades us that the seemingly purposeful construction of living things can very often, and perhaps always, be attributed to the operation of natural selection. 

If you have things that are reproducing their kind; 
if there are sometimes random variations, nevertheless, in the offspring; 
if such variations can be inherited; 
if some such variations can sometimes confer an advantage on their owners; 
if there is competition between the reproducing entities;- 
if there is an overproduction so that not all will be able to produce offspring themselves- 

then these entities will get better at reproducing their kind. What is needed for natural selection are things that conform to those 'ifs'. Self-replicating cells are prerequisites for evolution. None of this was available prebiotically to explain the origin of the first life form.  1 

MARIO VANEECHOUTTE The scientific origin of life 2000
We hypothesize that the origin of life, that is, the origin of the first cell, cannot be explained by natural selection among self-replicating molecules, as is done by the RNA-world hypothesis.
The hypothesis espoused here states that it is virtually impossible that the highly complicated system cell developed gradually around simple self-replicating molecules (RNA-hypercycles or autocatalytic peptide networks) by means of natural selection; as is proposed by, for example, the RNA-world hypothesis.  Despite searching quadrillions of molecules, it is clear that a spontaneous RNAreplicator is unlikely to occur. Reports of nucleotide and peptide self-replication still depend upon human intervention (for instance, by changing the environmental conditions between two rounds of replication or by denaturing the double strands). The problem of denaturing the double-nucleotide strand in a nonenzymatic manner has been overlooked and has contributed to a failure to establish molecular self-replication. The first cell, life, was born and natural selection (selection among variations on the theme of autonomous duplication) commenced.

The hypothesis suggested here states that no such autonomous duplication existed before the first cell and, thus, natural selection started only with the first cell.
https://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.645.3011&rep=rep1&type=pdf

Jonathan Sarfati Natural selection cannot explain the origin of life 31 March 2021
Natural selection requires pre-existing life.
https://creation.com/ns-origin-of-life

The first life could emerge by chance in a depression or tide pool, as one of countless reaction systems.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4810237/#:~:text=The%20bottom%2Dup%20approach%20is,%2C%20genetic%20code%2C%20and%20proteins.

Evolution by mutations and natural selection do not explain the origin of life, since evolution depends on the Darwinian dynamic of replication with a heritable variation. The only alternative to design are random unguided lucky events.

Or through the direct intervention and creative force of an intelligent agency, a powerful creator.

In an attempt to explain the origin of life, scientists propose a two-stage process of natural chemical evolution:  formation of organic molecules, which combine to make larger biomolecules; self-organization of these molecules into a living organism. The origin of life can not be explained through biological nor chemical evolution. Adaptation, mutation, and natural selection depend on DNA replication. Heredity is guaranteed by faithful DNA replication whereas evolution depends upon errors accompanying DNA replication. Neither can it be explained through physical laws. Life depends on codes and instructional complex information. This information can only be generated by when the arrangement of the code is free and unconstrained, and any of the four bases of the genetic code can be placed in any of the positions in the sequence to generate the information. The only alternative, if the action of a creative agency is excluded, would be spontaneous self-assembly by orderly aggregation of prebiotic elements and building blocks in a sequentially correct manner without external direction.

Origin of life: A prebiotic route to DNA
The first polymeric molecules capable of storing information and reproducing themselves were randomly assembled from organic precursors that were available on the early Earth.
https://www.sciencedaily.com/releases/2019/06/190618103721.htm

Albert L. Lehninger described how inanimate matter crossed the great divide to become alive. “We now come to the critical moment in evolution,” he wrote in 1970, “in which the first semblance of ‘life’ appeared, through the chance association of a number of abiotically formed macromolecular components.”

Natural selection is not a possible mechanism to explain the origin of life, since evolution depends on DNA replication

Life's Origins: What Was the Origin Of Complex Organic Molecules?  We are going to make an assumption: the chemical components found in all living prokaryotic and eukaryotic cells was present in the ancestral organism from which all life derived. In other words: the spontaneous interaction of the molecules present in the early earth's atmosphere formed more complex organic molecules, such as amino acids, sugars, fatty acids, and nitrogen bases - the building blocks of life as we know it today.
https://www2.gwu.edu/~darwin/BiSc151/Origin/origin.html

Question : Was there natural selection prior life starting?
Reply: No, natural selection as a mechanism of evolution cannot exist prior to the existence of life. Natural selection is a process by which certain traits that are better suited to an organism's environment become more prevalent in a population over time. This process depends on the existence of organisms that can reproduce, pass on traits to their offspring, and have variations in traits that can be selected for or against based on their survival and reproductive success.

In order for natural selection to occur, there must first be life, and this is where the question of the origin of life becomes relevant. While natural selection can explain the evolution of species once life has arisen, it cannot explain the initial emergence of life from non-living matter.

Stephen C. Meyer, The return of the God hypothesis
The process of natural selection presupposes the differential reproduction of already living organisms and thus a preexisting mechanism of self-replication. Yet self-replication in all extant cells depends upon functional (and therefore sequence-specific, information-rich) proteins and nucleic acids. And the origin of such information-rich molecules is precisely what Oparin needed to explain. Thus, many rejected his postulation of prebiotic natural selection as question-begging. As the evolutionary biologist Theodosius Dobzhansky insisted, “Pre-biological natural selection is a contradiction in terms.” Or as Christian de Duve explained, theories of prebiotic natural selection “need information which implies they have to presuppose what is to be explained in the first place.”

The Origin of the First Hereditary Replicators
This process is still an unsolved problem. By itself, this transition is not an evolutionary one because, without hereditary replicators, no Darwinian evolution is possible.
https://www.pnas.org/content/112/33/10104

Alemi Mario: The Amazing Journey of Reason from DNA to Artificial Intelligence 2020
Darwin probably didn’t propose a theory for the origin of life simply because applying Darwin’s mechanism of natural selection to the emergence of life, as done by Dawkins (1976), is like comparing apples with pears (Johnson 2010). What’s more, the idea that a self-replicating molecule with an information content casually appeared in a primordial soup, as imagined by Dawkins (1976) (“At some point a particularly remarkable molecule was formed by accident. We will call it the Replicator.”) appears to be statistically groundless (Yockey 1977).
https://link.springer.com/book/10.1007%2F978-3-030-25962-4

Is life a gamble? Scientist models universe to find out April 21, 2020
Scientists suspect that the complex life that slithers and crawls through every nook and cranny on Earth emerged from a random shuffling of non-living matter that ultimately spit out the building blocks of life.
https://www.livescience.com/origin-of-life-rna-universe-model.html

A. G. CAIRNS-SMITH Seven clues to the origin of life, page  36:
And if you ask me how the next stage happened, how the smallish 'molecules of life' came together to make the first reproducing evolving being, I will reply: 'With time, and more time, and the resource of oceans.' I will sweep my arms grandly about. 'Because you see. in the absence of oxygen the oceans would have accumulated "the molecules of life". The oceans would have been vast bowls of nutritious soup. Chance could do the rest.

The role of natural selection in the origin of life
Unlike living systems that are products of and participants in evolution, these prebiotic chemical structures were not products of evolution. Not being yet intricately organized, they could have emerged as a result of ordinary physical and chemical processes.
https://www.ncbi.nlm.nih.gov/pubmed/20407927

Alternative Pathways of Carbon Dioxide Fixation: Insights into the Early Evolution of Life? July 6, 2011
The fixation of inorganic carbon into organic material (autotrophy) is a prerequisite for life and sets the starting point of biological evolution.
https://sci-hub.ren/https://www.annualreviews.org/doi/10.1146/annurev-micro-090110-102801

Jack W. Szostak Functional proteins from a random-sequence library
Functional primordial proteins presumably originated from random sequences
https://molbio.mgh.harvard.edu/szostakweb/publications/Szostak_pdfs/Keefe_Szostak_Nature_01.pdf?fbclid=IwAR0giOg_aZfFRKQALk7CB22nVIx32ShiN0Vp78cwtAYwmwQ_0RJicfxpR1M

LIFE The Science of Biology, TENTH EDITION, page 3
When we consider how life might have arisen from nonliving matter, we must take into account the properties of the young Earth’s atmosphere, oceans, and climate, all of which were very different than they are today. Biologists postulate that complex biological molecules first arose through the random physical association of chemicals in that environment.

Neither Evolution nor physical necessity are a driving force prior dna replication. The only two alternatives are either a) creation by an intelligent agency, or b) Random, unguided, undirected natural events by a lucky "accident". 

Koonin, the logic of chance, page 246
Evolution by natural selection and drift can begin only after replication with sufficient fidelity is established. Even at that stage, the evolution of translation remains highly problematic. The emergence of the first replicator system, which represented the “Darwinian breakthrough,” was inevitably preceded by a succession of complex, difficult steps for which biological evolutionary mechanisms were not accessible . The synthesis of nucleotides and (at least) moderate-sized polynucleotides could not have evolved biologically and must have emerged abiogenically—that is, effectively by chance abetted by chemical selection, such as the preferential survival of stable RNA species. Translation is thought to have evolved later via an ad hoc selective process.  Did you read this ???!! An ad-hoc process ?? 

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

Heredity is guaranteed by faithful DNA replication whereas evolution depends upon errors accompanying DNA replication.  ( Furusawa, 1998 ) We hypothesize that the origin of life, that is, the origin of the first cell, cannot be explained by natural selection among self-replicating molecules, as is done by the RNA-world hypothesis. ( Vaneechoutte M )

Chance and necessity do not explain the origin of life
https://www.academia.edu/1204161/Trevors_J.T._Abel_D.L._2004_Chance_and_necessity_do_not_explain_the_origin_of_life_Cell_Biology_International_28_729-739
Selection pressure cannot select nucleotides at the digital programming level where primary structures form. Genomes predetermine the phenotypes which natural selection only secondarily favors. Contentions that offer nothing more than long periods of time offer no mechanism of explanation for the derivation of genetic programming. No new informationis provided by such tautologies. The argument simply says it happened. As such, it is nothing more than blind belief. Science must provide rational theoretical mechanism, empirical support, prediction fulfillment, or some combination of these three. If none of these three are available, science should reconsider that molecular evolution of genetic cybernetics is a proven fact and press forward with new research approaches which are not obvious at this time. 5

I would like to plead with you, simply, please realize you cannot use the words `natural selection' loosely. Prebiological natural selection is a contradiction of terms."
(Dobzhansky, T.G., Discussion of "Synthesis of Nucleosides and Polynucleotides with Metaphoric Esters,", Oct. 27-30, 1963, Academic Press: New York NY, 1965, pp.309-310).

B.Alberts, Molecular Biology of the Cell, 5th edition, page 406
Self-Replicating Molecules Undergo Natural Selection
The three-dimensional folded structure of a polynucleotide affects its stability, its actions on other molecules, and its ability to replicate. Therefore, certain polynucleotides will be especially successful in any self-replicating mixture. Because errors inevitably occur in any copying process, new variant sequences of these polynucleotides will be generated over time.



Stephen Meyer, Darwin's doubt, page 6: 
Natural selection assumes the existence of living organisms with a capacity to reproduce. Yet self-replication in all extant cells depends upon information-rich proteins and nucleic acids (DNA and RNA), and the origin of such information-rich molecules is precisely what origin-of-life research needs to explain. That’s why Theodosius Dobzhansky, one of the founders of the modern neo-Darwinian synthesis, can state flatly, “Pre-biological natural selection is a contradiction in terms.”5 Or, as Nobel Prize–winning molecular biologist and origin-of-life researcher Christian de Duve explains, theories of prebiotic natural selection fail because they “need information which implies they have to presuppose what is to be explained in the first place.

That means, evolution was not a driving force and acting for the emergence and origin of the first living organisms. The only remaining possible mechanisms are chemical reactions acting upon unregulated, aleatory events ( luck, chance), or physical necessity.  ( where chemical reactions are forced into taking a certain course of action. )  

Morowitz: THE ORIGIN AND NATURE OF LIFE ON EARTH page 18
The Darwinian framework for selection requires support from other error-correcting mechanisms that operate in simpler contexts, to arrive at a mechanism sufficient to explain the emergence, overall organization, and long-term persistence of life from non-living precursors.

In a relatively short time, the ocean became a broth of these molecules, and given enough time, the right combination of molecules came together by pure chance to form a replicating entity of some kind that evolved into modern life.
https://www.americanscientist.org/article/the-origin-of-life

Physical necessity & Physical laws

Stephen C.Meyer, The return of the God hypothesis, page 216: 
Rather than having a genetic molecule capable of unlimited novelty, with all the unpredictable and aperiodic sequences that characterize informative texts, we would have a highly repetitive text awash in redundant sequences—much as happens in crystals. Indeed, in a crystal the forces of mutual chemical attraction do completely explain the sequential ordering of the constituent parts. Consequently, crystals cannot convey novel information. Bonding affinities, to the extent they exist, cannot be used to explain the origin of information. Self-organizing chemical affinities generate highly repetitive “order,” but not information; they create mantras, not messages

The nucleotide sequence of DNA and RNA  have an instructional function to make proteins and is NOT random but complex and specified, and not due to physical necessity or physical laws. And this is what events in a prebiotic land would need to produce: a minimal set of proteins .... and this kind of specification does not arise through chemical reactions ...... the result of a chemical reaction is not random. But the events dealing with an eventual chemical reaction would have been if there was not a mind guiding the events.

Consider, for example, what would happen if the individual nucleotide bases (A, C, G, T) in the DNA molecule did interact by chemical necessity (along the information-bearing axis of DNA). Suppose that every time adenine (A) occurred in a growing genetic sequence, it attracted cytosine (C) to it,26 which attracted guanine (G), which attracted thymine (T), which attracted adenine (A), and so on. If this were the case, the longitudinal axis of DNA would be peppered with repetitive sequences of ACGT. Rather than being a genetic molecule capable of virtually unlimited novelty and characterized by unpredictable and aperiodic sequences, DNA would contain sequences awash in repetition or redundancy—much like the arrangement of atoms in crystals. 

Michael Polanyi: Life's Irreducible Structure, 
Science mag, 1968
In Galileo's experiments on balls rolling down a slope, the angle of the slope was not derived from the laws of mechanics, but was chosen by Galileo. And as this choice of slopes was extraneous to the laws of mechanics, so is the shape and manufacture of test tubes extraneous to the laws of chemistry. The same thing holds for machinelike boundaries; their structure cannot be defined in terms of the laws which they harness. Nor can a vocabulary determine the content of a text, and so on. Therefore, if the structure of living things is a set of boundary conditions, this structure is extraneous to the laws of physics and chemistry which the organism is harnessing. Thus the morphology of living things transcends the laws of physics and chemistry.the codelike structure of DNA must be assumed to have come about by a sequence of chance variations established by natural selection. But this evolutionary aspect is irrelevant here; whatever may be the origin of a DNA configuration, it can function as a code only if its order is not due to the forces of potential energy. It must be as physically indeterminate as the sequence of words is on a printed page. As the arrangement of a printed page is extraneous to the chemistry of the printed page, so is the base sequence in a DNA molecule extraneous to the chemical forces at work in the DNA molecule. It is this physical indeterminacy of the sequence that produces the improbability of occurrence of any particular sequence and thereby enables it to have a meaning-a meaning that has a mathematically determinate information content equal to the numerical improbability of the arrangement.

A deterministic answer assumes that the laws of physics and chemistry have causally and sequentially determined the obligatory series of events leading from inanimate matter to life – that each step is causally linked to the previous one and to the next one by the laws of nature. In principle, in a strictly deterministic situation, the state of a system at any point in time determines the future behavior of the system – with no random influences. To invoke a guided determinism toward the formation of life would only make sense if the construction of life was demonstrably a preferential, highly probable natural pathway.
Luisi, The Emergence of Life; From Chemical Origins to Synthetic Biology, page 21

Just like computer codes, the genetic code is arbitrary. There is no law of physics that says “1” has to mean “on” and “0” has to mean “off.” There’s no law of physics that says 10000001 has to code for the letter “A.” Similarly, there is no law of physics that says three Guanine molecules in a row have to code for Glycine. In both cases, the communication system operates from a freely chosen, fixed set of rules.
In all communication systems it is possible to label the encoder, the message and the decoder and determine the rules of the code.
The rules of communication systems are defined in advance by conscious minds. There are no known exceptions to this. Therefore we have 100% inference that the Genetic Code was designed by a conscious mind.

Physical laws which result in physical constraints,  where chemical reactions are forced into taking a certain course of action is an often cited possible mechanism for the origin of life. 
We are moving from chemistry to biology. Henceforward, life, it goes without saying, is independent of its chemical substrate, and its evolution does not follow paths that are predictable solely based on the laws of physics.
M. Gargaud · H. Martin · P. López-García T. Montmerle · R. Pascal Young Sun, Early Earth and the Origins of Life, page 95

Laurent Boiteau Prebiotic Chemistry: From Simple Amphiphiles to Protocell Models, page 3:
Spontaneous self-assembly occurs when certain compounds associate through noncovalent hydrogen bonds, electrostatic forces, and nonpolar interactions that stabilize orderly arrangements of small and large molecules.  The argument that chemical reactions in a primordial soup would not act upon pure chance, and that chemistry is not a matter of "random chance and coincidence, finds its refutation by the fact that the information stored in DNA is not constrained by chemistry. Yockey shows that the rules of any communication system are not derivable from the laws of physics.  He continues: “there is nothing in the physicochemical world that remotely resembles reactions being determined by a sequence and codes between sequences.” In other words, nothing in nonliving physics or chemistry obeys symbolic instructions.

Ulrich E. Stegmann:  The arbitrariness of the genetic code March 2004 5
Some of the processes expected to involve semantic information are certainly not chemically arbitrary and, therefore, chemical arbitrariness is not a necessary condition for a semantic relation.


The problem of information to explain the origin of life

Norbert Weiner - MIT Mathematician - Father of Cybernetics
"Information is information, not matter or energy. No materialism which does not admit this can survive at the present day."

It has to be explained: 

- a library index and fully automated information classification, storage and retrieval program ( chromosomes, and the gene regulatory network )
- The origin of the complex, codified, specified, instructional information stored in the genome and epigenetic codes to make the first living organism
- The origin of the genetic Code
- How it got nearly optimal for allowing additional information within protein-coding sequences
- How it got more robust than 1 million alternative possible codes
- The origin of the over twentythree epigenetic codes
- The origin of the information transmission system, that is the origin of the genetic code itself, encoding, transmission, decoding and translation
- The origin of the genetic cipher/translation, from digital ( DNA / mRNA ) to analog ( Protein )
- The origin of the hardware, that is DNA, RNA, amino acids, and carbohydrates for fuel generation
- The origin of the replication/duplication of the DNA
- The origin of the signal recognition particle
- The origin of the tubulin Code for correct direction to the final destination of proteins


Information theory cannot normally be used to predict how chemicals will react because some chemicals react with each other readily, and others only react very slowly. Others do not react with each other at all. Thus, the likelihood of two chemicals joining together depends on both the quantity of the chemicals present and their chemical properties. Information theory can easily deal with the effects of quantity, but it has no way to deal with chemical properties.
Stuart Pullen, Intelligent Design or Evolution? Why the Origin of Life and the Evolution of Molecular Knowledge Imply Design, page 88
http://lifesorigin.com/prebiotic-evolution4.pdf

Stephen C. Meyer observed:
“There are neither bonds nor bonding affinities—differing in strength or otherwise—that can explain the origin of the base sequencing that constitutes the information in the DNA molecule”
(Signature in the Cell, 243).

As Paul Davies lamented,
“We are still left with the mystery of where biological information comes from.… If the normal laws of physics can’t inject information, and if we are ruling out miracles, then how can life be predetermined and inevitable rather than a freak accident? How is it possible to generate random complexity and specificity together in a lawlike manner? We always come back to that basic paradox”
(Fifth Miracle, 258).

A law of nature could not alone explain how life began, because no conceivable law would compel a legion of atoms to follow precisely a prescribed sequence of assemblage.
Paul Davies, The origin of Life, page 17

Werner Gitt summarized it this way:
“A necessary requirement for generating meaningful information is the ability to select from alternatives and this requires an intelligent, volitional entity.… Unguided, random processes cannot do this—not in any amount of time because this selection process demands continuous guidance by intelligent beings that have a purpose”
(Without Excuse, 50–51).

Let's assume that we begin with the sequence R-T-X, and will add two amino acids "B" and "A" to it. If amino acid "B" is the most reactive amino acid, the sequence would be R-T-X-B-A. However, if "A" is the most reactive amino acid, then the sequence would be R-T-X-A-B. In a random chemical reaction, the sequence of amino acids would be determined by the relative reactivity of the different amino acids. The polymer chain found in natural proteins and DNA has a very precise sequence that does not correlate with the individual components' reaction rates. Since all of the amino acids have relatively similar structures, they all have similar reaction rates; they will all react at about the same rate making the precise sequence by random chemical reactions unthinkably unlikely. This is the problem of Chemical Reactivity.
http://www.icr.org/article/evolution-hopes-you-dont-know-chemistry-problem-co/

The Genetic Code
http://hyperphysics.phy-astr.gsu.edu/hbase/Organic/gencode.html
DNA contains a true code. Being a true code means that the code is free and unconstrained; any of the four bases can be placed in any of the positions in the sequence of bases. Their sequence is not determined by the chemical bonding. There are hydrogen bonds between the base pairs and each base is bonded to the sugar phosphate backbone, but there are no bonds along the longitudional axis of DNA. The bases occur in the complementary base pairs A-T and G-C, but along the sequence on one side the bases can occur in any order, like the letters of a language used to compose words and sentences. Since nucleotides can be arranged freely into any informational sequence, physical necessity could not be a driving mechanism.

Abiogenesis is the process by which life arises naturally from non-living matter. Scientists speculate that life may have arisen as a result of random chemical processes happening to produce self-replicating molecules.
http://rationalwiki.org/wiki/Abiogenesis

Paul Davies conceded, “Unfortunately, before Darwinian evolution can start, a certain minimum level of complexity is required. But how was this initial complexity achieved? When pressed, most scientists wring their hands and mutter the incantation ‘Chance.’ So, did chance alone create the first self-replicating molecule?” (Fifth Miracle, 138).

If design or physical necessity is discarded, the only remaining possible mechanism for the origin of life is chance/luck.

Emergent properties
Claim: The origin of life could be an emergent property of basic chemical reactions
Reply: An emergent property is a property that a collection or complex system has, but which the individual members do not have. In biology, for example, heart is made of heart cells, heart cells on their own don't have the property of pumping blood. You will need the whole heart to be able to pump blood. Thus, the pumping property of the heart is an emergent or a supervenient property of the heart. Claiming that an individual heart cell can pump blood because the heart can would be an example of fallacy of division.

1. When we see complexification, that is: Interconnecting parts, weaving together, aggregating subunits, wrapping around, encompassing, interlinking, interlocking, twisting, interlacing, fusing, assembling related things, intricately combining things, where the system is greater than the sum of their parts. then it is logical to attribute such actions to intelligently acting mind with foresight and foreknowledge, and distant goals.
2. Making systems with the hallmark of complexity depends on the careful elaboration and design in detail of many elementary parts and interconnecting them in a meaningful way conferring a specific purpose or function. Not rarely, small changes in one part of the system can cause sudden and unexpected outputs in other parts of the system, system-wide reorganization, or breaking down of the higher function.
3. Random accidents are not the best case-adequate explanation for the origin of emerging properties of a complex system. intelligent design is.

Question: How could/would natural selection pressures operate, if there was no intent for these molecules to become part of living cells in a distant future?
Answer:  Indeed, we find ourselves grappling with a profound question. As we delve into the realm of heterocycles and molecular structures, we must tread carefully, recognizing the limitations of metaphorical language. Nature, devoid of intent or decision-making capabilities, does not possess the faculties of choice or selection. The conundrum lies in the presence of specific heterocycles within the realms of biological systems—a puzzle that defies the boundaries of chemistry, physical necessity, and even the mechanisms of evolution. In the primordial days of our planet, a diverse array of conditions fostered the occurrence of chemical reactions. The Earth, with its mélange of elements and energy sources like lightning, volcanic activity, and the touch of UV radiation, served as a fertile crucible. Within this crucible, an assortment of chemical reactions unfolded, yielding a vast repertoire of molecules, including enigmatic heterocycles. However, we must pause and reflect upon the essence of natural selection, the supposed driving force that shapes and molds life as we know it. Within the context of early Earth's chemistry, there was no grand arbiter of selection, no force guiding the preservation of one molecule over another. The absence of higher-order systems poised for preservation or propagation leaves us pondering the fate of these molecular entities. Without a complex system to be favored and perpetuated, without the advantages of survival and competition, the notion of selection becomes a hollow echo. Thus, we confront the enigma of the molecular realm, particularly when it comes to the selection of molecules destined to become the bearers of information—such as DNA and RNA. Can we attribute this selection solely to the capricious whims of natural processes and chance? The intricate design and bewildering complexity that pervade these molecules suggest otherwise—they beckon us to consider the involvement of an intelligent creator. Nucleobases, those wondrous components that harbor the potential to store and transmit genetic information, engage in the delicate dance of base-pairing interactions, and facilitate the emergence of self-replicating systems, are bestowed with remarkable properties. These properties, far from emerging haphazardly, appear purposefully woven into the very fabric of their being—a tapestry of intentionality. As the quest for unguided mechanisms to explain the selection of life-permitting molecules continues, we find ourselves at an impasse—an impasse that beckons us to contemplate the alternative perspective of intelligent design. Within this perspective lies an acknowledgment of the profound complexity and deliberate arrangement that pervades the molecular realm, including the enigmatic nucleobases. Such intricate building blocks of life are best understood as the result of intentional design by a higher intelligence—an intelligence that transcends the bounds of the natural world. In our pursuit of understanding, we navigate the realms of science and philosophy, seeking glimpses of truth amidst the enigmatic foundation of existence. The intricate dance of molecules and their purposeful arrangement hints at a profound narrative—a narrative that invites us to explore the realms beyond naturalistic explanations and embrace the possibility of a guiding hand—an intelligence that shapes and breathes life into the very essence of our being.

How might life have originated on the early Earth? In 1859, Charles Darwin speculated that life might have begun in a “warm little pond” but most research since has focused on understanding how the basic chemicals of life might have formed. There was almost no investigation of how the first life forms appeared and then evolved into the complex biochemical systems we see today.

Source: Deamer D.W. and Damer B. (2017) Can Life Begin on Enceladus? A Perspective from Hydrothermal Chemistry. Astrobiology, 17(9). https://www.liebertpub.com/doi/10.1089/ast.2016.1588

Abiogenesis is a historical event that cannot be reproduced experimentally. Therefore, the pathways leading to the origin of life remain unknown.

Source: Pross A. (2021) Toward solving the mystery of the origin of life. Life, 11(9). https://www.mdpi.com/2075-1729/11/9/900

The emergence of life from inanimate matter was a singularity, a unique event in history, which physics and chemistry cannot explain.

Source: Wickramasinghe C. (2015) The search for our cosmic ancestry. World Scientific.

How life emerged from nonlife remains a fundamental unsolved problem.

Source: Ruiz-Mirazo K., Briones C., and de la Escosura A. (2014) Prebiotic Systems Chemistry: New Perspectives for the Origins of Life. Chemical Reviews, 114(1). https://pubs.acs.org/doi/10.1021/cr2004844

There is no generally accepted description of how life on Earth originated. All existing theories of abiogenesis fall short of completeness.

Source: Trevors J.T. and Pollack G.H. (2012) Chance and necessity do not explain the origin of life. Cell Biology International, 36(7). https://onlinelibrary.wiley.com/doi/10.1042/CBI20110348



Calculations of life beginning through unguided, natural, random events.
http://reasonandscience.heavenforum.org/t2508-calculations-of-life-beginning-through-unguided-natural-random-events

1. https://webcache.googleusercontent.com/search?q=cache:Y7wv8TsUEQkJ:https://osf.io/7ke83/download/%3Fversion%3D4%26displayName%3DOrigin%2520of%2520Life%2520%2520%2520Stout%2520%2520Matzko%2520%25202018%2520%2520OSF-2019-05-05T05%253A50%253A03.408Z.pdf+&cd=1&hl=en&ct=clnk&gl=br

Apparently, the “mechanism worldview” was formulated as a bedrock of scientific method by Henry Oldenburg, the first secretary of the influential Royal Society, who claimed that all phenomena can be explained
exhaustively by the mechanical operation of physicochemical forces. Physical forces can arise as effects of causes arising at two basic levels:

(1) due to interactions between physical objects (which are, of course, mediated by physical laws) and
(2) interactions between physical objects directly with the physical laws. A third element is also allowed:
(3) “random,” “spontaneous,” or “acausal” phenomena.

Examples are collision of physical objects (1), free fall (2), and radioactive decay or spontaneous emission (3).

As a test of our new classification of teleologies, we now compare it to that of Mayr ( 2004 ) . He defined five classes:

(1) teleomatic,
(2) teleonomic,
(3) purposive behavior,
(4) adapted features, and
(5) cosmic teleology.

It is straightforward that Mayr’s first teleomatic class

(1) corresponds to cases when physical laws determine the output “automatically.” His teleonomic class
(2) corresponds to cases when the behavior is determined by programs. “All teleonomic behavior is characterized by two components. It is guided by ‘a program’ and it depends on the existence of some endpoint, goal, or terminus that is ‘foreseen’ in the program that regulates the behavior or process. This endpoint might be a structure (in development), a physiological function, the attainment of a geographic position (in migration), or a ‘consummatory act’ in behavior” Mayr ( 2004 , 51). He also includes the behavior of human artifacts like machines into this class. With the recognition that tortoises have short stocky legs adapted for a certain function (namely, climbing, crawling, and walking), and as such represent behavioral programs, we can classify the legs of tortoises as corresponding to our class (B). It is easy to see that physiological functions like the heart pumping blood, migration of birds, or consummatory acts, as well as the complexity of machines, can be characterized by algorithmic complexity, which can be measured in bits, con firming the classification of teleonomic behavior into our class (B).
Mayr’s category
(3) is that of purposeful behavior. We classified purposeful behavior into class (C) and gave it a somewhat definite meaning.
(4) His fourth category “adapted features” is classified into our class (B). This classification is confirmed by the fact that the complexity of adapted features can be characterized by algorithmic complexity and can be measured in bits. Mayr refutes his own fifth class,
(5) “cosmic teleology,” with the following argument: “Natural selection provides a satisfactory explanation for the course of organic evolution and makes an invoking of supernatural teleological forces unnecessary. The removal of the mentioned four material processes from the formerly so heterogeneous category ‘teleological’ leaves no residue. This proves the nonexistence of cosmic teleology” (Mayr, 2004 ). 

 “Neither teleomatic nor teleonomic ( mindless programs ) determinism nor Natural selection does provide a satisfactory explanation for the course of physicochemical origin of life nor organic evolution and makes an invoking of supernatural teleological forces necessary. No material processes are capable of the feat. This proves the existence of cosmic teleology”

Genetic programs provide a clear demarcation between inanimate and living processes.

Genetic and epigenetic information controls and determines the generation of algorithmic complexity, organismal form and architecture, and the characteristically biological behavior and processes. Control based on information is manifest and observable in the trajectory of the living. Genetic and epigenetic programs play an important part in governing dynamic biological behavior, they are tools for the activity of the biological principle that continuously
generates the algorithmic complexity of biological behavior which permits change and adaptation to the environment.

Intelligent design is always tracked back to the intention of agents. In the case of man-made artifacts such as instructional complex blueprints of a factory, and the factory thereof made based on the information of these blueprints, both are the product of an intelligent engineer. It makes no sense, in the case of naturally occurring instructional information stored in DNA, and cell factories, made based on that information stored in DNA, to conclude that the designer was not an intelligent engineer. It is obviously the solution to postulate God, even if we cannot fathom or understand why there is eternal existence, rather than not. Life is eternal and ultimate, and a necessary intelligent designer is at the bottom of all existence. The existence of the first principle, an intelligent conscious mind, is validated based on all our empirical and theoretical knowledge. Therefore, a creator is not improbable but, on the contrary, the most probable, actually, universally reliable fact derived from all scientific facts. 

No scientific experiment has been able to come even close to synthesize the basic building blocks of life and reproduce a  self-replicating Cell in the Laboratory through self-assembly and autonomous organization.  The total lack of any kind of experimental evidence leading to the re-creation of life; not to mention the spontaneous emergence of life… is the most humiliating embarrassment to the proponents of naturalism and the whole so-called “scientific establishment” around it… because it undermines the worldview of who wants naturalism to be true. Darwinian evolution by natural selection, drift, and gene flow, the gene-centric view has failed to offer a consistent powerful explanatory scope in the biological sciences. The evidence has unraveled far more complex mechanisms, namely pre-programmed instructional complex INFORMATION encoded in various genetic and epigenetic languages and communication by various signaling codes through various signaling networks which leads us to the requirement of implementation by an intelligent designer. We can now safely say that the appearance of design in living creatures points straightforward to a designer. 

Selection and the Origin of Cells David A. Baum
https://academic.oup.com/bioscience/article/65/7/678/258308

Self-organization vs. self-ordering events in life-origin models. Physics of Life Reviews 3:211-228. Abel, D.L. and J.T. Trevors. (2006)
https://sci-hub.tw/https://www.sciencedirect.com/science/article/abs/pii/S1571064506000224

Measuring the functional sequence complexity of proteins Durston, K.K., D.K.Y. Chiu, D.L. Abel and J.T. Trevors (2007)
https://tbiomed.biomedcentral.com/articles/10.1186/1742-4682-4-47

Chance and necessity do not explain the origin of life Trevors, J.T. and Abel, D.L. (2004)
https://sci-hub.tw/https://www.ncbi.nlm.nih.gov/pubmed/15563395

Roscoe T Kane Life might well be an inevitable consequence of the laws of nature. Consider the Everett Interpretation of Quantum Mechanics. In it, life needs no maker and has no luck, everything that could possibly happen must happen in some world.

Dynamic kinetic stability (DKS) 1

Recently, one of us (A.P.) has described a new stability kind in nature, seemingly overlooked in modern scientific thought, which we have termed dynamic kinetic stability (DKS) . That stability kind, applicable solely to persistent replicating systems, whether chemical or biological, derives directly from the powerful kinetic character and the inherent unsustainability of the replication process. However, for the replication reaction to be kinetically unsustainable, the reverse reaction, in which the replicating system reverts back to its component building blocks, must be very slow when compared with the forward reaction; the replication reaction must be effectively irreversible. That condition, in turn, means the system must be maintained in a far-from-equilibrium state , and that continuing requirement is satisfied through the replicating system being open and continually fed activated component building blocks. Note that the above description is consistent with Prigogine's non-equilibrium thermodynamic approach, which stipulates that self-organized behaviour is associated with irreversible processes within the nonlinear regime . From the above, it follows that the DKS term would not be applicable to an equilibrium mixture of some oligomeric replicating entity together with its interconverting component building blocks.

1. http://rsob.royalsocietypublishing.org/content/3/3/120190#sec-5

Selforganization 1

In the book: Young Sun, Early Earth and the Origins of Life, we read:
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.

Since the authors apply methodological naturalism and exclude design a priori, they are left with the only alternative to design, that is self-organisation. 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 the cycle oself-replication, , which had to be fully setup as well right from the beginning, to perpetuate life for millennia, if not millions of years, but living organisms die? If the unbound drive of atoms to self-organize and get alive, why not the unbound drive to KEEP alive? We know for instance, that lobsters don't die. They just get bigger. 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 and 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


1. M. Gargaud · H. Martin · P. López-García -  Young Sun, Early Earth and the Origins of Life page 92

The possible mechanisms to explain the origin of life
In an attempt to explain the origin of life, scientists propose a two-stage process of natural chemical evolution:  formation of organic molecules, which combine to make larger biomolecules; self-organization of these molecules into a living organism. The origin of life can not be explained through biological nor chemical evolution. Adaptation, mutation, and natural selection depend on DNA replication. Heredity is guaranteed by faithful DNA replication whereas evolution depends upon errors accompanying DNA replication. Neither can it be explained through physical laws. Life depends on codes and instructional complex information. This information can only be generated by when the arrangement of the code is free and unconstrained, and any of the four bases of the genetic code can be placed in any of the positions in the sequence to generate the information. The only alternative, if the action of a creative agency is excluded, would be spontaneous self-assembly by orderly aggregation of prebiotic elements and building blocks in a sequentially correct manner without external direction.

Natural selection is not a possible mechanism to explain the origin of life since evolution depends on DNA replication
When we consider how life might have arisen from non-living matter, we must take into account the properties of the young Earth’s atmosphere, oceans, and climate, all of which were very different than they are today. Biologists postulate that complex biological molecules first arose through the random physical association of chemicals in that environment.
LIFE The Science of Biology, TENTH EDITION, page 3

Neither Evolution nor a physical necessity is a driving force prior to DNA replication. The only two alternatives are either a) creation by an intelligent agency, or b) Random, unguided, undirected natural events by a lucky "accident". 

Koonin, the logic of chance, page 266
Evolution by natural selection and drift can begin only after replication with sufficient fidelity is established. Even at that stage, the evolution of translation remains highly problematic. The emergence of the first replicator system, which represented the “Darwinian breakthrough,” was inevitably preceded by a succession of complex, difficult steps for which biological evolutionary mechanisms were not accessible. The synthesis of nucleotides and (at least) moderate-sized polynucleotides could not have evolved biologically and must have emerged abiogenically—that is, effectively by chance abetted by chemical selection, such as the preferential survival of stable RNA species. Translation is thought to have evolved later via an ad hoc selective process.  Did you read this ???!! An ad-hoc process ?? 

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

Heredity is guaranteed by faithful DNA replication whereas evolution depends upon errors accompanying DNA replication.  ( Furusawa, 1998 ) We hypothesize that the origin of life, that is, the origin of the first cell, cannot be explained by natural selection among self-replicating molecules, as is done by the RNA-world hypothesis. ( Vaneechoutte M )

Ann N Y Acad Sci. 2000;901:139-47.
The scientific origin of life. Considerations on the evolution of information, leading to an alternative proposal for explaining the origin of the cell, a semantically closed system
MARIO VANHOUTTE
We hypothesize that the origin of life, that is, the origin of the first cell, cannot be explained by natural selection among self-replicating molecules, as is done by the RNA-world hypothesis.
The hypothesis espoused here states that it is virtually impossible that the highly complicated system cell developed gradually around simple self-replicating molecules (RNA-hypercycles or autocatalytic peptide networks) by means of natural selection; as is proposed by, for example, the RNA-world hypothesis.  Despite searching quadrillions of molecules, it is clear that a spontaneous RNA replicator is unlikely to occur. Reports of nucleotide and peptide self-replication still depend upon human intervention (for instance, by changing the environmental conditions between two rounds of replication or by denaturing the double strands). The problem of denaturing the double-nucleotide strand in a non-enzymatic manner has been overlooked and has contributed to a failure to establish molecular self-replication. The first cell, life, was born and natural selection (selection among variations on the theme of autonomous duplication) commenced.

Chance and necessity do not explain the origin of life
Selection pressure cannot select nucleotides at the digital programming level where primary structures form. Genomes predetermine the phenotypes which natural selection only secondarily favours. Contentions that offer nothing more than long periods of time offer no mechanism of explanation for the derivation of genetic programming. No new information is provided by such tautologies. The argument simply says it happened. As such, it is nothing more than blind belief. Science must provide a rational theoretical mechanism, empirical support, prediction fulfillment, or some combination of these three. If none of these three is available, science should reconsider that molecular evolution of genetic cybernetics is a proven fact and press forward with new research approaches which are not obvious at this time. 5

Paul Davies: Why Darwinian evolution does NOT explain the origin of life Sep 2, 2021
I think in all honesty a lot of people even confuse it the people who aren't familiar with the area that oh I presume Darwinian evolution sort of accounts for the origin of life but of course, you don't get an evolutionary process until you've got a self-replicating molecule. ( Darwin )  gave us a theory of evolution about how life has evolved but he uh didn't want to tangle with how you go from non-life to life and for me, that's a much bigger step.
https://www.youtube.com/watch?v=q4LnWlOKQFA

In order for life to exist, the four fundamental forces have to be selected amongst a limitless possible number of alternative forces.
The same applies to life's four basic building blocks: Nucleotides, amino acids, phospholipids, and carbohydrates. There was also a limitless number of possible molecular combinations on the early earth. Besides natural selection in biology, it is also proposed regarding the origin of life, and cosmology.
The problem is, mindless, non-intelligent random events have no foresight and no goal. They will never sort out what promotes life randomly.

Cosmological natural selection
Cosmological natural selection also called the fecund universes, is a hypothesis proposed by Lee Smolin intended as a scientific alternative to the anthropic principle.
https://en.wikipedia.org/wiki/Cosmological_natural_selection

The role of natural selection in the origin of life
Unlike living systems that are products of and participants in evolution, these prebiotic chemical structures were not products of evolution. Not being yet intricately organized, they could have emerged as a result of ordinary physical and chemical processes.
https://www.ncbi.nlm.nih.gov/pubmed/20407927

An argument from ignorance asserts that a proposition is true because it has not yet been proven false. It excludes the possibility that there may have been an insufficient investigation to prove that the proposition is either true or false. In our case, scientific researchers have tried for over 70 years to explain the origin of life by unguided means, and failed. So it’s not that they have not tried. They have, but all attempts led to dead ends. Eliminative induction is sound when there are two competing hypotheses, and one can be shown with high certainty false. Provided the proposition, together with its competitors, forms a mutually exclusive and exhaustive class. Since either there is a God, or not, either one or the other is true. When you have eliminated the impossible, whatever remains, however not fully comprehensible, but logically possible, must be the truth. Eliminative inductions, in fact, become deductions. Naturalism rests on blind beliefs: Not science. Random events have never been demonstrated to impose, guide, or direct chemical selection to give life the first go.

An ID proponent does not make an assertion as exemplified with Russell’s teapot: There is a teapot revolving in an elliptical orbit around Mars. Because nobody can prove otherwise, it’s true. Nobody believes that, of course. People make wild claims and often get away with them, simply on the fact that the converse cannot otherwise be proven. Not so with Intelligent Design.

Synonym for selecting is: choosing, picking, handpicking, sorting out, discriminating, choosing something from among others, and giving preference to something over another. We know that we, as intelligent beings, do make choices to get the desired outcome all the time - and there is no demonstrated and known alternative to conscious intelligent selection for functional outcomes. Therefore, it is logical and plausible, and probable, that an intelligent agent created the first genome and stored instructional information, created the metabolic pathways to synthesize the building blocks of life, and energy turbines to make ATP. And he was remarkably good at that. So this is an entirely positive case. Not a case of ignorance.

As we witness complexity arise,
Interweaving parts before our eyes,
Aggregating subunits, fusing tight,
Encompassing, interlocking, a sight
Of systems greater than their parts,
Intricately combining, works of art.

It's logical to attribute,
Such actions to an intelligent pursuit,
With foresight, foreknowledge, and goals,
In the design, intricacy unfolds.

Careful elaboration, detailed design,
Meaningful interconnections, we find,
Creating purpose, function, and more,
Small changes causing effects galore.

Why would a molecule self-replicate,
Without DNA machinery to duplicate?
No natural selection, no survival need,
So why would a goal of replication lead?

Random assembly, chemical force,
No drive or goal, no guiding source,
Why should molecules strive to be,
Complex building blocks of life, we see?

Emerging properties, system-wide,
Random accidents can't coincide,
With the intricate complexity, we find,
Intelligent design, a more adequate kind.

Comparing Natural Selection and Chemoselectivity: Distinct Processes in Biology and Chemistry


Natural selection and chemoselectivity are two distinct concepts operating in different domains - biology and chemistry.

Natural Selection

1. Domain: Biology, specifically evolutionary biology
2. Definition: The process by which organisms better adapted to their environment tend to survive and produce more offspring
3. Mechanism:
  - Relies on hereditary variations in a population
  - Differential survival and reproduction based on these variations
  - Gradual accumulation of beneficial traits over generations
4. Timescale: Operates over many generations, typically long periods of time
5. Complexity: Involves complex living systems with the ability to reproduce and pass on genetic information

Chemoselectivity

1. Domain: Chemistry
2. Definition: The preferential formation of one chemical product over others in a reaction when multiple outcomes are possible
3. Mechanism:
  - Based on differences in reactivity between functional groups
  - Influenced by factors like molecular structure, reaction conditions, and catalysts
4. Timescale: Occurs during individual chemical reactions, typically on very short timescales
5. Complexity: Involves molecules and their interactions, not living systems

Key Differences

1. Scope: Natural selection applies to populations of living organisms, while chemoselectivity applies to individual chemical reactions.
2. Complexity: Natural selection involves complex biological systems capable of reproduction and inheritance, whereas chemoselectivity deals with simpler molecular interactions.
3. Timescale: Natural selection typically operates over long periods (many generations), while chemoselectivity occurs during individual chemical reactions.
4. Mechanism: Natural selection relies on random genetic variations and differential survival/reproduction, while chemoselectivity is based on chemical properties and reaction conditions.
5. Outcome: Natural selection leads to changes in populations over time, potentially resulting in evolution. Chemoselectivity results in the preferential formation of specific chemical products.
6. Intent: Natural selection is an unguided process with no predetermined goal. Chemoselectivity can be manipulated by chemists to achieve desired outcomes.

Some scientific papers have proposed chemoselectivity as a potential mechanism in the origin of life, but this hypothesis has since been largely discarded.

Key papers proposing chemoselectivity in the origin of life:

Joyce, G. F. (1989). RNA evolution and the origins of life. Nature, 338(6212), 217-224. Link. (This paper explores the potential role of RNA in early life and its evolution, suggesting chemoselectivity as a factor in prebiotic molecular evolution.)

Eschenmoser, A. (1999). Chemical etiology of nucleic acid structure. Science, 284(5423), 2118-2124. Link. (Eschenmoser discusses the chemical origins of nucleic acid structure, considering chemoselectivity in the context of prebiotic chemistry.)

Orgel, L. E. (2004). Prebiotic chemistry and the origin of the RNA world. Critical Reviews in Biochemistry and Molecular Biology, 39(2), 99-123. Link. (This review examines prebiotic chemistry and the RNA world hypothesis, touching on chemoselectivity in the formation of early biological molecules.)

Ricardo, A., & Szostak, J. W. (2009). Origin of life on earth. Scientific American, 301(3), 54-61. Link. (Ricardo and Szostak provide an overview of origin of life theories, including the potential role of chemoselectivity in early chemical evolution.)

These papers and others suggested that chemoselectivity could have played a role in the preferential formation of biologically relevant molecules in prebiotic conditions. Reasons why the idea was classified as not plausible:

1. Lack of specificity: While chemoselectivity can lead to the preferential formation of certain products, it's not specific enough to account for the precise molecular structures required for life. The level of selectivity observed in prebiotic chemistry experiments is far lower than what would be needed to produce complex biomolecules.
2. Absence of a driving force: Chemoselectivity alone doesn't provide a mechanism for the continuous improvement and complexification of molecular systems, which is necessary for the origin of life.
3. Insufficient complexity: Chemoselectivity might explain the formation of simple organic molecules, but it fails to account for the emergence of complex, information-rich polymers like DNA, RNA, and proteins.
4. Concentration problem: Prebiotic oceans were likely too dilute for effective chemoselectivity to occur. The concentrations of organic compounds would have been too low for significant selective reactions.
5. Lack of experimental support: Attempts to demonstrate significant chemoselectivity in plausible prebiotic conditions have largely been unsuccessful.
6. Chirality issue: Chemoselectivity doesn't adequately explain the homochirality observed in biological molecules.
7. Energetic barriers: Many of the reactions required for the formation of complex biomolecules are energetically unfavorable and wouldn't occur spontaneously, even with chemoselectivity.
8. Interference from side reactions: In a complex prebiotic "soup," many side reactions would occur, interfering with any selective processes.
9. Inability to explain information content: Chemoselectivity doesn't provide a mechanism for the origin of the genetic code or the information content in nucleic acids.
10. Lack of a self-replicating system: Chemoselectivity alone can't explain the emergence of self-replicating systems, which are crucial for the origin of life.

These limitations led to the recognition that it's insufficient as a primary mechanism for the origin of life. More recent research has focused on other hypotheses, such as RNA world hypothesis, metabolism-first scenarios, or membrane-first approaches, often in combination with concepts from systems chemistry and non-equilibrium thermodynamics. However, while addressing some of the limitations of chemoselectivity, these more recent hypotheses have not resolved either the fundamental challenges in explaining the origin of life.

Irreducible Complexity

The concept of irreducible complexity suggests that all essential components of a living system must be present simultaneously for it to function. This remains a significant challenge for origin of life theories. For example:

- The RNA World hypothesis struggles to explain how a self-replicating RNA system could arise without proteins to catalyze reactions and without a membrane to contain the system.
- Metabolism-first scenarios face the challenge of explaining how a metabolic network could be maintained and replicated without an information storage system like DNA or RNA.
- Membrane-first approaches must account for how a primitive cell membrane could form and persist without the complex lipid synthesis pathways found in modern cells.

As noted by Ruiz-Mirazo et al. (2014) in "Prebiotic Systems Chemistry: New Perspectives for the Origins of Life" (Chemical Reviews, 114(1), 285-366), these approaches often struggle to explain the emergence of an integrated system capable of both catalysis and information storage.

Polymerization Problem

The formation of long, information-rich polymers like DNA, RNA, and proteins in prebiotic conditions remains a significant challenge. Recent research has made some progress, but major hurdles persist:

- Strand separation: Once formed, polymer strands tend to stick together, inhibiting replication.
- Monomer purity: Prebiotic environments likely contained a mix of molecules, many of which could interfere with polymerization.
- Energy requirements: Many polymerization reactions are not thermodynamically favorable under prebiotic conditions.

Sutherland (2017) in "Opinion: Studies on the origin of life — the end of the beginning" (Nature Reviews Chemistry, 1, 0012) discusses some progress in prebiotic synthesis but acknowledges that significant challenges remain.

Information Problem

The origin of the genetic code and the information content in nucleic acids remains one of the most perplexing issues in origin of life research. This includes:

- The emergence of a system to translate genetic information into functional proteins.
- The origin of the specific sequence information in nucleic acids that codes for functional proteins.
- The development of error correction mechanisms to maintain genetic integrity.

As highlighted by Kun and Szathmáry (2015) in "Weak convergence to simplicity in evolution and tinkering" (Nature Communications, 6, 7789), the transition from chemical evolution to biological evolution, with its reliance on coded information, remains poorly understood.

Concentration Problem

Many origin of life scenarios require relatively high concentrations of precursor molecules, which is unlikely in a prebiotic ocean. While some propose concentration mechanisms (e.g., mineral surfaces, hydrothermal vents), maintaining these concentrations over time remains problematic.

Chirality

The homochirality observed in biological molecules (e.g., L-amino acids, D-sugars) is still not fully explained by current theories.

Integration of Subsystems

Even if individual components (e.g., replicators, metabolic cycles, membranes) could form independently, explaining how they became integrated into a functional whole remains challenging. These persistent issues highlight the complexity of the origin of life problems. A comprehensive and widely accepted explanation for the origin of life remains elusive. The challenges posed by irreducible complexity, polymer formation, and the origin of biological information continue to be an unbridgeable problem. The ongoing difficulties in explaining the origin of life through purely naturalistic processes point to intelligent design as the most plausible explanation, since intelligence can solve all these problems.

1. Complexity and Information Content: Intelligent agents are known to create complex, information-rich systems. The genetic code, with its intricate information storage and processing capabilities, bears hallmarks of designed systems we observe in human technology.
2. Problem-Solving Capability: Intelligence can foresee and solve multiple interconnected problems simultaneously. This addresses the issue of irreducible complexity, where multiple components need to be present and functional from the start.
3. Overcoming Probabilistic Barriers: The extremely low probabilities associated with the spontaneous formation of functional proteins or self-replicating systems are more easily explained by intentional design rather than chance events.
4. Fine-Tuning: The precise conditions required for life, both at the cosmic and molecular levels, appear finely tuned. Intelligent design could explain this apparent fine-tuning more readily than chance.
5. Goal-Directed Processes: Unlike undirected natural processes, intelligence can work towards specific goals, potentially explaining the apparent purposefulness observed in biological systems.
6. Analogy to Human Design: We observe that complex, functional systems in our experience (e.g., computers, engines) invariably result from intelligent design, not undirected processes.
7. Integration of Subsystems: Intelligence can conceptualize and implement the integration of various subsystems (replication, metabolism, encapsulation) into a functional whole.
8. Overcoming Chemical Obstacles: An intelligent agent could potentially overcome issues like the water paradox (where water is necessary for life but also hydrolyzes important biological polymers) through clever chemical engineering.
9. Solving the Chirality Problem: Intelligence could selectively use molecules of a specific chirality, explaining the homochirality observed in biological systems.
10. Information Processing and Storage: The origin of the genetic code and its translation machinery is more readily explained by an intelligent process capable of creating symbolic information systems.

Premise 1: Complex, information-rich systems that exhibit irreducible complexity, goal-directed processes, and integrated subsystems are invariably the product of intelligent design in our observable experience.
Premise 2: Living systems display complex, information-rich characteristics, irreducible complexity, goal-directed processes, and integrated subsystems that cannot be adequately explained by known naturalistic processes.
Conclusion: Therefore, living systems are most plausibly the product of intelligent design.

A Critical Analysis of Proposed Mechanisms for the Origin of Life: Challenges to Naturalistic Explanations

Otangelo Grasso email:otangelograsso@gmail.com

Abstract

This paper examines various proposed mechanisms for the origin of life, focusing on the fundamental dichotomy between intelligence-based and non-intelligence-based explanations. We review key hypotheses including chemoselectivity, early energy sources, ATP synthesis, the contact surface hypothesis, chance, physical necessity, and natural selection. The challenges faced by non-intelligent explanations are analyzed, including issues of molecular complexity, energy requirements, and the emergence of information-rich systems. We conclude that while naturalistic proposals offer thought-provoking possibilities, they face significant explanatory hurdles, particularly in accounting for the origin of complex, interdependent biological systems.

1. Introduction

The origin of life remains one of the most profound and challenging questions in science. Despite decades of research, a comprehensive and widely accepted explanation for how life arose from non-living matter continues to elude us. The proposed mechanisms for abiogenesis can be broadly categorized into two fundamental approaches: those invoking intelligent causation and those relying solely on undirected natural processes. This paper examines several key hypotheses within the naturalistic framework, including chemoselectivity, early energy sources, the evolution of ATP synthesis, the contact surface hypothesis, chance, physical necessity, and natural selection. We analyze these proposals in light of the challenges they face, particularly in explaining the emergence of complex, information-rich biological systems. The dichotomy between intelligence-based and non-intelligence-based explanations forms the central theme of our analysis. While naturalistic explanations have dominated mainstream scientific discourse, they continue to grapple with significant explanatory gaps. On the other hand, intelligence-based explanations, while often considered outside the realm of traditional scientific inquiry, offer a perspective that addresses some of the key challenges in the origin of life research. Our goal is to provide a critical evaluation of these competing explanations, highlighting the strengths and weaknesses of each approach. By doing so, we aim to contribute to a more comprehensive understanding of the origin of life problems and stimulate further research and discussion in this vital area of scientific inquiry.

Mechanisms to Explain the Origin of Life

1. Chemoselectivity: Proposes that specific chemical reactions and pathways favored the formation of life-essential molecules.
2. Early Energy Sources: Investigates how primitive energy sources, such as light and inorganic compounds, could drive early metabolic reactions.
3. ATP Synthesis Evolution: Explores the gradual evolution of ATP synthesis as a critical component of bioenergetic systems.
4. Contact Surface Hypothesis: Suggests that surfaces, such as minerals, could facilitate the organization and assembly of prebiotic molecules.
5. Chance: Considers the possibility that life emerged through highly improbable random events.
6. Physical Necessity: Argues that life is a result of inevitable physical and chemical laws.
7. Natural Selection: Applies the principles of natural selection to prebiotic chemistry, suggesting that advantageous molecular traits were preserved.
8. Radiation-Driven Synthesis: Proposes that radiation, such as UV light, played a role in synthesizing prebiotic compounds.
9. Thermodynamics-Based Proposals: Includes various theories on how thermodynamic principles and energy gradients could drive the self-organization of life.
   - Self-Organization through Dissipative Structures
   - Thermal Gradients as Energy Sources
   - Entropy-Driven Self-Assembly
   - Non-Equilibrium Thermodynamics
   - Maximum Entropy Production Principle
   - Thermodynamic Efficiency and Natural Selection
   - Free Energy Transduction
10. Hydrothermal Systems: Examines the role of hydrothermal vents and similar environments in providing energy and materials for the origin of life.
11. Thioester World Hypothesis: Proposes that thioesters served as the primary energy currency before ATP.
12. Information-Theoretic Approaches: Focuses on how genetic information and complex specified systems could arise.

2. The distinction between abiogenesis and evolution

Rational Wiki states: "Let's get something abundantly clear: abiogenesis and evolution are two completely different things. The theory of evolution says absolutely nothing about the origin of life. It merely describes the processes that take place once life has started."

This quote highlights a crucial point often misunderstood in discussions about life's origins. Evolution by natural selection requires pre-existing self-replicating entities. It cannot explain how the first such entities came into existence.

3. The Chemical Nature of the Origin of Life Problem

Addy Pross (2012) states: "Darwinian theory is a biological theory and therefore deals with biological systems, whereas the origin of life problem is a chemical problem, and chemical problems are best solved with chemical (and physical) theories. Attempting to explain chemical phenomena with biological concepts is methodologically problematic."

This quote emphasizes that the origin of life is fundamentally a question of chemistry, not biology. We need to understand how complex, self-replicating chemical systems could arise from simpler precursors without invoking biological mechanisms that didn't yet exist.

4. The challenge of prebiotic chemistry

Alan W. Schwartz (2007) points out: "Although the Miller–Urey reaction produces an impressive set of amino acids and other biologically significant compounds, a large fraction of the starting material goes into a brown, tar-like residue that remains uncharacterized; i.e., gunk."

This highlights a significant challenge in origin of life research. While we can produce some biologically relevant molecules under simulated prebiotic conditions, we also get many other products. The challenge is explaining how life-essential molecules could have been selected and concentrated from this complex mixture.

5. The problem of chirality

A.G. Cairns-Smith (1985) notes: "It is one of the most singular features of the unity of biochemistry that this mere convention is universal. Where did such agreement come from? You see non-biological processes do not as a rule show any bias one way or the other."

This quote addresses the chirality problem - the fact that life uses only left-handed amino acids and right-handed sugars. This uniformity is crucial for life's functions, but it's difficult to explain how it could have arisen through non-biological processes.

6. The role of chance

Sean Carroll refers to the emergence of life as "the mother of all accidents" and "the accident of all mothers."

This view represents one extreme in origin of life theories - that life arose through an extremely improbable chance event. However, as Gennady Shkliarevsky points out: "invoking chance even once is highly problematic; invoking it twice to explain the same phenomenon makes an explanation very questionable."

7. The limitations of self-organization

William Dembski (2002) argues: "The problem is that natural mechanisms are too unspecific to determine any particular outcome. Natural processes could theoretically form a protein, but also compatible with the formation of a plethora of other molecular assemblages, most of which have no biological significance."

This critique of self-organization theories points out that while physical and chemical laws can produce complex structures, they don't specify the particular complexity we see in living systems.

8. The absence of prebiotic natural selection

As the document states: "There was no prebiotic natural selection to survive and reproduce. Why should be assumed that molecules - that are randomly assembled by chemical/physical forces/happenstance and just happened to stay in place - have the drive or goal to self-replicate, to become the complex macromolecular building blocks of living cells?"

This is a crucial point. Natural selection as we understand it in biology requires self-replication and heredity. These didn't exist before the first life forms, so we can't invoke natural selection to explain their origin.

9. The challenge of explaining the first cell

Mario Vaneechoutte (2000) hypothesizes: "The origin of life, that is, the origin of the first cell, cannot be explained by natural selection among self-replicating molecules, as is done by the RNA-world hypothesis."

This underscores the difficulty of explaining how we get from simple self-replicating molecules (if they could even exist in a prebiotic environment) to a fully functioning cell.

While significant progress has been made in understanding potential chemical pathways to life, major challenges remain. These include explaining the origin of biological information, the emergence of complex self-replicating systems, and the transition from chemistry to biology. Current hypotheses, while providing valuable insights, still struggle to fully account for these phenomena without invoking extremely improbable chance events or assuming capabilities (like natural selection) that weren't present before life existed.

10. Claim: Chemoselectivity as an Explanation for the Origin of Life


Claim: Chemoselectivity as an Explanation for the Origin of Life

1. Definition: Chemoselectivity refers to the preferential formation of one chemical product over others in a reaction when multiple outcomes are possible.
2. Application to origin of life: Proposal: Chemoselectivity could have led to the preferential formation of biologically relevant molecules in prebiotic conditions.
3. Mechanism: Based on differences in reactivity between functional groups, influenced by factors like molecular structure, reaction conditions, and catalysts.
4. Timescale: Occurs during individual chemical reactions, typically on very short timescales.
5. Complexity: Involves molecules and their interactions, not living systems.

Response:

1. Lack of specificity: Chemoselectivity is not specific enough to account for the precise molecular structures required for life.
2. Absence of driving force: It doesn't provide a mechanism for continuous improvement and complexification of molecular systems.
3. Insufficient complexity: Fails to explain the emergence of complex, information-rich polymers like DNA, RNA, and proteins.
4. Concentration problem: Prebiotic oceans were likely too dilute for effective chemoselectivity to occur.
5. Lack of experimental support: Attempts to demonstrate significant chemoselectivity in plausible prebiotic conditions have been largely unsuccessful.
6. Chirality issue: Doesn't adequately explain the homochirality observed in biological molecules.
7. Energetic barriers: Many required reactions are energetically unfavorable and wouldn't occur spontaneously, even with chemoselectivity.
8. Interference from side reactions: In a complex prebiotic "soup," many side reactions would interfere with selective processes.
9. Inability to explain information content: Provides no mechanism for the origin of the genetic code or information content in nucleic acids.
10. Lack of self-replicating system: Can't explain the emergence of self-replicating systems crucial for life.
11. Time scale mismatch: Chemoselectivity occurs rapidly, while the origin of life likely required long periods of molecular evolution.
12. No mechanism for adaptation: Doesn't explain how early chemical systems could adapt to changing environmental conditions.
13. Oversimplification: Reduces the complex problem of life's origin to simple chemical preferences, ignoring many critical aspects of living systems.
14. Integration problem: Fails to address how various components (replication, metabolism, compartmentalization) became integrated.
15. Limited scope: At best, could explain the formation of some simple organic molecules, not the emergence of life itself.

While chemoselectivity is an important concept in chemistry, it is insufficient as a primary explanation for the origin of life. The process lacks the complexity, specificity, and driving force necessary to account for the emergence of living systems. Chemoselectivity might play a role in certain prebiotic reactions, but it fails to address the fundamental challenges of creating complex, self-replicating, information-rich systems characteristic of life. More comprehensive theories incorporating multiple aspects of chemistry, physics, and biology are needed to adequately tackle the origin of life problem.

11. Early Energy Sources

Claim: The first proto-cellular systems would not have used ATP. 
Response: Pyrophosphate as an early energy currency:  Some scientists suggest that pyrophosphate would have preceded ATP as an energy carrier.
Problems: 
- The instability of pyrophosphate in water
- Lack of evidence for ancient pyrophosphate-using enzymes
- Difficulty explaining the transition to ATP-based systems

Iron-sulfur world hypothesis:
Proposal: Early metabolism was based on iron-sulfur clusters, with energy derived from redox reactions.
Problems:
- Limited range of reactions possible
- Difficulty in explaining the transition to more complex organic molecules
- Challenges in maintaining the required chemical gradients in early Earth conditions

RNA World hypothesis:
Proposal: RNA served both as genetic material and as catalysts, including for energy transfer.
Problems:
- Instability of RNA in prebiotic conditions
- Difficulty in explaining the synthesis of ribonucleotides
- Lack of efficient RNA-based energy transfer systems

Membrane-based energy systems:
Proposal: Early cells used proton gradients across primitive membranes for energy.
Problems:
- Difficulty in forming stable membranes in prebiotic conditions
- Lack of sophisticated protein machinery for efficient energy transduction
- Challenges in evolving the complex ATP synthase from simpler precursors

Thermal gradients as energy sources:
Proposal: Temperature differences, such as those found in hydrothermal vents, provided energy for early life.
Problems:
- Limited availability of such environments
- Difficulty in harnessing thermal energy without complex molecular machinery
- Challenges in transitioning from thermal to chemical energy systems

6. Chemiosmotic energy in alkaline hydrothermal vents:
Proposal: pH gradients in these vents could have driven early metabolism.
Problems:
- Limited to specific geological settings
- Difficulty in concentrating and organizing molecules in such environments
- Challenges in evolving more complex energy systems from this starting point

Thioester world hypothesis:
Proposal: Thioesters served as early high-energy compounds before the advent of ATP.
Problems:
- Instability of thioesters in aqueous environments
- Limited range of reactions compared to ATP
- Difficulty explaining the transition to phosphate-based energy currencies

Each of these proposals faces significant challenges in explaining the origin and early origin of life's energy systems. The main overarching problems include:

- Lack of experimental evidence replicating prebiotic conditions
- Difficulty in explaining the transition from simple chemical systems to complex biological ones
- Challenges in maintaining the stability and organization required for early life in harsh prebiotic environments
- The "chicken and egg" problem: many energy systems require complex proteins, which themselves require energy to be synthesized

These issues highlight why the origin of life's energy systems remains one of the most challenging questions in science. Research continues to explore new possibilities and refine existing hypotheses, but a fully satisfactory explanation remains elusive.

Claim: Energy sources for early life: Early life forms would have relied on simpler energy sources available in their environment, such as chemical gradients or geothermal energy.
Response: There are several proposed energy sources and environments that have been suggested for the origin of early life, with hydrothermal vents being a prominent hypothesis. However, there are significant challenges with this and other proposed scenarios:

Hydrothermal Vents: While hydrothermal vents provide chemical energy and minerals, they face several issues as a site for abiogenesis:

1. High temperatures: The extreme heat would rapidly break down any organic molecules formed, including amino acids and nucleotides essential for life.
2. Water problem: The abundance of water inhibits the formation of critical chemical bonds needed to build complex biomolecules. Polymerization reactions that form proteins and nucleic acids produce water as a byproduct, making them thermodynamically unfavorable in aqueous environments.
3. Dilution: The vast ocean volume would dilute any organic compounds formed, making it difficult to achieve concentrations needed for further reactions.
4. Lack of evidence: We do not observe protocells or early life forms developing at hydrothermal vents today, even though the conditions are thought to be similar to early Earth.
5. Instability of key molecules: RNA and DNA are unstable at high temperatures without sophisticated repair mechanisms.

Other Proposed Energy Sources:

UV radiation: While UV light can provide energy for certain reactions, it would also rapidly degrade organic molecules.
Electrical discharges (lightning): Similar issues with degradation of formed molecules and lack of consistent energy supply.
Radioactivity: Proposed as an energy source, but likely insufficient and would cause mutations in early replicators.

12. The Evolution of ATP Synthesis

Claim: ATP and protein function: While it's true that many modern proteins require ATP to function, this wasn't necessarily the case for early, simpler biomolecules.
Response:  The claim that early, simpler biomolecules didn't require ATP to function is not well-supported by our current understanding of biochemistry and the origins of life. 

Fundamental role of ATP: ATP (adenosine triphosphate) is not just a simple energy source; it's a fundamental component of cellular metabolism. It serves as a universal energy currency in all known living organisms. The ubiquity of ATP across all domains of life suggests that it was likely present and crucial even in the earliest forms of life.
Chemical properties of ATP: ATP's chemical structure makes it uniquely suited for energy transfer in biological systems. Its high-energy phosphate bonds allow for efficient energy storage and release. It's unlikely that early life forms could have functioned effectively without a similar energy transfer mechanism.
Metabolic complexity: Even the simplest known organisms today have complex metabolic pathways that depend on ATP. These pathways are so fundamental and conserved across species that they likely evolved very early in the history of life. It's difficult to conceive of a functioning metabolism without an ATP-like molecule.
Chicken-and-egg problem: Many of the processes required to synthesize proteins and other complex biomolecules require energy input, often in the form of ATP. Without ATP or a similar energy-rich molecule, it's unclear how these essential biomolecules could have been synthesized in the first place.
RNA World hypothesis: Many scientists believe that RNA preceded proteins in the evolution of life (the RNA World hypothesis). RNA can catalyze chemical reactions and store genetic information, but these functions often require energy input. ATP or similar molecules would have been necessary even in an RNA-based proto-life.
Evolutionary conservation: The fact that ATP is used so universally in modern organisms suggests that it was likely present very early in the evolution of life. If early life forms had used a different energy system, we would expect to see more diversity in energy currencies across different lineages.

It's highly unlikely that functional proteins or other complex biomolecules could have evolved without an ATP-like energy currency. The transition from simple chemical systems to living organisms almost certainly required a versatile, high-energy molecule like ATP.

Claim: ATP synthesis: Modern ATP synthesis primarily occurs through phosphorylation, often driven by chemiosmotic gradients (as in ATP synthase). This is indeed a sophisticated system that evolved over time.
Response:  ATP synthesis is a fundamental process for life, involving complex systems like ATP synthase and chemiosmotic gradients. This system presents an origin of life problem, not an evolutionary one, as it must have existed before life began. Therefore, evolutionary mechanisms cannot explain its origin. ATP synthase and the proton gradient form an irreducibly complex system. Both components are necessary for function, and neither has a useful purpose on its own. The ATP synthase itself is irreducibly complex, consisting of multiple subunits that must be precisely arranged to function. The system exhibits both specified complexity (in its information content) and irreducible complexity (in its structure and function). Our experience suggests that such complex, interdependent systems are typically the product of intelligent design rather than random processes. Given that ATP synthesis is universal in life and essential for its origin, its complexity poses a significant challenge to naturalistic explanations of life's beginnings. The argument concludes that the existence of ATP synthase and related systems is evidence for an intelligent creator rather than the result of unguided processes. The complexity and interdependence of ATP synthesis systems are better explained by intelligent design than by chance or evolutionary processes, particularly given their necessity at life's very inception.

Claim:  Early life existed in an anaerobic environment, and fermentation or similar processes might have been crucial early energy-generating pathways.
Response:  
1. Energy inefficiency: Fermentation yields only about 2 ATP molecules per glucose, compared to up to 38 in aerobic respiration. This low energy yield would severely limit the metabolic capabilities and complexity of early life forms.
2. Limited substrate availability: Fermentation requires organic molecules as substrates. In the prebiotic world, the availability of complex organic molecules would have been limited, making it difficult for early life to sustain itself solely through fermentative processes.
3. Waste product accumulation: Fermentation produces waste products like lactic acid or ethanol, which can be toxic in high concentrations. Without efficient means of waste removal, early organisms relying solely on fermentation would quickly poison their environment.
4. Lack of metabolic flexibility: Fermentation is a relatively simple process compared to complex electron transport chains. This lack of complexity would limit the evolutionary potential and adaptability of early life forms.
5. Incompatibility with RNA World hypothesis: Many origin of life theories, including the RNA World hypothesis, require more energy-rich environments than fermentation alone could provide. The synthesis and maintenance of complex molecules like RNA would likely require more efficient energy generation.
6. Absence of precursor molecules: The enzymes and pathways required for fermentation, while simpler than those for aerobic respiration, are still complex molecular machines. It's unclear how these could have arisen without pre-existing energy generation systems.
7. Geological evidence: While early Earth was indeed largely anaerobic, there's evidence of other potential energy sources like chemolithotrophy that could have been more plausible for early life.
8. Universal conservation of ATP synthase: The fact that ATP synthase is universally conserved across all domains of life suggests that it, or a similar system, was present very early in life's history, predating the divergence of major lineages.
9. Thermodynamic constraints: Fermentation alone might not provide sufficient energy to overcome the thermodynamic barriers involved in self-organization and self-replication, which are crucial for the emergence of life.
10. Lack of evolutionary trajectory: There's no clear evolutionary path from simple fermentative processes to the complex, chemiosmotic energy generation systems seen in all modern life forms.

Claim: Energy in abiogenesis: The origin of life (abiogenesis) likely involved simpler energy transduction mechanisms before the evolution of complex systems like ATP synthase or fermentation pathways.
Response:  Here's an explanation of the proposed simpler energy transduction mechanisms for abiogenesis and why they fall short in explanatory power:

1. Proton gradients across mineral surfaces:
Proposal: Early proto-cells could have used naturally occurring proton gradients across mineral surfaces (like those in hydrothermal vents) for energy.
Shortcomings: 
- Lacks a mechanism for harnessing this energy for useful cellular work.
- Doesn't explain how cells transitioned to generating their own gradients.
- Doesn't account for the origin of complex biomolecules needed to utilize such gradients.

2. Chemiosmosis using simpler molecules:
Proposal: Primitive versions of chemiosmosis using simpler molecules than ATP.
Shortcomings:
- Still requires complex molecular machinery to couple ion gradients to chemical reactions.
- Doesn't explain the origin of the necessary semi-permeable membranes.
- Fails to address how the transition to ATP-based systems occurred.

3. Thioester world hypothesis:
Proposal: Thioesters as primitive energy currency before ATP.
Shortcomings:
- Doesn't explain how thioester chemistry could support the complex reactions needed for early life.
- Lacks evidence for a plausible prebiotic source of thioesters in sufficient quantities.
- Fails to address the transition from thioester-based to ATP-based metabolism.

4. Iron-sulfur world hypothesis:
Proposal: Energy from redox reactions involving iron-sulfur minerals.
Shortcomings:
- Doesn't provide a clear mechanism for coupling these reactions to biosynthesis.
- Fails to explain how this system could support the formation of complex biomolecules.
- Lacks a plausible transition to modern cellular energetics.

5. Pyrophosphate as an energy source:
Proposal: Inorganic pyrophosphate as a simpler phosphate-based energy carrier.
Shortcomings:
- Doesn't explain the origin of pyrophosphate in prebiotic conditions.
- Fails to address how early systems could have efficiently utilized pyrophosphate.
- Lacks a clear evolutionary pathway to ATP-based systems.

6. UV-driven carbon fixation:
Proposal: UV light as an energy source for carbon fixation in early life.
Shortcomings:
- Doesn't explain how this energy could be stored or used for other cellular processes.
- Fails to address how life transitioned to chemical energy sources.
- Lacks a mechanism for protecting early biomolecules from UV damage.

7. Thermal gradients:
Proposal: Temperature differences as an energy source for early life.
Shortcomings:
- Doesn't provide a mechanism for converting thermal energy into chemical energy.
- Fails to explain how this could support complex biochemical reactions.
- Lacks a plausible transition to modern bioenergetics.

All these proposals fall short because they:
- Fail to provide a complete picture of early cellular energetics.
- Don't adequately explain the transition to more complex energy systems.
- Often require pre-existing complex molecules or structures.
- Lack convincing experimental evidence.
- Don't address the simultaneous need for energy, information storage, and self-replication in early life.

The origin of life's energy systems remains a significant challenge in abiogenesis research, with no fully satisfactory explanation to date.

Claim: Gradual evolution: The sophisticated energy systems we see in modern cells, including ATP synthesis and utilization, likely evolved gradually from simpler precursor systems.
Response: Here's an explanation of the proposals for gradual evolution of energy systems in early life and why they fall short:

1. Step-wise assembly of ATP synthase:
Proposal: ATP synthase evolved gradually from simpler rotary motors.
Shortcomings:
- Doesn't explain the origin of the initial rotary motor.
- Fails to address how partial assemblies would be functional and selectable.
- Ignores the need for a pre-existing proton gradient and ATP-utilizing enzymes.

2. Evolution from simpler phosphate-based energy carriers:
Proposal: Transition from pyrophosphate or acetyl phosphate to ATP.
Shortcomings:
- Lacks explanation for the origin of these simpler phosphate compounds.
- Doesn't address how early systems could efficiently use these alternatives.
- Fails to explain the universality of ATP in modern life.

3. Gradual development of electron transport chains:
Proposal: Electron transport chains evolved from simpler redox reactions.
Shortcomings:
- Doesn't account for the complex, interdependent nature of electron transport chains.
- Fails to explain how partially formed chains would be beneficial.
- Ignores the need for sophisticated membrane structures and proteins.

4. Evolution of metabolic pathways:
Proposal: Modern metabolic pathways evolved from simpler chemical reactions.
Shortcomings:
- Doesn't explain how these pathways became coupled to energy production.
- Fails to address the origin of enzymes needed for each step.
- Ignores the problem of how incomplete pathways could be beneficial.

5. Transition from heterotrophy to autotrophy:
Proposal: Early life forms evolved from consuming organic molecules to producing their own.
Shortcomings:
- Doesn't explain the initial source of organic molecules.
- Fails to address how early organisms could switch energy sources.
- Ignores the complexity of autotrophic pathways like photosynthesis or chemosynthesis.

6. RNA world to DNA/protein world transition:
Proposal: Energy systems evolved as life transitioned from RNA-based to DNA/protein-based.
Shortcomings:
- Doesn't explain how RNA-based life forms could have sufficient energy.
- Fails to address the energy requirements for this major transition.
- Ignores the need for complex energy systems in even RNA-based life.

7. Emergence of chemiosmosis:
Proposal: Chemiosmosis evolved gradually from simpler ion gradients.
Shortcomings:
- Doesn't explain the origin of semi-permeable membranes.
- Fails to address how partial chemiosmotic systems would be beneficial.
- Ignores the need for complex proteins to utilize ion gradients.

These proposals fall short in explaining the origin of energy production in early life because:

- They often require pre-existing complex structures or molecules.
- They don't adequately explain how partial or incomplete systems would be beneficial and selected for.
- They fail to address the chicken-and-egg problem of needing energy to produce the components of energy-producing systems.
- They don't account for the universality and complexity of core energy production systems across all life.
- They lack experimental evidence demonstrating the proposed transitions.
- They often ignore the interdependence of energy production with other crucial cellular processes.
- They fail to explain how the information for these systems could have originated and been preserved.

The gradual evolution of such complex, interdependent systems remains a significant challenge to explain, particularly in the context of early life where sophisticated enzymes and genetic systems were not yet present. The origin of life's energy systems continues to be a major unanswered question in the field of abiogenesis.

13. The Contact Surface Hypothesis

Claim: This hypothesis suggests that the interfaces between different phases (like liquid-solid or liquid-gas) could have played a crucial role in the origin of life. The key proposals include:

1. Concentration of molecules: Surfaces could concentrate organic molecules, increasing the likelihood of reactions.
2. Catalytic effects: Mineral surfaces might catalyze important prebiotic reactions.
3. Self-assembly: Interfaces could promote the self-assembly of complex molecules and protocells.
4. Energy gradients: Surfaces might create local energy gradients that could drive reactions.
5. Protection: Surfaces could protect fragile molecules from degradation.

Response: Why these proposals don't withstand scrutiny:

1. Concentration problem:
- While surfaces can concentrate molecules, they also limit diffusion and reaction space.
- It's unclear how surface-bound molecules could transition to form free-living cells.
2. Catalytic limitations:
- Mineral catalysis is often non-specific, leading to a mixture of products rather than the specific molecules needed for life.
- Many crucial prebiotic reactions require specific organic catalysts, not just mineral surfaces.
3. Self-assembly challenges:
- Self-assembly at interfaces doesn't explain the origin of the complex, specific sequences needed in biological polymers.
- It doesn't address how self-assembled structures could become capable of replication and evolution.
4. Energy gradient insufficiency:
- Local energy gradients at surfaces are typically too weak to drive the complex chemistry required for life.
- They don't explain how cells could have evolved to generate their own energy gradients.
5. Protection paradox:
- While surfaces might protect some molecules, they also expose them to potentially damaging surface chemistry.
- It's unclear how protected molecules could participate in the dynamic processes necessary for life.
6. Lack of information generation:
- Surface chemistry doesn't explain the origin of the genetic information required for life.
- It doesn't address how a surface-based system could transition to a genetic system.
7. Selectivity issues:
- Surfaces tend to adsorb a wide variety of molecules, potentially interfering with the specific chemistry needed for life.
8. Scale problem:
- While effects might be observed in laboratory settings, scaling these up to be relevant in prebiotic oceans is problematic.
9. Transition to cellular life:
- The hypothesis doesn't adequately explain how surface-bound chemistry could lead to free-living cells.
10. Experimental limitations:
- Many experiments supporting this hypothesis use highly controlled conditions and purified reagents, unlike the messy prebiotic environment.

While the contact surface hypothesis offers some interesting insights into possible prebiotic chemistry, it falls short of explaining the origin of life. It doesn't adequately address the origins of genetic information, metabolic pathways, or cellular structures. Like many origin of life hypotheses, it struggles with the transition from simple chemical processes to the complex, interrelated systems that characterize even the simplest forms of life.

13. The Radiation Hypotheses

Claim:  Radiation in various forms could have played a decisive role in the origin of life
Response:

1. UV radiation as an energy source:
Proposal: UV light from the early Sun could have driven prebiotic chemical reactions.
Shortcomings:
- UV radiation is more likely to break down complex molecules than build them up.
- Doesn't explain how early life forms could have protected themselves from UV damage.
- Fails to address how UV-driven reactions could lead to self-replicating systems.

2. Ionizing radiation from radioactive decay:
Proposal: Radiation from naturally occurring radioactive elements could have provided energy for prebiotic synthesis.
Shortcomings:
- The energy from radioactive decay is generally too unfocused to drive specific chemical reactions.
- Ionizing radiation can damage organic molecules, potentially destroying nascent life forms.
- Doesn't explain how this energy could be harnessed in a controlled manner.

3. Cosmic radiation:
Proposal: High-energy particles from space could have initiated chemical reactions in the early atmosphere or oceans.
Shortcomings:
- Cosmic radiation is more likely to cause random chemical changes rather than build complex, ordered molecules.
- Doesn't address how these reactions could lead to the specific molecules needed for life.
- Fails to explain how cosmic radiation could drive the formation of self-replicating systems.

4. Radiolysis of water:
Proposal: Radiation splitting water molecules could produce reactive species for prebiotic chemistry.
Shortcomings:
- The reactive species produced are often more likely to degrade organic molecules than build them.
- Doesn't explain how this process could lead to the complex, interrelated systems required for life.
- Fails to address the origin of genetic information.

5. Radiation-driven polymerization:
Proposal: Radiation could drive the formation of polymers like primitive proteins or nucleic acids.
Shortcomings:
- Radiation-induced polymerization typically produces random sequences, not the specific sequences needed for biological function.
- Doesn't explain how these polymers could become self-replicating.
- Fails to address how radiation-stable polymers could have the flexibility needed for life processes.

6. Radiation hormesis in early life:
Proposal: Low levels of radiation might have stimulated the development of early life forms.
Shortcomings:
- Lacks a clear mechanism for how radiation could stimulate the specific developments needed for life.
- Doesn't explain the origin of the complex systems needed to benefit from hormesis.
- Fails to address how early life could have controlled its radiation exposure.

These proposals fall short in explaining the origin of life for several key reasons:

1. Lack of specificity: Radiation generally causes random changes, not the specific, ordered processes needed for life.
2. Destructive potential: Many forms of radiation are more likely to break down complex molecules than build them up.
3. Energy coupling problem: These proposals don't adequately explain how radiation energy could be efficiently coupled to the specific chemical reactions needed for life.
4. Information problem: Radiation-based theories don't address the origin of the genetic information required for life.
5. Complexity issue: They fail to explain how radiation could lead to the development of complex, interrelated biochemical systems.
6. Protection paradox: Early life forms would need protection from radiation, but the proposals don't explain how this protection could evolve.
7. Selective pressure: These theories don't account for how natural selection could act on radiation-induced changes in prebiotic systems.
8. Experimental limitations: Laboratory experiments demonstrating radiation-driven prebiotic synthesis often use conditions unlikely in the prebiotic world.
9. Transition problem: The proposals don't adequately explain the transition from radiation-driven chemistry to self-sustaining biological processes.
10. Cellular organization: Radiation-based theories struggle to explain the origin of cellular structure and organization.

While radiation may have played some role in prebiotic chemistry, it falls far short of explaining the origin of life. The complexity, specificity, and information content of even the simplest life forms remain a significant challenge to explain through radiation-based mechanisms alone.

13. Thermodynamics-based Proposals

Claim: Thermodynamics-based Proposals

1. Self-organization through dissipative structures: Proposal: Life emerged as a dissipative structure to more efficiently dissipate energy gradients.
2. Thermal gradients as energy sources: Proposal: Temperature differences, such as those found in hydrothermal vents, could drive early metabolic reactions.
3. Entropy-driven self-assembly: Proposal: The formation of complex structures could be driven by entropy increases in the surrounding environment.
4. Non-equilibrium thermodynamics: Proposal: Life originated in systems far from thermodynamic equilibrium, allowing for the emergence of complex structures.
5. Maximum entropy production principle: Proposal: Life emerged as a way to maximize the rate of entropy production in a given environment.
6. Thermodynamic efficiency and natural selection: Proposal: Early chemical systems that were more thermodynamically efficient were naturally selected, leading to life.
7. Free energy transduction: Proposal: The ability to couple exergonic and endergonic reactions was key to the origin of life.

Response:

1. Lack of specificity: These proposals don't explain how general thermodynamic principles could lead to the specific molecular structures and information content found in life.
2. Information problem: Thermodynamic theories struggle to explain the origin and preservation of genetic information, which is crucial for life.
3. Complexity issue: While these proposals might explain simple self-organization, they don't account for the immense complexity of even the most basic living systems.
4. Catalysis unexplained: These theories don't address the origin of the specific catalysts (enzymes) needed for life's chemical reactions.
5. Selective processes unclear: It's not evident how thermodynamic principles alone could lead to the selective processes required for evolution.
6. Cellular organization: Thermodynamic proposals struggle to explain the emergence of cellular structure and compartmentalization.
7. Metabolic pathways: These theories don't adequately explain the origin of complex, interconnected metabolic pathways.
8. Replication mechanisms: The emergence of self-replication, a key characteristic of life, is not clearly explained by thermodynamic principles alone.
9. Time scale problem: Many of these processes would occur too slowly to be relevant on geological time scales without highly specific catalysts.
10. Experimental limitations: Laboratory demonstrations of these principles often use conditions or materials unlikely to have existed in the prebiotic world.
11. Transition to autonomy: These proposals don't clearly explain how thermodynamically driven systems could transition to the autonomous, self-maintaining systems characteristic of life.
12. Genetic takeover unexplained: They fail to address how a system based purely on thermodynamics could transition to one controlled by genetic information.
13. Homochirality problem: Thermodynamic theories struggle to explain the origin of homochirality in biological molecules.
14. Specificity of interactions: These proposals don't account for the highly specific molecular interactions required for life processes.
15. Energy coupling mechanisms: They don't adequately explain the origin of sophisticated energy coupling mechanisms found in all living systems.

While thermodynamic principles undoubtedly play a crucial role in living systems, they alone are insufficient to explain the origin of life. The emergence of life requires not just energy flow and self-organization, but also information storage, replication, and the ability to evolve. Thermodynamic proposals, while offering insights into some aspects of life's operations, fall short of providing a comprehensive explanation for how life could have originated from non-living matter.

13. Various Other Proposals

Claim: Equilibrium-based Proposals

1. Chemical equilibrium in primordial soup: Proposal: Life emerged from a complex mixture of organic compounds in chemical equilibrium.
2. Steady-state systems: Proposal: Early proto-life existed in a steady state, with inputs and outputs balanced.
3. Equilibrium fluctuations: Proposal: Small, random fluctuations around equilibrium led to the emergence of self-replicating systems.
4. Quasi-equilibrium polymerization: Proposal: The formation of early biopolymers occurred under near-equilibrium conditions.
5. Equilibrium self-assembly: Proposal: Complex structures like protocells self-assembled under equilibrium conditions.
6. Thermodynamic equilibrium as a selection pressure: Proposal: Systems that could maintain internal equilibrium while external conditions changed were selected for.

Response:

1. Violation of thermodynamic principles: Life is fundamentally a non-equilibrium phenomenon. Equilibrium systems lack the energy flow necessary for life's processes.
2. Lack of energy for biosynthesis: Equilibrium conditions don't provide the energy needed to drive the synthesis of complex biomolecules.
3. No mechanism for information increase: Equilibrium systems can't explain the origin and increase of genetic information, crucial for life and evolution.
4. Inability to perform work: Living systems must perform work to maintain themselves, which is impossible in true equilibrium.
5. No driving force for self-organization: Equilibrium lacks the thermodynamic driving forces needed for the self-organization of complex structures.
6. Conflict with observed prebiotic chemistry: Most prebiotic chemistry experiments require energy input and non-equilibrium conditions to produce biologically relevant molecules.
7. Incompatibility with metabolism: Metabolic pathways require constant energy input and are inherently non-equilibrium processes.
8. No explanation for cellular compartmentalization: The formation and maintenance of cell-like structures require energy input, contradicting equilibrium conditions.
9. Lack of selectivity: Equilibrium conditions don't provide a mechanism for selecting specific molecules or reactions over others.
10. Inconsistency with the RNA world hypothesis: The formation and function of catalytic RNA molecules, often proposed as precursors to life, require non-equilibrium conditions.
11. Contradiction with the second law of thermodynamics: The increase in order and complexity associated with life seems to contradict the second law under equilibrium conditions.
12. No mechanism for adaptation: Equilibrium systems can't explain how early life could have adapted to changing environmental conditions.
13. Inconsistency with observed life: All known life forms operate far from equilibrium, making equilibrium-based origins unlikely.
14. Lack of experimental support: Laboratory experiments have failed to demonstrate the emergence of life-like properties under equilibrium conditions.
15. Time scale problem: Any fluctuations around equilibrium would be too small and short-lived to allow for the emergence of complex, life-like systems.

Equilibrium-based scenarios for the origin of life are fundamentally flawed. Life is an inherently non-equilibrium phenomenon, requiring constant energy input and material flow. While certain aspects of living systems may approach steady states, true equilibrium is incompatible with the dynamic, self-organizing, and evolving nature of life. The origin of life almost certainly required far-from-equilibrium conditions to provide the necessary energy and driving forces for the emergence of complex, self-replicating systems.

Claim: The RNA World Hypothesis
Proposal: RNA molecules served as both the genetic material and catalysts for early life, before the evolution of DNA and proteins.

Response:
1. RNA synthesis problem: Nucleotides are difficult to synthesize under prebiotic conditions.
2. Chirality issue: RNA requires homochiral sugars, which are unlikely to form spontaneously.
3. Instability: RNA is unstable and degrades quickly, especially in the conditions of early Earth.
4. Catalytic inefficiency: RNA enzymes (ribozymes) are generally less efficient than protein enzymes.
5. Information paradox: Complex RNA needed for life requires even more complex systems to produce it.

Claim: The Lipid World Hypothesis
Proposal: Self-replicating lipid vesicles were the first step towards cellular life.

Response:
1. Lack of information: Lipids alone cannot store or transmit genetic information.
2. Limited functionality: Lipid-based systems lack the catalytic versatility needed for metabolism.
3. Replication fidelity: Lipid replication lacks the accuracy needed for Darwinian evolution.
4. Energy requirements: Formation of complex lipids requires energy input and catalysts.
5. Transition problem: No clear path from lipid-based to nucleic acid-based systems.

Claim: The Iron-Sulfur World Hypothesis
Proposal: Life began in iron and sulfur-rich environments, like hydrothermal vents, with metal sulfides as catalysts.

Response:
1. Limited chemistry: The range of reactions possible is too narrow for complex life.
2. Extreme conditions: High temperatures and pressures can degrade organic molecules.
3. Concentration problem: Dilution in the ocean makes it difficult to achieve necessary concentrations.
4. Energy coupling: No clear mechanism for coupling geochemical energy to biochemical reactions.
5. Transition issue: Difficulty in explaining the move from mineral-based to organic-based life.

Claim: The Zinc World Hypothesis
Proposal: Zinc sulfide in shallow waters acted as a photocatalyst for carbon fixation and the synthesis of biomolecules.

Response:
1. Availability: Zinc sulfide deposits may not have been widespread enough.
2. Efficiency: Photocatalysis by ZnS is not efficient enough for significant organic synthesis.
3. Specificity: Lacks explanation for the specific molecules needed for life.
4. Energy storage: No clear mechanism for storing the captured light energy.
5. Evolutionary pathway: Doesn't address the transition to more complex biological systems.

Claim: The PAH World Hypothesis
Proposal: Polycyclic aromatic hydrocarbons (PAHs) served as templates for early replication and metabolism.

Response:
1. Limited information: PAHs lack the information-carrying capacity of nucleic acids.
2. Toxicity: Many PAHs are toxic to living systems.
3. Specificity: PAHs don't explain the origin of specific biomolecules.
4. Metabolic limitations: PAHs don't provide a clear path to complex metabolism.
5. Transition problem: No clear evolution from PAH-based to nucleic acid-based systems.

Claim: The Formose Reaction World
Proposal: The formose reaction, which produces sugars from formaldehyde, was key to early prebiotic chemistry.

Response:
1. Lack of selectivity: The reaction produces a complex mixture of sugars, not just those used in biology.
2. Inefficiency: The reaction has low yields of biologically relevant sugars.
3. Side reactions: Destructive side reactions often dominate.
4. Chirality problem: Doesn't explain the homochirality of biological sugars.
5. Limited scope: Focuses only on sugar synthesis, ignoring other crucial biomolecules.

Claim: The Thioester World Hypothesis
Proposal: Thioesters served as the primary energy currency before the advent of ATP.

Response:
1. Stability issues: Thioesters are unstable in aqueous environments.
2. Synthesis problem: Prebiotic synthesis of thioesters is challenging.
3. Limited versatility: Thioesters are less versatile than ATP for energy transfer.
4. Transition issue: No clear path from thioester-based to ATP-based metabolism.
5. Specificity: Doesn't explain the origin of other specific biomolecules.

Claim: The Peptide-RNA World
Proposal: Short peptides and RNA molecules coevolved, leading to more complex life.

Response:
1. Synthesis problem: Both peptides and RNA are difficult to synthesize prebiotically.
2. Chicken-and-egg problem: Each component seems to require the other to function effectively.
3. Catalytic limitations: Short peptides have limited catalytic abilities.
4. Stability issues: Both peptides and RNA are unstable under early Earth conditions.
5. Complexity hurdle: Doesn't fully address how complex, specific sequences arose.

Claim: The Autocatalytic Sets Theory
Proposal: Networks of mutually catalytic molecules could have initiated life.

Response:
1. Specificity problem: Autocatalytic sets tend to produce a wide range of molecules, not just those needed for life.
2. Information storage: Lacks a clear mechanism for storing and transmitting genetic information.
3. Evolution mechanism: Difficult to explain how such sets could evolve into more complex systems.
4. Experimental limitations: Difficult to demonstrate emergence of complex autocatalytic sets under prebiotic conditions.
5. Energy requirements: Doesn't address the energy needs of maintaining and replicating the set.

Claim: The Gard Model (Graded Autocatalysis Replication Domain)
Proposal: Compositional information in molecular assemblies could have preceded sequence-based information.

Response:
1. Information limitations: Compositional information is less specific than sequence information.
2. Evolvability: Limited capacity for evolution compared to nucleic acid-based systems.
3. Catalytic limitations: Doesn't explain the origin of efficient, specific catalysts.
4. Transition problem: No clear path to nucleic acid-based life.
5. Complexity issue: Difficulty in achieving the complexity needed for life.

These proposals, like the others, face significant challenges in explaining the origin of life. They often address only part of the problem, lack experimental support, or fail to provide a clear path to the complex, information-rich systems characteristic of life as we know it. The origin of life remains a formidable scientific challenge, with no current hypothesis fully explaining all aspects of the transition from non-living to living systems.

Claim: Multiple mechanisms explain the origin of life
Proposal: The combined action of chemoselectivity, simple energy sources, gradual evolution of energy systems, and the contact surface hypothesis, working together over long periods, can explain the emergence of life.

Response:
1. Compounding improbabilities: Combining unlikely events reduces overall likelihood.
2. Lack of coordination: No mechanism for processes to coordinate towards a common goal.
3. Insufficient complexity: Can't account for the complexity of even the simplest living systems.
4. Information problem: Fails to explain the origin of genetic code or information in DNA/RNA.
5. Integration issue: Doesn't address how cellular components became integrated.
6. Thermodynamic challenges: Doesn't overcome barriers to spontaneous organization.
7. Chicken-and-egg dilemmas: Many processes require pre-existing complex structures.
8. Lack of empirical evidence: No demonstration of these processes leading to life.

Missing ingredient: A guiding intelligent agency with foresight

Importance of intelligent agency

1. Purposeful direction: Guides processes towards specific goals.
2. Information input: Provides information for complex, specified systems.
3. Problem-solving: Anticipates and solves problems that stymie undirected processes.
4. Integration of systems: Allows coordinated development of interdependent systems.
5. Overcoming barriers: Devises strategies to overcome thermodynamic and chemical barriers.
6. Efficient resource use: Utilizes resources more efficiently than random processes.
7. Complex specification: Explains highly specific arrangements in biological systems.
8. Irreducible complexity: Accounts for systems exhibiting irreducible complexity.

Conclusion: Combining mechanisms fails to address fundamental issues in explaining life's origin. The complexity, specificity, and integrated functionality of living systems suggest the involvement of an intelligent agent with foresight.

14. Concluding Remarks

The origin of life remains one of the most challenging problems in science, sitting at the intersection of chemistry, biology, geology, and physics. Our review of various naturalistic proposals for the origin of life reveals significant challenges in explaining the emergence of complex, interdependent biological systems through undirected processes alone. While hypotheses such as chemoselectivity, primitive energy sources, and surface-mediated reactions offer thought-provoking and interesting possibilities, they struggle to fully account for the complexity, specificity, and information content observed in even the simplest living systems. The origin of sophisticated energy production systems, like ATP synthesis, poses particularly difficult questions for non-intelligent explanations. The alternative perspective, that of intelligent causation, addresses some of these challenges by invoking a source of complex specified information. However, this approach raises its own set of questions and often falls outside traditional scientific methodologies. As we continue to explore the origin of life, it is crucial to remain open to multiple explanatory frameworks while rigorously testing all hypotheses against empirical evidence. Future research should focus on bridging the gap between simple chemical systems and the complexity of living organisms, potentially exploring new paradigms that transcend the current status quo based on purely naturalistic mechanisms, and extending the possibility of intelligence-based explanations. The quest to understand life's origins not only drives scientific progress but also touches on fundamental questions about our place in the universe. As such, it remains a vital and exciting area of research that will likely continue to challenge and inspire scientists for generations to come.

References: 

1. Ryan, A., Shenvi, D.P., O'Malley, P.S., Baran. (2009). Chemoselectivity: The Mother of Invention in Total Synthesis. ChemInform, 40(34). Link. (This paper discusses the importance of chemoselectivity in total synthesis, highlighting its role in developing new synthetic strategies.)

2. Nicholas, A., McGrath, Ronald, T., Raines. (2011). Chemoselectivity in chemical biology: acyl transfer reactions with sulfur and selenium. Accounts of Chemical Research, 44(9), 752-761. Link. (This review explores chemoselective acyl transfer reactions involving sulfur and selenium, emphasizing their applications in chemical biology.)

3. Daniel, Milshteyn, George, Cooper, David, W., Deamer. (2019). Chemiosmotic energy for primitive cellular life: Proton gradients are generated across lipid membranes by redox reactions coupled to meteoritic quinones. Scientific Reports, 9, 12447. Link. (This study investigates how proton gradients, essential for early cellular life, could have been generated through redox reactions involving meteoritic quinones.)

4. Nicholas, A., McGrath, Ronald, T., Raines. (2011). Chemoselectivity in chemical biology: acyl transfer reactions with sulfur and selenium. Accounts of Chemical Research, 44(9), 752-761. Link. (This review explores chemoselective acyl transfer reactions involving sulfur and selenium, emphasizing their applications in chemical biology.)

5. Daniel, Milshteyn, George, Cooper, David, W., Deamer. (2019). Chemiosmotic energy for primitive cellular life: Proton gradients are generated across lipid membranes by redox reactions coupled to meteoritic quinones. Scientific Reports, 9, 12447. Link. (This study investigates how proton gradients, essential for early cellular life, could have been generated through redox reactions involving meteoritic quinones.)

6. Powner, M.W., Sutherland, J.D. (2023). Nucleotide Photochemistry on the Early Earth. ChemSystemsChem, 5(2), e202200050. Link. (This paper explores the potential role of photochemistry in the formation of nucleotides on the early Earth.)

7. Koch, A.L., Schmidt, T.M. (1991). The first cellular bioenergetic process: primitive generation of a proton-motive force. Journal of Molecular Evolution, 33, 297–304. Link. (This article proposes a model for the primitive generation of proton-motive force in early cellular life.)

8. Boiteau, L., Pascal, R. (2011). Energy sources, self-organization, and the origin of life. Origins of Life and Evolution of Biospheres, 41, 23–33. Link. (This paper discusses various energy sources and self-organization processes that may have been crucial in the origin of life.)

9. Baltscheffsky, H. (1989). Early evolution of bioenergetic reactions. Origins of Life and Evolution of Biospheres, 19, 465–470. Link. (This article explores the early evolution of bioenergetic reactions in primitive life forms.)

10. Berry, S. (2002). The chemical basis of membrane bioenergetics. Journal of Molecular Evolution, 54, 595–613. Link. (This paper discusses the chemical principles underlying membrane bioenergetics in living systems.)

11. Usher, D.A. (1977). Early chemical evolution of nucleic acids: a theoretical model. Science, 196(4290), 311-313. Link. (This article proposes a theoretical model for the early chemical evolution of nucleic acids.)

12. Amend, J.P., McCollom, T.M. (2009). Energetics of Biomolecule Synthesis on Early Earth. ACS Symposium Series, 1025, 63-94. Link. (This chapter examines the energetics of biomolecule synthesis in the context of early Earth conditions.)

13. Aleksandrova, M., Sousa, F.L. (2022). Bioenergetics of early life. EMBO Reports, 23( 8 ), e55475. Link. (This review discusses the bioenergetic processes that may have been important in early life forms.)

14. Russell, M.J., Arndt, N.T. (2005). The onset and early evolution of life. Geological Society of America Memoirs, 198, 1-32. Link. (This chapter provides an overview of theories and evidence related to the onset and early evolution of life.)

15. Sousa, F.L., et al. (2013). Early bioenergetic evolution. Philosophical Transactions of the Royal Society B, 368(1622), 20130088. Link. (This paper discusses the early evolution of bioenergetic processes in living systems.)

16. Russell, M.J., Hall, A.J. (2009). The hydrothermal source of energy and materials at the origin of life. In: Zaikowski, L., Friedrich, J.M., Seidel, S.R. (eds) Chemical Evolution II: From the Origins of Life to Modern Society. ACS Symposium Series, 1025, 45-62. Link. (This chapter explores the potential role of hydrothermal systems in providing energy and materials for the origin of life.)

17. Fitz, D., Reiner, H., Rode, B.M. (2007). Chemical evolution toward the origin of life. Pure and Applied Chemistry, 79(12), 2101-2117. Link. (This paper provides an overview of chemical evolution processes that may have led to the origin of life.)

18. Milshteyn, D., Damer, B., Havig, J., Deamer, D. (2018). Amphiphilic Compounds Assemble into Membranous Vesicles in Hydrothermal Hot Spring Water but Not in Seawater. Life, 8(2), 11. Link. (This study examines the formation of membranous vesicles in hydrothermal hot spring water, suggesting potential environments for the origin of cellular life.)

19. Baltscheffsky, H., Baltscheffsky, M. (1986). Light and inorganic pyrophosphate as possible key components in the development of the earliest bioenergetic systems. Origins of Life and Evolution of the Biosphere, 16, 377–378. Link. (This paper proposes light and inorganic pyrophosphate as potential key components in early bioenergetic systems.)

20. Xie, P. (2020). The ATP Hypothesis Discovers the Missing "Matchmaker" between Proteins and Nucleic Acids. Preprints, 2020090233. Link. (This preprint proposes a new hypothesis for the origin of the genetic code, focusing on ATP as a crucial intermediary.)

21. Muller, A.W.J. (2005). Thermosynthesis as energy source for the RNA World: a model for the bioenergetics of the origin of life. Biosystems, 82(1), 93-102. Link. (This paper proposes thermosynthesis as a potential energy source for early life in the RNA World scenario.)

22. Skulachev, V.P. (1991). Chapter 2 Chemiosmotic systems and the basic principles of cell energetics. New Comprehensive Biochemistry, 22, 37-73. Link. (This book chapter discusses the fundamental principles of chemiosmotic systems in cell energetics.)

23. Kovalenko, S.P. (2020). Physicochemical Processes That Probably Originated Life. Russian Journal of Bioorganic Chemistry, 46, 847–858. Link. (This paper reviews physicochemical processes that may have been involved in the origin of life.)

24. Akbari, A., Arrieta, J., Arre, E., Olsson, P. (2021). Origin of electroneutrality in living system. bioRxiv. Link. (This preprint explores the origin of electroneutrality in living systems, a fundamental property of cells.)

25. Arrhenius, G. (1998). Prebiotic Evolution of Nitrogen Compounds. In: Brack, A. (eds) The Molecular Origins of Life. Cambridge University Press, Cambridge. Link. (This chapter discusses the prebiotic evolution of nitrogen compounds, which are crucial for the formation of biomolecules.)

26. Agarwal, B. (2013). Revisiting the Chemiosmotic Theory: Coupled Transport of Anion and Proton for ATP Synthesis. Journal of Theoretical Biology, 338, 20-29. Link. (This paper proposes a revision to the chemiosmotic theory, suggesting a coupled transport mechanism for ATP synthesis.)

27. Mauzerall, D. (1992). Light, Iron, Sam Granick and the Origin of Life. Photosynthesis Research, 33, 163–170. Link. (This article discusses the potential role of light and iron in the origin of life, drawing on the work of Sam Granick.)

28. Kaback, H.R. (1985). Studies of a Biological Energy Transducer. In: Martonosi A.N. (eds) The Enzymes of Biological Membranes. Springer, Boston, MA. Link. (This book chapter explores biological energy transducers, which are crucial for understanding early bioenergetics.)

29. Elshimy, M., El-Asar, K.M. (2020). Carbon footprint, renewable energy, non-renewable energy, and livestock: testing the environmental Kuznets curve hypothesis for the Arab world. Environment, Development and Sustainability, 23, 7995–8012. Link. (While not directly related to origin of life, this paper discusses energy sources and environmental impacts, which may have implications for early Earth conditions.)

30. Lu, A., Li, Y., Ding, H. et al. (2014). Mineral photoelectrons and their implications for the origin and early evolution of life on Earth. Science China Earth Sciences, 57, 897–902. Link. (This paper explores the potential role of mineral photoelectrons in the origin and early evolution of life.)

31. Parkinson, B.A., Spitler, M.T. (2013). The Potential Contribution of Photoelectrochemistry in the Global Energy Future. In: Giménez, S., Bisquert, J. (eds) Photoelectrochemical Solar Fuel Production. Springer, Cham. Link. (While focused on future energy solutions, this chapter discusses photoelectrochemistry, which may have relevance to prebiotic chemistry.)

32. Ryan, A., Shenvi, D.P., O'Malley, P.S., Baran. (2009). Chemoselectivity: The Mother of Invention in Total Synthesis. ChemInform, 40(34). Link. (This paper discusses the importance of chemoselectivity in total synthesis, highlighting its role in developing new synthetic strategies.)

A Critical Analysis of Proposed Mechanisms for the Origin of Life: Challenges to Naturalistic Explanations

This paper critically examines various naturalistic explanations for the origin of life, highlighting key challenges and limitations in current theories. It argues that while significant progress has been made in understanding potential chemical pathways to life, major obstacles remain in explaining the emergence of complex, self-replicating biological systems without invoking improbable chance events or assuming capabilities that weren't present before life existed.

1. Introduction to the Origin of Life Problem

The question of how life originated on Earth is one of the most fundamental and challenging problems in science. It sits at the intersection of chemistry, biology, physics, and even philosophy. This paper will examine various proposed mechanisms for the origin of life, focusing on the challenges these naturalistic explanations face.

2. The Distinction Between Abiogenesis and Evolution

Before delving into specific theories, it's crucial to clarify the distinction between abiogenesis (the origin of life) and biological evolution.

Rational Wiki states: "Let's get something abundantly clear: abiogenesis and evolution are two completely different things. The theory of evolution says absolutely nothing about the origin of life. It merely describes the processes that take place once life has started."

This quote highlights a crucial point often misunderstood in discussions about life's origins. Evolution by natural selection requires pre-existing self-replicating entities. It cannot explain how the first such entities came into existence.

Paul Davies: "Darwin gave us a theory of evolution about how life has evolved but he didn't want to tangle with how you go from non-life to life and for me, that's a much bigger step."

Eugene V. Koonin: "The emergence of the first replicator system, which represented the 'Darwinian breakthrough,' was inevitably preceded by a succession of complex, difficult steps for which biological evolutionary mechanisms were not accessible."

These quotes reinforce the key point that the origin of life (abiogenesis) and the subsequent evolution of life are separate scientific questions that require different explanatory frameworks. This distinction is crucial for understanding the specific challenges faced by origin of life research.

I apologize for the misunderstanding. Let me provide a more focused response on chemical evolution:

2.1. Challenges in Understanding Chemical Evolution

Claim: Chemical evolution explains the origin of complex biomolecules and early metabolic processes through a series of chemical reactions occurring on the early Earth.

Chemical evolution refers to the idea that complex organic molecules necessary for life arose from simpler inorganic compounds through chemical reactions driven by energy sources available on the primitive Earth, such as UV radiation, lightning, or hydrothermal activity. This process is proposed to have occurred before the emergence of biological evolution and is considered a crucial step in the origin of life.

Response: this concept faces several significant challenges and open questions:

1. Prebiotic Synthesis of Complex Molecules:
- How did complex organic molecules like nucleotides and amino acids form under prebiotic conditions?
- What was the source of chemical precursors in sufficient concentrations?
- How were these molecules protected from degradation in harsh early Earth environments?

2. Chirality Problem:
- How did the homochirality observed in biological molecules (e.g., L-amino acids, D-sugars) arise from presumed racemic mixtures?
- What mechanisms could have led to the selection and amplification of specific chiral forms?

3. Concentration and Polymerization:
- How did simple monomers concentrate sufficiently to form polymers like proteins and nucleic acids?
- What environmental conditions or mechanisms facilitated the polymerization of these molecules?

4. Self-Organization and Complexity:
- How did simple chemical systems transition to more complex, self-organizing structures?
- What drove the emergence of primitive metabolic cycles from random chemical reactions?

5. Energy Sources and Coupling:
- What were the primary energy sources driving prebiotic chemical reactions?
- How did early chemical systems develop mechanisms to capture and utilize this energy efficiently?

6. Selective Pressures:
- In the absence of biological evolution, what factors determined which chemical pathways persisted and complexified?
- How did functional chemical systems emerge and outcompete non-functional ones?

7. Environmental Constraints:
- How did early Earth conditions (temperature, pH, radiation levels) influence chemical evolution?
- What role did specific environments (e.g., hydrothermal vents, mineral surfaces) play in facilitating key reactions?

8. Transition to Biological Systems:
- How did chemically evolving systems transition to self-replicating, living entities?
- What was the nature of the first self-replicating molecules or systems?

These challenges highlight the significant gaps in our understanding of chemical evolution. The complexity of the proposed processes, the lack of direct evidence from the early Earth, and the difficulty in recreating prebiotic conditions in laboratory settings all contribute to the ongoing scientific debate surrounding this concept.

3. The Chemical Nature of the Origin of Life Problem

Having established the distinction between abiogenesis and evolution, we can now focus on the chemical nature of the origin of life problem.

Addy Pross (2012) states: "Darwinian theory is a biological theory and therefore deals with biological systems, whereas the origin of life problem is a chemical problem, and chemical problems are best solved with chemical (and physical) theories. Attempting to explain chemical phenomena with biological concepts is methodologically problematic."

This quote emphasizes that the origin of life is fundamentally a question of chemistry, not biology. We need to understand how complex, self-replicating chemical systems could arise from simpler precursors without invoking biological mechanisms that didn't yet exist.

The chemical nature of the problem leads us to examine various proposed mechanisms, each facing its own set of challenges.

4. Comprehensive Mechanisms to Explain the Origin of Life

1. Chemoselectivity - The acting agent is the chemical properties and reactivity of molecules, influenced by factors like structure, reaction conditions, and catalysts.
Challenge: While chemoselectivity can explain the preferential formation of certain molecules, it lacks the specificity required to account for the precise molecular structures found in living systems. It also doesn't provide a mechanism for the continuous improvement and complexification of molecular systems.

2. Early Energy Sources - The acting agent is the inherent chemical properties and reactions of compounds and systems like pyrophosphate, iron-sulfur, and RNA World.
Challenge: While these sources provide potential energy for prebiotic reactions, they don't explain how this energy was harnessed and directed towards the formation of complex, self-replicating systems.

3. ATP Synthesis Evolution - The acting agent is the complex, interdependent systems like ATP synthase and chemiosmotic gradients.
Challenge: The evolution of ATP synthesis presents a chicken-and-egg problem. The complex machinery required for ATP synthesis seems to require the energy provided by ATP itself, making its origin difficult to explain.

4. Contact Surface Hypothesis - The acting agent is the physical and chemical properties of interfaces between different phases (liquid-solid, liquid-gas).
Challenge: While interfaces can concentrate molecules and catalyze certain reactions, they don't provide a mechanism for the emergence of complex, self-replicating systems.

5. Chance - Considers the possibility that life emerged through highly improbable random events.
Challenge: As Gennady Shkliarevsky (2021) points out: "invoking chance even once is highly problematic; invoking it twice to explain the same phenomenon makes an explanation very questionable." The extreme improbability of life arising by chance makes this an unsatisfying explanation.

6. Physical Necessity - Argues that life is a result of inevitable physical and chemical laws.
Challenge: While physical laws certainly constrain how molecules and chemical elements interact, they aren't sufficient to explain the specific complexity of life. As William Dembski (2002) argues: "The problem is that natural mechanisms are too unspecific to determine any particular outcome."

7. Natural Selection - Applies the principles of natural selection to prebiotic chemistry, suggesting that advantageous molecular traits were preserved.
Challenge: Natural selection as we understand it in biology requires self-replication and heredity. These didn't exist before the first life forms, so we can't invoke natural selection to explain their origin.

8. Radiation-Driven Synthesis - The acting agent is various forms of radiation (UV, ionizing, cosmic) and the chemical reactions they can induce.
Challenge: While radiation can drive certain chemical reactions, it can also break down complex molecules. Explaining how radiation could lead to the build-up of complex biological molecules remains a challenge.

9. Thermodynamics-Based Proposals - The acting agent is the principles of thermodynamics, including energy gradients, entropy, and non-equilibrium conditions.
Challenge: While thermodynamics can explain how energy flows might have driven certain processes, it doesn't account for the specific information content of biological systems.

10. Hydrothermal Systems - Examines the role of hydrothermal vents and similar environments in providing energy and materials for the origin of life.
Challenge: While these environments provide interesting conditions for prebiotic chemistry, they don't fully explain the transition from simple chemical reactions to self-replicating systems.

5. The Challenge of Prebiotic Chemistry

One of the fundamental challenges in origin of life research is reproducing the conditions and reactions that could have led to the first life forms. This is exemplified by the challenges faced in prebiotic chemistry experiments.

Alan W. Schwartz (2007) points out: "Although the Miller–Urey reaction produces an impressive set of amino acids and other biologically significant compounds, a large fraction of the starting material goes into a brown, tar-like residue that remains uncharacterized; i.e., gunk."

This highlights a significant challenge in origin of life research. While we can produce some biologically relevant molecules under simulated prebiotic conditions, we also get many other products. The challenge is explaining how life-essential molecules could have been selected and concentrated from this complex mixture.

6. The Problem of Chirality

Another significant challenge in explaining the origin of life is the problem of chirality - the fact that life uses only left-handed amino acids and right-handed sugars.

A.G. Cairns-Smith (1985) notes: "It is one of the most singular features of the unity of biochemistry that this mere convention is universal. Where did such agreement come from? You see non-biological processes do not as a rule show any bias one way or the other."

This uniformity is crucial for life's functions, but it's difficult to explain how it could have arisen through non-biological processes. Recent research has proposed several mechanisms for how this chirality might have emerged, including:

1. Influence of circularly polarized light in space
2. Asymmetric adsorption on mineral surfaces
3. Amplification of tiny initial imbalances through autocatalytic reactions

However, a fully satisfactory explanation for the origin of biological homochirality remains elusive.

7. The Absence of Prebiotic Natural Selection

A key challenge in explaining the origin of life is the absence of natural selection before the emergence of self-replicating systems.

Mario Vaneechoutte (2000) argues: "We hypothesize that the origin of life, that is, the origin of the first cell, cannot be explained by natural selection among self-replicating molecules, as is done by the RNA-world hypothesis."

This is a crucial point. Natural selection as we understand it in biology requires self-replication and heredity. These didn't exist before the first life forms, so we can't invoke natural selection to explain their origin.

Iris Fry (2010) analyzed various theories on the origin of life, including RNA-first and metabolism-first hypotheses. She concluded that while none of these paradigms have decisive experimental support, gene-first theories show potential. However, as of her writing, no functioning system of genetic replication had been achieved without the addition of an external protein enzyme.

While significant progress has been made in understanding potential chemical pathways to life, major challenges remain. These include explaining the origin of biological information, the emergence of complex self-replicating systems, and the transition from chemistry to biology.

Current hypotheses, while providing valuable insights, still struggle to fully account for these phenomena without invoking extremely improbable chance events or assuming capabilities (like natural selection) that weren't present before life existed.

Future research directions might include:

1. Further exploration of non-equilibrium thermodynamics in prebiotic systems
2. Investigation of potential autocatalytic networks that could lead to self-replication
3. Examination of the role of information theory in understanding the origin of biological information
4. Development of more sophisticated models of prebiotic chemical evolution

8. Chemoselectivity as an Explanation for the Origin of Life

Claim: Chemoselectivity as an Explanation for the Origin of Life
1. Definition: Chemoselectivity refers to the preferential formation of one chemical product over others in a reaction when multiple outcomes are possible.
2. Application to origin of life: Proposal: Chemoselectivity could have led to the preferential formation of biologically relevant molecules in prebiotic conditions.
3. Mechanism: Based on differences in reactivity between functional groups, influenced by factors like molecular structure, reaction conditions, and catalysts.
4. Timescale: Occurs during individual chemical reactions, typically on very short timescales (microseconds to seconds).
5. Complexity: Involves molecular interactions and reaction kinetics, but not the emergent properties of living systems.

Critical Analysis:
1. Insufficient specificity: While chemoselectivity can explain preferential product formation, it lacks the precision required for the complex molecular structures in biological systems.
2. Absence of evolutionary mechanism: Chemoselectivity provides no inherent mechanism for the continuous improvement and complexification necessary for the emergence of life.
3. Limited complexity generation: Falls short in explaining the formation of information-rich polymers (e.g., DNA, RNA, proteins) crucial for life.
4. Concentration constraints: The dilute nature of prebiotic oceans likely hindered effective chemoselectivity, as demonstrated by Miller-Urey type experiments.
5. Experimental challenges: Reproducing significant chemoselectivity under plausible prebiotic conditions has proven difficult, limiting empirical support.
6. Homochirality puzzle: Fails to adequately account for the uniform chirality observed in biological molecules, a key feature of life.
7. Thermodynamic hurdles: Many essential reactions for life are energetically unfavorable and wouldn't proceed spontaneously, even with chemoselectivity.
8. Competitive side reactions: In a complex prebiotic environment, numerous side reactions would likely interfere with selective processes.
9. Information origin unexplained: Provides no mechanism for the emergence of the genetic code or the information content in nucleic acids.
10. Self-replication gap: Does not address the crucial transition to self-replicating systems, a defining characteristic of life.
11. Temporal scale discrepancy: The rapid nature of chemoselectivity contrasts with the extended timescales likely required for life's origin.
12. Adaptability unexplained: Lacks a framework for explaining how early chemical systems could adapt to environmental changes.
13. Reductionist approach: Oversimplifies the multifaceted challenge of life's origin by focusing solely on chemical preferences.
14. Systems integration problem: Does not account for the integration of various life components (e.g., replication, metabolism, compartmentalization).
15. Scope limitations: At best, explains the formation of simple organic molecules, falling short of elucidating the emergence of life itself.

While chemoselectivity undoubtedly played a role in prebiotic chemistry, it is insufficient as a comprehensive explanation for the origin of life. The process lacks the complexity, specificity, and driving force necessary to account for the emergence of living systems. Chemoselectivity may have contributed to the formation of certain prebiotic molecules, but it fails to address the fundamental challenges of creating complex, self-replicating, information-rich systems characteristic of life. Future research should focus on integrating chemoselectivity with other concepts such as autocatalysis, non-equilibrium thermodynamics, and information theory. Additionally, exploring the potential for chemoselectivity in structured environments (e.g., mineral surfaces, lipid membranes) may yield insights into how this process could have contributed to the emergence of more complex prebiotic systems. Ultimately, a more holistic approach incorporating multiple aspects of chemistry, physics, and proto-biology is needed to adequately address the origin of life problem.

9. Early Energy Sources

Claim: The first proto-cellular systems would not have used ATP.

Response: Pyrophosphate as an early energy currency: Some scientists suggest that pyrophosphate would have preceded ATP as an energy carrier.
Problems:
- The instability of pyrophosphate in water
- Lack of evidence for ancient pyrophosphate-using enzymes
- Difficulty explaining the transition to ATP-based systems

Iron-sulfur world hypothesis:
Proposal: Early metabolism was based on iron-sulfur clusters, with energy derived from redox reactions.
Problems:
- Limited range of reactions possible
- Difficulty in explaining the transition to more complex organic molecules
- Challenges in maintaining the required chemical gradients in early Earth conditions

RNA World hypothesis:
Proposal: RNA served both as genetic material and as catalysts, including for energy transfer.
Problems:
- Instability of RNA in prebiotic conditions
- Difficulty in explaining the synthesis of ribonucleotides
- Lack of efficient RNA-based energy transfer systems

Membrane-based energy systems:
Proposal: Early cells used proton gradients across primitive membranes for energy.
Problems:
- Difficulty in forming stable membranes in prebiotic conditions
- Lack of sophisticated protein machinery for efficient energy transduction
- Challenges in evolving the complex ATP synthase from simpler precursors

Thermal gradients as energy sources:
Proposal: Temperature differences, such as those found in hydrothermal vents, provided energy for early life.
Problems:
- Limited availability of such environments
- Difficulty in harnessing thermal energy without complex molecular machinery
- Challenges in transitioning from thermal to chemical energy systems

Chemiosmotic energy in alkaline hydrothermal vents:
Proposal: pH gradients in these vents could have driven early metabolism.
Problems:
- Limited to specific geological settings
- Difficulty in concentrating and organizing molecules in such environments
- Challenges in evolving more complex energy systems from this starting point

Thioester world hypothesis:
Proposal: Thioesters served as early high-energy compounds before the advent of ATP.
Problems:
- Instability of thioesters in aqueous environments
- Limited range of reactions compared to ATP
- Difficulty explaining the transition to phosphate-based energy currencies

Each of these proposals faces significant challenges in explaining the origin and early origin of life's energy systems. The main overarching problems include:
- Lack of experimental evidence replicating prebiotic conditions
- Difficulty in explaining the transition from simple chemical systems to complex biological ones
- Challenges in maintaining the stability and organization required for early life in harsh prebiotic environments
- The "chicken and egg" problem: many energy systems require complex proteins, which themselves require energy to be synthesized

These issues highlight why the origin of life's energy systems remains one of the most challenging questions in science. Research continues to explore new possibilities and refine existing hypotheses, but a fully satisfactory explanation remains elusive.

Claim: Energy sources for early life: Early life forms would have relied on simpler energy sources available in their environment, such as chemical gradients or geothermal energy.

Response: There are several proposed energy sources and environments that have been suggested for the origin of early life, with hydrothermal vents being a prominent hypothesis. However, there are significant challenges with this and other proposed scenarios:

Hydrothermal Vents: While hydrothermal vents provide chemical energy and minerals, they face several issues as a site for abiogenesis:
1. High temperatures: The extreme heat would rapidly break down any organic molecules formed, including amino acids and nucleotides essential for life.
2. Water problem: The abundance of water inhibits the formation of critical chemical bonds needed to build complex biomolecules. Polymerization reactions that form proteins and nucleic acids produce water as a byproduct, making them thermodynamically unfavorable in aqueous environments.
3. Dilution: The vast ocean volume would dilute any organic compounds formed, making it difficult to achieve concentrations needed for further reactions.
4. Lack of evidence: We do not observe protocells or early life forms developing at hydrothermal vents today, even though the conditions are thought to be similar to early Earth.
5. Instability of key molecules: RNA and DNA are unstable at high temperatures without sophisticated repair mechanisms.

Other Proposed Energy Sources:
UV radiation: While UV light can provide energy for certain reactions, it can also rapidly degrade organic molecules.
Electrical discharges (lightning): Similar issues with degradation of formed molecules and lack of consistent energy supply.
Radioactivity: Proposed as an energy source, but likely insufficient and would cause mutations in early replicators.

10. The Origin of ATP Synthesis

Claim: ATP and protein function: While it's true that many modern proteins require ATP to function, this wasn't necessarily the case for early, simpler biomolecules.

Response: The claim that early, simpler biomolecules didn't require ATP to function is not well-supported by our current understanding of biochemistry and the origins of life.

The fundamental role of ATP: ATP (adenosine triphosphate) is not just a simple energy source; it's a fundamental component of cellular metabolism. It serves as a universal energy currency in all known living organisms. The ubiquity of ATP across all domains of life suggests that it was likely present and crucial even in the earliest forms of life.

Chemical properties of ATP: ATP's chemical structure makes it uniquely suited for energy transfer in biological systems. Its high-energy phosphate bonds allow for efficient energy storage and release. It's unlikely that early life forms could have functioned effectively without a similar energy transfer mechanism.

Metabolic complexity: Even the simplest known organisms today have complex metabolic pathways that depend on ATP. These pathways are so fundamental and conserved across species that they likely evolved very early in the history of life. It's difficult to conceive of a functioning metabolism without an ATP-like molecule.

Chicken-and-egg problem: Many of the processes required to synthesize proteins and other complex biomolecules require energy input, often in the form of ATP. Without ATP or a similar energy-rich molecule, it's unclear how these essential biomolecules could have been synthesized in the first place.

RNA World hypothesis: Many scientists believe that RNA preceded proteins in the evolution of life (the RNA World hypothesis). RNA can catalyze chemical reactions and store genetic information, but these functions often require energy input. ATP or similar molecules would have been necessary even in an RNA-based proto-life.

Evolutionary conservation: The fact that ATP is used so universally in modern organisms suggests that it was likely present very early in the evolution of life. If early life forms had used a different energy system, we would expect to see more diversity in energy currencies across different lineages.

It's highly unlikely that functional proteins or other complex biomolecules could have evolved without an ATP-like energy currency. The transition from simple chemical systems to living organisms almost certainly required a versatile, high-energy molecule like ATP.

Claim: ATP synthesis: Modern ATP synthesis primarily occurs through phosphorylation, often driven by chemiosmotic gradients (as in ATP synthase). This is indeed a sophisticated system that evolved over time.

Response: ATP synthesis is a fundamental process for life, involving complex systems like ATP synthase and chemiosmotic gradients. This system presents an origin of life problem, not an evolutionary one, as it must have existed before life began. Therefore, evolutionary mechanisms cannot explain its origin. ATP synthase and the proton gradient form an irreducibly complex system. Both components are necessary for function, and neither has a useful purpose on its own. The ATP synthase itself is irreducibly complex, consisting of multiple subunits that must be precisely arranged to function. The system exhibits both specified complexity (in its information content) and irreducible complexity (in its structure and function). Our experience suggests that such complex, interdependent systems are typically the product of intelligent design rather than random processes.

Given that ATP synthesis is universal in life and essential for its origin, its complexity poses a significant challenge to naturalistic explanations of life's beginnings. The argument concludes that the existence of ATP synthase and related systems is evidence for an intelligent creator rather than the result of unguided processes. The complexity and interdependence of ATP synthesis systems are better explained by intelligent design than by chance or evolutionary processes, particularly given their necessity at life's very inception.

Claim: Early life existed in an anaerobic environment, and fermentation or similar processes might have been crucial early energy-generating pathways.

Response:
1. Energy inefficiency: Fermentation yields only about 2 ATP molecules per glucose, compared to up to 38 in aerobic respiration. This low energy yield would severely limit the metabolic capabilities and complexity of early life forms.
2. Limited substrate availability: Fermentation requires organic molecules as substrates. In the prebiotic world, the availability of complex organic molecules would have been limited, making it difficult for early life to sustain itself solely through fermentative processes.
3. Waste product accumulation: Fermentation produces waste products like lactic acid or ethanol, which can be toxic in high concentrations. Without efficient means of waste removal, early organisms relying solely on fermentation would quickly poison their environment.
4. Lack of metabolic flexibility: Fermentation is a relatively simple process compared to complex electron transport chains. This lack of complexity would limit the evolutionary potential and adaptability of early life forms.
5. Incompatibility with RNA World hypothesis: Many origins of life theories, including the RNA World hypothesis, require more energy-rich environments than fermentation alone could provide. The synthesis and maintenance of complex molecules like RNA would likely require more efficient energy generation.
6. Absence of precursor molecules: The enzymes and pathways required for fermentation, while simpler than those for aerobic respiration, are still complex molecular machines. It's unclear how these could have arisen without pre-existing energy generation systems.
7. Geological evidence: While early Earth was indeed largely anaerobic, there's evidence of other potential energy sources like chemolithotrophy that could have been more plausible for early life.
8. Universal conservation of ATP synthase: The fact that ATP synthase is universally conserved across all domains of life suggests that it, or a similar system, was present very early in life's history, predating the divergence of major lineages.
9. Thermodynamic constraints: Fermentation alone might not provide sufficient energy to overcome the thermodynamic barriers involved in self-organization and self-replication, which are crucial for the emergence of life.
10. Lack of evolutionary trajectory: There's no clear evolutionary path from simple fermentative processes to the complex, chemiosmotic energy generation systems seen in all modern life forms.

Claim: Energy in abiogenesis: The origin of life (abiogenesis) likely involved simpler energy transduction mechanisms before the evolution of complex systems like ATP synthase or fermentation pathways.

Response: Here's an explanation of the proposed simpler energy transduction mechanisms for abiogenesis and why they fall short in explanatory power:

1. Proton gradients across mineral surfaces:
Proposal: Early proto-cells could have used naturally occurring proton gradients across mineral surfaces (like those in hydrothermal vents) for energy.
Shortcomings: 
- Lacks a mechanism for harnessing this energy for useful cellular work.
- Doesn't explain how cells transitioned to generating their own gradients.
- Doesn't account for the origin of complex biomolecules needed to utilize such gradients.

2. Chemiosmosis using simpler molecules:
Proposal: Primitive versions of chemiosmosis using simpler molecules than ATP.
Shortcomings:
- Still requires complex molecular machinery to couple ion gradients to chemical reactions.
- Doesn't explain the origin of the necessary semi-permeable membranes.
- Fails to address how the transition to ATP-based systems occurred.

3. Thioester world hypothesis:
Proposal: Thioesters as primitive energy currency before ATP.
Shortcomings:
- Doesn't explain how thioester chemistry could support the complex reactions needed for early life.
- Lacks evidence for a plausible prebiotic source of thioesters in sufficient quantities.
- Fails to address the transition from thioester-based to ATP-based metabolism.

4. Iron-sulfur world hypothesis:
Proposal: Energy from redox reactions involving iron-sulfur minerals.
Shortcomings:
- Doesn't provide a clear mechanism for coupling these reactions to biosynthesis.
- Fails to explain how this system could support the formation of complex biomolecules.
- Lacks a plausible transition to modern cellular energetics.

5. Pyrophosphate as an energy source:
Proposal: Inorganic pyrophosphate as a simpler phosphate-based energy carrier.
Shortcomings:
- Doesn't explain the origin of pyrophosphate in prebiotic conditions.
- Fails to address how early systems could have efficiently utilized pyrophosphate.
- Lacks a clear evolutionary pathway to ATP-based systems.

6. UV-driven carbon fixation:
Proposal: UV light as an energy source for carbon fixation in early life.
Shortcomings:
- Doesn't explain how this energy could be stored or used for other cellular processes.
- Fails to address how life transitioned to chemical energy sources.
- Lacks a mechanism for protecting early biomolecules from UV damage.

7. Thermal gradients:
Proposal: Temperature differences as an energy source for early life.
Shortcomings:
- Doesn't provide a mechanism for converting thermal energy into chemical energy.
- Fails to explain how this could support complex biochemical reactions.
- Lacks a plausible transition to modern bioenergetics.

All these proposals fall short because they:
- Fail to provide a complete picture of early cellular energetics.
- Don't adequately explain the transition to more complex energy systems.
- Often require pre-existing complex molecules or structures.
- Lack of convincing experimental evidence.
- Don't address the simultaneous need for energy, information storage, and self-replication in early life.

The origin of life's energy systems remains a significant challenge in abiogenesis research, with no fully satisfactory explanation to date.

Claim: Gradual evolution: The sophisticated energy systems we see in modern cells, including ATP synthesis and utilization, likely evolved gradually from simpler precursor systems.
Response: Here's an explanation of the proposals for the gradual evolution of energy systems in early life and why they fall short:

1. Step-wise assembly of ATP synthase:
Proposal: ATP synthase evolved gradually from simpler rotary motors.
Shortcomings:
- Doesn't explain the origin of the initial rotary motor.
- Fails to address how partial assemblies would be functional and selectable.
- Ignores the need for a pre-existing proton gradient and ATP-utilizing enzymes.

2. Evolution from simpler phosphate-based energy carriers:
Proposal: Transition from pyrophosphate or acetyl phosphate to ATP.
Shortcomings:
- Lacks explanation for the origin of these simpler phosphate compounds.
- Doesn't address how early systems could efficiently use these alternatives.
- Fails to explain the universality of ATP in modern life.

3. Gradual development of electron transport chains:
Proposal: Electron transport chains evolved from simpler redox reactions.
Shortcomings:
- Doesn't account for the complex, interdependent nature of electron transport chains.
- Fails to explain how partially formed chains would be beneficial.
- Ignores the need for sophisticated membrane structures and proteins.

4. Evolution of metabolic pathways:
Proposal: Modern metabolic pathways evolved from simpler chemical reactions.
Shortcomings:
- Doesn't explain how these pathways became coupled to energy production.
- Fails to address the origin of enzymes needed for each step.
- Ignores the problem of how incomplete pathways could be beneficial.

5. Transition from heterotrophy to autotrophy:
Proposal: Early life forms evolved from consuming organic molecules to producing their own.
Shortcomings:
- Doesn't explain the initial source of organic molecules.
- Fails to address how early organisms could switch energy sources.
- Ignores the complexity of autotrophic pathways like photosynthesis or chemosynthesis.

6. RNA world to DNA/protein world transition:
Proposal: Energy systems evolved as life transitioned from RNA-based to DNA/protein-based.
Shortcomings:
- Doesn't explain how RNA-based life forms could have sufficient energy.
- Fails to address the energy requirements for this major transition.
- Ignores the need for complex energy systems in even RNA-based life.

7. Emergence of chemiosmosis:
Proposal: Chemiosmosis evolved gradually from simpler ion gradients.
Shortcomings:
- Doesn't explain the origin of semi-permeable membranes.
- Fails to address how partial chemiosmotic systems would be beneficial.
- Ignores the need for complex proteins to utilize ion gradients.

These proposals fall short in explaining the origin of energy production in early life because:
- They often require pre-existing complex structures or molecules.
- They don't adequately explain how partial or incomplete systems would be beneficial and selected for.
- They fail to address the chicken-and-egg problem of needing energy to produce the components of energy-producing systems.
- They don't account for the universality and complexity of core energy production systems across all life.
- They lack experimental evidence demonstrating the proposed transitions.
- They often ignore the interdependence of energy production with other crucial cellular processes.
- They fail to explain how the information for these systems could have originated and been preserved.

The gradual evolution of such complex, interdependent systems remains a significant challenge to explain, particularly in the context of early life where sophisticated enzymes and genetic systems were not yet present. The origin of life's energy systems continues to be a major unanswered question in the field of abiogenesis.

11. The Contact Surface Hypothesis

Claim: This hypothesis suggests that the interfaces between different phases (like liquid-solid or liquid-gas) could have played a crucial role in the origin of life. The key proposals include:
1. Concentration of molecules: Surfaces could concentrate organic molecules, increasing the likelihood of reactions.
2. Catalytic effects: Mineral surfaces might catalyze important prebiotic reactions.
3. Self-assembly: Interfaces could promote the self-assembly of complex molecules and protocells.
4. Energy gradients: Surfaces might create local energy gradients that could drive reactions.
5. Protection: Surfaces could protect fragile molecules from degradation.

Response: Why these proposals don't withstand scrutiny:

1. Concentration problem:
- While surfaces can concentrate molecules, they also limit diffusion and reaction space.
- It's unclear how surface-bound molecules could transition to form free-living cells.

2. Catalytic limitations:
- Mineral catalysis is often non-specific, leading to a mixture of products rather than the specific molecules needed for life.
- Many crucial prebiotic reactions require specific organic catalysts, not just mineral surfaces.

3. Self-assembly challenges:
- Self-assembly at interfaces doesn't explain the origin of the complex, specific sequences needed in biological polymers.
- It doesn't address how self-assembled structures could become capable of replication and evolution.

4. Energy gradient insufficiency:
- Local energy gradients at surfaces are typically too weak to drive the complex chemistry required for life.
- They don't explain how cells could have evolved to generate their own energy gradients.

5. Protection paradox:
- While surfaces might protect some molecules, they also expose them to potentially damaging surface chemistry.
- It's unclear how protected molecules could participate in the dynamic processes necessary for life.

6. Lack of information generation:
- Surface chemistry doesn't explain the origin of the genetic information required for life.
- It doesn't address how a surface-based system could transition to a genetic system.

7. Selectivity issues:
- Surfaces tend to adsorb a wide variety of molecules, potentially interfering with the specific chemistry needed for life.

8. Scale problem:
- While effects might be observed in laboratory settings, scaling these up to be relevant in prebiotic oceans is problematic.

9. Transition to cellular life:
- The hypothesis doesn't adequately explain how surface-bound chemistry could lead to free-living cells.

10. Experimental limitations:
- Many experiments supporting this hypothesis use highly controlled conditions and purified reagents, unlike the messy prebiotic environment.

While the contact surface hypothesis offers some interesting insights into possible prebiotic chemistry, it falls short of explaining the origin of life. It doesn't adequately address the origins of genetic information, metabolic pathways, or cellular structures. Like many origin of life hypotheses, it struggles with the transition from simple chemical processes to the complex, interrelated systems that characterize even the simplest forms of life.

12. The Radiation Hypotheses

Claim: Radiation in various forms could have played a decisive role in the origin of life

Response:

1. UV radiation as an energy source:
Proposal: UV light from the early Sun could have driven prebiotic chemical reactions.
Shortcomings:
- UV radiation is more likely to break down complex molecules than build them up.
- Doesn't explain how early life forms could have protected themselves from UV damage.
- Fails to address how UV-driven reactions could lead to self-replicating systems.

2. Ionizing radiation from radioactive decay:
Proposal: Radiation from naturally occurring radioactive elements could have provided energy for prebiotic synthesis.
Shortcomings:
- The energy from radioactive decay is generally too unfocused to drive specific chemical reactions.
- Ionizing radiation can damage organic molecules, potentially destroying nascent life forms.
- Doesn't explain how this energy could be harnessed in a controlled manner.

3. Cosmic radiation:
Proposal: High-energy particles from space could have initiated chemical reactions in the early atmosphere or oceans.
Shortcomings:
- Cosmic radiation is more likely to cause random chemical changes rather than build complex, ordered molecules.
- Doesn't address how these reactions could lead to the specific molecules needed for life.
- Fails to explain how cosmic radiation could drive the formation of self-replicating systems.

4. Radiolysis of water:
Proposal: Radiation-splitting water molecules could produce reactive species for prebiotic chemistry.
Shortcomings:
- The reactive species produced are often more likely to degrade organic molecules than build them.
- Doesn't explain how this process could lead to the complex, interrelated systems required for life.
- Fails to address the origin of genetic information.

5. Radiation-driven polymerization:
Proposal: Radiation could drive the formation of polymers like primitive proteins or nucleic acids.
Shortcomings:
- Radiation-induced polymerization typically produces random sequences, not the specific sequences needed for biological function.
- Doesn't explain how these polymers could become self-replicating.
- Fails to address how radiation-stable polymers could have the flexibility needed for life processes.

6. Radiation hormesis in early life:
Proposal: Low levels of radiation might have stimulated the development of early life forms.
Shortcomings:
- Lacks a clear mechanism for how radiation could stimulate the specific developments needed for life.
- Doesn't explain the origin of the complex systems needed to benefit from hormesis.
- Fails to address how early life could have controlled its radiation exposure.

These proposals fall short in explaining the origin of life for several key reasons:
1. Lack of specificity: Radiation generally causes random changes, not the specific, ordered processes needed for life.
2. Destructive potential: Many forms of radiation are more likely

These proposals fall short in explaining the origin of life for several key reasons:

Response:
1. Lack of specificity: Radiation generally causes random changes, not the specific, ordered processes needed for life.
2. Destructive potential: Many forms of radiation are more likely to break down complex molecules than build them up.
3. Energy coupling problem: These proposals don't adequately explain how radiation energy could be efficiently coupled to the specific chemical reactions needed for life.
4. Information problem: Radiation-based theories don't address the origin of the genetic information required for life.
5. Complexity issue: They fail to explain how radiation could lead to the development of complex, interrelated biochemical systems.
6. Protection paradox: Early life forms would need protection from radiation, but the proposals don't explain how this protection could evolve.
7. Selective pressure: These theories don't account for how natural selection could act on radiation-induced changes in prebiotic systems.
8. Experimental limitations: Laboratory experiments demonstrating radiation-driven prebiotic synthesis often use conditions unlikely in the prebiotic world.
9. Transition problem: The proposals don't adequately explain the transition from radiation-driven chemistry to self-sustaining biological processes.
10. Cellular organization: Radiation-based theories struggle to explain the origin of cellular structure and organization.

While radiation may have played some role in prebiotic chemistry, it falls far short of explaining the origin of life. The complexity, specificity, and information content of even the simplest life forms remain a significant challenge to explain through radiation-based mechanisms alone.

13. Thermodynamics-based Proposals

Claim: Thermodynamics-based Proposals
1. Self-organization through dissipative structures: Proposal: Life emerged as a dissipative structure to more efficiently dissipate energy gradients.
2. Thermal gradients as energy sources: Proposal: Temperature differences, such as those found in hydrothermal vents, could drive early metabolic reactions.
3. Entropy-driven self-assembly: Proposal: The formation of complex structures could be driven by entropy increases in the surrounding environment.
4. Non-equilibrium thermodynamics: Proposal: Life originated in systems far from thermodynamic equilibrium, allowing for the emergence of complex structures.
5. Maximum entropy production principle: Proposal: Life emerged as a way to maximize the rate of entropy production in a given environment.
6. Thermodynamic efficiency and natural selection: Proposal: Early chemical systems that were more thermodynamically efficient were naturally selected, leading to life.
7. Free energy transduction: Proposal: The ability to couple exergonic and endergonic reactions was key to the origin of life.

Response:
1. Lack of specificity: These proposals don't explain how general thermodynamic principles could lead to the specific molecular structures and information content found in life.
2. Information problem: Thermodynamic theories struggle to explain the origin and preservation of genetic information, which is crucial for life.
3. Complexity issue: While these proposals might explain simple self-organization, they don't account for the immense complexity of even the most basic living systems.
4. Catalysis unexplained: These theories don't address the origin of the specific catalysts (enzymes) needed for life's chemical reactions.
5. Selective processes unclear: It's not evident how thermodynamic principles alone could lead to the selective processes required for evolution.
6. Cellular organization: Thermodynamic proposals struggle to explain the emergence of cellular structure and compartmentalization.
7. Metabolic pathways: These theories don't adequately explain the origin of complex, interconnected metabolic pathways.
8. Replication mechanisms: The emergence of self-replication, a key characteristic of life, is not clearly explained by thermodynamic principles alone.
9. Time scale problem: Many of these processes would occur too slowly to be relevant on geological time scales without highly specific catalysts.
10. Experimental limitations: Laboratory demonstrations of these principles often use conditions or materials unlikely to have existed in the prebiotic world.
11. Transition to autonomy: These proposals don't clearly explain how thermodynamically driven systems could transition to the autonomous, self-maintaining systems characteristic of life.
12. Genetic takeover unexplained: They fail to address how a system based purely on thermodynamics could transition to one controlled by genetic information.
13. Homochirality problem: Thermodynamic theories struggle to explain the origin of homochirality in biological molecules.
14. Specificity of interactions: These proposals don't account for the highly specific molecular interactions required for life processes.
15. Energy coupling mechanisms: They don't adequately explain the origin of sophisticated energy coupling mechanisms found in all living systems.

While thermodynamic principles undoubtedly play a crucial role in living systems, they alone are insufficient to explain the origin of life. The emergence of life requires not just energy flow and self-organization, but also information storage, replication, and the ability to evolve. Thermodynamic proposals, while offering insights into some aspects of life's operations, fall short of providing a comprehensive explanation for how life could have originated from non-living matter.

14. Various Other Proposals

Claim: Equilibrium-based Proposals
1. Chemical equilibrium in primordial soup: Proposal: Life emerged from a complex mixture of organic compounds in chemical equilibrium.
2. Steady-state systems: Proposal: Early proto-life existed in a steady state, with inputs and outputs balanced.
3. Equilibrium fluctuations: Proposal: Small, random fluctuations around equilibrium led to the emergence of self-replicating systems.
4. Quasi-equilibrium polymerization: Proposal: The formation of early biopolymers occurred under near-equilibrium conditions.
5. Equilibrium self-assembly: Proposal: Complex structures like protocells self-assembled under equilibrium conditions.
6. Thermodynamic equilibrium as a selection pressure: Proposal: Systems that could maintain internal equilibrium while external conditions changed were selected for.

Response:
1. Violation of thermodynamic principles: Life is fundamentally a non-equilibrium phenomenon. Equilibrium systems lack the energy flow necessary for life's processes.
2. Lack of energy for biosynthesis: Equilibrium conditions don't provide the energy needed to drive the synthesis of complex biomolecules.
3. No mechanism for information increase: Equilibrium systems can't explain the origin and increase of genetic information, crucial for life and evolution.
4. Inability to perform work: Living systems must perform work to maintain themselves, which is impossible in true equilibrium.
5. No driving force for self-organization: Equilibrium lacks the thermodynamic driving forces needed for the self-organization of complex structures.
6. Conflict with observed prebiotic chemistry: Most prebiotic chemistry experiments require energy input and non-equilibrium conditions to produce biologically relevant molecules.
7. Incompatibility with metabolism: Metabolic pathways require constant energy input and are inherently non-equilibrium processes.
8. No explanation for cellular compartmentalization: The formation and maintenance of cell-like structures require energy input, contradicting equilibrium conditions.
9. Lack of selectivity: Equilibrium conditions don't provide a mechanism for selecting specific molecules or reactions over others.
10. Inconsistency with the RNA world hypothesis: The formation and function of catalytic RNA molecules, often proposed as precursors to life, require non-equilibrium conditions.
11. Contradiction with the second law of thermodynamics: The increase in order and complexity associated with life seems to contradict the second law under equilibrium conditions.
12. No mechanism for adaptation: Equilibrium systems can't explain how early life could have adapted to changing environmental conditions.
13. Inconsistency with observed life: All known life forms operate far from equilibrium, making equilibrium-based origins unlikely.
14. Lack of experimental support: Laboratory experiments have failed to demonstrate the emergence of life-like properties under equilibrium conditions.
15. Time scale problem: Any fluctuations around equilibrium would be too small and short-lived to allow for the emergence of complex, life-like systems.

Equilibrium-based scenarios for the origin of life are fundamentally flawed. Life is an inherently non-equilibrium phenomenon, requiring constant energy input and material flow. While certain aspects of living systems may approach steady states, true equilibrium is incompatible with the dynamic, self-organizing, and evolving nature of life. The origin of life almost certainly required far-from-equilibrium conditions to provide the necessary energy and driving forces for the emergence of complex, self-replicating systems.

Claim: The RNA World Hypothesis
Proposal: RNA molecules served as both the genetic material and catalysts for early life, before the evolution of DNA and proteins.

Response:
1. RNA synthesis problem: These proposals, like the others, face significant challenges in explaining the origin of life. They often address only part of the problem, lack experimental support, or fail to provide a clear path to the complex, information-rich systems characteristic of life as we know it. The origin of life remains a formidable scientific challenge, with no current hypothesis fully explaining all aspects of the transition from non-living to living systems.

Claim: Multiple mechanisms explain the origin of life
Proposal: The combined action of chemoselectivity, simple energy sources, gradual evolution of energy systems, and the contact surface hypothesis, working together over long periods, can explain the emergence of life.

Response:
1. Compounding improbabilities: Combining unlikely events reduces overall likelihood.
2. Lack of coordination: No mechanism for processes to coordinate towards a common goal.
3. Insufficient complexity: Can't account for the complexity of even the simplest living systems.
4. Information problem: Fails to explain the origin of genetic code or information in DNA/RNA.
5. Integration issue: Doesn't address how cellular components became integrated.
6. Thermodynamic challenges: Doesn't overcome barriers to spontaneous organization.
7. Chicken-and-egg dilemmas: Many processes require pre-existing complex structures.
8. Lack of empirical evidence: No demonstration of these processes leading to life.

Claim: The characteristics of the genetic code, coupled with the rapidity by which the LUCA emerged, can all be accounted for, in principle, by assuming the existence of an earlier communal epoch of life in which HGT was rampant even among the components of core cellular functions such as the translation machinery [10]. Here, we have shown how this communal epoch would have come to a graceful end, without requiring any fine tuning or other extraneous mechanisms. Simply put, HGT ceases to be effective beyond a certain time, since there is nothing new to transfer. The resulting dynamics is then characterized purely by vertical evolution of the core cellular functions, leading to the possibility to define species and lineages, and permitting the phylogeny and evolutionary trajectory of organisms to be tracked. Link

Response:
1. Compounding improbabilities: The claim relies on a series of highly improbable events occurring in sequence: the emergence of self-replicating molecules, the development of a proto-genetic code, and widespread horizontal gene transfer (HGT) among primitive cells. Each step compounds the unlikelihood, making the overall scenario extremely improbable.
2. Lack of coordination: The hypothesis assumes that random HGT events would somehow lead to the coordinated development of complex cellular machinery. There's no mechanism explained for how these transfers would be directed towards creating functional, integrated systems rather than chaotic, non-functional combinations.
3. Insufficient complexity: Even the simplest known living cells are incredibly complex, with hundreds of interacting genes and proteins. The proposed model doesn't adequately explain how such complexity could arise from simpler precursors through undirected HGT processes.
4. Information problem: The claim doesn't address the fundamental issue of how genetic information and the genetic code itself originated. HGT can only transfer existing information, not create new, functional genetic sequences from scratch.
5. Integration issue: The hypothesis fails to explain how transferred genetic elements would become properly integrated into existing cellular systems. Successful integration of foreign genes into a coherent, functional cellular framework is a significant challenge even in modern organisms with sophisticated regulatory systems.
6. Thermodynamic challenges: The scenario doesn't address how early life forms overcame thermodynamic barriers to self-organization and maintained themselves as distinct entities while supposedly engaging in rampant HGT.
7. Chicken-and-egg dilemmas: Many cellular processes, including those involved in HGT itself, require pre-existing complex cellular machinery. The claim doesn't resolve how these interdependent systems could have arisen simultaneously.
8. Lack of empirical evidence: There is no experimental evidence demonstrating that the proposed mechanisms can actually lead to the emergence of life or even to the development of simpler self-sustaining, replicating systems. The hypothesis remains purely theoretical without supporting empirical data.

Missing ingredient: A guiding intelligent agency with foresight

Importance of intelligent agency
1. Purposeful direction: Guides processes towards specific goals.
2. Information input: Provides information for complex, specified systems.
3. Problem-solving: Anticipates and solves problems that stymie undirected processes.
4. Integration of systems: Allows coordinated development of interdependent systems.
5. Overcoming barriers: Devises strategies to overcome thermodynamic and chemical barriers.
6. Efficient resource use: Utilizes resources more efficiently than random processes.
7. Complex specification: Explains highly specific arrangements in biological systems.
8. Irreducible complexity: Accounts for systems exhibiting irreducible complexity.

Conclusion: Combining mechanisms fails to address fundamental issues in explaining life's origin. The complexity, specificity, and integrated functionality of living systems suggest the involvement of an intelligent agent with foresight.

Certainly. I'll add persistent shortcomings and challenges to each section of the recent advances. Here's the updated version:

15. Concluding Remarks

The origin of life remains one of the most challenging problems in science, sitting at the intersection of chemistry, biology, geology, and physics. Our review of various naturalistic proposals for the origin of life reveals significant challenges in explaining the emergence of complex, interdependent biological systems through undirected processes alone. While hypotheses such as chemoselectivity, primitive energy sources, and surface-mediated reactions offer thought-provoking and interesting possibilities, they struggle to fully account for the complexity, specificity, and information content observed in even the simplest living systems. The origin of sophisticated energy production systems, like ATP synthesis, poses particularly difficult questions for non-intelligent explanations. The alternative perspective, that of intelligent causation, addresses some of these challenges by invoking a source of complex specified information. However, this approach raises its own set of questions and often falls outside traditional scientific methodologies. As we continue to explore the origin of life, it is crucial to remain open to multiple explanatory frameworks while rigorously testing all hypotheses against empirical evidence. Future research should focus on bridging the gap between simple chemical systems and the complexity of living organisms, potentially exploring new paradigms that transcend the current status quo based on purely naturalistic mechanisms, and extending the possibility of intelligence-based explanations. The quest to understand life's origins not only drives scientific progress but also touches on fundamental questions about our place in the universe. As such, it remains a vital and exciting area of research that will likely continue to challenge and inspire scientists for generations to come.