Open questions in prebiotic chemistry to explain the origin of the four basic building blocks of life https://reasonandscience.catsboard.com/t1279p75-abiogenesis-is-mathematically-impossible#7759Prevital RNA and DNA synthesisRNA & DNA: It's prebiotic synthesis: Impossible !! Part 1https://www.youtube.com/watch?v=-ZFlmL_BsXE
RNA & DNA: It's prebiotic synthesis: Impossible !! Part 2https://www.youtube.com/watch?v=dv4mUjmuRRU
How would the primitive Earth have generated and maintained organic molecules? All that can be said is that there might have been prevital organic chemistry going on, at least in special locations.
How would prebiotic processes have
purified the starting molecules to make RNA and DNA which were grossly impure? They would have been present in complex mixtures that contained a great variety of reactive molecules.
How did the synthesis of the nitrogenic nucleobases in prebiotic environments occur?
How did fortuitous accidents
select the five just-right nucleobases to make DNA and RNA, Two purines, and three pyrimidines?
How did unguided random events
select purines with two rings, with nine atoms, forming the two rings: 5 carbon atoms and 4 nitrogen atoms, amongst almost unlimited possible configurations?
How did stochastic coincidence
select pyrimidines with one ring, with six atoms, forming its ring: 4 carbon atoms and 2 nitrogen atoms, amongst an unfathomable number of possible configurations?
How did random trial and error foresee that this specific atomic arrangement of the nucleobases is required to get the right strength of the hydrogen bond to join the two DNA strands and form Watson–Crick base-pairing?
How did mechanisms without external direction foresee that this specific atomic arrangement would convey one of, if not the best possible genetic system to store information?
How would these functional bases have been
separated from the confusing jumble of similar molecules that would also have been made?
How were high-energy precursors to produce purines and pyrimidines produced in a sufficiently concentrated form and joined to the assembly site?
How could the adenine-uracil interaction function in any specific recognition scheme under the chaotic conditions of a "prebiotic soup" considering that its interaction is weak and nonspecific?
How could sufficient uracil nucleobases accumulate in prebiotic environments in sufficient quantities, if it has a half-life of only 12 years at 100◦C ?
How could the ribose 5 carbon sugar rings which form the RNA and DNA backbone have been
selected, if 6 or 4 carbon rings, or even more or less, are equally possible but non-functional?
How would the functional ribose molecules have been separated from the non-functional sugars?
How were the correct nitrogen atom of the base and the correct carbon atom of the sugar
selected to be joined together?
How could right-handed configurations of RNA and DNA have been
selected in a racemic pool of right and left-handed molecules? Ribose must have been in its D form to adopt functional structures ( The homochirality problem )
How could random events have
brought all the 3 parts together and bonded them in the right position ( probably over one million nucleotides would have been required ?)
How could prebiotic reactions have
produced functional nucleosides? (There are no known ways of bringing about this thermodynamically uphill reaction in aqueous solution)
How could prebiotic
glycosidic bond formation between nucleosides and the base have occurred if they are thermodynamically unstable in water, and overall intrinsically unstable?
How could
RNA nucleotides have accumulated, if they degrade at warm temperatures in time periods ranging from nineteen days to twelve years? These are extremely short survival rates for the four RNA nucleotide building blocks.
How was
phosphate, the third element, concentrated at reasonable concentrations?. (The concentrations in the oceans or lakes would have been very low)
How would prebiotic mechanisms
phosphorylate the nucleosides at the correct site (the 5' position) if, in laboratory experiments, the 2' and 3' positions were also phosphorylated?
How could phosphate have been
activated somehow? In order to promote the energy dispendious nucleotide polymerization reaction, and (energetically uphill) phosphorylation of the nucleoside had to be possible.
How was the
energy supply accomplished to make RNA? In modern cells, energy is consumed to make RNA.
How could a transition from
prebiotic to biochemical synthesis have occurred? There are a huge gap and enormous transition that would be still ahead to arrive at a fully functional interlocked and interdependent metabolic network.
How could RNA have formed, if it requires water to make them, but RNA cannot emerge in water and cannot replicate with sufficient fidelity in water without sophisticated repair mechanisms in place?
How would the
prebiotic synthesis transition of RNA to the highly regulated cellular metabolic synthesis have occurred? The pyrimidine synthesis pathway requires six regulated steps, seven enzymes, and energy in the form of ATP.
The starting material for purine biosynthesis is Ribose 5-phosphate, a product of the highly complex pentose phosphate pathway, which uses 12 enzymes. De novo purine synthesis pathway requires ten regulated steps, eleven enzymes, and energy in the form of ATP.
How would the primitive earth have produced high-energy precursors of purines and pyrimidines in a sufficiently concentrated form? (for example at least 0.01 M HCN).
How would the bases have been separated from the confusing jumble of similar molecules that would also have been made? - and the solutions had to be sufficiently concentrated.
How did formaldehyde concentration of above 0.01 M build up?
How did accumulated formaldehyde oligomerise to sugars?
How did the sugars separate and resolve, so as to give a moderately good concentration of, for example, D-ribose?
How did bases and sugars come together?
How were they induced to react to make nucleosides? (There are no known ways of bringing about this thermo dynamically uphill reaction in aqueous solution: purine nucleosides have been made by dry phase synthesis, but not even this method has been successful for condensing pyrimidine bases and ribose to give nucleosides
How was joining base and sugar achieved correctly ? It had to be between the correct nitrogen atom of the base and the correct carbon atom of the sugar. This junction will fix the pentose sugar as either the a- or fl-anomer of either the furanose or pyranose forms. For nucleic acids it has to be the fl-furanose. (In the dry-phase purine nucleoside syntheses referred to above, all four of these isomers were present with never more than 8 ‘Z, of the correct structure.)
How could phosphate have been present at sufficient concentrations? (The concentrations in the oceans would have been very low, so we must think about special situations—evaporating lagoons and such things
How could phosphate have been activated? — for example as a linear or cyclic polyphosphate — so that (energetically uphill) phosphorylation of the nucleoside is possible?
How would only the standard nucleotides, the 5’- hydroxyl of the ribose be phosphorylated? (In solid-state reactions with urea and inorganic phosphates as a phosphorylating agent, this was the dominant species to begin with.
How did the activated nucleotides (or the nucleotides with coupling agent) polymerise?. Initially this must have happened without a pre-existing polynucleotide template (this has proved very difficult to simulate ; but more important, it must have come to take place on pre-existing polynucleotides if the key function of transmitting information to daughter molecules was to be achieved by abiotic means. This has proved difficult too. Orgel & Lohrmann give three main classes of problem.
(i) While it has been shown that adenosine derivatives form stable helical structures with poly(U) — they are in fact triple helixes — and while this enhances the condensation of adenylic acid with either adenosine or another adenylic acid — mainly to di(A) - stable helical structures were not formed when either poly(A) or poly(G) Were used as templates.
(ii) It was difficult to find a suitable means of making the internucleotide bonds. Specially designed water-soluble carbodiimides were used in the experiments described above, but the obvious pre-activated nucleotides — ATP or cyclic 2’,3’-phosphates — were unsatisfactory. Nucleoside 5'-phosphorimidazolides, for example: N/\ n K/N/P-r’o%OHN/\N were more successful, but these now involve further steps and a supply of imidazole, for their synthesis.
(iii) Internucleotide bonds formed on a template are usually a mixture of 2’—5’ and the normal 3’—5’ types. Often the 2’—5’ bonds predominate although it has been found that Zn“, as well as acting as an eflicient catalyst for the templatedirected oligomerisation of guanosine 5’-phosphorimidazolide also leads to a preference for the 3’—5’ bonds.
How could the physical and chemical environment have been at all times suitable — for example the pH, the temperature, the M2+ concentrations?
How could all reactions have taken place well out of the ultraviolet sunlight? that is, not only away from its direct, highly destructive effects on nucleic acid-like molecules, but away too from the radicals produced by the sunlight, and from the various longer lived reactive species produced by these radicals.
If not already activated — for example as the cyclic 2’,3’-phosphate — how were the nucleotides be activated? (for example with polyphosphate) and a reasonably pure solution of these species created of reasonable concentration. Alternatively, a suitable coupling agent must now have been fed into the system.
Longer heating gave the nucleoside cyclic 2’,3’-phosphate as the major product although various dinucleotide derivatives and nucleoside polyphosphates are also formed
DNA is more stable than RNA. uracil (U) is replaced in DNA by thymine (T)
At the C2' position of ribose, an oxygen atom is removed by hypercomplex RNR molecular machines. The thymine-uracil exchange is the major chemical difference between DNA and RNA. Before being incorporated into the chromosomes, this essential modification takes place. The synthesis of thymine requires seven enzymes. De novo biosynthesis of thymine is an intricate and energetically expensive process.
All in all, not considering the metabolic pathways and enzymes required to make the precursors to start RNA and DNA synthesis, at least 26 enzymes are required. How did these enzymes emerge, if DNA is required to make them?
Prebiotic Amino acid synthesisChemical evolution of amino acids and proteins ? Impossible !! https://www.youtube.com/watch?v=1L1MfGrtk0A
How could ammonia (NH3), the precursor for amino acid synthesis, have accumulated on prebiotic earth, if the lifetime of ammonia would be short because of its photochemical dissociation?
How could prebiotic events have delivered organosulfur compounds required for a few amino acids used in life, if in nature sulfur exists only in its most oxidized form (sulfate or SO4), and only some unique groups of procaryotes mediate the reduction of SO4 to its most reduced state (sulfide or H2S)?
How did unguided stochastic coincidence select the right amongst over 500 that occur naturally on earth?
How was the concomitant synthesis of undesired or irrelevant by-products avoided?
How were bifunctional monomers, that is, molecules with two functional groups, so they combine with two others selected, and unifunctional monomers (with only one functional group) sorted out?
How did prebiotic events produce the twenty amino acids used in life? Eight proteinogenic amino acids were never abiotically synthesized under prebiotic conditions.
How did a prebiotic synthesis of biological amino acids avoid the concomitant synthesis of undesired or irrelevant by-products?
How could achiral precursors of amino acids have produced and concentrated only left-handed amino acids? ( The homochirality problem )
How did the transition from prebiotic enantiomer selection to the enzymatic reaction of transamination occur that had to be extant when cellular self-replication and life began?
How would natural causes have selected twenty, and not more or less amino acids to make proteins?
How did natural events have foreknowledge that the selected amino acids are best suited to enable the formation of soluble structures with close-packed cores, allowing the presence of ordered binding pockets inside proteins?
How did nature "kHow could ammonia (NH3), the precursor for amino acid synthesis, have accumulated on prebiotic earth, if the lifetime of ammonia would be short because of its photochemical dissociation?
How could prebiotic events have delivered organosulfur compounds required in a few amino acids used in life, if in nature sulfur exists only in its most oxidized form (sulfate or SO4), and only some unique groups of procaryotes mediate the reduction of SO4 to its most reduced state (sulfide or H2S)?
How was the concomitant synthesis of undesired or irrelevant by-products avoided?
How were bifunctional monomers, that is, molecules with two functional groups so they combine with two others selected, and unifunctional monomers (with only one functional group) sorted out?
How did prebiotic events produce the twenty amino acids used in life? Eight proteinogenic amino acids were never abiotically synthesized under prebiotic conditions.
How did a prebiotic synthesis of biological amino acids avoid the concomitant synthesis of undesired or irrelevant by-products?
How could achiral precursors of amino acids have produced and concentrated only left-handed amino acids? (The homochirality problem)
How did the transition from prebiotic enantiomer selection to the enzymatic reaction of transamination occur that had to be extant when cellular self-replication and life began?
How would natural causes have selected twenty, and not more or less amino acids to make proteins?
How did natural events have foreknowledge that the selected amino acids are best suited to enable the formation of soluble structures with close-packed cores, allowing the presence of ordered binding pockets inside proteins?
How did nature "know" that the set of amino acids selected appears to be near ideal and optimal?
How did Amino acid synthesis regulation emerge? Biosynthetic pathways are often highly regulated such that building blocks are synthesized only when supplies are low.
How did the transition from prebiotic synthesis to cell synthesis of amino acids occur? A minimum of 112 enzymes is required to synthesize the 20 (+2) amino acids used in proteins.now" that the set of amino acids selected appears to be near ideal and optimal?
How did Amino acid synthesis regulation emerge? Biosynthetic pathways are often highly regulated such that building blocks are synthesized only when supplies are low.
How did the transition from prebiotic synthesis to cell synthesis of amino acids occur? A minimum of 112 enzymes is required to synthesize the 20 (+2) amino acids used in proteins.
Prebiotic cell membrane synthesisHow could simple amphiphiles, which are molecules containing a nonpolar hydrophobic region and a polar hydrophilic region will self-assemble in aqueous solutions to form distinct structures such as micelles have been available in the prebiotic inventory if there has never been evidence for this? Furthermore, sources of compounds with hydrocarbon chains sufficiently long to form stable membranes are not known.
How could prebiotic mechanisms have transported and concentrated organic compounds to the pools and construction site?
How could membranous vesicles have self-assembled to form complex mixtures of organic compounds and ionic solutes, if science has no solution to this question?
How could there have been a prebiotic route of lipid compositions that could provide a membrane barrier sufficient to maintain proton gradients? Proton gradients are absolutely necessary for the generation of energy.
How to explain that lipid membranes would be useless without membrane proteins but how could membrane proteins have emerged or evolved in the absence of functional membranes?
How did prebiotic processes select hydrocarbon chains which must be in the range of 14 to 18 carbons in length? There was no physical necessity to form carbon chains of the right length nor hindrance to join chains of varying lengths. So they could have been existing of any size on the early earth.
How could there have been an "urge" for prebiotic compounds to add unsaturated cis double bonds near the center of the chain?
How is there a feasible route of prebiotic phospholipid synthesis, to the complex metabolic phospholipid and fatty acid synthesis pathways performed by multiple enzyme-catalyzed steps which had to be fully operational at LUCA?
How would random events start to attach two fatty acids to glycerol by ester or ether bonds rather than just one, necessary for the cell membrane stability?
How would random events start to produce biological membranes which are not composed of pure phospholipids, but instead are mixtures of several phospholipid species, often with a sterol admixture such as cholesterol? There is no feasible prebiotic mechanism to join the right mixtures.
How did unguided events produce the essential characteristic of living cells which is homeostasis, the ability to maintain a steady and more-or-less constant chemical balance in a changing environment? The first forms of life required an effective Ca2+ homeostatic system, which maintained intracellular Ca2+ at comfortably low concentrations—somewhere ∼10,000–20,000 times lower than that in the extracellular milieu. There was no mechanism to generate this gradient.
How was the transition generated from supposedly simple vesicles on the early earth to the ultracomplex membrane synthesis in modern cells, which would have to be extant in the last universal common ancestor, hosting at least over 70 enzymes?
Physico-Chemical and Evolutionary Constraints for the Formation and Selection of First Biopolymers: Towards the Consensus Paradigm of the Abiogenic Origin of Life 21 September 2007 1
It was suggested that the accumulation and interaction of increasingly complex compounds, formed under primordial conditions, could eventually lead to the origin of life. This initial paradigm did not contain much detail on the particular chemical routes involved.
Absence of a consensus among the members of the scientific community is causing problems outside science by opening the window for the proponents of the intelligent design as another, supposedly equally plausible hypothesis of origin of life. Therefore, we see an urgent task to formulate a consensus scenario for the abiogenic origin of life that 1) would be scientifically plausible, 2) could serve as a common basis/paradigm for the scientists with different views, and 3) could eventually be offered to the general public. the replication first and metabolism first hypotheses complement, rather than contradict, each other. Further, we suggest that life on Earth has started from a metabolism-driven replication and attempt to reconstruct the conditions under which such a replication could have occurred.
An important chemical constraint, which often remains unrecognized, is the reversibility of most (bio)chemical reactions. Therefore, any scheme that explains biopolymer formation under certain environmental conditions should also be able to explain why the synthesis of the given biopolymers would not be followed by their immediate hydrolysis. One cannot help noting that, in virtually all papers describing origin of life, the corresponding schemes contain unidirectional arrows, instead of bidirectional ones. However, the mechanisms that underlie that unidirectionality are almost never described. In a way, the mechanisms for formation and maintenance of
biopolymers require some kind of Maxwell's Demon that would allow the reaction to go in the direction of increasingly complex compounds.
Such a demon is hard to imagine, which serves as fertile ground for ideas of some kind of Supreme Being that was needed to breathe life into disorganized organic matter. The simplest substitution for this kind of Maxwell's Demon would be a Darwin's Demon, a selective mechanism that favors complex molecules (structures) over simple ones. Obviously, it would require external source(s) of energy. However, such a selective mechanism acting for a sufficiently long period of time appears to be a necessary condition for sustaining abiogenic evolution that could have produced a variety of pre-biological molecules and eventually brought about the first living organisms.
My comment: It is remarkable how the authors see the hypothesis of intelligent design as a problem ( a problem to whom??). Also, if, as the authors propose that metabolism and replication had to emerge together, than this is a nice admittance of irreducible complexity, which i fully agree with.
Formation and maintaining of increasingly complex biopolymers could proceed only if supported by a constant flow of utilizable energy. This consideration severely constrains otherwise plausible hypotheses of origin of life
under impact bombardment that tend to treat emergence of life as a one-time event. The second law of thermodynamics imposes an additional, less obvious constraint on the origin of life, namely, that heat cannot be used
as an energy source for the formation of increasingly complex chemical compounds. Hence, the ultimate source of energy must be external and constant, which effectively leaves solar radiation as the most likely candidate.
Prebiotic source of hydrocarbonsHow would an ensemble of minerals present anywhere on the primitive Earth be capable of catalyzing each of the many steps of the reverse citric acid cycle? How would a cycle mysteriously organize itself topographically on a metal sulfide surface? How would such a cycle, despite the lack of evidence of its existence, a transition to the “life-like” complexity of the Wood-Ljundahl cycle, or reverse TCA cycle, commonly proposed as the first carbon fixing cycles on earth?
In this work, we emphasize the role of selection during the prebiological stages of evolution and focus on the constraints that are imposed by physical, chemical, and biological laws. The key feature of the scenario is the
participation of the UV irradiation both as driving and selecting forces during the earlier stages of evolution.
Ultraviolet radiation was then already considered as an energy source but was not used, since it was difficult to generate radiation of appropriate wavelength with sources available at that time (Miller and Urey 1959). 2 The prebiotic UV environment was exposed to high levels of UV radiation relative to the present day due to lack of UV-shielding O2 and O3. 3. High environmental fluxes of UV–C and UV–B restricting protocyanobacteria to refuges. J.B.S. Haldane (1892-1962) independently proposed the existence of a prebiotic soup in the oceans (Haldane 1954) and suggested that subjecting a mixture of water, carbon dioxide and ammonia to UV light should produce a variety of organic substances. Dauvillier (1947) was one of the first in suggesting UV radiation as an energy source for the synthesis of organic matter. In the words of Sagan & Khare (1971),
“the availability of the ultraviolet solar radiation was some 100 times greater that of all the others”. It is a paradox how the molecule responsible for the replication of information has such a large absorption in the damaging UV spectral range. Sagan (1973) suggested the existence of a protecting layer of purines and pyrimidines surrounding the primitive organisms.The
decrease in UV surface fluxes was essential for the access of living beings to the land and the subsequent evolution of complex life forms. 4
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1. Life requires the use of a limited set of complex biomolecules, a universal convention, and unity which is composed of the four basic building blocks of life ( RNA and DNA's, amino acids, phospholipids, and carbohydrates). They are of a very specific complex functional composition and made by cells in extremely sophisticated orchestrated metabolic pathways, which were not extant on the early earth. If abiogenesis were true, these biomolecules had to be prebiotically available and naturally occurring ( in non-enzyme-catalyzed ways by natural means ) and then somehow join in an organized way and form the first living cells. They had to be available in big quantities and concentrated at one specific building site.
2. Making things for a specific purpose, for a distant goal, requires goal-directedness. And that's a big problem for naturalistic explanations of the origin of life. There was a potentially unlimited variety of molecules on the prebiotic earth. Competition and selection among them would never have occurred at all, to promote a separation of those molecules that are used in life, from those that are useless. Selection is a scope and powerless mechanism to explain all of the living order, and even the ability to maintain order in the short term and to explain the emergence, overall organization, and long-term persistence of life from non-living precursors. It is an error of false conceptual reduction to suppose that competition and selection will thereby be the source of explanation for all relevant forms of the living order.
3. We know that a) unguided random purposeless events are unlikely to the extreme to make specific purposeful elementary components to build large integrated macromolecular systems, and b) intelligence has goal-directedness. Bricks do not form from clay by themselves, and then line up to make walls. Someone made them. Phospholipids do not form from glycerol, a phosphate group, and two fatty acid chains by themselves, and line up to make cell membranes. Someone made them. That is God.
No prebiotic selection !! If a machine has to be made out of certain components, then the components have to be made first.'
Molecules have nothing to gain by becoming the building blocks of life. They are "happy" to lay on the ground or float in the prebiotic ocean and that's it. Being incredulous that they would concentrate at one building site in the right mixture, and in the right complex form, that would permit them to complexify in an orderly manner and assembly into complex highly efficient molecular machines and self-replicating cell factories, is not only justified but warranted and sound reasoning. That fact alone destroys materialism & naturalism. Being credulous towards such a scenario means to stick to blind belief. And claiming that "we don't know (yet), but science is working on it, but the expectation is that the explanation will be a naturalistic one ( No God required) is a materialism of the gaps argument.
A Few Experimental Suggestions Using Minerals to Obtain Peptides with a High Concentration of L-Amino Acids and Protein Amino Acids 10 December 2020
The prebiotic seas contained L- and D-amino acids, and non-Polar AAs and Polar AAs, and minerals could adsorb all these molecules. Besides amino acids,
other molecules could be found in the primitive seas that competed for mineral adsorption sites. Here, we have a huge problem that could be a double-edged sword for prebiotic chemistry. On the one hand, this may lead to more complex prebiotic chemistry, due to the large variety of species, which could mean more possibilities for the formation of different and more complex molecules. On the other hand, this complex mixture of molecules may not lead to the formation of any important molecule or biopolymer in high concentration to be used for molecular evolution. Schwartz, in his article “Intractable mixtures and the origin of life”, has already addressed this problem, denominating this mixture the “gunk”. 5
Intractable Mixtures and the Origin of Life 2007
A problem which 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. 6
Life: What A Concept! https://jsomers.net/life.pdf
Craig Venter: To me the key thing about Darwinian evolution is selection. Biology is a hundred percent dependent on selection. No matter what we do in synthetic biology, synthetic genomes, we're doing selection. It's just not
natural selection anymore. It's an intelligently designed selection, so it's a unique subset. But selection is always part of it.
My comment: What natural mechanisms lack, is goal-directedness. And that's a big problem for naturalistic explanations of the origin of life. There was a potentially unlimited variety of molecules on the prebiotic earth. Why should competition and selection among them have occurred at all, to promote a separation of those molecules that are used in life, from those that are useless? Selection is a scope and powerless mechanism to explain all of the living order, and even the ability to maintain order in the short term, and to explain the emergence, overall organization, and long-term persistence of life from non-living precursors. It is an error of false conceptual reduction to suppose that competition and selection will thereby be the source of explanation for all relevant forms of order.The problem of lack of a selection mechanism extends to the homochirality problem.
A. G. CAIRNS-SMITH Seven clues to the origin of life, page 40: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.
In regards to the prebiotic synthesis of the basic building blocks of life, I list 23 problems directly related to the lack of a selection mechanism on the prebiotic earth. This is one of the unsolvable problems of abiogenesis.
Selecting the right materials is absolutely essential. But a prebiotic soup of mixtures of impure chemicals would never purify and select those that are required for life. Chemicals and physical reactions have no "urge" to join, group, and start interacting in a purpose and goal-oriented way to produce molecules, that later on would perform specific functions, and generate self-replicating factories, full of machines, directed by specified, complex assembly information. This is not an argument from ignorance, incredulity, or gaps of knowledge.
William Dembski: 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.
http://www.discovery.org/a/1256
Out of the 27 listed problems of
prebiotic RNA synthesis, 8 are directly related to the lack of a mechanism to select the right ingredients.
1.How would prebiotic processes have
purified the starting molecules to make RNA and DNA which were grossly impure? They would have been present in complex mixtures that contained a great variety of reactive molecules.
2.How did fortuitous accidents
select the five just-right nucleobases to make DNA and RNA, Two purines, and three pyrimidines?
3.How did unguided random events
select purines with two rings, with nine atoms, forming the two rings: 5 carbon atoms and 4 nitrogen atoms, amongst almost unlimited possible configurations?
4.How did stochastic coincidence
select pyrimidines with one ring, with six atoms, forming its ring: 4 carbon atoms and 2 nitrogen atoms, amongst an unfathomable number of possible configurations?
5.How would these functional bases have been
separated from the confusing jumble of similar molecules that would also have been made?
6.How could the ribose 5 carbon sugar rings which form the RNA and DNA backbone have been
selected, if 6 or 4 carbon rings, or even more or less, are equally possible but non-functional?
7.How were the correct nitrogen atom of the base and the correct carbon atom of the sugar
selected to be joined together?
8.How could right-handed configurations of RNA and DNA have been
selected in a racemic pool of right and left-handed molecules? Ribose must have been in its D form to adopt functional structures ( The homochirality problem )
Out of the 27 listed problems of
prebiotic amino acid synthesis, 13 are directly related to the lack of a mechanism to select the right ingredients.
1. How did unguided stochastic coincidence select the right amongst over 500 that occur naturally on earth?2. How were bifunctional monomers, that is, molecules with two functional groups, so they combine with two others selected, and unifunctional monomers (with only one functional group) sorted out?3. How could achiral precursors of amino acids have produced/selected and concentrated only left-handed amino acids? ( The homochirality problem )4. How did the transition from prebiotic enantiomer selection to the enzymatic reaction of transamination occur that had to be extant when cellular self-replication and life began?5. How would natural causes have selected twenty, and not more or less amino acids to make proteins?6. How did natural events have foreknowledge that the selected amino acids are best suited to enable the formation of soluble structures with close-packed cores, allowing the presence of ordered binding pockets inside proteins?7. How were bifunctional monomers, that is, molecules with two functional groups so they combine with two others selected, and unifunctional monomers (with only one functional group) sorted out?8. How could achiral precursors of amino acids have produced and concentrated/selected only left-handed amino acids? (The homochirality problem)9. How did the transition from prebiotic enantiomer selection to the enzymatic reaction of transamination occur that had to be extant when cellular self-replication and life began?10. How would natural causes have selected twenty, and not more or less amino acids to make proteins?11. How did natural events have foreknowledge that the selected amino acids are best suited to enable the formation of soluble structures with close-packed cores, allowing the presence of ordered binding pockets inside proteins?12. How did nature "know" that the set of amino acids selected appears to be near ideal and optimal?Out of the 12 listed problems of
prebiotic cell membrane synthesis, 2 are directly related to the lack of a mechanism to select the right ingredients.
1. How did prebiotic processes
select hydrocarbon chains which must be in the range of 14 to 18 carbons in length? There was no physical necessity to form carbon chains of the right length nor hindrance to join chains of varying lengths. So they could have been existing of any size on the early earth.
2. How would random events start to produce biological membranes which are not composed of pure phospholipids, but instead are mixtures of several phospholipid species, often with a sterol admixture such as cholesterol? There is no feasible prebiotic mechanism to
select/join the right mixtures.
Claim: Even if we take your unknowns as true unknowns or even unknowable, the answer is always going to be “We don’t know yet.”
Reply: Science HATES saying confessing "we don't know". Science is about knowing and getting knowledge and understanding. The scientists mind is all about getting knowledge and diminishing ignorance. Confessing of not knowing, when there is good reason for it, is ok. But claiming of not knowing, despite the evident facts easy at hand and having the ability to come to informed well-founded conclusions based on sound reasoning, and through known facts and evidence, is not only willful ignorance but plain foolishness. In special, when the issues in the discussion are related to origins and worldviews, and eternal destiny is at stake. If there were hundreds of possible statements, then claiming of not knowing which makes most sense could be justified. In the quest of origins and God, there are just two possible explanations. Either there is a God, or there is not a God. That's it. There is however a wealth of evidence in the natural world, which can lead us to informed, well-justified conclusions. We know for example that nature has no "urge" to select things and to complexify, but its natural course is to act upon the laws of thermodynamics, and molecules disintegrate. That is their normal course of action. To become less complex. Systems, given energy and left to themselves, DEVOLVE to give uselessly complex mixtures, “asphalts”. The literature reports (to our knowledge) exactly ZERO CONFIRMED OBSERVATIONS where evolution emerged spontaneously from a devolving chemical system. it is IMPOSSIBLE for any non-living chemical system to escape devolution to enter into the Darwinian world of the “living”. Such statements of impossibility apply even to macromolecules. Both monomers and polymers can undergo a variety of decomposition reactions that must be taken into account because biologically relevant molecules would undergo similar decomposition processes in the prebiotic environment.
CAIRNS-SMITH 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 the primitive Earth?
Claim: That’s called the Sherlock fallacy. It's a false dichotomy
Reply: No. Life is either due to chance, or design. There are no other options.
One of the few biologists,
Eugene Koonin, Senior Investigator at the National Center for Biotechnology Information, a recognized expert in the field of evolutionary and computational biology, is honest enough to recognize that abiogenesis research has failed. He wrote in his book: The Logic of Chance page 351:
" Despite many interesting results to its credit, when judged by the straightforward criterion of reaching (or even approaching) the
ultimate goal, the origin of life field is a failure—we still do not have even a plausible coherent model, let alone a validated scenario, for the emergence of life on Earth. Certainly, this is due not to a lack of experimental and theoretical effort, but to the extraordinary intrinsic difficulty and complexity of the problem. A succession of exceedingly unlikely steps is essential for the origin of life, from the synthesis and accumulation of nucleotides to the origin of translation; through the multiplication of probabilities, these make
the final outcome seem almost like a miracle.Eliminative inductions argue for the truth of a proposition by demonstrating that competitors to that proposition are false. Either the origin of the basic building blocks of life and self-replicating cells are the result of the creative act by an intelligent designer, or the result of unguided random chemical reactions on the early earth. Science, rather than coming closer to demonstrate how life could have started, has not advanced and is further away to generating living cells starting with small molecules. Therefore, most likely, cells were created by an intelligent designer.
I have listed 27 open questions in regard to the origin of RNA and DNA on the early earth, 27 unsolved problems in regard to the origin of amino acids on the early earth, 12 in regard to phospholipid synthesis, and also unsolved problems in regard to carbohydrate production. The open problems are in reality far greater. This is just a small list. It is not just an issue of things that have not yet been figured out by abiogenesis research, but deep conceptual problems, like the fact that there were no natural selection mechanisms in place on the early earth.
https://reasonandscience.catsboard.com/t1279p75-abiogenesis-is-mathematically-impossible#77591. https://onlinelibrary.wiley.com/doi/abs/10.1002/cbdv.200790167
2. https://sci-hub.ren/10.1007/978-1-4939-1468-5_27
3. https://arxiv.org/ftp/arxiv/papers/1511/1511.00698.pdf
4. https://link.springer.com/book/10.1007%2Fb136268
5. https://www.mdpi.com/2073-8994/12/12/2046
