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Defending the Christian Worlview, Creationism, and Intelligent Design

This is my personal virtual library, where i collect information, which leads in my view to the Christian faith, creationism, and Intelligent Design as the best explanation of the origin of the physical Universe, life, and biodiversity


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Defending the Christian Worlview, Creationism, and Intelligent Design » Origin of life » Abiogenesis is mathematically impossible

Abiogenesis is mathematically impossible

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Otangelo


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The gap is enormous between the simplicity-toward- complexity models,which can suggest how simple replication of small sets of polymers may have emerged,and complexity-toward-simplicity models,which suggest a minimum of several hundred genes and their products networked within specialized metabolic compartments. What kind of evolvable entities might bridge this gap?
https://sci-hub.ren/10.1016/j.jtbi.2014.11.025


Simple prebiotic synthesis of high diversity dynamic combinatorial polyester libraries
31 May 2018
The generation and selection of molecules with activities including catalysis and replication from random complex mixtures remains a major challenge in origin of life research
https://www.nature.com/articles/s42004-018-0031-1



Last edited by Otangelo on Sat Jan 30, 2021 11:50 am; edited 1 time in total

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Otangelo


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The beauty of Abiogenesis ("Chemical evolution"), in an Origins debate context, is both the simplicity of the facts and the magnitude of its black and white starkness. There's "0" middle ground. Biomacromolecules, hundreds of millions strong in the biosphere, cannot be shown to abiotically self synthesize in 1) Nature, 2) the laboratory (even with ridiculous [60+ years!!] high level human interventionism):

https://retractionwatch.com/2017/12/05/definitely-embarrassing-nobel-laureate-retracts-non-reproducible-paper-nature-journal/?fbclid=IwAR1KdmyAK1yChhcTNEQhtIDcVdDbkC_EG4N0l4W4SQwsyRPJxlpCYbW9fic

and 3) nor can they be shown, oceans strong, to have **ever** existed, deeply buried in geologic history.

Three strikes, you're done!! Life did't create or self arise apart from outside "super" natural interventionism.

Now, what was that about "appealing to ignorance" and incredulity? You mean blind, fairytale beliefism in foundationless evolutionism? That's about right.

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Otangelo


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In a living cell, abasic sites left by depurination are quickly repaired by the action of specific enzymes, but in prebiotic conditions adenine and guanine would be lost at a certain rate from any nucleotide or nucleic acid. Another spontaneous reaction is the deamination of cytosine to produce uracil. This was recognized by Shapiro [80] as an important problem related to the origin of a genetic code.

Carbohydrates are also subject to chemical damage. For instance, amine groups can react with ribose and other sugars to produce cross linking in the Maillard reaction. Reducing sugars can also react with other sugar molecules at higher temperatures, a process called caramelization. In both cases this produces the familiar brown polymer present in all baked or grilled food, but would interfere with the synthesis of biologically relevant bonds.

Undesired crosslinking reactions. At ordinary temperature ranges in aqueous solution there is insufficient activation energy to drive random crosslinking between biologically relevant monomers, and the thermodynamically favored decomposition reaction is hydrolysis. When solutions are dehydrated by evaporation, solutes become concentrated, and in the anhydrous state the thermodynamic balance shifts from hydrolysis to the condensation reactions described earlier.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5370405/

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Otangelo


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https://www.flickr.com/photos/truth-in-science/16208667768/in/photolist-qGiEe7-ntpng3-p47acs-v2h544-pVpvA2-qLrk28-pVCjgF-ptctWq-pQYvD8-GC7wCj-r9SUPL-prfnyL-pw4eKS-kJEHCU-pkvDrJ-obZFsS-nVM5f7-kwT4qB-mBQN2N-q4AvLr-kmqhat-kmpZ5r-kjQn6r-kmstMU-kJVYxn

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Otangelo


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In an article in 2014, The Richard Dawkins Foundation asked:  How did the eye evolve?  They cited an article published at pbs.org where they wrote:

Zoologist Dan-Erik Nilsson demonstrates how the complex human eye could have evolved through natural selection acting on small variations. Starting with a simple patch of light-sensitive cells, Nilsson's model "evolves" until a clear image is produced.

In the last sentence of Nilsson’s paper, which has been used since it was published in 1994 as a reference to back up the claim that eyes could have evolved, Nilsson wrote:

"the eye was never a real threat to Darwin's theory of evolution."

Back in 1997, Professor Michael J. Behe wrote an article entitled: Molecular Machines: Experimental Support for the Design Inference, where he pointed out that:

In order to say that some function is understood, every relevant step in the process must be elucidated. The relevant steps in biological processes occur ultimately at the molecular level, so a satisfactory explanation of a biological phenomenon such as sight must include a molecular explanation. It is no longer sufficient, now that the black box of vision has been opened, for an ‘evolutionary explanation’ of that power to invoke only the anatomical structures of whole eyes, as Darwin did in the 19th century and as most popularizers of evolution continue to do today. Anatomy is, quite simply, irrelevant.

This is a landmark observation and has guided many of my investigations in regards to Intelligent Design. Has Nilsson’s paper not failed precisely on that very point?

Following Behe’s guideline, I took the same starting point as Nilsson, but not considering the eyespot as an initial stage of the evolutionary trajectory, and then showing a lineup of anatomical development,  but rather attempting to understand how evolution could have operated at a molecular level, culminating in supposedly “ primitive” eyespots. What was conveniently ignored by Nilsson, is that eyespots do only perform a function, for example in green algae, like Chlamydomonas, when embedded in a visual system useful for a higher functional end. Phototaxis is essential for green algae; They either move towards light upon which they depend for energy and nutrition, yet also undergoing negative phototaxis to protect themselves against too intense sources of illumination.  The eyespot is not the photoreceptor itself but rather a mass of carotenoid pigment shading the photoreceptor from light from one direction. A photosensitive organism needs a photoreceptor that detects the light. But that alone would not allow the organism to determine the direction of the light source. A pigmented spot reduces the illumination from one direction or changes the wavelength of the incident light falling on the photoreceptor, thus allowing the organism to move in the direction of the light or away of it. So next, a mechanism to promote movement is essential. To detect the light is one thing but to move towards or away from it requires a motor system; in green algae, the famous flagellum. But also a mechanism is required by which detection of light can be translated into a change in flagellar movement, generally an ion flux of one kind or another

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Otangelo


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- factory portals with fully automated security checkpoints ( membrane proteins )
- factory compartments ( organelles )
- a library index program ( the gene regulatory network )
- molecular computers, hardware ( DNA ) 
- software ( the genetic and over a dozen epigenetic codes )
- information retrieval ( RNA polymerase )
- transmission ( messenger RNA )
- translation ( Ribosome ) 
- signalling ( hormones ) 
- complex machines ( proteins )
- taxis ( dynein, kinesin, transport vesicles )
- molecular highways ( tubulins, used by dynein  for transport to various destinations )
- tagging programs ( each protein has a tag, which is an amino acid sequence )
- factory assembly lines ( fatty acid synthase, non-ribosomal peptide synthase )
- error check and repair systems  ( exonucleolytic proofreading, mismatch repair ) 
- recycling methods ( endocytic recycling )
- waste grinders and management  ( Proteasome Garbage Grinders )  
- power generating plants ( mitochondria )
- power turbines ( ATP synthase )
- electric circuits ( the metabolic network )



Last edited by Otangelo on Sun Jan 17, 2021 9:14 am; edited 1 time in total

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Otangelo


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Jack Szostak, Scientific American, 2009
It is virtually impossible to imagine how a cell’s machines, which are mostly protein-based catalysts called enzymes, could have formed spontaneously as life first arose from nonliving matter around 3.7 billion years ago.
https://www.commackschools.org/Downloads/Origin%20of%20Life%20article%20Scientific%20American.pdf

George Whiteside
I don't understand how you go from a system that's random chemicals to something that becomes in a sense the Darwinian set of chemical reactions that are getting more complicated spontaneously I just don't understand how that works
https://www.technologyreview.com/s/428793/three-questions-for-george-whitesides/

Origins of life | George M. Whitesides | TEDxBoston
https://www.youtube.com/watch?v=0fJffUkViOQ

Imagine a chicken looking skeptically at a bowl of chicken soup and you know how we all know how to as it was disassembled a chicken into the pieces to make chicken soup you boil it and the molecules that make up the chicken make chicken soup think about the problem of going backward how would you go from chicken soup to chicken? no idea? but that's the problem of the origin of life because something like that must have happened

A Replicator Was Not Involved in the Origin of Life Robert Shapiro
a profound difficulty exists however with the idea of RNA or any other replicator at the start of life existing replicators can serve as templates for the sense of the synthesis of additional copies of themselves but this device cannot be used for the preparation of the very next such molecule which must arise spontaneously from an unorganized mixture the formation of an information-bearing homo polymer through undirected chemical synthesis appears to be very improbable
https://iubmb.onlinelibrary.wiley.com/doi/pdf/10.1080/713803621

Richard Dawkins
The universe could so easily have remain lifeless it is an astonishing stroke of luck that we were here that's a big concession isn't it coming from him I mean that's a really big concession a stroke of luck

Abiogenesis is mathematically  impossible - Page 4 Sem_tz45



Last edited by Otangelo on Fri Jan 22, 2021 7:35 pm; edited 2 times in total

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83Abiogenesis is mathematically  impossible - Page 4 Empty Paradoxes in the Origin of Life Sat Mar 21, 2020 4:37 pm

Otangelo


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Paradoxes in the Origin of Life

https://reasonandscience.catsboard.com/t1279p75-abiogenesis-is-virtually-impossible#7309

Steven A. Benner

https://www.ncbi.nlm.nih.gov/pubmed/25608919

Discussed here is an alternative approach to guide research into the origins of life, one that focuses on “paradoxes”, pairs of statements, both grounded in theory and observation, that (taken together) suggest that the “origins problem” cannot be solved.

The Asphalt Paradox 
Systems, given energy and left to themselves, DEVOLVE to give uselessly complex mixtures, “asphalts”.  the literature reports (to our knowledge) exactly  ZERO CONFIRMED OBSERVATIONS where “replication involving replicable imperfections” (RIRI) evolution emerged spontaneously from a devolving chemical system. it is IMPOSSIBLE for any non-living chemical system to escape devolution to enter into the Darwinian world of the “living”. Such statements of impossibility apply even to macromolecules not assumed to be necessary for RIRI evolution. 

Decomposition of Monomers, Polymers and Molecular Systems: An Unresolved Problem 2017 Jan 17
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5370405/
It is clear that non-activated nucleotide monomers can be linked into polymers under certain laboratory conditions designed to simulate hydrothermal fields. However, both monomers and polymers can undergo a variety of decomposition reactions that must be taken into account because biologically relevant molecules would undergo similar decomposition processes in the prebiotic environment.

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?

Intractable Mixtures and the Origin of Life 2007
Whatever the exact nature of an RNA precursor which may have become the first selfreplicating molecule, how could the chemical homogeneity which seems necessary to permit this kind of mechanism to even come into existence have been achieved? What mechanism would have selected for the incorporation of only threose, or ribose, or any particular building block, into short oligomers which might later have undergone chemically selective oligomerization? Virtually all model prebiotic syntheses produce mixtures. 6

OPEN QUESTIONS IN ORIGIN OF LIFE: EXPERIMENTAL STUDIES ON THE ORIGIN OF NUCLEIC ACIDS AND PROTEINS WITH SPECIFIC AND FUNCTIONAL SEQUENCES BY A CHEMICAL SYNTHETIC BIOLOGY APPROACH February 2014
Attempts to obtain copolymers, for instance by a random polymerization of monomer mixtures, yield a difficult to characterize mixture of all different products. To the best of our knowledge, there is no clear approach to the question of the prebiotic synthesis of macromolecules with an ordered sequence of residues.
https://www.sciencedirect.com/science/article/pii/S2001037014600076

The Water Paradox:
The hydrolytic deamination of DNA and RNA nucleobases is rapid and irreversible, as is the base-catalyzed cleavage of RNA in water.  RNA requires water to function, but RNA CANNOT emerge in water and does not persist in water without repair. Life seems to need a substance (water) that is inherently toxic to  RNA necessary for life.

The Information-Need Paradox.
Biopolymers that might plausibly support “replication involving replicable imperfections” RIRI evolution ARE TOO LONG TO HAVE ARISEN SPONTANEOUSLY from the amounts of building blocks that might plausibly (again by theory) have escaped asphaltic devolution in water.

The Single Biopolymer Paradox.
Even if we can make biopolymers prebiotically, it IS HARD TO IMAGINE making two or three (DNA, RNA, proteins) at the same time. 

The Probability Paradox.
Experiments show that RNA molecules that catalyze the destruction of RNA are more likely to arise in a pool of random (with respect to fitness) sequences than RNA molecules that catalyze the replication of RNA, with or without imperfections.  Thus, even if we solve the asphalt paradox, the water paradox, the information need paradox, and the single biopolymer paradox, we still must mitigate or set aside chemical theory that makes destruction, not biology, the natural outcome of are already magical chemical system.

Paradoxes in the Origin of Life Steven A. Benner
https://sci-hub.st/https://www.ncbi.nlm.nih.gov/pubmed/25608919

“replication involving replicable imperfections” (RIRI)

(a) The Asphalt Paradox (Neveu et al. 2013).
An enormous amount of empirical data have established, as a rule, that organic systems, given energy and left to themselves, devolve to give uselessly complex mixtures, “asphalts”. Theory that enumerates small molecule space, as well as Structure Theory in chemistry, can be construed to regard this devolution a necessary consequence of theory. Conversely, the literature reports (to our knowledge) exactly zero confirmed observations where “replication involving replicable imperfections” (RIRI) evolution emerged spontaneously from a devolving chemical system. Further, chemical theories, including the second law of thermodynamics, bonding theory that describes the “space” accessible to sets of atoms, and structure theory requiring that replication systems occupy only tiny fractions of that space, suggest that it is impossible for any non-living chemical system to escape devolution to enter into the Darwinian world of the “living”. Such statements of impossibility apply even to macromolecules not assumed to be necessary for RIRI evolution. Again richly supported by empirical observation, material escapes from known metabolic cycles that might be viewed as models for a “metabolism first” origin of life, making such cycles short-lived. Lipids that provide tidy compartments under the close supervision of a graduate student (supporting a protocell first model for origins) are quite non-robust with respect to small environmental perturbations, such as a change in the salt concentration, the introduction of organic solvents, or a change in temperature.

b) The Water Paradox:
Water is commonly viewed as essential for life, and theories of water are well known to support this as a requirement. So are biopolymers, like RNA, DNA, and proteins. However, these biopolymers are corroded by water. For example, the hydrolytic deamination of DNA and RNA nucleobases is rapid and irreversible, as is the base-catalyzed cleavage of RNA in water. This allows us to construct a paradox: RNA requires water to function, but RNA cannot emerge in water, and does not persist in water without repair. Any solution to the “origins problem” must manage the paradox forced by pairing this theory and this observation; life seems to need a substance (water) that is inherently toxic to polymers (e.g. RNA) necessary for life.

(c) The Information-Need Paradox.
Theory can estimate the amount of information required for a chemical system to gain access to replication with imperfections that are themselves replicable. These estimates vary widely. However, by any current theory, biopolymers that might plausibly support RIRI evolution are too long to have arisen spontaneously from the amounts of building blocks that might plausibly (again by theory) have escaped asphaltic devolution in water. If a biopolymer is assumed to be necessary for RIRI evolution, we must resolve the paradox arising because implausibly high concentrations of building blocks generate biopolymers having inadequate amounts of information. These propositions from theory and observation also force the conclusion that the emergence of (in this case, biopolymer-based) life is impossible.

(d) The Single Biopolymer Paradox.
Even if we can make biopolymers prebiotically, it is hard to imagine making two or three (DNA, RNA, proteins) at the same time. For several decades, this simple observation has driven the search for a single biopolymer that “does” both genetics and catalysis. RNA might be such a biopolymer. However, genetics versus catalysis place very different demands on the behavior of a biopolymer. According to theory, catalytic biopolymers should fold; genetic biopolymers should not fold. Catalytic biopolymers should contain many building blocks; genetic biopolymers should contain few. Perhaps most importantly, catalytic biopolymers must be able to, catalyze reactions, while genetic biopolymers should not be able to catalyze reactions and, in particular, reactions that destroy the genetic biopolymer. Any “biopolymer first” model for origins must resolve these paradoxes, giving us a polymer that both folds and does not fold, has many building blocks at the same time as having few, and has the potential to catalyze hard-but-desired reactions without the potential to catalyze easy-but undesired reactions.

(e) The Probability Paradox.
Some biopolymers, like RNA, strike a reasonable compromise between the needs of genetics and the needs of catalysis. Further, no theory creates a paradox that excludes the possibility that some RNA might catalyze the replication of RNA, with imperfections, where the imperfections are replicable. However, experiments show that RNA molecules that catalyze the destruction of RNA are more likely to arise in a pool of random (with respect to fitness) sequences than RNA molecules that catalyze the replication of RNA, with or without imperfections. Chemical theory expects this to be the case, as the base-catalyzed cleavage of RNA is an “easy” reaction (stereoelectronically), while the SN2 reaction that synthesizes a phosphodiester bond is a “difficult” reaction. Thus, even if we solve the asphalt paradox, the water paradox, the information need paradox, and the single biopolymer paradox, we still must mitigate or set aside chemical theory that makes destruction, not biology, the natural outcome of are already magical chemical system.



Last edited by Otangelo on Sat Feb 27, 2021 11:01 am; edited 11 times in total

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84Abiogenesis is mathematically  impossible - Page 4 Empty Prebiotic chemistry and human intervention Wed Apr 01, 2020 2:26 pm

Otangelo


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Prebiotic chemistry and human intervention

12 December 2018
https://www.nature.com/articles/s41467-018-07219-5?fbclid=IwAR326klkI5xfGPxLjXbHTM_uJoM1toQkKUFcbiiNcbhJMk_-nMgLZLoXB6Q

For experiments aimed at demonstrating chemically complex processes, such as multistep syntheses mimicking biochemical pathways or genetic replication, repeated interventions by the experimentalist have been necessary. Each step needs a specific chemical environment or set of conditions to occur in high yield. For example, an elimination reaction needs other conditions than an addition reaction, and assuming that both will occur simultaneously in the same solution is unrealistic.

In the cell, the individual steps of a biosynthetic pathway are usually catalyzed by different enzymes. Each enzyme creates a specific microenvironment for a reaction in its active site. For potentially prebiotic, enzyme-free multistep syntheses, a chemical work-up at the end of a reaction is often required, involving steps such as precipitation, crystallization or other forms of handling and purification, and an often drastic change in chemical conditions from one synthetic transformation to the next.

Life is a non-equilibrium phenomenon. It requires an energy source that drives its reactions. Assuming that simple heating/cooling cycles could have driven the formation of functional biomacromolecules that were then able to harness the energy emitted by the sun via photosynthesis, seems unrealistic to me. Achieving the level of specificity required to successfully operate a protocell with genetic apparatus, metabolism, and cell division under strongly denaturing conditions is not easy, certainly when it comes to enzyme-free replication relying on the intrinsic specificity of small molecule interactions. So, the periodic addition of a chemical condensing agent may be unavoidable to drive biochemical reactions that are endergonic, even in “minimal intervention” experiments. Without the chemical activation, equilibrium (death) sets in. So, some level of human intervention may always be required for complex, multistep processes. After all, what the dominant activation agent was before enzymes began to use ATP will remain an enigma to many of us for the foreseeable future.

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Otangelo


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How did life begin? Abiogenesis. Origin of life from nonliving matter.
https://www.youtube.com/watch?v=nNK3u8uVG7o&feature=youtu.be&fbclid=IwAR2RgT7KvOntGEnHKiFNYfU4T2Fwyg1R2oZq4loVM5bUqdSgsQN_9INXOEM


At the fundamental level all living things contain a trinity of elements. First, nucleic acids, which make up the DNA or it's simpler form called RNA. These contain the blueprints of life and are self-replicating molecules. Second, there
are proteins, which are the workhorses that perform the important functions of your body. And third, are lipids which encapsulate the cells of your body.So these fatty membranes composed of lipids were critical components for abiogenesis.

My comment: All living things contain a trinity of elements implies irreducible complexity. Without at least these three elements, life could not exist ( there are many more, however )


Before any living things existed, before animals, plants and even bacteria existed, these three things had to have been present in the primordial soup in order for life to start.

My comment: What the author conveniently does not say, is that none of the basic building blocks of life have ever been synthesized in the laboratory. 


However, just this year, in 2019 researchers at the University of Washington showed that lipid spheres do not disassemble if they are in the presence of amino acids, which are precursors to protein molecules. In addition, the enclosing of amino acids within cell walls allows amino acids to concentrate within the walls and interact with each other to form proteins.

My comment: In order to have the amino acids used in life, you have to select the right ones amongst over 500 that occur naturally on earth. To get functional ones, you need to sort them out between left-handed and right-handed ones ( the homochirality problem). Only left-handed amino acids are used in cells. There is no selection process known besides the one used in cells by sophisticated enzymes, which produce only left-handed amino acids. This is just a tiny problem to form proteins. 

So now we see that lipids and proteins can potentially form in the presence of each other. 

My comment: This is pure pseudo-scientific nonsense. Far more is required for proteins. Instructional/specified complex information is required to get the right amino acid sequence which is essential to get the functionality in a vast sequence space ( amongst trillions os possible sequences, rare are the ones that provide function ) Chance of random chemical reactions to setup amino-acid polypeptide chains to produce  functional proteins, a minimal proteome on early earth external to cellular biosynthesis: 1 in 10^350.000 That's virtually the same as 0%. There are 10^80 atoms in the universe.


In a 2009 study, researchers at Rensselaer Polytechnic Institute in Troy New York, showed that current-day RNA could have formed on the surface of clays which act like catalyst to bring RNA bases together, as shown in this animation. A 2017 paper by scientists from McMaster University in Canada, and the Max Planck Institute in Germany, showed that the building blocks of RNA could have polymerized in the early Earth using organic molecules from meteorites and interplanetary dust in shallow ponds.

My comment: Although Sutherland has shown that it is possible to build one part of RNA from small molecules, objectors to the RNA-world theory say the RNA molecule as a whole is too complex to be created using early-Earth geochemistry. "The flaw with this kind of research is not in chemistry. The flaw is in the logic — that this experimental control by researchers in a modern laboratory could have been available on the early Earth," says Robert Shapiro


The wet/dry cycle of these ponds, they showed, is conducive to RNA polymerization. They also theorized that such polymers were probably present on earth shortly after its formation as early as 4.17 billion years ago.

My comment: This leaves out that there are many other unsolved problems of how to make RNA prebiotically. None of the bases have been synthesized in the lab either. Nor the reaction to join the three parts together. The author leaves this information conveniently out in his narrative. 

In the 1950s, several experiments by Stanley Miller and Harold Urey verified that the natural formation of amino acids, components of proteins, and other organic compounds, out of organic materials, was possible under the atmospheric conditions of the primordial earth.

My comment: An interview from 1998 with exobiology pioneer, Dr. Stanley L. Miller, University of California San Diego 3
We've shown that either you have a reducing atmosphere or you are not going to have the organic compounds required for life. If you don't make them on Earth, you have to bring them in on comets, meteorites or dust. Certainly, some material did come from these sources. In my opinion, the amount from these sources would have been too small to effectively contribute to the origin of life.

The amount of useful compounds you are going to get from meteorites is very small. The dust and comets may provide a little more. Comets contain a lot of hydrogen cyanide, a compound central to prebiotic synthesis of amino acids as well as purines. Some HCN came into the atmosphere from comets. Whether it survived impact, and how much, are open to discussion. I'm skeptical that you are going to get more than a few percent of organic compounds from comets and dust.

it was trillions upon trillions of amino acids reacting in countless places, over millions of years, that resulted in simple protein molecules. There are about 4x10^47 molecules of water in Earth's oceans. Even if there was one amino acid among 1 million water molecules, that would be 10 to the power 41 molecules of amino acids that had the opportunity to interact with each other, and to form proteins in numerous environments, in numerous places,
and in numerous trials, over millions of years, to produce proteins. 

My comment: That would still not be enough. If we sum up the total number of amino acids for a minimal Cell, there would have to be about 400 proteins x average 400 amino acids  =  160.000 amino acids, which would have to be bonded in the right sequence, choosing for each position amongst 20 different amino acids, and selecting only the left-handed, while sorting out the right-handed ones. That means each position would have to be selected correctly from 40 variants !! that is 1 right selection out of 40^160.000 possibilities or 10^350.000 !! Obviously, a gigantic number far above any realistic probability to occur by unguided events. Even a trillion universes, each hosting a trillion planets, and each shuffling a trillion times in a trillionth of a second, continuously for a trillion years, would not be enough. Such astronomically unimaginably gigantic odds are in the realm of the utmost extremely impossible. 

In 2014 Jeremy England, physics professor at MIT, showed mathematically that the driving force for chemical evolution may be hidden in physics, in Newton's second law of thermodynamics. that's our old friend "entropy." From a physics point of view, the one thing that distinguishes living things from nonliving things is its ability to capture energy and convert it to heat. England argues that when exposed to an external source of energy, such as the sun, any group of molecules will restructure themselves to dissipate more and more energy. 

My comment: life in any form is a very serious enigma and conundrum. It does something, whatever the biochemical pathway, machinery, enzymes, etc. are involved, that should not and honestly could not ever "get off the ground". It SPONTANEOUSLY recruits Gibbs free energy from its environment so as to reduce its own entropy. That is tantamount to a rock continuously recruiting the wand to roll it up the hill, or a rusty nail "figuring out" how to spontaneously rust and add layers of galvanizing zinc on itself to fight corrosion. Unintelligent simple chemicals can't self-organize into instructions for building solar farms (photosystems 1 and 2), hydroelectric dams (ATP synthase), propulsion (motor proteins), self-repair (p53 tumor suppressor proteins) or self-destruct (caspases) in the event that these instructions become too damaged by the way the universe USUALLY operates. Abiogenesis is not an issue that scientists simply need more time to figure out but a fundamental problem with materialism

https://reasonandscience.catsboard.com/t1279p75-abiogenesis-is-virtually-impossible#7582

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Otangelo


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Evolution, Origin of Life, Concepts and Methods Kunio Kawamura page 10
The origin-of-life problem has been well accepted as a practical scientific problem through the achievements by Pasteur, Oparin, and Miller. The difference between modern organisms and RNA-based life-like systems is quite large. Therefore, the uncertainty on how the RNA-based life-like system could have evolved to the modern method including the complicated assignment mechanism between DNA sequence and amino acid sequence of proteins is currently an important issue. 

My comment: Why does the author mention evolution, if there was not such a mechanism at disposal at this stage? 

The gap between the assignment methods between genotype and phenotype in the RNA-based life-like system and that in modern organisms involves the emergence of tRNA, rRNA, and aminoacyl-tRNA synthetase.

My comment: Agreed. And all these different RNA's,  tRNA, rRNA, and aminoacyl-tRNA synthetase had to be operational together to get to a translation process as used in modern life forms. One would have had no function without the other. 

Different kinds of functional RNA molecules should have been present for the construction of the RNA-based life-like systems. However, it is unclear what kinds of functions were necessary to make a life-like system.

My comment: It is unclear because there is no feasible way to reduce the pathway from genes to proteins.

The whole process of the spontaneous formation of RNA polymerase ribozymes from nucleotide monomers under prebiotic conditions is not yet clear. Presumably, primitive RP ribozymes would have been produced spontaneously as the model RP ribozymes can be constructed by using the in vitro selection engineering method of RNA

My comment: presumably based on what evidence? There is no evidence that this would have been possible.

Here, we briefly consider proteins from the viewpoint of the RNA world hypothesis. Thus, an argument that the difficulty for solving the connective pathway between the RNA-based lifelike systems to the modern systems is evidence to deny the RNA world hypothesis is not correct. The hypothetical protein-like-molecule-based life-like system should have possessed an assignment method between genotype and phenotype at least if it was present before the modern system. Protein or protein-like molecules are considered as key molecules during the chemical evolution from the RNA-based life-like system to the most primitive organism.

My comment: How to assign 64 codons to 20 amino acids is an intractable abiogenesis problem. There was no affinity, since the binding of codons to tRNAs is not directly physically connected, and there is another, third player,  aminoacyl-tRNA synthetases, which must also have the right assignment, and recognize which tRNA belongs to which amino acids.

For the spontaneous formation of oligopeptides, it was shown that peptides could have formed under such extreme Earth conditions. However, the peptide formation found by the simulation experiments was not efficient, as the yields of oligopeptides remain 0.1–1%

My comment: These are figures of "success" that obviously demonstrate remote success.

https://reasonandscience.catsboard.com

Otangelo


Admin
This was my introduction discourse in my debate with Leophilius:

Intelligent Design in Abiogenesis? DEBATE | Otangelo Vs Leophilius
https://www.youtube.com/watch?v=eb1YWZz4-d0&lc=z23zub5o0sznuvfyn04t1aokgo0f1ajzwhxo0vjnxnxpbk0h00410.1594768575517304

The origin of life is widely regarded as one of the most difficult open problems in science.  ‘Bottom-up’ approaches in the laboratory have not generated anything nearly as complex as a living cell. And what has been achieved, is a far cry from the complexity of anything living. The total lack of any kind of experimental evidence leading to the re-creation of life; not to mention the spontaneous emergence of life…  undermines the worldview of who wants materialism to be true. But of course, there is always an excuse: Science is working on it. But is it really justified to put hope that one day a materialistic explanation will be found?

David Denton stated:
We now know not only of the existence of a break between the living and non-living world but also that it represents the most dramatic and fundamental of all the discontinuities of nature. Between a living cell and the most highly ordered non-biological systems, such as a crystal or a snowflake, there is a chasm as vast and absolute as it is possible to conceive.

And Lynn Margulis stated: To go from a bacterium to people is less of a step than to go from a mixture of amino acids to a bacterium.

And Eugene Koonin advisory editorial board of Trends in Genetics stated:
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. The difficulties remain formidable. For all the effort, we do not currently have coherent and plausible models for the path from simple organic molecules to the first life forms. Most damningly, the powerful mechanisms of biological evolution were not available for all the stages preceding the emergence of replicator systems. Given all these major difficulties, it appears prudent to seriously consider radical alternatives for the origin of life. "

And in fact, there are basically just two options to consider: Either life emerged by a lucky accident, spontaneously through self-organization by unguided natural events, or through the direct intervention, creative force, and activity of an intelligent designer. Evolution is not a possible explanation, because evolution depends on DNA replication. Many have claimed that physical necessity could have promoted chemical reactions, which eventually resulted in the emergence of life. The problem here however is, that the genetic sequence that specifies the arrangement of proteins can be of any order, there is no constraint by physical needs.

To understand why random events are not a good explanation, we best have a look at the deepest level, on an atomic scale. Life uses just five nucleobases to make DNA and RNA. Two purines, and three pyrimidines. Purines use two rings with nine atoms, pyrimidines use just one ring with six atoms. Hydrogen bonding between purine and pyrimidine bases is fundamental to the biological functions of nucleic acids, as in the formation of the double-helix structure of DNA. This bonding depends on the selection of the right atoms in the ring structure. Pyrimidine rings consist of six atoms: 4 carbon atoms and 2 nitrogen atoms. Purines have nine atoms forming the ring: 5 carbon atoms and 4 nitrogen atoms.

Remarkably, it is the composition of these atoms that permit that the strength of the hydrogen bond that permits to join the two DNA strands and form Watson–Crick base-pairing, and well-known DNA ladder.  Neither transcription nor translation of the messages encoded in RNA and DNA would be possible if the strength of the bonds had different values. Hence, life, as we understand it today, would not have arisen.

Now, someone could say, that there could be no different composition, and physical constraints and necessity could eventually permit only this specific order and arrangement of the atoms. Now, in a recent science paper from 2019, Scientists explored how many different chemical arrangements of the atoms to make these nucleobases would be possible. Surprisingly, they found well over a million variants.   The remarkable thing is, among the incredible variety of organisms on Earth, these two molecules are essentially the only ones used in life. Why? Are these the only nucleotides that could perform the function of information storage? If not, are they perhaps the best? One might expect that molecules with smaller connected Carbon components should be easier for abiotic chemistry to explore.

According to their scientific analysis, the natural ribosides and deoxyribosides inhabit a fairly redundant ( in other words, superfluous, unnecessary, needless,  and nonminimal region of this space.  This is a remarkable find and implicitly leads to design. There would be no reason why random events would generate complex, rather than simple, and minimal carbon arrangements. Nor is there physical necessity that says that the composition should be so. This is evidence that a directing intelligent agency is the most plausible explanation. The chemistry space is far too vast to select by chance the right finely-tuned functional life-bearing arrangement.

In the mentioned paper, the investigators asked if other, perhaps equally good, or even better genetic systems would be possible.  Their chemical experimentations and studies concluded that the answer is no. Many nearly as good, some equally good, and a few stronger base-pairing analog systems are known. There is no reason why these structures could or would have emerged in this functional complex configuration by random trial and error. There is a complete lack of scientific-materialistic explanations despite decades of attempts to solve the riddle.

What we can see is, that direct intervention, a creative force, the activity of an intelligent agency, a powerful creator, is capable to have the intention and implement the right arrangement of every single atom into functional structures and molecules in a repetitive manner, in the case of DNA, at least 500 thousand nucleotides to store the information to kick-start life, exclusively with four bases, to produce a storage device that uses a genetic code, to store functional, instructional, complex information, functional amino acids, and phospholipids to make membranes, and ultimately, life.  Lucky accidents, the spontaneous self-organization by unguided coincidental events, that drove atoms into self-organization in an orderly manner without external direction, chemical non-biological are incapable and unspecific to arrange atoms into the right order to produce the four classes of building blocks, used in all life forms.

https://reasonandscience.catsboard.com

Otangelo


Admin
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#7759

Prevital RNA and DNA  synthesis

RNA & DNA: It's prebiotic synthesis: Impossible !! Part 1
https://www.youtube.com/watch?v=-ZFlmL_BsXE

RNA & DNA: It's prebiotic synthesis: Impossible !! Part 2
https://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 synthesis

Chemical 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 synthesis
How 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 hydrocarbons
How 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#7759
1. 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



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Biological Cell factories point overwhelmingly to set up by intelligent design

https://reasonandscience.catsboard.com/t1279p75-abiogenesis-is-mathematically-impossible#7761

factory portals with fully automated security checkpoints and control ( membrane proteins )
factory compartments ( organelles )
a library index and fully automated information classification, storage, and retrieval program ( chromosomes, and the gene regulatory network )
molecular computers, hardware ( DNA )
software, a language using signs and codes like the alphabet, an instructional blueprint, ( the genetic and over a dozen epigenetic codes )
information retrieval ( RNA polymerase )
transmission ( messenger RNA )
translation ( Ribosome )
signaling ( hormones )
complex machines ( proteins )
taxis ( dynein, kinesin, transport vesicles )
molecular highways ( tubulins, used by dynein and kinesin proteins for molecular transport to various destinations )
tagging programs ( each protein has a tag, which is an amino acid sequence ) informing other molecular transport machines where to transport them.
factory assembly lines ( fatty acid synthase, non-ribosomal peptide synthase )
error check and repair systems  ( exonucleolytic proofreading, strand-directed mismatch repair )
recycling methods ( endocytic recycling )
waste grinders and management  ( Proteasome Garbage Grinders )  
power generating plants ( mitochondria )
power turbines ( ATP synthase )
electric circuits ( the metabolic network )

1. Factory portals - factory compartments - a library index and fully automated information classification systems, storage and retrieval programs - molecular computers - hardware ( DNA )- software, a language using signs and codes like the alphabet, an instructional blueprint - information retrieval - transmission - translation - signaling - the make of complex machines - taxis - transport highways - tagging programs - factory assembly lines - error check and repair systems - recycling methods - waste grinders and management  - power generating plants - power turbines - electric circuits - machines - robots - fully automated manufacturing production lines - transport carriers - turbines - transistors - computers - and factories are always set up by intelligent designers.
2. Science has discovered, that cells are literally chemical nano factories, that operate based on molecular machines, protein robots, kinesin protein carriers, autonomous self-regulated production lines, generate energy through turbines, neuron transistors, and computers.
3. Therefore, with extremely high probability, cell factory complexes containing all those things are the product of an intelligent designer.

Engineering requires an engineer. An artificial cell or minimal cell is an engineered particle that mimics one or many functions of a biological cell. Mimicking a living cell requires engineers. 1
Architecture requires an architect.  Biological Cells demonstrate a complex architectural structure like a factory complex in a building  2
Orchestration requires a director. Gene regulatory networks orchestrate the expression of genes 3
Organization requires an organizer. Cells are organized into tissues, which are organized into organs, which are organized into organ systems 4
Programming languages are always set up by programmersGenes together form the master DNA program 5
Translation programs are always set up by translation programmers. 64 Codons of the genetic code are assigned to 20 amino acids during translation in the Ribosome.  6
Communication systems require network engineers. Cells give and receive messages with its environment and with itself. 7
Electrical networks require electrical engineers. Biological cells contain bioelectric circuits 8
Logistics require a logistic specialist. The cytoskeleton and microtubules serve as tracks for motor protein-based intracellular transport 9
Modular organization requires a modular project manager. Proteins and protein complexes organize intracellular interactions into networks of modules 10
Setting up recycling systems require a recycling technician. Cells sort out usable proteins for recycling 11
Setting up power plants requires systems engineers of power plants. Mitochondria are unusual organelles. They act as the power plants of the cell 12
Nanoscale technology requires nano processes, development engineers Living systems use biological nanomotors to build life’s essential molecules—such as DNA and proteins 13
Product planning and control require a production control coordinator. Eukaryotic cells have intricate regulatory control over the production of proteins and their RNA intermediates. 14
Product Quantity and Variant Flexibility control require product management engineers. Cells are extremely good at making products with high robustness, flexibility, and efficiency. 15
Waste disposal and management require a waste logistics manager.   Cells use proteasomes as "garbage disposal," 16
Creating a language requires intelligence. Cells use a remarkable variety of languages and communication methods 17
Creating Instructional information requires intelligent specialistsSoluble cues, cell-cell contact-dependent signals coordinate, encode and transmit regulatory information to instruct single-cell behavior18
Coordination requires a coordinator Circadian clocks are cell-autonomous timing mechanisms that organize and coordinate cell functions in a 24-h periodicity.19
Setting up strategies requires a strategist.    Cells use strategies to minimize energy consumption, by employing a number of common metabolic pathways for a variety of intermediate products before the pathway splits into different final products.  20
Regulation requires a regulator.  Regulatory circuits responsible for the function of individual genes or gene sets are at the lowest regulatory level. Then, there are circuits underlying the functions of cells, tissues, organs, and entire organisms. Endocrine and nervous systems are the regulatory circuits of the highest hierarchical level. 21
Controlling requires intelligence that sets up and programs the automatic control functions. Various cell cycle regulators control the Cell Cycle. 22
Recruiting requires intelligence which instructs autonomous programs how to do it. Proteins are for example recruited to fix DNA lesions. 23
Interpretation and response require intelligence which creates an interpretation program.  Cells monitor, interpret and respond to internal and external cues. 24
Setting up switch mechanisms based on logic gates with on and off states require intelligent setup. DNA binding proteins work based on circuit principles and logic gates 25
Setting up transport highways requires  Transportation Development engineers. Microtubules can act as specific transport roads for the trafficking of signaling factors 26
Controlled factory implosion programming requires an Explosive Safety Specialist Apoptosis is a form of programmed cell death that occurs in multicellular organisms. 27

Actions like engineering, architecting, orchestrating, organizing, programming, translating, setting up communication channels, electric networks, logistic networks, organizing modular systems, recycling systems, making power plants in nanoscale dimensions, product planning and control, establishing product quality and variant flexibility, setting up waste disposal and management systems, creating languages and instructional information, coordinating, setting up strategies, regulating, controlling, recruiting, interpreting and responding, setting up switch mechanisms based on logic gates, setting up transport highways and GPS systems, and controlled factory implosion, are ALWAYS and EXCLUSIVELY assigned to the action of intelligent agents. No exceptions

We can conclude, therefore, that biological systems, which cleverly perform all the demanding, multifaceted job activities described above, are most likely due to the set up of an intelligent designer(s). It is extraordinarily unlikely, statistically, and chemically, that blind fortune would be up to the task. Only a master player with foresight guided by superb chemical wisdom, putting all those systems together in a proper way is an explanation that makes sense.

1. https://en.wikipedia.org/wiki/Artificial_cell
2. https://www.nature.com/articles/nrm2460
3. https://www.nature.com/articles/nrm2428
4. https://flexbooks.ck12.org/cbook/ck-12-biology-flexbook-2.0/section/2.10/primary/lesson/organization-of-cells-bio
5. https://www.quantamagazine.org/how-the-dna-computer-program-makes-you-and-me-20180405/
6. https://pubmed.ncbi.nlm.nih.gov/29870756/
7. https://www.nature.com/scitable/topic/cell-communication-14122659/
8. https://www.ncbi.nlm.nih.gov/books/NBK549549/
9. https://sci-hub.tw/https://www.annualreviews.org/doi/full/10.1146/annurev-cellbio-100818-125149
10. https://www.pnas.org/content/100/3/1128
11. https://phys.org/news/2020-01-cells-recycle-components.html
12. https://www.nature.com/scitable/topicpage/mitochondria-14053590/
13. https://www.researchgate.net/profile/Viola_Vogel/publication/23154570_Harnessing_Biological_Motors_to_Engineer_Systems_for_Nanoscale_Transport_and_Assembly/links/551ab0590cf2bb754076cac6/Harnessing-Biological-Motors-to-Engineer-Systems-for-Nanoscale-Transport-and-Assembly.pdf
14. https://www.nature.com/scitable/topicpage/eukaryotic-cells-14023963/
15. https://ink.library.smu.edu.sg/cgi/viewcontent.cgi?article=2060&context=lkcsb_research
16. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3524306/
17. http://jonlieffmd.com/blog/the-remarkable-language-of-cells
18. https://advances.sciencemag.org/content/6/12/eaay5696
19. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5057284/
20. http://pubsonline.informs.org/doi/pdf/10.1287/msom.1030.0033
21. http://www.bionet.nsc.ru/meeting/bgrs_proceedings/papers/1998/27/index.html
22. https://courses.lumenlearning.com/suny-biology1/chapter/control-of-the-cell-cycle/
23. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1317637/
24. https://europepmc.org/article/med/27856508
25. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4230274/
26. https://jcs.biologists.org/content/126/11/2319
27. https://en.wikipedia.org/wiki/Apoptosis

Abiogenesis is mathematically  impossible - Page 4 Image010



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International Society for the Study of the Origin of Life (ISSOL) Conference

Regarding abiogenesis lab experiemtns, Robert Shapiro pointed out how much intelligent intervention and design were needed to produce laboratory outcomes. He added that if his peers could not produce chemical outcomes known to be vital for any conceivable OOL model with far less experimenter interference then they simply were proving that the origin of life requires an intelligent designer.
Sixteen years later chemist Clemens Richert published an article in Nature Communications in which he more fully articulated Shapiro’s point. He began by explaining that the reputed goal of experimental biochemists doing origin-of-life research is “to re-enact what may have happened when life arose from inanimate material.” However, he noted that such reenactments are unrealistic if one or more human interventions are required.

One such intervention that inevitably occurs arises from the experimenters’ desires that their results be reproducible by other biochemists. If their results cannot be reproduced, there is little, if any, likelihood that they will be published in any reputable science journal. This need for reproducibility forces the biochemists to begin with known quantities of pure chemicals. However, such fixed, pure quantities are unrealistic in any conceivable natural prebiotic scenario. The second law of thermodynamics inevitably introduces mixtures of structurally related but chemically interfering molecular aggregates.
Furthermore, to be relevant to any conceivable natural origin-of-life scenario the experiment must not involve any human intervention after the start of a reaction. There cannot be any addition or subtraction of chemicals during the reaction. The reaction must be allowed to unfold and samples drawn only after the reaction is completely finished.
Toward the end of his article Richert takes to task the now popular experiments of unending cycles of hydration and dehydration and/or cooling and heating. Richert points out, for example, that for cooling and heating cycles to be productive requires repeated specified transitions in a single locale from arctic to volcanic conditions then back to arctic within just hours or a few days. Such requirements, he understates, seem unrealistic for natural scenarios.

In his article, Richert coined a phrase for the experimenter intervention. He called it “the Hand of God dilemma.” His point is that experimenter intervention is akin to claiming that God did it. In saying this, he admits that “most of us [OOL researchers] are not comfortable with the idea of divine intervention in this context.”

Richert, nevertheless, makes a strong appeal to his fellow OOL researchers. So as not to deceive researchers in other disciplines, and especially the lay public, or to exaggerate their successes to their research peers, he recommends that his peers reveal the level of experimenter intervention. In their publications, they should state as accurately as possible how many times and exactly when and where in their experiments they commit the Hand of God dilemma.

https://reasons.org/.../is-the-hand-of-god-evident-in...

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Question: what is the better explanation for the origin of the following things?

- factory portals with fully automated security checkpoints and control
- factory compartments
- a library index and fully automated information classification, storage, and retrieval program
- computer hardware
- software, a language using signs and codes like the alphabet, an instructional blueprint,
- information retrieval systems
- information transmission systems
- translation systems
- complex robotlike machines
- taxis adapted for cargo transport and delivery, with GPS systems
- highways
- tagging programs informing taxis were to transport goods
- factory assembly lines
- error check and repair systems
- recycling machines
- waste grinders and management
- power generating plants
- power turbines
- electric circuits

Chance, or intelligent design ?

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Origin of life research faces three major problems

Awe-inspiring evidence of design in biochemistry !!
https://www.youtube.com/watch?v=zETY76qFzdk

1. The making of the basic building blocks of life, and complexification
At its most fundamental level, life is made of matter. In a putative prebiotic soup or hydrothermal vents, there is the random chaotic floating around of all sorts of chemicals and molecules in an aqueous environment, in non-purified and racemic form. In order to start the trajectory to complexification to get supposed protocells, and continuing, through chemical evolution, getting to a last universal common ancestor, capable of starting self-replication, and evolution, not only would the basic building blocks have to be purified, but also concentrated in sufficient quantity at the building site. The concentration would have to go hand in hand with sorting out molecules that are useless and keeping molecules used in life. There was no such mechanism on the early earth. There would have to be as well an enormously distant and steep trajectory from the prebiotic synthesis of those basic building blocks ( through electric discharges, synthesis on clay, metals, etc ), to the production performed in a superb manner by modern cells, which use extremely complex metabolic pathways, consistent of highly intricate, veritable molecular production lines, full of marvelous molecular machines, driven by energy in the form of ATP molecules, which require carefully crafted energy gradients and awe-inspiring nano energy turbines to be energetically charged, working in a robot-like fashion, producing all chemicals that life needs.  
 
Lynn Margulis: To go from a bacterium to people is less of a step than to go from a mixture of amino acids to a bacterium. 

Further problems arise by the fact that these basic molecules need to polymerize to become information-bearing genomes and proteins with specific functions and come into a functional relationship and interdependence. An organizational structure would have to be established between the domain of information and computation ( the genome and epigenetic information orchestrating gene expression ) and the mechanistic domain, where proteins and enzymes work based on the direction and information flow of the beforementioned blueprint-like information. The puzzle lies with the problem of creating a causal organization, the interrelationship of informational and mechanical aspects into interdependent narratives. One of the challenges of life’s origin is thus to explain how instructional information control systems emerge naturally and spontaneously from mere chemical interactions and start taking over the clever making and control of molecular mechanical dynamics. 
In modern cells, to make proteins, at least 25 unimaginably complex biosyntheses and production-line like manufacturing steps through large multimolecular machines are required. Each step requires exquisitely engineered molecular machines composed of an enormous number of subunits and co-factors, which require the very own processing procedure described, which makes its origin an irreducible  catch22 problem.

2. Randomization of molecules, and the energy problem
Virtually every task performed by living organisms requires energy. Complexification would not get "off the hook" based on thermodynamic considerations.  Maintenance of the low entropy state of living systems requires the persistent infusion of energy, first, to enable the system to maintain its complex organization and resist dissipation toward randomness. But if there even were a trajectory to get the basic building blocks of life prebiotically: 

As Steve Benner noted: Systems, given energy and left to themselves, DEVOLVE to give uselessly complex mixtures, “asphalts”.  the literature reports (to our knowledge) exactly  ZERO CONFIRMED OBSERVATIONS where “replication involving replicable imperfections” (RIRI) evolution emerged spontaneously from a devolving chemical system. it is IMPOSSIBLE for any non-living chemical system to escape devolution to enter into the Darwinian world of the “living”. Such statements of impossibility apply even to macromolecules not assumed to be necessary to start evolution.

Energy flow in non-living systems tends to result in greater disorder among all elements of the system.  The energy transformations of living systems serve primarily to harvest and store the levels of free energy necessary for maintaining the highly ordered structure of the organism and performing the work that living cells carry out. The net effect for living systems, in contrast to that for non-living systems, is to maintain and often increase order at local levels and on microscopic scales. The function of a living organism depends critically on precisely how it is put together. Its component parts function in a coordinated manner, to generate a complex array of emergent properties, both structurally and functionally. The second consequence of biological energy transformations is to create one or more additional microenvironments within the natural environment.  PH, solute composition, and structural complexity of the living cell are maintained at levels different from the extracellular environment because of the autonomous functions carried out by the cell, but not in the abiotic environment surrounding the cell.  There is a dual requirement of living systems: to resist an increase in entropy and to perform work. Both requirements are essential for the definition of a living entity. Any fabrication or machine is, for the time being, at a lower state of entropy than, and in disequilibrium with, its environment. 


3. The information problem
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." 
For explaining the origin of life we must also explain the origin of the genetic cipher/translation, from digital ( DNA / mRNA ) to analog ( Protein ), the origin of the epigenetic codes ( modern cells use over 20),  the specified instructional complex codified information contained in each life form's unique DNA and RNA, the origin of the network that orchestrates gene expres​sion( the gene regulatory network) through transcriptional regulation, the origin of the information transmission system, that is the genetic code itself, encoding, transmission, decoding, and translation, and furthermore, the origin of the codes, signaling and information, for correct direction of proteins to the final destination in the cell. When no prescriptive information exists it is impossible for information, languages, and information transmission systems to arise naturally in a mindless world. Instructional Information is more than just matter and independent of its storage medium. Like a language has a sender and a receiver who both understand the message and act according to it, the medium can be of various sorts, like a piece of paper, written on a sand dune, etc.  All communication and data processing, as is also done in the cell, is achieved through the use of symbols. When a computer processes code it has to decode it in order to convert the code into the corresponding action. Hubert P. Yockey wrote: A satisfactory scenario for spontaneous biogenesis requires the generation of “complexity” not “order”. The probability of selecting the right sequence of cytochrome c at random is about 2·1 ×10^65.  Belief in currently accepted scenarios of spontaneous biogenesis is based on faith, contrary to conventional wisdom.

Abiogenesis is mathematically  impossible - Page 4 Matter11



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93Abiogenesis is mathematically  impossible - Page 4 Empty Eric Smith on the Origin of Life Wed Sep 30, 2020 8:24 am

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Eric Smith on the Origin of Life

The Origins and Evolution of the Ribosome
https://www.youtube.com/watch?v=ei6qGLBTsKM

Ribosome Origins and Evolution - Prof. George Fox, University of Houston
https://www.youtube.com/watch?v=-ROJOBDCCLE

Central Dogma & Origin of the Ribosome
https://www.youtube.com/watch?v=x2DaEyfN0Ws

Difference between 70S and 80S Ribosomes (Prokaryotic vs Eukaryotic ribosomes) Subtitled
https://www.youtube.com/watch?v=MkfThTO-mj0

BIOGENESIS: The Emergence of the Fourth Geosphere by Eric Smith
https://www.youtube.com/watch?v=BgSal2Cv9qw

Inevitable Life ?
https://www.youtube.com/watch?v=ElMqwgkXguw

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How Did Life Begin?  By Jack Szostak on June 1, 2018:  A review

https://reasonandscience.catsboard.com/t1279p75-abiogenesis-is-mathematically-impossible#8140

Following is a classic example of how wellknown scientists with a high reputation author highly deceptive articles in regards to the origin of life, making believe that the solution is right around the corner waiting for science to discover. Nothing could be farther from the truth. He know more than almost anyone else, that the Origin of life is a huge, unsolved problem. And science has not even an explanation of a prebiotic route to the basic building blocks of life.

https://www.scientificamerican.com/article/how-did-life-begin1/

Untangling the origins of organisms will require experiments at the tiniest scales and observations at the vastest

By Jack Szostak on June 1, 2018

JS: Is the existence of life on Earth a lucky fluke or an inevitable consequence of the laws of nature? 
My comment:  Or was it divine creation? Why does JS not include tha possibility as well?

JS: Is it simple for life to emerge on a newly formed planet, or is it the virtually impossible product of a long series of unlikely events?
My comment:  The simplest free-living bacteria is Pelagibacter ubique. It is known to be one of if not the smallest and simplest, self-replicating, and free-living cell.  It has complete biosynthetic pathways for all 20 amino acids.  These organisms get by with about 1,300 genes and 1,308,759 base pairs and code for 1,354 proteins.  If we take a model size of 1,200,000 base pairs, the chance to get the sequence randomly would be 4^1,200,000 or 10^722,000.

JS: Advances in fields as disparate as astronomy, planetary science and chemistry now hold promise that answers to such profound questions may be around the corner. 
My comment:  Nothing could be farther from the truth. Eugene Koonin  writes 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.

JS: If life turns out to have emerged multiple times in our galaxy, as scientists are hoping to discover, the path to it cannot be so hard. Moreover, if the route from chemistry to biology proves simple to traverse, the universe could be teeming with life.The discovery of thousands of exoplanets has sparked a renaissance in origin-of-life studies. In a stunning surprise, almost all the newly discovered solar systems look very different from our own. Does that mean something about our own, very odd, system favors the emergence of life? Detecting signs of life on a planet orbiting a distant star is not going to be easy, but the technology for teasing out subtle “biosignatures” is developing so rapidly that with luck we may see distant life within one or two decades.
My comment: False again. Exotic Life Sites: The Feasibility of Far-Out Habitats
The data demonstrate that the probability of finding even one planet with the capacity to support life falls short of one chance in 10^140 (that number is 1 followed by 140 zeros)
https://reasons.org/explore/publications/facts-for-faith/read/facts-for-faith/2001/10/01/exotic-life-sites-the-feasibility-of-far-out-habitats

JS: To understand how life might begin, we first have to figure out how—and with what ingredients—planets form. A new generation of radio telescopes, notably the Atacama Large Millimeter/submillimeter Array in Chile's Atacama Desert, has provided beautiful images of protoplanetary disks and maps of their chemical composition. This information is inspiring better models of how planets assemble from the dust and gases of a disk. Within our own solar system, the Rosetta mission has visited a comet, and OSIRIS-REx will visit, and even try to return samples from, an asteroid, which might give us the essential inventory of the materials that came together in our planet.
My comment: Again, not true. Stellar evolution and the problem of the ‘first’ stars
https://reasonandscience.catsboard.com/t1922-chronology-and-timeline-of-origins-of-the-universe-life-and-biodiversity-the-lack-of-explanatory-power-open-questions-and-refuted-claims-of-naturalism#3212
Fred Hoyle, The Intelligent Universe, London, 1984, p. 184-185
The big bang theory holds that the universe began with a single explosion. Yet as can be seen below, an explosion merely throws matter apart, while the big bang has mysteriously produced the opposite effect–with matter clumping together in the form of galaxies.

JS:  Once a planet like our Earth—not too hot and not too cold, not too dry and not too wet—has formed, what chemistry must develop to yield the building blocks of life? In the 1950s the iconic Miller-Urey experiment, which zapped a mixture of water and simple chemicals with electric pulses (to simulate the impact of lightning), demonstrated that amino acids, the building blocks of proteins, are easy to make.
My comment: Again, false. Not easy to make. At all. I list 27 unsolved problems in regard to the origin of amino acids on the early earth, In regard to 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.
https://reasonandscience.catsboard.com/t1279p75-abiogenesis-is-mathematically-impossible#7759

JS: Other molecules of life turned out to be harder to synthesize, however, and it is now apparent that we need to completely reimagine the path from chemistry to life. The central reason hinges on the versatility of RNA, a very long molecule that plays a multitude of essential roles in all existing forms of life. RNA can not only act like an enzyme, it can also store and transmit information. Remarkably, all the protein in all organisms is made by the catalytic activity of the RNA component of the ribosome, the cellular machine that reads genetic information and makes protein molecules. This observation suggests that RNA dominated an early stage in the evolution of life.
My comment: It takes ribosomes to make ribosomes. How did everything start?  The ribosome, both looking at the past and at the future, is a very significant structure — it's the most complicated thing that is present in all organisms.  if we take all the life forms we have so far,  the minimum for the ribosome about 53 proteins and 3 polynucleotides.  And that is the kind of already reaching a plateau where adding more genomes doesn't reduce that number of proteins. Thats called irreducible complexity. ( A dialogue between Craig Venter, and George Church )
https://reasonandscience.catsboard.com/t1661-translation-through-ribosomes-amazing-nano-machines

JS:  Today the question of how chemistry on the infant Earth gave rise to RNA and to RNA-based cells is the central question of origin-of-life research. Some scientists think that life originally used simpler molecules and only later evolved RNA.
My comment: Here, JS, implicitly suggests, that RNA's would be the product of evolution. But there was no evolution in action at this stage. He admits that elswere:
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

JS: Other researchers, however, are tackling the origin of RNA head-on, and exciting new ideas are revolutionizing this once quiet backwater of chemical research. Favored geochemical scenarios involve volcanic regions or impact craters, with complex organic chemistry, multiple sources of energy, and dynamic light-dark, hot-cold and wet-dry cycles. Strikingly, many of the chemical intermediates on the way to RNA crystallize out of reaction mixtures, self-purifying and potentially accumulating on the early Earth as organic minerals—reservoirs of material waiting to come to life when conditions change.
My comment: Genetic takeover, Cairns Smith, page 66:
Now you may say that there are alternative ways of building up nucleotides, and perhaps there was some geochemical way on the early Earth. But what we know of the experimental difficulties in nucleotide synthesis speaks strongly against any such supposition. However it is to be put together, a nucleotide is too complex and metastable a molecule for there to be any reason to expect an easy synthesis.

If you were to consider in more detail a process such as the purification of an intermediate ( to form amide bonds between amino acids and nucleotides ) you would find many subsidiary operations — washings, pH changes and so on. (Remember Merrifield’s machine: for one overall reaction, making one peptide bond, there were about 90 distinct operations required.)

JS: Assuming that key problem is solved, we will still need to understand how RNA was replicated within the first primitive cells. Researchers are just beginning to identify the sources of chemical energy that could enable the RNA to copy itself, but much remains to be done. If these hurdles can also be overcome, we may be able to build replicating, evolving RNA-based cells in the laboratory—recapitulating a possible route to the origin of life.
My comment:  Koonin, the logic of chance: 2012
All this progress notwithstanding, the ribozyme polymerases that are currently available are a far cry from processive, sufficiently accurate (in terms of the Eigen threshold) replicases, capable of catalyzing the replication of exogenous templates and themselves. Thirty years ago, no catalytic activity was reported for any RNA molecule to catalyze any reaction at all; now we are aware of dozens of ribozyme activities, including some, such as highly efficient aminoacylation, that get the translation system going. However, this is about all the good news; the rest is more like a sobering cold shower.
https://reasonandscience.catsboard.com/t2234-the-origin-of-replication-and-translation-and-the-rna-world

What next? Chemists are already asking whether our kind of life can be generated only through a single plausible pathway or whether multiple routes might lead from simple chemistry to RNA-based life and on to modern biology. Others are exploring variations on the chemistry of life, seeking clues as to the possible diversity of life “out there” in the universe. If all goes well, we will eventually learn how robust the transition from chemistry to biology is and therefore whether the universe is full of life-forms or—but for us—sterile.



Abiogenesis: An unsolved mystery is not evidence of a creator
https://thelogicofscience.com/2017/06/05/abiogenesis-an-unsolved-mystery-is-not-evidence-of-a-creator/

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The Emergence of Life
The organization of various biological forms and their interrelationships, vis-à-vis biochemical and molecular networks, is characterized by the interlinked processes of flow of information between the information-bearing macromolecular semantides, namely DNA and RNA, and proteins (Zuckerkandl and Pauling 1965).
https://link.springer.com/article/10.1007/s11214-019-0624-8

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To bake a cake, the right procedure has to be applied. So as well, in order to make the basic building blocks of life

A. G. CAIRNS-SMITH genetic takeover, page54

The impurity problem:
First of all there is a problem which is seldom discussed. The starting monomers would have been grossly impure. On the basis of Simulation experiments they would have been present in complex mixtures that contained a great variety of variously reactive molecules. N0 sensible organic chemist would hope to get much out of a reaction from starting materials that were tars containing the reactants as minor constituents.

To bake the cake:
In organic chemistry it is often the work-up rather than the reaction that causes most of the trouble. Think about the techniques that are used: pH adjustments, solvent extractions, chromatography, evaporation to dryness, recrystallization, filtration and so on. Now you can say that such things might have taken place fortuitously under primitive geological conditions. Each individual operation can be imagined — a transfer of a solution, a washing of a precipitate, an evaporation, and so on. But very many such operations would have had to take place consistently and in the right order. In a typical work-up procedure there are subtle things that can make the difference between success and mess — how long to wait, say, after the pH adjustment before filtering. Practical organic chemistry is not easy. Very much has to be engineered. It is not sensible to suppose that an uninformed geochemistry would fortuitously be an expert in such things.

The concentration problem:
Next there is the problem of the concentrations of the monomers in primordial waters. It has been emphasized repeatedly that the idea of an oceanic primordial soup is difficult to sustain on thermodynamic and kinetic grounds. For example Hull (1960) says: ‘First, thermodynamic calculations predict vanishingly small concentrations of even the smallest organic compounds. Second, the reactions invoked to synthesize such compounds are seen to be much more effective in decomposition.’ Hull was discussing particularly the effects of ultraviolet radiation which he calculated would have destroyed 97 3/", of amino acids produced in the atmosphere before they reached the oceans.

The condensation problem: 
There is a third difficulty in prevital synthesis of biopolymers, and this is the most generally recognized: all the major biopolymers are metastable in aqueous solution in relation to their (deactivated) monomers. Left to itself in water, a polypeptide will hydrolyze to its constituent amino acids. 

Perhaps there is some other way of making peptides with more or less specified amino acid sequences; and perhaps this way does not need detailed control. Perhaps it could then have operated before there was life
on Earth, before that engineer, natural selection, appeared on the scene. But it is difficult to see how this could have been so. I think we would know by now if there was some much easier way. It is similarly difficult to imagine anything like polysaccharide being accumulated in primordial waters. As we saw, the monosaccharides could only have been made easily from formaldehyde, as far as anyone knows, and there is doubt if there could have been sufficient concentrations of that. In any case, as we saw, the product of the formose reaction is a very complex mixture that easily leads to higher polymers and to caramel.



Last edited by Otangelo on Sun Jan 24, 2021 7:58 pm; edited 1 time in total

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Abiogenesis is mathematically  impossible - Page 4 Curren10

Current central questions in origin of life (OoL) research.
In order to find answers, each of the natural sciences illustrated has to play a role by converting these questions into hypotheses and theories, while constantly testing them experimentally. The fundamental roles of philosophy, mathematics and informatics are portrayed in the background.

Abiogenesis is mathematically  impossible - Page 4 Timeli11
Abiogenesis is mathematically  impossible - Page 4 Timeli10
Timeline of recent multidisciplinary achievements that build bridges in OoL research.
Included are examples from the past 10 years of OoL research that bridge disciplines, approaches and/or methods, biomolecules/single-world scenarios, simulations and experiments. The choice of studies does not aim to cover (exclusively) novel findings, but those that build bridges.


1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7151616/

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Robert P. Bywater On dating stages in prebiotic chemical evolution 15 February 2012
Despite the wide repertoire of chemical and biological properties of RNA, which make it such an appealing contender for being the first type of molecular species to usher in life onto this planet, there is no explanation for how such a complex chemical species could have arisen in the absence of sophisticated chemical machinery. The generation of complex chemicals require many millions of cycles of synthesis, partial degradation, concentration, selection and reannealing in combinatorially new ways such that sufficiently diverse species could be produced and reproduced, from which particularly suitable entities survived 34

The following list of essential requirements is deemed to be necessary. 

(1) Catalytic activity, to accelerate synthetic reactions for needed products and in order to compensate for degradation processes. 
(2) Energy supply and management. 
(3) Storage system for synthesized products. 
(4) Controlled material transport across cell membranes. 
(5) Communication between the cell interior and the outside world. 
(6) Molecular recognition and selectivity/ affinity. 
(7) Replication of molecular species and ultimately of entire cells.

These are in turn catered for, in the prebiotic world, in the following way. 
(1) Catalytic material abounds in the mineral world, and while these catalysts do not possess the efficiency and selectivity of enzymes or ribozymes, they would be sufficient, during the eons of time that we are considering, for catalyzing the synthetic pathways to the earliest prebiotic chemicals. It is known that primitive metal ion catalysts were abundant on the early Earth. In our model, the first key synthetic steps were purported to take place on tidal beaches where there are myriads of catalytic particles. We are of course aware of other hypotheses whereby libraries of potential prebiotic compounds could have been produced by deep-sea vents or delivered from space . Both would have access to adequate energy sources and catalytic functions but both also lack key functions such as concentration, cyclical segregation, renewed mixing and combinatorial synthesis that the beach model provides

(2) Energy supplies were abundant—solar, geothermal, cosmic and terrestrial radiation, etc. In particular, the conflict between the thermodynamical imperatives, which require a drive towards increased entropy, and the need for living systems for the accumulation of order and reduced entropy must be considered. Energy must be consumed in order to favour the latter. 

(3) The importance of lipids has been stressed by several authors and we have also made a case for this. The protocells referred to above played a key role in all of this. Further, it is not only the space enclosed by the lipid bilayer that is important for storage but, even more importantly, the lipid bilayer itself, especially since many of the early biochemicals would have been lipophilic in nature. 

(4) The lipid bilayer presents a barrier to material transport, but there are mechanisms of passive transport that could easily operate, both peptide channel-based and diffusive. Active transport would be a much later development. 

(5) Communications across membranes can be accomplished through material transport, but more importantly for the development of future communication systems in a cellular world is the development of signal transduction mechanisms. These are taken care of by assemblies of transmembrane peptides recognition really has a chance to flourish. 

(7) Replication is of course an absolute requirement of biological systems and their potential for development and evolution. Obviously, RNA fulfills most of the requirements for this admirably, but as has been stated already, there was no RNA at the earliest stages

It is proposed here that as a first approximation, the order in which these organic compounds begin to appear depends on their molecular complexity and to the thermodynamics of their formation. Of course, the formation of any given compound depends on the nature and concentration of precursors, but these in turn will owe their existence to complexity-dependent natural-synthetic processes. This ordering suggests a time when they could have appeared on Earth, the dating scheme referred to in the “Introduction”. In regard to the seventh of the above-named functionalities, the replication issue, it has been stated that OoL could have got underway without templatebased replication.

Molecular complexity
Experiments and theoretical considerations have directed attention towards a collection of candidate chemicals that could have been produced prebiotically, and that these later, in various combinations, could react in ways that generated molecular species of ever-increasing complexity, the reactions being powered by solar and geothermal energy and radiation. This collection of chemicals would have to include some lipids, of sufficient complexity to be able to form the protocells referred to above. In addition, peptides would form that can assemble inside the enveloping membranes of these protocells and exert some of the key functions that will ultimately be required by more advanced living systems. The conditions that were needed to support the synthesis of the necessary organic chemicals were adequate for the production of the simplest peptides and lipids—energy sources and catalysts already referred to—and a feedstock of simple chemicals. In order to be able to estimate how early a given compound could have been produced, and to order these on a timescale, it is necessary to quantify this concept of “simplest”. In this work, this is done by defining molecular complexity according to a chemoinformatic score of information content based on Shannon entropy (see “Methods”). In the present case, several more complex and more recent compounds have been added. According to this complexity score, 12 of the now 20 natural (i.e. in the biology of today) amino acid types would have been produced early on, prebiotically. These are shown in Table 1. A cutoff of 100 defines this “minimal set”. This may seem arbitrary, but there are several other criteria that have been published elsewhere that lend support to this selection. In particular, it was stated by Miller: "Just turning on the spark in a basic pre-biotic experiment will yield 11 out of 20 amino acids." These 11 are included in the 12 identified here. (Of course, there could have been other amino acid types that have not survived.. One particularly significant feature of this minimal subset is that the majority of its members are hydrophobic in character, consistent with their preference for lipid-rich media and conducive o a propensity to populate polypeptides that are embedded in lipid. This observation led to the notion of a “transmembrane-peptide-first” model for OoL, but this would only earn any credence if the membrane-spanning peptides could exert useful biological functions. This is precisely what they can do (i.e. the fourth, fifth, sixth and even seventh of the above-defined functions). This emphasis on membrane-spanning peptides presupposes a supply of membranes and these are in turn based on lipids which would result from esterification (or etherification) of glycerol by fatty acids of various chain lengths (reckoned here as the number of methylenes), typically up to 17. The chemicals required to make up phospholipids (such as are found in lipid bilayers) are also “simple” by the criteria applied here (complexity score 95 and 121 for typical alkyl chain precursors, 116 for glycerol phosphate). To construct a phospholipid comparable to those in typical “modern” membranes requires the production of relatively complex molecules (score 551) but the lipids lining the earliest protocells would have been much simpler.

Fitting complexity scores to a timescale
The classical Miller experiment suggests that the simplest precursors to biomolecules could have been produced very early on, but it is surmised that more complex molecules will take more time to be generated in the first place and later to accumulate in sufficient quantities and concentrations, and then to evolve into further new species. The hypothesis presented here is that the emergence of these more complex species is dependent on molecular complexity. The minimal set of amino acids would have been produced very quickly and be present in some abundance. Lipid precursors and pyrimidine and purines (nucleobases) would also have been produced early on. But nucleobases on their own have no functions that are useful for replication; they need to be integrated into a polymeric structure. At some point a ribose-phosphate backbone became the favoured construct for this, but it can be seen that the nucleotides needed to form these polynucleotides are now ~4 times more complex than their parent nucleobases by virtue of the need to append ribose and phosphate onto them. In fact, it is very unlikely that nucleotides were ever produced in this way. While it is easy to sketch plausible synthetic pathways for the peptides, sugars and lipids and even for nucleobases, and indeed, these compounds are produced experimentally in systems designed to mimic the chemistry of the early Earth, it is not immediately obvious how nucleotides could be correctly assembled. It is unlikely that the nucleoside could be formed from the corresponding nucleobase correctly connected to a ribose moiety without the aid of a sophisticated catalyst. An interesting and highly plausible, synthetic path has been proposed. This is a very novel idea that nucleotides developed not from nucleobases, but rather, from ribose. The compounds in the proposed synthetic pathway to nucleotides from arabinose aminooxazolines via arabinose anhydronucleoside (“Product_2”) to an activated ribonucleotide β- ribocytidine-2′,3′-cyclic phosphate (“Product_3”) have complexity scores that increase as one proceeds from a ribose-based structure to a nucleotide-like structure, as one would expect, and these scores are in themselves very much in line with the scores for ribose phosphate itself and nucleotides, respectively. This is of course encouraging, but we have to compare polypeptides with RNA. The heavy burden, chemoinformatically speaking, of producing a full coding sequence for a given polypeptide or small protein becomes clear when one considers the complexity scores shown in Tables 3 and 4. Scores for both RNA and its corresponding DNA are given and they are clearly much larger compared to the polypeptide/protein they code for. It has to be remembered that the genetic code for proteins is a triplet code, but in practice, this means that for every amino acid residue there are six nucleobases, since DNA has to exist in a duplex ( +/- strand ) form. The consequences of this are very clearly seen in the enormously large values for complexity in the DNAcoding regions for (Ile)25 (Table 3) and crambin (Table 4), respectively. These complexity scores are of course related to how proteins are coded for “today” and do not take into account, nor preclude, that there could have been an “RNA world” without the need for DNA duplex structures. Still, RNA as such would be very much more complex than the proteins that it codes for, and therefore be a later arrival than oligopeptide and even some small proteins. 


RNA has been held to reign supreme in the OoL research world despite the need to explain the complexity, how it is synthesized in the first place, how it can be protected (during synthesis and certainly afterwards) from degradation and dilution in the oceans. These objections have never been satisfactorily defended. 

It remains the case that RNA is, with good reason, credited with many attributes that are essential for the maintenance of life. Principles among these are catalytic activity (“ribozyme”) and the replication function. As far as the former is concerned, there is nothing unique about that function in itself and examples of ribozyme activity are not common in the modern world. They operate when they are needed as in ribosomes. The appearance of the oldest living organisms on Earth— cyanobacteria as found in stromatolites—has been estimated to have taken place 3.5 Gyrs ago. This is 0.7 Gyrs after the earliest time for anything resembling life to have emerged, at the transition from the Hadean to the Archaean era. Doublestranded DNA (complexity ~322,100 for a small protein) must have been in place before that time, so we can at least put that as a lower limit. It is known that the moon is receding, so it is not strictly correct to assume a linear timescale for, e.g. the evolution of complexity. But over a restricted period, if this assumption can be allowed, then it is possible to give approximate times for the appearance of different types of compounds. Starting from the simpler substances (complexity ~100) that were in abundance 4.2 Gyr ago to duplex DNA at 3.5 Gyrs ago, we can, by interpolation, put the time of appearance of phospholipids (complexity ~550) at 1.2 Myr, a transmembrane peptide (~3,800) 8.3 Myr, a small protein (~6,500) 14 Myr and its corresponding RNA (~143,000) at 0.31 Gyr. Thus, the “RNA world” would have started about 3.9 Gyrs ago and then from 3.5 Gyrs the emergence of duplex DNA would start to take place.

Evolution of lipid structures
According to the complexity-based timescale being proposed here, the earliest lipids would have emerged at about the same time as the simplest amino acids, glycerol etc.. The presence of lipids leads to the formation of vesicles which are generally accepted as being critical. Ultimately, there would emerge complex lipids similar to “modern” lipids based on derivatives of phosphoglyceryl esters (and ethers) for example. But much simpler lipid-like molecules such as long-chain alcohols can also form vesicles. It is clear that this represents an important early stage in the steady evolution of ever more complex systems. This in turn exerts constraints on which oligopeptides emerged first. For example, in lipid vesicles made of only alcohols there would not be any way, at least under pH conditions close to neutral, to accommodate helical oligopeptides containing lysine. The complexity of, e.g. heptadecanol would be comparable to that of the very simplest amino acid types. This would have affected the very earliest expressions of peptide evolution and by no means invalidates the argument outlined above.

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Even for a single protein to be successfully expressed in the cell, a huge number of molecules need to interact with one another in exactly the right way, at exactly the right time, and in exactly the right order. And it should not be surprising that the likelihood that all of this happens in a perfectly efficient and precisely timed fashion (as one would expect of the programmatic execution of an algorithmic sequence of coded instructions) is virtually zero once we take into account the random and ferocious buffeting that all molecules are subject to inside the cell by virtue of their size.



1. https://philpapers.org/archive/NICOBT-2.pdf

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Dose, Klaus, "The Origin of Life: More Questions Than Answers," Interdisciplinary Science Reviews, Vol. 13, No. 4, 1988, p.348.
"More than 30 years of experimentation on the origin of life in the fields of chemical and molecular evolution have led to a better perception of the immensity of the problem of the origin of life on Earth rather than to its solution. At present all discussions on principal theories and experiments in the field either end in stalemate or in a confession of ignorance. New lines of thinking and experimentation must be tried."

Newman, 1967, p. 662: 
How did something so immensely complicated, so finessed, so exquisitely clever, come into being all on its own? How can mindless molecules, capable only of pushing and pulling their immediate neighbors, cooperate to form and sustain something as ingenious as a living organism?

Alberts, 1992, pp. xii, xiv

Before the explosive growth of our knowledge of the cell during the last 30 years, it was known that "the simplest bacteria are extremely complex, and the chances of their arising directly from inorganic materials, with no steps in between, are too remote to consider seriously. A typical eukaryote cell consists of an estimated 40,000 different protein molecules and is so complex that to acknowledge that the "cells exist at all is a marvel… even the simplest of the living cells is far more fascinating than any human-made object. 

Klaus Dose, the president of the Institute of Biochemistry at the University of Johannes Gutenberg, said : 
“ it has become abundantly clear that the power of self-organization inherent in macromolecules synthesized in cells is based on extremely subtle physical and chemical, and particularly stereochemical, properties [that] have never been observed in this highly organized form in pre-biotic molecules.… It appears that the field has now reached a stage of stalemate”
(“The Origin of Life: More Questions Than Answers,” Interdisciplinary Science Reviews 13 [1988]: 348–49).

Jeffrey Bada, "Life's Crucible," Earth, February 1998, p. 40.
Today, as we leave the twentieth century, we still face the biggest unsolved problem that we had when we entered the twentieth century: How did life originate on Earth?

Bill Faint
life in any form is a very serious enigma and conundrum. It does something, whatever the biochemical pathway, machinery, enzymes etc. are involved, that should not and honestly could not ever "get off the ground". It SPONTANEOUSLY recruits Gibbs free energy from its environment so as to reduce its own entropy. That is tantamount to a rock continuously recruiting the wand to roll it up the hill, or a rusty nail "figuring out" how to spontaneously rust and add layers of galvanizing zinc on itself to fight corrosion. Unintelligent simple chemicals can't self-organize into instructions for building solar farms (photosystems 1 and 2), hydroelectric dams (ATP synthase), propulsion (motor proteins) , self repair (p53 tumor suppressor proteins) or self-destruct (caspases) in the event that these instructions become too damaged by the way the universe USUALLY operates. Abiogenesis is not an issue that scientists simply need more time to figure out but a fundamental problem with materialism

Chemist Wilhelm Huck, professor at Radboud University Nijmegen
A working cell is more than the sum of its parts. "A functioning cell must be entirely correct at once, in all its complexity,"

Lynn Margulis:
To go from a bacterium to people is less of a step than to go from a mixture of amino acids to a bacterium. 

Douglas Futuyma, a prominent American biologist admits as much:(1983, p. 197).
“Organisms either appeared on the earth fully developed or they did not. If they did not, they must have developed from preexisting species by some process of modification. If they did appear in a fully developed state, they must indeed have been created by some omnipotent intelligence” 

In fact, Futuyma’s words underline a very important truth. He writes that when we look at life on Earth, if we see that life emerges all of a sudden, in its complete and perfect forms, then we have to admit that life was created, and is not a result of chance. As soon as naturalistic explanations are proven to be invalid, then creation is the only explanation left.

Neither Evolution nor physical necessity is a driving force prior DNA replication :The origin of the first cell, cannot be explained by natural selection (Ann N Y Acad, 2000) DNA replication had  to be previously, before life began, fully setup, working, and fully operating, in order for evolution to act upon the resulting mutations. The remaining possible mechanisms are chemical reactions acting upon unguided random events ( luck, chance), or physical necessity. It could not be physical necessity because that would constrain the possible gene sequences, but they are free and unconstrained; any of the bases can be interlinked into any sequence. If design or physical necessity is excluded, the only remaining possible mechanism for the origin of life is chance/luck.

Hoyle: 
The possibility that life might have emerged through unguided, aleatory, random chemical reactions is comparable to the chance that a tornado sweeping through a junkyard might assemble a Boeing 747 from the materials therein. It's as well extremely unlikely that chance/luck can write a book, or produce instructional complex information. Nor will unguided, random events produce cells that are more complex than a 747, and contain more information than an encyclopedia Britannica. Life as we know it is, among other things, dependent on at least 2000 different enzymes. How could the blind forces of the primal sea manage to put together the correct chemical elements to build enzymes?

George Wald, Harvard University biochemist and Nobel Laureate,  stated in 1954:
"One has to only contemplate the magnitude of this task to concede that the spontaneous generation of a living organism is impossible. Yet we are here as a result, I believe, of spontaneous generation. However improbable we regard this event [evolution], or any of the steps which it involves, given enough time it will almost certainly happen at least once… Time is in fact the hero of the plot… Given so much time, the ‘impossible’ becomes possible, the possible probable, the probable virtually certain. One has only to wait; time itself performs the miracles.”

Steven A. Benner, Ph.D. Chemistry, Harvard, prominent origin-of-life researcher, said: 
"We have failed in any continuous way to provide a recipe that gets from the simple molecules that we know were present on early Earth to RNA."  "The first paradox is the tendency of organic matter to devolve and to give tar.  If you can avoid that, you can start to try to assemble things that are not tarry, but then you encounter the water problem, which is related to the fact that every interesting bond that you want to make is unstable, thermodynamically, with respect to water.  If you can solve that problem, you have the problem of entropy, that any of the building blocks are going to be present in a low concentration; therefore, to assemble a large number of those building blocks, you get a gene-like RNA -- 100 nucleotides long -- that fights entropy.  And the fourth problem is that even if you can solve the entropy problem, you have a paradox that RNA enzymes, which are maybe catalytically active, are more likely to be active in the sense that destroys RNA rather than creates RNA."

 P. L. Luisi, research biologist In preparation for a 2014 conference in Japan :
The scientific question about the origin of life is still unanswered: it is still one of the great mysteries that science is facing… Which conceptual progress have we made…? It is too much to say that we didn’t really make any, if we look at data under really and honest prebiotic conditions? Adding that this situation is not due to shortage of means and finances in the field—but to a real lack of difficulty to conceive conceptually how this nonliving-living passage really took place?

PIER LUIGI LUISI: The Origin of Life on Earth An unsolved problem or a mystery? 23 OCTOBER 2016
https://wsimag.com/science-and-technology/21279-the-origin-of-life-on-earth
Who or what made this highly ordered state? Obviously there must be a preliminary mechanism, a black box, capable to make such ordered macromolecules. This black box, I call “origin of life”. Seriously, consider that you cannot be asking how life arises from non-life, and start with sequentially well ordered macromolecules- or viruses or viroid.

Opinion: Studies on the origin of life — the end of the beginning

Karl Popper: 
‘What makes the origin of life and of the genetic code a disturbing riddle is this: the genetic code is without any biological function unless it is translated; that is, unless it leads to the synthesis of the proteins whose structure is laid down by the code. But … the machinery by which the cell (at least the non-primitive cell, which is the only one we know) translates the code consists of at least fifty macromolecular components which are themselves coded in the DNA. Thus the code can not be translated except by using certain products of its translation. This constitutes a baffling circle; a really vicious circle, it seems, for any attempt to form a model or theory of the genesis of the genetic code.


John Lennox:
We have only to see a few letters of the alphabet spelling our name in the sand to recognize at once the work of an intelligent agent. How much more likely, then is the existence of an intelligent Creator behind human DNA, the colossal biological database that contains no fewer than 3.5 billion "letters" - the longest "word" yet discovered? 

If we consider as the most complex machine ever built by man and take as a parameter :
then the Large Hadron Collider is the most expensive and complex scientific machine ever built. It took  10,000 scientists and engineers from over 100 countries, as well as hundreds of universities and laboratories.
As another example, the Airbus A380. Huge airliners are incredibly complex. The A380 has about 4 million parts, with 2.5 million part numbers produced by 1,500 companies from 30 countries around the world,  including 800 companies from the United States. compared to this, the most simple cell is still far more complex. Advocates of naturalism often try to sidestep and state either that a) evolution explains the feat, or b) " we don't know yet how life emerged, but one day science will know ", as if natural mechanisms would explain life's origin, no matter what. That's a classic example of " evolution of the gaps ". We don't know yet, therefore evolution.

The Mystery of Life’s Origin 
A number of researchers have concluded that the spontaneous origin of life cannot be explained by known laws of physics and chemistry. Many seek “new” laws which can account for life’s origin. Why are so many unwilling to simply accept what the evidence points to: that the theory of evolution itself is fundamentally implausible? Dean Kenyon answers, “Perhaps these scientists fear that acceptance of this conclusion would leave open the possibility (or the necessity) of a supernatural origin of life” (p.viii).
https://cogmessenger.org/wp-content/uploads/2013/06/Mystery_of_Life_Origin.pdf

Fred Hoyle and Chandra Wickramsinghe
From the beginning of this book we have emphasized the enormous information content of even the simplest living systems. The information cannot in our view be generated by what are often called 'natural' processes, as for instance through meteorological and chemical processes. . . Information was also needed. We have argued that the requisite information came from an 'intelligence'.
Evolution from Space (1981), p. 148, 150

Sir Fred Hoyle and Chandra Wickramasinghe
"It is quite a shock. From my earliest training as a scientist I was very strongly brainwashed to believe that science cannot be consistent with any kind of deliberate creation. That notion has had to be very painfully shed. I am quite uncomfortable in the situation, the state of mind I now find myself in. But there is no logical way out of it.  I now find myself driven to this position by logic. There is no other way in which we can understand the precise ordering of the chemicals of life except to invoke the creations on a cosmic scale. . . .  We were hoping as scientists that there would be a way round our conclusion, but there isn't.
"There Must Be A God," Daily Express, Aug. 14, 1981 and Hoyle on Evolution, Nature, Nov. 12, 1981, p. 105

Carl Sagan, astronomer, "Life," in 10 Encyclopedia Britannica: Macromedia, 15th ed.
(Chicago: Encyclopedia Britannica, 1974), 893-894:

A living cell is a marvel of detailed and complex architecture. Seen through a microscope there is an appearance of almost frenetic activity. On a deeper level it is known that molecules are being synthesized at an enormous rate. . . . The information content of a simple cell has been estimated as around 10^12 bits, comparable to about a hundred million pages of the Encyclopedia Britannica.

What if I told you, I believed it possible (not probable but possible) that a hundred million pages of the Encyclopedia could come together without assistance from intelligence given enough time in the universe. Would you think me to be a logical person?

https://reasonandscience.catsboard.com

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