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Intelligent Design, the best explanation of Origins

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


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Intelligent Design, the best explanation of Origins » Origin of life » Abiogenesis is mathematically impossible

Abiogenesis is mathematically impossible

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76Abiogenesis is mathematically  impossible - Page 4 Empty Re: Abiogenesis is mathematically impossible on Sat Mar 09, 2019 8:59 am

Otangelo


Admin
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

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77Abiogenesis is mathematically  impossible - Page 4 Empty Re: Abiogenesis is mathematically impossible on Wed Mar 20, 2019 5:27 am

Otangelo


Admin
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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78Abiogenesis is mathematically  impossible - Page 4 Empty Re: Abiogenesis is mathematically impossible on Fri Mar 22, 2019 3:36 pm

Otangelo


Admin
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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79Abiogenesis is mathematically  impossible - Page 4 Empty Re: Abiogenesis is mathematically impossible on Mon Oct 21, 2019 7:42 pm

Otangelo


Admin
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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80Abiogenesis is mathematically  impossible - Page 4 Empty Re: Abiogenesis is mathematically impossible on Tue Dec 03, 2019 5:27 am

Otangelo


Admin
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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81Abiogenesis is mathematically  impossible - Page 4 Empty Re: Abiogenesis is mathematically impossible on Thu Dec 19, 2019 4:25 pm

Otangelo


Admin
- 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 )

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82Abiogenesis is mathematically  impossible - Page 4 Empty Re: Abiogenesis is mathematically impossible on Wed Mar 18, 2020 2:25 pm

Otangelo


Admin
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

See this deeply scientific image which is a chicken looking skeptically at a bowl of chicken soup and you know how we all know how to as it were 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 backwards 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


Abiogenesis is mathematically  impossible - Page 4 Sem_tz45

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

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83Abiogenesis is mathematically  impossible - Page 4 Empty Paradoxes in the Origin of Life on 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://sci-hub.st/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.

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.tw/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 Admin on Wed Sep 30, 2020 11:16 am; edited 5 times in total

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84Abiogenesis is mathematically  impossible - Page 4 Empty Prebiotic chemistry and human intervention on 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


Admin
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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86Abiogenesis is mathematically  impossible - Page 4 Empty Re: Abiogenesis is mathematically impossible on Wed Jul 01, 2020 7:02 am

Otangelo


Admin
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.

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87Abiogenesis is mathematically  impossible - Page 4 Empty Re: Abiogenesis is mathematically impossible on Tue Jul 21, 2020 7:30 am

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.

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Open questions in prebiotic chemistry to explain the origin of the four basic building blocks of life

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, 14 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.   

The implausibility of 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 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.

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? 


Amino acids

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 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 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 "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.

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?

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?


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Otangelo


Admin
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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90Abiogenesis is mathematically  impossible - Page 4 Empty Re: Abiogenesis is mathematically impossible on Mon Jul 27, 2020 4:43 pm

Otangelo


Admin
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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91Abiogenesis is mathematically  impossible - Page 4 Empty Re: Abiogenesis is mathematically impossible on Wed Aug 19, 2020 12:40 pm

Otangelo


Admin
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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92Abiogenesis is mathematically  impossible - Page 4 Empty Re: Abiogenesis is mathematically impossible on Wed Aug 19, 2020 2:52 pm

Otangelo


Admin
Biological Cell factories point overwhelmingly to set up by intelligent design

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

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.  
 
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

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.

- 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.

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

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93Abiogenesis is mathematically  impossible - Page 4 Empty Re: Abiogenesis is mathematically impossible on Sun Sep 06, 2020 8:59 am

Otangelo


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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.

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94Abiogenesis is mathematically  impossible - Page 4 Empty Eric Smith on the Origin of Life on Wed Sep 30, 2020 8:24 am

Otangelo


Admin
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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