E-mail debates

Jim

Jim: This article is not for scientists.  It’s for lay people. It discusses how thinking about DNA as software is useful. It does not mean dna is software. Mental models are not reality. This does nothing for your case.
Reply: Then why is Craig's description agreed upon in science papers?

Craig Venter is elaborating a box attached to a computer that receives DNA sequences over the internet to synthesize DNA. As a leading expert in the field of synthetic biology, he is convinced that “life is a DNA software system”, and all living things are reducible to DNA sequences. The DNA-based software creates as well as directs the more visible “hardware” of life, such as proteins and cells. Similar to the algorithm-based computing machines of Turing and von Neumann, Venter’s concept of DNA as a software system relies on these computation models. DNA organized in chromatin is far more complex than the human-made “software system”
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160521/

Jim: How about the parts where he gets actual origin of life scientists to debunk Dr tours claims?
Reply:  Can you mention how one of the scientists invited by "professor" Dave debunks James Tour's claims? Just one....

Jim: The best explanation has not been god yet.
Reply: How can we explain our existence without a creator?

Jim: Yes, but that doesn’t mean we can know which it is. This is true of any dichotomy.
Reply: Scientists HATE saying "we don't know. " They prefer to shut their face until they do know. Much less base their entire worldview on being "comfortable not knowing". Confessing of not knowing, when there are good reasons to confess ignorance, is ok. But claiming of not knowing of something, 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 God, there are just two possible explanations. Either there is a God, or not. There is however a wealth of evidence, which can lead us to informed, well-justified conclusions.

We KNOW HOW to detect the action of intelligence by a mind  when we see :

- written messages
- something made based on mathematical principles
- systems and networks functioning based on logic gates
- something purposefully made for specific goals
- specified complexity, the instructional blueprint or a codified message  
- irreducible complex and interdependent systems or artifacts composed of several interlocked, well-matched parts contributing to a higher end of a complex system that would be useful only in the completion of that much larger system.
- order or orderly patterns
- hierarchically arranged systems of parts
- artifacts which use might be employed in different systems ( a wheel is used in cars and airplanes )
- Fine-tuned things

We KNOW by observation and experience that the origin of blueprints containing the instructional complex information, and the fabrication of complex machines and interlinked factories based on these instructions, which produce goods for specific purposes, are both always the result of intelligent setup, and never the result of the spontaneous emergence through self-organization by unguided natural events in an orderly manner without external direction, chemical non-biological,  purely physicodynamic processes and reactions.  
 Living Cells store very complex genetic and epigenetic information through the genetic code, and over twenty epigenetic languages, translation systems, and signaling networks. These information systems instruct the making and operation of cells and multicellular organisms. Each cell hosts millions of interconnected molecular machines, production lines and factories analogous to factories made by man. They are of unparalleled gigantic complexity, able to process constantly a stream of data from the outside world through signaling networks. Cells operate robot-like,  autonomously. They adapt the production and recycle molecules on demand. The process of self-replication is the epitome of manufacturing advance and sophistication.
Therefore, the origin of biological information and self-replicating cell factories is best explained by the action of an intelligent designer, who created life for his own purposes.
https://reasonandscience.catsboard.com/t1810-its-not-justified-to-claim-ignorance-limited-causal-alternatives-for-origins-do-not-justify-to-claim-of-not-knowing

Jim: So far, earthquakes, hurricanes, tornadoes, plagues, frogs, locusts and everything else laid at gods doorstep has been proven to be natural. 
Reply:  Correct. That does not mean a creator was not involved/necessary to create those things, or the conditions for them to happen.

Jim: We know design by comparison to other things that are designed and are natural.  Not by complexity.  Not by how little we know how something works.
Reply: How to recognize the signature of (past) intelligent actions
https://reasonandscience.catsboard.com/t2805-how-to-recognize-the-signature-of-past-intelligent-action

Intelligence leaves behind a characteristic signature. The action or signature of an intelligent designer can be detected when we see :

1. Implementing things based on regular behavior, order, mathematical rules, laws, principles, physical constants, and logic gates

2. Something purposefully and intentionally developed and made to accomplish a specific goal(s). That includes specifically the generation and making of building blocks, energy, and information.  If an arrangement of parts is
1) perceptible by a reasonable person as having a purpose and 2) can be used for the perceived purpose then its purpose was correctly perceived and it was designed by an intelligent mind.

3. Repeating a variety of complex actions with precision based on methods that obey instructions, governed by rules.

4. An instructional complex blueprint (bauplan) or protocol to make objects ( machines, factories, houses, cars, etc.) which are irreducible complex, integrated, and an interdependent system or artifact composed of several interlocked, well-matched hierarchically arranged systems of parts contributing to a higher end of a complex system that would be useful only in the completion of that much larger system. The individual subsystems and parts are neither self-sufficient, and their origin cannot be explained individually, since, by themselves, they would be useless. The cause must be intelligent and with foresight, because the unity transcends every part, and thus must have been conceived as an idea, because, by definition, only an idea can hold together elements without destroying or fusing their distinctness. An idea cannot exist without a creator, so there must be an intelligent mind.

5. Artifacts which use might be employed in different systems ( a wheel is used in cars and airplanes )

6. Things that are precisely adjusted and finely-tuned to perform specific functions and purposes

7. Arrangement of materials and elements into details, colors, forms to produce an object or work of art able to transmit the sense of beauty, elegance, that pleases the aesthetic senses, especially the sight.

8. Establishing a language, code, communication, and information transmission system, that is 1. A language, 2. the information (message) produced upon that language, the 3 .information storage mechanism ( a hard disk, paper, etc.), 4. an information transmission system, that is: encoding - sending and decoding) and eventually fifth, sixth, and seventh ( not essential): translation, conversion, and transduction

9. Any scheme where instructional information governs, orchestrates, guides, and controls the performance of actions of constructing, creating, building, and operating. That includes operations and actions as adapting, choreographing, communicating, controlling product quality, coordinating, cutting, duplicating, elaborating strategies, engineering, error checking and detecting, and minimizing, expressing, fabricating, fine-tuning, foolproof, governing, guiding, implementing, information processing, interpreting, interconnecting, intermediating, instructing, logistic organizing, managing, monitoring, optimizing, orchestrating, organizing, positioning, monitoring and managing of quality, regulating, recruiting, recognizing, recycling, repairing, retrieving, shuttling, separating, self-destructing, selecting, signaling, stabilizing, storing, translating, transcribing, transmitting, transporting, waste managing.

10. Designed objects exhibit “constrained optimization.” The optimal or best-designed laptop computer is the one that is the best balance and compromise of multiple competing factors.

Jim: The probability is 1. Because it did happen.
Reply: The classic argument is given in response is that one shouldn't be surprised to observe life to exist, since if it wouldn't, we wouldn't exist. Therefore, the fact that we exist means that life exists should only be expected by the mere fact of our own existence - not at all surprising. This is obviously a response begging the question. 

This argument is like a situation where a man is standing before a firing squad of 10000 men with rifles who take aim and fire - - but they all miss him. According to the above logic, this man should not be at all surprised to still be alive because, if they hadn't missed him, he wouldn't be alive.  The nonsense of this line of reasoning is obvious. Surprise at the extreme odds of life emerging randomly, given the hypothesis of a mindless origin, is only to be expected - in the extreme.

A protein requires a threshold of minimal size to fold and become functional within its milieu where it will operate. That threshold is an average of 400 amino acids. That means until that minimal size is reached, the amino acids polypeptide chain bears no function. So each protein can be considered irreducibly complex. Practically everyone has identically the same kind of haemoglobin molecules in his or her blood, identical down to the last amino acid and the last atom.  Anyone having different haemoglobin would be seriously ill or dead because only the very slightest changes can be tolerated by the organism.

A. I. Oparin
Even the simplest of these substances [proteins] represent extremely complex compounds, containing many thousands of atoms of carbon, hydrogen, oxygen, and nitrogen arranged in absolutely definite patterns, which are specific for each separate substance.  To the student of protein structure the spontaneous formation of such an atomic arrangement in the protein molecule would seem as improbable as would the accidental origin of the text of irgil’s “Aeneid” from scattered letter type.¹

In order to start a probability calculation, it would have to be pre-established somehow, that the twenty amino acids used in life, would have been pre-selected out of over 500 different kinds of amino acids known in nature. They would have to be collected in one place, where they would be readily available. Secondly, amino acids are homochiral, that is, they are left and right-handed. Life requires that all amino acids are left-handed. So there would have to exist another selection mechanism, sorting the correct ones out, in order to remain only left-handed amino acids ( Cells use complex biosynthesis pathways and enzymes to produce only left-handed amino acids ).  So if we suppose that somehow, out of the prebiotic pond, the 20 amino acids, only with left-handed, homochiral, were sorted out,  

The probability of generating one amino acid chain with 400 amino acids in successive random trials is (1/20)400

Jim: You can, and do build complexity one simple piece at a time. 
Reply: https://reasonandscience.catsboard.com/t2245-abiogenesis-the-factory-maker-argument#6959

1. Living Cells store very complex genetic and epigenetic information through the genetic code, and over forty epigenetic languages, translation systems, and signaling networks. These information systems prescribe and instruct the making and operation of cells and multicellular organisms. The operation of cells is close to thermodynamic perfection, and its operation occurs analogously to computers. Cells ARE computers in a literal sense, using boolean logic. Each cell hosts millions of interconnected molecular machines, production lines and factories analogous to factories made by man. They are of unparalleled gigantic complexity, able to process constantly a stream of data from the outside world through signaling networks. Cells operate robot-like,  autonomously. They adapt the production and recycle molecules on demand. The process of self-replication is the epitome of manufacturing advance and sophistication.

2. The origin of blueprints containing the instructional complex information, and the fabrication of complex machines and interlinked factories based on these instructions, which produce goods for specific purposes, are both always the result of intelligent setup.

3. Therefore, the origin of biological information and self-replicating cell factories is best explained by the action of an intelligent designer, who created life for his own purposes.

Herschel 1830 1987, p. 148:
“If the analogy of two phenomena be very close and striking, while, at the same time, the cause of one is very obvious, it becomes scarcely possible to refuse to admit the action of an analogous cause in the other, though not so obvious in itself.”

A metaphor (“A biological cell is like a production system”) demonstrates that similar behaviors are driven by similar causal mechanisms.

Michael Denton’s 1985 Evolution: A Theory in Crisis:
The inference to design is a purely a posteriori induction based on a ruthlessly consistent application of the logic of analogy.

DNA Is Called The Blueprint Of Life: Here’s Why
OCTOBER 26, 2017
DNA is called the blueprint of life because it is the instruction manual to create, grow, function and reproduce life on Earth similar to a blueprint of a house. 10

The Molecular Fabric of Cells  BIOTOL, B.C. Currell and R C.E Dam-Mieras (Auth.)
Cells are, indeed, outstanding factories. Each cell type takes in its own set of chemicals and making its own collection of products. The range of products is quite remarkable and encompass chemically simple compounds such as ethanol and carbon dioxide as well as the extremely complex proteins, carbohydrates, lipids, nucleic acids and secondary products. Furthermore: Self-replication is the epitome of manufacturing advance and achievement, far from being realized by man-made factories.  

Self-replication had to emerge and be implemented first, which raises the unbridgeable problem that DNA replication is irreducibly complex. Evolution is not a capable driving force to make the DNA replicating complex, because evolution depends on cell replication through the very own mechanism we try to explain. It takes proteins to make DNA replication happen. But it takes the DNA replication process to make proteins. That’s a catch 22 situation.

Chance of intelligence to set up life: 
100% We KNOW by repeated experience that the origin of blueprints containing instructional complex assembly information, dictating the fabrication of complex machines, robotic production lines, computers, transistors, turbines, energy plants,  and interlinked factories based on these instructions, which produce goods for specific purposes, are both always the result of intelligent setup.

Jim: Yes.  If the physical constants were different, the universe would be different. That does not prove diddly. 
Reply: 1. God, which is the ultimate reference point, eternal and absolute, is the necessary precondition, the source of what is, can be, or not be, and to impose the regularity of nature.
2. The universe, in order to exist, and to operate in an orderly, stable manner, to permit atoms, planets, chemistry, molecules, and life, requires forces to be created, to have identity over time, the principle of identity, to be constant, to have the right strengths, and right coupling constants within each other.
3. If that were not the case, then these forces would and could adopt any spontaneous coincidental, values, coupling constants, and pop in and out in a stochastic chaotic manner.  
4. The universe operates based on four fundamental forces, which are stable, constant, secured, and permit a life-permitting universe.
5. Therefore, the instantiation of the fundamental forces, the coupling constants, and securing that they are constant, was instantiated by God.

1. The Laws of physics are like the computer software, driving the physical universe, which corresponds to the hardware. All the known fundamental laws of physics are expressed in terms of differentiable functions defined over the set of real or complex numbers. The properties of the physical universe depend in an obvious way on the laws of physics, but the basic laws themselves depend not one iota on what happens in the physical universe.There is thus a fundamental asymmetry: the states of the world are affected by the laws, but the laws are completely unaffected by the states. Einstein was a physicist and he believed that math is invented, not discovered. His sharpest statement on this is his declaration that “the series of integers is obviously an invention of the human mind, a self-created tool which simplifies the ordering of certain sensory experiences.” All concepts, even those closest to experience, are from the point of view of logic freely chosen posits. . .
2. The laws of physics are immutable: absolute, perfect mathematical relationships, infinitely precise in form. The laws were imprinted on the universe at the moment of creation, i.e. at the big bang, and have since remained fixed in both space and time. 
3. The ultimate source of the laws transcend the universe itself, i.e. to lie beyond the physical world. The only rational inference is that the physical laws emanate from the mind of God. 
 https://arxiv.org/pdf/math/0302333.pdf

https://reasonandscience.catsboard.com/t2895-syllogistic-arguments-of-gods-existence-based-on-positive-evidence#8178


Fine-tuning of the physical constants
https://reasonandscience.catsboard.com/t3134-fine-tuning-of-the-physical-constants#8607

 Fred C. Adams: The Degree of Fine-Tuning in our Universe – and Others  11 Feb 2019
Within our universe, the laws of physics have the proper form to support all of the building blocks that are needed for observers to arise. However, a large and growing body of research has argued that relatively small changes in the laws of physics could render the universe incapable of supporting life. In other words, the universe could be fine-tuned for the development of complexity. The list of required structures to have a life-permitting universe includes complex nuclei, planets, stars, galaxies, and the universe itself. In addition to their existence, these structures must have the right properties to support observers. Stable nuclei must populate an adequate fraction of the periodic table. Stars must be sufficiently hot and live for a long time. The galaxies must have gravitational potential wells that are deep enough to retain heavy elements produced by stars and not overly dense so that planets can remain in orbit. The universe itself must allow galaxies to form and live long enough for complexity to arise.

In order to make a full assessment of the degree of fine-tuning of the universe, one must address the following components of the problem: 

I   Specification of the relevant parameters of physics and astrophysics that can vary. 
II  Determination of the allowed ranges of parameters that allow for the development of complexity and hence observers. 
III Identification of the underlying probability distributions from which the fundamental parameters are drawn, including the full possible range that the parameters can take. 
IV Consideration of selection effects that allow the interpretation of observed properties in the context of the a priori probability distributions.
V  Synthesis of the preceding ingredients to determine the overall likelihood for universes to become habitable

Studying the degree of tuning necessary for the universe to operate provides us with a greater understanding of how it works.

Both the fundamental constants that describe the laws of physics and the cosmological parameters that determine the properties of our universe must fall within a range of values in order for the cosmos to develop astrophysical structures and ultimately support life. 1

Jim: When scientists wanted to know if the Higgs-boson existed, they didn’t rely on the math. They didn’t rely on the second hand evidence from other experiments that supported the math. That wasn’t good enough.  They built a collider and showed it to the world. That’s how you prove something exists. 
Reply: Fine-tuning of the Higgs-mass: It will knock your socks off.
https://reasonandscience.catsboard.com/t3142-fine-tuning-of-the-higgs-mass-it-will-knock-your-socks-off

The Higgs Boson is a unique particle unlike any other: it is the particle that all other known particles interact with that gives them mass. Without the Higgs, there would be nothing with mass at all! But, here's the really crazy thing. Although the Standard Model did not predict the Higgs' mass, its mass was found to be in literally the most improbable place you could expect to find it.

the LHC found the Higgs but no evidence for anything new besides that. No supersymmetry, no extra-dimensions, no black holes, no fourth generation, nothing. This means that the Higgs-mass just sits there, boldly unnatural. Since theoretical physicists haven’t found an explanation for the smallness of the Higgs-mass, they now try to accept that there simply may be no explanation.

The basic idea is that the more improbable the world is--the more we find the world's parameters *could* have been one way, but instead occupy the most improbable values across a range of phenomena--the more reason we have to think that something fishy is going on. If you found one pile of rocks on a path in the shape of an arrow, you might reasonably chalk it up to happenstance. If you found two sets of rocks miles apart pointing in the same direction, you still might do so. If you found not only rocks shaped like arrows, but also arrows carved into trees, and so on, you would probably get suspicious that something fishy is going on. It *could* all just be chance, but all the same, the *chance* that it is just chance seems progressively smaller the more improbable coincidences one finds.

One 'instance' of fine-tuning (e.g. carbon fine-tuning) would be remarkable. But dozens of different, independent instances? This is like picking up one coin, flipping it a gazillion times, it landing 'heads' every single time; then picking up a six sided die, flipping it a gazillion times, it landing on '1' every single time; then picking up a twelve-sided die, flipping it a gazillion times, it landing on '11' *every* single time; and so on.

Jim: I’ve pointed out in a number of papers you’ve sent me the very clear linguistic markers that show the paper is using metaphors.
Reply: I don't understand why you keep insisting in an assertion which I have shown you clearly, that it is not the case.

When we are talking about genetic code, we are talking about a translation program, where 64 codons are assigned to 20 amino acids. That assignment is not metaphorically an assignment, but literally. 

The genetic code is the set of rules used by living cells to translate information encoded within genetic material (DNA or mRNA sequences of nucleotide triplets, or codons) into proteins. The codons specify which amino acid will be added next during protein synthesis.
https://en.wikipedia.org/wiki/Genetic_code

If you think there is something metaphorically described, please point it out.

When we talk about codified information stored in DNA, then we mean an information-bearing sequence of DNA/mRNA nucleotides which is not the same as the genetic code. 

Sang Yup Lee DNA Data Storage Is Closer Than You Think July 1, 2019
DNA—which consists of long chains of the nucleotides A, T, C and G—is life’s information-storage material. Data can be stored in the sequence of these letters, turning DNA into a new form of information technology.
https://www.scientificamerican.com/article/dna-data-storage-is-closer-than-you-think/

Richard Dawkins River Out of Eden: A Darwinian View of Life 1996
What is truly revolutionary about molecular biology in the post-Watson-Crick era is that it has become digital.   After Watson and Crick, we know that genes themselves, within their minute internal structure, are long strings of pure digital information. What is more, they are truly digital, in the full and strong sense of computers and compact disks, not in the weak sense of the nervous system. The genetic code is not a binary code as in computers, nor an eight-level code as in some telephone systems, but a quaternary code, with four symbols. The machine code of the genes is uncannily computerlike. Apart from differences in jargon, the pages of a molecular-biology journal might be interchanged with those of a computer-engineering journal. . . .Our genetic system, which is the universal system of all life on the planet, is digital to the core. With word-for-word accuracy, you could encode the whole of the New Testament in those parts of the human genome that are at present filled with “junk” DNA – that is, DNA not used, at least in the ordinary way, by the body. Every cell in your body contains the equivalent of forty-six immense data tapes, reeling off digital characters via numerous reading heads working simultaneously. In every cell, these tapes – the chromosomes – contain the same information, but the reading heads in different kinds of cells seek out different parts of the database for their own specialist purposes.  Genes are pure information – information that can be encoded, recoded and decoded, without any degradation or change of meaning. Pure information can be copied and, since it is digital information, the fidelity of the copying can be immense. DNA characters are copied with an accuracy that rivals anything modern engineers can do. What lies at the heart of every living thing is not a fire, warm breath, not a ‘spark of life’. It is information, words, instructions…Think of a billion discrete digital characters…If you want to understand life think about technology – Richard Dawkins (Dawkins 1996, 112)
https://3lib.net/book/807573/de593a

Leroy Hood  The digital code of DNA   23 January 2003
Hubert Yockey, the worlds' foremost biophysicist and foremost authority on biological information contradicts you 100%.:
"Information, transcription, translation, code, redundancy, synonymous, messenger, editing, and proofreading are all appropriate terms in biology. They take their meaning from information theory (Shannon, 1948) AND ARE NOT SYNONYMS, METAPHORS, OR ANALOGIES." (Hubert P. Yockey, Information Theory, Evolution, and the Origin of Life, Cambridge University Press, 2005) "It is important to understand that WE ARE NOT REASONING BY ANALOGY. the sequence hypothesis [that the exact order of symbols records the information] APPLIES DIRECTLY TO THE PROTEIN AND THE GENETIC TEXT AS WELL AS TO WRITTEN LANGUAGE AND THEREFORE THE TREATMENT IS MATHEMATICALLY IDENTICAL."
Yockey continued, "Like all messages, _the life message is NON-MATERIAL_ but has an information content measurable in bits and bytes".

Furthermore:
The base sequences in DNA and amino acids in proteins have functional specificity. The term “information” as used in biology refers to two real and contingent properties: complexity and specificity which bears functionality. In other words, the DNA nucleobase sequence prescribes, specifies, instructs how to build and join correctly amino acids, resulting in complex polymer macromolecules that fold into correct 3D folds, that bear machine-like functions.
Since the correlation confers not simply subjective meaning, DNA cannot be understood simply as a metaphor in biology. Where it refers to complex functional instructional specificity, it defines a feature of living systems that calls for an explanation every bit as much as, say, a mysterious set of inscriptions on the hieroglyphs on an ancient Egyptian inscription. Saying that it is a true code involves the idea that the code is free and unconstrained; any of the four bases can be placed in any of the positions in the sequence of bases. Their sequence is not determined by the chemical bonding. There are hydrogen bonds between the base pairs and each base is bonded to the sugar-phosphate backbone, but there are no bonds along the longitudinal axis of DNA. The bases occur in the complementary base pairs A-T and G-C, but along the sequence on one side, the bases can occur in any order, like the letters of a language used to compose words and sentences.

If you think there is something metaphorically described, please point it out.

Jim:  If you’re going to claim that some entity did something, step one is prove they exist. 
Reply: Aquinas first way proves God's existence LOGICALLY. There is motion. Things move when potential motion becomes actual motion. Only when potential motion exists ( the possibility to instantiate actual motion ), actual motion can be instantiated. Each thing beginning to move is moved by a cause. The sequence of motion cannot extend infinitely. Therefore, there must be a first mover, that puts motion in motion which is God.

Asking for empirical proof, however, is a silly thing to do.

Why it`s an irrational demand to ask for proof of God's existence
https://reasonandscience.catsboard.com/t2717-godwhy-its-an-irrational-demand-to-ask-proofs-of-his-existence

Atheist: All that theists ever offer is arguments sans any demonstration whatsoever. Provide verifiable evidence for any God, demonstrating his existence.
Answer: Atheists cannot prove either, that the natural world is all there is. Neither view, theism, nor materialism can be proven. Science will never demonstrate how reality came about. We can only look at the science available to us and find adequate philosophical explanations based on the evidence. The Scientific method nor any other will never be able to demonstrate God's existence or the claim that the material universe is all there is. Historical events cannot be repeated. From what we know, we can decide which is the bigger leap of faith - which materialism as well requires. Any view, conclusion, and position, is based on a leap of faith. It is just that - a leap of faith. Upon my understanding, there is extraordinary evidence FOR a creator, therefore, theism requires the smallest leap of faith and that points to a creator.

If there would be no God, then anything would/should be possible, arbitrary, and nothing would be impossible. Without God, nothing can be established, imposed, and secured. The laws of physics could be instantiated, and disappear at any moment. God is ultimate and singular and that means to be the source of all facts and possibilities.

Without God's hiddenness, we would not have any significant freedom. Even those that hate God would be unable to fully live according to their wishes; much like a criminal would find it intolerable living in the police station. God stays hidden to a degree, He gives people the free will to either respond to His tugging at their hearts or remain autonomous from Him. There is enough light for those who desire to find him, and enough darkness for those that prefer to live autonomously to HIM. If you prefer being an atheist, God values your free will more than His desires for you. If you are really after truth, then have an open mind and follow the evidence wherever it leads, even if you don’t like the conclusion.

Matthew 7:8 For everyone who asks receives; the one who seeks finds; and to the one who knocks, the door will be opened.
But when you seek, it's actually not, that you will find the truth. But the truth will find you.

Revelation 3:20 Here I am! I stand at the door and knock. If anyone hears my voice and opens the door, I will come in and eat with that person, and they with me.

Jim: The good news is that origin of life research is making great leaps and bounds.
Answer: The consensus view is that there is no solution at sight. 


Abiogenesis is mathematically  impossible
https://reasonandscience.catsboard.com/t1279-abiogenesis-is-mathematically-impossible



Jack W. Szostak: 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.mrgscience.com/uploads/2/0/7/9/20796234/origin_of_life_sci_am.pdf

Eugene V. Koonin: The Logic of Chance: page 252:
" 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.

Steve Benner:  Paradoxes in the origin of life
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.

Graham Cairns-Smith: Genetic takeover, 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.

Garrett: Biochemistry, 6th ed,  page 665
Key compounds, such as arginine, lysine, and histidine; the straight-chain fatty acids; porphyrins; and essential coenzymes, have not been convincingly synthesized under simulated prebiotic conditions.

Robert Shapiro: A Replicator Was Not Involved in the Origin of Life
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 synthesis of additional copies of themselves, but this device cannot be used for the preparation of the very first such molecule, which must arise spontaneously from an unorganized mixture. The formation of an information-bearing homopolymer through undirected chemical synthesis appears very improbable.

Jim: It shows how chemicals “make decisions”, and debunks Tour. 
Answer: Chemicals are PREPROGRAMMED to make decisions.... that confirms intelligent design, and not random emergence of consciousness and decision-making of chemicals. 

Preprogrammed decision making of the gene regulatory network 
1. Cells continuously process a multitude of input signals to make decisions about their appropriate responses that lead to changes in gene expression, enzymatic activity, rewiring of their signaling networks, migration, growth, or division, as well as programmed cell death as the output information. In a computing device, the input information is mathematically processed into a digital signal. This signal is a code representation of the physical cues and assumes a sequence of discrete values. For instance, in the case of a binary code, the basic unit of information is denoted as a series of “0” and “1” digits. The binary digits indicate the two states of the logic circuit. A threshold is implemented to define the input and output range that can be categorized under each logic set. If the value is either lower or higher than the threshold, the state of the circuit is defined as either “0” or “1”, respectively. Digital circuits make extensive use of logic elements that are interconnected to create logic gates, capable of executing Boolean logic functions including NOT, OR, AND, and all their possible combinations
2. Molecular and biomolecular logic gates and their networks process chemical input signals similar to human-made computers. The similarities in the processing of information by biological systems and human-designed devices are broadly recognized by many researchers.
3. Decision making is either a) something performed directly by intelligence, or b) programmed by intelligence to be performed by machines, like computers. It has never been observed, that unguided, evolutionary mechanisms could produce a decision making machine with the purpose to generate specific outcomes further ahead. Foresight is a quality exclusively performed by intelligence.  If the analogy of two phenomena be very close and striking, while, at the same time, the cause of one is very obvious, it becomes scarcely possible to refuse to admit the action of an analogous cause in the other, though not so obvious in itself. A metaphor (“A biological cell is like a production system”) demonstrates that similar behaviors are driven by similar causal mechanisms.
4. Therefore, the decision-making process observed in the cell is most probably the result of divine superintelligent design.


Jim: Let me know when you can show god exists, and don’t have a bunch of bad arguments.
Answer:  As said. You make the claim that God is not necessary. Give me a concise, plausible, logical, rational explanation of how we can exist without a creator.

Some questions to proponents of naturalism
https://reasonandscience.catsboard.com/t2408-some-questions-for-atheists

Atheists frequently ignore to analyze the alternative and consequence if there is no God - they usually only focus on supposed lack of evidence of God, or try to poke holes in the Genesis account, but, the alternative to a creator would be - either an eternal universe, or the causation of the universe out of absolutely nothing, as well as the origin of computers, hardware, software, a language using signs and codes like the alphabet, an instructional blueprint, complex machines, factory assembly lines, error check and repair systems, recycling methods, waste grinders and management, power generating plants, power turbines, and electric circuits could emerge randomly, by unguided, accidental events. That would be their causal alternative, once intelligent planning, invention, design, and implementation are excluded, to explain the origin of biological Cells, which are literally miniaturized, ultracomplex, molecular, self-replicating factories. When atheists claim, that science will elucidate how natural mechanisms did the job, it is an act of blind faith.

This is why Dawkins concludes things like "..but, aliens!"

1. What caused the universe to exist?
2. The universe works orderly based on physical laws. What emerged first, the physical
laws, or the physical universe, if they are interdependent? Physical laws have no business without the physical world, and
the physical world cannot exist orderly without physical laws. One is physical, the other is not.
3. The original conditions of the universe, the fundamental forces, our galaxy,
and the earth are finely tuned to permit life. How comes?
4. Stars and planets exist. How did they come to be, if gas cannot clump upon gravitational forces?
5. Life exists. How comes, if a minimal number of proteins and proteome and genome are required?
6. Cells are complex factories, full of molecular machines, and assembly lines. Does randomness produce factories - facing the fact that there was no natural selection prior to replication?
7. Cells use various codes and hierarchical levels of information, based on complex
hardware/information processing machines ( computers ). Unguided forces do not produce blueprints... How did
the blueprints in biological cells come to be?
8. Genes have two layers of codes and information. How did they emerge?
9. DNA has the highest information storage density physically possible. How comes?
10. Cells use metabolic pathways and literally manufacturing and production assembly lines. How comes?
11. Cells are interdependent and irreducible complex ( a minimal genome,
proteome, and metabolome size is required to give life a first go ). How did it come to be? randomly? How and why would self-assembly spontaneously by orderly aggregation and sequentially correct manner without external direction be a reasonable, compelling scenario, and make sense?
12. Cells are self-replicating. DNA replication is irreducibly complex. How did it emerge?
13. Cells have error detection and check mechanisms. Life could not have "taken off" without them. How did they emerge?
14. Cells require homeostasis. How did it emerge?
15. There are 3 domains of life and the virus world. Biological cells and viruses are interdependent. There would be no viruses without life, and vice-versa. How comes ?
16. There is consciousness. How comes, if matter does not produce it?
17. There are objective moral values. Where did they come from?
18. Language, logic, reasoning, free will, and moral values are not grounded in physics. How did they come to be?
19. How did DNA and amino acids arise? how did homochirality in amino acids arise?
20. How do irreducibly complex enzyme chains emerge?
21. How do we account for the origin of 116 distinct language families?
22. Why did cities suddenly appear all over the world between 3,000 and 1,000BC?
23. How is independent thought possible in a world ruled by chance and necessity?
24. How do we account for self-awareness?
25. How is free will possible in a material universe?
26. How do we account for conscience?
27. On what basis can we make moral judgments?
28. Why does suffering matter?
29. Why do human beings matter?
30. Why care about justice?
31. How do we account for the almost universal belief in the supernatural?
32. What is the evidence that the natural world is all there is?
33. How can we know if there is no conscious existence after death?
34. What accounts for the empty tomb, resurrection appearances, and growth of the church?
35. Is the Bible just fiction?

My quote: DNA cannot be understood simply as a metaphor in biology. Where it refers to complex functional instructional specificity, it defines a feature of living systems that calls for an explanation every bit as much as, say, a mysterious set of inscriptions on the hieroglyphs on an ancient Egyptian inscription.
Jim: Ok I was wrong.
Reply:  Good. Since you agree with the premise, here again, is the argument with the inference to the best explanation:

1.The information stored in DNA is a template. It is equal to a recipe or program. Nucleic acids contain information in a semantic (meaningful) sense. Instructing consists in an advance specification of the kind and order of steps yielding a certain outcome if the steps are carried out. The amino acid arrangement and sequence to make functional proteins is the product of the information stored in DNA. 
2. Recipes and programs do not just bring about a particular outcome; they are designed to do so. They are usually formulated with a purpose. The computer program output is the result of executing a pre-specified series of operations.  A purely physical description does not capture the instructional nature of the process. Instructional information is not a tangible entity, and as such, it is beyond the reach of, and cannot be created by any undirected physical process. This is not an argument about probability. Conceptual semiotic information is simply beyond the sphere of influence of any undirected physical process. To suggest that a physical process can create semiotic code is like suggesting that a rainbow can write poetry... it is never going to happen!  Physics and chemistry alone do not possess the tools to create a concept. The only cause capable of creating conceptual semiotic information is a conscious intelligent mind.
3. Therefore, the instructional information stored in DNA comes most likely from an intelligent designer. 

Jim: This is a claim. You need to provide evidence that this is there case. Your making two fallacious arguments here;  an argument from analogy, and an argument from ignorance.  Before you can claim a god, designer, or bob, does anything, first prove they exist.
Reply: Analogy Viewed from Science

https://reasonandscience.catsboard.com/t2809-analogy-viewed-from-science

The Argument from Simple Analogy
https://iep.utm.edu/design/#SH1b
David Hume is the most famous critic of these arguments. In Part II of his famous Dialogues Concerning Natural Religion, Hume formulates the argument as follows:
Look round the world: contemplate the whole and every part of it: you will find it to be nothing but one great machine, subdivided into an infinite number of lesser machines, which again admit of subdivisions to a degree beyond what human senses and faculties can trace and explain. All these various machines, and even their most minute parts, are adjusted to each other with an accuracy which ravishes into admiration all men who have ever contemplated them. The curious adapting of means to ends, throughout all nature, resembles exactly, though it much exceeds, the productions of human contrivance; of human designs, thought, wisdom, and intelligence. Since, therefore, the effects resemble each other, we are led to infer, by all the rules of analogy, that the causes also resemble; and that the Author of Nature is somewhat similar to the mind of man, though possessed of much larger faculties, proportioned to the grandeur of the work which he has executed. By this argument a posteriori, and by this argument alone, do we prove at once the existence of a Deity, and his similarity to human mind and intelligence.

If the causes are known that are efficacious in those other, similar phenomena, then this may give us clues concerning the causes in the phenomenon under consideration. Of course, whether this strategy works depends on the availability of closely analogous phenomena that are already explained (Herschel [1830] 1987, p. 148). Herschel (ibid., p. 149) wrote:

“If the analogy of two phenomena be very close and striking, while, at the same time, the cause of one is very obvious, it becomes scarcely possible to refuse to admit the action of an analogous cause in the other, though not so obvious in itself.”

Let us suppose we arrive at a parking lot, and a car is parked there. It is from a well-known American car maker, and you know the model, type, when it was made, etc.  Then, you observe a second object, which you immediately recognize as a car as well. It is far far better build, with similar functionalities, but of unknown manufacturer. Now someone approaches you and asks: Hey, what do you think, was the second car made by another car manufacturer, or did some natural unguided processes build the car? We will obviously without thinking twice answer: What a foolish question. It is OBVIOUS that an unknown car maker made the Car. Biological Cells use instructional codes to make the building blocks of life and are full of molecular machines, which resemble machines made by humans through intelligent design with specific goals. We can, therefore, infer that, since like effects have most probably similar causes, that the agency which created biological Cells, and life, must be of intelligent nature.

1. Intelligent minds make factory plants full of machines with specific functions, set up for specific purposes. Each fabric can be full of robotic production lines where the product of one factory is handed over to the next for further processing until the end product is made. Each of the intermediate steps is essential. If any is mal or non-functioning, like energy supply, or supply of the raw materials, the factory as a whole ceases its production.
2. Biological cells are a factory complex of interlinked high-tech fabrics, fully automated and self-replicating, hosting up to over 2 billion molecular fabrics like Ribosomes & chemical production lines, full of proteins that act like robots, each with a specific task, function or goal, and completing each other, the whole system has the purpose to survive and perpetuate life. At least 560 proteins and a fully setup metabolome and genome is required, and they are interdependent. The probability, that such complex nano-factory plant could have emerged by unguided chemical reactions, no matter in what primordial environment, is beyond the chance of one to 10^150.000. The universe hosts about 10^80 atoms.   
3. Biological Cells are of unparalleled gigantic complexity and adaptive design, vastly more complex and sophisticated than any man-made factory plant. Self-replicating cells are, therefore, with extremely high probability, the product of an intelligent designer.


Is intelligent design merely an "argument from ignorance?"

https://reasonandscience.catsboard.com/t1720-is-intelligent-design-merely-an-argument-from-ignorance

Origins can be explained either by a conscient intelligent designer, which is the grounding necessary foundation of all contingent existence like our universe, or not, in other words, either there is a God, or not. Verificationism is the claim that ONLY what can be experimentally demonstrated is true. This is self-refuting since it cannot be experimentally proven that the truth of the metaphysical claim that "ONLY what can be experimentally proven " is True.

The truth is, science is limited in that it does not grant absolute truth, but only yields degrees of probability or likelihood. A solid epistemological framework that is consistent must carefully be chosen and use an elaborated methodology permitting to come to a meaningful, and most accurate possible conclusions in regards to origins and reality. Instead of looking only for scientific "proof" or confirmation in an absolute sense, better is to proceed with examining the available evidence-based on science, philosophy, and theology, which should point with confidence to the worldview that best accounts for that evidence using the bayesian method of abductive reasoning.

The (past) action or signature of an intelligent designer can be detected when we recognize things in nature very similar to human-made artifacts, things made based on mathematical principles, and made with an end goal in mind. The construction of functional irreducibly complex multipart-machines,  integrated circuits that require a blueprint to build the object. Furthermore, Computers integrate software/hardware that store high levels of instructional complex coded information. In our experience, systems that require and store large amounts of data through codes and languages, and which are constructed in the interdependence of hard and software invariably originate from an intelligent source. No exception.

DNA, epigenetic codes, and metabolic circuits indicate that biological molecular machines and factories ( Cells ) are full of information-rich, language-based codes and code/blueprint-based structures. Biologists have performed mutational sensitivity tests in proteins and determined that their amino acid sequences, in order to provide function, require highly instructional complex coded information stored in the Genome.   Cells also require and use over two dozen epigenetic codes, like Splicing Codes,  Metabolic Codes,   The Glycomic Code, etc. Furthermore, all kinds of irreducibly complex molecular machines and biosynthesis performing and metabolic pathways are necessary, which could not keep their basic functions without a minimum number of parts and complex inter-wined and interdependent structures. That indicates these biological machines and pathways had to emerge fully operational, all at once. Furthermore, the real mechanisms that explain biodiversity and complex organismal architecture are preprogrammed instructional complex INFORMATION encoded in various genetic and epigenetic languages and communication by various signaling codes through various signaling networks

Furthermore, the Origin of life research during over half a century has demonstrated that there are no viable explanations in regards to the prebiotic origin of the four classes of the basic building blocks of life by random, unguided processes, and consequently, living self-replicating cells is extremely unlikely. Also, statistical calculations have demonstrated, that getting a minimal cell proteome of 438 proteins total to make a first living cell, the probability would be  438/10^520.  We arrive at a probability of about 1 in 10^350.000 which is in the realm of the virtually impossible.  
Eliminative inductions argue for the truth of a proposition by demonstrating that competitors to that proposition are false. 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.  Darwin's theory of evolution by natural selection in regards of first-degree speciation & macroevolutionary level has been falsified. Instead of evolving, organisms devolve. And there is not enough time for evolution to establish even the most trivial amount of new information. Even a coordinated pair of mutations that first inactivates a binding site and then creates a new one is very unlikely to occur on a reasonable timescale. For example, the odds of getting two mutations right, to give hemoglobin C Harlem in one generation in an individual whose parents have normal hemoglobin, are about a hundred million times a hundred million (10^16). On average, then, nature needs about that many offspring in order to find just one that has the right double mutation. With a generation time of ten years and an average population size of one million, on average it should take about a hundred billion years for that particular mutation to arise—more than the age of the universe.

As a conclusion, the evidence that natural, unguided random events are too unlikely to occur, and the experience that intelligence can bring forward the systems described above and encountered in nature, applying bayesian abductive reasoning, and not merely based on lack of knowledge, or ignorance, an Intelligent Designer is the most plausible explanation of origins.


BAYESIAN PROBABILITY AND SCIENCE
Demand: All you have, is a great opinion, no evidence or proofs. Just an opinion, not fact.
Reply:  Proofs exist only in mathematics and logic, not in science.  Atheists repeatedly claim that a solid view or position, in order to be acceptable and valid, must be capable in principle of being empirically verified. The inadequacy of this epistemological approach led to the complete collapse amongst philosophers of science during the second half of the twentieth century, helping to spark a revival of interest in Metaphysics. Today’s Flew’s sort of challenge, which loomed so large in mid-century discussions, is scarcely a blip on the philosophical radar screen. Asking for 100 percent,  to truly know what occurred in the past is unrealistic. We believe lots of things with confidence even though we do not have absolute certainty. It is up to logic and the factors of different lines of evidence to determine what causes best to explain our origins.  Every worldview, without exception, is a faith-based belief system, consisting of a set of statements the holder adopts as being true. Starting from this view, we can dispense with the foolish notion of "proof," as some are so quick to require. Instead of "proof" in the absolute sense, we proceed with examining the available evidence, which should point with confidence to the worldview that best accounts for that evidence.

Science provides us with evidence. Based on it, we can make post-dictions in regard to the past.  Historical sciences cannot go back with a time-machine and observe what happened back in the past. As such, abiogenesis, and macroevolution ( primary speciation ) cannot be demonstrated in as much as ID/creationism. This is not a dispute between religion and science, but good interpretations of the scientific evidence, and inadequate interpretations, which do eventually not fit well the data.

… we can never have perfectly clean-cut knowledge of anything. It is a general consequence of the approximate character of all measurement that no empirical science can ever make exact statements.
P. W. Bridgman; (1882-1961); The Logic of Modern Physics; 1927/1951; p33, 34

A typical epistemological lack of understanding common to atheists is how to setup a correct methodology to find the best answers in regards of origins and reality, and to assume that given further investigations, science will or can discover with absolute certainty and tell us what has happened in the past. The truth is, science is limited in that it does not grant absolute truth, but only yields degrees of probability or likelihood. Asking theists to prove that there is a God is silly.

Science isn’t in the business of proving things. Rather, science judges the merits of competing models in terms of their simplicity, clarity, comprehensiveness, and fit to the data.

Science observes the Universe, records evidence, and strives to draw conclusions about what has happened in the past, is happening now, and what will potentially happen in the future, given the current state of scientific knowledge—which is often times woefully incomplete, and even inaccurate. The late, prominent evolutionist George Gaylord Simpson discussed the nature of science and probability several years ago in the classic textbook, Life: An Introduction to Biology, stating:

We speak in terms of “acceptance,” “confidence,” and “probability,” not “proof.” If by proof is meant the establishment of eternal and absolute truth, open to no possible exception or modification, then proof has no place in the natural sciences.

https://reasonandscience.catsboard.com/t2721-bayesian-probability-and-science

Jim: The phenomena aren’t even close.  Naturally occurring chemicals that act as human made electronics, are only analogous in function.  Not in origin.
Reply: Paul C. W. Davies The algorithmic origins of life 2013 Feb 6
We need to explain the origin of both the hardware and software aspects of life, or the job is only half finished. Explaining the chemical substrate of life and claiming it as a solution to life’s origin is like pointing to silicon and copper as an explanation for the goings-on inside a computer. It is this transition where one should expect to see a chemical system literally take on “a life of its own”, characterized by informational dynamics which become decoupled from the dictates of local chemistry alone (while of course remaining fully consistent with those dictates). Thus the famed chicken-or-egg problem (a sole hardware issue) is not the true sticking point. Rather, the puzzle lies with something fundamentally different, a problem of a causal organization having to do with the separation of informational and mechanical aspects into parallel causal narratives. The real challenge of life’s origin is thus to explain how instructional information control systems emerge naturally and spontaneously from mere molecular dynamics.

But now we hit a snag. The second step on the road to life, or at least the road to proteins, is for amino acids to link together to form molecules known as peptides. A protein is a long peptide chain, or a polypeptide. Whereas the spontaneous formation of amino acids from an inorganic chemical mixture is an allowed downhill process, coupling amino acids together to form peptides is an uphill process. It therefore heads in the wrong direction, thermodynamically speaking. Each peptide bond that is forged requires a water molecule to be plucked from the chain. In a watery medium like a primordial soup, this is thermodynamically unfavorable. Consequently, it will not happen spontaneously: work has to be done to force the newly extracted water molecule into the water saturated medium. Obviously, peptide formation is not impossible because it happens inside living organisms. But there the uphill reaction is driven along by the use of customized molecules that are pre-energized to supply the necessary work. In a simple chemical soup, no such specialized molecules would be on hand to give the reactions the boost they need. So a watery soup is a recipe for molecular disassembly, not self-assembly.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3565706/

Jim: Chemicals don’t need this intervention. They do things on their own.   Because they obey the laws of physics.
Reply: 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


Steven A. Benner Paradoxes in the Origin of Life 2012
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. 
https://www.ncbi.nlm.nih.gov/pubmed/25608919

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

https://reasonandscience.catsboard.com/t1279-abiogenesis-is-mathematically-impossible#7309

Jim: If I put a tree and a car together, which one is designed?
Reply:  A better comparison would be a photovoltaic system with photosynthesis

The make of Chlorophyll, and what it tells us about intelligent design
https://reasonandscience.catsboard.com/t1546-the-make-of-chlorophyll-and-what-it-tells-us-about-intelligent-design

Photovoltaic Power systems as illustration and comparison to Photosynthesis
Biological cell factories and molecular machines find often their equivalents in human-made artifacts. Photosynthesis finds its equivalent in human-made Solar Electric Power Systems which make electricity from sunlight.  It would be meaningless to produce Solar panels without the other parts required in the process to produce electrical energy. Solar panels by their own are useless. In Solar Electric Power Systems, a minimal number of five interdependent and interconnected parts is required, or the process is not functional. In a similar manner, the making of solar panels requires complex factories and machines, and at least seven processing steps, of which each requires complex machines which produce the intermediate products. The process must go all through, or functional Solar panels are not produced.   In the same manner, as Solar panels require complex manufacturing processes to be made, and to become functional, all other parts of the Solar Power Systems, to be made, require equally complex manufacturing processes. 

Human-made solar panels exercise the same function as chlorophyll. A solar power system is designed to supply usable solar power, using solar panels in the first step to capturing solar energy. We can draw interesting parallels between human-made solar panels and power systems, to its equivalent in nature, chlorophylls, and photosynthesis, and point out, why they provide an excellent illustration of intelligent design.

In order to gain electricity through solar power,  the installation of a solar power system is required. It consists of an arrangement of several components, including solar panels, a solar inverter, cabling,  solar tracking system, and an integrated battery solution to store the energy produced. If any of the mentioned components are missing, solar energy cannot be gained and stored. The final goal cannot be achieved. Each of the components is essential, and need to be interconnected correctly. One of the indispensable components are solar panels. 

The make of solar panels requires complex factories and machines  
The basic component of solar panels,  pure silicon,  is not pure in its natural state. It must be brought to the manufacturing site, the solar panel factory, cleaned, and prepared for further steps. The same happens in cells, where raw material must be imported in complex mechanisms, through gates in the cell membrane.   The manufacturing process goes from Purification of silicon , Making single crystal silicon, silicon wafers , doping,  placing electrical contacts, anti-reflective coating, and finally encapsulating the cell. Finally, the panel goes through a quality control process and implantation. That's an eight-step production process, which must go all the way through; each step is essential and requires also several complex machines, which are specifically designed for specific processing and manufacturing goals. 

It's evident that the whole process requires the invention and implementation of intelligence. That is, engineers, which first make scientific research, and based on the findings and inventions, experience and collected data, elaborate the relevant blueprints of the whole production process of every single machine, interconnections, and conceptualization as how the functional whole will provide the desired outcome. Functional parts are only meaningful within a whole, in other words, it is the whole that gives meaning to its parts. The information is based on a language system which must be pre-established. To define a specific subpart of a machine that requires a specific shape, size, material etc. the initial requirement is the language or code system, and the information based on that language to specify the part in question. In that way, the workers in the factory know how to decipher and understand the blueprint, its meaning, to produce the panels.   Intelligent agents think with an "end goal" in mind, allowing them to solve complex problems by taking many parts and arranging them in intricate patterns that perform a specific function. They need to be able to organize parts availability, synchronization, manufacturing and assembly coordination and interface compatibility of the single parts and subunits. The individual parts must precisely fit together and be correctly interconnected. The production process usually takes place in complex factories  which also must be fully built, and ready for production. The raw materials are sourced, transported to the factory, selected and prepared for use at the right facility.  Without solar panels, no energy could be captured, a solar power system would be non-functional.

What humans invented a few decades ago, was implemented much before through photosynthesis.

Chlorophyll, by evolution? 
The evolutionary model is day by day…step by step…we are getting better and better slowly with time, adding to get more complexity. But that suggested manufacturing process raises serious questions in face of the challenge to produce Chlorophyll molecules and photosynthesis. 

Evolution has no foresight. So let's suppose, hundreds of millions of years would produce chlorophylls.  SO WHAT ???! - on their own, there is no function for them, and if they don't have a function, natural selection would not select them. Chlorophyll by its own, without the other proteins used in the photosynthesis pathway, would have no use.

There relies on the BIG flaw in Darwin's idea: ‘Why would evolution produce a series of enzymes that only generate useless intermediates until all of the enzymes needed for the end product exist, fully functional, and  interlinked in a useful manner ?’ A minimal amount of precise instructional information is required for a gene regulatory network, and genes to instruct for the orderly setup of the whole system. If a gene and epigenetic information do not contain sufficient instructions for an end function, there would be no selective advantage, and no end goal would be achieved only useless intermediary products. Thus, before a region of DNA and epigenetic codes and signalling network contain the required information to produce functional multi-part protein complexes, natural selection plays no role in guiding its making. The step by step selective mechanism is not a sufficient nor adequate and too unspecific to explain for the complex molecular proceedings observed in living cells and organisms. Intelligent pre-programming is the most adequate explanation for the origin of Chlorophyll, and photosynthesis. 

What good would it be to make complex manufacturing machines to produce intermediate products for solar panel production, without all the other machines and a functional factory fully setup and in place? 
What good would there be for natural selection to select and produce enzymes, used in this complex manufacturing process, without all the other enzymes in place, and the whole process coordinated to get a useful end product? 
What good would it be, if solar panels would be produced, but all other parts would be missing to transform solar energy into useful energy? 
What good would there be, if the chlorophyll pathway would go all the way through the 17th step? Chlorophyll would be produced, BUT:
What good for survival would there be for chlorophyll on its own, if not fully embedded in the photosynthesis process? none.
What good would there be for photosynthesis without chlorophyll in place, capturing light, and transmitting it to the photosystem? none, since capturing light is essential for the whole process. 

The thing is, there's no driver for any of the pieces to emerge individually because single parts confer no advantage in and of themselves. The necessity for the parts of the system to be in place all at once is simply evidence of a planning organizing creative intelligence.

Natural selection would not select for components of a complex system that would be useful only in the completion of the much larger system.

Jim:  Here’s another: which was designed the Sun or the space heater?  At least they both produce heat and light.
Reply: The sun - just right for life 
https://reasonandscience.catsboard.com/t2550-the-sun-just-right-for-life

The Nuclear Weak Coupling Force - Tuned to Give an Ideal Balance Between Hydrogen (as Fuel for Sun) and Heavier Elements as Building Blocks for Life
The weak force governs certain interactions at the subatomic or nuclear level. If the weak force coupling constant were slightly larger, neutrons would decay more rapidly, reducing the production of deuterons, and thus of helium and elements with heavier nuclei. On the other hand, if the weak force coupling constant were slightly weaker, the Big Bang would have burned almost all of the hydrogen into helium, with the ultimate outcome being a universe with little or no hydrogen and many heavier elements instead. This would leave no long-lived stars and no hydrogen-containing compounds, especially water. In 1991, Breuer noted that the appropriate mix of hydrogen and helium to provide hydrogen-containing compounds, long-term stars, and heavier elements is approximately 75 percent hydrogen and 25 percent helium, which is just what we find in our universe.

Jim:  Car factories and cells are not analogous either.
Reply: Genome information, protein synthesis,  the biosynthesis pathways in biology, and the analogy of human programming, engineering, and factory robotic assembly lines
https://reasonandscience.catsboard.com/t1987-information-biosynthesis-analogy-with-human-programming-engeneering-and-factory-robotic-assembly-lines

 The best and most advanced result that intelligent and capable minds, thousands and hundred thousands of the most brilliant and inventive men and women from all over the globe have been able to come up with after over one hundred years of technologic advance and progress, of what is considered one of the greatest innovations of the 20th century, is the construction of complex factories with fully automated assembly lines which use programmed robots in the manufacturing, assembly, quality control and packing process of the most diverse products, in the most economical, efficient and effective way possible,  integrating different facilities and systems, and using advanced statistical methods of quality control, making from cell phones, to cars, to power plants, etc.,  but the constant intervention of intelligent brain power is required to get the whole process done and obtain the final products. The distribution of the products is also based on complex distribution networks and companies, which all require huge efforts of constant human intervention and brainpower.  

Amazingly, the highest degree of manufacturing performance, excellence, precision, energy efficiency, adaptability to external change, economy, refinement, and intelligence of production automatization ( at our scale = 100 )  we find in proceedings adopted by each cell,  analogous to our factory, and biosynthesis pathways and processes in biology.  A cell uses a complex web of metabolic pathways, each composed of chains of chemical reactions in which the product of one enzyme becomes the substrate of the next. In this maze of pathways, there are many branch points where different enzymes compete for the same substrate. The system is so complex that elaborate controls are required to regulate when and how rapidly each reaction occurs. Like a factory production line, each enzyme catalyzes a specific reaction, using the product of the upstream enzyme, and passing the result to the downstream enzyme. 

If just one of the enzymes is not present or otherwise not functioning then the entire process doesn’t work. We now know that nearly every major process in a cell is carried out by assemblies of 10 or more protein molecules. And, as it carries out its biological functions, each of these protein assemblies interacts with several other large complexes of proteins. Indeed, the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines. Cells adopt the highest advanced Mass-Craft production techniques, which yield products with the ability of high adaptability to the environment ( microevolution ) while being produced with high efficiency of production, advanced error checking mechanisms, low energy consumption, and automatization, and so is generally being far far more advanced, complex,  better structured and organized in every aspect, than the most advanced robotic assembly facility ever created by man. Unlike our own pseudo-automated assembly plants, where external controls are being continually applied, the cell's manufacturing capability is entirely self-regulated . . . . I advocate that this fact is strong evidence of a planning, super-intelligent mind, which conceptualized and created life right from scratch.

Considerations of the planning of the layout of an assembly line facility.

My comment: Important considerations for a high economic,  effective, and proper material flow are required and must be considered, though, and brought in when planning the concepts and layout design of a new factory assembly line, as for example maximal flexibility in the line for demand and supply fluctuation,  planning deep enough to answer all possible aspects of a new line to get max efficiency afterward.   There should be simple material delivery routes and pathways throughout the facility that connect the processes. Also, there needs to be a plan for flexibility and changes, since volumes and demand are variable. Awareness of the many factors involved right in the planning process of the factory is key. Right-sized equipment and facilities must be planned and considered as well. All equipment and facilities should be designed to the demand rate or takt time projects and facility designs that do not take these considerations into the account,  start out great, but quickly bog down in unresolved issues, lack of consensus, confusion, and delay.  3)

Denton, p. 329.
We would see [in cells] that nearly every feature of our own advanced machines had its analog in the cell: artificial languages and their decoding systems, memory banks for information storage and retrieval, elegant control systems regulating the automated assembly of parts and components, error fail-safe and proof-reading devices utilized for quality control, assembly processes involving the principle of prefabrication and modular construction. In fact, so deep would be the feeling of deja-vu, so persuasive the analogy, that much of the terminology we would use to describe this fascinating molecular reality would be borrowed from the world of late-twentieth-century technology.
    “What we would be witnessing would be an object resembling an immense automated factory, a factory larger than a city and carrying out almost as many unique functions as all the manufacturing activities of man on earth. However, it would be a factory that would have one capacity not equaled in any of our own most advanced machines, for it would be capable of replicating its entire structure within a matter of a few hours. To witness such an act at a magnification of one thousand million times would be an awe-inspiring spectacle.”

1) http://money.cnn.com/gallery/technology/2015/04/29/ford-factory-assembly-line-robots/
2) http://robohub.org/the-evolution-of-assembly-lines-a-brief-history/
3) http://www.assemblymag.com/articles/89974-9-line-layout-mistakes-to-avoid
4) http://alumnus.caltech.edu/~raj/writing/mass-craft.html

Jim: You spend all this time on evidence, and then claim it’s silly. Cognitive dissonance.
Reply: Evidence and empirical proofs ( demonstration ) is not the same. Evidence is what we observe, and based on the evidence, we can make inductive, deductive, or abductive arguments. Proofs are what can be empirically observed. When you demand for evidence, it is not the same as to demand for empirical proofs. That is a fundamental difference, which I expected you to know.

Jim:  every piece of evidence for the supernatural presented to me so far has a natural explanation.
Reply: Presuppositionalism
https://reasonandscience.catsboard.com/t3116-presuppositionalism

Naturalism cannot ground fundamentally anything. That is: 1. Existence itself 2. The meaning of life  3. The value of human life 4. Moral values 5. Knowing what is objectively ( ontologically) true in regards to reality 
6. Sound reasoning 7. Logic 8. Intelligibility 9. His mind and consciousness 10. Uniformity in nature.

Comparing worldviews - there are basically just two
https://reasonandscience.catsboard.com/t2793-worldviews-there-are-basically-just-two-in-regards-of-origins

Naturalism & materialism:
“the philosophical belief that everything arises from natural properties and causes, and supernatural or spiritual explanations are excluded or discounted.”

Materialism is an atheistic worldview that sees all reality as the result of accidental collisions and combinations of elementary particles governed by a mysteriously fortuitous set of laws that control how matter interacts. It’s a worldview devoid of higher meaning and purpose.

“the doctrine that nothing exists except matter and its movements and modifications.”

- Multiverse
- Steady-state universe
- Oscillating universes
- Virtual particles
- Big Bang
- Accretion theory
- Abiogenesis
- Common ancestry
- Evolution
- Monism

In regards of the origin of the universe, it was either eternal or had a beginning, in that case, the proponent of naturalism would have to give an explanation of the cause of the universe, and/or explain how it could exist eternally, without a beginning.  The universe is finely tuned, so then he has the option of multiverses, where one would be life-permitting ( ours ). In regards to abiogenesis, he has random chance, and afterward, evolution. He has to provide good reasons why these alternatives have more/better explanatory power than design.

I don't think you can back up rationally ANY of these naturalistic propositions, or, if you propose any other, those alternatives. I have never seen an atheist capable of doing it. Try if you like. Lets see..... 

Jim: That for the last 1,000 years no supernatural claim has been proven.
Reply:  WOW!! Right after I explained that demanding for proofs is an unsophisticated epistemological approach, you go and ask again for proof. Did you forget what I wrote in my previous email ? Do YOU have proof that the natural world is all there is? No? Can you provide proof? No? Then it is moot to demand proof of God's existence. There is no proof either way.

Jim: The time to believe something is true, is when you have sufficient good evidence.
Reply:  Are you still conflating proof, with evidence ?

125 reasons to believe in God
https://reasonandscience.catsboard.com/t1276-125-reasons-to-believe-in-god

Syllogistic - Arguments of Gods existence based on positive evidence
https://reasonandscience.catsboard.com/t2895-syllogistic-arguments-of-gods-existence-based-on-positive-evidence

Arguments for Gods existence in in short sentences
https://reasonandscience.catsboard.com/t3026-evidence-of-god-in-short-sentences

Presuppositionalism
https://reasonandscience.catsboard.com/t3116-presuppositionalism

The obviousness of Creation is hidden from those who reject God. There is no evidence that we can exist without a creator. 
Since there is being, being has always been. Beginning requires a cause. Movement and change a prime mover. Contingent beings depend on a necessary cause. Creation requires a creator. Design requires a designer. Laws require a lawmaker. Mathematics requires a mathematician. Fine-tuning requires a fine-tuner, Codes require a coder. Information requires an Informer. Translation requires a translator.  Life has only been observed to come from life. Logic comes from logic, Consciousness comes from consciousness, machines require a machine-maker.  Factories require a factory-maker.  Objective moral values come from a moral giver. The "God of the gaps" is an invalid refutation of arguments for the existence of God. And so, that there is no evidence for God(s). 

To be ultimate and singular means to be the source of all possibilities. How can you establish what is possible and impossible without referencing God? If there is no God, then how can the laws of physics which are imported on the physical universe be stable, and continuous, and be secured? Atheists cannot ground fundamentally anything, that is:  1. Existence itself
2. The meaning of life  3. The value of human life 4. Moral values 5. Knowing what is objectively ( ontologically) true in regards to reality  6. Sound reasoning 7. Logic 8. Intelligibility 9. Mind and consciousness 10. Uniformity in nature.


Scientists, most of them not believing in God, had to acknowledge and admit the overwhelming evidence pointing to the overwhelming appearance of design in the natural world:
https://reasonandscience.catsboard.com/t1276p25-125-reasons-to-believe-in-god#8282

Following a list of positive evidence of God's existence, not depending on gaps or lack of knowledge. 

1. Existence of the universe. The universe had a beginning, therefore a cause
2. The universe obeys the laws and rules of mathematics and physics. Its implementation depends on the action of an intelligent rational agency.
3. The physical universe and the laws of physics are interdependent and irreducible. There would not be one without the other.
4. Fine-Tuning. The fundamental physical constants, the universe, and the earth are finely tuned for life. Over 100 constants must be just right.
5. Formation of life. Life comes only from life. Abiogenesis has never been demonstrated to be possible despite over half a century of intensive scientific research.
6. Cells ARE literally factories. Biological cells ARE an industrial park of millions of interconnected complex factories, full of machines. Factories are always designed.
7. A minimal free-living Cell requires 1300 proteins with an average size of 400 amino acids. That requires to select 1 out of 10^722.000! 
8. Irreducible complexity. Biological cells require a minimal number of parts, which have no use by themselves, and would never accumulate on a prebiotic earth
9. The appearance of design. The universe and biological systems appear designed. Therefore, most probably, they are designed. 
10. Codified Information. DNA has the highest storage density known, and stores the blueprint of life. Blueprints can always be traced back to intelligence
11. The Fossil Record. The Fossil record, and in special the Cambrian explosion, demonstrates the sudden appearance of lifeforms, without intermediates. 
12. Consciousness and language. Conscience, mental reality, language, logic, free will, moral values, are immaterial entities, and cannot emerge from physical matter. 
13. Objective moral values exist. They are "ought to be"s, imprinted in our conscience. 
14. Human objective logic depends and can only derive from a pre-existing necessary first mind with objective logic.
15. Theology and philosophy. Both lead to an eternal, self-existent, omnipresent transcendent, conscious, intelligent, personal and moral Creator.
16. The Bible. The Old Testament is a catalog of fulfilled prophecies of Jesus Christ, and his mission, death, and resurrection foretold with specificity.
17. Archaeology. Demonstrates that all events described in the Bible are historical facts. 
18. History. Historical evidence reveals that Jesus Christ really did come to this earth, and really did physically rise from the dead
19. The Bible's witnesses. There are many testimonies of Jesus doing miracles still today, and Jesus appearing to people all over the globe, still today.
20. End times. The signs of the end times that were foretold in the Bible are occurring in front of our eyes. New world order, Israel as a nation, microchip implant, etc.
21. After-life experiences. Credible witnesses have seen the afterlife and have come back and reported to us that the afterlife is real.

Jim: Does nothing exist?  Can you show it?  No of course not. The universe exists, everything we’ve discovered so far points to natural causes. Without proof of the supernatural, to claim a supernatural cause for anything is dubious at best.
Reply: The point is that a state of affairs of absolutely nothing has never been, otherwise it would still be the same state of affairs, because nothing has no causal powers. 

Nothing is the thing that stones think of
https://reasonandscience.catsboard.com/t2817-nothing-is-the-thing-that-stones-think-of

Existence cannot come from non-existence. Reality cannot come from Non-reality. Something cannot come from Nothing. The law of cause and effect is the most universal law of all laws known. That is something that can be inferred by the explicit nature of non-being. It is the absence of anything. Therefore, the claim: Something cannot come into existence from absolutely nothing, stands on its own, and does not require any further proof or demonstration. 

1. The physical universe exists. 
2. Existence cannot come from non-existence. 
3. Since we exist, then being has always been in one form or another.
4. The universe had a beginning. It cannot be the product of an infinite serie of regress, nor be caused by nothing. 
5. Therefore, a non-physical being must have existed beyond the universe, causing the universe into existence.
6. That being is God.

Jim:  I have heard several quantum physicists say that cause and effect aren’t fundamental (https://www.quantamagazine.org/quantum-mischief-rewrites-the-laws-of-cause-and-effect-20210311/ google for more).
Reply: There is tons of hocus pocus, and speculation in the article. they talk about quantum gravity, photons, superposition etc. First, they would have to explain where all the elementary particles, and elementary particles came from.

Jim: Playing with infinity is fun. Here’s a useless thought experiment:  in order to go from point a, to point b, you first have to cross the half-way point. But, before that the quarter way point. I can keep dividing by two, creating halfway points to halfway points, infinitely.
Reply: Right. But you cannot go below planck time which is subject to the laws of physics:

The Fundamental Properties of Nature, the universal constants—the cosmic numbers which define our Universe where did they come from ?
https://reasonandscience.catsboard.com/t3165-the-fundamental-properties-of-nature-where-did-they-come-from

CODATA RECOMMENDED VALUES OF THE FUNDAMENTAL PHYSICAL CONSTANTS: 2018
https://physics.nist.gov/cuu/pdf/wall_2018.pdf

Wolfram: As of Today, the Fundamental Constants of Physics (c, h, e, k, NA) Are Finally… Constant! November 16, 2018
Representatives of more than 100 countries agreed on a new definition of the base units for all weights and measures. An important vote for the future weights and measures used in science, technology, commerce and even daily life happened. The agreement was the culmination of at least 230 years of wishing and labor by some of the world’s most famous scientists. Units appear in any real-world measurement, and fundamental constants are of crucial importance for the laws of physics. Why do the constants have the values they have? Is humankind lucky that the constants have the values they have (e.g. only minute changes in the values of the constants would not allow stars to form)?
https://blog.wolfram.com/2018/11/16/as-of-today-the-fundamental-constants-of-physics-c-h-e-k-na-are-finally-constant/

Laws of Physics, fine-tuned for a life-permitting universe 
https://reasonandscience.catsboard.com/t1336-laws-of-physics-fine-tuned-for-a-life-permitting-universe
1. The Laws of physics are like the computer software, driving the physical universe, which corresponds to the hardware. All the known fundamental laws of physics are expressed in terms of differentiable functions defined over the set of real or complex numbers. The properties of the physical universe depend in an obvious way on the laws of physics, but the basic laws themselves depend not one iota on what happens in the physical universe.There is thus a fundamental asymmetry: the states of the world are affected by the laws, but the laws are completely unaffected by the states. Einstein was a physicist and he believed that math is invented, not discovered. His sharpest statement on this is his declaration that “the series of integers is obviously an invention of the human mind, a self-created tool which simplifies the ordering of certain sensory experiences.” All concepts, even those closest to experience, are from the point of view of logic freely chosen posits. . .
2. The laws of physics are immutable: absolute, perfect mathematical relationships, infinitely precise in form. The laws were imprinted on the universe at the moment of creation, i.e. at the big bang, and have since remained fixed in both space and time. 
3. The ultimate source of the laws transcend the universe itself, i.e. to lie beyond the physical world. The only rational inference is that the physical laws emanate from the mind of God. 
https://arxiv.org/pdf/math/0302333.pdf

Jim: I’m unaware of any cosmologist that suggests the universe is infinite.
Reply: 
PHYSICIST: THE UNIVERSE HAS LIKELY BEEN EXPANDING “ETERNALLY” WHAT IF THE UNIVERSE DIDN'T ACTUALLY HAVE A BEGINNING?
https://futurism.com/the-byte/physicist-universe-expanding-eternally

But since you don't believe that, then you must stick to the proposition that the universe actually had a beginning. What caused it into existence ?

JMike: what example do you have at the beginning at which you could observe and know that that is the case or what is the novel predictions from an indirect observation basis at which you can make that conclusion
Reply: B.Alberts: Molecular Biology of the Cell. 4th edition.
If left uncorrected when the DNA is replicated, most of these changes would be expected to lead either to the deletion of one or more base pairs or to a base-pair substitution in the daughter DNA chain. ( see below ) The mutations would then be propagated throughout subsequent cell generations. Such a high rate of random changes in the DNA sequence would have disastrous consequences for an organism
https://www.ncbi.nlm.nih.gov/books/NBK26879/

PHILIP HEMME: Nobel Prize in Chemistry 2015: DNA Repairing Mechanisms that Keep you Alive 07/10/2015
The 2015 Nobel Prize in Chemistry has been awarded to three scientists for their truly amazing discoveries about the DNA code of life. An article from the Swedish Academy of Science highlights the significance of these discoveries for understanding how our cells can copy the DNA code millions of times with hardly ever making a mistake. 1 ( See article 32 )
DNA repair mechanisms are crucial to our existence. Without them, we would not survive because of DNA damage caused by the environment (e.g UV light damage, radiation etc.)
https://www.labiotech.eu/trends-news/nobel-prize-2015-dna-repairing-mechanism-keeps-alive-rewarded/

JMike: like catalytic functions of uh ribozymes or anything like that 
Reply: The origin of replication and translation and the RNA World
https://reasonandscience.catsboard.com/t2234-the-origin-of-replication-and-translation-and-the-rna-world

The phrase "RNA World" was first used by Nobel laureate Walter Gilbert in 1986, in a commentary on how recent observations of the catalytic properties of various forms of RNA fit with this hypothesis.
https://en.wikipedia.org/wiki/RNA_world

Leslie Orgel: Prebiotic chemistry and the origin of the RNA world Mar-Apr 2004
It is possible that all of these, and many other difficulties, will one day be overcome and that a convincing prebiotic synthesis of RNA will become available. However, many researchers in the field, myself included, think that this is unlikely
https://pubmed.ncbi.nlm.nih.gov/15217990/

Christian de Duve: The Beginnings of Life on Earth   September-October 1995 issue of American Scientist.
Contrary to what is sometimes intimated, the idea of a few RNA molecules coming together by some chance combination of circumstances and henceforth being reproduced and amplified by replication simply is not tenable. There could be no replication without a robust chemical underpinning continuing to provide the necessary materials and energy.
https://www2.nau.edu/~gaud/bio372/class/readings/beglifeerth.htm

Robert Shapiro: Small Molecule Interactions were Central to the Origin of Life  (June 2006),
The myth of a small RNA molecule that arises de novo and can replicate efficiently and with high fidelity under plausible prebiotic conditions . . . [is] unrealistic in light of current understanding of prebiotic chemistry
https://www.jstor.org/stable/10.1086/506024

JMike: or polymerizing on hot clay like you would disagree with that or is that is that
Reply: RNA & DNA: It's prebiotic synthesis: Impossible !!
https://reasonandscience.catsboard.com/t2865-rna-dna-it-s-prebiotic-synthesis-impossible#6847

Robert Shapiro Do natural clays catalyze this reaction? June 2006
The attractiveness of this oligonucleotide synthesis rests in part in the ready availability of the catalyst. Montmorillonite is a layered clay mineral-rich in silicate and aluminum oxide bonds. It is widely distributed in deposits on the contemporary Earth. If the polymerization of RNA subunits was a common property of this native mineral, the case for RNA at the start of life would be greatly enhanced.
However, the “[c]atalytic activity of native montmorillonites before being converted to their homoionic forms is very poor” (Ertem 2004:567). The native clays contain bound polyvalent cations, such as Cu2, Fe3, and Zn2, that interfere with phosphorylation reactions. This handicap was overcome in the synthetic experiments by titrating the clays to a monoionic form, generally sodium, before they were used. Even after this step, the activity of the montmorillonite depended strongly on its physical source, with samples from Wyoming yielding the best results (Ferris et al. 1989; Ertem 2004). Eventually the experimenters settled on Volclay, a commercially processed Wyoming montmorillonite provided by the American Colloid Company. Further purification steps were applied to obtain the catalyst used for the “prebiotic” formation of RNA.
https://www.jstor.org/stable/10.1086/506024

JMike: you know it seems like if we took like a meme of it it's like they're working in a lab and you're on your phone like on the toilet researching things you know what i mean it seems to just seems to be you're assuming things that other models don't agree with
Reply: The Lab experiments warrant the conclusion that abiogenesis is not possible.

Abiogenesis is mathematically  impossible
https://reasonandscience.catsboard.com/t1279-abiogenesis-is-mathematically-impossible

Jack W. Szostak: 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.mrgscience.com/uploads/2/0/7/9/20796234/origin_of_life_sci_am.pdf

Eugene V. Koonin: The Logic of Chance: page 252:
" 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.

Steve Benner:  Paradoxes in the origin of life
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.

Graham Cairns-Smith: Genetic takeover, 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.

Garrett: Biochemistry, 6th ed,  page 665
Key compounds, such as arginine, lysine, and histidine; the straight-chain fatty acids; porphyrins; and essential coenzymes, have not been convincingly synthesized under simulated prebiotic conditions.

Robert Shapiro: A Replicator Was Not Involved in the Origin of Life
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 synthesis of additional copies of themselves, but this device cannot be used for the preparation of the very first such molecule, which must arise spontaneously from an unorganized mixture. The formation of an information-bearing homopolymer through undirected chemical synthesis appears very improbable.


Question: Let's suppose you see a machine made for specific functions. And you see nearby another machine, that is set up constantly to monitor the function of the first machine, and knows when it performs properly, and when an error occurs. And then, when something goes havoc, that machine knows immediately what error occurred, and has the know-how to fix it. Is it more rational to infer that intelligence was required to set up both machines, or rather that both are the product of random unguided events?

1. Organisms are constantly exposed to different environments, and in order to survive, require to be able to adapt to external conditions. 
2. Life, in order to perpetuate, has to replicate. That includes DNA, which must be replicated with extreme accuracy. Somehow, the cell knows when DNA is accurately replicated, and when not. There are extremely complex quality control mechanisms in place, which constantly monitor the process. At least 3 error check and repair mechanisms keep error during replication down to 1 error in 10 billion nucleotides replicated. 
3. These repair mechanisms, sophisticated proteins, are also encoded in DNA. So proteins are required to error check and repair DNA but accurately replicated DNA is necessary to make the proteins that repair DNA. 
4. That is an all-or-nothing business. Therefore, these sophisticated systems had to emerge all at once, and require a designer.  

1. The origin of life, and perpetuation of life, depends on the accurate replication of DNA. At least 3 error check and repair mechanisms keep error during replication down to 1 error in 10 billion nucleotides replicated. 
2. That depends on very sophisticated error check and repair proteins, which had to be in operation from day one. 
3. Instructions in DNA are required to make error check and repair proteins, but these proteins have to be there from day one to error check and repair DNA. That is an all or nothing business. 
4. The complexity of the first living cell had to be set up fully formed right from the beginning, and that requires intelligence.

DNA and RNA error checking and  repair, amazing evidence of design
https://reasonandscience.catsboard.com/t2043-dna-and-rna-error-checking-and-repair-amazing-evidence-of-design

Error check and repair mechanisms require foresight
https://reasonandscience.catsboard.com/t3105-error-check-and-repair-mechanisms-require-foresight

Error detection and repair during the biogenesis & maturation of the ribosome, tRNA's, Aminoacyl-tRNA synthetases, and translation: by chance, or design?
https://reasonandscience.catsboard.com/t2984-error-check-and-repair-during-messengerrna-translation-in-the-ribosome-by-chance-or-design

Kreodebunk: 1) Okay it is the standart fallacy of comparing the living organism with mechanisms, what could not emerge through evolution process, for example here: ”The same problem-solving processes apply to chemical cell factories.”
Reply: Science describes proteins as molecular machines. Biological cells as chemical factories. Neurons as computers. Metabolic pathways as production lines. 

Nature's Robots point to design
https://reasonandscience.catsboard.com/t2978-nature-s-robots-point-to-design

Are Cells factories in a literal sense?
https://reasonandscience.catsboard.com/t2245-abiogenesis-the-factory-maker-argument#4490

1. 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, most probably, Cell factories containing all those things are the product of an intelligent designer.

Kreodebunk: There is important difference between mechanism and chemical process, what I would like you to remember.
The the mechanical parts must fir perfectly with respect to each other, be places in right location by the creator, what for certain do not emerge naturally.
But chemicals do not need precise positioning and size matching towards each other. You just drop chemicals - even complex ones in the solution, and they find each other through Bround movement, randomly floating here and there,until they get right location. Watch the interesting video about the proteing performing its action when the molecule gets into the “hole” on his surface.

And no, probability of it is not  very low, since chemical reactions DO happen.

Reply: So the alternative mechanism, once an intelligent designer is removed from the picture, is either 1. physical necessity, 2. random, non-designed, unguided events, or 3. When DNA replication starts, evolution.

Kreodebunk:  2) The next part is about abiogenesis and you must properly familiarize yourself with the hot springs hypothesis and facts, what are claimed by mainstream science be hints to it, including UV-radiation from nucleotydes, chemical composition comparison, the greater concentration of chemicals due to evaporation, etc. Without having real knowledge of this topic and generally in chemistry, you argue by drawing in broad, household presentation of processes like

“That part has still to be directed to a location inside the cell where it can exercise its new function in a joint venture with other molecules, or substrates. That requires meta-data. “

You just invent this statement about requirement on no basis.

Reply: Signal Recognition Particle: An essential protein targeting machine

https://reasonandscience.catsboard.com/t2651-signal-recognition-particle-an-essential-protein-targeting-machine

The argument of the zip-codes within the cell
1.  Proteins are the workhorses of the cell, but to get the most work out of them, they need to be in the right place.  In neurons, for example, proteins needed at axons differ from those needed at dendrites, while in budding yeast cells, the daughter cell needs proteins the mother cell does not.  In each case, one strategy for making sure a protein gets where it belongs is to shuttle its messenger RNA to the right spot before translating it. The destination for such an mRNA is encoded in a set of so-called “zipcode” elements, which loop out of the RNA string to link up with RNA-binding proteins.  In yeast, these proteins join up with a myosin motor that taxis the complex to the encoded location.
2. All the above speaks about amazing, irreducible complexity and intelligent design of one of the simplest cells, the yeast. How this complex system evolved was not explained. This complexity found in the simple cell of yeast is one more example out of innumerable complex systems that are necessary for the existence of the cell.
3. The irreducibly complex systems are evidence of an intelligent design that could have been made only by a super-intelligent person all men call God.

Kreodebunk: 3) The final part is about  misunderstanding of information, language and code. I remember this bullshit quotes.
I would argue that “syntax” has everything. The night sky has a syntax what carries information about stars from far away. But  DNA and other natural processes have no semantic, because that means having some relation, unrelated to natural process from syntax carrying object. For example written text - to real objects, there is no relation from written word “cat” to the real cat object, unless you intentionally invent or know this connection.
Do you see how is it different from simple nucleotyde to aminoacid relation, what is based on natural process - chemistry.

Reply:

The five levels of information in DNA
https://reasonandscience.catsboard.com/t1311-the-five-levels-of-information-in-dna

Syntax 
If we look at a text in any particular language, we see that only certain combinations of letters form permissible words of that particular language. This is determined by a pre-existing, wilful, convention. All other conceivable combinations do not belong to that language’s vocabulary. Syntax encompasses all of the structural characteristics of the way information is represented. This second level involves only the symbol system itself (the code) and the rules by which symbols and chains of symbols are combined (grammar, vocabulary). This is independent of any particular interpretation of the code.

To this end, they compared the rules of syntax (the way in which words are put together to form phrases and sentences), semantics (the study of meaning in language forms) and the basic rules of grammar. They found that the alkalines of our DNA follow a regular grammar and do have set rules just like our languages. So human languages did not appear coincidentally but are a reflection of our inherent DNA. 2

The 'grammar' of the human genetic code is more complex than that of even the most intricately constructed spoken languages in the world. The findings explain why the human genome is so difficult to decipher -- and contribute to the further understanding of how genetic differences affect the risk of developing diseases on an individual level.   A new study from Sweden's Karolinska Institutet shows that the 'grammar' of the human genetic code is more complex than that of even the most intricately constructed spoken languages in the world. The findings, published in the journal Nature, explain why the human genome is so difficult to decipher -- and contribute to the further understanding of how genetic differences affect the risk of developing diseases on an individual level.  knowing just the order of the letters is not sufficient for translating the genomic discoveries into medical benefits; one also needs to understand what the sequences of letters mean. In other words, it is necessary to identify the 'words' and the 'grammar' of the language of the genome. Their analysis reveals that the grammar of the genetic code is much more complex than that of even the most complex human languages. Instead of simply joining two words together by deleting a space, the individual words that are joined together in compound DNA words are altered, leading to a large number of completely new words.

Complex grammar of the genomic language
https://phys.org/news/2015-11-complex-grammar-genomic-language.html

Immutiable Destiny There is no such thing as something seeking or desiring to become some other kind of thing. To answer your question, where you go from there are various combinations of peptides and RNA that interact mutually with each other. Some pairings may be good, and others not so stable.

Reply: There is no reason to presuppose that there was a large pool of RNAs extant prebiotically. The scenario falls short right here, right from the beginning. For a detailed justification of that conclusion, see here

Some may interact in such a way where its structure makes the Replication of both a Peptide and an RNA easier, and in such cases, because both of them have a symbiotic effect on each others survival, there is a bias in the system to produce more of that kind of thing.

Reply: If a self-replicating RNA molecule has never been observed, as outlined here, what makes you believe, it would be different with RNA-peptides?

 You are correct to point out that it is a long stretch to go to fully operational translation machinery. What we are looking for are plausible scenarios that explain why amino acids/peptides and RNA have this relationship between them.

Reply: Ok. So lets suppose that was even the case. So what? Where do you want to go from there?

 If there is ever a gain in the survivability of some chemical species, you can then imagine other things within some protocell or whatever system you envision, that further allows that system to perform its function easier, and so the process goes, becoming more efficient each time.

Reply: These are just unsupported hypotheses. Speculation & guesswork.

And even IF such a miracle would happen, a ribosome itself, on its own, has no business. The entire chain of players has to be present, fully connected, and operational, from gene regulation to transcription to translation to be fully set up to have anything meaningful going on. The synthesis of proteins is an irreducible, interdependent, highly complex process. This contention was already addressed, irreducible complexity is a drawn out and failed argument. Nobody in OOL research believes all components need to be necessary,

Reply: Then why are periodically new science papers published, that try to establish what a minimal cells part would have to be, in order to be able to keeps its minimal vital functions? And once going lower than that threshold, these basic functions are not kept anymore? That is in its very essence what irreducible complexity means.

Jim Bendewald Irreducible Complexity  SEPTEMBER 21, 2019
The cell is the ultimate example of irreducible complexity. My book Evolution Shot Full of Holes with co-author Frank Sherwin, contains a chapter on the topic of the origin of life.The cell is an interdependent functional city. We state, “The cell is the most detailed and concentrated organizational structure known to humanity. It is a lively microcosmic city, with factories for making building supplies, packaging centers for transporting the supplies, trucks that move the materials along highways, communication devices, hospitals for repairing injuries, a massive library of information, power stations providing usable energy, garbage removal, walls for protection and city gates for allowing certain materials to come and go from the cell.” The notion of the theoretical first cell arising by natural causes is a perfect example of irreducibly complexity. Life cannot exist without many numerous interdependent complex systems, each irreducibly complex on their own, working together to bring about a grand pageant for life to exist.
https://evidencepress.com/irreducible-complexity/

More here

we are looking for scenarios that explain why the relationship between RNA and amino acids(peptides) exist at all. Once you have scenario that is plausible, you can very easily begin to see other components of cells and other things in prebiotic chemistry act in such a way that are mutually beneficial, this generates a selection pressure 

Reply: I understand why you guys constantly attempt to smuggle natural selection into abiogenesis. If you cancel it, all you have left as an alternative to a designer is  nonintelligent stochastic chance. But that is a big no. 

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

more here

and by consequence, those things reproduce better than things not as good, and over time new interactions that form which aid the system to do its things become more integrative and the system develops as needed.

Reply: and so, the storytelling and wishful thinking goes.... anything is acceptable. Just not God.

2nd claim: Shubin Liu: Homochirality Originates from the Handedness of Helices 20 November 2020
Homochirality is a common feature of amino acids and carbohydrates, and its origin is still unknown.  

https://pubs.acs.org/doi/10.1021/acs.jpclett.0c02144. So you are quoting the abstract. The purpose of an abstract is to inform its reader of the issue in question, in this case homochirality, things that have been done to approach the issue, and how this research team aims to solve the issue. Unless you are going to read sutherlands papers on how he solves homochirality and why these proposals are unfeasible(if you can by all means do), quoting the abstract doesn't help you here. 

Reply: I know the end notes. Did you read them. Did they solve the problem? If so, why have they not generated world news, solving a problem that persists since Louis Pasteur, and why is a Nobel prize in chemistry not on the table? 

3rd claim: "Your RNR argument also falls apart, because every process you can argue actually can be performed in a simpler system."
in order to "charge" RNR enzymes, you require an oxidation–reduction cycle involving ribonucleotide reductase, thioredoxin, thioredoxin reductase, and NADPH. Which of these players do you think was not necessary in your simpler system, and why? And here we see another instance of dragging the cart before the horse. Simply because those cofactors were necessary for the Modern function, why must that be how it was when the system was first developing. 

Reply: What warrants the belief that a stepwise pathway would have been possible even in principle? Did you have a look at the monstrosity of the complexity of that molecular machine?

What this effectively boils down to is, you need things that will donate and give back electrons from certain chemical species to make certain reactions easier. The obvious thing to note is, if there are simpler chemicals on prebiotic earth that perform this function, they will under the right types of conditions. Various molecular species can act as oxidizers and reductants. The modern cofactors are the product of modern cells being able to perform very complex biosynthesis pathways, and they are thus able to create molecules that do this better given the range of chemistry available to a cell given the chemistry of its proteins.

Reply: I see you are fond to blind speculation, and wishful thinking. That is, IMHO, not how science works, and how one can draw solid, warranted, plausible conclusions. I have all good reasons not to buy your story.

 How do you explain the selection of the correct metals as co-factors, and the selection of the correct binding site in the active site, by unguided means? The basic answer to this is, inorganic chemistry is thing. And thats hard to explain in simple terms. To try and make it easier, think about a lock and a key. All Atoms have an atomic radii(effectively how large the atom is), some metals are not suitable to fit in the active site of chemical species which are trying to react, others fall into a kind of goldilocks zone, where their size can be accommodated by the chemicals trying to react. 

Reply: Your scenario falls short based on the fact that there is no plausible route to have non-enzymatically synthesized functional proteins on the prebiotic earth. If you want to inform yourself, see here and here

In addition, sometimes the interactions between a metal and molecular species trying to reacts acts as a kind of anchor in the sense that, it stabilizes the molecules trying to react, making it easier for them to do so. Specific protein factors include a metal insertase or chaperone to deliver the metal, specific redox proteins such as flavodoxins or ferredoxins that control the oxidation state of the metal, and GTPases or ATPases involved in protein unfolding/refolding to allow metal entrance into deeply buried active sites. There are always molecular species that chelate a metal and can transport it by making sure it doesn't react until it goes where its needed. It may well be the case that in prebiotic settings, a metal is chelated by native molecular species in a protocell, and that specific interactions when other molecular species come into contact with it, allow that metal to become reactive, appropriate to how the reaction needs to proceed. 

Reply: First you need the complex machinery to chelate and import metals into the cell ( which wasn't even there yet, btw.). How do you get all these hypercomplex systems prebiotically?

Amazing molecular assembly lines and non-ribosomal amino-acid chain formation pathways come to light
Iron Uptake and Homeostasis in Cells


Fourth claim: "It was shown clearly that RNA replication can occur without enzymes"

That is another, factually false assertion. Many found the metaphor appealing: a world with a jack-of-all-trades RNA molecule, catalyzing the formation of indispensable cellular scaffolds, from which somehow then cells emerged. Others were quick to notice several difficulties with that scenario. These included the lack of templates enabling the polymerization of RNA in the prebiotic complex mixture  and RNA’s extreme lability at moderate to high temperatures and susceptibility to base-catalyzed hydrolysis https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7151616/?fbclid=IwAR0RQGnrvfMnW3qaQeRHIYtAdVwyS3KhBjoLlAjAOccF0H9-Phgv7acaME0. Curiously the paper you reference claims no such thing about that being false. What IS discussed however is if the scenarios concerning RNA replication occuring autocatalytically is feasible, and that the approach to answering this question must be by encouraging OOL researchers to interact more with each other and test their hypothesis.

Reply: Steve Benner:  Paradoxes in the origin of life. 2015 Jan 22 Benner SA1.
We are now 60 years into the modern era of prebiotic chemistry. That era has produced tens of thousands of papers attempting to define processes by which “molecules that look like biology” might arise from “molecules that do not look like biology” …. For the most part, these papers report “success” in the sense that those papers define the term…. And yet, the problem remains unsolved
http://sci-hub.ren/https://www.ncbi.nlm.nih.gov/pubmed/25608919

Is feasible does not mean, they solved it. They didn't. So positing that they think it is feasible, is confirming my point. There is no confirmed, demonstrated case. Just hope, and wishful thinking. 

Neeraja Sankaran: Revisiting the RNA World with its inventor September 6, 2017
Gilbert himself expressed some disappointment that “a self-replicating RNA has not yet been synthesized or discovered” in the years since he predicted his hypothesis, but he remains optimistic that it will emerge eventually.
[url=https://atlasofscience.org/revisiting-the-rna-world-with-its-inventor/#:~:text=The RNA World Hypothesis is,composed entirely of RNA molecules.]https://atlasofscience.org/revisiting-the-rna-world-with-its-inventor/#:~:text=The%20RNA%20World%20Hypothesis%20is,composed%20entirely%20of%20RNA%20molecules.[/url]

As explained many times now, there is no foresight, it is a stochastic process, things that work get selected for,


Reply: Work for what? Even if a miracle would generate tRNAs on a prebiotic earth, what would they be good for, without a functioning cell, where they are used in the translation process? You are like in Alice in wonderland with your fantasy. Nothing else. 

Reply: Contrary to what you may think, there are quite a number of papers that give synthetic pathways for the production of nitrogenous bases and nucleotides. 

Reply: Making the right nucleobases is requires a true professional. One that truly knows his business, and knows what it takes to have them in a functional isomeric form. Mindless chance does not fine-tune anything.

Barrow, FITNESS OF THE COSMOS FOR LIFE,  Biochemistry and Fine-Tuning, page 154
If (in the sense of a “counterfactual variation”) the difference between the average bond energy of a carbon-oxygen double bond and that of a carbon-carbon and carbon-nitrogen double bond were smaller by a few kcal per mol, then the nucleobases guanine, cytosine, and thymine would exist as “enols” and not as “ketones,” and Watson–Crick base-pairing would not exist – nor would the kind of life we know. It looks as though this is providing a glimpse of what might appear (to those inclined) as biochemical fine-tuning of life.

The cascade of coincidences embodied in nature’s canonical nucleobases will remain, from a chemical point of view, an extraordinary case of evolutionary contingency on the molecular level (even to those unconcerned about the question of a biocentric universe). The generational simplicity of these bases when compared with their relative constitutional complexity,  their capacity to communicate with one another in specific pairs through hydrogen bonding within oligonucleotides, and, finally, the role they were to take over at the dawn of life and to play at the heart of biology ever since is extraordinary. I have little doubt that Henderson – could he have known it – would have added these coincidences to his list of facts that were, to him, convincing evidence for the environment’s fitness to life.

Graham Cairns-Smith: Fine-tuning in living systems: early evolution and the unity of biochemistry   11 November 2003
We return to questions of fine-tuning, accuracy, and specificity. Any competent organic synthesis hinges on such things. In the laboratory, the right materials must be taken from the right bottles and mixed and treated in an appropriate sequence of operations. In the living cell, there must be teams of enzymes with specificity built into them. A protein enzyme is a particularly well-tuned device. It is made to fit beautifully the transition state of the reaction it has to catalyze. Something must have performed the fine-tuning necessary to allow such sophisticated molecules as nucleotides to be cleanly and consistently made in the first place.
https://www.cambridge.org/core/journals/international-journal-of-astrobiology/article/abs/finetuning-in-living-systems-early-evolution-and-the-unity-of-biochemistry/193313763244F9E6D085A3F062110389

Yitzhak Tor: On the Origin of the Canonical Nucleobases: An Assessment of Selection Pressures across Chemical and Early Biological Evolution 2013 Jun; 5
How did nature “decide” upon these specific heterocycles? Evidence suggests that many types of heterocycles could have been present on the early Earth. It is therefore likely that the contemporary composition of nucleobases is a result of multiple selection pressures that operated during early chemical and biological evolution. The persistence of the fittest heterocycles in the prebiotic environment towards, for example, hydrolytic and photochemical assaults, may have given some nucleobases a selective advantage for incorporation into the first informational polymers.

The prebiotic formation of polymeric nucleic acids employing the native bases remains, however, a challenging problem to reconcile. Two such selection pressures may have been related to genetic fidelity and duplex stability. Considering these possible selection criteria, the native bases along with other related heterocycles seem to exhibit a certain level of fitness. We end by discussing the strength of the N-glycosidic bond as a potential fitness parameter in the early DNA world, which may have played a part in the refinement of the alphabetic bases. Even minute structural changes can have substantial consequences, impacting the intermolecular, intramolecular and macromolecular “chemical physiology” of nucleic acids 4

My comment: For the well-intended above has clear teleological implications. Fine-tuning things in order to achieve specific functions that play critical roles in higher-order functions of a system has always been associated with conscious, goal-orientated action by intelligence. 

This has been done for a variety of scenarios such as Deep-Sea-Hydrothermal Vents, Volcanic Tidal Pools, etc... So yes there is precedent to say that RNA was present prebiotically. There are even studies which study the synthesis of that class and further classes of significant biomolecules in nebulae and meteorites, which are relevant for the reason of the late bombardment period in earths history, which more than likely acted as a significant carrier of biomolecules.  

Reply: Dr. Stanley L. Miller, University of California San Diego  14
What about submarine vents as a source of prebiotic compounds?
I have a very simple response to that . Submarine vents don't make organic compounds, they decompose them. Indeed, these vents are one of the limiting factors on what organic compounds you are going to have in the primitive oceans. At the present time, the entire ocean goes through those vents in 10 million years. So all of the organic compounds get zapped every ten million years. That places a constraint on how much organic material you can get. Furthermore, it gives you a time scale for the origin of life. If all the polymers and other goodies that you make get destroyed, it means life has to start early and rapidly. If you look at the process in detail, it seems that long periods of time are detrimental, rather than helpful.

Reply: Once more, the paper DOES NOT SAY THAT. The paper tries to ascertain the plausibility of different models and find means by which researchers can do better in approaching this question. As for the second part of your question, it turns out to be one of the main reasons why RNA-world scenarios are compelling. RNA itself is not extremely stable. This is useful though, because it means a system using RNA as its genetic information storage system, will need to replicate quickly. With that said, there are studies which have indicated self-replicating RNA that are facilitated by ribozymes that are in the hundreds of nucleotides range. That scenario is plausible under certain hydrothermal vent models where thermophoresis increases the yield of RNA substantially up to 800fold, but i t fails to account for the genetic code. As Dimiters model argues, there is a plausible mechanism for which small peptides and RNA can induce replication of each. The predominant reason why this is feasible is, it makes the RNA less susceptible to hydrolysis so it allows the RNA to stay around longer. Given the chemistry that already is understood between RNA and Amino Acids, this isn't that much of a leap in terms of proposals.  

Reply:  What does this hypothesis even explain that would be relevant to get closer to the origin of life? There are so many other problems, that remain unexplained, and even to join one amino acid to another is a huge challenge, as I report here:

Peptide Bond Formation of amino acids in prebiotic conditions: another unsurmountable problem of protein synthesis on early earth
https://reasonandscience.catsboard.com/t2130-peptide-bonding-of-amino-acids-to-form-proteins-and-its-origins#6664

Reply: I answered this last time. The moment you have that kind of system, you will have things floating around alongside it. When it is the case that small peptides stabilize and thereby increase the reaction rate by making it more easy to occur, you generate selection pressure for that kind of addition to the system, to be further proliferated. This occurs up and to the point where replication becomes reliable, and then you can start to talk about error correction mechanisms. 

Reply:  Error correction mechanisms are variegated ultrasophisticated molecular machines, and depend on a fully developed system. These proteins need to know what a correct state of affairs looks like, how to do the checking, and need to have the know-how to repair when things are not as should be. This is powerful evidence of design by a designer that has the aim from the beginning to convey robustness to the system.

DNA and RNA error checking and  repair, amazing evidence of design
https://reasonandscience.catsboard.com/t2043-dna-and-rna-error-checking-and-repair-amazing-evidence-of-design

1. Organisms are constantly exposed to different environments, and in order to survive, require to be able to adapt to external conditions. 
2. Life, in order to perpetuate, has to replicate. That includes DNA, which must be replicated with extreme accuracy. Somehow, the cell knows when DNA is accurately replicated, and when not. There are extremely complex quality control mechanisms in place, which constantly monitor the process. At least 3 error check and repair mechanisms keep error during replication down to 1 error in 10 billion nucleotides replicated. 
3. These repair mechanisms, sophisticated proteins, are also encoded in DNA. So proteins are required to error check and repair DNA but accurately replicated DNA is necessary to make the proteins that repair DNA. 
4. That is an all-or-nothing business. Therefore, these sophisticated systems had to emerge all at once, and require a designer.  

Error detection and repair during the biogenesis & maturation of the ribosome, tRNA's, Aminoacyl-tRNA synthetases, and translation: by chance, or design?
https://reasonandscience.catsboard.com/t2984-error-check-and-repair-during-messengerrna-translation-in-the-ribosome-by-chance-or-design

Reply: I can tell you for a fact that you are not reading the articles you are reading, in part because you do not understand them and some of the techniques occuring.

Reply: Whoever belittles his neighbor lacks sense, But a man of understanding remains silent.-Proverbs 11:12

Criticizing the opponent's knowledge, intelligence or education is not the best way to establish a point. I hear often critiques like You need a basic understanding of science, you don't understand evolution nor biology,  take a science class, where is your published work, we're trying to educate you, you are spouting ignorance of the subject,  you refuse to learn, Head well and truly in the sand, willful ignorance is your decision, you don't understand what you're copying and pasting, or go over to explicit insults of various forms and degrees. Mock and ridicule with contempt are not new to me. That are responses put forward frequently by Atheists in the attempt to hide their own ignorance, and avoid providing substance. Rather than address the specific issues in question, and provide compelling scenarios that would underline their own views, they resort to that implicit personal attacks and try to discredit the opponent. Not only does it hide their ignorance on the subject, but they expose also their ignorance of their opponent's knowledge and education, which cannot be known after a few sentences and posts made on a specific topic.   Fact is, even IF their opponent were ignorant on the issue, that would not make their views become more credible or correct. That's a logical fallacy. The best way for them to deal with the arguments brought forward by proponents of ID/creationism, is 1. educate themselves about the issue in question, and 2. if they disagree with the inference drawn, provide a better explanation based on their views.

Unless you are referencing an opinion or perspective piece or an article that is positing a new hypothesis, this statement is not correct. The hypothesis being put forth such as metabolism first and RNA first  are hypotheses which have data that lend credence to accepting that theory as more likely to be true or less likely. What is always true, is that when a hypothesis is put forth, testing will be done on it, and based on the results, we modify the  hypothesis and update it to make better predictions, in the hopes of honing in on the true answer the more this occurs. This is how science works. So again, actually read the papers which support the hypothesis, it is not blind speculation, these hypotheses are being put forth to try and resolve issues occuring in OOL studies as more experiments are being done.

Reply: Right. They adjust the hypotheses, but what, when there is a fundamental flaw, namely a decisive ingredient is a priory being excluded from the picture, namely intelligent implementation? Then, ALL hypotheses will lead to DEAD ends. And that is precisely what is observed. That's why abiogenesis research has not gone forward to solve the problems, but they are ever increasing, the more complexity that science unravels.

The RNA world hypothesis, in as much as the RNA-peptide world hypothesis, are both not "delivering the goods", as already shown here. With the metabolism first hypothesis, it is not different.  

How Cellular Enzymatic and Metabolic networks  point to design
https://reasonandscience.catsboard.com/t2371-how-cellular-enzymatic-and-metabolic-networks-point-to-design

The development of the metabolic system, which, as the primordial soup thinned, must have "learned" to mobilize chemical potential and to synthesize the cellular components, poses Herculean problems.
J.Monod Chance and Necessity: An Essay on the Natural Philosophy of Modern Biology 1972

1. Cells contain high information content that directs and controls integrated metabolic pathways which if altered are inevitably damaged or destroy their function. They also require regulation and are structured in a cascade manner, similar to electronic circuit boards.
2. There is always an observable consequence if a circuit is interrupted. Since these consequences are always catastrophically bad, flexibility is minimal, and since the circuits are all interconnected, the whole network partakes in the quality that there is only one way for things to work. ( Davidson)
3. Naturalistic mechanisms or undirected causes do not suffice to explain the origin and set up of information (instructional prescribing complex information), integrated complex circuits with little tolerance of change.
4. There is no way to write the code for all the enzymes unless one knows the 3D shapes of the substrates they act upon, and one can't know this unless one sees "the big picture" of the context within which and WHY they are needed for each life-essential product (or the final end products would not be produced), it becomes very clear that believing it could "evolve" without deliberate planning, foreknowledge, etc. stretches plausibility, reason, and logic, to say the least. Therefore, intelligent design constitutes the best explanation for the origin of these systems.

Reply: For two reasons, 1) because the more we examine cells, the more we recognize that level of sophistication modern cells use is not always necessary for a cell to perform some basic functions that a cell goes through, being able to do this helps you in understanding what is the bare minimum for the first forms of cellular life. However, we must assume in that process that a protocell will utilize chemistry to that of its descendants, and that is not always a reliable assumption given what was argued earlier. It is expected that earlier cells were a fair bit more lenient in terms of requirements with proteins the way modern cells are.

Reply: Life cannot start simple.

Fouad El Baidouri (2021) Along with two robust prokaryotic phylogenetic trees we are able to infer that the last universal common ancestor of all living organisms was likely to have been a complex cell with at least 22 reconstructed phenotypic traits probably as intricate as those of many modern bacteria and archaea. 

Protein Superfamily Evolution and the Last Universal Common Ancestor (LUCA) 31 May 2006
We know that the LUCA, or the primitive community that constituted this entity, was functionally and genetically complex. Life achieved its modern cellular status long before the separation of the three kingdoms. we can affirm that the LUCA held representatives in practically all the essential functional niches currently present in extant organisms, with a metabolic complexity similar to translation in terms of domain variety.   

LUCA—The Last Universal Common Ancestor 
https://reasonandscience.catsboard.com/t2176-lucathe-last-universal-common-ancestor

When certain basic bare-minimum requirements are not kept it can mean that the modern cell will die.

Reply:  Right. Functional parts are only meaningful within a whole, in other words, it is the whole that gives meaning to its parts. This recursive dependency really seals off the system from deterministic bottom-up causation. The top-down causation constitutes an irreducible structure.
https://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.94.171&rep=rep1&type=pdf

Irreducible Complexity: The existence of irreducible interdependent structures in biology is an undeniable fact
https://reasonandscience.catsboard.com/t1468-irreducible-complexity-the-existence-of-irreducible-interdependent-structures-in-biology-is-an-undeniable-fact#2133

The predominant claim of irreducible complexity is that some structure existent in the biological world must not be able to change at all and that its function must that of the function it possesses now. This is false because you can take away portions of a protein from a modern cell, and it tolerates it just fine, usually. The second reason it is false, is in a myriad of experiments, we can observe the function of a protein changing or diversifying to accommodate some new pressure acting on a cell. The third reason there are people investigating minimal cell requirements is because there are known flaws with the current model, and science is in the interest of updating and improving our understanding of these systems. 

Reply: A minimal amount of instructional complex information is required for a gene to produce useful proteins. A minimal size of a protein is necessary for it to be functional.   Thus, before a region of DNA contains the requisite information to make useful proteins, natural selection would not select for a positive trait and play no role in guiding its evolution. ( In OoL scenarios it's even worse, where there was no natural selection )

The simplest free-living bacteria is Pelagibacter ubique. It is known to be one of the smallest and simplest, self-replicating, and free-living cells.  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. They survive without any dependence on other life forms. Incidentally, these are also the most “successful” organisms on Earth. They make up about 25% of all microbial cells.   If a chain could link up, what is the probability that the code letters might by chance be in some order which would be a usable gene, usable somewhere—anywhere—in some potentially living thing? 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.


Reply: I'm not entirely sure where this angst is coming from. The majority of creationists accept the existence of natural selection. 

Reply: It has nothing to do with fear. It has to do with the fact that natural selection does not belong to the origin of life, as explained in today's previous email , and outlined here

And what exactly is natural selection? Natural selection just means that things which are best suited to some environment or niche, are going to be those best able to survive and replicate. 

Reply: Right. And you need to remove the idea that there was replication, and life, prior living cells were extant, and started self-replicating. Molecules do not attempt to survive.

The same is true of chemicals. Chemicals exist in environments, and there are conditions in which chemicals are formed or replicated. When you have systems that behave synergistically and this in turn allows both systems to proliferate and replicate more often than other things, this is one form of natural selection.

Reply: Steven A. Benner Paradoxes in the Origin of Life 5 Dec. 2014


The Asphalt Paradox 
An enormous amount of empirical data have established, as a rule, that organic systems, given energy and left to themselves, devolve to give uselessly complex mixtures, “asphalts”. The literature reports (to our knowledge) 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”. 
https://sci-hub.ren/10.1007/s11084-014-9379-0

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.

Paradoxes in the Origin of Life
https://reasonandscience.catsboard.com/t1279-abiogenesis-is-mathematically-impossible#7309

A designer may be present, but at its core, that hypothesis can not be tested or invalidated, so it holds no explanatory power or virtue when we are talking about scientific models for the origin of life. 

Reply: Chance of intelligence to set up life: 

100% We KNOW by repeated experience that the origin of blueprints containing instructional complex assembly information, dictating the fabrication of complex machines, robotic production lines, computers, transistors, turbines, energy plants,  and interlinked factories based on these instructions, which produce goods for specific purposes, are both always the result of intelligent setup. 

Reply: Are you telling me, that when there are incidental improvements to a system by means of stochastic processes, that these things are not actually improvements? because you can simulate and test experimentally what happens when you introduce random strains of peptides or prebiotically relevant molecules to systems. You can measure whether or not there has been an improvement in catalytic efficiency or its ability to stabilize some molecule. So these things are actually experimentally ascertainable, and worth consideration as ideas. Remind me again how I would know or could test if a god has been monkeying with physics? I'll wait for your reply. 

Reply: Understanding that God must have had his hands in play is not difficult to understand, if you remove your naturalistic blinkers, bias, sit down for a minute, and think carefully. You are a smart person. Following is not hard to grasp: 

Cells have a codified description of themselves in digital form stored in genes and have the machinery to transform that blueprint through information transfer from genotype to phenotype, into an identical representation in analog 3D form, the physical 'reality' of that description. The cause leading to a machine’s and factory's functionality has only been found in the mind of the engineer and nowhere else.

Reply: if you read the endnotes on the paper, you would understand that this critique doesn't make sense. The goal of the paper was to find approaches that further induce the cooperation of groups involved in OOL research. Second, you are not reciting the correct law here that you are trying to disprove. The goal of Pasteur's work was to disprove the notion of vitalism and spontaneous generation which stated that decaying flesh gave rise to things like mosquitoes and flies and rodents such as mice and rats.

Reply:  Apparently you don't know that it was Pasteur that discovered that molecules are chiral. You can read about the history here:

Pasteur’s Crystals and the Beauty of Simplicity
https://reasonandscience.catsboard.com/t2668-pasteurs-crystals-and-the-beauty-of-simplicity

Reply: Please show me where I mentioned the word protein once in the context of abiogenesis in my previous reply, I did not. By and large, what you need for chemical reactivity, is an arrangement of certain compounds in space. This can occur when peptides(small strings of amino acids that are joined) interact with one another. Proteins are folded by many-many-peptides folding together, so in-fact, it entirely merited to say that having small peptides interact in the right way with some molecule to promote some reaction is appropriate for prebiotic purposes, because as cells generate more energy and can replicate reliably, the length of peptides and soon-to-be-proteins can be increased. 

Reply:  If you are at a stage of a RNA-peptides, you are still far far away from a system that is capable of generating energy with ATP as its currency. That is, btw. another huge problem for abiogenesis, which you are certainly aware of. I write about it here

The challenge to start harvesting energy
https://reasonandscience.catsboard.com/t1394-the-hydrothermal-vent-hypothesis-and-why-it-fails#9499

Reply: This is why I said inorganic chemistry(the chemistry of anything not carbon) is needed, this statement is wrong. Various classes of molecules will chelate different metals, and some of those arrangements are likely to be permeable to the membrane of a protocell,

Reply: Good luck getting prebiotic cell membranes. I outline the problems here

Reply: Work in terms of performing whatever function those molecules happen to be doing. I think explained to you already that tRNA and aminoacyl tRNA's are candidates as linker molecules for stabilizing RNA Replication, this notion has been put forth and is being tested by Szostak et al. tRNA's may act also to stabilize some molecular species in a protocell. 

Reply:  There is no way to get functional tRNAs prebiotically. RNA disintegrates very fast. Ribose in 40 days.

Good interacting with you Otangello, but let's ease off on the insults and keep this cordial. 

Reply:  Agreed. Let's keep it cordial. Also, don't tell me what I understand, or don't understand. That's a kind of presumptuous criticism that atheists frequently do. You can do better than that.

Biochemical fine-tuning - essential for life
https://reasonandscience.catsboard.com/t2591-biochemical-fine-tuning-essential-for-life

The hydrothermal-vent hypothesis , and why it fails
https://reasonandscience.catsboard.com/t1394-the-hydrothermal-vent-hypothesis-and-why-it-fails

Taylor:  Selection exists prebiotically, this isn't arguable.

Reply:  NS is not only arguable but actually argued against by many different sources.

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

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

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

Taylor: Before I go on, this is the most important part of this message:  I could quibble with every detail, but the point here is that you always conclude abiogenesis is impossible, using the god of the gaps FALLACY, and that's your main hurdle.

Reply: 1. if there is no money in the wallet
2. It's an argument of knowledge to say: There is no money in the wallet after you check.
3. The same happens in biochemistry. Science is doing abiogenesis research, checked, investigated, made falsifiable predictions, attempting to solve the mystery of life, and investigating if life could have emerged naturally. But rather than solving the problem, the riddle is unraveling how unlikely the emergence of life is by unguided events and merely chemical reactions. DNA stores specified complex information, which is analogous to blueprints or a library full of books with instructions to make things, instructing the precise sequence of amino acids to make proteins, and how to operate a cell. Such information has never been observed to emerge by nonintelligent nonguided events, and therefore, we have evidence that something is extremely unlikely (e.g., that stochastic random events could inform the correct instructions to make proteins). Indeed, scientists will often debate whether an experiment's result should be considered evidence of absence. Something has proven not to be the result of X ( as chance, for example )
4. Intelligence can have the foresight and know-how to make things with a purpose, act towards achieving specific distant goals, and knows how to create codified language, and use that language to create blueprints, used to make complex machines, production lines, and interconnected factories. It can finely tune and arrange things to work in a precise fashion. it can shape and form parts that perform tasks by interacting like lock and key. None of all this has been observed to be achieved by any alternative non-intelligent mechanism. if anyone wants to propose an alternative to replace intelligence, it should meet the burden of proof, and falsify the claim of intelligent design based on empirical testing and falsification.
5. Hence, the argument of Intelligent Design as the best explanation of origins is based on experiments and observation, gained knowledge and experience. Not from ignorance.

Either an intelligent designer was involved in creating life, or not. Intelligent design wins in my view based on using eliminative induction and abductive reasoning to infer the best explanation. Abiogenesis research has failed to explain even in principle how life could have started on early earth without a powerful intelligent designer. For over 70 years, all hypotheses have failed. Following a few reasons:

General hurdles of the Origin of Life by unguided means
1. Natural selection: There was no selection on early earth. In the living world, complex molecular machines are pre-programmed to make the specified complex macromolecules, the building blocks of life, precisely as needed.
2. Time: Some chemical reactions are so unspecific that getting the right one by unguided means resorting to time leads to huge numbers of odds.
3. Getting pure materials: Evidently, what chemists do in the lab, namely using pure reagents, was not what happened on the early earth. Impure contamination in the pool of chemicals was the state of affairs.
4. Getting free Gibbs energy:  Spontaneous prebiotic reactions would have to "invent" ways to recruit Gibbs free energy from its environment so as to reduce its own entropy.
5. Activation and repetitive processes: Monomers need to be activated in order for polymerization and catenation to make amino acid strands, and genes, to be possible.
6. Information: Specified complex information, digital data, stored in genes through the language of the genetic code, dictates and directs the making of irreducibly complex molecular machines. Prescriptive information is statistically unlikely to be generated randomly. 
7. Polymerization: How did prebiotic polycondensation of amino acids and nucleotides in heterogeneous aqueous solutions or in interfaces with water-based media occur without the aid of biological catalysts? 
8. Eigens paradox:  is one of the most intractable puzzles in the study of the origins of life. It is thought that the error threshold concept limits the size of self-replicating molecules to perhaps a few hundred digits, yet almost all life on earth requires much longer molecules to encode their genetic information.
9. Muller's rachet: [url=https://bmcecolevol.biomedcentral.com/articles/10.1186/1471-2148-8-62#:~:text=The theory of Muller' Ratchet,that accompanies small population size.]The theory of Muller's Ratchet[/url] predicts that small asexual populations are doomed to accumulate ever-increasing deleterious mutation loads as a consequence of the magnified power of genetic drift and mutation that accompanies small population size.
10. Protected environments: If these chemical reactions had happened in places being exposed to UV radiation, no deal. If it was too cold, or too hot, too acidic, or too alkaline, in the wrong atmospheric conditions, no deal.
11. The right sequence of reactions: In metabolic pathways in the cell, enzymes must be lined up in the right sequence. Spontaneous events usually give chaotic results, not order and organization achieving specific functions. 
12. Getting an organized system out of chaos: Emergent processes such as growth, self-propagation, information processing, and adaptive evolution have never been observed to emerge randomly. 
13. Irreducible complexity: The cell is an irreducible, minimal entity of life. The individual parts by themselves bear no function unless integrated into a higher-order system. Random events have never shown to create irreducibly complex structures. 
14. Homeostasis:   The control of metabolism is a fundamental requirement for all life, with perturbations of metabolic homeostasis underpinning numerous disease-associated pathologies. Such an environment has never shown to emerge by chance. 

More here

The hallmark of intelligence is the ability to create order, function, laws, purpose, instructions, and fine-tuned devices to achieve a state of affairs that has a specific function/purpose. In the following link, I give 14 examples that characterize the hallmark of intelligent action, and how we recognize all 14 in the physical world

How to recognize the signature of (past) intelligent action
https://reasonandscience.catsboard.com/t2805-how-to-recognize-the-signature-of-past-intelligent-action

Taylor:You need to give that up.  It's fine to be skeptical of individual mechanisms of abiogenesis.  That's what origin of life scientists do all day long!  They criticize each others' ideas.  But never is it scientific to conclude that because one idea failed, that the science is stuck, will never advance, and only a god can solve the current unknowns.  

Reply: God is the best explanation based on what we DO know, not based on lack of knowledge.

Taylor: You said "molecules do no(t) survive."  This is false.  Some molecules are short-lived, others are stable and long-lasting.  Some, like catalysts, can interact with, and cause chemical reactions, without themselves changing their chemical composition.  So, a molecule being destroyed by its environment does not survive.  Survival just means existing.  It's also about production.  If a particular chemical system keeps producing nucleotides for example, and some combinations end up existing for longer than others, this is absolutely a selection force at work.

Reply:  Synonym for selecting is: choosing, picking, handpicking, sorting out, discriminating, choosing something from among others, and giving preference to something over another.

We know that we, as intelligent beings, do make choices to get the desired outcome all the time - and there is no alternative to conscious intelligent action. Therefore, it is logical and plausible, and probable, that an intelligent creator was in action, choosing the parameters of the laws of physics, the right equations, the right adjustments in the universe, the right building blocks of life, the right machinery to have given life a first go.  And he was remarkably good at that.

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.

Taylor: You then quotemine someone about a cell needing all its parts all at once.  This is a non-sequitur.  A cell does, yes.  But a protocell does not.  Parts of cells do not. 
Reply: Please give me a precise characterization of what a "protocell" is.

Taylor: The idea is that different parts of cells have their own fitness, and can be produced independently, and can combine.
Reply: 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. 

There was no prebiotic selection to get life originating
https://reasonandscience.catsboard.com/t3121-there-was-no-prebiotic-selection-to-get-life-originating

Taylor: Now, there is some success with some of these parts, but not all.  From this, you somehow conclude that it is impossible?  This is the god of the gaps FALLACY, which is why we HAVE TO reject your conclusion.  
Reply:  Well, it's actually YOU committing a fallacy. It's called naturalism of the gaps. Science has not been able to demonstrate how life could come from nonlife. But it is working on it, and one day, it will find out, and it will be a natural explanation. 

Taylor: You're also wrong on homochirality, there are multiple means of purifying chiral handedness and you know this.  I'm not sure why you're trying to argue this point.  There are natural samples that have a chiral bias, or near purity.  The mechanisms exist, many have been observed, some have not.  This isn't arguable.  If you even have a bias, this will help increase the selection for certain polymers, you do not need 100% purity.  Labs only do this to be as efficient as possible.  The earth doesn't need to be efficient, it has all the time in the world.  It doesn't matter if things are unknown about these processes.  You cannot conclude that it is unknowable or impossible, that is a FALLACY.  

Reply: No, I don't know this. But you can provide a scientific paper that backs up your claim. I am unaware of it. And we are not talking only about the homochirality of amino acids, but as well of nucleotides ( right-handed ribose), and the glycerol head in phospholipids.

Tan, Change; Stadler, Rob. The Stairway To Life:
In all living systems, homochirality is produced and maintained by enzymes, which are themselves composed of homochiral amino acids that were specified through homochiral DNA and produced via homochiral messenger RNA, homochiral ribosomal RNA, and homochiral transfer RNA. No one has ever found a plausible abiotic explanation for how life could have become exclusively homochiral.

Homochirality, an unresolved issue
https://reasonandscience.catsboard.com/t1309-homochirality

Taylor: You then quote Venter about how complex ribosomes are.  Okay?  And?  It's not the only molecule that has its function.  That's the problem you have, you always ignore the inefficient molecules that have similar or multiple functions to highly derived biological systems.  
Question: Let's suppose you see a machine made for specific functions. And you see nearby another machine, that is set up constantly to monitor the function of the first machine, and knows when it performs properly, and when an error occurs. And then, when something goes havoc, that machine knows immediately what error occurred, and has the know-how to fix it. Is it more rational to infer that intelligence was required to set up both machines, or rather that both are the product of random unguided events?

Translation through the ribosome is an irreducible, integrated complex process
1. The ribosome is the 3D printer of proteins. A human-made 3D printer is made of several functional parts, like the nozzle, the extruder, cooling fan, heated be, the painter's tape, etc. The 3D extruder has no use on its own. But only, when working inside the 3D printer in the right place. A bacterial cell depends upon a translation and coding system consisting of 106 distinct but functionally integrated proteins as well several distinct types of RNA molecules (tRNAs, mRNAs, and rRNAs). This system includes the ribosome (consisting of fifty distinct protein parts), the twenty distinct tRNA synthetases, twenty distinct tRNA molecules with their specific anticodons, about 200 ribosome assembly proteins and 75 co-factors, chaperones, free-floating amino acids, ATP molecules (for energy), and—last, but not least—information-rich mRNA transcripts for directing protein synthesis. Many of the proteins in the translation system perform multiple functions and catalyze coordinated multistep chemical transformations.
2. In the same sense, as an engineer would not project, invent, create and make a blueprint of a 3D printer extruder with no use by its own, but only conjoined, and together with all other parts while projecting a whole printer, envisioning its end function and use, its evident that unguided random natural events without foresight would not come up with an assemblage of tiny molecular machines, enzymatic structures with unique contours, which bear no function by their own, but only when inserted as part of the ribosome with higher ends, being essential for cells to translate DNA information into proteins, and being a key part participating to perpetuate life. Natural selection would not select for components of a complex system that would be useful only in the completion of that much larger system. In other words: Why would natural selection select an intermediate biosynthesis product, which has by its own no use for the organism, unless that product keeps going through all necessary steps, up to the point to be ready to be assembled in a larger system?  Never do we see blind, unguided processes leading to complex functional systems with integrated parts contributing to the overarching design goal. A minimal amount of instructional complex information is required for a gene to produce useful proteins. A minimal size of a protein is necessary for it to be functional.   Thus, before a region of DNA contains the requisite information to make useful proteins, natural selection would not select for a positive trait and play no role in guiding its evolution.
3. Naturalistic mechanisms or undirected causes do not suffice to explain the origin of information (instructed complex information), irreducible complexity, and the setup of complex machines with little tolerance of change.   Therefore, intelligent design constitutes the best explanations for the origin of the information guiding the making of the irreducible and integrated complex ribosome protein factory.


Syllogisms about the Ribosome
https://reasonandscience.catsboard.com/t1661p25-translation-through-ribosomes-amazing-nano-machines#8800

Taylor: This brings us back to survivability.  There are simple molecules that can self replicate, derived experimentally via random evolution.  
Reply: Please provide an example, and a scientific paper backing up your claim.

Taylor:  So, we know function can emerge from random combinations.  Anything that increases the number or the length of a molecule's existence acts as a selector.  End of story.
Again, not here to quibble with every detail, this is to point out that you rely on fallacies to critique abiogenesis.

Reply: What would you expect to see, in order to say: Now the story seems to shift to God being the best explanation ?

Dessel: I've been witness to too many examples of Otangelo deliberately mishandling papers and repeating points in the form of his own Donny Deals fallacy (Claim Y!  No, actually, it's X.  Claim Y anyway!) that I can't take him seriously, so this is going to be my only comment in this debate.

Reply: According to your claim, there are too many? So it shouldn't be difficult to give an example?

Dessel:  Otangelo quotes Stanley Miller about submarine vents destroying organic molecules.  What he doesn't tell you is that this interview took place in 1996 and is discussing the *black smoker* vents, not the alkaline vents proposed today as a model for the emergence of life.  The alkaline vents hadn't even been discovered yet.  Michael Russell predicted the existence of a much lower temperature vent that would operate as a proper "incubator" and "hatchery" for life and this was confirmed in December of 2000 with the discovery of Lost City.  Not only has it been confirmed that these vents abiotically produce organic molecules to this very day (see Menez [2018] on the Abiotic production of tryptophan via Friedel Crafts reactions within the serpentinized cracks underneath and around these vents)

Reply: Please give a plausible model/hypothesis of the transition from tryptophan made by your hatchery, to the metabolic pathway and its regulation that makes tryptophan, which is the most complex compared to all others, synthesizing the amino acids alphabet used in life. Here the entire pathway and the enzymes involved: 

Tryptophan biosynthesis:
https://reasonandscience.catsboard.com/t1740-amino-acids-origin-of-the-canonical-twenty-amino-acids-required-for-life#5731

Tan, Change; Stadler, Rob. The Stairway To Life:
E. coli can manufacture the amino acid tryptophan by producing the enzyme tryptophan synthase. Production of this enzyme requires precious resources that the cell would prefer to conserve. As a result, the cell carefully regulates production—a far better approach than continuous full-speed production of the enzyme. In the cell, freely available tryptophan produces negative feedback for production of tryptophan synthase, thus conserving resources. To accomplish this, E. coli have another gene that codes for a regulatory protein called “TrpR,” or “tryptophan repressor”. When the TrpR protein senses the presence of available tryptophan, the protein becomes activated (i.e., changes shape) and binds to the DNA immediately preceding the genes for tryptophan synthase. The attachment of activated TrpR to this regulatory segment of DNA inhibits tryptophan synthase production, thus stopping the production of tryptophan. The simple summary is that freely available tryptophan inhibits the production of tryptophan via specific information stored in DNA. As a result of this ingenious regulatory system with its multiple coordinated components, the level of tryptophan is maintained at the correct level for cellular function.

Furthermore:

 Unsolved issues:
Unsolved issues about the origin of amino acids on early earth:
How did unguided nondesigned coincidence select the right amino acids amongst over 300 ( known, but the number is theoretically limitless ) that occur naturally on earth? All life on Earth uses the same 20 ( in some cases, 22 genetically encoded) amino acids to construct its proteins even though this represents a small subset of the amino acids available in nature?
How would twenty amino acids be selected (+2)  and not more or less to make proteins?
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 unfunctional monomers (with only one functional group) sorted out?
How were β, γ, δ… amino acids sorted out?
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 did ammonia (NH3), the precursor for amino acid synthesis, accumulate 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 a prebiotic synthesis of biological amino acids avoid the concomitant synthesis of undesired or irrelevant by-products?
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 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 select the set of amino acids which appears to be near-optimal in regard to size, charge, and hydrophobicity more broadly and more evenly than in 16 million alternative sets?
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 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 the synthesis through metabolic pathways of amino acids occur? A minimum of 112 enzymes is required to synthesize the 20 (+2) amino acids used in proteins.

In order to have a functional protein, you need to have amino acids.
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.
Amino acids used for life have amino groups and carboxyl groups. To form a chain, it is necessary to have the reaction of bifunctional monomers, that is, molecules with two functional groups so they combine with two others. If a unifunctional monomer (with only one functional group) reacts with the end of the chain, the chain can grow no further at this end. If only a small fraction of unifunctional molecules were present, long polymers could not form. But all ‘prebiotic simulation’ experiments produce at least three times more unifunctional molecules than bifunctional molecules.
The useful amino acids would have to be joined and brought together at the same assembly site in enough quantity.
There are four different ways to bond them together by the side chains. if bonded to the wrong side chain, no deal.
The formation of amide bonds without the assistance of enzymes poses a major challenge for theories of the origin of life.
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 )
Before amino acids would join into a sequence providing functional folding, it would disintegrate if hit by UV radiation.
But even IF that would not be the case, most proteins become only functional, if they are joined into holo-enzymes, where various amino acid chains come together like lock and key.
If that would occur, the tertiary or quaternary structure in most cases would bear no function without the insertion of a co-factor inside the pocket, like retinal in the opsin pocket, forming rhodopsin.
But even IF there would emerge a functional protein on the early earth, by itself, it would be like a piston outside the engine block of an automobile. Many proteins bear only function once they are integrated in an assembly line, producing sophisticated molecular products used in life.
But even IF we had an assembly line of enzymes producing a functional product, what good would there be for that product, if the cell would not know where that product is required in the Cell?
For example, chlorophyll requires the complex biosynthesis process of 17 enzymes, lined up in the right order, each producing the substrate used by the next enzyme.  But chlorophyll has no function unless inserted in the light-harvesting antenna complex used in photosynthesis to capture light and funnel it to the reaction center.  
But even if that complex, chlorophyll and the LHC would be fully set up, they have no function without all over 30 protein complexes forming photosynthesis, used to make hydrocarbons, essential for all advanced life forms.  
Now, let's suppose all this would assemble by a freaky random accident on early earth, there would still be no mechanisms of transition from a prebiotic assembly, to Cell factory synthesis.

Tan; Stadler:  The Stairway To Life:
Countless biology textbooks describe the Miller-Urey experiment and others like it as strong evidence that life began spontaneously. This argument seemingly equates the simplicity of a handful of amino acids (formed by a natural process) with the unimaginable complexity of living organisms. This is like finding sand and concluding that microprocessors (computer chips based upon silicon) must be able to assemble spontaneously. Indeed, the chasm between simple organic molecules and living organisms is frequently dismissed in a single sentence. Take, for example, this quote from a popular biology textbook: “The first spark of life ignited when simple chemical reactions began to convert small molecules into larger, more complex molecules with novel 3-D structures and activities”. In his 2014 book, Undeniable, Bill Nye similarly applies “the spark of life” to dismiss complexity: “The origin of life just requires some raw material that could allow the spark of life to emerge”. Walt Disney made a movie about a wooden puppet that turned into a boy through a spark of life. Perhaps such fantasy inspired our current biology textbooks and Bill Nye because these statements are certainly not based on scientific evidence or rational thought. In The Vital Question, a 2015 book that Bill Gates praised as “an amazing inquiry into the origins of life,” biochemist Nick Lane expects his readers to join him in dismissing the great complexity separating simple building blocks and living cells: The formation of organic matter from H2 and CO2 is thermodynamically favoured under alkaline hydrothermal conditions, so long as oxygen is excluded…This means that organic matter should form spontaneously from H2 and CO2 under these conditions. The formation of cells releases energy and increases overall entropy! The average reader of The Vital Question may not have noticed the colossal leap that occurred in the last sentence, where Lane equates spontaneous formation of organic building blocks with the spontaneous formation of cells. This could indeed be possible if cells were “nothing more than a shapeless, mobile, little lump of mucus or slime, consisting of an albuminous combination of carbon,” as thought by Haeckel in the late nineteenth century, but each new year of research exposes previously unimagined layers of cellular complexity, even among the simplest known forms of life. Bestselling author Dan Brown, in his 2017 book Origin, includes a respected scholarly character Robert Langdon who concludes, “Life arose spontaneously from the laws of physics”. Addy Pross, a professor of chemistry at Ben Gurion University, concludes the following in his 2012 book, What is Life?: “Life then is just the chemical consequences that derive from the power of exponential growth operating on certain replicating systems”. Jeremy England, a professor of physics at MIT who also happens to appear in Dan Brown’s Origin, similarly sweeps all the complexity of life under the rug with one sentence: “You start with a random clump of atoms, and if you shine light on it for long enough, it should not be so surprising that you get a plant” . Carl Sagan offered similar words, which are strikingly discordant with all observable evidence: “The origin of life must be a highly probable affair; as soon as conditions permit, up it pops!” . Daily news articles on astronomy and astrobiology barrage us with suggestions that life probably exists on other planets. These articles lead us to believe that the simple discovery of water on a planet virtually guarantees the spontaneous formation of life. A reality check is long overdue. The fantastic complexity of all known life-forms stands in stark contrast to what our schools are teaching, what some scientists believe, and what popular media suggests.

Chemical evolution of amino acids and proteins ? Impossible !!
https://reasonandscience.catsboard.com/t2887-chemical-evolution-of-amino-acids-and-proteins-impossible

Dessel: but the experimental work confirms the production of each of the four classes of organic molecules (amino acids, lipids, carbohydrates, and nucleotides)
Reply: Let us suppose for a moment that your claim is true, how do you transition from the production of these building blocks through your black smokers, to the minimal metabolic network englobing over 400 reactions to make these building blocks ?

William Martin and colleagues from University Düsseldorf’s Institute of Molecular Evolution give us also an interesting number: The metabolism of cells contains evidence reflecting the process by which they arose. Here, we have identified the ancient core of autotrophic metabolism encompassing 404 reactions that comprise the reaction network from H2, CO2, and ammonia (NH3) to amino acids, nucleic acid monomers, and the 19 cofactors required for their synthesis. Water is the most common reactant in the autotrophic core, indicating that the core arose in an aqueous environment. Seventy-seven core reactions involve the hydrolysis of high-energy phosphate bonds, furthermore suggesting the presence of a non-enzymatic and highly exergonic chemical reaction capable of continuously synthesizing activated phosphate bonds. CO2 is the most common carbon-containing compound in the core. An abundance of NADH and NADPH-dependent redox reactions in the autotrophic core, the central role of CO2, and the circumstance that the core’s main products are far more reduced than CO2 indicate that the core arose in a highly reducing environment. The chemical reactions of the autotrophic core suggest that it arose from H2, inorganic carbon, and NH3 in an aqueous environment marked by highly reducing and continuously far from equilibrium conditions. 54 55

Supplementary Table 1. in the paper lists all 402 metabolic reactions: 
Biosynthetic core comprising 402 metabolic reactions 

Prevital unguided origin of the four basic building blocks of life: Impossible !!
https://reasonandscience.catsboard.com/t2894-prevital-unguided-origin-of-the-four-basic-building-blocks-of-life-impossible

Dessel:  with the means present to concentrate them heavily 
Reply: Polymer formation in aqueous environments would most likely have been necessary on early Earth because the liquid ocean would have been the reservoir of amino acid precursors needed for protein synthesis. 1

A thermodynamic analysis of a mixture of protein and amino acids in an ocean containing a 1 molar solution of each amino acid (100,000,000 times higher concentration than we inferred to be present in the pre-biological ocean) indicates the concentration of a protein containing just 100 peptide bonds (101 amino acids) at equilibrium would be 10-338 molar. Just to make this number meaningful, our universe may have a volume somewhere in the neighbourhood of 10^85 litres. At 10-338 molar, we would need an ocean with a volume equal to 10229 universes (100, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000) just to find a single molecule of any protein with 100 peptide bonds. So we must look elsewhere for a mechanism to produce polymers. It will not happen in the ocean.

Sidney Fox, an amino acid chemist, and one of my professors in graduate school recognized the problem and set about constructing an alternative. Since water is unfavourable to peptide bond formation, the absence of water must favour the reaction. Fox attempted to melt pure crystalline amino acids in order to promote peptide bond formation by driving off water from the mix. He discovered to his dismay that most amino acids broke down to a tarry degradation product long before they melted. After many tries, he discovered two of the 20 amino acids, aspartic and glutamic acid, would melt to a liquid at about 200oC. He further discovered that if he were to dissolve the other amino acids in the molten aspartic and glutamic acids, he could produce a melt containing up to 50% of the remaining 18 amino acids. It was no surprise then that the amber liquid, after cooking for a few hours, contained polymers of amino acids with some of the properties of proteins. He subsequently named the product proteinoids. The polymerized material can be poured into an aqueous solution, resulting in the formation of spherules of protein-like material which Fox has likened to cells. Fox has claimed nearly every conceivable property for his product, including that he had bridged the macromolecule to cell transition. He even went so far as to demonstrate a piece of lava rock could substitute for the test tube in proteinoid synthesis and claimed the process took place on the primitive earth on the flanks of volcanoes. However, his critics, as well as his own students, have stripped his credibility. Note the following problems:

1) Proteinoids are not proteins; they contain many non-peptide bonds and unnatural cross-linkages.
2) The peptide bonds they do contain are beta bonds, whereas all biological peptide bonds are alpha.
3) His starting materials are purified amino acids bearing no resemblance to the materials available in the "dilute soup." If one were to try the experiment with condensed "pre-biological soup," tar would be the only product.
4) The ratio of 50% Glu and Asp necessary for success in these experiments bears no resemblance to the vastly higher ratio of Gly and Ala found in nearly all primitive earth synthesis experiments.
5) There is no evidence of information contained in the molecules.


Dessel:  to facilitate and promote exponentially higher rates of polymerization,

Reply: 1. The synthesis of proteins and nucleic acids from small molecule precursors represents one of the most difficult challenges to the model of pre-biological ( chemical) evolution.
2. The formation of amide bonds without the assistance of enzymes poses a major challenge for theories of the orgin of life. 2
3. The best one can hope for from such a scenario is a racemic polymer of proteinous and non-proteinous amino acids with no relevance to living systems.
4. Polymerization is a reaction in which water is a product. Thus it will only be favoured in the absence of water. The presence of precursors in an ocean of water favours depolymerization of any molecules that might be formed.
5. Even if there were billions of simultaneous trials as the billions of building block molecules interacted in the oceans, or on the thousands of kilometers of shorelines that could provide catalytic surfaces or templates, even if, as is claimed, there was no oxygen in the prebiotic earth, then there would be no protection from UV light, which would destroy and disintegrate prebiotic organic compounds. Secondly, even if there would be a sequence, producing a functional folding protein, by itself, if not inserted in a functional way in the cell, it would absolutely no function. It would just lay around, and then soon disintegrate. Furthermore, in modern cells proteins are tagged and transported on molecular highways to their precise destination, where they are utilized. Obviously, all this was not extant on the early earth.
6. To form a chain, it is necessary to react bifunctional monomers, that is, molecules with two functional groups so they combine with two others. If a unifunctional monomer (with only one functional group) reacts with the end of the chain, the chain can grow no further at this end. If only a small fraction of unifunctional molecules were present, long polymers could not form. But all ‘prebiotic simulation’ experiments produce at least three times more unifunctional molecules than bifunctional molecules.

Peptide Bond Formation of amino acids in prebiotic conditions: another insurmountable problem of protein synthesis on early earth 
https://reasonandscience.catsboard.com/t2130-peptide-bonding-of-amino-acids-to-form-proteins-and-its-origins#6664

Dessel: to render a heavy chiral bias, with lower water activity and lower temperatures within the institial layers of clays or nanopores that stabilize organic molecules and allow for condensation reactions for greater complexity to occur.  The progress made by these researchers is substantive and they even hold themselves to much higher standards than most other people would (e.g. researcher Nick Lane has celebrated Saladino's experimental work demonstrating nucleobase and nucleotide formation, but still chooses to pursue an alternative pathway closer to what's used by acetogens and methanogens, bacteria and archaea that serve as inspiration for this model).

You have an option about what to believe: Otangelo doesn't know the difference between volcanic black smokers and alkaline vents, or he does and he chooses to lie to you.
Reply:  I know the difference, and following are my conclusions in regards of this proposal:

Inorganic compartments versus membrane-bounded cells as the means for confining the LUCA 
Eugene V. Koonin (2005): It has been repeatedly argued that the complex molecular composition inferred for LUCA could not have been attained without prior evolution of biogenic-membrane-bounded cells, mainly because (i) compartmentalization is a prerequisite for the evolution of any complex system; and (ii) certain key membrane-associated enzymes, such as the signal recognition particle (SRP) and the proton ATPase, are conserved in eubacteria and archaebacteria. The model of a compartmentalized, but inorganically confined LUCA obviates the first problem. However, the second problem – the conservation of certain membrane-associated functions in all modern forms of life – is more challenging. The ubiquity of the SRP (with its notable RNA component) and the proton ATPase across genomes, together with the clear split between archaebacterial–eukaryotic and eubacterial versions, suggests that these complexes were present in LUCA. Because the SRP inserts proteins into hydrophobic layers and ATPase requires a hydrophobic layer to function, this would seem to imply the existence of membranes in LUCA, apparently in contradiction to arguments concerning the late and independent emergence of lipid biosynthetic pathways. The essential distinction to be made is between a ‘hydrophobic layer’ and a ‘biogenic membrane’. The latter requires elaborate suites of lineage-specific enzymes (given the unrelated isoprene ether versus fatty acid ester chemistries of the membrane lipids in archaebacteria and eubacteria, respectively). 9

J. Baz Jackson (2016):  The hypothesis that a natural pH gradient across inorganic membranes lying between the ocean and fluid issuing from hydrothermal alkali vents provided energy to drive chemical reactions during the origin of life has an attractive parallel with chemiosmotic ATP synthesis in present-day organisms. However, such natural pH gradients are unlikely to have played a part in life’s origin. There is as yet no evidence for thin inorganic membranes holding sharp pH gradients in modern hydrothermal alkali vents at Lost City near the Mid-Atlantic Ridge. Proposed models of non-protein forms of the H+-pyrophosphate synthase that could have functioned as a molecular machine utilizing the energy of a natural pH gradient are unsatisfactory. Some hypothetical designs of non-protein motors utilizing a natural pH gradient to drive redox reactions are plausible but complex, and such motors are deemed unlikely to have assembled by chance in prebiotic times. Small molecular motors comprising a few hundred atoms would have been unable to function in the relatively thick (>1 μm) inorganic membranes that have hitherto been used as descriptive models for the natural pH gradient hypothesis. 11

Tan, Change; Stadler, Rob: The Stairway To Life (2020): The cell uses the proton gradient to charge “batteries” such as adenosine triphosphate (ATP), hence the “coupling” part of chemiosmotic coupling. ATP is a nearly universal battery in life. Once charged, it can be “plugged into” a wide variety of molecular machines to perform a wide variety of functions: activating amino acids for protein synthesis, copying DNA, untangling DNA, breaking bonds, transporting molecules, or contracting muscles. Like rechargeable batteries, ATP cycles frequently between powering gadgets and recharging. Although a human body contains only about sixty grams of ATP at any given moment, it is estimated that humans regenerate approximately their own weight in molecules of ATP every day. Because chemiosmotic coupling is essential for life and is highly conserved across all of life, abiogenesis must include a purely natural means to arrive at chemiosmotic coupling. This requires a membrane, a mechanism for pumping protons across the membrane, and a mechanism for producing or “recharging” ATP. The challenge is particularly onerous because these three components are highly complex in all of life and are interdependent to provide energy for life. In other words, the pumping of protons is of no use unless the membrane is there to maintain a gradient of protons. The membrane has no function for energy generation unless there is a mechanism for pumping protons across it. Similarly, the method of ATP production is of no use without a proton gradient across a membrane. 2

Rob Stadler (2022): The energy density required by life is about 100,000,000 times that which can be produced by the pH gradients of the vents. The small compartments in the rock structure have “membranes” that are far too thick for energy harnessing. And they would still require complex molecular machinery to make use of the free pH gradient. Energy harnessing in even the simplest forms of life requires extreme complexity and exhibits circular causality. Advocates for abiogenesis desperately seek to sidestep this complexity, but their best approach thus far requires placing blind faith in the wonders of natural selection. 23

Michael Marshall (2020): The biggest problem for the alkaline vent hypothesis is its most unique element, which at first sight seems the most convincing: the idea that a natural proton gradient could supply the energy to kick-start metabolism. This idea is a brilliant intuitive leap, but there is no experimental evidence. All life does use proton gradients, but all life also uses ribosomes and nobody thinks ribosomes were present at the very beginning. The problem is twofold. First, we do not know that there are sharp proton gradients within alkaline vents like Lost City. Instead, alkali may slowly blend into acid over the length of each chimney, in which case the proton gradient will be too gentle to generate useful power. Second, the enzymes that life uses, including the one that makes ATP, are big and complex. So far, nobody has found a simpler version that works and could plausibly have formed. This absence is glaring, just as the lack of a self-replicating RNA has been a problem for the RNA World. In the last few years Russell has tried to solve this problem. It seems unlikely that the first life used ATP itself, as the adenosine part of the molecule is elaborate. However, the key part is the chain of phosphates, and these ‘polyphosphate’ chains may simply have formed on their own. Indeed, Harold Morowitz pointed out in 1992 that many microorganisms make polyphosphates and used them to store chemical energy. Russell now suspects that the first life used the simplest possible polyphosphate: pyrophosphate, which is simply two phosphates strung together. To integrate pyrophosphate into his scheme, he has abandoned the idea of iron sulfide bubbles. ‘There were a lot of people who loved that because it looked like a cell,’ he says. However, he now thinks the pores in the rocks of alkaline vents were lined with multiple thin layers of ‘green rust’. Most of us have seen green rust, for instance on old iron ships that have long been exposed to seawater. It is a compound of iron, hydrogen, oxygen, and other chemicals, and Russell found it often formed when he tried to simulate conditions in the vents. He posits that these layers of green rust within the rock pores were the first cell membranes. This may seem an odd addition – surely the pores themselves were suitable containers for proto-life? – but Russell thinks the film of green rust could have been how the first life harnessed proton gradients to make pyrophosphate, without an enzyme. His proposal is that the proton gradient over the green rust membrane pulled phosphates and protons into narrow gaps in the green rust crystals, where they fused to form pyrophosphate. This was then released into the gaps between green rust layers, where it drove the synthesis of other biological molecules. It is an ingenious idea, which he is now trying to test. ‘If we can’t show in three years that that works, then we’re in dead trouble,’ he says. However, Russell is facing a new obstacle. In 2019 he lost his long-standing position at NASA’s Jet Propulsion Laboratory, and he is now living in Italy. He’s trying to get the experiments done at European Universities. Meanwhile, genetics has yielded a startlingly powerful piece of evidence in favor of the alkaline vent hypothesis.

In 2016, Martin’s team published a detailed reconstruction of the Last Universal Common Ancestor (LUCA) from which all modern organisms are descended. They did so by examining the genes of 1930 microorganisms, searching for genes that they all shared – which probably existed in LUCA. This was not easy, because microbes sometimes take a gene from an unrelated species; a process called horizontal gene transfer. This can make a gene appear universal and ancestral, when it actually evolved later and then spread. After the team had cleaned up the data as best they could, they were left with 355 gene families that seemingly existed in LUCA. These suggested that LUCA lived somewhere hot – which is compatible with an alkaline vent but doesn’t prove it – and that it used the Wood–Ljungdahl pathway to make biological molecules, as Martin predicted. Furthermore, it seems LUCA had the equipment to harness a proton gradient, but not to generate one – which fits with the idea that it relied on a natural proton gradient in a vent. This latter finding is striking, but must be taken with a pinch of salt because of the horizontal gene transfer problem. The alkaline vent hypothesis is beautiful and detailed and lines up with microbiology. But that doesn’t make it true. Plenty of beautiful, plausible seeming ideas have turned out to be wrong. It is not at all clear that the hypothesis can surmount its many problems. However, several of its key elements are so compelling that the true theory must surely incorporate them, or find some other solution to the problems they address. A source of chemical energy to fuel metabolism is obviously crucial, but possibly so is the ability to harness, or even generate, a proton gradient. Finally, it is striking that the hypothesis attempts to make two of the components of life – a metabolic cycle and a compartment – at once. It is this more holistic approach that is arguably most significant. Rather than trying to do everything with RNA, or with proteins, Russell’s idea endeavors to build something that looks more like a complete cell. In this, if nothing else, it hints at a better explanation for life on Earth. In the twenty-first century, many researchers followed Russell’s example and stopped trying to do everything with one kind of chemical. Instead, they would find ways to create all of life’s components at once. Even if Russell’s hypothesis turns out to be wrong, his work clearly foreshadowed this new approach. 24

Serpentinization
M. J. RUSSELL (2010): The alkaline nature of hydrothermal effluent in serpentinizing systems creates naturally formed pH and redox gradients across the precipitate at the vent-ocean interface, which could readily have served as the geochemical template upon which biological chemiosmotic harnessing evolved. More generally, hydrothermal vent precipitates provide natural three-dimensional microcompartments within which the products of serpentinization-driven organic synthesis could have been retained, so that the path to chemical complexity would not be faced with otherwise insurmountable problems of diffusion to the ocean. 26

Dr. Hideshi Ooka (2018): Deep-sea environments can harness thermal and chemical energy, and this may be used to drive specific chemical reactions such as CO2 reduction. This is possible due to the material properties of the chimney wall, namely their electrical conductivity and thermal insulation. These features allow the thermal and chemical gradients to be maintained, leading to variations in reaction environments which would likely create an environment suitable for the generation of a specific CO2 reduction product. In this way, hydrothermal vents occupy a large chemical reaction space, and may “search” for the optimum spatial and physicochemical environments for CO2 reduction. 27

D.Deamer (2019): Assumptions and conjectures not tested by experiments or observation: 

- The vent minerals can catalyze the reduction of CO2 by the dissolved hydrogen. 
- A substantial pH gradient develops between the alkaline fluid and relatively acidic seawater. 
- The porous minerals compartments can concentrate potential reactants and maintain products within their volume. 
- The reduced carbon compounds can act as a substrate to initiate a primitive version of metabolism. 
- A lipid film seals the otherwise porous mineral membranes so that pH gradients can be maintained. 
- The pH gradients can serve as a source of chemiosmotic energy coupled to pyrophosphate bond synthesis.

As is proper in scientific research, recent papers from other experts express skepticism about whether CO2 can actually be reduced under vent conditions, as well as the conclusions that follow from that assumption. For instance, Jackson (2016) makes the point that mineral membranes are much too thick to function as a chemiosmotic membrane because chemiosmosis requires a thin membrane to harvest the energy of a pH gradient. An analogy that may help clarify this point is to imagine a turbine and generator capturing the energy of a 10-meter waterfall over a cliff (a “sharp” gradient) and then putting the same generator into a river that falls the same distance—10 meters— but over a distance of one kilometer (analogous to a thick membrane). Virtually no energy can be captured from the slow-moving river. 25

Phosphate’s Role in Primitive Metabolism? 
ATP is an extraordinary molecule that has permeated all life as an energy currency, yet the origin of this particular molecule is a major gap in our understanding. Cells use ATP to gather energy from a source such as photosynthesis or respiration and then deliver it to energy-requiring reactions in the rest of the cytoplasm. The chemical-energy content of ATP is present in the pyrophosphate bond that links its second and third phosphate groups. This is called a high-energy bond because of its relatively large energy content, expressed as kilocalories per mole of ATP (kcal/ mol) or as kilojoules per mole (kJ/mol) in international units. To give a sense of the amount of energy available in the bond, the units were originally measured as calories, with units defined as the amount of heat that raises the temperature of a gram (approximately one cubic centimeter) of water by one degree Celsius. (This is simplified, but the technical definition is not necessary here.) A  kilocalorie will therefore raise the temperature of a liter of water (one thousand grams) by one degree C.  If one mole of ATP (507 grams) is dissolved in one liter of water and allowed to hydrolyze, the temperature of the water would increase by approximately 7 degrees C. This energy, by the way, is a chemist’s version which is measured under carefully defined conditions of temperature and concentration. In a living cell, the conditions are quite different and ATP makes a greater amount of energy available, closer to 10 kcal per mole. ATP hydrolysis is the primary source of the heat used by mammals and birds to maintain their body temperature at a fixed point above that of the environment. 

Dessel: I've seen enough from Otangelo that I know what I believe: he knows, but he doesn't care.  He's happy to lie because he's not interested in the truth, he's interested in evangelism, and he desperately wants to deceive both himself and others as much as he possibly can.  I am sure Otangelo will make excuses about his misuse of the Miller quote and copy-paste another wall of yellow journalism misconstruing the facts, but this kind of predictable lying bores me to tears and shows me he can't be taken seriously as anything more than a carnival clown side-show or a two-rate magician bent on playing tricks that rely on deception and distraction.  You guys have fun with him; I'm going to pursue genuine criticism from honest people, not propaganda from con men.  That's all.  Bye now.

Reply: One thing that I really can't stand is to be called intellectually dishonest, or when I am explicitly out called as a liar, but my opponent uses that tactic just to hide his incompetence to deal with the issues raised in a grown-up manner, as an adult. If my opponent feels I lied, he should first quote the sentence where he feels I was dishonest, and then clearly outline why he felt it was a lie. Unless he does this, I call such accusations coward and anti-intellectual. 


I have also invited you to a formal debate, despite your continuous hostility and accusations, and you refused. I have nothing to hide. You line up to a number of people who don't have to courage to debate me, but instead, resort to the kind of attacks on a personal level as you just did. I am vaccinated to that. You are not the first, and will not be the last. It is not the way I think an exchange of ideas should occur. Now let me see if you can refute the facts that I am bringing to the table here, and if you can't, let everybody see if you stand the manhood to admit that you were wrong. 

Taylor: Otangelo, you cited a paper that discusses the role of selection... to claim there is no selection!  Truly astounding!
Reply: Right. The paper DISCUSSES the role of selection. That does not mean there WAS selection before life started.

Taylor: From the paper you cited:    https://link.springer.com/article/10.1007/s11084-010-9214-1  " It is commonly accepted today by origin-of-life researchers that the emergence of life was an evolutionary process involving, at one stage or another, the working of natural selection.

Reply: You see, one can give different interpretations/meanings of a sentence, depending on what one highlights. I agree, many, if not most OoL researchers commonly accept it. So what? Does that mean, there actually was
NS? First of all, natural selection depends on a few things.

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

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

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

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

Taylor: The early systems, constituting the Last Universal Common Ancestor at the root of the evolutionary tree, were already highly complex. They could not have been the product of regular physical and chemical processes alone and had to be the consequence of evolution. 
Reply:  First, 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. Second, these structures were evolvable, i.e., capable of evolution by natural selection.

First of all, I do not need to agree with EVERYTHING that the author of a science paper claims, in order to be warranted to cite a paper, and quote it. Quoting without removing from the context, aka. quote-mining is unwarranted. Quoting in context, IMHO, is justified. I did not quote out of context. The quote stands on its own, and the next sentence does not give a different meaning to the quoted text if added. In fact, it continues with the following:

Second, these structures were evolvable, i.e., capable of evolution by natural selection.

This would be the case if these structures were incorporated into a living, self-replicating cell. Not before.

Taylor: "While convinced of the need for evolution in the emergence of life, researchers disagree on the nature of the required chemical infrastructure that could have formed on the primordial Earth."You cut out the italicized portion, ignoring the rest.  Did you think you could get away with this?
Reply:  Does the fact that some are convinced that evolution is needed for the emergence of life, make it factual, that evolution and natural selection was in fact THE driving force? No!!

Taylor: It clearly states that there was prebiotic selection occurring.  
Reply:  It states that prebiotic selection was occurring for prebiotic chemical structures, that could have emerged as a result of ordinary physical and chemical processes. So the author makes a distinction between prebiotic chemical structures that emerged as a result of ordinary physical and chemical processes, and then claims, that these structures were evolvable. Why? Because "The early systems, constituting the Last Universal Common Ancestor at the root of the evolutionary tree, were already highly complex."  So the author does not make this inference, because NS is warranted prior to DNA self-replication, but because he cannot fathom how ordinary physical and chemical processes could have given rise to such already highly complex early systems!! This is circular reasoning. He commits that logical fallacy because he does not consider that there could be OTHER POSSIBLE mechanisms that account for the arise of these highly ordered complex structures, NAMELY DESIGN. 

Taylor: Now, I understand how one could be confused that such systems did not evolve, and yet are capable of evolving, but... that's the point, you don't seem to understand the material.
Reply:  No. It's not that I don't understand the material. It's that I am not buying everything that is written in scientific papers, and you shouldn't either. But because you are indoctrinated and blindly believe in anything, just because a science paper says it, at it fits your preconceived views, you buy and endorse it.  I take every claim, coming from a science paper or not, with a grain of salt, and scrutinize if the claim is justified and true, or not. Why don't you do the same?

John Lennox: Nonsense remains nonsense, even when spoken by world-famous scientists

You start with a random clump of atoms, and if you shine light on it for long enough, it should not be so surprising that you get a plant,” England said. 16

Richard Terrile, NASA mission scientist: “Put those ingredients ( for the origin of life) together on Earth and you get life within a billion years 20

Wentao Ma (2017): When two or more functional RNAs emerged, for their efficient cooperation, there should have been a selective pressure for the emergence of protocells. 21

TED talk (2011): Lee Cronin: So many people think that life took millions of years to kick in we're proposing to do it in just a few hours once we've set up the right uh chemistry
Chris Anderson: So and when do you think that will happen?
Lee Cronin: Hopefully within the next two years 22

Jaques Monod: Chance and necessity 1972:  "In the final analysis language too was a product of chance."

Jessica L. E. Wimmer et al. (2021): Simple spontaneous geochemical reactions gave rise to the enzymatically catalyzed reaction network of microbial metabolism: a highly organized set of specific organic reactions that provides the amino acids, nucleotides and cofactors to sustain ribosomal protein synthesis and growth.

Peer review: a flawed process at the heart of science and journals
https://reasonandscience.catsboard.com/t1290-peer-review-a-flawed-process-at-the-heart-of-science-and-journals

Taylor: We could discuss it, but you're not even accurately reciting the contents of the paper, so how are we to discuss its contents?!?
Reply:  And now you are deliberately lying!! Nothing that I quoted, is out of context. The fact that according to the author, in a second state, evolution/NS supposedly occurred, does not take away the author's confirmation ( which is what I quoted),  that the prebiotic chemical structures were not the product of evolution. That alone, considering the complexity of the four vital basic building blocks of life, is a no-no for abiogenesis. But you obviously don't get it, even after having been provided with more than enough scientific material demonstrating this, outlining why it is unlikely to the extreme, to the point that it is warranted to say: It is impossible. 

Taylor: "To recapitulate, according to the prevailing thesis the emergence of life, entailing the development of complex organization, depended on a process of evolution by natural selection."
Reply: A prevailing thesis is not fact. It is OPINION.

Taylor:  You claimed the opposite was the conclusion of this paper, Otangelo!  Either you read the paper and are lying about it, or you're lying that you read the paper!  Not good! Sure, we could be having a discussion on whether or not these proposed mechanisms are viable, but you claim this paper argues AGAINST prebiotic selection!!
Reply: YOU are lying about what I said and quoted. Not the other way around. Nowhere did I claim anything about a conclusion. Not good.

Taylor:  "An inaccurate reproduction of such a metabolic system which still provided an infrastructure for natural selection could have functioned for a limited period of time, giving rise to more complex chemical structures. These structures could have later evolved into more accurate genetic systems."However, de Duve does not regard this protometabolism as providing an infrastructure for natural selection, which he claims could begin only when ribonucleotides were synthesized and polymerized (2005a)."

de Duve is still talking about prebiotic conditions, even though his idea of selection is more narrow than others in the field.   Again, the opposite of how you characterized this paper.  

You mischaracterize the literature, at best, so this is why no one thinks you can critique it!
Reply: No one? So now you have become a team speaker? You wear blinkers with the written text " naturalism" on them and are unwilling/unable to recognize the obviousness, that the origin of life could not be the product of non-intelligent mechanisms, and in order to protect and shield your self-delusional view, you attempt to accuse me of not understanding what I quote. Remarkable. I understand pretty well what the paper says, but I simply do not swallow everything, and you shouldn't either. 

Taylor: I know it sounds juicy to take out parts that say they're not products of evolution, but you ignore the part that says they're evolvable by natural selection and the part where researchers ARE CONVINCED that natural selection plays a role in the emergence of life, and you cite this as an example of researchers challenging the idea of prebiotic selection!  I really am astounded!  You can't be doing this!
Reply: Double down, Taylor!! Keep blaming. Sing victory. Remember. The emperor has no cloth. And you are still holding to the delusion that NS is the performer of miracles on early earth. A mindless, but super powerful agent that is more capable of creating structures that man, with all its intelligence, is not even close being able to instantiate. Remarkable faith you have. You are a fully indoctrinated person who is truly incapable of seeing, let alone questioning your core assumptions, sadly. Natural Selection creates NOTHING.  All it can do, at best, is act to preserve what already exists. What selective pressures, SPECIFICALLY, are acting in your “simple” prebiotic chemical structures?  SPECIFICALLY  selection acts to drive to the shortest possible, fastest replicating system that consumes the least energy and resources.  This means SELECTION ITSELF acts to PREVENT such a system from growing in complexity.  Not to kick start the evolutionary explosion that life actually displayed.  You believe and repeat this same core assumption so often that you no longer recognize it as a pure assumption in the first place, let alone question it. So, Taylor, please explain: How do copying errors actually produce coherent, functional, information-rich systems?  We can't just assume that they do, and then pull Darwin's rhetorical trick out of the bag and claim there is some selection out there "preserving and adding up all that is good."

Trevors, J.T.: Chance and necessity do not explain the origin of life 2004
Selection pressure cannot select nucleotides at the digital programming level where primary structures form. Genomes predetermine the phenotypes which natural selection only secondarily favors. Contentions that offer nothing more than long periods of time offer no mechanism of explanation for the derivation of genetic programming. No new informationis provided by such tautologies. The argument simply says it happened. As such, it is nothing more than blind belief. Science must provide rational theoretical mechanism, empirical support, prediction fulfillment, or some combination of these three. If none of these three are available, science should reconsider that molecular evolution of genetic cybernetics is a proven fact and press forward with new research approaches which are not obvious at this time. 5

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

Taylor:  Kondrashov tested one, and it effectively halts the ratchet indefinitely all on its own.  And Muller's ratchet only applies to SMALL and ASEXUAL populations.  Not remotely a problem here, as 1, this doesn't apply to anything prebiotic,
Reply: There is a supposed transition from a first, to a last universal common ancestor. Yes, we have a problem.

Muller's Ratchet The theory of Muller's Ratchet predicts that small asexual populations are doomed to accumulate ever-increasing deleterious mutation loads as a consequence of the magnified power of genetic drift and mutation that accompanies small population size. Evolutionary theory predicts that mutational decay is inevitable for small asexual populations, provided deleterious mutation rates are high enough. Such populations are expected to experience the effects of Muller's Ratchet where the most-fit class of individuals is lost at some rate due to chance alone, leaving the second-best class to ultimately suffer the same fate, and so on, leading to a gradual decline in mean fitness. The mutational meltdown theory built upon Muller's Ratchet to predict a synergism between mutation and genetic drift in promoting the extinction of small asexual populations that are at the end of a long genomic decay process. Since deleterious mutations are harmful by definition, accumulation of them would result in loss of individuals and a smaller population size. Small populations are more susceptible to the ratchet effect and more deleterious mutations would be fixed as a result of genetic drift. This creates a positive feedback loop that accelerates extinction of small asexual populations. This phenomenon has been called mutational meltdown.

Muller's Ratchet: Another hurdle in the hypothetical origin of life scenarios
E. V. Koonin (2017): Both the emergence of parasites in simple replicator systems and their persistence in evolving life forms are inevitable because the putative parasite-free states are evolutionarily unstable. 3 E. V. Koonin (2016): In the absence of recombination, finite populations are subject to irreversible deterioration through the accumulation of deleterious mutations, a process known as Muller’s ratchet, that eventually leads to the collapse of a population via mutational meltdown. 2

Dana K Howe (2008): The theory of Muller's Ratchet predicts that small asexual populations are doomed to accumulate ever-increasing deleterious mutation loads as a consequence of the magnified power of genetic drift and mutation that accompanies small population size. Evolutionary theory predicts that mutational decay is inevitable for small asexual populations, provided deleterious mutation rates are high enough. Such populations are expected to experience the effects of Muller's Ratchet where the most-fit class of individuals is lost at some rate due to chance alone, leaving the second-best class to ultimately suffer the same fate, and so on, leading to a gradual decline in mean fitness. The mutational meltdown theory built upon Muller's Ratchet to predict a synergism between mutation and genetic drift in promoting the extinction of small asexual populations that are at the end of a long genomic decay process. Since deleterious mutations are harmful by definition, accumulation of them would result in loss of individuals and a smaller population size. Small populations are more susceptible to the ratchet effect and more deleterious mutations would be fixed as a result of genetic drift. This creates a positive feedback loop that accelerates the extinction of small asexual populations. This phenomenon has been called mutational meltdown. From the onset, there would have had to be a population of diversified microbes, not just the population of one progenitor, but varies with different genetic make-ups, internally compartmentalized, able to perform Horizontal Gene Transfer and recombination. Unless these preconditions were met, the population would die. 1

The only escape would be that life started with a plurality of ancestors, as Koonin proposes:
The origin of life did not coincide with the organismal LUCA; rather, a profound gap in time, biological evolution, geochemical change, and surviving evidence separates the two. After life emerged from prebiotic processes, diversification ensued and the initial self-replicating and evolving living systems occupied a wide range of available ecological niches. From this time until the existence of the organismal LUCA, living systems, lineages and communities would have come and gone, evolving via the same processes that are at work today, including speciation, extinction, and gene transfer.  4
Eugene V. Koonin (2020): The LUCA was not a homogenous microbial population but rather a community of diverse microorganisms, with a shared gene core that was inherited by all descendant life-forms and a diversified pangenome that included various genes involved in virus–host interactions, in particular multiple defense systems. 8

Comment:  One would have to presume that the first universal common ancestor started as a diversified population, which is precisely the point of objection. If the origin of ONE OoL life event was extremely unlikely, imagine multiple diversified organisms, that would escape Muller's ratchet. That's a far stretch!! On top of that, this population would have to find a fully flourishing virus world, fully apt to start the evolutionary arms race necessary to have ecological homeostasis, essential for life to exist on earth. Good luck explaining the origin of over 20 separate virus lineages, polyphyly and multiple ancestry of viruses, and the capsid world!!

Taylor:  and 2, there is no reason to assume the population of the first organisms were small.  You seem to consistently ignore anything in the literature that contradicts your criticisms.
Reply: Haha, that's the best one. So you assume the origin of life started with a large population? Precious !! 

Taylor: So, I really don't see any other argument BUT god of the gaps.  The possibility of a god being entirely taken for granted; you have not shown that a god exists, or that it can create life.  Why do you not have the same level of skepticism for this god concept that you have for this abiogenesis concept?  
Reply: Well, after I demonstrated in my previous reply, why God is not a gap argument, but based on inference to the best explanation, and you entirely ignored all other points that I replied to, and after I have debated you before on the subject, and you never learn, I am diagnosing a strong confirmation bias on your side, and a strong unwillingness to learn, in order to keep your Zombie worldview alive. Be it. Anything more, would be a surprise. 

Taylor: Otangelo: "What would you expect to see, in order to say: Now the story seems to shift to God being the best explanation ?" The model of "God did it" would require to have within it, some principles or mechanisms with which some novel predictions can be derived.   If those predictions are then tested and observed, then this would scientifically verify this hypothesis, to the degree of how many predictions are met.
Reply:  Unique events that occurred in the past cannot be repeated in the lab. Intelligent design is an inference, outside of the scope of repetition and observation.

Observation: Intelligent agents act frequently with an end goal in mind, instantiating information storage devices like hard disks, and creating blueprints, instructional information, and codified descriptions of factories and machines. They also know how to instantiate information transmission machines, that encode, transmit, decode, or even translate that information, and subsequently, build factories that contain functional irreducibly complex machines made of multiple, integrated parts, and on top of that, assembly lines, where various machines are finely adjusted to each other, to produce useful end products, or intermediate products, that are later assembled in a system with higher functions. In our experience, such systems invariably originate from an intelligent source. No exception.

Hypothesis (Prediction): If structures in nature are found, that are analogous to hardware/software ( computers ) made by man, that direct the making of devices containing many parts arranged in intricate patterns, metabolic pathways similar to electronic circuits, and irreducible integrated systems and structures that perform specific functions, it is an indication that intelligence had to be present, instantiating these systems in the past. 

Experiment: Scientific research has unraveled that cells host the densest possible data storage mechanisms ( genes), optimized genetic and epigenetic codes, and languages ( the genetic code is more optimal than a million alternatives in regards to the robustness of information translation, furthermore, we know of over 45 epigenetic languages), information transmission, that is encoding through RNA polymerase transcription, transmission through messenger RNA, and decoding/translation through ribosomes ( the entire process is monitored, error-checked, repaired when needed), creating molecular machines (proteins) and lining them up and ordering them into metabolic circuits ( analogous to factory production lines) and compartments ( organelles),  creating irreducible self-replicating ( the epitome of engineering) chemical fabrics ( Cells ). Cells could not keep their basic functions without a minimum number of parts and complex inter-wined, integrated, and interdependent structures. That indicates these biological machines and pathways had to emerge fully operational, all at once. A stepwise manner is not possible. 

Conclusion: Unless someone can falsify the prediction ( and actually, confirmation), and point out a superior, more case-adequate, non-intelligent source of high levels of instructional complex codified information, irreducible complex and interdependent molecular systems, and complex metabolic circuits and biosynthesis pathways instantiated through these genetic instructions, their origin is best explained by the action of an intelligent agent. We do not need direct observed empirical evidence of the instantiation of these structures through an intelligent agency. What is observed ( the evidence) is the path to the cause in the past. We can stick to inference to the best explanation. 

Eliminative inductions argue for the truth of a proposition by arguing that competitors to that proposition are false. Provided the proposition, together with its competitors, form a mutually exclusive and exhaustive class, eliminating all the competitors entails that the proposition is true. Since either there is a God, or not, either one or the other is true. As Sherlock Holmes's famous dictum says: when you have eliminated the impossible, whatever remains, however not fully comprehensible, but logically possible, must be the truth. Eliminative inductions, in fact, become deductions.

The claim that intelligent design constitutes the best explanation of origins leads is also based on the fact that competing causal hypotheses will not demonstrate the power to produce these effects—just as they may not have done so to this point.

Matter, space, and time cannot create themselves.
The laws of physics cannot create themselves.
Life cannot create itself.
Languages and codes cannot create themselves
Blueprints, instructional complex information, data, and programs cannot create themselves
Information processing and transmission channels can not create themselves
Computers cannot create themselves
Transistors cannot create themselves
Complex machines, factory production lines, factories, and factory parks producing things with purpose cannot create themselves

The model of intelligent design makes predictions, and is testable
https://reasonandscience.catsboard.com/t1659-predictions-does-intelligent-design-make-predictions-is-it-testable

Taylor: That, or have god show up and show us how he did it.  If your god desires me to know this truth, I'm sure he can come up with something.
Reply:   Philosopher Michael Murray of Franklin & Marshall College makes the case that if God stays hidden to a degree, He gives people the free will to either respond to His tugging at their hearts or remain autonomous from Him. This is what happens in the narrative of the Garden of Eden. When Adam and Eve are tempted by the serpent, God’s immediate proximity to them is not evident. Perhaps the character is what you do when you think nobody is looking.

What if, in the words of Blaise Pascal, God has only revealed Himself enough to give us the choice of whether or not to believe? Pascal says, “There is enough light for those who desire only to see, and enough darkness for those of a contrary disposition.”

if you prefer being an atheist, God values your free will more than His desires for you. If you are really after truth, then have an open mind and follow the evidence wherever it leads, even if you don’t like the conclusion.

Why does God not simply show himself to us ?
https://reasonandscience.catsboard.com/t1422-show-why-does-god-not-simply-show-himself-to-us

Taylor: Otangelo... And I quote from you: "NS is not only arguable but actually argued against by many different sources." The citation I spent time quoting was, again, full of people exclusively SUPPORTING natural selection, THE EXACT OPPOSITE OF YOUR CLAIM that it argued AGAINST.  

Reply: The paper in question claimed that many are supportive of NS. No doubt about that, since there it is a more attractive mechanism than resignation that the only alternative to an intelligent designer is that life just coalesced from atomic building blocks through a random fluke collision of disorderly pieces, emerging by  “dumb, blind” mechanical processes, a fortuitous accident, spontaneously through self-organization by unguided, non-designed, unintended stochastic coincidence, natural events that turned into self-organization in an orderly manner without external direction. But there are many, and I cite the sources here that disagree, for the reasons already stated.

Taylor: Your only other citation to support this were a quote talking about how a standalone replicator just appearing out of nowhere is statistically improbable, (which all of us would agree with,) but which has NOTHING to do with supporting your claim that natural selection is "argued against" in the literature, either in prebiotic realms or otherwise.

Reply: Did you even care to open the link provided where I list several papers that disagree that NS had any play in the origin of life? You also do not address the two sources quoted, which disprove your claim, and demonstrate the conditions upon which NS can operate?  Did you ever educate yourself ? I googled for you: what are the conditions for natural selection to occur? The first answer:



You tell me if these conditions are met prior to life, and DNA replication exists. 

Taylor: You tried to shift the focus to why I accept these claims (because they're all experimentally demonstrated, just referenced in this review) but your actual first claim was that this paper "ARGUED AGAINST" natural selection!

Reply: Experimentally demonstrated ??? LOL. Really? Be my guest. Quote the experiments done that demonstrate that NS was operating prior DNA replication in living cells!!

Taylor: Again, I'd love to discuss the actual plausibility of these mechanisms, and whether implausible/incomplete mechanisms is evidence for intelligent design, but if you don't even represent the contents of the CLAIMS correctly, how are we to discuss their validity???

Reply: If NS was experimentally demonstrated, there is nothing more to be discussed. It's game over, and your refutation has experimental evidence in its favor, and I will remain obliged to acknowledge that NS was a driving force to explain the origin of life. Now back up your claim.....The fact that you don't address any of all the other reasons why I am supportive of ID, is telling.

Neil deGrasse Tyson:  The tenets of the big bang that the universe started out small hot dense uh where matter and energy were a primordial soup where the forces of nature had merged all of that is thoroughly supported by observations of this universe thoroughly supported.  Our universe would have started with a big bang okay?.
https://www.youtube.com/watch?v=nJLh6Wha76A&t=277s

Comment: It's great that Tyson admits that the universe had a beginning. 

Tyson: But big bang is not in trouble right i'm just saying it's not in trouble it is a whole thing that could conceivably fit in a deeper bigger idea right but it's not going to be swapped out tomorrow we're not going to find out tomorrow gee

Comment: It's If he's talking just about the fact that the Big bang points to a beginning of the universe, then, yes, I agree with Tyson. But if we are talking about what comes afterward, that's what is being questioned with the new data from the J Webb telescope.

In this video, Tyson does not address what the current buzz is all about. Here it is:

The Paradox: Grown-up Galaxies in an Infant Universe
https://reasonandscience.catsboard.com/t3091-the-paradox-grown-up-galaxies-in-an-infant-universe

Big Bang cosmology predicts that galaxies evolve over long periods of time:  If galaxies were all formed long ago, distant galaxies should look younger than those nearby because light from them requires a longer time to reach us. Such galaxies should contain more short-lived stars and more gas out of which future generations of stars will form.
https://www.scientificamerican.com/article/the-evolution-of-the-universe/

The Genesis model, where God "stretched out" the heavens and created a "mature" universe, (in the same sense as he created Adam looking "mature" and grown up, even after being created instants ago), predicts ensembles of galaxies close to us should look statistically the same as those far away.

And that is what is being observed through the new J.Webb telescope.


That the universe had a beginning is still questioned. For example, Brian Cox says here: https://www.youtube.com/watch?v=dE3dqlFzDeg

We don't know why the universe began in the way that it did if he indeed had a beginning
at the moment it's not able to answer even whether the universe had a beginning or not we don't even know that

Such confession makes only sense in light of the fact that Cox is an agnostic atheist, and, it seems, he does not want to admit that the universe had a beginning, to avoid the obvious implications. If it had a beginning, it had a cause. According to Hawking, Einstein, Rees, Vilenkin, Penzias, Jastrow, Krauss, and 100’s other physicists, the physical universe (time/space/matter) had a beginning.

Cox then goes on and says:

The universe started in a very highly ordered state.
And there are the laws of nature.
This is what science did find out.
This is the observational framework.
This is what science discovered. This is not what someone made up.

Then he goes and says: " We are humble and say: We don't know the why. Why it happened".

But is this true humility, or is it wilful ignorance?
Why not say: Order and laws of nature come from a mind.
Therefore, most probably, God exists?
That is a plausible, probable, logical answer.

The low entropy state of the universe at the beginning is indeed baffling. And so, by giving a closer look, at how the laws of physics are finely adjusted, to permit a life-permitting universe. We have indeed 3 powerful reasons to believe, that the universe was designed. 

1. The universe had a beginning, 
2. The universe is governed by laws of physics, and 
3. The universe is finely tuned to permit life. And now we can add: 
4. Galaxies close to the Big bang confirm a young earth creationism model. Not an old earth Big bang model. 


 
The Entropy of the Early Universe
The low-entropy condition of the early universe is extreme in both respects: the universe is a very big system, and it was once in a very low entropy state. The odds of that happening by chance are staggeringly small. Roger Penrose, a mathematical physicist at Oxford University, estimates the probability to be roughly 1/10^10^123. That number is so small that if it were written out in ordinary decimal form, the decimal would be followed by more zeros than there are particles in the universe! It is even smaller than the ratio of the volume of a proton (a subatomic particle) to the entire volume of the visible universe. Imagine filling the whole universe with lottery tickets the size of protons, then choosing one ticket at random. Your chance of winning that lottery is much higher than the probability of the universe beginning in a state with such low entropy! Huw Price, a philosopher of science at Cambridge, has called the low-entropy condition of the early universe “the most underrated discovery in the history of physics.”
http://www.faithfulscience.com/energy-and-entropy/entropy-of-the-early-universe.html

There are roughly 6.51×10^22 copper atoms in one cubic meter.
https://math.stackexchange.com/questions/287737/number-of-copper-atoms-in-1-mboxcm3-of-copper

If we take that the distance from Earth to the edge of the observable universe is about 14.26 gigaparsecs (46.5 billion light-years or 4.40×10^26 m) in any direction, and assuming that space is roughly flat (in the sense of being a Euclidean space), this size corresponds to a  volume of about  3.566×10^80 m3
https://en.wikipedia.org/wiki/Observable_universe

That means there would be roughly 10^100 copper atoms if we filled the entire volume of the observable universe with atoms without leaving any space. Getting the right initial low entropy state of our universe is like picking one red atom amongst all atoms in the universe. By chance, or design?   

JAY W. RICHARDS LIST OF FINE-TUNING PARAMETERS
Besides physical constants, there are initial or boundary conditions, which describe the conditions present at the beginning of the universe. Initial conditions are independent of the physical constants. One way of summarizing the initial conditions is to speak of the extremely low entropy (that is, a highly ordered) initial state of the universe. This refers to the initial distribution of mass energy. In The Road to Reality, 

Physicist Roger Penrose estimates that the odds of the initial low entropy state of our universe occurring by chance alone are on the order of 1 in 10 10^123. This ratio is vastly beyond our powers of comprehension. Since we know a life-bearing universe is intrinsically interesting, this ratio should be more than enough to raise the question: Why does such a universe exist? If someone is unmoved by this ratio, then they probably won’t be persuaded by additional examples of fine-tuning. In addition to initial conditions, there are a number of other, wellknown features about the universe that are apparently just brute facts. And these too exhibit a high degree of fine-tuning. Among the fine-tuned
(apparently) “brute facts” of nature are the following:

The ratio of masses for protons and electrons—If it were slightly different, building blocks for life such as DNA could not be formed.
The velocity of light—If it were larger, stars would be too luminous. If it were smaller, stars would not be luminous enough.
Mass excess of neutron over proton—if it were greater, there would be too few heavy elements for life. If it were smaller, stars would quickly collapse as neutron stars or black holes.
https://www.discovery.org/m/securepdfs/2018/12/List-of-Fine-Tuning-Parameters-Jay-Richards.pdf

David H Bailey: Is the universe fine-tuned for intelligent life?April 1st, 2017
The overall entropy (disorder) of the universe is, in the words of Lewis and Barnes, “freakishly lower than life requires.” After all, life requires, at most, a galaxy of highly ordered matter to create chemistry and life on a single planet. Physicist Roger Penrose has calculated (see The Emperor's New Mind, pg. 341-344) the odds that the entire universe is as orderly as our galactic neighborhood to be one in 10^10^123, a number whose decimal representation has vastly more zeroes than the number of fundamental particles in the observable universe. Extrapolating back to the big bang only deepens this puzzle.
https://mathscholar.org/2017/04/is-the-universe-fine-tuned-for-intelligent-life/

J. Warner Wallace: Initial Conditions in a Very Low Entropy State JULY 21, 2014
Entropy represents the amount of disorder in a system. Thus, a high entropy state is highly disordered – think of a messy teenager’s room. Our universe began in an incredibly low entropy state. A more precise definition of entropy is that it represents the number of microscopic states that are macroscopically indistinguishable. An egg has higher entropy once broken because you’re “opening” up many more ways to arrange the molecules. There are more ways of arranging molecules that would still be deemed an omelet than there are ways to arrange the particles in an unbroken egg in where certain molecules are confined to subsets of the space in the egg – such as a membrane or the yolk. Entropy is thus closely associated with probability. If one is randomly arranging molecules, it’s much more likely to choose a high entropy state than a low entropy state. Randomly arranged molecules in an egg would much more likely look like an omelet that an unbroken egg.

It turns out that nearly all arrangements of particles in the early universe would have resulted in a lifeless universe of black holes. Tiny inconsistencies in the particle arrangements would be acted on by gravity to grow in size. A positive feedback results since the clumps of particles have an even greater gravitational force on nearby particles. Penrose’s analysis shows that in the incredibly dense early universe, most arrangements of particles would have resulted basically in nothing but black holes. Life certainly can’t exist in such a universe because there would be no way to have self-replicating information systems. Possibly the brightest objects in the universe are quasars, which release radiation as bright as some galaxies due to matter falling into a supermassive black hole. The rotation rates near black holes and the extremely high-energy photons would non-life permitting.

Roger Penrose is the first scientist to quantify the fine-tuning necessary to have a low entropy universe to avoid such catastrophes. “In order to produce a universe resembling the one in which we live, the Creator would have to aim for an absurdly tiny volume of the phase space of possible universes, about 1/10^10123.” This number is incomprehensibly small – it represents 1 chance in 10 to the power of (10 to the power of 123). Writing this number in ordinal notational would require more zeroes than the number of subatomic particles in the observable universe, 10123 zeroes. Under the assumption of atheism, the particles in our universe would have been arranged randomly or at least not with respect to future implications for intelligent life. Nearly all such arrangements would not have been life-permitting so this fine-tuning evidence favors theism over atheism. We have a large but finite number of possible original states and rely on well-established statistical mechanics to assess the relevant probability.

The incredibly low entropy state of the initial conditions shows fine-tuning was required to avoid excessive black holes! This fact about the initial conditions also calls into question Smolin’s proposed scenario that universes with differing physical constants might be birthed out of black holes. Smolin suggests the possibility of an almost Darwinian concept in which universes that produce more black holes, therefore, more baby universes than those which don’t. But if our universe requires statistically miraculous initial conditions to be life-permitting by avoiding excessive black holes, universes evolving to maximize black hole production would be unlikely to lead to life! (Even if the evolution of universes were possible) Furthermore, the skeptic who thinks that black holes suggest a purposeless universe should consider that black holes can, in moderation and kept at distance, be helpful for life. While a universe comprised of mostly black holes would be life-prohibiting, having a large black hole at the center of a galaxy is actually quite helpful for life. Here is a Scientific American article that documents the benefits of Black Holes for life – it summarizes: “the matter-eating beast at the center of the Milky Way may actually account for Earth’s existence and habitability.”
https://crossexamined.org/fine-tuning-initial-conditions-support-life/




The universe had a beginning
https://reasonandscience.catsboard.com/t1297-beginning-the-universe-had-a-beginning

Energy was created at the Big bang
https://reasonandscience.catsboard.com/t3159-energy-was-created-at-the-big-bang

Fine-tuning of the Big Bang
https://reasonandscience.catsboard.com/t1866-fine-tuning-of-the-big-bang

Laws of Physics, fine-tuned for a life-permitting universe
https://reasonandscience.catsboard.com/t1336-laws-of-physics-fine-tuned-for-a-life-permitting-universe

Taylor: Otangelo, so are you now admitting that neither of these papers actually argue against prebiotic selection, despite your original claim?

Reply: I think I was pretty clear in my previous reply, so why do you ask? I think what you do not understand it,

Taylor: I agree a 100% with Vaneechoutte on this quote: 

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

It is right at the beginning of the abstract. Then comes the next sentence: 

To circumvent the chicken and egg problem associated with semantic closure of the cell—no replication of information molecules (nucleotide strands) without functional enzymes, no functional enzymes without encoding in information molecules—a prebiotic evolutionary process is proposed that, from the informational point of view, must somehow have resembled the current scientific process.

Reading the second sentence does not give another meaning to the first sentence, but points to another huge abiogenesis problem, namely a chicken & egg situation. The sentence seems  a bit convoluted to me, but that is what I crystallize out of it, and was already recognized and pointed out by Sidney Fox in 1965:



Which came first, proteins or protein synthesis?
Both the transcription and translation systems depend upon numerous proteins, many of which are jointly necessary for protein synthesis to occur at all. Yet all of these proteins are made by this very process. Proteins involved in transcription such as RNA polymerases, for example, are built from instructions carried on an RNA transcript. Translation of the RNA transcript depends upon other specialized enzymes such as synthetases, yet the information to build these enzymes is translated during the translation process that synthetases themselves facilitate. Biochemist David Goodsell describes the problem, "The key molecular process that makes modern life possible is protein synthesis, since proteins are used in nearly every aspect of living. The synthesis of proteins requires a tightly integrated sequence of reactions, most of which are themselves performed by proteins." Or as Jacques Monod noted in 1971: "The code is meaningless unless translated. The modern cell's translating machinery consists of at least fifty macromolecular components which are themselves coded in DNA: the code cannot be translated otherwise than by products of translation." (Scientists now know that translation actually requires more than a hundred proteins.) The integrated complexity of the cell's information-processing system has prompted some profound reflection. As Lewontin asks, "What makes the proteins that are necessary to make the protein?" As David Goodsell puts it, this "is one of the unanswered riddles of biochemistry: which came first, proteins or protein synthesis? If proteins are needed to make proteins, how did the whole thing get started?" The end result of protein synthesis is required before it can begin.

Catch22, chicken and egg problems in biology and biochemistry
https://reasonandscience.catsboard.com/t2059-catch22-chicken-and-egg-problems-in-biology-and-biochemistry

Vaneechoutte continues in the abstract: The cell was the outcome of interactions of a complex premetabolic community, with information molecules that were devoid of self-replicative properties.

Comment: As I said previously, I am not obligated to agree with everything claimed in a science paper, in order to quote a part that I agree with. I already disagree with above sentence of Vaneechoutte. The claim made is unsubstantiated and written as if it was a demonstrated fact. It's not. 



Vaneechoutte :  In a comparable manner, scientific progress is possible, essentially because of interaction between a complex cultural society and permanent information carriers like printed matter. This may eventually lead to self-replicating technology in which semantic closure occurs anew. Explaining the origin of life as a scientific process might provide a unifying theory for the evolution of information, wherebye at two moments symbolization/encoding of interactions into permanent information occurred: at one moment that of chemical interaction and at another moment that of animal behavior interaction. In one event this encoding led to autonomously duplicating chemistry (the cell), an event that possibly may be one of the outcomes of current scientific progress.

Comment: In other words: Science does not know today, but maybe it will find out tomorrow, and it will be an answer that warrants a natural nonguided process. That's called: naturalism of the gaps""

Tan, Change; Stadler, Rob. The Stairway To Life 2020:
In DNA and RNA, no chemical or physical forces impose a preferred sequence or pattern upon the chain of nucleotides. In other words, each base can be followed or preceded by any other base without bias, just as the bits and bytes of information on a computer are free to represent any sequence without bias. This characteristic of DNA and RNA is critical—in fact, essential—for DNA and RNA to serve as unconstrained information carriers. However, this property also obscures any natural explanation for the information content of life—the molecules themselves provide no explanation for the highly specific sequence of nucleotides required to code for specific biologic functions. Only two materialistic explanations have been proposed for the information content of life: fortuitous random arrangements that happen to be functional or the combination of replication, random mutations, and natural selection to improve existing functionality over time.

Hubert P. Yockey A calculation of the probability of spontaneous biogenesis by information theory   7 August 1977
The Darwin-Oparin-Haldane “warm little pond” scenario for biogenesis is examined by using information theory to calculate the probability that an informational biomolecule of reasonable biochemical specificity, long enough to provide a genome for the “protobiont”, could have appeared in 10^9 years in the primitive soup. Certain old untenable ideas have served only to confuse the solution of the problem. Negentropy is not a concept because entropy cannot be negative. The role that negentropy has played in previous discussions is replaced by “complexity” as defined in information theory. A satisfactory scenario for spontaneous biogenesis requires the generation of “complexity” not “order”. Previous calculations based on simple combinatorial analysis overestimate the number of sequences by a factor of 10^5. The number of cytochrome c sequences is about 3·8 × 10^61. The probability of selecting one such sequence at random is about 2·1 ×10^65. The primitive milieu will contain a racemic mixture of the biological amino acids and also many analogues and non-biological amino acids. Taking into account only the effect of the racemic mixture the longest genome which could be expected with 95 % confidence in 10^9 years corresponds to only 49 amino acid residues. This is much too short to code a living system so evolution to higher forms could not get started. Geological evidence for the “warm little pond” is missing. It is concluded that belief in currently accepted scenarios of spontaneous biogenesis is based on faith, contrary to conventional wisdom.
http://www.sciencedirect.com/science/article/pii/0022519377900443 

Coded information comes always from a mind
https://reasonandscience.catsboard.com/t1312-coded-information-comes-always-from-a-mind

Taylor: "Selection is a general principle. It occurs when variations on a theme exist. None, one, more or all variations will be able to exist in a given environment. Radioactive decay is an example of selection among variations on the theme of physically stable atomic configurations in a universe (environment) with certain parameters for fundamental laws. The difference with cultural and natural selection is that there is no amplification/replication of the fit variations. In cultural selection, different answers to a problem (variations on a theme) may be valued differently by the environment"

Otangelo!  Are you able to understand that selection STILL occurs whether or not the selected chemicals can then amplify themselves, and are simply selected by being the only ones left?

Reply:  It seems you have either not read, or not understood almost anything of what I replied to you previously.

Even the simplest of these substances [proteins] represent extremely complex compounds, containing many thousands of atoms of carbon, hydrogen, oxygen, and nitrogen arranged in absolutely definite patterns, which are specific for each separate substance.  To the student of protein structure the spontaneous formation of such an atomic arrangement in the protein molecule would seem as im- probable as would the accidental origin of the text of irgil’s “Aeneid” from scattered letter type.
– A. I. Oparin

David Goodsell gives a good example in his excellent book: Our Molecular Nature, page 26:
Dozens of enzymes are needed to make the DNA bases cytosine and thymine from their component atoms. The first step is a "condensation" reaction, connecting two short molecules to form one longer chain, performed by aspartate carbamoyltransferase. Other enzymes then connect the ends of this chain to form the six-sided ring of nucleotide bases, and half a dozen others shuffle atoms around to form each of the bases. In bacteria, the first enzyme in the sequence, aspartate carbamoyltransferase, controls the entire pathway. (In human cells, the regulation is more complex, involving the interaction of several of the enzymes in the pathway.) Bacterial aspartate carbamoyltransferase determines when thymine and cytosine will be made, through a battle of opposing forces. It is an allosteric enzyme, referring to its remarkable changes in shape (the term is derived from the Greek for "other shape"). The enzyme is composed of six large catalytic subunits and six smaller regulatory subunits. Take just a moment to ponder the immensity of this enzyme. The entire complex is composed of over 40,000 atoms, each of which plays a vital role. The handful of atoms that actually perform the chemical reaction are the central players. But they are not the only important atoms within the enzyme--every atom plays a supporting pan. The atoms lining the surfaces between subunits are chosen to complement one another exactly, to orchestrate the shifting regulatory motions. The atoms covering the surface are carefully picked to interact optimally with water, ensuring that the enzyme doesn't form a pasty aggregate, but remains an individual, floating factory. And the thousands of interior atoms are chosen to fit like a jigsaw puzzle, interlocking into a sturdy framework. Aspartate carbamoyltransferase is fully as complex as any fine automobile in our familiar world. And, just as manufacturers invest a great deal of research and time into the design of an automobile, enzymes like aspartate carbamoyltransferase have been finely tuned  and now, Goodsell adds just five words at the end of the sentence - over the course of evolution.

Comment:  After describing like an epic - how this enzyme is masterfully crafted down to the atomic scale, resorting to the analogy of the manufacturing of an automobile, he concludes that this life-essential enzyme was finely tuned by a process that does not operate based on intelligence - namely evolution. You did read that right. Worse than that:  Aspartate Carbamoyltransferase is part of the biosynthesis of pyrimidines - the nucleobases that make up RNA and DNA, life-essential molecules that had to be made prior to when life started, and as such, evolution as the mechanism to synthesize them cannot be invoked. There is a minimal number of proteins and enzymes that are required to start life, and the synthesis of RNA and DNA is life essential, and as such, the origin of  Aspartate Carbamoyltransferase is a question that belongs to the origin of life research, and an evolutionary process is inadequate to explain its origin. 

Taylor: " 2. ADDY PROSS: 
Pross himself states, in https://www.researchgate.net/publication/235880807_The_origin_of_life_What_we_know_what_we_can_know_and_what_we_will_never_know
"Its essence may be expressed as follows: All stable (persistent) replicating systems will tend to evolve over time towards systems of greater DKS. As we have described in some detail in previous publications, there are both empirical and theoretical grounds for believing that oligomeric replicating systems which are less stable (less persistent) will tend to be transformed into more stable (more persistent) forms"

So, what I've been telling you about selection this whole time.  Stability, persistence.

Reply: Once again you demonstrate that you did not pay attention to my previous replies: THERE IS NO EVIDENCE FOR SELF-REPLICATING RNA MOLECULES.

Today, thirty years after the RNA World was first proposed, no one has seen an actual living system that is completely based in RNA. Nevertheless, the hypothesis lives on in the origins of life research community, albeit in a hotly debated, highly contentious atmosphere. Although there are strong opponents, many researchers agree that although far from complete, it remains one of the best theories we have to understand “the backstory to contemporary biology.” Gilbert himself expressed some disappointment that “a self-replicating RNA has not yet been synthesized or discovered” in the years since he predicted his hypothesis, but he remains optimistic that it will emerge eventually.
[url=https://atlasofscience.org/revisiting-the-rna-world-with-its-inventor/#:~:text=The RNA World Hypothesis is,composed entirely of RNA molecules.]https://atlasofscience.org/revisiting-the-rna-world-with-its-inventor/#:~:text=The%20RNA%20World%20Hypothesis%20is,composed%20entirely%20of%20RNA%20molecules.[/url]

The origin of replication and translation and the RNA World
https://reasonandscience.catsboard.com/t2234-the-origin-of-replication-and-translation-and-the-rna-world

Some have accused me of cherry-picking are right: I cherry-pick what science paper authors say, that is substantiated, and discard unsubstantiated claims, that are based on bias that favors a naturalistic narrative, but which does not find supportive evidence. Obviously, you can't do that, if you don't understand the claims, or if you are uninformed in regards of the real state of affairs. 

Taylor:  He continues, "In fact that selection rule is just a particular application of the more general law of nature, almost axiomatic in character, that systems of all kinds tend from less stable to more stable. That law is inherent in the very definition of the term ‘stability’. So within the global selection rule in nature, normally articulated by the second law of thermodynamics, we can articulate a formulation specific to replicative systems, both chemical and biological"

Reply: Thermodynamics is not the naturalists friend when it comes to abiogenesis. Quite the contrary. Stability as a motor or basis of complexification is a myth, repeated by Dimiter Kunnev et al. but without a warrant.. Benner points out that:

The Asphalt Paradox 
An enormous amount of empirical data have established, as a rule, that organic systems, given energy and left to themselves, devolve to give uselessly complex mixtures, “asphalts”. The literature reports (to our knowledge) 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”. 
https://sci-hub.ren/10.1007/s11084-014-9379-0

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.

Paradoxes in the Origin of Life
https://reasonandscience.catsboard.com/t1279-abiogenesis-is-mathematically-impossible#7309

Taylor: 3. Exploring the Deep Mystery of Life's Origins Aug 8, 2022
Nick Lane: Our kind of cell arose once in four billion years of evolution. And it seems to have been something of a bit of a freak accident.


This isn't from any peer reviewed literaure, but a youtube video.  Did you watch it?  Because he discusses how energy flow makes life inevitable.  The "freak accident" part you take out of context is referring to the origin of our TYPE of cell... aka the EUKARYOTIC cells.  He was NOT referring to the origin of life... AT ALL. 

Reply: 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


The natural tendency of proteins is to fall apart; for proteins to be synthesized, the reaction must be driven up the thermodynamic hill, away from equilibrium. The same is true of other biochemical processes: the transport of nutrients against a concentration gradient, the generation of physical force or electrical potentials, even the accurate transmittal of genetic information, all represent work in the thermodynamic sense. They can take place only because of cells couple the work function to a source of energy. This, in fact, is how energy is defined: it is the capacity to do work. Bioenergetics revolves around the sources of biological energy and the mechanisms by which energy is coupled to useful work


Thermodynamics, and the origin of life
https://reasonandscience.catsboard.com/t2718-thermodynamics-and-the-origin-of-life

Taylor: He is referring to nuclei and the endosymbiosis events that lead to mitochondria (which itself proves evolution seeing as there is no design reason to have mitochondria to have separate genomes, as some organisms have mitochondrial DNA in their nucleus.)   Endosymbiosis is a rare, but observed and testable event in biology.  A freak accident, if you will, but nothing that would comment on abiogenesis or present any points against evolution, and nothing that contradicts any science.

Reply:  The origin of eukaryotes is one of the hardest and most intriguing problems in the study of the evolution of life, and arguably, in the whole of biology. On average, the volume of eukaryotic cells is about 15,000 times larger than that of prokaryotic cells. 4 A major problem faced by this scenario (and symbiogenetic scenarios in general) is the mechanistic difficulty of the engulfment of one prokaryotic cell by another.  The origin of eukaryotes is a fundamental, forbidding evolutionary puzzle. The scenario of eukaryogenesis, and in particular the relationship between endosymbiosis and the origin of eukaryotes, is far from being clear.  Compared to archaea and bacteria (collectively, prokaryotes), eukaryotic cells are three to four orders of magnitude larger in volume and display a qualitatively higher level of complexity of intracellular organization. Eukaryotic cells function on different physical principles compared to prokaryotic cells, which is directly due to their (comparatively) enormous size. The gulf between the cellular organizations of eukaryotes and prokaryotes is all the more striking because no intermediates have been found. So intimidating is the challenge of eukaryogenesis that the infamous notion of irreducible complexity’ has sneaked into serious scientific debate 2 . The diversity of the outcomes of phylogenetic analysis, with the origin of eukaryotes scattered around the archaeal diversity, has led to considerable frustration and suggested that a ‘phylogenomic impasse’ has been reached, owing to the inadequacy of the available phylogenetic methods for disambiguating deep relationships. The evolutionary trajectory of modern eukaryotes is  distinct from that of prokaryotes. Data from many sources give no direct evidence that eukaryotes evolved by genome fusion between archaea and bacteria. Nuclei, nucleoli, Golgi apparatus, centrioles, and endoplasmic reticulum are examples of cellular signature structures (CSSs) that distinguish eukaryote cells from archaea and bacteria.

On the Origin of Mitochondria: Reasons for Skepticism on the Endosymbiotic Story 
https://reasonandscience.catsboard.com/t1303-challenges-to-endosymbiotic-theory

Taylor: Again, you're conflating DARWINIAN EVOLUTION with selection.  Similar principles, but different process.  Selection can occur without inheritance.  Replication vs. production.  Both can be selected for fitness and longevity by natural forces.  Of course abiotic processes are not biological.  Thus these quotes are utterly misrepresented as somehow contradictory. 

Reply: Davies clearly addressed the claim that there was natural selection on prebiotic earth, as many, you included claim, and he clearly DENIES it.

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

So your accusation that I quoted and misrepresented what he said is a LIE. 

Taylor:  Otangelo, this is unacceptable!  I can't review every single reference you give, but starting from the top, and without exception, every single one is a misrepresentation of the science. Just understand the material, and THEN we can discuss the merits of it!  There is NOTHING wrong with disputing scientific results and speculation! You just need to accurately represent what it is, first and foremost.  Hopefully this helps.

Reply: You are demonstrating that 1. You are not able to distinguish warranted, from unwarranted claims, 2. You don't understand the science, and swallow everything, in special if it confirms what you already believe and wish to be true. 3. You accuse me of what you are guilty of. 4. You accused me several times of lying, which is unacceptable. If you keep replying one more time, and accusing me of lying, and I recognize that your accusation is unjustified, I see no motivation in responding again.