Defending the Christian Worlview, Creationism, and Intelligent Design
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Defending the Christian Worlview, Creationism, and Intelligent Design

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


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Defending the Christian Worlview, Creationism, and Intelligent Design » Origin of life » Abiogenesis: Uncertainty quantification of a primordial ancestor with a minimal proteome emerging through unguided, natural, random events

Abiogenesis: Uncertainty quantification of a primordial ancestor with a minimal proteome emerging through unguided, natural, random events

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Otangelo


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Uncertainty quantification of a primordial ancestor with a minimal proteome emerging through unguided, natural, random events

https://reasonandscience.catsboard.com/t2508-abiogenesis-uncertainty-quantification-of-a-primordial-ancestor-with-a-minimal-proteome-emerging-through-unguided-natural-random-events

Claim: the origin of life is overwhelmingly improbable, but as long as there is at least some chance of a minimal proteome to kick-start life arising by natural means, then we shouldn’t reject the possibility that it did.
Reply: Chance is a possible explanation for minimal a proteome to emerge by stochastic, unguided means, and as consequence, the origin of life, but it doesn’t follow that it is necessarily the best explanation. Here is why.
We can calculate the odds that a minimal functional proteome would arise by unguided random natural events, not considering all other essential things to get a first living self-replicating cell.

Assume that:
1.  the conditions of the primitive atmosphere were known.
2.  Nitrogen and carbon in fixed form, necessary elements of amino acids, was readily available, and that all of the twenty amino acids used in life did form naturally ( disregarding the lifetime of ammonia which would be short because of its photochemical dissociation)
3.  Organosulfur compounds required in a few amino acids used in life would be readily available, even if in nature sulfur exists only in its most oxidized form (sulfate or SO4), and only some unique groups of prokaryotes mediate the reduction of SO4 to its most reduced state (sulfide or H2S)
4.  Billions of each amino acid would be readily available. ( even if eight proteinogenic amino acids were never abiotically synthesized under prebiotic conditions)
5.  The amino acids would be concentrated all together at one assembly site.
6.  There would be selected twenty, and not more or less amino acids to make proteins.
7.  Only the best suited would have been selected to enable the formation of soluble structures with close-packed cores, allowing the presence of ordered binding pockets inside proteins
8.  Nature did somehow "know" that the set of amino acids selected appears to be near ideal and optimal.
9.  The amino acids were only in homochiral, that is the left-handed configuration.
10. They would be pure, and without contaminating reactants, somehow avoiding the concomitant synthesis of undesired or irrelevant by-products.
11. They would be all bifunctional monomers with amino groups and carboxyl groups. AA's with unifunctional monomers (with only one functional group) would have been sorted out somehow.
12. They would remain stable, and not DEVOLVE to give uselessly complex mixtures, “asphalts”
13. They would be able to bond and polymerize by non-enzymatic means, without the ribosome
14. There are four different ways to bond AA's together by the side chains. if bonded to the wrong side chain, no deal. They would, somehow, bond together at the right place.
15. The polypeptide chain would not hydrolyze to its constituent amino acids.
16. In each trial, the average protein would be  400 amino acid  units in length
17. The rate to form and test each chain would be just one-third of a ten-million-billionth of a second!  This is around 150 thousand trillion times the normal speed in living things.
18. If a usable sequence were obtained, the action would stop so that it would be preserved, and shuffling would restart to obtain all proteins required for life.
19. 1/3 of all proteins once folded require chaperones, other proteins, that help the protein to fold into its proper, functional shape. They were not required for the first protein folds.  
20. The synthesized proteins would be able to merge and interlink into assembly lines and metabolic pathways, ready for working together in a living system.
21. Somehow, nature knew how to transition from prebiotic synthesis to cell synthesis of amino acids.  A minimum of 112 enzymes is required to synthesize the 20 (+2) amino acids used in proteins.

What are the odds that a functional protein or a cell would arise given the chance hypothesis (i.e., given the truth of the chance hypothesis)?

Mycoplasma is a reference to the threshold of the living from the non-living, held as the smallest possible living self-replicating cell. It is, however, a pathogen, an endosymbiont that only lives and survives within the body or cells of another organism ( humans ).  As such, it IMPORTS many nutrients from the host organism. The host provides most of the nutrients such bacteria require, hence they do not need the genes for producing such compounds themselves. It does not require the same complexity of biosynthesis pathways to manufacturing all nutrients as a free-living bacterium.

Pelagibacter unique bacteria are known to be the smallest and simplest, self-replicating, and free-living cells. Pelagibacter genomes (~ 1,300 genes and 1,3 million base pairs ) devolved from a slightly larger common ancestor (~2,000 genes). Pelagibacter is an alphaproteobacterium. In the evolutionary timescale, its common ancestor supposedly emerged about 1,3 billion years ago. The oldest bacteria known however are Cyanobacteria,  living in the rocks in Greenland about 3.7-billion years ago.  With a genome size of approximately  3,2 million base pairs ( Raphidiopsis brookii D9) they are the smallest genomes described for free-living cyanobacteria. This is a paradox. The oldest known life-forms have a considerably bigger genome than Pelagibacter, which makes their origin far more unlikely from a naturalistic standpoint.  The unlikeliness to have just ONE protein domain-sized fold of 250amino acids is 1 in 10^77. That means, to find just one functional protein fold with the length of about 250AAs, nature would have to search amongst so many non-functional folds as there are atoms in our known universe ( about 10^80 atoms).   We will soon see the likeliness to find an entire functional of genome Pelagibacter with 1,3 million nucleotides, which was however based on the data demonstrated above, not the earliest bacteria....

Pelagibacter has complete biosynthetic pathways for all 20 amino acids.  These organisms get by with about 1,300 genes and 1,3 million base pairs and code for 1,300 proteins.  The chance to get its entire proteome would be 10^722,000.  The discrepancy between the functional space, and the sequence space, is staggering.

  ( To calculate the odds, you can see this website: https://web.archive.org/web/20170423032439/http://creationsafaris.com/epoi_c06.htm#ec06f12x

The chance hypothesis can be rejected as the best explanation of the origin of life not only because of the improbability of finding the functional amino acid sequence giving rise to a functional proteome but also because there are not sufficient resources to do the shuffling during the entire history of the universe. There would not be enough time available, even doing the maximum number of possible shuffling in parallel. There could be trillions and trillions of attempts at the same time, during the entire time span of the history of the universe, in parallel, and it would not be enough.   Here is why:

Signature in the Cell, chapter 10: There have been roughly 10^16 seconds since the big bang. ( 60 (seconds)x60 (minutes)x24 (hours)x365.24238 (days in a year)x13799000000 (years since the Big Bang) = 4.35454 x 10^16  seconds). Due to the properties of gravity, matter, and electromagnetic radiation, physicists have determined that there is a limit to the number of physical transitions that can occur from one state to another within a given unit of time. According to physicists, a physical transition from one state to another cannot take place faster than light can traverse the smallest physically significant unit of distance. That unit of distance is the so-called Planck length of 10–33 centimeters. Therefore, the time it takes light to traverse this smallest distance determines the shortest time in which any physical effect can occur. This unit of time is the Planck time of 10–43 seconds. Based on that, we can calculate the largest number of opportunities that any physical event could occur in the observable universe since the big bang. Physically speaking, an event occurs when an elementary particle does something or interacts with other elementary particles. But since elementary particles can interact with each other only so many times per second (at most 10^43 times), since there are a limited number (10^80) of elementary particles, and since there has been a limited amount of time since the big bang (10^16 seconds), there are a limited number of opportunities for any given event to occur in the entire history of the universe.

This number can be calculated multiplying the three relevant factors together: the number of elementary particles (10^80) times the number of seconds since the big bang (10^16) times the number of possible interactions per second (10^43). This calculation fixes the total number of events that could have occurred in the observable universe since the origin of the universe at 10^139.  This provides a measure of the probabilistic resources of the entire observable universe.

Emile Borel gave an estimate of the probabilistic resources of the universe at 10^50.
Physicist Bret Van de Sande calculated the probabilistic resources of the universe at a more restrictive 2.6 × 10^92
Scientist Seth Lloyd calculated that the most bit operations the universe could have performed in its history is 10^120, meaning that a specific bit operation with an improbability significantly greater than 1 chance in 10^120 will likely never occur by chance.

The probability of producing a single 150-amino-acid functional protein by chance stands at about 1 in 10^164. Thus, for each functional sequence of 150 amino acids, there are at least 10^164 other possible nonfunctional sequences of the same length. Therefore, to have a  chance of producing a single functional protein of this length by chance, a random process would have to shuffle up to 10^164 sequences. That number vastly exceeds the most optimistic estimate of the probabilistic resources of the entire universe—that is, the number of events that could have occurred since the beginning of its existence.

Comparing 10^164 to the maximum number of opportunities—10^139—for that event to occur in the history of the universe, 10^164 exceeds the second 10^139 by more than twenty-four orders of magnitude, by more than a trillion trillion times.

If every event in the universe over its entire history were devoted to producing combinations of amino acids of the correct length in a prebiotic soup (an extravagantly generous and even absurd assumption), the number of
combinations thus produced would still represent a tiny fraction—less than 1 out of a trillion trillion—of the total number of events needed to have a chance of generating just ONE functional protein—any functional protein of modest length of 150 amino acids by chance alone ( consider that the average length of a protein is about 400 amino acids ). 

Even taking the probabilistic resources of the whole universe into account, it is extremely unlikely that even a single protein of that length would have arisen by chance on the early earth.

We have crudely estimated a total of 100 protons, neutrons, and electrons on average per atom.
The number of protons, neutrons, and electrons in our solar system is  around 1.8 × 10^57
The number of protons, neutrons and electrons in our galaxy is around 1.8 × 10^68
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796651/

The odds to have the genome of the smallest known free-living cell ( Pelagibacter unique ) is 1 to 10^722000. The are 10^80 atoms in the universe. Life by chance is a ridiculously implausible plausibility assertion.

Imagine covering the whole of the USA with small coins, edge to edge. Now imagine piling other coins on each of these millions of coins. Now imagine continuing to pile coins on each coin until reaching the moon about 400,000 km away! If you were told that within this vast mountain of coins there was one coin different to all the others. The statistical chance of finding that one coin is about 1 in 10^50. In other words, the evidence that our universe is designed is overwhelming!

1. The more statistically improbable something is, the less it makes sense to believe that it just happened by blind chance.
2. Statistically, it is practically impossible, that the primordial genome, proteome, and metabolome of the first living cell arose by chance.
3. Furthermore, we see in biochemistry purposeful design.  
4. Therefore, an intelligent Designer is by far the best explanation of origins.  

Abiogenesis? Impossible !!
https://www.youtube.com/watch?v=ycJblRcgqXk

The cell is the irreducible, minimal unit of life
https://sci-hub.ren/https://link.springer.com/chapter/10.1007/978-3-319-56372-5_8

A. Graham Cairns-Smith: Chemistry and the Missing Era of Evolution:
We can see that at the time of the common ancestor, this system must already have been fixed in its essentials, probably through a critical interdependence of subsystems. (Roughly speaking in a domain in which everything has come to depend on everything else nothing can be easily changed, and our central biochemistry is very much like that.
https://sci-hub.ren/https://www.ncbi.nlm.nih.gov/pubmed/18260066

Wilhelm Huck, Chemist, professor at Radboud University Nijmegen
A working cell is more than the sum of its parts. "A functioning cell must be entirely correct at once, in all its complexity
https://sixdaysblog.com/2013/07/06/protocells-may-have-formed-in-a-salty-soup/

Bit by Bit: The Darwinian Basis of Life
Gerald F. Joyce  Published: May 8, 2012
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001323
Suppose that a  polymer  (like RNA) that is assembled into four chains of 40 subunits (quaternary heteropolymer) . Then there would be 10^24 possible compositions. To represent all of these compositions at least once, and thus to establish a certainty that this simple ribozyme could have materialized, requires 27 kg of RNA chains, which classifies spontaneous emergence as a highly implausible event.

For an enzyme to be functional, it must fold in a precise three-dimensional pattern. A small chain of 150 amino acids making up an enzyme must be tested within the cell for 10^12 different possible configurations per second, taking 10^26 ( 1,000,000,000,000,000,000,000,000,000) years to find the right one.  This example comprises a very, very, very small degree of the chemical complexity of a human cell.

My comment: The paper claims that quantum effects performed a sequence search to find functional enzymes !! Is that believable?  
https://sci-hub.ren/https://link.springer.com/chapter/10.1007/978-3-319-56372-5_8

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 intelligence produces all the things, as follows:
factory portals  ( membrane proteins ) factory compartments ( organelles ) a library index ( chromosomes, and the gene regulatory network ) molecular computers, hardware ( DNA ) software, a language using signs and codes like the alphabet, an instructional blueprint, ( the genetic and over a dozen epigenetic codes ) information retrieval ( RNA polymerase ) transmission ( messenger RNA ) translation ( Ribosome ) signaling ( hormones ) complex machines ( proteins ) taxis ( dynein, kinesin, transport vesicles ) molecular highways ( tubulins ) tagging programs ( each protein has a tag, which is an amino acid sequence  informing other molecular transport machines were to transport them.) factory assembly lines ( fatty acid synthase ) error check and repair systems  ( exonucleolytic proofreading ) recycling methods ( endocytic recycling ) waste grinders and management  ( Proteasome Garbage Grinders )   power generating plants ( mitochondria ) power turbines ( ATP synthase ) electric circuits ( the metabolic network ) computers ( neurons ) computer networks ( brain ) all with specific purposes.

Chance of unguided random natural events producing just a minimal functional proteome, not considering all other essential things to get a first living self-replicating cell,is:

Let's suppose, we have a fully operational raw material, and the genetic language upon which to store genetic information. Only now, we can ask: Where did the information come from to make the first living organism? Various attempts have been made to lower the minimal information content to produce a fully working operational cell. Often, Mycoplasma is mentioned as a reference to the threshold of the living from the non-living. Mycoplasma genitalium is held as the smallest possible living self-replicating cell. It is, however, a pathogen, an endosymbiont that only lives and survives within the body or cells of another organism ( humans ).  As such, it IMPORTS many nutrients from the host organism. The host provides most of the nutrients such bacteria require, hence the bacteria do not need the genes for producing such compounds themselves. As such, it does not require the same complexity of biosynthesis pathways to manufacturing all nutrients as a free-living bacterium. 

Mycoplasma are not primitive but instead descendants of soil-dwelling proteobacteria, quite possibly the Bacillus, which evolved into parasites. In becoming obligate parasites, the organisms were able to discard almost all biosynthetic capacity by a strategy of gaining biochemical intermediates from the host or from the growth medium in the case of laboratory culture.

The simplest free-living bacteria is Pelagibacter ubique. 13 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.  14 That would be the size of a book with 400 pages, each page with 3000 characters.  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. This probability is hard to imagine but an illustration may help.  

Life on earth: a cosmic origin?
http://bip.cnrs-mrs.fr/bip10/hoyle.htm
Hoyle and Wickramasinghe  examine the probability that an enzyme consisting of 300 residues could be formed by random shuffling of residues, and calculate a value of 10^250, which becomes 10^500.000 if one takes account of the need for 2000 different enzymes in a bacterial cell. Comparing this calculation with the total of 10^79 atoms in the observable universe, they conclude that life must be a cosmological phenomenon.

Imagine covering the whole of the USA with small coins, edge to edge. Now imagine piling other coins on each of these millions of coins. Now imagine continuing to pile coins on each coin until reaching the moon about 400,000 km away! If you were told that within this vast mountain of coins there was one coin different to all the others. The statistical chance of finding that one coin is about 1 in 10^55. 

Furthermore, what good would functional proteins be good for, if not transported to the right site in the Cell, inserted in the right place, and interconnected to start the fabrication of chemical compounds used in the Cell?  It is clear, that life had to start based on fully operating cell factories, able to self replicate, adapt, produce energy, regulate its sophisticated molecular machinery.

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

https://reasonandscience.catsboard.com/t2245-abiogenesis-the-factory-maker-argument

https://www.youtube.com/watch?v=f8oGda1JxKw


It is an interesting question, to elucidate what would be a theoretical minimal Cell, since based on that information, we can figure out what it would take for first life to begin on early earth. That gives us a probability, if someone proposes natural, unguided mechanisms, based on chemical reactions, and atmospheric - and geological circumstances. The fact that we don't know the composition of the atmosphere back then doesn't do harm and is not necessary for our inquiry.

We can take rather than one of the smallest freeliving cells, the one claimed by Science magazine to be a minimal bacterial genome. That would be however not have the metabolic pathways to synthesize the 20 amino acids uses in life. According to a peer-reviewed scientific paper published in Science magazine in 2016: Design and synthesis of a minimal bacterial genome, in their best approximation to a minimal cell, it has a 531000-base pairs genome that encodes 473 gene products, being substantially smaller than M. genitalium (580 kbp), which has the smallest genome of any naturally occurring cell that has been grown in pure culture, having a genome that contains the core set of genes that are required for cellular life. That means, all its genes are essential and irreducible. It encodes for 438 proteins

Regardless of whether the actual minimum is 100,000 or 500,000 nucleotides, this is all beyond a nucleic acid technology struggling with falling apart at 200 nucleotides. The current understanding of information can give many explanations of the difficulties of creating it. It cannot explain where it comes from. 1

Protein-length distributions for the three domains of life
The average protein length of these 110 clusters of orthologous genes COGs is 359 amino acids for the prokaryotes and 459 for eukaryotes.
https://pdfs.semanticscholar.org/5650/aaa06de4de11c36a940cf29c07f5f731f63c.pdf

Proteins are the result of the instructions stored in DNA, which specifies the complex sequence necessary to produce functional 3D folds of proteins. Both, improbability and specification are required in order to justify an inference of design.
1. According to the latest estimation of a minimal protein set for the first living organism, the requirement would be about 438 proteins, this would be the absolute minimum to keep the basic functions of a cell alive.  
2. According to the Protein-length distributions for the three domains of life, there is an average between prokaryotic and eukaryotic cells of about 400 amino acids per protein. 8
3. Each of the 400 positions in the amino acid polypeptide chains could be occupied by any one of the 20 amino acids used in cells, so if we suppose that proteins emerged randomly on prebiotic earth, then the total possible arrangements or odds to get one which would fold into a functional 3D protein would be 1 to 20^400 or 1 to 10^520. A truly enormous, super astronomical number. 
4. Since we need 1300 proteins total to make a first living cell, we would have to repeat the shuffle 520 times, to get all proteins required for life. The probability would be therefore 438/10^520.  We arrive at a probability of about 1 in 10^350.000 

Exemplification
Several famous physicists, including, Stephen Hawking worked out that the relationship between all the fundamentals of our universe is so finely tuned that even if we slightly changed the 55 th decimal point then our universe could not exist. Put another way, several leading scientists have calculated that the statistical probability against this fine-tuning being by chance is in the order of 1 in 10^55.

This probability is hard to imagine but an illustration may help. Imagine covering the whole of the USA with small coins, edge to edge. Now imagine piling other coins on each of these millions of coins. Now imagine continuing to pile coins on each coin until reaching the moon about 400,000 km away! If you were told that within this vast mountain of coins there was one coin different to all the others. The statistical chance of finding that one coin is about 1 in 10^55 . In other words, the evidence that our universe is designed is overwhelming!

How to make the calculations:
https://web.archive.org/web/20170423032439/http://creationsafaris.com/epoi_c06.htm#ec06f12x

Granted, the calculation does not take into consideration nor give information on the probabilistic resources available. But the sheer gigantic number os possibilities throw any reasonable possibility out of the window. 

If we sum up the total number of amino acids for a minimal Cell, there would have to be about 1300 proteins x average 400 amino acids  =  520.000 amino acids, which would have to be bonded in the right sequence, choosing for each position amongst 20 different amino acids, and selecting only the left-handed, while sorting out the right-handed ones. That means each position would have to be selected correctly from 40 variants !! that is 1 right selection out of 40^520.000 possibilities or 10^700.000 !! Obviously, a gigantic number far above any realistic probability to occur by unguided events. Even a trillion universes, each hosting a trillion planets, and each shuffling a trillion times in a trillionth of a second, continuously for a trillion years, would not be enough. Such astronomically unimaginably gigantic odds are in the realm of the utmost extremely impossible.  

https://reasonandscience.catsboard.com/t2508-abiogenesis-calculations-of-a-primordial-ancestor-with-a-minimal-proteome-emerging-through-unguided-natural-random-events

Helicase
Helicases are astonishing motor proteins which rotational speed is up to 10,000 rotations per minute, and are life essential.

How Many Genes Can Make a Cell: The Minimal-Gene-Set Concept
https://www.ncbi.nlm.nih.gov/books/NBK2227/

We propose a minimal gene set composed of 206 genes. Such a gene set will be able to sustain the main vital functions of a hypothetical simplest bacterial cell with the following features.

(i) A virtually complete DNA replication machinery, composed of one nucleoid DNA binding protein, SSB, DNA helicase, primase, gyrase, polymerase III, and ligase. No initiation and recruiting proteins seem to be essential, and the DNA gyrase is the only topoisomerase included, which should perform both replication and chromosome segregation functions.

Helicase are a class of enzymes vital to all living organisms. Their main function is to unpackage an organism's genes, and they are essential for dna replication, and evolution to be able to occur. They require 1000 left-handed amino acids in the right specified sequence. Each of the 1000 amino acids must be the right amongst 20 to chose from.  How did they emerge by natural processes? The chance to get them by random chemical reactions is 1 to 20^1000..... there are 10^80 atoms in the universe.

The odds are in reality much greater. There exist hundreds of different amino acids, which supposedly were extant on the early earth. Amongst these, an unknown selection process would have had to select the 20 amino acids used in life, select only left-handed ones from a mix of left and right handed ones. 

But the problems do not stop there. 

Cairns-Smith, the Genetic Takeover, page 59:
For one overall reaction, making one peptide bond, there about 90 distinct operations are required. If you were to consider in more detail a process such as the purification of an intermediate you would find many subsidiary operations — washings, pH changes and so on.

1. The synthesis of proteins and nucleic acids from small molecule precursors, and the formation of amide bonds without the assistance of enzymes represents one of the most difficult challenges to the model of pre-vital ( chemical) evolution, and for theories of the orgin of life.
2. 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.
3. 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.
4. 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.
5. 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.


Abiogenesis: Uncertainty quantification of a primordial ancestor with a minimal proteome emerging through unguided, natural, random events YK23Ods
9

Like the Holy Grail, a universal DNA ‘minimal genome’ has remained elusive despite efforts to define it. 10 Gene essentiality has to be defined within the specific context of the bacterium, growth conditions, and possible environmental fluctuations. Gene persistence can be used as an alternative because it provides a more general framework for defining the requirements for long-term survival via identification of universal functions. These functions are contained in the paleome, which provides the core of the cell chassis. The paleome is composed of about 500 persistent genes. 

We can take an even smaller organism, which is regarded as one of the smallest possible, and the situation does not change significantly:
The simplest known free-living organism, Mycoplasma genitalium, has the smallest genome of any free-living organism, has a genome of 580,000 base pairs. This is an astonishingly large number for such a ‘simple’ organism. It has 470 genes that code for 470 proteins that average 347 amino acids in length. The odds against just one specified protein of that length are 1:10^451. If we calculate the entire proteome, then the odds are 470 x 347 = 163090 amino acids, that is odds of 20^164090 , if we disconsider that nature had to select only left-handed amino acids, and bifunctional ones.

Common objections to the argument from Improbability

Objection: Arguments from probability are drivel. So far the likelihood that life would form the way it did is 1. 
Response: 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

=============================================================================================================================================

Objection: The physical laws, the laws of biochemistry, those aren't chance. The interaction of proteins, molecules, and atoms, their interaction is dictated by the laws of the universe.
Response: While it is true, that the chemical bonds that glue one amino acid to the other are subdued to chemical properties, there are neither bonds nor bonding affinities—differing in strength or otherwise—that can explain the origin of the specificity of the sequence of the 20 types of amino acids, that have to be put together in the right order and sequence, in order for a protein to bear function.  What dictates in modern cells the sequence of amino acids in proteins is the DNA code.

DNA contains true codified instructional information, or a blueprint.  Being instructional information means that the codified nucleotide sequence that forms the instructions is free and unconstrained; any of the four bases can be placed in any of the positions in the sequence of bases. Their sequence is not determined by the chemical bonding. There are hydrogen bonds between the base pairs and each base is bonded to the sugar-phosphate backbone, but there are no bonds along the longitudional axis of DNA. The bases occur in the complementary base pairs A-T and G-C, but along the sequence on one side the bases can occur in any order, like the letters of a language used to compose words and sentences. Since nucleotides can be arranged freely into any informational sequence, physical necessity could not be a driving mechanism.

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Objection: Logical Fallacy. Argument from Improbability. Just because a thing is highly unlikely to occur doesn't mean that its occurrence is impossible. No matter how low the odds, if there is a chance that it will happen, it will happen given enough tries, especially considering a large enough universe with countless potentially "living" planets. Nobody claims that winning the lottery doesn't happen just because the chance of a specific individual winning it is low.
Response: So you're saying there's a chance... Murphy's Law states given enough time and opportunity, anything THAT CAN HAPPEN will happen. That phrase "can happen" is very important. The natural, non thinking, random, void of purpose and reason cosmos is unable to produce what we see without information. Life without information is not only improbable but rather impossible from what we know about the nature of complexity, design, and purpose. Given a planet full of simpler non-self-replicating organic molecules, abundant but not excessive input of energy from the local star, and a few thousand million years one could imagine that the number of "tries" to assemble that one self-replicating organic molecule would easily exceed 5x10^30. You can't just vaguely appeal to vast and unending amounts of time (and other probabilistic resources) and assume that self-assembly, spontaneously by orderly aggregation and sequentially correct manner without external direction, given enough trials is possible, that it can produce anything "no matter how complex."  Rather, it has to be demonstrated that sufficient probabilistic resources or random, non-guided mechanisms indeed exist to produce the feature. Fact is, we know upon repeated experience and demonstration that intelligence can and does envision, project and elaborate complex blueprints, and upon its instructions, intelligence produces the objects in question. It has NEVER been demonstrated that unguided events without specific purposes can do the same. In such examples it is also not taken in consideration, that such shuffle requires energy applied in specific form, and the environmental conditions must permit the basic molecules not to be burned by UV radiation. The naturalistic proposal is more a matter of assaulting the intelligence of those who oppose it with a range assertions that proponents of naturalism really have no answer, how these mechanisms really work. To argue that forever is long enough for the complexity of life to reveal itself is an untenable argument. The numbers are off any scale we can relate to as possible to explain what we see of life. Notwithstanding, you have beings in here who go as far to say it's all accounted for already, as if they know something nobody else does. Fact is, science is struggling for decades to unravel the mystery of how life could have emerged, and has no solution in sight. 

Eugene Koonin, advisory editorial board of Trends in Genetics, writes in his book: The Logic of Chance: 
" The Nature and Origin of Biological Evolution, Eugene V. Koonin, page 351:
The origin of life is the most difficult problem that faces evolutionary biology and, arguably, biology in general. Indeed, the problem is so hard and the current state of 
the art seems so frustrating that some researchers prefer to dismiss the entire issue as being outside the scientific domain altogether, on the grounds that unique
events are not conducive to scientific study.


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Objection: What is entirely missing from such arguments as above is the demonstration that a specific modern "alive" configuration is the only possible one. Calculating probabilities starting with the end result commits the classic fallacy of painting the target after the arrow has been shot, pretending that a goal has been specified in advance; any event becomes arbitrarily improbable if specified with sufficient accuracy.
Response: We have taken as our premise what science has demonstrated to be the minimal requirement to start life. And therefore, the objection fails. 

Above calculation does not take into consideration that there are about 500 naturally occurring amino acids known. So let us suppose that they were extant on the prebiotic earth, and somehow, a selective process did chose and select, and concentrate just the 20 used in life. These 20 could still come in two versions, left-handed, and right-handed. Life uses only left-handed amino acids, so they would also have to be sorted out. Now let us suppose, that by freaky accident and crazy shuffling trillions of trillions of time, suddenly, the right protein set would be there, the right proteins, the right assortment. It is claimed, that there was no oxygen in the prebiotic earth. If that was so, 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 have 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.
 
Peptide bonding of amino acids to form proteins and its origins
https://reasonandscience.catsboard.com/t2130-peptide-bonding-of-amino-acids-to-form-proteins-and-its-origins

Most of the cell’s important functions are carried out by compounds called proteins which are a chain of amino acids linked together. There are 20 amino acids which can be arranged in any combination and the average protein consists of over 400 amino acids linked together. The protein’s characteristics and function is determined by the number and particular arrangement of amino acids. A protein can be represented by a sentence which derives its meaning from the particular arrangement of letters or amino acids. 4  According to evolutionary theories, amino acids were synthesized spontaneously and then linked together to form the first protein from a generic amino acid “soup.” In experiments attempting to synthesize amino acids, the products have been a mixture of right-handed and left-handed amino acids. (Amino acids, as well as other organic compounds, can exist in two forms which have the same chemical composition but are three-dimensional mirror images of each other; thus termed right and left-handed amino acids.) Every protein in a living cell is composed entirely of left-handed amino acids, even though the right-handed isomer can react in the same way. Thus, if both right and left-handed amino acids are synthesized in this primitive organic soup, we are faced with the question of how life has used only the left-handed amino acids for proteins.

We can represent this dilemma by picturing a huge container filled with millions of white (left-handed amino acids) and black (right-handed amino acids) jelly beans. What would be the probability of a blind-folded person randomly picking out 410 white jelly beans (representing the average sized protein) and no black jelly beans? The odds that the first 410 jelly beans would be all one color are one in 2^410 or 109^123. To put the odds in perspective, there are only about 10^18 seconds in 4.5 billion years, the approximate claimed age of the earth, and it has been estimated that there are only 10^80 particles in the universe.

Yet the probability of choosing all left-handed amino acids, without even considering their particular order or specific arrangement, is much larger than that!

So let us suppose that there are about 500 different amino acids on the prebiotic earth, and somehow, a selective process did chose and select, and concentrate just the 20 used in life. And sorted out all right-handed amino acids, 
so only left-handed would have remained. 

About 500 naturally occurring amino acids are known (though only 20 appear in the genetic code) and can be classified in many ways
https://en.wikipedia.org/wiki/Amino_acid

We had a theoretical average size of 400 amino acids per protein,  Since each of the 400 positions in the chain could be occupied by any one of the 20 amino acids, the total possible arrangements is 20^400, a truly enormous, super astronomical number. Applying the formula below, the odds for one protein with 400 amino acids to emerge randomly are 1 to 10^520.

Abiogenesis: Uncertainty quantification of a primordial ancestor with a minimal proteome emerging through unguided, natural, random events Z3uo2dj

Abiogenesis: Uncertainty quantification of a primordial ancestor with a minimal proteome emerging through unguided, natural, random events ClbAktZ
7

Abiogenesis: Uncertainty quantification of a primordial ancestor with a minimal proteome emerging through unguided, natural, random events CQAsIBY

Considering the first one as already obtained, we need 559 more. The probability is therefore 559/10520.  The third one could be any of the 558 still needed, so its probability would be 558 /10520.  Calculating all of these, and allowing for one substitution per chain, we arrive at a probability far beyond  of 1 in 10^100.000

To link two amino acids together requires the removal of a water molecule and the supply of some 150 times more energy than heat in the Earth's oceans could supply. In the absence of a joining enzyme used by biology or without an excessively large flux of ultraviolet light at the ocean surface, no new arrangements could be achieved. But even if chemical barriers for the linkages are artificially and miraculously removed, the really vast improbability of 1 in 10 ^40,000 poses a serious dilemma for the whole of evolutionary science. 6

For a protein made from scratch in a prebiotic soup, the odds of finding such globally optimal solutions are infinitesimally small- somewhere between 1 in 10^140 and 1 in 10^164 for a 150 amino acid long sequence if we factor in the probabilities of forming peptide bonds and of incorporating only left handed amino acids. 5

Proteins families are grouped into Clusters of Orthologous Groups, or COGs, which typically serve the same function. This Clusters of Orthologous Groups 561-COG set gives a low-end estimate for the LUCA proteome.
Prebiotic Evolution and Astrobiology 2009 Landes Bioscience Austin Texas

A minimal estimate for the gene content of the last universal common ancestor—exobiology from a terrestrial perspective
A truly minimal estimate of the gene content of the last universal common ancestor, obtained by three different tree construction methods and the inclusion or not
of eukaryotes (in total, there are 669 ortholog families distributed in 561 functional annotation descriptions, including 52 which remain uncharacterized)
http://sci-hub.ren/https://www.ncbi.nlm.nih.gov/pubmed/16431085/

The proteomic complexity and rise of the primordial ancestor of diversified life
A more recent study of 184 genomes identified 669 orthologous protein families, which cover 561 detailed functional classes that are involved in almost all essential biological processes of extant life, including translation, transcription and its regulation, DNA replication, recombination, and repair, transport and membrane-associated functions, electron transfer, and metabolism
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3123224/

Protein-length distributions for the three domains of life
The average protein length of these 110 clusters of orthologous genes COGs is 359 amino acids for the prokaryotes and 459 for eukaryotes.
https://pdfs.semanticscholar.org/5650/aaa06de4de11c36a940cf29c07f5f731f63c.pdf

So let us suppose and make a theoretical assumption that the threshold to have a first living cell is 560 proteins with an average length of 400 amino acids.

The length of the average protein in the smallest known living thing is at least 400 amino acid links, containing more than 7,000 atoms.
https://web.archive.org/web/20170423032439/http://creationsafaris.com/epoi_c06.htm

Lies, Damned Lies, Statistics, and Probability of Abiogenesis Calculations
http://www.talkorigins.org/faqs/abioprob/abioprob.html
Claim: Firstly, the formation of biological polymers from monomers is a function of the laws of chemistry and biochemistry, and these are decidedly not random.
Response: The amino acid sequence of a polypeptide, together with the laws of chemistry and physics, cause a polypeptide to fold into a more compact structure, but the sequence that permits proteins to fold to a stable fold is not determined by the laws of chemistry, but the complex, specified, code in DNA, which is a functional Cell dictates the amino acids which will be synthesized in the Ribosome. The instruction for the 3-D structure of a protein is embedded in the sequences of amino acids and the electrochemical attractive forces among them, and these are determined by the genetic Code. Most proteins include all of the usual twenty kinds of amino acids.  Each protein has a specific exact sequence of these units.

Wiki: The genetic code is the set of rules used by living cells to translate information encoded within genetic material (DNA or mRNA sequences) into proteins. Translation is accomplished by the ribosome, which links amino acids in an order specified by messenger RNA (mRNA)

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Objection: The entire premise is incorrect to start off with, because in modern abiogenesis theories the first "living things" would be much simpler, not even a protobacteria, or a preprotobacteria (what Oparin called a protobiont and Woese calls a progenote), but one or more simple molecules probably not more than 30-40 subunits long.
Response: In his book: The Fifth Miracle: The Search for the Origin and Meaning of Life, Paul Davies describes life with the following characteristics of life:
Reproduction. Metabolism.  Homeostasis Nutrition. Complexity. Organization.  Growth and development. Information content.  Hardware/software entanglement.  Permanence and change.

The paper: The proteomic complexity and rise of the primordial ancestor of diversified life describes :
The last universal common ancestor as the primordial cellular organism from which diversified life was derived. This urancestor accumulated genetic information before the rise of organismal lineages and is considered to be a complex 'cenancestor' with almost all essential biological processes.
http://europepmc.org/articles/pmc3123224

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

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Objection: Another view is the first self-replicators were groups of catalysts, either protein enzymes or RNA ribozymes, that regenerated themselves as a catalytic cycle. It's not unlikely that a small catalytic complex could be formed. Each step is associated with a small increase in organisation and complexity, and the chemicals slowly climb towards organism-hood, rather than making one big leap
Response:   The Logic of Chance: The Nature and Origin of Biological Evolution By Eugene V. Koonin
Hence, the dramatic paradox of the origin of life is that, to attain the minimum complexity required for a biological system to start on the Darwin-Eigen spiral, a system of a far greater complexity appears to be required. How such a system could evolve is a  puzzle that defeats conventional evolutionary thinking, all of which is about biological systems moving along the spiral; the solution is bound to be unusual. 

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Objection: As to the claim that the sequences of proteins cannot be changed, again this is nonsense. There are in most proteins regions where almost any amino acid can be substituted, and other regions where conservative substitutions (where charged amino acids can be swapped with other charged amino acids, neutral for other neutral amino acids and hydrophobic amino acids for other hydrophobic amino acids) can be made.
Response: A protein requires a threshold of minimal size to fold and become functional within its milieu where it will operate. That threshold is average 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 a 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

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Objection: We were examining sequential trials as if there was only one protein/DNA/proto-replicator being assembled per trial. In fact there would be 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.
Response: It is claimed, that there was no oxygen in the prebiotic earth. If that was so, 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 early earth.


[url=https://servimg.com/view/20268040/224][img:f053]https://i.servimg.com



Last edited by Otangelo on Tue Mar 16, 2021 8:12 am; edited 117 times in total

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Leading scientists have calculated that the statistical probability of the fine-tuning of the universe, and life emerging by random unguided events, is far beyond the limit of Borel's law, which is in the order of 1 in 10^50.

This probability is hard to imagine but an illustration may help. Imagine covering the whole of the USA with small coins, edge to edge. Now imagine piling other coins on each of these millions of coins. Now imagine continuing to pile coins on each coin until reaching the moon about 400,000 km away! If you were told that within this vast mountain of coins there was one coin different to all the others. The statistical chance of finding that one coin is about 1 in 10^50. In other words, the evidence that our universe is designed is overwhelming!

A statistical impossibility is a probability that is so low as to not be worthy of mentioning. Sometimes it is quoted as 10^50 although the cutoff is inherently arbitrary. Although not truly impossible the probability is low enough so as to not bear mention in a rational, reasonable argument.  If the probability of an event is an infinitesimally small, then, for all practical purposes, the probability is equal to zero.
https://www.conservapedia.com/Statistical_impossibility

The Criterion : The "Cosmic Limit" Law of Chance

To arrive at a statistical "proof," we need a reasonable criterion to judge it by :
As just a starting point, consider that many statisticians consider that any occurrence with a chance of happening that is less than one chance out of 10^50, is an occurrence with such a slim a probability that is, in general, statistically considered to be zero. (10^50 is the number 1 with 50 zeros after it, and it is spoken: "10 to the 50th power"). This appraisal seems fairly reasonable, when you consider that 10^50 is about the number of atoms which make up the planet earth. --So, overcoming one chance out of 10^50 is like marking one specific atom out of the earth, and mixing it in completely, and then someone makes one blind, random selection, which turns out to be that specific marked atom. Most mathematicians and scientists have accepted this statistical standard for many purposes.

LES PROBABILITIES DINOMBRABLES ET LEURS APPLICATIONS ARITHMtTIOUES.
Par M. EmiIe BoreI (Paris) 8 novembre 1908
http://sci-hub.tw/https://link.springer.com/article/10.1007/BF03019651

Strong law of large numbers
https://www.encyclopediaofmath.org/index.php/Strong_law_of_large_numbers

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Proteins are structures of complex semantophoretic macromolecules that carry genetic information.

How Did Protein Synthesis Evolve?
The molecular processes underlying protein synthesis in present-day cells seem inextricably complex. Although we understand most of them, they do not make conceptual sense in the way that DNA transcription, DNA repair, and DNA replication do. It is especially difficult to imagine how protein synthesis evolved because it is now performed by a complex interlocking system of protein and RNA molecules; obviously the proteins could not have existed until an early version of the translation apparatus was already in place. As attractive as the RNA world idea is for envisioning early life, it does not explain how the modern-day system of protein synthesis arose.
Molecular biology of the cell, 6th ed. pg. 365

The corresponding DNA sequences dictate the amino acid sequences.  Specific functionality of a given protein is defined by a unique spatial positioning of its amino acid side chains and prosthetic groups, suggesting that such a specific spatial arrangement of functional groups in biologically active proteins is defined by their unique 3D structures predetermined by the unique amino acid sequences encoded in unique genes.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7014577/

Estimating the prevalence of protein sequences adopting functional enzyme folds.
Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10(77), adding to the body of evidence that functional folds require highly extraordinary sequences.
https://www.ncbi.nlm.nih.gov/pubmed/15321723?fbclid=IwAR2WqQIOoD3Opw1tmhd6Z5K76yAcJ-w_DbwlWnPml5jVxM34YxC9l7N3PHw
.
Abiogenesis: Uncertainty quantification of a primordial ancestor with a minimal proteome emerging through unguided, natural, random events Ribonu10

Calculations of life beginning through unguided, natural, random events

https://reasonandscience.catsboard.com/t2508-calculations-of-life-beginning-through-unguided-natural-random-events

Proteins are the result of the DNA blueprint, which specifies the complex sequence necessary to produce functional 3D folds of proteins. Both, improbability and specification are required in order to justify an inference of design.
1. According to the latest estimation of a minimal protein set for the first living organism, the requirement would be about 560 proteins, this would be the absolute minimum to keep the basic functions of a cell alive. 
2. According to the Protein-length distributions for the three domains of life, there is an average between prokaryotic and eukaryotic cells of about 400 amino acids per protein. 8
3. Each of the 400 positions in the amino acid polypeptide chains could be occupied by any one of the 20 amino acids used in cells, so if we suppose that proteins emerged randomly on prebiotic earth, then the total possible arrangements or odds to get one which would fold into a functional 3D protein would be 1 to 20^400 or 1 to 10^520. A truly enormous, super astronomical number.
4. Since we need 560 proteins total to make a first living cell, we would have to repeat the shuffle 560 times, to get all proteins required for life. The probability would be therefore 560/10520.  We arrive at a probability far beyond  of 1 in 10^100.000  ( A proteome set with 239 proteins yields odds of approximately 1/10^119614 ) 7
Granted, the calculation does not take into consideration nor give information on the probabilistic resources available. But the sheer gigantic number os possibilities throw any reasonable possibility out of the window.   

Helicases are astonishing motor proteins which rotational speed is up to 10,000 rotations per minute, and are life essential. They require 1000 left-handed amino acids in the right specified sequence. Each of the 1000 amino acids must be the right amongst 20 to chose from. How did they emerge by natural processes? Chance to get them by random chemical reactions is 1 to 20^1000..... there are 10^80 atoms in the universe.

Above calculation does not take into consideration that there are about 500 naturally occurring amino acids known. So let us suppose that they were extant on the prebiotic earth, and somehow, a selective process did chose and select, and concentrate just the 20 used in life. These 20 could still come in two versions, left-handed, and right-handed. Life uses only left-handed amino acids, so they would also have to be sorted out. Now let us suppose, that by freaky accident and crazy shuffling trillions of trillions of time, suddenly, the right protein set would be there, the right proteins, the right assortment. It is claimed, that there was no oxygen in the prebiotic earth. If that was so, 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.

As of 2014, Koonin serves on the advisory editorial board of Trends in Genetics and is co-Editor-in-Chief of the open access journal Biology Direct. He served on the editorial board of Bioinformatics from 1999-2001. Koonin is also an advisory board member in bioinformatics at Faculty of 1000.

Let us see what he writes in regard of the origin of life:

The Logic of Chance: The Nature and Origin of Biological Evolution, Eugene V. Koonin, page 351:
The origin of life is the most difficult problem that faces evolutionary biology and, arguably, biology in general. Indeed, the problem is so hard and the current state of the art seems so frustrating that some researchers prefer to dismiss the entire issue as being outside the scientific domain altogether, on the grounds that unique events are not conducive to scientific study.

A succession of exceedingly unlikely steps is essential for the origin of life, from the synthesis and accumulation of nucleotides to the origin of translation; through the multiplication of probabilities, these make the final outcome seem almost like a miracle. The difficulties remain formidable. For all the effort, we do not currently have coherent and plausible models for the path from simple organic molecules to the first life forms. Most damningly, the powerful mechanisms of biological evolution were not available for all the stages preceding the emergence of replicator systems. Given all these major difficulties, it appears prudent to seriously consider radical alternatives for the origin of life

The Logic of Chance: The Nature and Origin of Biological Evolution, Eugene V. Koonin page 435:
The requirements for the emergence of a primitive, coupled replication-translation system, which is considered a candidate for the breakthrough stage in this paper, are much greater. At a minimum, spontaneous formation of the following is required:
• Two rRNAs, with a total size of at least 1,000 nucleotides.
• Approximately 10 primitive adaptors of about 30 nucleotides
each, for a total of approximately 300 nucleotides.
• At least one RNA encoding a replicase, about 500 nucleotides (low bound) required. Under the notation used here, n = 1,800, resulting in E <10^1018.
In other words, even in this toy model that assumes a deliberately inflated rate of RNA production, the probability that a coupled translation replication emerges by chance in a single O-region is P < 10^1018. Obviously, this version of the breakthrough stage can be considered only in the context of a universe with an infinite (or, at the very least, extremely vast) number of O-regions ( observable regions ).
The model considered here is not supposed to be realistic, by any account. It only illustrates the difference in the demands on chance for the origin of different versions of the breakthrough system and, hence, the connections between this version and different cosmological models of the universe.

All things considered, my assessment of the current state of the art in the study of the origins of replication and translation is rather somber. Notwithstanding relevant theoretical models and suggestive experimental results, we currently do not have a credible solution to these problems and do not even see with any clarity a path to such a solution. Any even remotely realistic origin of life scenario must incorporate well-defined pre-cellular, abiogenic compartmentalization; inorganic catalysts to catalyze “pre-biochemical” reactions prior to the emergence of bona fide enzymes; thermal and/or electrochemical potential gradients required for the generation of energy in accessible forms; a solution to the extremely difficult problem of the origin of genetic information (see the discussion earlier in this chapter). In general, the early concepts underestimated the dimensions of the origin of life problem and failed to investigate special abiogenic conditions that must have been a prerequisite for the jump-start of biological evolution. Subsequently, several groups of researchers attempted to get away from the concept of the homogeneous primary soup, replacing it with some form of inorganic compartments, and sought to address all the origin of life problems in conjunction by combination of modeling, experiment, and observation in nature. The common idea of these hypotheses is the existence of a single framework that could simultaneously provide compartmentalization, energy gradients, and catalysts.

A 'review' of The Logic of Chance by Gert Korthof
https://web.archive.org/web/20180820034559/http://wasdarwinwrong.com/korthof98.htm

The probability of the spontaneous origin of this is: P < 10-10^18. The spontaneous origin of 1,800 nucleotides is the Koonin-threshold for the origin of life and evolution. No Origin of Life (OOL) researcher put it more clearly and dramatically than Koonin. Please note 1,800 nucleotides is a minimum. Every OOL researcher that skips over the Koonin threshold makes a serious scientific oversight.

At most ribozymes could spontaneously originate, but not a coupled replication-translation system (the DNA-protein world). So, if ribozymes are the beginnings of the RNA-world, Koonin claims that the RNA-world would come to a halt before a replication-translation system emerged. In our universe, certainly on our earth, the RNA-world would be a dead end.

Abiogenesis: Uncertainty quantification of a primordial ancestor with a minimal proteome emerging through unguided, natural, random events Quote-12

The estimated number of elementary particles in the universe is 10^80. The most rapid events occur at an amazing 10^45 per second. Thirty billion years contains only 10^18 seconds. By totaling those, we find that the maximum elementary particle events in 30 billion years could only be 10^143.

The simplest known free-living organism, Mycoplasma genitalium,
has the smallest genome of any free-living organism, has a genome of 580,000 base pairs. This is an astonishingly large number for such a ‘simple’ organism.It has 470 genes that code for 470 proteins that average 347 amino acids in length. The odds against just one specified protein of that length are 1:10^451.

According to Borel's law, any occurrence with a chance of happening that is less than one chance out of 10^50, is an occurrence with such a slim a probability that is, in general, statistically considered to be zero. (10^50 is the number 1 with 50 zeros after it, and it is spoken: "10 to the 50th power")


Estimating the probability of just a single 150-amino acid functional protein coming into existence by random chance at 10E164.
To show how utterly improbable this is, he gave the example: If every elementary particle in the universe (10E80) interact with each other 10E43 times per second and each interaction produced a 150-amino acid combination every second since the big bang (10E17), the total maximum number of combinations that could have been generated by now is 10E140. 

Someone did an estimate that helped put these numbers in perspective: To demonstrate how far 10E140 combinations are from all 10E164 total combinations, consider that if 10E164 was represented by the distance from Earth to the star Sirius A (8.6 LY away), and the 10E140 maximum possible combinations generated since the big bang represented the distance we've traveled toward Sirius A so far, then we have traveled about the width of a single hydrogen atom. 

Achieving a 50/50 probability of generating a single functional protein by sampling half of all combinations would occur at the halfway point (4.3 LY away). But with the maximum 10^140 combinations that could possibly have been generated by now, we've still traveled less than the width of a single hydrogen atom, And all this is for the probability of SINGLE functional protein coming into existence by random chance. The simplest living cell needs somewhere around 250 minimum unique proteins.


Objection: every sequence is just as improbable as another.
Answer: It's true that any particular equal-length sequence is just as improbable as any other. But if the goal is to have a sequence, a particular string starting at 1, then 2,3,4,5,6 ............ 500, then intuitively you know there sequence has a specific order. The relevant point to be outlined here is: The sequence 1,2,3,4 ..........  500, exhibits a specification or particular pattern. What must be explained, is the origin not of any kind of sequence, but a particular, specific sequence.
Suppose you see a blueprint to make a car engine with 100 horse powers to drive a BMW 5X. Not any blueprint will produce this particular car engine with the right size and fit and power. Only a blueprint with the precise, specific, complex arrangement of orders that is understood by the common pre-established agreement between the engineer, and the manufacturer, will permit to be encoded, transmitted, decoded and transformed in an equivalent artifact that has the specific, recognizable function which meets the pre-established goal. The information for that particular car engine can be encoded in Bits. Lets suppose its the size of a CD, 600mb. What has to be calculated, are the odds to get that specific sequence of instructions, which permit to give rise to that particular car engine. Not any sequence will do.
We know by experience, that intelligence is able to produce factories, engines, machines, codes, computers, software, hardware etc. The odds are 1, since it happens and are a proven, it's a fact.Now you take a random character generator. The odds to have a specific string of 470 characters, equivalent of a medium-sized protein of that length are 1:10^451. So there would have to be this number of trials and errors to get the right sequence. 

Answering the Lottery fallacy fallacy
The fine tuning argument is not driven by the improbability of just any universe coming into existence, like the probability of someone winning the lottery, which might be high. Instead the argument is driven by the specified probability of a life-permitting universe coming into existence. A useful illustration that’s sometimes used is that of a gigantic swimming pool, filled with hundreds of billions of white marbles (representing life-prohibiting universes or failed universes), but containing only one black marble (representing a successful and life permitting universe). While it is true that the probability of pulling out any particular marble is the same as that of pulling out any other particular marble and provided we are going to pull out a marble, then the probability of pulling out a marble is 1 (i.e. it is certain that it will happen), it is also true that the probability of pulling out a black marble is mind bogglingly lower than the probability of pulling out a white marble.
http://rightreason.org/2010/the-lottery-fallacy-fallacy/

Enzymes: The Cell's Miniature Factories 1
The importance of the three-dimensional structure of proteins can best be illustrated by the function of enzymes. Virtually all of the complex chemical reactions in living cells involve special proteins called enzymes. Enzymes act to speed up (catalyze) chemical reactions in biological systems. Enzymes are employed in the production of DNA, RNA, proteins, and nearly every chemical reaction in the cell. Digestion, thought, sight, and the function of nerve and muscles all require the use of enzymes. In fact, these activities would be impossible without them.
Enzymatic reactions occur like "lock and key" mechanisms. An enzyme (the lock) has a highly specific three-dimensional shape which will only allow chemicals with the correct three-dimensional fit (the key) to bind and result in a chemical reaction.

Since all spark and soup experiments produce a 50/50 mix of right and left-handed amino acids, chemists have tried to decipher how only left-handed amino acids became integrated into the proteins of living systems. For decades chemists have attempted to separate out a pure mixture of left-handed amino acids from a racemic mix by chance chemistry alone. Chance or un-directed chemistry has, however, consistently proven to be an inadequate mechanism for the separation of the right and left-handed amino acid forms.31 So, how did it happen? Mathematically, random-chance would never select such an unlikely pure molecule out of a racemic primordial soup.
The solution is simple, yet it has profound implications. To separate the two amino acid forms requires the introduction of biochemical expertise or know-how, which is the very antithesis of chance! However, biochemical expertise or know-how comes only from a mind. Without such know-how or intelligent guidance, the right and left-handed building blocks of life will never separate. Consequently, enzymes, with their lock and key mechanisms, and ultimately, life, are impossible!32
However, the existence of a mind or a Creator involved in the creation of life is anathema to the atheist's scenario. But the volume of biochemical knowledge supports this fact: To produce pure mixtures of left-handed amino acids and right-handed nucleotides, requires intelligent guidance. And since no human chemists were around before the origin of life on earth, the source of this intelligent guidance must have been extraterrestrial!

Objection:
How many observable universes do we have? One. Does that universe host stars and life? Yes. One shouldn't be surprised to find these precisely sequenced proteins because if they would not exist, we wouldn't exist. Therefore, the fact that they exist means it should only be expected by the mere fact of our own existence - not at all surprising. That means that the current probability that our universe hosts stars and life is 100%.
Answer: this argument is like a situation where a man is standing before a firing squad of one thousand 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 highly unlikely  instructional complex coded information stored in the Genome and irreducible complex cell structures, given the hypothesis of a mindless origin, is only to be expected - in the extreme.

Biological molecular machines and factories ( Cells ) are full of information-rich, language-based codes and code/blueprint-based structures.  Instructional/specified complex information is required to get the right amino acid sequence which is essential to get functionality in a vast sequence space ( amongst trillions os possible sequences, rare are the ones that provide function ), and every protein is irreducibly complex in the sense, that a minimal number of amino acids are required for each protein to get function. One  objection is given in response to this argument is that

Joseph Mastropaolo, Ph.D.
According to the most generous mathematical criteria, abiogenesis and monogenesis are impossible to unimaginable extremes.

Abiogenic Origin of Life: A Theory in Crisis, 2005 Arthur V. Chadwick, Ph.D. Professor of Geology and Biology
To give you an idea of how incomprehensible, I use the following illustration. An ameba starts out at one side of the universe and begins walking towards the other side, say, 100 trillion light years away. He travels at the rate of one meter per billion years. He carries one atom with him. When he reaches the other side, he puts the atom down and starts back. In 10^186 years, the ameba will have transported the entire mass of the universe from one side to the other and back a trillion trillion trillion trillion trillion trillion times. That is my definition of impossible. And what resulted from success, if it did occur would not be a living cell or even a promising combination. Spontaneous origin of life on a prebiological earth is IMPOSSIBLE!


To arrive at a statistical "proof," we need a reasonable criterion to judge it by:
As just a starting point, consider that many statisticians consider that any occurrence with a chance of happening that is less than one chance out of 10^50, is an occurrence with such a slim a probability that is, in general, statistically considered to be zero. (10^50 is the number 1 with 50 zeros after it, and it is spoken: "10 to the 50th power"). This appraisal seems fairly reasonable when you consider that 10^50 is about the number of atoms which make up the planet earth. --So, overcoming one chance out of 10^50 is like marking one specific atom out of the earth, and mixing it in completely, and then someone makes one blind, random selection, which turns out to be that specific marked atom. Most mathematicians and scientists have accepted this statistical standard for many purposes.     The Criterion: The "Cosmic Limit" Law of Chance 3

A calculation of the probability of spontaneous biogenesis by information theory
Hubert P. Yockey
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 109 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 over estimate the number of sequences by a factor of 105. 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 109 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


The origin of the first cell, cannot be explained by natural selection
The cell is irreducible complex, and hosts a hudge amount of codified, complex, specified information. The probability of useful DNA, RNA, or proteins occurring by chance is extremely small. Calculations vary somewhat but all are extremely small (highly improbable). If one is to assume a hypothetical prebiotic soup to start there are at least three combinational hurdles (requirements) to overcome. Each of these requirements decreases the chance of forming a workable protein. First, all amino acids must form a chemical bond (peptide bond) when joining with other amino acids in the protein chain. Assuming, for example a short protein molecule of 150 amino acids, the probability of building a 150 amino acids chain in which all linkages are peptide linkages would be roughly 1 chance in 10^45. The second requirement is that functioning proteins tolerate only left-handed amino acids, yet in abiotic amino acid production the right-handed and left-handed isomers are produced in nearly the same frequency. The probability of building a 150-amino-acid chain at random in which all bonds are peptide bonds and all amino acids are L-form is roughly 1 chance in 10^90. The third requirement for functioning proteins is that the amino acids must link up like letters in a meaningful sentence, i.e. in a functionally specified sequential arrangement. The chance for this happening at random for a 150 amino acid chain is approximately 1 chance in 10^195. It would appear impossible for chance to build even one functional protein considering how small the likelihood is. By way of comparison to get a feeling of just how low this probability is consider that there are only 10^65 atoms in our galaxy.
http://www.ncbi.nlm.nih.gov/pubmed/10818565



Paul Davies, the fifth miracle, page 54:
Chance and the origin of life
Ask the simple question: Given the conditions that prevailed on the Earth four billion years ago, how likely was it that life arose?
The following answer won’t do: “Life was inevitable, because we are here.” Obviously life did originate—our existence proves that much. But did it have to originate? In other words, was the emergence of life from a chemical broth or whatever inevitable, given millions of years? Nobody knows the answer to this question. The origin of life may have been a sheer fluke, a chemical accident of stupendous improbability, an event so unlikely that it would never happen twice in the entire universe. Or it may have been as unremarkable and predetermined as the formation of salt crystals. How can we know which explanation is the right one? Let’s take a look at the chemical-fluke theory. Terrestrial life is based on some very complicated molecules with carefully crafted structures. Even in simple organisms, DNA contains millions of atoms. The precise sequence of atoms is crucial. You can’t have an arbitrary sequence, because DNA is an instruction manual for making the organism. 

Change a few atoms and you threaten the structure of the organism. Change too many and you won’t have an organism at all. The situation may be compared to the word sequence of a novel. Change a few words here and there at random, and the text will probably be marred. Scramble all the words and there is a very high probability that it won’t be a novel any more. There will be other novels with similar words in different combinations, but the set of word sequences that make up novels is an infinitesimal fraction of all possible word sequences. The odds are fantastic  against shuffling amino acids at random into the right sequence to form a protein molecule by accident. That was a single protein. Life as we know it requires hundreds of thousands of specialist proteins, not to mention the nucleic acids. The odds against producing just the proteins by pure chance are something like 1^40.000 to 1. This is one followed by forty thousand zeros, which would take up an entire chapter of this book if I wanted to write it out in full. Dealing a perfect suit at cards a thousand times in a row is easy by comparison. In 40000 a famous remark, the British astronomer Fred Hoyle likened the odds against the spontaneous assembly of life to those for a whirlwind sweeping through a junkyard and producing a fully functioning Boeing 747.



With a half-trillion stars wheeling through the spiral patterns of the Milky Way Galaxy, it seems illogical to assume that among them only one world supports intelligent life.’ The use of the word ‘illogical’ was unfortunate, because the logic is perfectly clear. There are indeed a lot of stars – at least ten billion billion in the observable universe. But this number, gigantic though it may appear to us, is nevertheless trivially small compared to the gigantic odds against the random assembly of even a single protein molecule. The universe may be big, but if life formed solely by random agitation in a molecular junkyard, there is scant chance it will have happened twice.

With such a extraordinary elucidation, it would/should be a easy leap of faith to infer =====>>>> DESIGN !! Why Davies does not do it, but keeps a agnostic standpoint, is a mistery to me.



Objection:  Chance can create life, despite the small possibility. There are 31 million seconds in a single year, meaning that if you multiply that by ten billion you get an astronomical amount of chances and don't forget just because something is largely unlikely doesn't mean it's impossible
Answer:

Talking about life getting together is similar to talking about cars forming themselves, or even basic computer programs making themselves. These things are not just improbable, they are impossible without intelligence. 

Paul Davies once said :
How did stupid atoms spontaneously write their own software … ? Nobody knows …… there is no known law of physics able to create information from nothing.

Literature from those who posture in favor of creation abounds with examples of the tremendous odds against chance producing a meaningful code. For instance, the estimated number of elementary particles in the universe is 10^80. The most rapid events occur at an amazing 10^45 per second. Thirty billion years contains only 10^18 seconds. By totaling those, we find that the maximum elementary particle events in 30 billion years could only be 10^143. Yet, the simplest known free-living organism, Mycoplasma genitalium, has 470 genes that code for 470 proteins that average 347 amino acids in length. The odds against just one specified protein of that length are 1:10^451.

The protein that enables a firefly to glow, and also reproduce (as its illuminated abdomen also serves as a visible mating call), is a protein made up of a chain of 1,000 amino acids. The full range of possible proteins that can be coded with such a chain is 17 times the number of atoms in the visible universe. This number also represents the odds against the RANDOM coding of such a protein. Yet, DNA effortlessly assembles that protein, in the exactly correct, and absolutely necessary sequence and number of amino acids for the humble firefly. What are we to say of the 25,000 individual, highly specialized, absolutely necessary, and exactly correctly coded proteins in the human body? 

Dembsky : We also know from broad and repeated experience that intelligent agents can and do produce information-rich systems: we have positive experience-based knowledge of a cause that is sufficient to generate new instructing complex information, namely, intelligence.  the design inference  does not constitute an argument from ignorance. Instead, it constitutes an "inference to the best explanation" based upon our best available knowledge.  It asserts the superior explanatory power of a proposed cause based upon its proven—its known—causal adequacy and  based upon a lack of demonstrated efficacy among the competing proposed causes.  The problem is that nature has too many options and without design couldn’t sort them all out. Natural mechanisms are too unspecific to determine any particular outcome. Mutation and natural selection or luck/chance/probablity could theoretically form a new complex morphological feature like a  leg or a limb with the right size and form , and arrange to find out the right body location to grow them , but it could  also produce all kinds of other new body forms, and grow and attach them anywhere on the body, most of which have no biological advantage or are most probably deleterious to the organism. Natural mechanisms have no constraints, they could produce any kind of novelty. Its however that kind of freedom that makes it extremely unlikely that mere natural developments provide new specific evolutionary arrangements that are advantageous to the organism.  Nature would have to arrange almost a infinite number of trials and errors until getting a new positive  arrangement. Since that would become a highly  unlikely event, design is a better explanation. 

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.1
– A. I. Oparin

Mondore, The Code Word
What is the probability of complex biochemicals like proteins and DNA arising by chance alone?
The chance that amino acids would line up randomly to create the first hemoglobin protein is 1 in 10^850. The chance that the DNA code to produce that hemoglobin protein would have randomly reached the required specificity is 1 in 10^78,000.



Harold Urey, a founder of origin-of-life research, describes evolution as a faith which seems to defy logic:
“All of us who study the origin of life find that the more we look into it, the more we feel that it is too complex to have evolved anywhere. We believe as an article of faith that life evolved from dead matter on this planet. It is just that its complexity is so great, it is hard for us to imagine that it did.

― Michael Denton, Evolution: A Theory In Crisis
“The complexity of the simplest known type of cell is so great that it is impossible to accept that such an object could have been thrown together suddenly by some kind of freakish, vastly improbable, event. Such an occurrence would be indistinguishable from a miracle.”

[size=13]Hoyle and Wickramasinghe, p. 24.

“The trouble is that there are about two thousand enzymes, and the chance of obtaining them all in a random trial is only one part in (10^20)2,000 = 10^40,000, an outrageously small probability that could not be faced even if the whole universe consisted of organic soup. If one is not prejudiced either by social beliefs or by a scientific training into the conviction that life originated on the Earth [by chance or natural processes], this simple calculation wipes the idea entirely out of court.”

Ibid., p. 130. http://hyperphysics.phy-astr.gsu.edu/nave-html/faithpathh/hoyle.html
Any theory with a probability of being correct that is larger than one part in 10^40,000 must be judged superior to random shuffling [of evolution]. The theory that life was assembled by an intelligence has, we believe, a probability vastly higher than one part in 10^40,000 of being the correct explanation of the many curious facts discussed in preceding chapters. Indeed, such a theory is so obvious that one wonders why it is not widely accepted as being self-evident. The reasons are psychological rather than scientific.

Hoyle and Wickramasinghe, p. 3.

Biochemical systems are exceedingly complex, so much so that the chance of their being formed through random shufflings of simple organic molecules is exceedingly minute, to a point indeed where it is insensibly different from zero.

In the 1970s Hoyle calculated the mathematical probability of the coincidental formation of only the 2,000 types of proteins found in a single amoeba. (There are some 200,000 different types of proteins in a human cell.) The figure that he calculated was 1 over 10^40,000—an incredible number obtained by putting 40,000 zeros after the 1 (Eastman&Missler, 1996, p. 61).

The Universe: Past and Present Reflections Sir Fred Hoyle
When you consider that a typical enzyme has a chain of perhaps 200 links and that there are 20 possibilities for each link, it's easy to see that the number of useless arrangements is enormous, more than the number of atoms in all the galaxies visible in the largest telescopes. This is for one enzyme, and there are upwards of 2000 of them, mainly serving very different purposes. So how did the situation get to where we find it to be? This is, as I see it, the biological problem - the information problem. Some super-calculating intellect must have designed the properties of the carbon atom, otherwise, the chance of my finding such an atom through the blind forces of nature would be utterly minuscule. Of course, you would, and if you were a sensible superintellect you would conclude that the carbon atom is a fix. 
http://calteches.library.caltech.edu/527/2/Hoyle.pdf

― Stephen C. Meyer, Darwinism, Design and Public Education
“The information contained in an English sentence or computer software does not derive from the chemistry of the ink or the physics of magnetism, but from a source extrinsic to physics and chemistry altogether. Indeed, in both cases, the message transcends the properties of the medium. The information in DNA also transcends the properties of its material medium.”

― Jonathan Wells, The Politically Incorrect Guide to Darwinism And Intelligent Design

“The secret of DNA's success is that it carries information like that of a computer program, but far more advanced. Since experience shows that intelligence is the only presently acting cause of information, we can infer that intelligence is the best explanation for the information in DNA.”

Kuhn, J. A. 2012. Dissecting Darwinism. Baylor University Medical Center Proceedings. 25 (1): 41-47.
Based on an awareness of the inexplicable coded information in DNA, the inconceivable self-formation of DNA, and the inability to account for the billions of specifically organized nucleotides in every single cell, it is reasonable to conclude that there are severe weaknesses in the theory of gradual improvement through natural selection (Darwinism) to explain the chemical origin of life. Furthermore, Darwinian evolution and natural selection could not have been causes of the origin of life, because they require replication to operate, and there was no replication prior to the origin of life.


According to Dembski and Borel  (Dembski, 1998, pp. 5, 62, 209, 210).
specified events of small probability do not occur. Dembski estimated 10^80 elementary particles in the universe and asked how many times per second an event could occur. He used the Planck value of 10^45. He then calculated the number of seconds from the beginning of the universe to the present and for good measure multiplied by ten million for 10^25 seconds in all. He thereby obtained 10^80 x 10^45 x 10^25 = 10^150, or more exactly 0.5 x 10^150, for his Law of Small Probability to eliminate chance
Currently, there does not seem to be a scientific criterion more generous to evolution than Dembski’s one chance in 0.5 x 10^150. Anything as rare as that probability had absolutely no possibility of happening by chance at any time by any conceivable specifying agent by any conceivable process throughout all of cosmic history. To test against that criterion, we take one chance in 2.3 x 10^75 for one protein (Yockey, 1992, pp. 255, 257) and multiply by the 60,000 proteins required for the abiogenesis of a minimal cell (Denton, 1986, p. 263; Morowitz, 1966, pp. 446-459) and obtain one chance in more than 104,478,296 (Mastropaolo, 1999, p. iii). That exceeds Dembski’s most generous criterion for impossible by more than 104,478,146. Or if 0.5 x 10^150 to 1 is the most generous probability science can provide to demarcate possibility from miracle, then with more than four million orders of magnitude to spare abiogenesis must be considered miraculous. To put abiogenesis in biology textbooks as evolutionists have done throughout the United States is to teach evolution religion as science and that violates the requirement of the U.S. Constitution prohibiting the establishment of a state religion (Constitution of the United States of America, 1787, Amendment I, see note).

Richard Dawkins,(Dawkins, 1996, pp. 144, 146).
Suppose we want to suggest, for instance, that life began when both DNA and its protein- based replication machinery spontaneously chanced to come into existence. We can allow ourselves the luxury of such an extravagant theory, provided that the odds against this coincidence occurring on a planet do not exceed 100 billion billion to one”  (Dawkins, 1996, pp. 144, 146).

Paul Davies, the fifth miracle, page 54:
Life as we know it requires hundreds of thousands of specialist proteins, not to mention the nucleic acids. The odds against producing just the proteins by pure chance are something like 1O^40000 to 1.
There are indeed a lot of stars—at least ten billion billion in the observable universe. But this number, gigantic as it may appear to us, is nevertheless trivially small compared with the gigantic odds against the random assembly of even a single protein molecule. Though the universe is big, if life formed solely by random agitation in a molecular junkyard, there is scant chance it has happened twice.

Regarding the probability of spontaneous generation, Harvard University biochemist and Nobel Laureate, George Wald stated in 1954:
"One has to only contemplate the magnitude of this task to concede that the spontaneous generation of a living organism is impossible. Yet we are here-as a result, I believe, of spontaneous generation."

The late Nobel prize winning scientist George Wald once wrote,
 “However improbable we regard this event [evolution], or any of the steps which it involves, given enough time it will almost certainly happen at least once… Time is in fact the hero of the plot… Given so much time, the ‘impossible’ becomes possible, the possible probable, the probable virtually certain. One has only to wait; time itself performs the miracles.”

1. http://xwalk.ca/origin.html#fn15

If you took thousands of letters of the alphabet, threw them high up into the air, watched them all fall to the ground, and they somehow formed themselves into Tolstoy’s War and
Peace, that would be as likely to occur as life being formed by the chance mixing of molecules.

Of all the ways that molecules can fall together by chance, we are told, an extraordinarily small proportion constitute the kind of self-replication machinery required for a process of natural selection to get going and lead to life as we know it. So the chance of life arising by chance, even given the basic organic chemical ingredients and a hospitable environment, is said to be incredibly low. w. Now let’s suppose that the process by which these complex molecules arose was not just a matter of chance, but rather was (non-intentionally) biased towards certain molecular configurations. Are self-replicating, life-producing molecules more likely to appear on this assumption? I am unable to see any reason to think so. We can think up any number of ways that the process could be biased. We can speculate about a range of possible laws and physical conditions such that simple atoms and molecules tend to cluster in certain ways rather than others. Some of these may favour life’s emergence; others will disfavour it. As in the cosmological case, what makes certain molecular configurations stand out from the multitude of possibilities seems to be that they are capable of developing into something which strikes us as rather marvellous, namely a world of living creatures. But there is no conceivable reason that blind forces of nature or physical attributes should be biased toward the marvelous. Where does this leave us? If life’s existence is no more to be expected on the assumptions of either intentional or non-intentional biasing than it is on chance, then we have no reason to doubt the Chance hypothesis.
http://web.mit.edu/rog/www/papers/does_origins.pdf

more reading:
Confusing Probability: The “Every-Sequence-Is-Equally-Improbable” Argument
https://uncommondescent.com/intelligent-design/confusing-probability-the-every-sequence-is-equally-improbable-argument/

Abiogenic Origin of Life: A Theory in Crisis

http://origins.swau.edu/papers/life/chadwick/default.html
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Infinite monkey theorem
https://en.wikipedia.org/wiki/Infinite_monkey_theorem
For physically meaningful numbers of monkeys typing for physically meaningful lengths of time the results are reversed. If there were as many monkeys as there are atoms in the observable universe typing extremely fast for trillions of times the life of the universe, the probability of the monkeys replicating even a single page of Shakespeare is unfathomably minute.

Ignoring punctuation, spacing, and capitalization, a monkey typing letters uniformly at random has a chance of one in 26 of correctly typing the first letter of Hamlet. It has a chance of one in 676 (26 × 26) of typing the first two letters. Because the probability shrinks exponentially, at 20 letters it already has only a chance of one in 2620 = 19,928,148,895,209,409,152,340,197,376 (almost 2 × 10^28). In the case of the entire text of Hamlet, the probabilities are so vanishingly small as to be inconceivable. The text of Hamlet contains approximately 130,000 letters. Thus there is a probability of one in 3.4 × 10183,946 to get the text right at the first trial. The average number of letters that needs to be typed until the text appears is also 3.4 × 10183,946, or including punctuation, 4.4 × 10360,783.

Even if every proton in the observable universe were a monkey with a typewriter, typing from the Big Bang until the end of the universe (when protons might no longer exist), they would still need a still far greater amount of time – more than three hundred and sixty thousand orders of magnitude longer – to have even a 1 in 10^500 chance of success. To put it another way, for a one in a trillion chance of success, there would need to be 10360,641 universes made of atomic monkeys.[note 6] As Kittel and Kroemer put it in their textbook on thermodynamics, the field whose statistical foundations motivated the first known expositions of typing monkeys, "The probability of Hamlet is therefore zero in any operational sense of an event...", and the statement that the monkeys must eventually succeed "gives a misleading conclusion about very, very large numbers."

In fact there is less than a one in a trillion chance of success that such a universe made of monkeys could type any particular document a mere 79 characters long.
the guys who invented these types of mathematical analogies disagree...once the chance of an event occurring exceeds a particular threshold...the chance of success is equal to zero in any operational sense of the word.

Why a Living Cell Cannot Arise by Chance
12 Reasons Why Evolution Cannot 
Explain the Origin of Life on Earth pg.39:

So how can we know that it is impossible for a living cell to arise by chance? The answer lies in understanding that a single cell is vastly more complicated than anything human minds have ever engineered. Let us consider the components of a simple cell using the well-studied organism Escherichia coli, which is a single-celled organism found in the human gastrointestinal tract. In 1996 a two-volume, 2,800-page set of articles that summarized some of our knowledge of the biochemistry and biology of this organism was published. Using this data, George Javor, professor of biochemistry at Loma Linda University, calculated the following statistics:

[size=12]A single living E. coli contains around 2.4 million protein molecules made up of approximately 4,000 different types of proteins. Along with these proteins, the cell contains around 255,000 nucleic acid molecules made up of 660 different types of nucleic acids. Included with these nucleic acids are around 1.4 million polysaccharides (long chains of sugar-type molecules) molecules made up of three different types of polysaccharides. Associated with these polysaccharides are around 22 million lipid molecules made up of 50 to 100 different types of lipids. These lipids also cooperate with many millions of metabolic intermediate molecules made up of about 800 different types of compounds that have to be at just the right concentration, otherwise the cell will die. Along with the metabolic intermediates, there are many millions of mineral molecules made up of 10 to 30 different types of minerals.[/size]

We know that intelligence is able to create high-information containing codes, like books, computer codes, and complex machines and factories. We observe in the natural world organisms made by the same principles, namely codified specified information, and irreducible and interdependent molecular machines and cell factories, while the only possible natural mechanisms, namely chance or random chemical reactions, do not have this broad range of intelligence-like capabilities. Its safe therefore to conclude, that the origin of life is best explained through a intelligent creator, and not well explained through natural mechanisms. This is not a inference based on what we do not know, commonly called " argument from ignorance", as proponents of naturalism frequently like to argue, but it is a conclusion based on what science has discovered in the last few decades about how cells work, and how they are build up. The only rational explanation for the origin of cells, and life, is creation through a intelligent designer. 

According to Dembski and Borel  (Dembski, 1998, pp. 5, 62, 209, 210).

specified events of small probability do not occur. Dembski estimated 10^80 elementary particles in the universe and asked how many times per second an event could occur. He used the Planck value of 10^45. He then calculated the number of seconds from the beginning of the universe to the present and for good measure multiplied by ten million for 10^25 seconds in all. He thereby obtained 10^80 x 10^45 x 10^25 = 10^150, or more exactly 0.5 x 10^150, for his Law of Small Probability to eliminate chance

Currently, there does not seem to be a scientific criterion more generous to evolution than Dembski’s one chance in 0.5 x 10^150. Anything as rare as that probability had absolutely no possibility of happening by chance at any time by any conceivable specifying agent by any conceivable process throughout all of cosmic history. To test against that criterion, we take one chance in 2.3 x 10^75 for one protein (Yockey, 1992, pp. 255, 257) and multiply by the 60,000 proteins required for the abiogenesis of a minimal cell (Denton, 1986, p. 263; Morowitz, 1966, pp. 446-459) and obtain one chance in more than 104,478,296 (Mastropaolo, 1999, p. iii). That exceeds Dembski’s most generous criterion for impossible by more than 104,478,146. Or if 0.5 x 10^150 to 1 is the most generous probability science can provide to demarcate possibility from miracle, then with more than four million orders of magnitude to spare abiogenesis must be considered miraculous. To put abiogenesis in biology textbooks as evolutionists have done throughout the United States is to teach evolution religion as science and that violates the requirement of the U.S. Constitution prohibiting the establishment of a state religion (Constitution of the United States of America, 1787, Amendment I, see note).

Having calculated the staggering improbability of life’s emergence by chance, Manfred Eigen (1992) concludes:  

The genes found today cannot have arisen randomly, as it were by the throw of a dice. There must exist a process of optimization that works toward functional efficiency. Even if there are several routes to optimal efficiency, mere trial and error can not be one of them. (p. 11)

It is from this conclusion that Eigen motivates his search for a physical principle that does not leave the emergence of life up to blind chance, hence making it reproducible in principle: The physical principle that we are looking for should be in a position to explain the complexity typical of the phenomena of life at the level of molecular structures and syntheses. It should show how such complex molecular arrangements are able to form reproducibly in Nature. (p. 11)

In considering how the first self-replicating machinery arose, Dawkins asks: 

“Whatis the largest single event of sheer naked coincidence, sheer unadulterated miraculous luck, that we are allowed to get away with in our theories, and still say that we have a satisfactory explanation of life?” (p. 141) 

And he answers that there are strict limits on the “ration of luck” that we are allowed to postulate in our theories. According to Dawkins, an examination of the immense complexity of the most basic mechanisms required for DNA replication is sufficient to see that any theory which makes its existence a highly improbable fluke is unbelievable, quite apart from what alternative explanations are on the table

http://web.mit.edu/rog/www/papers/does_origins.pdf



Chance
If someone were to ask why the pebbles fell in this specific pattern, we should be satisfied with the response “They just fell that way by chance. A car wheel kicked up the stones and they happened to land this way.” Of course it is highly improbable that a random scattering of pebbles should result in precisely this arrangement on the path, but this is no reason to doubt that their arrangement was due to anything but chance. Random improbabilities are commonplace—people win lotteries, hands of cards are dealt, and so on—without giving us any reason to suspect that there is a deeper reason for their occurrence than blind chance 1

Physical necessity
The correct explanation presumably has something to do with the lawful correlations between physical properties such as volume, mass, and inertia (my rough guess is that as the waves and tides wash in and out, the smaller stones being lighter are more easily swept back to the shoreline). But even if we know next to nothing about the physics involved, the simple regularity of the pattern suggests that these pebbles didn’t get that way by accident.

Intelligent design
There can be little doubt about the general form of the correct explanation here, namely that the positioning of the pebbles was influenced on purpose by an agent. Perhaps a full explanation would require more details as to who arranged the pebbles and how 1


1. http://web.mit.edu/rog/www/papers/does_origins.pdf



Last edited by Admin on Mon Mar 18, 2019 9:10 am; edited 1 time in total

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Otangelo


Admin
Abiogenesis and Probability

https://www.patheos.com/blogs/tippling/2017/08/28/abiogenesis-and-probability/

Problems with the creationists’ “it’s so improbable” calculations

1) They calculate the probability of the formation of a “modern” protein, or even a complete bacterium with all “modern” proteins, by random events. This is not the abiogenesis theory at all.

2) They assume that there is a fixed number of proteins, with fixed sequences for each protein, that are required for life.

3) They calculate the probability of sequential trials, rather than simultaneous trials.

4) They misunderstand what is meant by a probability calculation.

5) They seriously underestimate the number of functional enzymes/ribozymes present in a group of random sequences.

I will try and walk people through these various errors, and show why it is not possible to do a “probability of abiogenesis” calculation in any meaningful way.

A primordial protoplasmic globule

So the calculation goes that the probability of forming a given 300 amino acid long protein (say an enzyme like carboxypeptidase) randomly is (1/20)300 or 1 chance in 2.04 x 10390, which is astoundingly, mind-beggaringly improbable. This is then cranked up by adding on the probabilities of generating 400 or so similar enzymes until a figure is reached that is so huge that merely contemplating it causes your brain to dribble out your ears. This gives the impression that the formation of even the smallest organism seems totally impossible. However, this is completely incorrect.

Firstly, the formation of biological polymers from monomers is a function of the laws of chemistry and biochemistry, and these are decidedly not random.

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Calculations of a primordial ancestor with a minimal proteome emerging through unguided, natural, random events

https://reasonandscience.catsboard.com/t2508-abiogenesis-calculations-of-life-beginning-through-unguided-natural-random-events#6665

It is an interesting question, to elucidate what would be a theoretical minimal Cell, since based on that information, we can figure out what it would take for first life to begin on early earth. That gives us a number of  probability, if someone proposes natural, unguided mechanisms, based on chemical reactions, and atmospheric - and geological circumstances. The fact that we don't know the composition of the atmosphere back then doesn't do harm, and is not necessary in our inquiry.

The proteomic complexity and rise of the primordial ancestor of diversified life
A more recent study of 184 genomes identified 669 orthologous protein families, which cover 561 detailed functional classes that are involved in almost all essential biological processes of extant life, including translation, transcription and its regulation, DNA replication, recombination, and repair, transport and membrane-associated functions, electron transfer, and metabolism
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3123224/

Protein-length distributions for the three domains of life
The average protein length of these 110 clusters of orthologous genes COGs is 359 amino acids for the prokaryotes and 459 for eukaryotes.
https://pdfs.semanticscholar.org/5650/aaa06de4de11c36a940cf29c07f5f731f63c.pdf

Proteins are the result of the DNA blueprint, which specifies the complex sequence necessary to produce functional 3D folds of proteins. Both, improbability and specification are required in order to justify an inference of design.
1. According to the latest estimation of a minimal protein set for the first living organism, the requirement would be about 560 proteins, this would be the absolute minimum to keep the basic functions of a cell alive.  
2. According to the Protein-length distributions for the three domains of life, there is an average between prokaryotic and eukaryotic cells of about 400 amino acids per protein. 8
3. Each of the 400 positions in the amino acid polypeptide chains could be occupied by any one of the 20 amino acids used in cells, so if we suppose that proteins emerged randomly on prebiotic earth, then the total possible arrangements or odds to get one which would fold into a functional 3D protein would be 1 to 20^400 or 1 to 10^520. A truly enormous, super astronomical number. 
4. Since we need 560 proteins total to make a first living cell, we would have to repeat the shuffle 560 times, to get all proteins required for life. The probability would be therefore 560/10^520.  We arrive at a probability far beyond  of 1 in 10^200.000  ( A proteome set with 239 proteins yields odds of approximately 1/10^119.614 ) 7
Granted, the calculation does not take into consideration nor give information on the probabilistic resources available. But the sheer gigantic number os possibilities throw any reasonable possibility out of the window. 

If we sum up the total number of amino acids for a minimal Cell, there would have to be 560 proteins x 400 amino acids  =  224.000 amino acids, which would have to be bonded in the right sequence, choosing for each position amongst 20 different amino acids, and selecting only the left-handed, while sorting out the right-handed ones. That means each position would have to be selected correctly from 40 variants !! that is 1 right selection out of 40^224.000 possibilities !! Obviously, a gigantic number far above any realistic probability to occur by unguided events. Even a trillion universes, each hosting a trillion planets, and each shuffling a trillion times in a trillionth of a second, continuously for a trillion years, would not be enough. Such astronomically unimaginably gigantic odds are in the realm of the utmost extremely impossible.  

Helicases are astonishing motor proteins which rotational speed is up to 10,000 rotations per minute, and are life essential. 

How Many Genes Can Make a Cell: The Minimal-Gene-Set Concept
https://www.ncbi.nlm.nih.gov/books/NBK2227/

We propose a minimal gene set composed of 206 genes. Such a gene set will be able to sustain the main vital functions of a hypothetical simplest bacterial cell with the following features.

(i) A virtually complete DNA replication machinery, composed of one nucleoid DNA binding protein, SSB, DNA helicase, primase, gyrase, polymerase III, and ligase. No initiation and recruiting proteins seem to be essential, and the DNA gyrase is the only topoisomerase included, which should perform both replication and chromosome segregation functions.

Helicase are a class of enzymes vital to all living organisms. Their main function is to unpackage an organism's genes. They require 1000 left-handed amino acids in the right specified sequence. Each of the 1000 amino acids must be the right amongst 20 to chose from.  How did they emerge by natural processes? The chance to get them by random chemical reactions is 1 to 20^1000..... there are 10^80 atoms in the universe.  

Abiogenesis: Uncertainty quantification of a primordial ancestor with a minimal proteome emerging through unguided, natural, random events YK23Ods
9

Like the Holy Grail, a universal DNA ‘minimal genome’ has remained elusive despite efforts to define it. 10 Gene essentiality has to be defined within the specific context of the bacterium, growth conditions, and possible environmental fluctuations. Gene persistence can be used as an alternative because it provides a more general framework for defining the requirements for long-term survival via identification of universal functions. These functions are contained in the paleome, which provides the core of the cell chassis. The paleome is composed of about 500 persistent genes. 

We can take an even smaller organism, which is regarded as one of the smallest possible, and the situation does not change significantly:
The simplest known free-living organism, Mycoplasma genitalium,  has the smallest genome of any free-living organism, has a genome of 580,000 base pairs. This is an astonishingly large number for such a ‘simple’ organism. It has 470 genes that code for 470 proteins that average 347 amino acids in length. The odds against just one specified protein of that length are 1:10^451. If we calculate the entire proteome, then the odds are 470 x 347 = 163090 amino acids, that is odds of 20^164090 , if we disconsider that nature had to select only left-handed amino acids, and bifunctional ones. 

Argument: The physical laws, the laws of biochemistry, those aren't chance. The interaction of proteins, molecules, and atoms, their interaction is dictated by the laws of the universe. 
Response: While it is true, that the chemical bonds that glue one amino acid to the other are subdued to chemical properties, there are neither bonds nor bonding affinities—differing in strength or otherwise—that can explain the origin of the specificity of the sequence of the 20 types of amino acids, that have to be put together in the right order and sequence, in order for a protein to bear function.  What dictates in modern cells the sequence of amino acids in proteins is the DNA code. 

DNA contains true codified instructional information, or a blueprint.  Being instructional information means that the codified nucleotide sequence that forms the instructions is free and unconstrained; any of the four bases can be placed in any of the positions in the sequence of bases. Their sequence is not determined by the chemical bonding. There are hydrogen bonds between the base pairs and each base is bonded to the sugar-phosphate backbone, but there are no bonds along the longitudional axis of DNA. The bases occur in the complementary base pairs A-T and G-C, but along the sequence on one side the bases can occur in any order, like the letters of a language used to compose words and sentences. Since nucleotides can be arranged freely into any informational sequence, physical necessity could not be a driving mechanism.


Objection: Logical Fallacy. Argument from Improbability. Just because a thing is highly unlikely to occur doesn't mean that its occurrence is impossible. No matter how low the odds, if there is a chance that it will happen, it will happen given enough tries, especially considering a large enough universe with countless potentially "living" planets. Nobody claims that winning the lottery doesn't happen just because the chance of a specific individual winning it is low.
Response: So you're saying there's a chance... Murphy's Law states given enough time and opportunity, anything THAT CAN HAPPEN will happen. That phrase "can happen" is very important. The natural, non thinking, random, void of purpose and reason cosmos is unable to produce what we see without information. Life without information is not only improbable but rather impossible from what we know about the nature of complexity, design, and purpose. Given a planet full of simpler non-self-replicating organic molecules, abundant but not excessive input of energy from the local star, and a few thousand million years one could imagine that the number of "tries" to assemble that one self-replicating organic molecule would easily exceed 5x10^30. You can't just vaguely appeal to vast and unending amounts of time (and other probabilistic resources) and assume that self-assembly, spontaneously by orderly aggregation and sequentially correct manner without external direction, given enough trials is possible, that it can produce anything "no matter how complex."  Rather, it has to be demonstrated that sufficient probabilistic resources or random, non-guided mechanisms indeed exist to produce the feature. Fact is, we know upon repeated experience and demonstration that intelligence can and does envision, project and elaborate complex blueprints, and upon its instructions, intelligence produces the objects in question. It has NEVER been demonstrated that unguided events without specific purposes can do the same. In such examples it is also not taken in consideration, that such shuffle requires energy applied in specific form, and the environmental conditions must permit the basic molecules not to be burned by UV radiation. The naturalistic proposal is more a matter of assaulting the intelligence of those who oppose it with a range assertions that proponents of naturalism really have no answer, how these mechanisms really work. To argue that forever is long enough for the complexity of life to reveal itself is an untenable argument. The numbers are off any scale we can relate to as possible to explain what we see of life. Notwithstanding, you have beings in here who go as far to say it's all accounted for already, as if they know something nobody else does. Fact is, science is struggling for decades to unravel the mystery of how life could have emerged, and has no solution in sight.  

Eugene Koonin, advisory editorial board of Trends in Genetics, writes in his book: The Logic of Chance: 
" The Nature and Origin of Biological Evolution, Eugene V. Koonin, page 351:
The origin of life is the most difficult problem that faces evolutionary biology and, arguably, biology in general. Indeed, the problem is so hard and the current state of 
the art seems so frustrating that some researchers prefer to dismiss the entire issue as being outside the scientific domain altogether, on the grounds that unique
events are not conducive to scientific study.


Objection: What is entirely missing from such arguments as above is the demonstration that a specific modern "alive" configuration is the only possible one. Calculating probabilities starting with the end result commits the classic fallacy of painting the target after the arrow has been shot, pretending that a goal has been specified in advance; any event becomes arbitrarily improbable if specified with sufficient accuracy.
Response: We have taken as our premise what science has demonstrated to be the minimal requirement to start life. And therefore, the objection fails. 

Above calculation does not take into consideration that there are about 500 naturally occurring amino acids known. So let us suppose that they were extant on the prebiotic earth, and somehow, a selective process did chose and select, and concentrate just the 20 used in life. These 20 could still come in two versions, left-handed, and right-handed. Life uses only left-handed amino acids, so they would also have to be sorted out. Now let us suppose, that by freaky accident and crazy shuffling trillions of trillions of time, suddenly, the right protein set would be there, the right proteins, the right assortment. It is claimed, that there was no oxygen in the prebiotic earth. If that was so, 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 have 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.
 
Peptide bonding of amino acids to form proteins and its origins
https://reasonandscience.catsboard.com/t2130-peptide-bonding-of-amino-acids-to-form-proteins-and-its-origins

Most of the cell’s important functions are carried out by compounds called proteins which are a chain of amino acids linked together. There are 20 amino acids which can be arranged in any combination and the average protein consists of over 400 amino acids linked together. The protein’s characteristics and function is determined by the number and particular arrangement of amino acids. A protein can be represented by a sentence which derives its meaning from the particular arrangement of letters or amino acids. 4  According to evolutionary theories, amino acids were synthesized spontaneously and then linked together to form the first protein from a generic amino acid “soup.” In experiments attempting to synthesize amino acids, the products have been a mixture of right-handed and left-handed amino acids. (Amino acids, as well as other organic compounds, can exist in two forms which have the same chemical composition but are three-dimensional mirror images of each other; thus termed right and left-handed amino acids.) Every protein in a living cell is composed entirely of left-handed amino acids, even though the right-handed isomer can react in the same way. Thus, if both right and left-handed amino acids are synthesized in this primitive organic soup, we are faced with the question of how life has used only the left-handed amino acids for proteins.

We can represent this dilemma by picturing a huge container filled with millions of white (left-handed amino acids) and black (right-handed amino acids) jelly beans. What would be the probability of a blind-folded person randomly picking out 410 white jelly beans (representing the average sized protein) and no black jelly beans? The odds that the first 410 jelly beans would be all one color are one in 2^410 or 109^123. To put the odds in perspective, there are only about 10^18 seconds in 4.5 billion years, the approximate claimed age of the earth, and it has been estimated that there are only 10^80 particles in the universe.

Yet the probability of choosing all left-handed amino acids, without even considering their particular order or specific arrangement, is much larger than that!

So let us suppose that there are about 500 different amino acids on the prebiotic earth, and somehow, a selective process did chose and select, and concentrate just the 20 used in life. And sorted out all right-handed amino acids, 
so only left-handed would have remained. 

About 500 naturally occurring amino acids are known (though only 20 appear in the genetic code) and can be classified in many ways
https://en.wikipedia.org/wiki/Amino_acid

We had a theoretical average size of 400 amino acids per protein,  Since each of the 400 positions in the chain could be occupied by any one of the 20 amino acids, the total possible arrangements is 20^400, a truly enormous, super astronomical number. Applying the formula below, the odds for one protein with 400 amino acids to emerge randomly are 1 to 10^520.

Abiogenesis: Uncertainty quantification of a primordial ancestor with a minimal proteome emerging through unguided, natural, random events Z3uo2dj

Abiogenesis: Uncertainty quantification of a primordial ancestor with a minimal proteome emerging through unguided, natural, random events ClbAktZ
7

Abiogenesis: Uncertainty quantification of a primordial ancestor with a minimal proteome emerging through unguided, natural, random events CQAsIBY

Considering the first one as already obtained, we need 559 more. The probability is therefore 559/10520.  The third one could be any of the 558 still needed, so its probability would be 558 /10520.  Calculating all of these, and allowing for one substitution per chain, we arrive at a probability far beyond  of 1 in 10^100.000

To link two amino acids together requires the removal of a water molecule and the supply of some 150 times more energy than heat in the Earth's oceans could supply. In the absence of a joining enzyme used by biology or without an excessively large flux of ultraviolet light at the ocean surface, no new arrangements could be achieved. But even if chemical barriers for the linkages are artificially and miraculously removed, the really vast improbability of 1 in 10 ^40,000 poses a serious dilemma for the whole of evolutionary science. 6

For a protein made from scratch in a prebiotic soup, the odds of finding such globally optimal solutions are infinitesimally small- somewhere between 1 in 10^140 and 1 in 10^164 for a 150 amino acid long sequence if we factor in the probabilities of forming peptide bonds and of incorporating only left handed amino acids. 5

Proteins families are grouped into Clusters of Orthologous Groups, or COGs, which typically serve the same function. This Clusters of Orthologous Groups 561-COG set gives a low-end estimate for the LUCA proteome. 
Prebiotic Evolution and Astrobiology 2009 Landes Bioscience Austin Texas

A minimal estimate for the gene content of the last universal common ancestor—exobiology from a terrestrial perspective
A truly minimal estimate of the gene content of the last universal common ancestor, obtained by three different tree construction methods and the inclusion or not
of eukaryotes (in total, there are 669 ortholog families distributed in 561 functional annotation descriptions, including 52 which remain uncharacterized)
http://sci-hub.tw/https://www.ncbi.nlm.nih.gov/pubmed/16431085/

The proteomic complexity and rise of the primordial ancestor of diversified life
A more recent study of 184 genomes identified 669 orthologous protein families, which cover 561 detailed functional classes that are involved in almost all essential biological processes of extant life, including translation, transcription and its regulation, DNA replication, recombination, and repair, transport and membrane-associated functions, electron transfer, and metabolism
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3123224/

Protein-length distributions for the three domains of life
The average protein length of these 110 clusters of orthologous genes COGs is 359 amino acids for the prokaryotes and 459 for eukaryotes.
https://pdfs.semanticscholar.org/5650/aaa06de4de11c36a940cf29c07f5f731f63c.pdf

So let us suppose and make a theoretical assumption that the threshold to have a first living cell is 560 proteins with an average length of 400 amino acids.

The length of the average protein in the smallest known living thing is at least 400 amino acid links, containing more than 7,000 atoms.
https://web.archive.org/web/20170423032439/http://creationsafaris.com/epoi_c06.htm

Lies, Damned Lies, Statistics, and Probability of Abiogenesis Calculations
http://www.talkorigins.org/faqs/abioprob/abioprob.html
Claim: Firstly, the formation of biological polymers from monomers is a function of the laws of chemistry and biochemistry, and these are decidedly not random.
Response: The amino acid sequence of a polypeptide, together with the laws of chemistry and physics, cause a polypeptide to fold into a more compact structure, but the sequence that permits proteins to fold to a stable fold is not determined by the laws of chemistry, but the complex, specified, code in DNA, which is a functional Cell dictates the amino acids which will be synthesized in the Ribosome. The instruction for the 3-D structure of a protein is embedded in the sequences of amino acids and the electrochemical attractive forces among them, and these are determined by the genetic Code.  Most proteins include all of the usual twenty kinds of amino acids.  Each protein has a specific exact sequence of these units.

Wiki: The genetic code is the set of rules used by living cells to translate information encoded within genetic material (DNA or mRNA sequences) into proteins. Translation is accomplished by the ribosome, which links amino acids in an order specified by messenger RNA (mRNA)

Objection: The entire premise is incorrect to start off with, because in modern abiogenesis theories the first "living things" would be much simpler, not even a protobacteria, or a preprotobacteria (what Oparin called a protobiont and Woese calls a progenote), but one or more simple molecules probably not more than 30-40 subunits long.
Response: In his book: The Fifth Miracle: The Search for the Origin and Meaning of Life, Paul Davies describes life with the following characteristics of life:
Reproduction. Metabolism.  Homeostasis Nutrition. Complexity. Organization.  Growth and development. Information content.  Hardware/software entanglement.  Permanence and change.

The paper: The proteomic complexity and rise of the primordial ancestor of diversified life describes :
The last universal common ancestor as the primordial cellular organism from which diversified life was derived. This urancestor accumulated genetic information before the rise of organismal lineages and is considered to be a complex 'cenancestor' with almost all essential biological processes.
http://europepmc.org/articles/pmc3123224

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

Objection: Another view is the first self-replicators were groups of catalysts, either protein enzymes or RNA ribozymes, that regenerated themselves as a catalytic cycle. It's not unlikely that a small catalytic complex could be formed. Each step is associated with a small increase in organisation and complexity, and the chemicals slowly climb towards organism-hood, rather than making one big leap
Response:   The Logic of Chance: The Nature and Origin of Biological Evolution By Eugene V. Koonin
Hence, the dramatic paradox of the origin of life is that, to attain the minimum complexity required for a biological system to start on the Darwin-Eigen spiral, a system of a far greater complexity appears to be required. How such a system could evolve is a  puzzle that defeats conventional evolutionary thinking, all of which is about biological systems moving along the spiral; the solution is bound to be unusual. 

Objection:As to the claim that the sequences of proteins cannot be changed, again this is nonsense. There are in most proteins regions where almost any amino acid can be substituted, and other regions where conservative substitutions (where charged amino acids can be swapped with other charged amino acids, neutral for other neutral amino acids and hydrophobic amino acids for other hydrophobic amino acids) can be made.
Response: A protein requires a threshold of minimal size to fold and become functional within its milieu where it will operate. That threshold is average 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 a 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

Claim: We were examining sequential trials as if there was only one protein/DNA/proto-replicator being assembled per trial. In fact there would be 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.
Response: It is claimed, that there was no oxygen in the prebiotic earth. If that was so, 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 early earth.

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Otangelo


Admin
As a simple measure of the difficulty of creating information, consider the example of the average archaea protein of 270 nucleotides. Even under realistically favorable assumptions, it should take a googol of googol years to generate a single instance of this molecule. It would take three times this many, i.e., 780 nucleotides, to code for it. Prebiotic appearance of nucleotides and long polymers is more difficult than appearance of amino acids and proteins. Hence, it should take longer than a googol of googol years to for the appearance of a 780 nt gene able to code for a specifically required protein. Yet, a 200 nt ribonucleic acid degrades in a matter of days. It is implausible that a googol of googol years would be enough time. On a practical basis this discussion is nonsense. These numbers are so extreme that the human mind cannot comprehend their significance.

https://osf.io/p5nw3/

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Otangelo


Admin
Claim: What I have never seen from creationists is any actual barrier to the natural origin of life. If the chemistry of OOL was impossible, then the chemistry of all cells today would be impossible. Every fart would be an act of god.”

Reply: Actually, the barrier is information. Even if conditions of the prebiotic Earth were suitable, even if plausible scenarios for monomer synthesis were demonstrated in the necessary concentrations, purity and supply, even if a vaguely possible hypothesis for the simultaneous formation of the trinity of membrane, RNA/DNA and proteins were proposed, no amount of creative conjecture can overcome the information barrier.

A minimal self-replicating and metabolising protocell requires genetic information of tens or hundreds of thousands of base pairs, highly specific and complex in terms their direct enzymatic etc function or the proteins for which they code.

The only claimed naturalistic mechanism to accomplish the creation of this amount and type of information is natural selection, but natural selection only begins to operate at this point. Appeals to “prebiotic selection” or “chemical selection” are oxymoronic.

History will judge this as the dark ages of materialism blinding us from the scientifically unavoidable truth.

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Otangelo


Admin
So for calculations of the probability of something as fundamental as a single enzyme that digests a single molecular bond of, for instance a fat molecule, the assumptions go something like this:

Given that the oceans are full of amino acids only; no bases, no alcohols, no toxins, no interfering compounds, oils, ketones, aromatics, aliphatics,  nitrogenous bases, sugars etc…,
Given that these amino acids are found in concentrations favorable to collisions that would allow some form of covalent bond formation from some source of energy; typically heat,
And given ideal conditions of the aqueous medium (water in which the reactions will occur) such as the proper pH, osmolality (salt), turbulence, heat, or lightening or any one of hundreds of environmental conditions favorable to the formation of the peptide bond (the covalent bond between amino acid residues),
And given that none of the assumed favorable environmental conditions are at all detrimental to the formation of such peptide bonds (another completely ridiculous consideration),
And given all the Hubble Time (the life of a universe is one Hubble Time or about 30 billion years) in multiple universes to be unrestricted,
And given that the only chemical reactions that will occur will be between the primary amino group of one amino acid and the primary carboxy-terminal group of the next amino acid (literally thousands of other chemical bonds could form between the 20 essential amino acids even in an sublime chemical soup as described here),
And given that all and only the 20 essential amino acids are available to participate in the chemical reactions under consideration,
And given that all the amino acids available are only left handed residues; the only kind that are chemically made by biological systems (in a world where such chemicals are created synthetically or theoretically by materialistic means this is and would be impossible to control for),

Then and only then, can we ask the question, “what is the statistical probability of a single polypeptide chain being randomly formed in the correct linear sequence of amino acids that would form say the lipase enzyme?”  It turns out that it is somewhere in the neighborhood of 1 chance in 2.04 x 10^390.  This can be spread over as much time as you want with as many conceivable worlds all simultaneously undergoing prebiotic synthesis concurrently.  This number is ridiculously large and no amount of storytelling helps to improve the chances of this occurring.  The visible universe is not sufficiently large or old enough to improve the statistically probability number.  Add as many more universes as you like and the probability does not improve by very much.  The conclusion is clearly that a materialistic means for the formation of a biological molecule literally requires a miracle; or the programming of cellular chemistry as is found in living cells.  Neither of these ideas help the materialistic method of chemical evolution. Theoretical abiogenic processes do not contribute to an answer for life.  The answer becomes a metaphysical one.  Science supports a metaphysical reality since even the simplest form of biochemistry requires a complex program (DNA) and a complete decoding system (the cell) to manufacture specified proteins.  It is proven that this is what is required to make a single protein. No molecular stories aid the abiogenic hypothesis.

Ian asserts that: Firstly, the formation of biological polymers from monomers is a function of the laws of chemistry and biochemistry, and these are decidedly not random.

This statement is patently false.  Ian may not know the chemistry of any kind or he may be deliberate in this deception. Any chemist or biochemist knows that polymerization of any monomeric unit requires highly controlled and near pristine conditions and sometimes a catalyst must be available to create a thermodynamically favorable direction for the polymeric reaction to take place. There are only two sources that are currently known for polymer formation: synthetic polymers that are man-made and biopolymers made by biology.

Many polymers used in DNA or Protein research such as the formation of polyacrylamides require extremely pure acrylamide subunits and a catalyst that drives the reaction to the formation of polymerization.  In this

case, the polyacrylamide formed is a random network of strands that create a gelatinous mesh. This gel is used to strain or sieve other molecules when an electric field is generated through the mesh by a power supply.  The effect is to separate molecules or fractionate them based upon there size.

However, in the formation of DNA, RNA, or protein molecules, which are all polymers, many types of monomeric units are involved in the synthesis of each type of molecule.  Random networks are not made in the polymerization of biomolecules, but a linear arrangement of monomers is required.  Large multimeric enzymatic catalysts called polymerases or transcriptases or ribosomes are involved in polymer formation and this, at the expense of enormous amounts of cellular energy.  The formation of the DNA polymer requires not just a random string of monomers but also a template of DNA to begin the polymerization.  The code of information for DNA polymerization is found in the specified linear arrangement of data on the template.  The catalysts duplicate the information, which results in the functional double-stranded genetic code replicated for the purpose of directing protein synthesis.

In the case of proteins, each sequence of say 300 residues (monomers) is the result of highly ordered linearly alignment of molecules based upon a transcript (dictated information) to create a highly specific three-dimensional biomolecular machine.  Such a protein (molecular machine) possesses a catalytic site favorable to perform a single, well-defined enzymatic reaction using the free energy of the universe to drive a reaction to a point of equilibrium… a minimum requirement for any enzyme.   There are typically many other important and well-defined regions of the protein other than the catalytic site that forms other domains. These carry out specific biophysical jobs in the activity, control, longevity, and structural integrity of the protein.

As stated, there are no known chemical reactions that result in the linear polymerization of amino acids to form a polypeptide chain (protein) under any natural conditions other than living systems.  This type of polymerization does not take place outside the living cell unless an intelligently designed machine such as a peptide synthesizer is constructed.  Such a device comes with a highly refined and specifically designed resin from which single residues are automatically added using well known organic chemistry that is favorable to a single, highly reactive covalent bonding event between an amino-terminal of one amino acid and a carboxyterminal of another amino acid residue. This process is repeated by computer control until a polypeptide chain is made.  After the first addition event the resin must be washed free of the excess unreacted residue and prepared for the second addition by a computer-controlled system so that the next defined monomer can be added to the growing linear chain of residues.  The result is a polypeptide chain of some 80 residues, which is the best we have been able to do to produce to protein synthetically. Otherwise, genetic engineers like myself use biological systems like living bacteria or plants to produce kilogram quantities of a single, valuable protein.

One of the simplest lipase molecules comes from a bacterium.  It digests lipid, fats and oils and has around 306 amino acids residues in fairly exact linear sequence in order to be useful to a living system like the bacterium.  There are many forms of the same protein but their fundamental structures provide the key elements to both recognize and digest lipids.  Below is the number 1, written 306 times (Figure 1).

1111111111111111111111111111111111111111111111111111111111111111111

1111111111111111111111111111111111111111111111111111111111111111111

1111111111111111111111111111111111111111111111111111111111111111111

1111111111111111111111111111111111111111111111111111111111111111111

1111111111111111111111111111111111111111111111111111111111

Linear arrangement of single type of unit.  A graphic example of polymerization.

Under the most pristine conditions in nature you will not find polymerization of a single organic monomer to take place such that the monomer will be chemically attached to form a linear (a straight line) of polymeric structure; like beads on a string.  It must be under the direction of a biological process. There are some theories in regards to the origin of petroleum that suggest this oil may not be of biological origin but rather the result of collections of a methane gas molecules that have undergone polymerization in the depths of the earth.  Not many petrochemical engineers really care how the oil got there though such a polymerization reaction can be performed in the laboratory, under the direction of an intelligent agent.

Now consider Figure 2 where 20 amino acids are placed in a specified order to give rise to a recognizable and functional entity, a lipase protein from a bacterium.

GADNIDVSFQ TILQQERNWA GLQSKSLKVG DITWSYSEGG SSTKPTLLLI HGLAGSRDNW NRVAHYLTTN YHVIIPDLPG SGETIVSQDF DYSVPNLAEK LRRFVEAANL KGPIHIAGHSLGGSIALLYA GQYPFETKSL FLVDSGGIFR SANTIYLKDP TYLKQLLVSK KGDFNYLLKQ TGFNPPFIPK EFLQAQEKLX INQAPQTQKL DQLIALNKVYTPDSFAVLT KTIDAPTLILWGKQDKIINV EVANELKRLL KNAQPPVILE NVGHXPILEA EQLVIQQYVP FLLKVETNQS SKTTTP

This protein has specified arrangements of amino acids that then fold and twist to form a globular protein having the ability to recognize and digest lipids (oils and fats) (Figure 3).  The linear arrangement of amino acids is called the primary structure of the protein.  Depending on the linear arrangement, portions of the protein may form higher-ordered structures called secondary structures.  The protein may coil creating alpha-helical structures.  One or more amino acids may allow a bend in the protein; the severity of the bend is determined by the particular amino acid or acids placed at that particular position.  Other structures form sheets where the residues alternate the angle of their peptide bonds to form features much like this:  VVVVVVVVV.  These are called beta-sheets.  Other alignments of the amino acids give rise to finger domains, hand loops, and catalytic sites and there are many other well defined structural features or “motifs” (meaning image, pattern or theme).  Some of these motifs have the function of holding the protein in three-dimensional space such that its molecular form allows highly specified interactions with a very limited number of other molecules.  For the enzyme lipase, there is a specified site of the molecule that recognizes fats and oils and binds to that site, breaking the bonds of the molecule.  This is the catalytic site and it reduces the lipid to smaller compounds that can be absorbed or transported into the bacterium.

https://blueprintsforliving.com/origin-life-research/

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Otangelo


Admin
According to the Protein-length distributions for the three domains of life, there is an average between prokaryotic and eukaryotic cells of about 400 amino acids per protein. 8 Each of the 1354 positions in the amino acid polypeptide chains could be occupied by anyone of the 20 amino acids used in cells, so if we suppose that proteins emerged randomly on prebiotic earth, then the total possible arrangements or odds to get one which would permit successful folding into a functional 3D forms would be 1 to 20^400 or 1 to 10^520. A truly enormous, super astronomical number.  Since we need 1354 proteins total to make our model organism, we would have to repeat the shuffle 1354 times, to get all proteins required. The probability would be therefore 1354/10^520.  We arrive at a probability of about 1 in 10^704.000 There are 10^80 atoms in the universe.

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10Abiogenesis: Uncertainty quantification of a primordial ancestor with a minimal proteome emerging through unguided, natural, random events Empty The Number of Possible Orders in a Gene Fri Jul 31, 2020 10:38 am

Otangelo


Admin
The Number of Possible Orders in a Gene

There are three different ways to determine the number of possible sequences in a DNA chain.  The general formula, it may be recalled, is the number of kinds to the power of the number of units in the chain.  If each order is equally likely, the probability of a particular sequence will then be one in the total of possible orders. With four kinds of nucleotides and a chain 1,200 long, the total of possible arrangements would be 4^1200, which is approximately 10^722.  The letters of a gene, however, are read in triplet codons (comprising sixty-four kinds of triplets) of which there are 400 in this size chain.  If computed in this way, there would be a total of 64^400 possible orders, and this turns out to be the same as when figured by individual letters, namely 10^722. Many of the twenty amino acids are coded by more than one triplet.  The duplicate codons are thought by some to be “a historical accident,” Others believe they may be “perhaps a regulatory factor in some cases,” since nature is “seldom redundant” for very long.  As mentioned in the preceding chapter, the evidence is accumulating that these seeming duplicates may serve the vital purpose of regulating the synthesis of proteins.  If that turns out to be true, then there would be no useless duplicates among the 64 codons, and the total real sequences would be the 10^722 figure. Since research is not yet final on that point, however, let’s again give chance the benefit of the doubt and figure it as if all the duplicates were useless extras. There are only twenty-one different possible primary outcomes for each codon position.  Those potential outcomes which are signaled by codons are the twenty amino acids plus “end of chain.”  We will, therefore, figure on the basis of twenty-one kinds, for a chain 400 amino acids long.  The figure 21^400 is approximately 10^528.  If we allow one substitution per chain (without limiting it to the active site—another boost for chance), then the equivalent total of different sequences is 10^524.

https://web.archive.org/web/20170706223248/http://www.creationsafaris.com/epoi_c10.htm

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Otangelo


Admin
We do not need a model to predict and test if intelligence is a capable potent causal principle and agency to make life and biodiversity. We KNOW by repeated experience that following things are both always the result of intelligent setup. 

1. Blueprints containing instructional complex assembly information, dictating the 
2. 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. 


We see all these things in biochemistry, and biology, and much more.....

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

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

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Otangelo


Admin
How much of protein sequence space has been explored by life on Earth?
A typical estimate of the size of sequence space is 20^100 (approx. 10^130) for a protein of 100 amino acids in which any of the normally occurring 20 amino acids can be found. This number is indeed gigantic
[url=https://royalsocietypublishing.org/doi/10.1098/rsif.2008.0085#:~:text=A typical estimate of the,size of protein sequence space.]https://royalsocietypublishing.org/doi/10.1098/rsif.2008.0085#:~:text=A%20typical%20estimate%20of%20the,size%20of%20protein%20sequence%20space.[/url]

Bit by Bit: The Darwinian Basis of Life Gerald F. Joyce  Published: May 8, 2012
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001323
Suppose that a  polymer  (like RNA) that is assembled into four chains of 40 subunits (quaternary heteropolymer) . Then there would be 10^24 possible compositions. To represent all of these compositions at least once, and thus to establish a certainty that this simple ribozyme could have materialized, requires 27 kg of RNA chains, which classifies spontaneous emergence as a highly implausible event.

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
There is a conceptual problem, namely the emergence of specific sequences among a vast array of possible ones, the huge “sequence space”, leading to the question “why these macromolecules, and not the others?” One of the main open questions in the field of the origin of life is the biogenesis of proteins and nucleic acids as ordered sequences of monomeric residues, possibly in many identical copies. The first important consideration is that functional proteins and nucleic acids are chemically speaking copolymers, i.e., polymer formed by several different monomeric units, ordered in a very specific way.

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. The copolymeric nature of proteins and nucleic acid challenges our understanding of origin of life also from a theoretical viewpoint. The number of all possible combinations of the building blocks (20 amino acids, 4 nucleotides) forming copolymers of even moderate length is ‘astronomically’ high, and the total number of possible combinations it is often referred as the “sequence space”. Simple numerical considerations suggest that the exhaustive exploration of the sequence spaces, both for proteins and nucleic acid, was physically not possible in the early Universe, both for lack of time and limited chemical material. There are no methods described in the literature to efficiently generate long polypeptides, and we also lack a theory for explaining the origin of some macromolecular sequences instead of others.

The theoretical starting point is the fact that the number of natural proteins on Earth, although apparently large, is only a tiny fraction of all the possible ones. Indeed, there are thought to be roughly 10^13 proteins of all sizes in extant organisms. This number, however, is negligible when compared to the number of all theoretically possible different proteins. The discrepancy between the actual collection of proteins and all possible ones stands clear if one considers that the number of all possible 50-residues peptides that can be synthesized with the standard 20 amino acids is 20^50, namely 10^65. Moreover, the number of theoretically possible proteins increases with length, so that the related sequence space is beyond contemplation; in fact, if we take into account the living organisms, where the average length of proteins is much greater, the number of possible different proteins becomes even bigger. The difference between the number of possible proteins (i.e. the sequence space) and the number of those actually present in living organisms is comparable, in a figurative way, to the difference that exists between a drop of water and an entire Ocean. This means that there is an astronomically large number of proteins that have never been subjected to the long pathway of natural evolution on Earth: the “Never Born Proteins” (NBPs). Furthermore, the question whether a functionality is a common feature in the sequence space, or a rare result of natural selection, is of the utmost importance to elucidate the role of proteins in the origin of life and to fully exploit its biological potential and find new scaffolds for biological activities.
https://www.sciencedirect.com/science/article/pii/S2001037014600076


The Universe: Past and Present Reflections Fred Hoyle
https://calteches.library.caltech.edu/527/2/Hoyle.pdf
The big problem in biology, as.I see it, is to understand the origin of the information carried by the explicit structures of biomolecules. The issue isn't so much the rather crude fact that a protein consists of a chain of amino acids linked together in a certain way, but that the explicit ordering of the amino acids endows the chain with remarkable properties, which other orderings wouldn't give. The case of the enzymes is well known. Enzymes act as catalysts in speeding up chemical reactions that would otherwise go far too slowly, as in the breakdown, for example, of starch into sugar. If amino acids were linked at random, there would be a vast number of arrangements that would be useless in serving the purposes of a living cell. When you consider that a typical enzyme has a chain of perhaps 200 links and that there are 20 possibilities for each link, it's easy to see that the number of useless arrangements is enormous, more than the number of atoms in all the galaxies visible in the largest telescopes. This is for one enzyme, and there are upwards of 2000 of them, mainly serving very different purposes. So how did the situation get to where we find it to be? This is, as I see it, the biological problem - the information problem. It's easy to frame a deceitful answer to it. Start with much simpler, much smaller enzymes, which are sufficiently elementary to be discoverable by chance; then let evolution in some chemical environment cause the simple enzymes to change gradually into the complex ones we have today. The deceit here comes from omitting to explain what is in the environment that causes such an evolution. The improbability of finding the appropriate orderings of amino acids is simply being concealed in the behavior of the environment if one uses that style of argument.

I was constantly plagued by the thought that the number of ways in which even a single enzyme could be wrongly constructed was greater than the number of all the atoms in the universe.  So try as I would, I couldn't convince myself that even the whole universe would be sufficient to find life by random processes - by what are called the blind forces of nature. The thought occurred to me one day that:

The human chemical industry doesn't chance on its products by throwing chemicals at random into a stewpot. To suggest to the research department at DuPont that it should proceed in such a fashion would be thought ridiculous.

Wasn't it even more ridiculous to suppose that the vastly more complicated systems of biology had been obtained by throwing chemicals at random into a wildly chaotic astronomical stewpot? By far the simplest way to arrive at the correct sequences of amino acids in the enzymes would be by thought, not by random processes. And given a knowledge of the appropriate ordering of amino acids, it would need only a slightly superhuman chemist to construct the enzymes with 100 percent accuracy. It would need a somewhat more superhuman scientist, again given the appropriate instructions, to assemble it himself, but not a level of scale outside our comprehension. Rather than accept the fantastically small probability of life having arisen through the blind forces of nature, it seemed better to suppose that the origin of life was a deliberate intellectual act. By "better" I mean less likely to be wrong. Suppose a spaceship approaches the earth, but not close enough for the spaceship's imaginary inhabitants to distinguish individual terrestrial animals. They do see growing crops, roads, bridges, however, and a debate ensues. Are these chance formations or are they the products of an intelligence? Taking the view, palatable to most ordinary folk but exceedingly unpalatable to scientists, that there is an enormous intelligence abroad in the universe, it becomes necessary to write blind forces out of astronomy.

Now imagine yourself as a superintellect working through possibilities in polymer chemistry. Would you not be astonished that polymers based on the carbon atom turned out in your calculations to have the remarkable properties of the enzymes and other biomolecules? Would you not be bowled over in surprise to find that a living cell was a feasible construct? Would you not say to yourself, in whatever language supercalculating intellects use: Some supercalculating intellect must have designed the properties of the carbon atom, otherwise the chance of my finding such an atom through the blind forces of nature would be utterly minuscule. Of course you would, and if you were a sensible superintellect you would conclude that the carbon atom is a fix.

A common sense interpretation of the facts suggests that a superintellect has monkeyed with physics, as well as with chemistry and biology, and that there are no blind forces worth speaking about in nature. The numbers one calculates from the facts seem to me so overwhelming as to put this conclusion almost beyond question.

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Otangelo


Admin
Steve Meyer, Signature in the Cell:
The conditional probability that just one of these information-rich molecules arose by chance—in effect, the chance that chance is true—is much less than one-half. It is less than one in a trillion trillion. Thus, I concluded that it is more reasonable to reject the chance hypothesis than to accept it.

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