Defending the Christian Worldview, Creationism, and Intelligent Design
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Defending the Christian Worldview, 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 Worldview, Creationism, and Intelligent Design » Intelligent Design » Information Theory, Coded Information in the cell » Coded information comes always from a mind

Coded information comes always from a mind

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Otangelo


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Coded information comes always from a mind

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

Albert Voie  Biological function and the genetic code are interdependent  2006
Subsystems of the mind as functional objects or formal systems are unique in respect to other phenomena that follow the laws of nature and are subsystems of the universe. Life express both function and sign systems, which indicates that it is not a subsystem of the universe, since chance and necessity cannot explain sign systems, meaning, purpose, and goals . The human mind also possesses other properties that do not have these limitations, the property of creativity with ability to create through choice with intent. This choice doesn’t violate any laws. It merely uses dynamically inert configurable switches to record into physicality the nonphysical choices of mind. It is therefore very natural that many scientists believe that life is a subsystem of some Mind greater than humans or symbolic number cruncher referred to by Svozil. At least as observers we are left taking life as an axiom as Nils Bohr suggested in a lecture published in Nature “life is consistent with, but underivable from physics and chemistry”
http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.94.171&rep=rep1&type=pdf


PAUL DAVIES The Fifth Miracle The Search for the Origin and Meaning of Life 1999
"Yet, the scientists arguing for intelligent design do not do so merely because natural processes-chance, laws or the combination of the two-have failed to explain the origin of the information and information processing systems in cells. Instead, they also argue for design because we know from experience that systems possessing these features invariably arise from intelligent causes. The information on computer screen can be traced back to a user or programmer. The information in a newspaper ultimately came from a writer-from a mental, rather than a strictly material, cause. As the pioneering information theorist Henry Quastler observed, "information habitually arises from conscious activity." This connection between information and prior intelligence enables us to detect or infer intelligent activity even from unobservable sources in the distant past. Archeologists infer ancient scribes from hieroglyphic inscriptions. SETI's search for extraterrestrial intelligence presupposes that information imbedded in electromagnetic signals from space would indicate an intelligent source. As yet, radio astronomers have not found information-bearing signals from distant star systems. But closer to home, molecular biologists have discovered information in the cell, suggesting--by the same logic that underwrites the SETI program and ordinary scientific reasoning about other informational artifacts--an intelligent source for the information in DNA. DNA functions like a software program. We know from experience that software comes from programmers. We know generally that information-whether inscribed in hieroglyphics, written in a book or encoded in a radio signal-always arises from an intelligent source. So the discovery of information in the DNA molecule, provides strong grounds for inferring that intelligence played a role in the origin of DNA, even if we weren't there to observe the system coming into existence."
http://www.nytimes.com/books/first/d/davies-miracle.html

Tan, Change; Stadler, Rob. The Stairway To Life 2020:
In DNA and RNA, no chemical or physical forces impose a preferred sequence or pattern upon the chain of nucleotides. In other words, each base can be followed or preceded by any other base without bias, just as the bits and bytes of information on a computer are free to represent any sequence without bias. This characteristic of DNA and RNA is critical—in fact, essential—for DNA and RNA to serve as unconstrained information carriers. However, this property also obscures any natural explanation for the information content of life—the molecules themselves provide no explanation for the highly specific sequence of nucleotides required to code for specific biologic functions. Only two materialistic explanations have been proposed for the information content of life: fortuitous random arrangements that happen to be functional or the combination of replication, random mutations, and natural selection to improve existing functionality over time.
https://3lib.net/book/14907523/eda416

Stephen C.Meyer, The return of the God hypothesis 2021, page 253
For every one DNA sequence that generates a short functional protein fold of just 150 amino acids in length, there are 10^77 nonfunctional combinations—combinations that will not form a stable three-dimensional protein fold capable of performing a specific biological function. In other words, there are vastly more ways of arranging nucleotide bases that will produce nonfunctional amino-acid chains than there are ways of arranging nucleotide bases that will produce folded and functional proteins. Indeed, for every functional gene capable of coding for a protein fold there is an almost unimaginably large number of corresponding nonfunctional sequences. Clearly, 10^77 represents a huge number. To put it in context, there are only 10^65 atoms in our galaxy. During the 3.85-billion-year history of life, biologists estimate that about 10^40 individual organisms—a huge number—have lived on our planet. That means that, at most, about 1040 such opportunities to mutate a gene that might ultimately produce a new protein fold could have occurred. Yet 10^40 represents only a tiny fraction of 10^77—the number of non-functional sequences corresponding to each protein fold of modest length. Indeed, the fraction 10^40 divided by 10^77 equals 1 part in 10^37, or 1 part in ten trillion times a trillion times a trillion, to be exact. This means that for even one relatively modest-size novel protein fold to arise, the mechanism of random mutation and natural selection would have time to search just a tiny fraction of the total number of relevant sequences. In other words, the number of trials available to the evolutionary process turns out to be incredibly small in relation to the number of possible sequences that need to be searched. Or to put it differently, the size of the relevant spaces that need to be searched by the evolutionary process dwarfs the time available for searching—even taking into account life’s 3.85-billion-year history. It follows that the mechanism of random mutation and natural selection has not had enough time to generate or search but a minuscule fraction (one ten trillion trillion trillionth, to be precise) of the total number of possible nucleotide base or amino-acid sequences corresponding to a single protein fold. It is therefore overwhelmingly more likely than not that a random mutational search would have failed to produce even one new functional (information-rich) DNA sequence capable of coding for one new protein fold in the entire history of life on earth. Consequently, the hypothesis that such a random search succeeded is more likely to be false than true. And, of course, building new animals would require the creation of many new proteins and protein folds, not just one. It follows that the standard neo-Darwinism mechanism does not provide an adequate explanation for the origin of the genetic information necessary to produce the major innovations in biological form that have arisen in the history of life on earth.
https://3lib.net/book/15644088/9c418b

Robert L. Crowther By Design, Not By Chance December 2, 2005
All historical, observational, testable and repeatable examples PROVE information and operational functionality come from intelligent sources.
"The inadequacy of proposed materialistic causes forms only a part of the basis of the argument for intelligent design. 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 specified information, namely, intelligence. We are not ignorant of how information arises. According to information theorist Henry Quastler...'the creation of new information is habitually associated with conscious activity' "....I described indirect evidence which is a recognized form of proof for a causal agent...if you have no theory which explains the formation of complex specified information or functional operational activity without an intelligent origin then you cannot dismiss a known cause for such phenomena. Seen or unseen such phenomena require a sufficient cause.
http://www.evolutionnews.org/2005/12/by_design_not_by_chance001687.html#sthash.hSJbItWP.dpuf

B.Alberts: Molecular Biology of the Cell. 4th edition.
Few of the Many Possible Polypeptide Chains Will Be Useful
Since each of the 20 amino acids is chemically distinct and each can, in principle, occur at any position in a protein chain, there are 20 × 20 × 20 × 20 = 160,000 different possible polypeptide chains four amino acids long, or 20n different possible polypeptide chains n amino acids long. For a typical protein length of about 300 amino acids, more than 10^390 (20^300) different polypeptide chains could theoretically be made. This is such an enormous number that to produce just one molecule of each kind would require many more atoms than exist in the universe.
https://www.ncbi.nlm.nih.gov/books/NBK26830/

Steve Meyer, Signature in the Cell:
Whatever information is—whether thought or an elaborate arrangement of matter—one thing seems clear. What humans recognize as information certainly originates from thought—from conscious or intelligent activity. A message received via fax by one person first arose as an idea in the mind of another. The software stored and sold on a compact disc resulted from the design of a software engineer. The great works of literature began first as ideas in the minds of writers—Tolstoy, Austen, or Donne. Our experience of the world shows that what we recognize as information invariably reflects the prior activity of conscious and intelligent persons.
https://3lib.net/book/917961/a3d8cc

Douglas Axe Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds 2004
The likelihood of randomly arranging 153 amino acids into a protein domain that performed a similar function as β-lactamase was on the order of one in 10^77 similar to the chance of finding one specific atom in the universe.
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://sci-hub.ren/10.1016/j.jmb.2004.06.058

A protein domain is a region of the protein's polypeptide chain that is self-stabilizing and that folds independently from the rest. In general, domains vary in length from between about 50 amino acids up to 250 amino acids in length
https://en.wikipedia.org/wiki/Protein_domain

David L Abel The Universal Plausibility Metric (UPM) & Principle (UPP)  2009 Dec 3
Even if multiple physical cosmoses existed, it is a logically sound deduction that linear digital genetic instructions using a representational material symbol system (MSS) cannot be programmed by the chance and/or fixed laws of physicodynamics. This fact is not only true of the physical universe, but would be just as true in any imagined physical multiverse. Physicality cannot generate non-physical Prescriptive Information (PI). Physicodynamics cannot practice formalisms (The Cybernetic Cut). Constraints cannot exercise formal control unless those constraints are themselves chosen to achieve formal function.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796651/

Edward J. Steele Cause of Cambrian Explosion - Terrestrial or Cosmic? August 2018
The transformation of an ensemble of appropriately chosen biological monomers (e.g. amino acids, nucleotides) into a primitive living cell capable of further evolution appears to require overcoming an information hurdle of superastronomical proportions, an event that could not have happened within the time frame of the Earth except, we believe, as a miracle. All laboratory experiments attempting to simulate such an event have so far led to dismal failure. It would thus seem reasonable to go to the biggest available “venue” in relation to space and time. A cosmological origin of life thus appears plausible and overwhelmingly likely to us
https://sci-hub.ren/10.1016/j.pbiomolbio.2018.03.004

David T.F Dryden How much of protein sequence space has been explored by life on Earth? 15 April 2008
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
https://royalsocietypublishing.org/doi/10.1098/rsif.2008.0085

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.

KatarzynaAdamala 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

Sir Fred Hoyle: The Universe: Past and Present Reflections November 1981
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.
https://calteches.library.caltech.edu/527/2/Hoyle.pdf

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

Charles L. Sanders Heuristic View on Quantum Bio-Photon Cellular Communication 2017
The paper claims that quantum effects performed a sequence search to find functional enzymes !! Is that believable?  
https://sci-hub.ren/10.1007/978-3-319-56372-5_8

Robert T. Pennock Intelligent Design Creationism and Its Critics: Philosophical, Theological, and Scientific Perspectives 2001
If chance and necessity left to themselves cannot generate CSI, is it possible that chance and necessity working together might generate CSI? The answer is No. Whenever chance and necessity work together, the respective contributions of chance and necessity can be arranged sequentially. But by arranging the respective contributions of chance and necessity sequentially, it becomes clear that at no point in the sequence is CSI generated. Consider the case of trial-and-error (trial corresponds to necessity and error to chance). Once considered a crude method of problem-solving, trial-and-error has so risen in the estimation of scientists that it is now regarded as the ultimate source of wisdom and creativity in nature. The probabilistic algorithms of computer science all depend on trial-and-error. So too, the Darwinian mechanism of mutation and natural selection is a trial-and-error combination in which mutation supplies the error and selection the trial. An error is committed after which a trial is made. But at no point is CSI generated.

All historical, observational, testable and repeatable examples PROVE information and operational functionality come from intelligent sources.

"The inadequacy of proposed materialistic causes forms only a part of the basis of the argument for intelligent design. We know from broad and repeated experience that intelligent agents can and do produce information rich systems: we have positive experience based on knowledge of a cause that is sufficient to generate new specified information, namely, intelligence. We are not ignorant of how information arises. According to information theorist Henry Quastler...'the creation of new information is habitually associated with conscious activity' "....I described indirect evidence which is a recognized form of proof for a causal agent...if you have no theory which explains the formation of complex specified information or functional operational activity without an intelligent origin then you cannot dismiss a known cause for such phenomena. Seen or unseen such phenomena require a sufficient cause.

The cell expresses the information contained in DNA (which forms its genetic material) such that it is able to construct its own proteins. This synthesis takes place in the ribosomes, where the peptide bond forms. Peptide bonds are covalent links between amino acids, giving rise to polypeptides which, in turn, form proteins. How is the information contained in a DNA sequence, that is, in a combination of nucleotides containing the four DNA bases (A, C, G, T), translated into the right combination of amino acids from among the twenty possible amino acids that can make up a protein? Thanks to the genetic code. Each of those twenty amino acids is coded by a triplet of bases (nucleotides), known as a codon. The signals for the start and end of the synthesis of a protein are equally marked by codons. The genetic code, which establishes the correspondence between a given codon and an amino acid, has three fundamental properties. It is:
– universal: every living organism uses the same code (there are some exceptions, but they correspond to minor derived changes). Certain computer simulations suggest that the genetic code corresponds to the optimum code, taking account of the physical and chemical properties of the amino acids coded by the different codons;
– redundant: several codons may correspond to a single amino acid. This is the consequence of the fact that there are sixty-four possible codons for only twenty amino acids to be coded;
– unambiguous: a single, unique amino acid corresponds to a single codon.
For the message contained within the DNA to be efficiently translated into proteins, each gene must first be transcribed into messenger RNA (mRNA). The message is then still in the form of combination of four nucleotides carrying the bases A, C, G and U (uracil, U, replaces thymine, T). It then needs an “adaptor” capable of making the link between a codon and a specific amino acid. This function is fulfilled by transfer RNAs (tRNA), specific to each amino acid. In the ribosome, positioned opposite to each codon of the mRNA comes a tRNA bearing the corresponding amino acid according to the genetic code. The tRNA recognizes its specific codon thanks to a sequence known as an anticodon (a complementary triplet sequence to the codon). In this way, a message in an alphabet with just four letters (the four bases) can be translated into an alphabet with twenty letters (the twenty amino acids).
https://3lib.net/book/1015290/17c02d

Paul Davies Transition from Inorganic to Organic Life was Based on Information, Not Chemistry" October 18, 2013
"We propose that the transition from non-life to life is unique and definable," added Davies. "We suggest that life may be characterized by its distinctive and active use of information, thus providing a roadmap to identify rigorous criteria for the emergence of life. This is in sharp contrast to a century of thought in which the transition to life has been cast as a problem of chemistry, with the goal of identifying a plausible reaction pathway from chemical mixtures to a living entity."

In a nutshell, the authors shift attention from the "hardware" – the chemical basis of life – to the "software" – its information content. To use a computer analogy, chemistry explains the material substance of the machine, but it won't function without a program and data. Davies and Walker suggest that the crucial distinction between non-life and life is the way that living organisms manage the information flowing through the system.
"When we describe biological processes we typically use informational narratives – cells send out signals, developmental programs are run, coded instructions are read, genomic data are transmitted between generations and so forth," Walker said. "So identifying life's origin in the way information is processed and managed can open up new avenues for research."
http://www.dailygalaxy.com/my_weblog/2013/10/radical-theory-says-transition-from-inorganic-to-organic-life-was-based-on-information-not-chemistry.html

What Davies missed to point out, is, that this information input could have come only from an intelligent designer. Repeated and uniform OBSERVATIONAL science has also shown us that coded information systems have been shown to be the sole product of an intelligent source. If you disagree with this assertion, then provide documented proof this is not true. Otherwise ... You have to come to grips with the fact that there is absolutely no OBSERVABLE evidence that coded information can be produced by random chance processes and natural selection (evolution). Therefore, coded information can only be produced by intelligence and if natural processes combined with natural selection are not capable of producing coded information

https://web.archive.org/web/20131019024024/https://dailygalaxy.com/my_weblog/2013/10/radical-theory-says-transition-from-inorganic-to-organic-life-was-based-on-information-not-chemistry.html

Paul davies The Algorithmic Origins of Life 19 Jul 2012
If life is more than just complex chemistry, its unique informational management properties may be the crucial indicator of this distinction, which raises the all-important question of how the informational properties characteristic of living systems arose in the first place. This key question of origin may be satisfactorily answered only by first having a clear notion of what is meant by “biological information”. Unfortunately, the way that information operates in biology is not easily characterized. While standard information-theoretic
measures, such as Shannon information, have proved useful, biological information has an additional quality which may roughly be called “functionality” – or “contextuality” – that sets it apart from a collection of mere bits as characterized by Shannon Information content. Biological information shares some common ground with the philosophical notion of semantic information (which is more commonly – and rigorously – applied in the arena of “high-level” phenomena such as language, perception and cognition). We, therefore, identify the transition from non-life to life with a fundamental shift in the causal structure of the system, specifically, a transition to a state in which algorithmic information gains direct, context-dependent, causal efficacy over matter.
http://arxiv.org/pdf/1207.4803v2.pdf

Perry Marshall, Evolution 2.0 page 170
Information possesses another very interesting property that distinguishes it from matter and energy. That property is freedom of choice. In communication, your ability to choose whether “1 = on and 0 = off” or “1 = off and 0 = on” is the most elementary example of the human capacity to choose. Mechanical encoders and decoders can’t make choices, but their very existence shows that the choice was made. By definition, none of these decisions can be derived from the laws of physics because they are freely chosen. In the history of the computer industry, somewhere along the way, somebody got to decide that 1 = “on” and 0 = “off.” Then everyone else decided to adopt that standard. Physics and chemistry alone want us to be fat, lazy, and unproductive. Gravity pulls us down. Entropy makes us old and tired. Clocks wind down. Cars rust. Signals get static. LPs scratch. Desks become cluttered. Bedrooms get strewn with dirty clothes. Choice rises up against this. Evolution 2.0, far from mindless, is literally mind over matter. The unfit adapt. Order and structure increase. Cells exert control over their environments. That means materialism cannot explain the origin of information, the nature of information, or the ability to create a code or language from scratch. It can’t explain thought, feeling, mind, will, or communication.
https://3lib.net/book/2603914/e82d50

Werner Gitt Scientific laws of information and their implications—part 1
Every information transmission chain can be traced back to an intelligent sender It is useful to distinguish here between the original and the intermediate sender. We mean by the original sender the author of the information, and he must always be an individual equipped with intelligence and a will. If, after the original sender, there follows a machine-aided chain consisting of several links, the last link in the chain might be mistaken for the originator of the message. Since this link is only apparently the sender, we call this the intermediate sender (but it is not the original one!).

The original sender is often not visible: in many cases the author of the information is not or no longer visible. It is not in contradiction to the requirement of observability when the author of historical documents is no longer visible—in such a case he was, however, observable once upon a time. Sometimes the information received has been carried via several intermediate links. Here, too, there must have been an intelligent author at the beginning of the chain. Take the example of a car radio: we receive audible information from the loud speakers, but these are not the actual source; neither is the transmission tower that also belongs to the transmission chain. An author (an intelligent originator) who created the information is at the head of the chain. In general we can say that there is an intelligent author at the beginning of every information transmission chain.

The actual (intermediate) sender may not be an individual: we could gain the impression that, in systems with machine-aided intermediate links, that the last observed member is the sender: The user of a car auto-wash can only trace the wash program back to the computer—but the computer is only the intermediate sender; the original sender (the programmer) is nowhere to be seen. The internet-surfer sees all kinds of information on his screen, but his home computer is not the original sender, but rather someone who is perhaps at other end of the world has thought out the information and put it on the internet. It is by no means different in the case of the DNA molecule. The genetic information is read off a material substrate, but this substrate is not the original sender; rather, it is only the intermediate sender. It may seem obvious that the last member of the chain is the sender because it seems to be the only discernible possibility. But it is never the case in a system with machine-aided intermediate links that the last member is the original sender (= author of the information)—it is an intermediate sender. This intermediate sender may not be an individual, but rather only part of a machine that was created by an intelligence. Individuals can pass on information they have received and in so doing act as intermediate senders. However, they are in actuality only intermediate senders if they do not modify the information. If an intermediate changes the information, he may then be considered the original sender of a new piece of information.

Even in the special case where the information was not transmitted via intermediaries, the author may remain invisible. We find in Egyptian tombs or on the obelisks numerous hieroglyphic texts, but the authors are nowhere to be found. No one would conclude that there had been no author. Intelligent Source always refers to an individual who is equipped with a will and consciousness. It is not in contradiction to SLI-4c if the author of the information cannot always be specifically identified, but, rather, sometimes only identified generally, as in the following examples: texts in Egyptian Pharaoh’s tombs (Egyptians), historical documents (unknown author), secret radio messages (the military), computer viruses in the internet (criminals), graffiti (graffiti artists), information in biological systems (creator).

The physicalist thesis is valid only in spontaneous systems whereas genes and proteins are never formed by spontaneous reactions. They are invariably manufactured by molecular machines, and all manufacturing processes do not require only physical quantities but also additional entities like sequences and codes. 1
Genes and proteins are never formed spontaneously in real life. They are invariably manufactured by molecular machines, and all manufacturing processes do not require only physical quantities but also additional entities like sequences and coding rules.
http://creation.com/laws-of-information-1

Biola: Can DNA Prove the Existence of an Intelligent Designer? May 31, 2010
We now know that what runs the show in biology is what we call digital information or digital code. This was first discovered by [James] Watson and [Francis] Crick. In 1957, Crick had an insight which he called “The Sequence Hypothesis,” and it was the idea that along the spine of the DNA molecule there were four chemicals that functioned just like alphabetic characters in a written language or digital characters in a machine code. The DNA molecule is literally encoding information into alphabetic or digital form. And that’s a hugely significant discovery, because what we know from experience is that information always comes from an intelligence, whether we’re talking about hieroglyphic inscription or a paragraph in a book or a headline in a newspaper. If we trace information back to its source, we always come to a mind, not a material process. So the discovery that DNA codes information in a digital form points decisively back to a prior intelligence.
http://magazine.biola.edu/article/10-summer/can-dna-prove-the-existence-of-an-intelligent-desi/

Paul Davies The Fifth Miracle: The Search for the Origin and Meaning of Life 1998 page 82 
The theory of self-organization as yet gives no clue how the transition is to be made between spontaneous, or self-induced, organization—which in even the most elaborate nonbiological examples still involves relatively simple structures—and the highly complex, information-based, genetic organization of living things. An explanation of this genetic takeover must account for more than merely the origin of nucleic acids and their potent entanglement with proteins at some later stage. It is not enough to know how these giant molecules arose or started to interact. We also need to know how the system’s software came into existence. Indeed, we need to know how the very concept of software control was discovered by nature.

The Question of the Origin of Natural Codes
But how did all these optimized and stringent codes of biological communication come about? Here we are up against one of the great enigmas of biology, which thus far has defied all efforts of penetration. Darwinian evolutionary theory offers no help here. Its principle of natural selection or survival of the fittest, as even staunch evolutionists do concede, entails a tautology: it identifies the fittest with the survivors, and so boils down to no more than a "survival of the survivors." Modern molecular biological versions of the principle, where the survivors are less sweepingly described in terms of preservation (and recombination) of genetic information, do somewhat better.3 Still they are good only for treading in place, and that won't change until we have at least an operational definition, some measure of the fitness. Outside biology, the question how codes get to be hardly comes up. It is usually uncalled for; the origins are obvious in the case of man-made codes. Take our telegraph code, for instance, or the codes bankers or military men use. Those are concocted more or less arbitrarily, arising almost fully fledged from the cryptographer's mind. But no one but the most die-hard creationist would believe that the codes of biological communication—the natural codes—have such one-fell-swoop beginnings. The question of the origins of natural codes has haunted two generations of information theorists interested in human languages and, regarding biomolecular communication, the question has loomed large ever since the genetic code was found. Indeed, one cannot help being drawn to something that speaks so eloquently for the unity of life and the early origin of its master code, like the fact that all living beings use the same four-letter alphabet for their genetic information, the same twenty-letter alphabet for their proteins, and the same code to translate from one language to the other. Each of the 64 possible triplets of the 4 RNA bases here is a "codon" that assigns one of the 20 amino acids in the polypeptide chain. Such a code and the hardware that executes it are surely too complex to have started with one swoop.
https://3lib.net/book/3321549/ce8c35

Thomas D. Schneider Evolution of biological information 2000 Jul 15
Here this method is used to observe information gain in the binding sites for an artificial ‘protein’ in a computer simulation of evolution. The simulation begins with zero information and, as in naturally occurring genetic systems, the information measured in the fully evolved binding sites is close to that needed to locate the sites in the genome. The transition is rapid, demonstrating that information gain can occur by punctuated equilibrium.
Discussion:
The results, which show the successful simulation of binding site evolution, can be used to address both scientific and pedagogical issues. Rsequence approaches and remains around Rfrequency (Fig. ​(Fig.2b),2b), supporting the hypothesis that the information content at binding sites will evolve to be close to the information needed to locate those binding sites in the genome, as observed in natural systems (4,6). That is, one can measure information in genetic systems, the amount observed can be predicted, and the amount measured evolves to the amount predicted. This is useful because when this prediction is not met (4,6,28,29) the anomaly implies the existence of new biological phenomena. Simulations to model such anomalies have not been attempted yet.  
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC102656/

Edward J. Steele: Cause of Cambrian Explosion - Terrestrial or Cosmic? August 2018
The transformation of an ensemble of appropriately chosen biological monomers (e.g. amino acids, nucleotides) into a primitive living cell capable of further evolution appears to require overcoming an information hurdle of superastronomical proportions, an event that could not have happened within the time frame of the Earth except, we believe, as a miracle. All laboratory experiments attempting to simulate such an event have so far led to dismal failure. It would thus seem reasonable to go to the biggest available “venue” in relation to space and time. A cosmological origin of life thus appears plausible and overwhelmingly likely to us
https://sci-hub.ren/10.1016/j.pbiomolbio.2018.03.004

Koonin: Genomes and the Protein Universe 2003
The theoretical size of the sequence space, i.e. the total number of possible protein sequences is, for all practical purposes, infinite. Assuming that an average protein length is 200 amino acids, there can be 20^200 different protein sequences, a number that is much greater than, for example, the number of protons in our Universe.
https://www.ncbi.nlm.nih.gov/books/NBK20267/

Matthew K. Matlock Evolution and Functional Information March 05, 2017.
The fantastic rarity of functional proteins computed by this approach emboldens some to argue that evolution is impossible.
https://www.biorxiv.org/content/10.1101/114132v1.full

Nir Hecht Exploring Protein Space: From Hydrolase to Ligase by Substitution 01 September 2020
About one third of random mutations in proteins have severe effects on their function (>90% loss of activity) For natural selection to act as a driving force for molecular evolution, the enzyme catalytic activity must be retained at some level, as an inactive enzyme is a dead end for natural selection. Hence, protein space represents the continuous network of viable sequence combinations via a stepwise mutational process. The mutational trajectory in which protein evolution occurs—while retaining catalytic activity and stability—is complex, given the stochastic nature of mutation and the vast sequence space of proteins. 
https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msaa215/5900267

Mark Eastman, M.D. and Chuck Missler The Origin of Information 1996
http://xwalk.ca/origin2.html

Argument by information 
1. There is matter or energy.
2. It is useless or inactive to direct the origin and make of complex life forms without information and consciousness.
3. DNA stores  huge quantities of coded, specified/instructional, complex information. Many DNA strands have 100 million, or even billions of  segments (one segment is called a nucleotide. Nucleotides are the building blocks, namely purines: adenine, guanine; and pyrimidines: cytosine, thymine and uracil).
4.  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 to emerge without guiding specifying intelligence  are 1:10^451.
5. Proponents of materialism have no answer to the question what generated the first DNA strands, and the information stored in it.
6. Intelligent agents  act frequently  with an end goal in mind, inventing complex machines using many sub-parts that are specified in size, fit, materials, to integrate in a functional whole using  a blueprint to build the object.
7. Therefore, the best causal-adequate answer to explain the origin of the DNA blueprint required for make a organism is a intelligent agency

Argument from the genetic code-like (GCL) binary representation
1. The 64 codons (sequences of 3 nucleotides: adenine, uracil, guanine) and the 20 amino acids are for research by scientists assigned to numerical elements within a system, referred to as the genetic code-like (GCL) binary representation.
2. It is a mathematical model of the underlining physical/chemical processes related to genetic information processing—a so-called structural isomorphism namely, identity or similarity of form or appearance.
3. The GCL binary representation and the genetic code are both isomorphic systems. Thus, the characteristics that are true of the GCL binary representation must also be true of the genetic code.
4. The characteristics of the mathematically modeled GCL binary representation are:
a. Palindromic symmetry (a symmetry like that of the word that reads same backward and forward).
b. Parity symmetry.
c. Organized redundancy (Repetition of messages to reduce the probability of errors).
d. A rich mathematical structure.
5. Such a graceful symmetry, organization, and structure indicates a code that has been designed for a purpose.
6. God necessarily exists.

The argument of Francis Collins
1. Francis Collins is one of the most respected research scientists in the world and was the head of the Human Genome Project. He authored the book "The Language of God."
2. In the beginning of his book he describes his doubts in God and strong belief in the theory of evolution. He was then an atheist.
3. As the project of the human genome advanced, seeing the wonderful complexities of genes changed his scientific conviction in evolution and he became a believer in God.
3a. The human genome consists of all the DNA of our species, the hereditary code of life. This newly revealed text was 3 billion letters long, and written in a strange and cryptographic four-letter code. Such is the amazing complexity of the information carried within each cell of the human body, that a live reading of that code at a rate of one letter per second would take thirty-one years, even if reading continued day and night. Printing these letters out in regular font size on normal bond paper and binding them all together would result in a tower the height of the Washington Monument.
4. Announcing the completion of the first phase of the project in year 2000 he said: "Today we are learning the language in which God created life."
5. Collins insists that "science is not threatened by God; it is enhanced" and "God is most certainly not threatened by science; He made it all possible."
6. The book argues that belief in a transcendent, personal God—and even the possibility of an occasional miracle—can and should coexist with a scientific picture of the world that includes evolution. Thus he follows the footsteps of the Kantian tradition, attempting the great synthesis of the empirical and the spiritual, the pure reason and the practical reason.
7. To give an example: The human genome consists of about 3 billion letters. One letter wrong can cause illnesses like cystic fibrosis. How could anybody generate 3 billion letters describing something capable of living in 3 billion or so years if random mutations are the only thing you have at your disposal?
8. Thus after a detailed research of a reputed scientist, Mr. Collins on the complexity of the genome we must conclude that God exists.

The argument of complex and specified information (CSI)
1. The scientific method consists of a four-step process involving observations, hypothesis, experiments, and conclusion. .
2. Performing many scientific experiments upon natural objects, now already for decades, in many of them, scientists discovered so highly complex and specified information (CSI) that it is very difficult or even impossible to make imitation of such complex units.
3. If scientists cannot make copies of complex and specified units what to say about the dull material nature, natural selection, and mutation creating these.
4. Natural objects containing a high level of CSI means they were produced by a super designer.
5. That super designer can be only God.
6. God exists.

Objection: Organic chemicals are everywhere in the cosmos. Life is probably a fair ordinary development. Complex organic chemicals are regularly detected in nebulae. Organic chemistry is everywhere. The bridge from organic chemicals to self-replicating molecules is small.
Answer:  That's like saying that magnetic medium is widespread in the universe, so musical recordings or software must be ubiquitous. Information, extremely complex and highly ordered information, cannot be explained by the existence of the medium that contains it.

Objection: Arguments from Incredulity and Arguments from Ignorance are useless. Anyway, the scientific community doesn't see a problem with the development of life. If they did, it would be a major news story in scientific journals. It isn't.
Answer: "Self replicating" is not the same thing as information creation


Coded information comes always from a mind Dna_in10



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Stephen C. Meyer Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design pg.268 2013

Intelligent agents, due to their rationality and consciousness, have demonstrated the power to produce specified or functional information in the form of linear sequence-specific arrangements of characters. Digital and alphabetic forms of information routinely arise from intelligent agents. A computer user who traces the information on a screen back to its source invariably comes to a mind— a software engineer or programmer. The information in a book or inscription ultimately derives from a writer or scribe. Our experience-based knowledge of information flow confirms that systems with large amounts of specified or functional information invariably originate from an intelligent source.  The generation of functional information is "habitually associated with conscious activity." Our uniform experience confirms this obvious truth.  It also suggests, therefore, that intelligent design meets the key "causal adequacy" requirement of a good historical scientific explanation. Certainly, intelligence is a "cause now in operation" capable of generating functional or specified information in a digital form. As I write this, my mind is generating specified information. Intelligent agents generate information in the form of software code, ancient inscriptions, books, encrypted military codes, and much else. And since we know of no "presently acting" materialistic cause that also generates large amounts14 of specified information  (especially in a digital or alphabetic form), only intelligent design meets the causal adequacy requirement of a historical scientific explanation. In other words, our uniform experience of cause and effect shows that intelligent design is the only known cause of the origin of large amounts of functionally specified digital information. It follows that the great infusion of such information in the Cambrian explosion points decisively to an intelligent cause.

Intelligent design stands alone as an explanation for the origin of genetic information for another reason: purposive agents have just those necessary powers that natural selection lacks as a condition of its causal adequacy. We have seen that natural selection lacks the ability to generate novel information precisely because it can only act after new functional information has arisen. Natural selection can favor new proteins and genes, but only after they perform some function (influencing reproductive output). The job of generating new functional genes, proteins, and systems of proteins therefore falls entirely to random mutations. Yet without functional criteria to guide a search through the space of possible sequences, random variation is probabilistically doomed. What is needed is not just a source of variation (i.e., the freedom to search a space of possibilities) or a mode of selection that can operate after the fact of a successful search, but instead a means of selection that (a) operates during a search—before success—and that (b) is guided by information about or knowledge of a functional target.

Demonstration of this requirement has come from an unlikely quarter: genetic algorithms. Genetic algorithms are programs that allegedly simulate the creative power of mutation and selection. Richard Dawkins, Bernd-Olaf Küppers, and others have developed computer programs that putatively simulate the production of genetic information by mutation and natural selection.15 Yet these programs succeed only by the illicit expedient of providing the computer with a "target sequence" and then treating proximity to future function (i.e., the target sequence), not actual present function, as a selection criterion. As mathematician David Berlinski shows, genetic algorithms need something akin to a "forward-looking memory" in order to succeed.16 Yet such foresighted selection has no analogue  in nature. In biology, where differential survival depends upon maintaining function, natural selection cannot occur before new functional sequences arise. Natural selection lacks foresight; the process, as evolutionary theorists Rodin and Szathmáry note, works strictly " 'in the present moment,' right here and right now . . . lacking the foresight of potential future advantages."

What natural selection lacks, intelligent design—purposive, goal-directed selection—provides. Rational agents can arrange both matter and symbols with distant goals in mind. They also routinely solve problems of combinatorial inflation. In using language, the human mind routinely "finds" or generates highly improbable linguistic sequences to convey an intended or preconceived idea. In the process of thought, functional objectives precede and constrain the selection of words, sounds, and symbols to generate functional (and meaningful) sequences from a vast ensemble of meaningless alternative possible combinations of sound or symbol.

Similarly, the construction of complex technological objects and products, such as bridges, circuit boards, engines, and software, results from the application of goal-directed constraints. Indeed, in all functionally integrated complex systems where the cause is known by experience or observation, designing engineers or other intelligent agents applied constraints on the possible arrangements of matter to limit possibilities in order to produce improbable forms, sequences, or structures. Rational agents have repeatedly demonstrated the capacity to constrain possible outcomes to actualize improbable but initially unrealized future functions. Repeated experience affirms that intelligent agents (minds) uniquely possess such causal powers.  Analysis of the problem of the origin of biological information, therefore, exposes a deficiency in the causal powers of natural selection and other undirected evolutionary mechanisms that corresponds precisely to powers that agents are uniquely known to possess.

Intelligent agents have foresight. Such agents can determine or select functional goals before they are physically instantiated. They can devise or select material means to accomplish those ends from among an array of possibilities. They can then actualize those goals in accord with a preconceived design plan or set of functional requirements. Rational agents can constrain combinatorial space with distant information-rich outcomes in mind. The causal powers that natural selection lacks—by definition—are associated with the attributes of consciousness and rationality—with purposive intelligence. Thus, by invoking intelligent design to overcome a vast combinatorial search problem and to explain the origin of new specified information, contemporary advocates of intelligent design are not positing an arbitrary explanatory element unmotivated by a consideration of the evidence.
https://3lib.net/book/15198129/3fa8c6

David T.F Dryden How much of protein sequence space has been explored by life on Earth? 15 April 2008
https://royalsocietypublishing.org/doi/10.1098/rsif.2008.0085

Claim: it is instead quite plausible for all of functional protein sequence space to have been explored
Reply: There have supposedly past about 10^16 seconds since the big bang ( 14.7 billion years). There is a limit to the number of things that can occur within the smallest unit of time. Atoms can interact with each other only at most 10^43 times per second. There are about 10^80 atoms in the universe, so there are a limited number of opportunities for any given event to occur in the entire history of the universe. Now let us suppose, that each atom in the entire universe (10^80) would perform that maximal number of possible interactions ( 10^43) per second.  The maximal number of possible events can be calculated by multiplying the three relevant factors: the number of atoms (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 its beginning at 10^139.  This provides a measure of the probabilistic resources of the entire observable universe.

The probability of producing a single 150-amino-acid functional protein by chance stands at about 1 in 10^164.

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

Claim: As an extreme method to reduce the size of sequence space, Dill (1999) suggested that only two types of amino acid were needed to form a protein structure, hydrophilic and hydrophobic, and that furthermore it was critical to define only the surface of the protein.
Reply: Before even starting to incorporate amino acids in a putative polypeptide chain to make proteins, the following hurdles would have to be solved:


Nitrogen and carbon was not readily available in fixed form, necessary elements of amino acids, which were no readily available. The lifetime of ammonia would also be short because of its photochemical dissociation. 
Organosulfur compounds required in a few amino acids used in life had to be readily available. 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)
Eight proteinogenic amino acids were never, or in very small amounts abiotically synthesized under prebiotic conditions.
There was no mechanism to concentrate the amino acids all together at one assembly site.
There was no selection process to select twenty, and not more or less amino acids to make proteins.
Only the best suited could/should/would have been selected to enable the formation of soluble structures with close-packed cores, allowing the presence of ordered binding pockets inside proteins
Nature would not have "known" which would have been the set of amino acids near ideal and optimal to make proteins.
No selective process is known to get only homochiral, which is left-handed configuration amino acids.
There was no process avoiding the concomitant synthesis of undesired or irrelevant by-products.
There was no selection process of only bifunctional monomers with amino groups and carboxyl groups. AA's with unifunctional monomers (with only one functional group) disrupt the polymer chains.
Amino acids would DEVOLVE to give uselessly complex mixtures, “asphalts”
They would not be able to bond and polymerize by non-enzymatic means, without the ribosome
There are four different ways to bond AA's together by the side chains. if bonded to the wrong side chain, no deal. 
The polypeptide chain would hydrolyze to its constituent amino acids.
In a hypothetical prebiotic assembly process, in each trial, the average protein would have had to be  400 amino acid  units in length
If a usable sequence were obtained, the action would have had to stop so that it would be preserved, and shuffling would have had to restart to obtain all proteins required for life.
1/3 of all proteins once folded require chaperones, other proteins, that help the protein to fold into its proper, functional shape. They were had also to emerge somehow prebiotically.
The synthesized proteins would have had to be able to merge and interlink into assembly lines and metabolic pathways, ready for working together in a living system.
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.

Frozen, but no accident – why the 20 standard amino acids were selected 07 December 2016
https://febs.onlinelibrary.wiley.com/doi/full/10.1111/febs.13982
Which amino acids came first?
It is plausible that the first proteins used a subset of the 20 and a simplified Genetic Code, with the first amino acids acquired from the environment. Several studies agree on a consensus set of these amino acids, comprising Ala, Asp, Glu, Gly, Ile, Leu, Pro, Ser, Thr and Val. It is likely that folded proteins, with some desirable function, can be produced from a subset of the 20, although this has not yet been demonstrated for this set of 10. For example, Longo et al. [20] showed that β‐trefoil proteins can be produced using just these 10 plus Asn, Gln and Arg in high salt. Their set is notable for amino acids with a high propensity for α‐helices (e.g. Ala and Leu) and β‐sheets (e.g. β‐branched Val, Ile and Thr), although no positively charged side chains. Additional amino acids required the evolution of metabolic pathways, increasing the set to 20. As additional amino acids are added to the code, the advantage of adding a further amino acid decreases compared to the risk of adding too many deleterious mutations simultaneously. While these 10 might be readily available for the first proteins, they were not the only amino acids present. The question still remains as to why these 10 were selected from a much larger pool of amino acids.

B.Alberts: Molecular Biology of the Cell. 4th edition.
https://www.ncbi.nlm.nih.gov/books/NBK26830/
Few of the Many Possible Polypeptide Chains Will Be Useful
Since each of the 20 amino acids is chemically distinct and each can, in principle, occur at any position in a protein chain, there are 20 × 20 × 20 × 20 = 160,000 different possible polypeptide chains four amino acids long, or 20n different possible polypeptide chains n amino acids long. For a typical protein length of about 300 amino acids, more than 10^390 (20^300) different polypeptide chains could theoretically be made. This is such an enormous number that to produce just one molecule of each kind would require many more atoms than exist in the universe.

Paul Davies , the fifth miracle, page 82
The theory of self-organization as yet gives no clue how the transition is to be made between spontaneous, or self-induced, organization—which in even the most elaborate nonbiological examples still involves relatively simple structures—and the highly complex, information-based, genetic organization of living things. An explanation of this genetic takeover must account for more than merely the origin of nucleic acids and their potent entanglement with proteins at some later stage. It is not enough to know how these giant molecules arose or started to interact. We also need to know how the system’s software came into existence. Indeed, we need to know how the very concept of software control was discovered by nature.

The Question of the Origin of Natural Codes
But how did all these optimized and stringent codes of biological communication come about? Here we are up against one of the great enigmas of biology, which thus far has defied all efforts of penetration. Darwinian evolutionary theory offers no help here. Its principle of natural selection or survival of the fittest, as even staunch evolutionists do concede, entails a tautology: it identifies the fittest with the survivors, and so boils down to no more than a "survival of the survivors." Modern molecular biological versions of the principle, where the survivors are less sweepingly described in terms of preservation (and recombination) of genetic information, do somewhat better.3 Still they are good only for treading in place, and that won't change until we have at least an operational definition, some measure of the fitness. Outside biology, the question how codes get to be hardly comes up. It is usually uncalled for; the origins are obvious in the case of man-made codes. Take our telegraph code, for instance, or the codes bankers or military men use.

Those are concocted more or less arbitrarily, arising almost fully fledged from the cryptographer's mind. But no one but the most die-hard creationist would believe that the codes of biological communication—the natural codes—have such one-fell-swoop beginnings. The question of the origins of natural codes has haunted two generations of information theorists interested in human languages and, regarding biomolecular communication, the question has loomed large ever since the genetic code was found. Indeed, one cannot help being drawn to something that speaks so eloquently for the unity of life and the early origin of its master code, like the fact that all living beings use the same four-letter alphabet for their genetic information, the same twenty-letter alphabet for their proteins, and the same code to translate from one language to the other. Each of the 64 possible triplets of the 4 RNA bases here is a "codon" that assigns one of the 20 amino acids in the polypeptide chain. Such a code and the hardware that executes it are surely too complex to have started with one swoop.

Po-Ssu Huang The coming of age of de novo protein design 2016
https://sci-hub.ren/10.1038/nature19946

Claim: It is useful to begin by considering the fraction of protein sequence space that is occupied by naturally occurring proteins. The number of distinct sequences that are possible for a protein of typical length is 20^200 sequences (because each of the protein’s 200 residues can be one of 20 amino acids), and the number of distinct proteins that are produced by extant organisms is on the order of 10^12because evolution proceeds by incremental mutation and selection, naturally occurring proteins are not spread uniformly across the full sequence space; instead, they are clustered tightly into families.
My comment: First of all, evolution by natural selection was not a driving force prior DNA replication. Secondly: Why should natural forces have restricted their search to functional clusters? Any search for a target that has less than 1 chance in 10^139 exceeds the universal probability bound; it exhausts and is far beyond the total number of events that could have occurred in the observable universe since the origin of the universe, supposedly 13,7 billion years ago.

Since 20^200 is about 10^260, and the space actually sampled by living organisms is 10^12, the numbers differ by at least 240 orders of magnitude for proteins of length 200, or about 183 orders of magnitude the 150-amino-acid chains

Claim:  Despite the advances in technology of the past 100 years, human-made machines cannot compete with the precision of function of proteins at the nanoscale and they cannot be produced by self-assembly. The properties of naturally occurring proteins are even more remarkable when considering that they are essentially accidents of evolution. Instead of a well-thought-out plan to develop a machine to use proton flow to convert ADP to ATP, selective pressure operated on randomly arising variants of primordial proteins, and there were also hundreds of millions of years in which to get it right.
My comment: Now think about that ??!! They acknowledge that molecular machines used in life are superior to manmade design, yet they believe that random stochastic occurrences on prebiotic earth would explain the feat. Their worldview does not allow them to consider this as evidence for design. How can such a conclusion be taken seriously??!!



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Information in DNA, evidence of a intelligent cause

https://reasonandscience.catsboard.com/t2270-information-in-dna-evidence-of-a-intelligent-cause

Whether you’re creating codes or adapting them to new circumstances, you must create new rules. The only thing we know of that creates or re-creates codes is volitional beings. In all man-made systems, the only thing that makes them evolve is . . . intelligence.” Codes are not matter and they’re not energy. Codes don’t come from matter, nor do they come from energy. Codes are information, and information is in a category by itself.

"All *life forms* definitely must have an enormous amount  of information to keep all their structures functioning." 
                                                                 

1.  No information can exist without a code. 

2.  No code can exist without a free and deliberate convention. 

3.  No information can exist without the five hierarchical levels: 
     statistics, syntax, semantics, pragmatics, and apobetics. 

4.  No information can exist in purely statistical processes. 

5.  No information can exist without a transmitter. 

6.  No information chain can exist without a mental origin. 

7.  No information can exist without an initial mental source; 
     that is, information is, by its nature, a mental and not a material quantity. 

8.  No information can exist without a will. 

These theorems are similar to the laws of gravity and the laws of  thermodynamics, in that no counterexample has 'ever' been found.



Last edited by Otangelo on Sun 3 Jan 2021 - 14:43; edited 1 time in total

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Biology Shows us that Codes Cannot be Randomly Generated


Codes are the product of a mind. A thinking entity outside the cell has to be responsible for the double dose of the DNA and the Protein , which use different languages and yet can communicate with each other. One would never dare insist that random ordering could create the Morse Code or the Braille reading method. That would be utterly irrational.

The protein molecule, as it turns out, has what biologists refer as sequence specificity. The sequence of those amino acids determines its specific function. If the function of the system as a whole depends critically upon the specific arrangement of the parts, then it is a code. Both proteins and the DNA have a language. But they are different from one another. Languages have this same property.

So does a computer program. The sentence, “My name is Henry,” is written in the English language. Each of the letters in that sentence have specific information that when placed together performs a function. The code allows the reader that must also know that code to decipher the meaning.

If the reader understands the code that interprets each letter, he is able to understand the sentence. This is viewed as specified complexity because it transfers functional information in asymmetrical codes. It is not the simple complexity of repetitive symmetrical patterns created by nature. Such as in crystals or wave patterns in sand that form simple complexity due to electrical affinities in atoms and molecules. These patterns are periodic and predictable. A code on the other hand must be aperiodic and each element must have a specific meaning understood by the reader. “My Name is Henry” is a code in the English language that can be understood by those who know the code.

The numerical sequence, “100 1101 101 1001 100 1110 100 0001 100 1101 100 0101 100 1001 101 0011 100 1000 100 0101 100 1110 101 0010 101 1001,” says, “My name is Henry,” in the American Standard Code for Information Interchange (ASCII). This is the binary code that my computer is using to store the data I input when I am writing.

Both these have complexity and specific information. The sentence, “Xt morh br kturs,” has the same number of letters as “My name is Henry.” It has irregular unrepeatable complexity, it is also asymmetrical, but it has no specific information because it does not have a code. This exhibits what information scientists call “mere complexity” as opposed to “specified complexity.”

Codes that exhibit specified complexity (that is, it carries functional information) are not found anywhere in the natural world outside of living things. Specified complexity cannot appear through random chaotic processes. They must be imputed by a mind that understands the symbols and the code.

The existence of a code automatically presupposes two minds, but at minimum one mind. The mind of the message giver is the essential component and the mind of the message receiver is the secondary element.

In 1977 scientists sent out Voyager1 to space with many coded messages on a plate. They did so with the hope that the second mind would see those codes and infer that intelligence exists on planet earth. Why? Because random ordering does not create codes, they provide to any who might come upon it the evidence of intelligence existing in our planet. It was basically our note in a bottle thrown into the cosmic ocean.

Included in the many images portrayed in that golden disk is that of the DNA. In the back of the golden record are symbols that instruct the “receiver” how to use the record player with the stylus in the right position at the exterior of the record. Beyond that even the numbers 1, 2, 3 are noted in the code of binary numbers. There are coded instructions in how to read the pictures, etc. Our astrophysicists understood that such specific information conveyed in codes would be understood as a sign of intelligence by any “alien” that would happen upon our little satellite.

The fundamental presupposition to the mission of Voyager1 is that any alien that by chance might come upon it would assume that random ordering could not have created such specified complexity. The coded symbols prove that a conscious mind sent the message. Whether or not a conscious mind will receive the message is another story. But, the point is that a code automatically presupposes a code inventor and message giver. In this we are in complete agreement with the astrophysicists that designed and engineered the coded message in this gold disk sent on Voyager 1.

The complexity of the hardware of the Voyager satellite, combined with the specified complexity of the coded messages inscribed on its golden plate, proves to any alien that might happen upon it that an intelligent mind sent it. In exactly the same way, the gene-expression system in the cell is the “Voyager” sent by God to humankind that proves to us that intelligence designed life. The cell is our golden record engineered by the Creator for those with eyes to see and ears to hear.

“Apart from the molecules comprising the gene-expression system and machinery of the cell, sequences or structures exhibiting such specified complexity or specified information are not found anywhere in the natural- that is the non-human world. Sequences and structures exhibiting either redundant order or mere complexity are common in the chemical substrate of nature. But structures exhibiting specified complexity are completely unknown there apart from DNA, RNA, and proteins. As the origin-of-life biochemist Leslie Orgel observes, ‘Living organisms are distinguished by their specified complexity. Crystals…fail to qualify as living because they lack complexity; mixtures of random polymers fail to qualify because they lack specificity.’” (Signature in the Cell by Stephen C. Meyer, Harper Collins Publishers, New York, 2009, pg.110)

Polypeptide chains that do not become proteins exhibit mere complexity, but not specified complexity. They are like, “Xt morh br kturs.” From the thousands of possible combinations of amino acids relatively few can carry specific information in the form of proteins. Both the proteins and nucleotides exhibit specified complexity. Moreover, they have a code that is mutually compatible and allows them to function together for they are both mutually interdependent. The secret of their intercommunication is a marvel to understand.

The language of the DNA would be meaningless if it could not interface with the language of proteins. Hence, if random processes were responsible for their origin, they would have to evolve simultaneously. How did random chaotic processes manage that miracle of the first magnitude? What selective pressure could carry out such a feat?

It seems infinitely more plausible to account for this unique phenomenon, as an exhibited common design by the common Designer, leaving His fingerprint in the evidence of His previsioned design. Here, is yet another vital thread in the intricate tapestry of life that bears witness to His genius design of our creation and specifically of life itself.

As we shall see, the insurmountable problem for the evolutionist is that there is a mutual interdependence that exists between the basic molecules and components of the cell, which would require of evolution to develop each of them simultaneously in order for them to function, as they are all needed in the cell, at the same time.

Only a Master Designer could have imagined the two languages and the ability of each to interpret the other. Evolution has no answer for this.

Coded information comes always from a mind Geneti13

CODES - RANDOM EVOLUTION VS DIVINE DESIGN·WEDNESDAY, JANUARY 30, 2019

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