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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 » Information: Main topics on complex, specified/instructional coded information in biochemical systems and life

Information: Main topics on complex, specified/instructional coded information in biochemical systems and life

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Otangelo


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Main topics on complex, specified/instructional coded information in biochemical systems and life

https://reasonandscience.catsboard.com/t2625-information-main-topics-on-complex-specified-instructional-coded-information-in-biochemical-systems-and-life

Is the Genetic Code a) an information-bearing sequence of DNA nucleotides or b) a translation program? ( Don't google)

George Gilder, a proponent of ID, co-founder of the Discovery Institute,  vs Richard Dawkins:  Podcast from 2005
Dawkins talk starts at 22:18
https://dcs.megaphone.fm/BUR9801030455.mp3?key=d621210697253d413a8a1148a524b6c7

Dawkins: DNA Information, in a sense, comes first. He ( Gilder) then said: Information implies intelligence. Now we come really down to the wire. Information DOES NOT imply intelligence. That was the genius of Darwin. Superficially though, it looks like information implies intelligence. But if you are going to postulate a supernatural intelligence, as the origin of complexity of life, ( complexity is just another word for complexity ) It was the genius of Darwin to show, organized complexity can come about from primeval simplicity. If it required God, then we would have an infinite regress, saying: Where does the original intelligence come from?  

Perry Marshall: Where life came from, according to Richard Dawkins March 9, 2016
https://evo2.org/richard-dawkins/

Michael Levin:  Living Things Are Not (20th Century) Machines: Updating Mechanism Metaphors in Light of the Modern Science of Machine Behavior 16 March 2021
Biology and computer science are not two different fields; they are both branches of information science, working in distinct media with much in common.
https://www.frontiersin.org/articles/10.3389/fevo.2021.650726/full

Biosemiotics is a field of semiotics and biology that studies the meaning-making or production and interpretation of signs and codes in the biological realm. Biosemiotics attempts to integrate the findings of biology and semiotics and proposes a paradigmatic shift in the scientific view of life, in which semiosis (sign process, including meaning and interpretation) is one of its immanent and intrinsic features.
https://en.wikipedia.org/wiki/Biosemiotics

Chance to find a message written on a cloud in the sky: "Jesus loves you" randomly,  is as DNA creating its own software, and upon it, writing a complex algorithm to make a protein by accident.
https://www.youtube.com/watch?v=FT-RsCo1Flg

David L Abel Dichotomy in the definition of prescriptive information suggests both prescribed data and prescribed algorithms: biosemiotics applications in genomic systems 2012 Mar 14
"Functional Information (FI)" has now been formalized into two subsets: Descriptive Information (DI) and Prescriptive Information (PI). This formalization of definitions precludes the prevailing confusion of informational terms in the literature. The more specific and accurate term "Prescriptive Information (PI)" has been championed by Abel to define the sources and nature of programming controls, regulation and algorithmic processing. Such prescriptions are ubiquitously instantiated into all known living cells
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3319427/

The problem of information Norbert Weiner - MIT Mathematician - Father of Cybernetics
"Information is information, not matter or energy. No materialism which does not admit this can survive at the present day."

Sankar Chatterjee The Origin of Prebiotic Information System in the Peptide/RNA World: A Simulation Model of the Evolution of Translation and the Genetic Code  2019 Mar; 9
The origin of prebiotic information remains a mystery
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6463137/


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 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 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 


We need to explain the origin of both the hardware and software aspects of life, or the job is only half-finished. Explaining the chemical substrate of life and claiming it as a solution to life’s origin is like pointing to silicon and copper as an explanation for the goings-on inside a computer. It is this transition where one should expect to see a chemical system literally take on “a life of its own”, characterized by informational dynamics which become decoupled from the dictates of local chemistry alone (while of course remaining fully consistent with those dictates). Thus the famed chicken-or-egg problem (a solely hardware issue) is not the true sticking point. Rather, the puzzle lies with something fundamentally different, a problem of causal organization having to do with the separation of informational and mechanical aspects into parallel causal narratives. The real challenge of life’s origin is thus to explain how instructional information control systems emerge naturally and spontaneously from mere molecular dynamics.

For explaining the origin of life scientists must also explain the origin of specified information contained in each life form's unique DNA and RNA. Just like the whole universe, information is subject to entropy. See information entropy. When no information exists it is impossible for information to arise naturally in a mindless world. Information is more than just matter, it contains a message encoded by other parts of the cell. Like a language has a sender and a receiver who both understand the message and act according to it. Another irreducibly complex factor of life. On top of that meaningful information itself is not materially based. See also Semiotics. All communication and data processing, as is also done in the cell, is achieved through the use of symbols. When a computer processes code it has to decode it in order to convert the code into a corresponding action.

It has to be explained:

- a library index and fully automated information classification, storage and retrieval program ( chromosomes, and the gene regulatory network )
- The origin of the complex, codified, specified, instructional information stored in the genome and epigenetic codes to make the first living organism
- The origin of the genetic Code
- How it got nearly optimal for allowing additional information within protein-coding sequences
- How it got more robust than 1 million alternative possible codes
- The origin of the over twentythree epigenetic codes
- The origin of the information transmission system, that is the origin of the genetic code itself, encoding, transmission, decoding and translation
- The origin of the genetic cipher/translation, from digital ( DNA / mRNA ) to analog ( Protein )
- The origin of the hardware, that is DNA, RNA, amino acids, and carbohydrates for fuel generation
- The origin of the replication/duplication of the DNA
- The origin of the signal recognition particle
- The origin of the tubulin Code for correct direction to the final destination of proteins

none of the above items can be explained by evolution since evolution depends on all this.

https://reasonandscience.catsboard.com/t2625-information-main-topics-on-complex-specified-instructional-coded-information-in-biochemical-systems-and-life


Claim: The claim that DNA contains blueprints, instructional complex information is an assumption but even if true, is not analogous to DNA and comes down to an argument from ignorance (DNA is really so complex we don't fully understand it therefore god).
Reply: The problem of DNA is manyfold: It is about how the hardware, that is mononucleotides came to be on prebiotic earth equivalent to single alphabetic letters, and the software, how they polymerized to become genetic information carriers, in the same sense as single letters are joined to form words, sentences, and paragraphs, and finally blueprints, instructional information, and moreover, on top of that,  the origin of the machinery, apt to process the algorithmic information, which is by itself encoded in by genetic information (  giving rise to a catch22 situation: It takes encoding and transcription ( DNA & RNA polymerase machines ) transmission (mRNA) and decoding ( Ribosome ) systems to set up this very own information transmission system & machinery which we try to explain ). It had to emerge all together since one has no function without the other.

Paul Davies: the fifth miracle page 62: Due to the organizational structure of systems capable of processing algorithmic (instructional) information, it is not at all clear that a monomolecular system – where a single polymer plays the role of catalyst and informational carrier – is even logically consistent with the organization of information flow in living systems, because there is no possibility of separating information storage from information processing (that being such a distinctive feature of modern life). As such, digital-first systems (as currently posed) represent a rather trivial form of information processing that fails to capture the logical structure of life as we know it.

Cells must be created and be functional, all at once. As Graham Cairns-Smith noted, this system has to be fixed in its essentials through the critical interdependence of subsystems. Irreducibly complex and interdepend systems cannot evolve but depend on intelligence with foreknowledge on how to build discrete parts with distant goals.


1. Regulation, governing, controlling, recruiting, interpretation, recognition, orchestrating, elaborating strategies, guiding, instruct are all tasks of the gene regulatory network.
2. Such activity can only be exercised if no intelligence is present if the correct actions were pre-programmed by intelligence.
3. Therefore, most probably, the gene regulatory network was programmed by an intelligent agency.

1. The setup of functional Information retrieval systems, like a library classification system, is always tracked back to intelligence
2. The gene regulatory network is a fully automated, pre-programmed, ultra-complex gene information extraction system
3. Therefore, its origin is best explained through intelligent setup

1. DNA stores information based on a code system, and codified, complex, instructional information, with the same function as a blueprint.  
2. All codes and blueprints come from intelligence.
3. Therefore, the genetic code and the instructions to build cells and complex biological organisms, stored in DNA, were most likely created by an intelligent agency.

1. Cells use sophisticated information transmission and amplification systems (signalling pathways), information interpretation, combination and selection ( the Gene regulatory network ) encoding and transcription ( DNA & RNA polymerase machines ) transmission (mRNA), and decoding ( Ribosome ) systems.
2. Setup of information transmission systems, aka.  transmission, amplification, interpretation, combination, selection, encoding, transmission, and decoding are always a deliberate act of intelligence
3. The existence of the genetic information transmission system is best explained by the implementation of an intelligent designer.

1. yeast, crustacea, onion roots, and algae use languages  and sophisticated communication channels even through light photons
2. The setup of languages, and information transmission systems is always tracked back to intelligence.
3. Therefore, the origin of these organisms using these sophisticated languages, and communication channels, is best explained by design.

The Laws of information
1. Anything material such as physhical/chemical processes cannot create something non-material
2. Information is a non-material fundamental entity and not a property of matter
3. Information requires an material medium for storage and transmission
4. Information cannot arise fRom Statistical processes
5. There can be no information without a code ie. No knowledge can be shared without a code
6. All codes result from an intentional choice and agreement between sender and recipient 
7. The determination of meaning for and from a set of symbols is a mental process that requires intelligence
8. There can be no new information without an intelligent purposeful sender
9. Any given chain of information can be traced back to an intelligent source
10. Information comprises the non-material foundation for all 
a. Technological systems
b. Works of art
c. Biological systems

Therefore:
A. since the DNA code of all life is clearly within the definition domain of information, we can conclude there must be a sender.
B. Since the density and complexity of the DNA encoded information is billions of times greater than man's present technology , we conclude that the sender must be extremely intelligent
C. Since the sender must have
- encoded (stored) the information into the DNA molecules
- Constructed the molecular biomachines required for the encoding, decoding and synthesizing process and
- Designed all the features for the original life forms
We conclude that 
• the sender must be purposeful and supremely powerful.
• Since information is a non-material fundamental entity and cannot originate from material quantities, The sender must have a non-material component
• Since information is a non-material fundamental entity and cannot originate from material quantities and since information also originates from man then mans nature must have a non-material component or SPIRIT.
• Since information is a non-material entity then the assumption that the Universe is comprised solely of mass and energy is false
• Since biological information originates only from an intelligent sender and all theories of chemical and biological evolution require that information must originate solely from mass and energy alone (without a sender) then al, theories or concepts of biological evolution is false.
• Just 2mm of a DNA strand contains as much information as 100 million 40GB hard drives, think about that a little, do you really think that is the result of pure Undirected random natural processes?

1. D
2. D -> A & B & C
3. A & B & C -> requires Intelligence
4. Therefore Intelligence

A: Information, Biosemiotics ( instructional complex mRNA codon sequences transcribed from DNA )
B: Translation mechanism ( adapter, key, or process of some kind to exist prior to translation = ribosome )
C: Genetic Code
D: Functional proteins

1. Life depends on proteins ( molecular machines ) (D). Their function depends on the correct arrangement of a specified complex sequence of amino acids.
2. That depends on the translation of genetic information (A) through the ribosome (B) and the genetic code (C), which assigns 61 codons and 3 start/stop codons to 20 amino acids
3. Instructional complex Information ( Biosemiotics: Semantics, Synthax, and pragmatics (A)) is only generated by intelligent beings with foresight. Only intelligence with foresight can conceptualize and instantiate complex machines with specific purposes, like translation using adapter keys (ribosome, tRNA, aminoacyl tRNA synthetases (B)) All codes require arbitrary values being assigned and determined by agency to represent something else ( genetic code (C)).
4. Therefore, Proteins being the product of semiotics/algorithmic information including translation through the genetic code, and the manufacturing system ( information directing manufacturing ) are most probably the product of a divine intelligent designer.


The problem of translation through the Ribosome is threefold:

1. The origin of Information stored in the genome.

1. Semiotic functional information is not a tangible entity, and as such, it is beyond the reach of, and cannot be created by any undirected physical process.
2. This is not an argument about probability. Conceptual semiotic information is simply beyond the sphere of influence of any undirected physical process. To suggest that a physical process can create semiotic code is like suggesting that a rainbow can write poetry... it is never going to happen!  Physics and chemistry alone do not possess the tools to create a concept. The only cause capable of creating conceptual semiotic information is a conscious intelligent mind.
3. Since life depends on the vast quantity of semiotic information, life is no accident and provides powerful positive evidence that we have been designed. A scientist working at the cutting edge of our understanding of the programming information in biology, he described what he saw as an “alien technology written by an engineer a million times smarter than us”

2. The origin of the adapter, key, or process of some kind to exist prior to translation = ribosome

1. Ribosomes have the function to translate genetic information into proteins. According to Craig Venter, the ribosome is “an incredibly beautiful complex entity” which requires a minimum of 53 proteins. It is nothing if not an editorial perfectionist…the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products…  They are molecular factories with complex machine-like operations. They carefully sense, transfer, and process, continually exchange and integrate information during the various steps of translation, within itself at a molecular scale, and amazingly, even make decisions. They communicate in a coordinated manner, and information is integrated and processed to enable an optimized ribosome activity. Strikingly, many of the ribosome functional properties go far beyond the skills of a simple mechanical machine. They can halt the translation process on the fly, and coordinate extremely complex movements. The whole system incorporates 11 ingenious error check and repair mechanisms, to guarantee faithful and accurate translation, which is life-essential.
2. For the assembly of this protein-making factory, consisting of multiple parts, the following is required: genetic information to produce the ribosome assembly proteins, chaperones, all ribosome subunits, and assembly cofactors. a full set of tRNA's, a full set of aminoacyl tRNA synthetases, the signal recognition particle, elongation factors, mRNA, etc. The individual parts must be available,  precisely fit together, and assembly must be coordinated. A ribosome cannot perform its function unless all subparts are fully set up and interlocked.
3. The making of a translation machine makes only sense if there is a source code, and information to be translated. Eugene Koonin: Breaking the evolution of the translation system into incremental steps, each associated with a biologically plausible selective advantage is extremely difficult even within a speculative scheme let alone experimentally. Speaking of ribosomes, they are so well-structured that when broken down into their component parts by chemical catalysts (into long molecular fragments and more than fifty different proteins) they reform into a functioning ribosome as soon as the divisive chemical forces have been removed, independent of any enzymes or assembly machinery – and carry on working.  Design some machinery that behaves like this and I personally will build a temple to your name! Natural selection would not select for components of a complex system that would be useful only in the completion of that much larger system. The origin of the ribosome is better explained through a brilliant intelligent and powerful designer, rather than mindless natural processes by chance, or/and evolution since we observe all the time minds capabilities producing machines and factories.

3. The origin of the genetic code

1. A code is a system of rules where a symbol, letters, words, etc. are assigned to something else. Transmitting information, for example, can be done through the translation of the symbols of the alphabetic letters, to symbols of kanji, logographic characters used in Japan.  In cells,  the genetic code is the assignment ( a cipher) of 64 triplet codons to 20 amino acids.
2. Assigning meaning of characters through a code system, where symbols of one language are assigned to symbols of another language that mean the same, requires a common agreement of meaning. The assignment of triplet codons (triplet nucleotides) to amino acids must be pre-established by a mind.
3. Therefore, the origin of the genetic code is best explained by an intelligent designer.

The algorithmic origins of life
https://reasonandscience.catsboard.com/t3061-the-algorithmic-origins-of-life

The central problem in biology
https://reasonandscience.catsboard.com/t2826-the-central-problem-in-biology

Complex Specified/instructing Information – It’s not that hard to understand
https://reasonandscience.catsboard.com/t2374-complex-instructing-specified-information-its-not-that-hard-to-understand

DNA stores literally coded information
https://reasonandscience.catsboard.com/t1281-dna-stores-literally-coded-information

The language of the genetic code
https://reasonandscience.catsboard.com/t1472-the-language-of-the-genetic-code

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

The genetic code cannot arise through natural selection
https://reasonandscience.catsboard.com/t1405-the-genetic-code-cannot-arise-through-natural-selection

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

The genetic code, insurmountable problem for non-intelligent origin
https://reasonandscience.catsboard.com/t2363-the-genetic-code-unsurmountable-problem-for-non-intelligent-origin

Wanna Build a Cell? A DVD Player Might Be Easier
https://reasonandscience.catsboard.com/t2404-wanna-build-a-cell-a-dvd-player-might-be-easier

The amazing DNA information storage capacity
https://reasonandscience.catsboard.com/t2052-the-amazing-dna-information-storage-capacity

The different genetic codes
https://reasonandscience.catsboard.com/t2277-the-different-genetic-codes

The various codes in the cell
https://reasonandscience.catsboard.com/t2213-the-various-codes-in-the-cell

DNA - the instructional blueprint of life
https://reasonandscience.catsboard.com/t2544-dna-the-instructional-blueprint-of-life

Is calling DNA code just a metaphor?
https://reasonandscience.catsboard.com/t1466-is-calling-dna-a-code-just-a-metaphor#2131

The algorithmic origins of life
https://reasonandscience.catsboard.com/t3061-the-algorithmic-origins-of-life

More links:
https://biosemiosis.net/?fbclid=IwAR0B_bZLCzCWkziNuoich1DfoNtswa5nY5HGEAdf9aOYzctflmDCHdKZmVY
https://web.archive.org/web/20170614142752/http://www.biosemiosis.org/index.php/why-is-this-important

Biological Information Processing
https://www.evolutionofcomputing.net/Multicellular/BiologicalInformationProcessing.html?fbclid=IwAR3nq-fkfjN9vbqzDKVekzIwG1kNm91XmGWc__paDt3IAEewmeRgsxXPZHY



Last edited by Otangelo on Sat Nov 13, 2021 9:41 am; edited 39 times in total

https://reasonandscience.catsboard.com

2Information: Main topics on complex, specified/instructional coded information in biochemical systems and life Empty The Information Theory of Life Sat Jul 11, 2020 8:44 pm

Otangelo


Admin

The Information Theory of Life

The polymath Christoph Adami is investigating life’s origins by reimagining living things as self-perpetuating information strings.

Life, he argues, should not be thought of as a chemical event. Instead, it should be thought of as information. The shift in perspective provides a tidy way in which to begin tackling a messy question. In the following interview, Adami defines information as “the ability to make predictions with a likelihood better than chance,” and he says we should think of the human genome — or the genome of any organism — as a repository of information about the world gathered in small bits over time through the process of evolution.

My comment: It is remarkable how proponents of materialism tap dance in regards of abiogenesis. They propose metabolism first scenarios, then replication first, Information first, and so forth. They cannot go over it, that a stepwise, evolutionary manner of the origin of life is not feasible. But try, and try, and try, and never give up an idea that is obviously never going to work. They avoid admitting that the Cell is irreducibly complex, because, if doing so, they are giving to us, bad creationists, pseudo-scientific hoodlums, a free lunch, which is committing the greatest sin for a materialistic oriented mind.

Think of evolution as a process where information is flowing from the environment into the genome. The genome learns more about the environment.

My comment: This is pure nonsense !! Environments DO NOT produce information !! And genomes do not learn. Only conscient minds learn.

We of course know that all life on Earth has enormous amounts of information that comes from evolution, which allows information to grow slowly.

My comment: Genetic information had to be present to generate the first living Cell. And there was no evolution since it depends on DNA replication.

How Does Life Come From Randomness?
https://www.youtube.com/watch?v=k9QYtbjzjAw


" Could it be life – RNA molecules and everything that comes after that. They’re delicate little beings and you might worry that, put in a little soup, the random motion would destroy them. But perhaps they’re not so delicate. And perhaps they’re even a predictive consequence of a random Earth but with energy imposed into the system. That is something we can’t answer now, but is an exciting new vein or way of people are thinking about the problem and hope to solve it. "

My comment: Why putting hope in something that can be demonstrated - will never work? This is the kind of nebulous information, that the uninformed with swallow, believing that there is justification for hope when there is not.

Life is information stored in a symbolic language. The secret of all life is that through the copying process, we take something that is extraordinarily rare and make it extraordinarily abundant. Before evolution, you couldn’t have the process of evolution. As a consequence, the first piece of information has to have arisen by chance.

My comment: Did you read that ? The first information came by chance !! This is pure irrationality driven by ideology.

On the one hand, the problem is easy; on the other, it’s difficult. We don’t know what that symbolic language was at the origins of life. It could have been RNA or any other set of molecules. But it has to have been an alphabet. The easy part is asking simply what the likelihood of life is, given absolutely no knowledge of the distribution of the letters of the alphabet. In other words, each letter of the alphabet is at your disposal with equal frequency.

Even simple words are very rare. Then you can do a calculation: How likely would it be to get 100 bits of information by chance? It quickly becomes so unlikely that in a finite universe, the probability is effectively zero.

My comment: Then why not admit intelligent design, rather than to insist to chance ?

The letters of the alphabet, the monomers of hypothetical primordial chemistry, don’t occur with equal frequency. The rate at which they occur depends tremendously on local conditions like temperature, pressure and acidity levels.

My comment: This is another totally irrational and illogic inference. Only minds give symbolic representative attributes to alphabetic letters. Not mindless nature.

I’ve been under attack from creationists from the moment I created life when designing [the artificial life simulator] Avida. I was on their primary target list right away. I’m used to these kinds of fights. They’ve made kind of timid attacks because they weren’t really understanding what I’m saying, which is normal because I don’t think they’ve ever understood the concept of information.

My comment: Well, we do know information theory, and these hypotheses are not backed up by evidence and facts. Just baseless speculation.

https://www.quantamagazine.org/the-information-theory-of-life-20151119/?fbclid=IwAR1fYEcdSpZauuz-RVc2QV7d94dqa1DYV_uqZUctFOsP__C8FecLEfLoqwo



Last edited by Otangelo on Wed Jul 07, 2021 11:32 am; edited 1 time in total

https://reasonandscience.catsboard.com

Otangelo


Admin

The Code of Life
The cell has its own sophisticated information-processing system, much like a computer. Computer programs require programmers, conscious agents with knowledge and foresight who can code the needed instructions, in the right sequence, to generate a functioning and information-rich program. Is there any reason to think that the information in cells also was programmed by a programmer rather than by random processes? 

Foresight in DNA
The cell’s genetic information is a foundational and most ancient characteristic of life. It is essential to how all living things on Earth are formed, move, and reproduce. Without it, no cellular organism would produce the biomolecules essential to life. If matter evolved into living cells through purely blind processes, as evolutionary theory holds, then this information somehow was generated from matter and energy, through unguided natural processes. origin-of-life theorists committed to a purely naturalistic account of life must, therefore, explain how both this genetic information and the cell’s information processing system appeared virtually all at once, since such things, by their very nature, work in direct synergy and thus cannot evolve bit by bit. This impossibility shouldn’t be surprising, since the genetic information and the genetic code together include features like semantic logic and the meaningful ordering of characters—things not dictated by any laws of physics or chemistry. The genome sequence of a cell is essentially an operating system, the code that specifies the cell’s various genetic functions, affecting everything from the cellular chemistry and structure to replication machinery and timing. Because certain functions are shared by all forms of life, genomes are all similar to a considerable extent. For example, all mammals share more than 90% of their genomes. It has been estimated that even life forms as distinctive as humans and bananas share 60% of their genetic information. The unique portions are specific instructions for the varying needs of different genera and species. Because it is so crucial to life on Earth, genetic information had to be transmitted and stored in a way that was as compact, efficient, and error-free as possible. This need presents a set of problems that had to be solved and implemented virtually simultaneously, so that molecules able to store and transmit genetic information was ready to go in the very first organism. DNA (deoxyribonucleic acid) is made up of three classes of chemical. One is the phosphate anion PO4 3- , with its four oxygen atoms distributed in a tetrahedral fashion around the phosphorous atom, producing a triple-negative charge. Another is the five-membered cyclic sugar molecule—ribose—with four available OH linking sites. (DNA uses a special form of ribose called deoxyribose. Deoxyribose has an OH replaced with an H.) The third class of chemical comprises four different kinds of stable, rigid, and heterocyclic bases, two purines and two pyrimidines, each with the ability to firmly attach to ribose via covalent bonds and to each other via two or three H-bonding “supramolecular” arms. The attachments form ribose-plus-base “ribonucleotides” that turn out to be ideal for transmitting the information. Why is that? Let’s take it in stages. 

The Phosphate Anion
If it’s to be viable, life’s long-term storehouse of genetic information cannot break down in the presence of water. The hydrolysis problem, in other words, has to be solved in advance or life’s information storehouse would dissolve as quickly as a sandcastle struck by the incoming tide. How DNA meets this challenge is a wonder of engineering finesse. DNA is what’s known as a polymeric ester, composed of a very long phosphate (PO4 3-) wire—the wire runs close to two meters in humans— interspersed with ribonucleotides. This molecular architecture is perfectly suited for DNA. The 3-D chemical structure of phosphate PO4 3-, with four terminal O-atoms and three net charges, allows it to bind to two ribonucleotides (using two of these O- atoms) while one of the extra O- stays single-charged. If “R” represents a ribonucleotide, this can be written as (R 1O)(R 2O) P(=O)-O-. This remaining negative charge at the end is in resonance with two oxygen atoms. That charge resonance is essential since it stabilizes the DNA molecule against reaction with water (hydrolysis) by forming an electrical shield around the entire double helix. This encompassing electrical field also holds DNA inside the cell nucleus, preventing the precious DNA from escaping via membrane permeation. These properties make PO4 3- the perfect link to construct a stable DNA macromolecule, bonded to the right sugars and bases, well protected against hydrolysis, and perfectly encapsulated inside the nuclear membrane. This exquisitely engineered molecular arrangement, which protects DNA, had to be present for any cell to live. It’s make or break. For DNA to function properly, still another problem had to be solved. Inorganic phosphate PO43- is the perfect link for DNA, but as a link for the long, polymeric molecule, its reaction with deoxyribose is too slow. The cell needed therefore a proper catalyst to speed up this slow but crucial reaction. Enzymes—large, exquisitely designed biomolecules—fulfill this task by accelerating the formation of such links by many orders of magnitude. Making enzymes is another whole incredible process. They would have been needed from the very beginning to make DNA. Yet they themselves have to be made using the DNA sequence they “were born” to make. So we have two ingenious solutions to do-or-die challenges: an engineering marvel—an electrical shield—that protects DNA from breaking down in the presence of water; and another engineering marvel—enzymes— that speeds a crucial reaction that would otherwise be far too slow. And these two ingenious solutions could not come one after the other, because the DNA sequence is necessary to making the enzyme, while the enzyme is necessary for making the DNA. Both the polymeric DNA, with its multiple phosphate-sugar bonds and very slow kinetics, and the proper enzymes to accelerate the formation of the DNA phosphate- sugar bonds, have to be in place at the same time. If only one exists without the other, no cell at all.

Ribose
Another bit of engineering cleverness was needed to cinch the stability of DNA. When forming the phosphate wire, PO4 3- should be able to react with ribose at any of its four OH groups extending from the sugar molecule; but the intrinsic nature of the phosphodiester bonds found in DNA make exclusive use of 5’-3’ OH groups. ( biochemists number the carbon atoms in them. The phosphate backbone of DNA binds the 5’ carbon in one sugar to the 3’ carbon in the next.) It turns out that this 5’-3’ selectivity in OH binding increases DNA’s stability when compared to 5’-2’ linkages. In DNA the 2’ OH group is replaced by H, and is unavailable for binding, and for good reason. This change prevents hydrolysis of the DNA, which is essential for any molecule used for long-term storage of information. A recent article expanded on the criteria for selection: The reason that nature really chose phosphate is due to interplay between two counteracting effects: on the one hand, phosphates are negatively charged and the resulting charge-charge repulsion with the attacking nucleophile contributes to the very high barrier for hydrolysis, making phosphate esters among the most inert compounds known… [But] the same charge-charge repulsion that makes phosphate ester hydrolysis so unfavorable also makes it possible to regulate, by exploiting the electrostatics. This means that phosphate ester hydrolysis can not only be turned on, but also be turned off, by fine tuning the electrostatic environment… This makes phosphate esters the ideal compounds to facilitate life as we know it. 

Thus, only phosphates have the dual capacity needed to make DNA work. Researchers have constructed DNA analogues using sugars beside ribose and measured their properties. So was ribose, this very specific five-membered cyclic sugar, just one good option out of many? It appears not. The final molecule had to be both stable and capable of carrying the code of life. For these jobs, only ribose will do. DNA analogues using other sugars are not suitable information storage molecules. Some DNA made of the other sugars fails to form stable double helices, or their intermolecular interactions are too strong or too weak, or their associations are insufficiently selective. Other DNA analogues adopt various conformations that would hinder the cell machinery from replicating them. Effectively, ribose was the only choice that would work. Darwin suggested that life emerged by chance in a “warm little pond.” In other words, an accident formed a masterful informationstorage molecule equipped with the only sugar that could make it work. But judging from the myriad of molecules bearing two OH groups that could mimic it, the task of making, finding, and specifically selecting this particular and life-essential sugar at random in the “primordial soup” would be dauntingly improbable. Ribose is also ideal at forming a 3-D molecular structure. True, it is not the only sugar that allows for DNA to form a stable double helix, but it’s far and away the best. The resulting inner space within the double helix is about 25 Å, and this distance is just perfect for one monocyclic nitrogen base (T or C) and one bicyclic base (A or G). This perfect space allows the formation of base pairs, in which A pairs with T and C pairs with G, forming a crucial selective criteria of the genetic code. If any sugar other than ribose were used, that distance would be too wide or too narrow.

DNA’s Four Bases
Another crucial question: Why did life “choose” the very specific ATGC quartet of N bases? Another indication of the planning involved in the DNA chemical architecture arises from the choice of a four-character alphabet used for coding units three characters long. Why not more alphabetic characters, or longer units?  It’s fascinating work. But DNA should be as economical as possible, and for DNA to last, it had to be highly stable chemically. And these four bases are exactly what is needed. They are highly stable and can bind to ribose via strong covalent N-O bonds that are very secure. Each base of this “Fantastic Four” can establish perfect matchings with precise molecular recognition through supramolecular H-bonds. The members of the G≡C pair align precisely to establish three strong, supramolecular hydrogen bonds. The A=T pair align to form two hydrogen bonds. A and G do not work, and neither do C and T, or C and A, or G and T. Only G≡C and A=T work. But why don’t we see G≡G, C≡C, A=A or T=T pairings? After all, such pairs could also form two or three hydrogen bonds. The reason is that the 25 Å space between the two strands of the double helix cannot accommodate pairing between the two large (bicyclic) bases A and G, and the two small (monocyclic) bases T and C would be too far apart to form hydrogen bonds. A stable double helix formed by the perfect phosphate-ribose polymeric wire, with proper internal space in which to accommodate either A=T or G≡C couplings with either two or three H-bonds is necessary to code for life. And fortunately, that is precisely what we have. Ribose for RNA and Deoxyribose for DNA There is an even more striking example of potential problems in the DNA structure that had to be solved in advance. DNA must be highly stable, while RNA, as the temporary intermediate between DNA and protein must be dramatically less stable. RNA uses the intact ribose sugar molecule to make its polymeric wire, while DNA uses a de-oxygenated version of it—deoxyribose. Since an OH group has been replaced by an H at an apparently “chemically silent” 2’-position in the ribose ring, it seems strange at first sight to note such care for a seemingly trivial molecular detail. But it turns out that there is a crucial-for-life reason for this amazing chemical trick. The choice of D-ribose for m-RNA and D-deoxyribose for DNA increases the chemical stability of DNA while decreasing that of RNA in an alkaline medium. Both of these are for a reason. If nuclear DNA is the hard drive of life, storing information for the long term, messenger RNA (m-RNA) is life’s flash drive, transmitting information over short periods of time. RNA’s lifetime had therefore to be short, otherwise protein production would never stop. Life needed a way to quickly “digest” via hydrolysis and ideally recycle the components of RNA when its job is finished. When chemists analyzed this “mysterious” OH/H exchange, they discovered that the apparently “silent” 2’-OH group helps RNA undergo hydrolysis about one hundred times faster than DNA. So we see that ribose had to be used in RNA for easy digestion in an alkaline medium, and deoxyribose had to be used in DNA for longevity. Otherwise, life would be impossible. Again, by all appearances this stability control for both DNA and RNA had to be anticipated ahead of time and the solution provided with just-in-time delivery.

Homochirality and the U-to-T Exchange
There are other striking solutions within DNA and RNA. Like many other organic molecules, ribose can come in either a right-handed (D) or left-handed (L) form, and a random assemblage of the stuff would have a roughly equal mix of the two—what is known as a racemic mixture. But a racemic mixture of D-ribose and L-ribose would be biologically disastrous, rendering impossible the proper 3-D coherence of the double helix. Both DNA and RNA need either all D forms, or all L forms—not a mixture. So here’s the mystery: How could purely blind chemical forces have accomplished this challenging 3-D selection? Commenting on the puzzle, Philip Ball, a science writer and an editor of the journal Nature, once conceded, “On the 60th anniversary of the double helix, we should admit that we don’t fully understand how evolution works at the molecular level.” That’s putting it mildly. There is another crucial difference between RNA and DNA. Where DNA uses thymine (T) as one of its bases, RNA uses uracil (U). This U-to-T exchange is intriguing because the chemical structures of T and U are nearly identical, distinguished only by a single, small methyl group (CH3). As the editors of the NSTA WebNews Digest noted, converting uracil to thymine requires energy, so why do cells bother to methylate uracil into thymine for DNA? Additionally, the extra group is placed in what seems to be a rather inert position on the T ring. It seems therefore that such a rather small and inert CH3 group is there only to “differentiate” U and T while disturbing the chemical properties as little as possible. A number of evolutionary explanations have been offered for this U-to-T exchange, but it turns out this exchange maintains the integrity of the whole information storage system, so a fully evolved form of it would have been needed from the start. The four RNA bases—A, U, G, and C—are superb for the job they have, but they also cause a problem if used in the wrong context. The U-to-T exchange is the solution. The original quartet is fine for less stable RNA, but not the best choice for long-lasting DNA. The U base would still establish preferential pairing with A, but the A=U pair is not ideal for the role DNA fills, since U can also match efficiently with all the other bases, including itself. DNA’s T, on the other hand, is much more selective than U in its pairing with adenine (A), forming a more stable A=T pair. This specificity makes sense. DNA, which is made of nucleic acids, phosphate anions, and sugar molecules, is very hydrophilic (water-loving). The addition of a hydrophobic CH3 group to U (thus forming T) causes T to repel the rest of the DNA. This, in turn, shifts T to a specific location in the helix. This perfect positioning causes T to bind exclusively with A, making DNA a better, more accurate information replication system. This guarantees the long-lasting integrity of DNA information. So we see that the most fundamental design principles of the DNA helix are carefully tuned for the code to work properly, from the number of H-bonds between the A=T and G≡C interactions, to the exact fit of the molecules between the two wires that form the double helix.

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Three things are essential to have life: The basic building blocks of life, energy, and information. Cells use the most advanced computer information systems known.

https://reasonandscience.catsboard.com/t2625-information-main-topics-on-complex-specified-instructional-coded-information-in-biochemical-systems-and-life#7993

To have an information transmission system, following is required:
1. The rules of any communication system  must be established in advance through establishing in common agreement of the meaning of words, signs, or a code. There must be preestablished agreement between those that communicate with each other, otherwise the transmission of information is not possible. A message can only be created once a language has been established.  A code is an abstract, immaterial, nonphysical set of rules.
2. This set of rule, code, or language, permits to produce a blueprint, which is instructional complex information, that permits to produce goods for specific purposes. 
3. Then there has to be a device, that is the harddisk, a paper, or any hardware upon which the information can be recorded.
4. And there has to be a system to encode, send, and decode the message. These four things—language, transmitter of language, message, and receiver of language—all have to be precisely defined in advance before any form of communication can be possible at all.
5. Eventually, during the transmission of information, it can be translated from one language to another.

In Cells, we see all these things.
Setting up the rules of communication:
The translation of a word in one language, to another language, is always of mental origin. For example the assignment of the word chair, in English, to xizi, in Chinese, can only be made by intelligence upon common agreement of meaning.
In biology the genetic code is the assignment ( a cipher) of 64 triplet codons to 20 amino acids.
Eugene Koonin wrote in a science paper in 2009: In our opinion, despite extensive and, in many cases, elaborate attempts to model code optimization, ingenious theorizing along the lines of the coevolution theory, and considerable experimentation, very little definitive progress has been made. Summarizing the state of the art in the study of the code evolution, we cannot escape considerable skepticism. It seems that the two-pronged fundamental question: “why is the genetic code the way it is and how did it come to be?”, that was asked over 50 years ago, at the dawn of molecular biology, might remain pertinent even in another 50 years. Our consolation is that we cannot think of a more fundamental problem in biology.
Since we know only of intelligence to be able to establish a common agreement of meaning of words, this assignment is best explained by the deliberate, arbitrary action of a non-human intelligent agency.

Information stored in DNA
Chance of intelligence to set up the first blueprint for life: 
Mycoplasma  is one of the smallest self-replicating cells, and its genome has about 500 thousand base-pairs. It is, however, a pathogen, which has to be hosted by other organisms to survive.  It does not produce the twenty amino acids used in life. In order to know the threshold or minimal organismal complexity to sustain life, Pelagibacter ubique is a good candidate, since it is one the smallest self-replicating free-living cells, and produces all 20 amino acids used in life.  It has a genome size of 1,3 million base pairs which codes for about 1,300 proteins. That would be the size of a book with 400 pages, each page with 3000 characters. The chance to sequence each of the 1,3 million characters in the right order by unguided means, to get the precise instructional complex information to have a working self replicating cell is is 10^700,000. This is in the realm of the absolutely impossible.
The likelyhood of intelligence to set up an information system essential for life is  100% We KNOW by repeated experience that intelligence does elaborate blueprints, instructional information and constructs complex machines, production lines, transistors and computers and factories with specific purposes.

DNA has Ultra-High-Density Data Storage and Compression
Our cells contain at least 92 strands of DNA and 46 double-helical chromosomes. In total, they stretch 6 feet (1.8 meters) end to end. Every human DNA strand contains as much data as a CD. Every DNA strand in our body stretched end to end would reach from Earth to the sun and back 600 times. Cells store data at millions of times more density than hard drives. Not only that, they use that data to store instructions vastly more effectively than human-made programs; consider that Windows takes 20 times as much space (bits) as our genome. The genome is unfathomably more elegant, more sophisticated, and more efficient in its use of data than anything we have ever designed.  A single gene can be used a hundred times by different aspects of the genetic program, expressed in a hundred different ways.

Besides the information transmission system of DNA to make proteins, there is  the most amazing and advanced  information transmission system in operation in each of our cells, which works through light.  The more sophisticated and fast a Information transmission systems is, the more intelligence is required to project and implement it . Light-fidelity, or Li-Fi, is a 5th generation cutting edge technology, the fastest information transmission system so far invented by man. Life uses not only light, but quantum entanglement to transmit information, which occurs basically instantly. It is logical, therefore, to infer a super intelligent  agency created lifes awesome high-speed internet on a molecular  level.

The origin of such complex communication systems is best explained by an intelligent designer. Since no humans were involved in creating these complex computing systems, a suprahuman super intelligent agency must have been the creator. 



Last edited by Otangelo on Wed Jul 07, 2021 11:36 am; edited 1 time in total

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WHAT IS THE ORIGIN OF CODED BIOLOGICAL INFORMATION IN THE CELL?

The truth about the theory of evolution or (the Neo-Darwinian Theory of Evolution) is that no matter how you want to define evolution:
    1  Change in allele frequency.
    2  Mutations acted upon by natural selection.
    3  Change in the heritable characteristics of biological populations over successive generations.
    4  Descent with modification from preexisting species, or
    5  Genetic drift ….

None of these theories account for what we now know is the real driver of both the origin and diversity of life.
The crucial question that will decide the conclusion to the debate about biological origins is precisely the origin of prescriptive or coded information in DNA.  If you don’t have assembly instructions, if you don’t have biological assembly information, then you cannot build biological life.  
This is a scientific fact that atheists and evolutionists tend to ignore, deny, or reject from ignorance.
We know that coded information cannot self-generate.  It cannot just pop into existence.  So where did it come from?
The 4-character digital information code in DNA is sequenced to provide the assembly instructions for every part of the cell and in turn, every part of every biological organism.  These are precisely sequenced nucleotide bases along the backbone of the DNA molecule and cannot be produced by anything except an intelligent agent.  The sequencing cannot be produced by a blind, mindless, random chance process.
google:  “what are the nucleotide bases in dna”,
or
go here:  https://knowgenetics.org/nucleotides-and-bases/

Anyone who denies or ignores or rejects this scientific fact is doing so out of ignorance or intellectual dishonesty.  
Atheists/evolutionists, cannot explain HOW the DNA molecule evolved from a blind, mindless, purposeless, random chance natural process, which, has no idea what an assembly instruction code is or should be?  
These nucleotide bases function exactly like the letters of a written language or digital symbols in a section of computer code.  These comparisons are not just an analogy as many atheists/evolutionists claim. This is a functional, coded information storage and retrieval system and operates exactly like a computer operating system.  
The book Information Theory, Evolution and the Origin of Life, was written by Hubert Yockey, the foremost specialist in bioinformatics.  Yockey rigorously demonstrated that the coding process in DNA is identical to the coding process and mathematical definitions used in Electrical Engineering. This is not a subjective statement, nor is it debatable or even controversial. It is a brute fact.  To deny this fact is either willful ignorance or intellectually dishonest.
“Information, transcription, translation, code, redundancy, synonymous, messenger, editing, and proofreading are all appropriate terms in biology. They take their meaning from information theory (Shannon, 1948) and are not synonyms, metaphors, or analogies.” (Hubert P. Yockey,  Information Theory, Evolution, and the Origin of Life,  Cambridge University Press, 2005)

Coded sequential information that instructs for the construction, operation, maintenance, and modification of a machine are UNIQUE to the presence of a designing intelligence.  The nucleotide bases along the spine of the DNA molecule have been specifically sequenced to provide the assembly instructions for all of the other proteins and enzymes in the cell.  This is an observable fact and not a subjective statement or baseless opinion.
THEREFORE, DNA CONTAINS A CODED INFORMATION SYSTEM THAT WAS INTELLIGENTLY DESIGNED
Just as letters in the English alphabet can be formed to convey a specific message or instruction, depending on their arrangement, the sequences of chemical bases along the spine of the DNA molecule, convey precise instructions for the assembly of proteins.  Proteins are then assembled precisely to perform numerous functions or assembly instructions of structures in the cell.  
In 2010, the noted micro-biologist, Craig Venter and his team created the first computer designed, synthetically produced genome, which is the set of application programs for an organism. This artificial DNA had over 1,000,000 letters of genetic code that were then read, processed and executed by the computer systems in the target cell’s nucleus.  Thanks to Venter and his team, these biological computers are no longer theoretical, but have been experimentally observed, tested and verified.
In an interview with Venter, He stated:
“Life is basically the result of an information process, a software process. Our genetic code is our software, and our cells are dynamically, constantly reading that genetic code.”
(Watch this video documentary:  “Science Uprising”)
https://www.youtube.com/watch?v=qxhuxg3WRfg
According to evolutionary theory, new proteins, new animal functions, or new animal types of life, arise by random genetic mutations acted on by natural selection.  But random changes in a language text or computer code, always degrade the function of the text or computer code.  
So how can a degrading process such as mutations, improve an organism’s function or assemble a better or new function?  Quite simply … it can’t.  The discovery of coded information in DNA in 1957, has falsified evolution.
While a coded information system cannot be produced by a blind, mindless, purposeless, random chance process … the existence of that information system … IS … proof that there was an intelligent designer, because Coded Information Systems are only produced by intelligence.
To deny that the code in DNA exists, and that an intelligence is responsible for it’s existence …  is nothing short of intellectual ignorance or worse … intellectual dishonesty.
THREE WORDS THAT FALSIFY EVOLUTION:  
Integrated Functional Complexity

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Otangelo


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Paul Davies: It is the information content of the genome – the sequence of bits – and not the chemical nature of DNA as such that is (at least in part) “calling the shots.”

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