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Defending the Christian Worlview, Creationism, and Intelligent Design

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


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Defending the Christian Worlview, Creationism, and Intelligent Design » 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

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

Dichotomy in the definition of prescriptive information suggests both prescribed data and prescribed algorithms: biosemiotics applications in genomic systems
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3319427/
"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://biosemiosis.net/?fbclid=IwAR0B_bZLCzCWkziNuoich1DfoNtswa5nY5HGEAdf9aOYzctflmDCHdKZmVY

https://web.archive.org/web/20170614142752/http://www.biosemiosis.org/index.php/why-is-this-important

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

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."

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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6463137/
The origin of prebiotic information remains a mystery.

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

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.

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 

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.



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.



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

teleonomy, teleomatic

Information: Main topics on complex, specified/instructional coded information in biochemical systems and life Sdfsdf10



Last edited by Otangelo on Tue Feb 23, 2021 6:49 am; edited 27 times in total

https://reasonandscience.catsboard.com

Otangelo


Admin
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?

https://reasonandscience.catsboard.com

3Information: 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

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Otangelo


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

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.

https://reasonandscience.catsboard.com

Otangelo


Admin
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. 

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Otangelo


Admin
Claim: DNA is a product of material, chemical processes with no evidence of being intelligently designed.



Response: DNA is a physical medium encoded with Complex Specified Information which prescribes the features and biochemistry of organisms.1 This verifies they are adenine, cytozine, guinine, or thymine, are able to bond to any of the binding sites of the ribose backbone of DNA. Therefore, chemical determinacy has not organized the nucleotides of DNA as information-bearing symbols.

Information is a non-material entity which cannot be produced by material processes.
Information is a product of intelligence.
Therefore, DNA is a product of intelligence and not material processes.
Since all organisms are prescribed by information, all organisms are a product of Intelligent Design.
The properties of genetic information which verify that DNA is impirical evidence of Intelligent Design are:
It has an intended purpose which has been preconceived - the process of forethought
The intended purpose is to cause the recipient to have an intended response
The intended response is to assemble proteins or regulate cell processes
The instructions to assemble proteins and regulate cell processes employ a coded language that both the sender (designer) and recipient (cell) understand
The instructions are organized syntaxically and grammatically so that the assembly or regulation occurs as specified and in a prescribed order
The end result is that the intended purpose is achieved
Intentionality, purpose, instruction, code, language, and forethought are mental processes, not material ones
The value of the information is it's meaning and purpose, not in a material quantity, such as the number of digits or characters in a sequence
Examples:

A pound of gold is of greater value that a pound of sand
A string of 9 unvarying characters such as "AAAAAAAAA" does not convey meaning. However, a string of 9 characters such as "TURN_LEFT" conveys meaning.
A varying string 19 of letters such as "AFGOPHRQLBNCMRIDAKX" does not convert convey meaning because no syntax or grammar (languge) is present. However, a varying string of only 9 characters such as "TURN_ONCE" conveys meaning because it is organized syntaxically and grammatically (linguistically)
Information is a non-material entity. It is not comprised of matter or a property of matter - it is not a material quantity such as mass or the number of digits or characters in a string
Material processes cannot produce that which is non-material
The intentional volition of the sender to convey knowledge is the origin of information
The sender creates information by mental processes which are non-material
Intentional volition and mental processes are properties of intelligence
The origin of information is intelligence
Conclusion: Since information is created by intelligence, and since all biological forms are prescribed by genetic information, the Intelligent Design of all biological forms is empirically demonstrated, and all theories of abiogenesis and the evolution of biological forms are empirically false.
Genetic information is a product of a mind.
It is prescriptive - it prescribes the structural design and biochemistry of organisms
It prescribes function of proteins by prescribing their structural design, which determines their functions and relationships with other proteins and cell structures
It prescribes organismal features, such as organs, their arrangement in a body plan, and their relationship to each other
It prescribes the regulation of information expression in time (4th dimension of genetic information) to maintain and operate an organism
It possesses a code system which is the alphabet of it's language system
It possesses linguistics properties - phonetics, semantics, punctuation, syntax, and grammar
Language is physically represented by symbols
Symbolism is non-material - symbols represent objects, processes, or concepts which are external to themselves
The application of meaning to a symbol and interpretation of meaning from a symbol is a mental process, not a material process.
Minds apply meaning to matter, not the other way around.
It is illogical to apply mental properties to matter
Information is a non-material entity
Information is purposeful - it describes something meaningful such as data, function, concept, or process.
Information cannot be physically measured because it has no physical dimensions or mass - the concept of measuring one pound or one meter of information is nonsensical.
Information is not bound to whatever medium upon which it is encoded.
Example: The information in a book can be copied onto any other medium without the information changing in any way and without relocation of the material medium upon which it is encoded:

Reading a book: If information and minds were both physical, it would be impossible to receive (read) the information in a book without relocating the material of the book into the brain of the reader.
Reading a printed message to another person: If information and minds were both physical, it would be impossible to convey (read aloud) the information in a book without relocating the material of the book into the brain of the listener.
Speaking to an audience: If information and minds were both physical, it would be impossible to share information with an audience without relocating the material of the provider's brain to the brains of the each member of the audience.
10 Laws of Nature Regarding Information which verify that creation is true and evolution is false:
The following is a transcript of Dr. Werner Gitt from his book, "In the Beginning Was Information".

Premises:

Anything material, such as physical/chemical processes, cannot create something non-material
Information is a non-material fundamental entity and not a property of matter
Information requires a material medium for storage and transmission
Information cannot arise from statistical processes
There can be no information without a code - no thought or idea can be shared without a code
All codes result from an intentional choice and agreement between sender and recipient
The determination of meaning for and from a set of symbols is a mental process that requires intelligence
There can be no new information without an intelligent, purposeful sender
Any given chain of information can be traced back to an intelligent source
Information comprises the non-material foundation for all:
technological systems
works of art
biological systems
Therefore,

Since the DNA code of all life is clearly within the definition domain of information, we conclude that there must be a sender
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 supremely intelligent
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 the sender must be purposeful and supremely powerful,

Since information is a non-material fundamental entity and cannot originate from material quantities, we conclude that 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, we conclude man's nature must have a non-material component (spirit)
Since information is a non-material entity, we conclude that the assumption "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), we conclude that all theories or concepts of biological evolution are false.
Anyone who disagrees with these laws and conclusions must falsify them by demonstrating the initial origin of information from purely material sources. Therefore, the laws of nature about information have,

refuted the assumption of scientific materialism and the theories of chemical and biological evolution
all philosophies or theories based on the assumption of scientific materialism including chemical and biological evolution are falsified by the laws of nature about information.
Shannon Information
Shannon Information is not the type of information that DNA possesses, and does not require intelligence to be produced. Unlike Shannon Information, genetic information is complex, specified, prescriptive, functional, meaningful, purposeful, semiotic, and linguistic.

Information scientist Dr. Werner Gitt on Shannon Information:

"Shannon's definition of information exclusively concerns the statistical properties of sequences of symbols; meaning is completely ignored. It follows that this concept of information is unsuitable for evaluating the information content of meaningful sequences of symbols. A message which has been subject to interference or "noise", in general comprises more information than an error-free message, according to Shannon's theory. It follows that this concept of information is unsuitable for evaluating the information content of meaningful sequences of symbols."

- In the Beginning Was Information, Werner Gitt, former head of the Department of Information Technology at the German Federal Institute of Physics and Technology (Physikalisch-Technische Bundesanstalt [PTB], in Braunschweig). Seven years later he was promoted to Director and Professor at PTB.


Sources
"The information in DNA is stored as a code made up of four chemical bases: adenine (A), guanine (G), cytosine (C), and thymine (T). Human DNA consists of about 3 billion bases, and more than 99 percent of those bases are the same in all people. The order, or sequence, of these bases determines the information available for building and maintaining an organism, similar to the way in which letters of the alphabet appear in a certain order to form words and sentences." - What is DNA?, Genetics Home Reference, NLH, U.S. National Library of Medicine


"It should now be clear that information, being a fundamental entity, cannot be a property of matter, and its origin cannot be explained in terms of material processes. We therefore formulate the following fundamental theorem: Theorem 1: The fundamental quantity information is a nonmaterial (mental) entity. It is not a property of matter, so that purely material processes are fundamentally precluded as sources of information." - Werner Gitt, In the Beginning was Information. 2000, former Director, former head of the Department of Information Technology at the German Federal Institute of Physics and Technology (Physikalisch-Technische Bundesanstalt [PTB], in Braunschweig


"If there are more than several dozen nucleotides in a functional sequence, we know that realistically they will never just "fall into place"'. This has been mathematically demonstrated repeatedly. But as we will soon see, neither can such a sequence arise randomly one nucleotide at a time. A pre-existing "concept" is required as a framework upon which a sentence or a functional sequence must be built. Such a concept can only pre-exist within the mind of the author." - Genetic Entropy & the Mystery of the Genome, Dr, Johnathon Sanford, geneticist, Cornell University, 2005, pp. 124-125.


"No matter how many "bits" of possible combinations it has, there is no reason to call it "information" if it doesn't at least have the potential of producing something useful. What kind of information produces function? In computer science, we call it a "program." Another name for computer software is an "algorithm." No man-made program comes close to the technical brilliance of even Mycoplasmal genetic algorithms. Mycoplasmas are the simplest known organisms with the smallest known genome, to date. How was its genome and other living organisms' genomes programmed?" - , David L. Abel1 and Jack T. Trevors" Three subsets of sequence complexity and their relevance to biopolymeric information, David L. Abel and Jack T. Trevors, 2005


"The Common Fund's 4D Nucleome program aims to understand the principles behind the three-dimensional organization of the nucleus in space and time (the 4th dimension), the role nuclear organization plays in gene expression and cellular function, and how changes in the nuclear organization affect normal development as well as various diseases." - The 4D Nucleome Project, National Institutes of Health, https://commonfund.nih.gov/4Dnucleome


"There are no specific choices to be found anywhere within this mathematical definition of a "bit." Shannon worked only on general communication engineering problems. He deliberately made no attempt to quantify intuitive/semantic information by measuring specific functional choices with fixed units. That would be impossible." - Dichotomy in the definition of prescriptiveinformation suggests both prescribed data and prescribed algorithms: biosemiotics applications in genomic systems, David J D'Onofrio, David L Abel and Donald E Johnson, Theoretical Biology and Medical Modeling, 2012


The human genome takes shape and shifts over time, Sarah Schwartz, August 24, 2015 https://www.sciencenews.org/article/human-genome-takes-shape-and-shifts-over-time


"The digital linear coding carried by the base pairs in the DNA double helix is now known to have an important component that acts by altering, along its length, the natural shape and stiffness of the molecule. In this way, one region of DNA is structurally distinguished from another, constituting an additional form of encoded information manifest in three-dimensional space. These shape and stiffness variations help in guiding and facilitating the DNA during its three-dimensional spatial interactions. Such interactions with itself allow communication between genes and enhanced wrapping and histone-octamer binding within the nucleosome core particle. Meanwhile, interactions with proteins can have a reduced entropic binding penalty owing to advantageous sequence-dependent bending anisotropy. Sequence periodicity within the DNA, giving a corresponding structural periodicity of shape and stiffness, also influences the supercoiling of the molecule, which, in turn, plays an important facilitating role. In effect, the super-helical density acts as an analogue regulatory mode in contrast to the more commonly acknowledged purely digital mode."

http://rsta.royalsocietypublishing.org/content/370/1969/2960


"The creation of information is habitually associated with concious activity" - Henry Quastier, information theorist


Information is useless unless it can be read. But the decoding machinery is itself encoded on the DNA. The leading philosopher of science, Karl Popper (1902-1994), expressed the huge problem:

"What makes the origin of life and of the genetic code a disturbing riddle is this: the genetic code is without any biological function unless it is translated; that is, unless it leads to the synthesis of the proteins whose structure is laid down by the code. But . . . the machinery by which the cell (at least the non-primitive cell, which is the only one we know) translates the code consists of at least fifty macromolecular components which are themselves coded in the DNA. Thus the code can not be translated except by using certain products of its translation. This constitutes a baffling circle; a really vicious circle, it seems, for any attempt to form a model or theory of the genesis of the genetic code. Thus we may be faced with the possibility that the origin of life (like the origin of physics) becomes an impenetrable barrier to science, and a residue to all attempts to reduce biology to chemistry and physics." - 1974. Scientific Reduction and the Essential Incompleteness of All Science. In Ayala, F. and Dobzhansky, T., eds., Studies in the Philosophy of Biology, University of California Press, Berkeley, p. 270


"Did the code and the means of translating it appear simultaneously in evolution? It seems almost incredible that any such coincidences could have occurred, given the extraordinary complexities of both sides and the requirement that they be coordinated accurately for survival. By a pre-Darwinian (or a skeptic of evolution after Darwin) this puzzle surely would have been interpreted as the most powerful sort of evidence for special creation." - C. Haskins, "Advances and Challenges in Science" in American Scientist 59 (1971), pp. 298.


"The information content of amino acid sequences cannot increase until a genetic code with an adapter function has appeared. Nothing which even vaguely resembles a code exists in the physiochemical world. One must conclude that no valid scientific explanation of the origin of life exists at present." - H. Yockey, "Self Organization Origin of Life Scenarios and Information Theory," in Journal of Theoretical Biology 91 (1981), p. 13.


"On the possibility that random material causes could be the origin of proteins: If we have a tiny chain of only 10 amino acid molecules, and because there are 20 amino acid molecules that can be used to produce the chain, there are 10 trillion possible combinations! The probability that a sequence of amino acids could arise to produce even such a tiny protein are astronomical, and therefore beyond improbable. By the science of statistical analysis, this would be considered impossible times impossible times impossible. . . An average protein however, is 300-500 amino acid molecules in length and may be thousands, and results in trillons times trillions of potential combinations! Here we see that the improbability of material causes to arrange a sequence for a typical protein is far beyond improbable, so as to be unworthy of being considered possible by any manner of reasoning." - Stephen C. Meyer, PhD in Philosophy of Science and Mathematics, former geophysicist for Atlantic Richfield Company (ARCO). His PhD thesis offered a methodological interpretation of origin-of-life research. Meyer discovered that the odds of a protein forming naturally is 1:10^164 There are only 10^80 elementary particles in the known universe. There are only 10^18 seconds in the imagined 13.5 billions years since the big bang.


"Representation and processing of digital information in the form of DNA is essential to life in all organisms, no matter how large or tiny. Computing tools and computational thinking help us understand how DNA stores information and how that information directs activity in the cell." - Module 6: Digital DNA, University of British Columbia http://www.cs.ubc.ca/~condon/cpsc101/notes/digital-dna.pdf


"Genomes [all the DNA of a species] are remarkable in that they encode most of the functions necessary for their interpretation and propagation." - Anne-Claude Gavin et al., "Proteome Survey Reveals Modularity of the Yeast Cell Machinery," Nature, Vol. 440, 30 March 2006, p. 631.


"The discovery of the structure of DNA transformed biology profoundly, catalysing the sequencing of the human genome and engendering a new view of biology as an information science. Two features of DNA structure account for much of its remarkable impact on science: it's digital nature and its complementarity, whereby one strand of the helix binds perfectly with its partner. DNA has two types of digital information -- the genes that encode proteins, which are the molecular machines of life, and the gene regulatory networks that specify the behavior of the genes." - Hood L1, Galas D. The digital code of DNA, http://www.ncbi.nlm.nih.gov/pubmed/12540920


"Biologic systems and processes cannot be fully accounted for in terms of the principles and laws of physics and chemistry alone, but they require in addition the principles of semiotics - the science of symbols and signs, including linguistics." - Rutgers University professor Sungchul Ji's, "The Linguistics of DNA: Words, Sentences, Grammar, Phonetics, and Semantics"


The Information Theory textbook, "T. M. Cover and J. M. Thomas, Elements of Information Theory, 2nd, Wiley-Interscience, 2006." states information is knowledge transmitted from sender to receiver using a code.


"We now know that genes are made of DNA, a magnificently simple/complex molecule which actually encodes a language. It carries information just as a book does. The language has 4 letters which form 64 three letter words." The digital code of DNA http://www.ncbi.nlm.nih.gov/pubmed/12540920


"There is no such thing as physical information. Information is a nonmaterial fundamental entity and not a property of matter. Information is knowledge conveyed from a sender to a receiver using a language agreed upon by both parties. Nature has no potential to create information, and therefore cannot be the origin of living things. Information is a non-physical fundamental entity, which the laws of physics and matter cannot produce. Information is a product of a non-physical mind. No physical thing is itself information. Observing something allows us to gain knowledge of it's properties, which we can convey to someone else, thus producing information by sharing the knowledge we have gained by observation, investigation, or study." - Werner Gitt, former Director, former head of the Department of Information Technology at the German Federal Institute of Physics and Technology (Physikalisch-Technische Bundesanstalt [PTB], in Braunschweig


"Information is information, not matter or energy." - Norbert Wiener, Cybernetics; or, Control and Communication in the Animal and the Machine, 2nd edition (Cambridge, Massachusetts: MIT Press, 1948), p. 132.


"There is no known law of nature, no known process and no known sequence of events which can cause information to originate by itself in matter." - Werner Gitt, former Director, former head of the Department of Information Technology at the German Federal Institute of Physics and Technology (Physikalisch-Technische Bundesanstalt [PTB], in Braunschweig


"In all systems, there can be no new information without an intelligent, purposeful sender." - Werner Gitt, former Director, former head of the Department of Information Technology at the German Federal Institute of Physics and Technology (Physikalisch-Technische Bundesanstalt [PTB], in Braunschweig


"No matter how many "bits" of possible combinations it has, there is no reason to call it "nformation" if it doesn't at least have the potential of producing something useful. What kind of information produces function? In computer science, we call it a "program." Another name for computer software is an 'algorithm.' No man-made program comes close to the technical brilliance of even Mycoplasmal genetic algorithms. Mycoplasmas are the simplest known organisms with the smallest known genome, to date. How was its genome and other living organisms' genomes programmed?" Abel and Trevors, p. 8.


How can we measure information? A computer file might contain information for printing a story, reproducing a picture at a given resolution, or producing a widget to specified tolerances. Information can usually be compressed to some degree, just as the English language could be compressed by eliminating every "u" that directly follows a "q". If compression could be accomplished to the maximum extent possible (eliminating all redundancies and unnecessary information), the number of bits (0s or 1s) would be a measure of the information needed to produce the story, picture, or widget.


Each living system can be described by its age and the information stored in its DNA. Each basic unit of DNA, called a nucleotide, can be one of four types. Therefore, each nucleotide represents two (log24 = 2) bits of information. Conceptual systems, such as ideas, a filing system, or a system for betting on race horses, can be explained in books. Several bits of information can define each symbol in these books. The number of bits of information, after compression, needed to duplicate and achieve the purpose of a system will be defined as its information content. That number is also a measure of the system's complexity.


"No matter how many 'bits' of possible combinations it has, there is no reason to call it 'information' if it doesn't at least have the potential of producing something useful. What kind of information produces function? In computer science, we call it a 'program.' Another name for computer software is an 'algorithm.' No man-made program comes close to the technical brilliance of even Mycoplasmal genetic algorithms. Mycoplasmas are the simplest known organisms with the smallest known genome, to date. How was its genome and other living organisms' genomes programmed?" Abel and Trevors, p. 8.


"If there are more than several dozen nucleotides in a functional sequence, we know that realistically they will never just 'fall into place.' This has been mathematically demonstrated repeatedly. But as we will soon see, neither can such a sequence arise randomly one nucleotide at a time. A pre-existing 'concept' is required as a framework upon which a sentence or a functional sequence must be built. Such a concept can only pre-exist within the mind of the author." Sanford, pp. 124-125.


"The creation of information is habitually associated with conscious activity" - Henry Quastier, information theorist


On the possibility that random material causes could be the origin of proteins: If we have a tiny chain of only 10 amino acid molecues, and because there are 20 amino acid molecules that can be used to produce the chain, there are 10 trillion possible combinations! The probability that a sequence of amino acids could arise to produce even such a tiny protein are astronomical, and therefore beyond improbable. By the science of statistical analysis, this would be considered impossible times impossible times impossible. . . An average protein however, is 300-500 amino acid molecules in length and may be thousands, and results in trillons times trillions of potential combinations! Here we see that the improbability of material causes to arrange a sequence for a typical protein is far beyond improbable, so as to be unworthy of being considered possible by any manner of reasoning.


Stephen C. Meyer earned a PhD in Philosophy of Science and also Mathematics, former geophysicist for Atlantic Richfield Company (ARCO). His PhD thesis offered a methodological interpretation of origin-of-life research. Meyer discovered that the odds of a protein forming naturally is 1:10^164 There are only 10^80 elementary particles in the known universe. There are only 10^18 seconds in the imagined 13.5 billions years since the big bang.


Michael Polanyi (1891-1976), former chairman of physical chemistry at the University of Manchester (UK) who turned to philosophy, affirmed a very important point -- the information was something above the chemical properties of the building blocks:

"As the arrangement of a printed page is extraneous to the chemistry of the printed page, so is the base sequence in a DNA molecule extraneous to the chemical forces at work in the DNA molecule. It is this physical indeterminacy of the sequence that produces the improbability of any particular sequence and thereby enables it to have a meaning - a meaning that has a mathematically determinate information content."


University of British Columbia - Module 6: Digital DNA: "Representation and processing of digital information in the form of DNA is essential to life in all organisms, no matter how large or tiny. Computing tools and computational thinking help us understand how DNA stores information and how that information directs activity in the cell." http://www.cs.ubc.ca/~condon/cpsc101/notes/digital-dna.pdf


In 2010, another level of complexity was discovered in the genetic code. On a strand of DNA, a sequence of three adjacent nucleotides forms a unit in the genetic code called a codon. Prior to 2010, some codons were thought to have the same function as others. That turns out to not be the case:

"... synonymous codon changes can so profoundly change the role of a protein [that it] adds a new level of complexity to how we interpret the genetic code. Ivana Weygand-Durasevic and Michael Ibba, "New Roles for Codon Usage," Science, Vol. 329, 17 September 2010, p. 1474. Also see Fangliang Zhang et al., Differential Arginylation of Actin Isoforms Is Regulated by Coding Sequence-Dependent Degradation, Science, Vol. 329, 17 September 2010, p. 1734-1537.


"Genomes [all the DNA of a species] are remarkable in that they encode most of the functions necessary for their interpretation and propagation." Anne-Claude Gavin et al., "Proteome Survey Reveals Modularity of the Yeast Cell Machinery," Nature, Vol. 440, 30 March 2006, p. 631.


TRANSLATION PACKAGE NEEDED AT BEGINNING - The amount of information in the genetic code is so vast that it would be impossible to put together by chance. But, in addition, there must be a means of translating it so the tissues can use the code. "Did the code and the means of translating it appear simultaneously in evolution? It seems almost incredible that any such coincidences could have occurred, given the extraordinary complexities of both sides and the requirement that they be coordinated accurately for survival. By a pre-Darwinian (or a skeptic of evolution after Darwin) this puzzle surely would have been interpreted as the most powerful sort of evidence for special creation." - C. Haskins, "Advances and Challenges in Science" in American Scientist 59 (1971), pp. 298.


"Not only did the DNA have to originate itself by random accident, but the translation machinery already had to be produced by accident - and also immediately! Without it, the information in the DNA could not be applied to the tissues. Instant death would be the result. "The code is meaningless unless translated. The modern cell's translation machinery consists of at least fifty macromolecular components which are themselves encoded in DNA [!]; the code cannot be translated otherwise than by products of translation. It is the modern expression of omne vivum ex ovo ['every living thing comes from an egg']. When and how did this circle become closed? It is exceedingly difficult to imagine." - J, Monod, Chance and Necessity (1971), p. 143.


"The discovery of the structure of DNA transformed biology profoundly, catalysing the sequencing of the human genome and engendering a new view of biology as an information science. Two features of DNA structure account for much of its remarkable impact on science: it's digital nature and its complementarity, whereby one strand of the helix binds perfectly with its partner. DNA has two types of digital information--the genes that encode proteins, which are the molecular machines of life, and the gene regulatory networks that specify the behaviour of the genes." http://www.ncbi.nlm.nih.gov/pubmed/12540920


Shannon was keen to point out that the type of information he described did not relate to function. It was a reductionist approach to reducing improbability, and that the more possibilities of an event, the more information it could provide. An example might be the rolling of a die. Since the die has 5 sides, it provides 6 possible outcomes, and therefore 6 seperate pieces of information. When the die is rolled, the outcome has been reduced from 6 to 1, and the information has been reduced to 1 piece of information. However, genetic information is not based upon chance, necessity as it relates to chemistry, or statistical analysis. In fact, statistical analysis itself cannot produce information, but rather is a process of studying information. Genetic information is complex and specific, and relates to function. Shannon information does not describe genetic information. Complex specified information is a critical component of life and is not statistical or produced by chance events. Complex specified information is a product of mind and not random associations or events. Protein synthesis, gene expression, the precise structure of proteins which determines function, and meta-information of the cell are therefore not products of chance or random associations, but instead a feature of intentional design.


Receiver (information theory): The receiver in information theory is the receiving end of a communication channel. It receives decoded messages/information from the sender, who first encoded them. Sometimes the receiver is modeled so as to include the decoder. Real-world receivers like radio receivers or telephones can not be expected to receive as much information as predicted by the noisy channel coding theorem. https://en.wikipedia.org/wiki/Receiver_(information_theory)


Information: Information is that which informs. In other words, it is the answer to a question of some kind. It is thus related to data and knowledge, as data represents values attributed to parameters, and knowledge signifies understanding of real things or abstract concepts.[1] As it regards data, the information's existence is not necessarily coupled to an observer (it exists beyond an event horizon, for example), while in the case of knowledge, the information requires a cognitive observer. Information is conveyed either as the content of a message or through direct or indirect observation of anything. That which is perceived can be construed as a message in its own right, and in that sense, information is always conveyed as the content of a message. Information can be encoded into various forms for transmission and interpretation (for example, information may be encoded into a sequence of signs, or transmitted via a sequence of signals). It can also be encrypted for safe storage and communication. https://en.wikipedia.org/wiki/Information


DNA, RNA, and the Flow of Genetic Information http://www.ncbi.nlm.nih.gov/books/NBK21171/


Genetics - information properties https://ghr.nlm.nih.gov/primer/basics/dna


"Biologic systems and processes cannot be fully accounted for in terms of the principles and laws of physics and chemistry alone, but they require in addition the principles of semiotics - the science of symbols and signs, including linguistics." - Rutgers University professor Sungchul Ji's, "The Linguistics of DNA: Words, Sentences, Grammar, Phonetics, and Semantics"


The Information Theory (textbook), "T. M. Cover and J. M. Thomas, Elements of Information Theory, 2nd, Wiley-Interscience, 2006." states information is knowledge transmitted from sender to receiver using a code.


"We now know that genes are made of DNA, a magnificently simple/complex molecule which actually encodes a language. It carries information just as a book does. The language has 4 letters which form 64 three letter words." The digital code of DNA http://www.ncbi.nlm.nih.gov/pubmed/12540920


Websters Dictionary, Definition of algorithm: a procedure for solving a mathematical problem (as of finding the greatest common divisor) in a finite number of steps that frequently involves repetition of an operation; broadly :a step-by-step procedure for solving a problem or accomplishing some end especially by a computer


DNA is information organized to conform to linguistics laws which are more complex than Zipf's Law of Linguistics, it is digital code, is posesses algorithmic operations, and the human language properties of semantics, puntiuation, grammar, phonetics, and aprobatics.


INFORM: to communicate knowledge, to inform Definition of -ation: action or process flirtation : something connected with an action or process discoloration INFORM -ATION = INFORMATION


Websters Definition of knowledge 1 a (1): the fact or condition of knowing something with familiarity gained through experience or association (2): acquaintance with or understanding of a science, art, or techniqueb (1) : the fact or condition of being aware of something (2): the range of one's information or understanding answered to the best of my knowledgec: the circumstance or condition of apprehending truth or fact through reasoning: cognitiond: the fact or condition of having information or of being learned a person of unusual knowledge 2 a: the sum of what is known: the body of truth, information, and principles acquired by humankindb archaic: a branch of learning


The Heavy Hammer of Information http://nephilimfree.blogspot.com/


"Information is information, not matter or energy." - Norbert Wiener, Cybernetics; or, Control and Communication in the Animal and the Machine, 2nd edition (Cambridge, Massachusetts: MIT Press, 1948), p. 132.


"There is no known law of nature, no known process and no known sequence of events which can cause information to originate by itself in matter." - Werner Gitt, former Director, former head of the Department of Information Technology at the German Federal Institute of Physics and Technology (Physikalisch-Technische Bundesanstalt [PTB], in Braunschweig


"In all systems, there can be no new information without an intelligent, purposeful sender." - Werner Gitt, former Director, former head of the Department of Information Technology at the German Federal Institute of Physics and Technology (Physikalisch-Technische Bundesanstalt [PTB], in Braunschweig


Proceedings of the Symposium, Cornell University, USA, 31 May - 3 June 2011 http://www.worldscientific.com/worldscibooks/10.1142/8818#t=toc"


"In the spring of 2011, a diverse group of scientists gathered at Cornell University to discuss their research into the nature and origin of biological information. This symposium brought together experts in information theory, computer science, numerical simulation, thermodynamics, evolutionary theory, whole organism biology, developmental biology, molecular biology, genetics, physics, biophysics, mathematics, and linguistics. This volume presents new research by those invited to speak at the conference.

The contributors to this volume use their wide-ranging expertise in the area of biological information to bring fresh insights into the many explanatory difficulties associated with biological information. These authors raise major challenges to the conventional scientific wisdom, which attempts to explain all biological information exclusively in terms of the standard mutation/selection paradigm.

Several clear themes emerged from these research papers: 1) Information is indispensable to our understanding of what life is; 2) Biological information is more than the material structures that embody it; 3) Conventional chemical and evolutionary mechanisms seem insufficient to fully explain the labyrinth of information that is life. By exploring new perspectives on biological information, this volume seeks to expand, encourage, and enrich research into the nature and origin of biological information."


In the Beginning was Information - Werner Gitt, former Director, former head of the Department of Information Technology at the German Federal Institute of Physics and Technology (Physikalisch-Technische Bundesanstalt [PTB], in Braunschweig


DNA Study Forces Rethink of What It Means to Be a Gene, Eliizabeth Pennisi, Science 15 June 2007, Vol. 316 no. 5831 pp. 1556-1557: "According to a painstaking new analysis of 1% of the human genome, genes can be sprawling, with far-flung protein-coding and regulatory regions that overlap with other genes." http://www.sciencemag.org/content/316/5831/1556


Anzai, T. et al. 2003. Comparative sequencing of human and chimpanzee MHC class I regions unveils insertions/deletions as the major path to genomic divergence. Proceedings of the National Academy of Sciences. 100 (13): 7708-13.


Yale News: Yale Symposium Will Explore New Evidence Supporting The Theory of Intelligent Design http://news.yale.edu/2000/10/31/yale-symposium-will-explore-new-evidence-supporting-theory-intelligent-design


SYMPOSIUM PRELIMINARY PROGRAM Intelligent Design & Artificial Intelligence: The Ghost in the Machine http://sophiawarsaw.ippt.gov.pl/Symposium%202009%20Pasadena.pdf


The 2016 International Conference on Biological Information and Biomedical Engineering http://www.icbibe.org/


"Many biologists think of the developmental processes by which organisms progress from egg to adult in terms of the execution of a "developmental program" - Biological Information, Stanford Encyclopedia of Philosophy


"Since the 1950s, the concept of information has acquired a strikingly prominent role in many parts of biology." - Stanford Encyclopedia of Philosophy https://plato.stanford.edu/entries/information-biological/


Biological Information, New Perspectives, Proceedings of the Symposium, Cornell University, USA, 31 May - 3 June 2011


John W. Oller, Jr (2013) Pragmatic Information. Biological Information: pp. 64-86. doi: .1142/9789814508728_0003


Section one: Information Theory & Biology: Introductory Comments, Pragmatic Information, John W. Oller, Jr, Doris B. Hawthorne Board of Regents Support Fund Professor IV, Department of Communicative Disorders, University of Louisiana at Lafayette, Lafayette, LA 70504, USA

The goal of this paper is to define pragmatic information with a view toward measuring it. Here, pragmatic information means the content of valid signs - the key that unlocks language acquisition by babies and to human communication through language - also the content that enables biological "codes" in genetics, embryology, and immunology to work. In such systems, the inter-related layers appear to be ranked as in a hierarchy. Sounds are outranked by syllables, in turn outranked by words, and so on. In DNA, nucleotide pairs are outranked by codons, which are outranked by genes, and so on. As signs of lower rank combine to form signs of any higher rank, combinatorial "explosions" occur. With each increase in rank, the number of possible combinations grows exponentially, but the constraints on valid strings and, thus, their pragmatic value, sharpens their focus. As a result with each explosive increase in the number of possible combinations the relative proportion of meaningful ones diminishes. Consequently, random processes of forming strings or changing them must tend increasingly toward meaninglessness (invalid and nonviable) strings. The consequent outcome of random mutations is mortality of individuals and in deep time an increasing number of disorders, diseases, and the eventual extinction of populations.


Computational Aspects of Biological Information 2016 https://www.microsoft.com/en-us/research/event/computational-aspects-biological-information-2016/#


9th International Conference on Bioinformatics, November 13-14, 2017 Paris, France http://bioinformatics.conferenceseries.com/


Signal Transduction in the Immune System http://www.faseb.org/src/micro/Site/SigImm/home.aspx


Biochemistry. 5th edition: Chapter 5DNA, RNA, and the Flow of Genetic Information http://www.ncbi.nlm.nih.gov/books/NBK21171/


Biological Information, New Perspectives, Proceedings of the Symposium, Cornell University, USA, 31 May - 3 June 2011 Edited by: Robert J Marks II (Baylor University, USA), Michael J Behe (Lehigh University, USA), William A Dembski (Discovery Institute, USA), Bruce L Gordon (Houston Baptist University, USA), John C Sanford (Cornell)

Biological Information, New Perspectives http://www.worldscientific.com/worldscibooks/10.1142/8818#t=toc%22n the spring of 2011, a diverse group of scientists gathered at Cornell University to discuss their research into the nature and origin of biological information. This symposium brought together experts in information theory, computer science, numerical simulation, thermodynamics, evolutionary theory, whole organism biology, developmental biology, molecular biology, genetics, physics, biophysics, mathematics, and linguistics. This volume presents new research by those invited to speak at the conference.

The contributors to this volume use their wide-ranging expertise in the area of biological information to bring fresh insights into the many explanatory difficulties associated with biological information. These authors raise major challenges to the conventional scientific wisdom, which attempts to explain all biological information exclusively in terms of the standard mutation/selection paradigm.

Several clear themes emerged from these research papers: 1) Information is indispensable to our understanding of what life is; 2) Biological information is more than the material structures that embody it; 3) Conventional chemical and evolutionary mechanisms seem insufficient to fully explain the labyrinth of information that is life. By exploring new perspectives on biological information, this volume seeks to expand, encourage, and enrich research into the nature and origin of biological information.

Session One - Information Theory & Biology: Introductory Comments (Robert J Marks II): Biological Information - What is It? (Werner Gitt, Robert Compton and Jorge Fernandez), A General Theory of Information Cost Incurred by Successful Search (William A Dembski, Winston Ewert and Robert J Marks II), Pragmatic Information (John W Oller, Jr), Limits of Chaos and Progress in Evolutionary Dynamics (William F Basener), Tierra: The Character of Adaptation (Winston Ewert, William A Dembski and Robert J Marks II), Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation (George Montanez, Robert J Marks II, Jorge Fernandez and John C Sanford), Entropy, Evolution and Open Systems (Granville Sewell), Information and Thermodynamics in Living Systems (Andy C McIntosh)

Session Two - Biological Information and Genetic Theory: Introductory Comments (John C Sanford): Not Junk After All: Non-Protein-Coding DNA Carries Extensive Biological Information (Jonathan Wells) Can Purifying Natural Selection Preserve Biological Information? (Paul Gibson, John R Baumgardner, Wesley H Brewer and John C Sanford), Selection Threshold Severely Constrains Capture of Beneficial Mutations (John C Sanford, John R Baumgardner and Wesley H Brewer)

Using Numerical Simulation to Test the "Mutation-Count" Hypothesis (Wesley H Brewer, John R Baumgardner and John C Sanford), Can Synergistic Epistasis Halt Mutation Accumulation? Results from Numerical Simulation (John R Baumgardner, Wesley H Brewer and John C Sanford), Computational Evolution Experiments Reveal a Net Loss of Genetic Information Despite Selection (Chase W Nelson and John C Sanford), Information Loss: Potential for Accelerating Natural Genetic Attenuation of RNA Viruses (Wesley H Brewer, Franzine D Smith and John C Sanford), DNA.EXE: A Sequence Comparison between the Human Genome and Computer Code (Josiah Seaman), Biocybernetics and Biosemiosis (Donald Johnson)

Session Three - Theoretical Molecular Biology: Introductory Comments (Michael J Behe): An Ode to the Code: Evidence for Fine-Tuning in the Standard Codon Table (Jed C Macosko and Amanda M Smelser), A New Model of Intracellular Communication Based on Coherent, High-Frequency Vibrations in Biomolecules (L Dent), Getting There First: An Evolutionary Rate Advantage for Adaptive Loss-of-Function Mutations (Michael J Behe), The Membrane Code: A Carrier of Essential Biological Information That is Not Specified by DNA and is Inherited Apart from It (Jonathan Wells), Explaining Metabolic Innovation: Neo-Darwinism Versus Design (Douglas D Axe and Ann K Gauger)

Session Four - Biological Information and Self-Organizational Complexity Theory: Introductory Comments (Bruce L Gordon): Evolution Beyond Entailing Law: The Roles of Embodied Information and Self Organization (Stuart Kauffman), Towards a General Biology: Emergence of Life and Information from the Perspective of Complex Systems Dynamics (Bruce H Weber)


Werner Gitt (Professor of Information Systems) describes man as the most complex information processing system on earth. Gitt estimated that about 3 x 1024 bits of information are processed daily in an average human body. That is thousands of times more than all the information in all the world's libraries. [See Werner Gitt, In the Beginning Was Information, 2nd edition (Bielefeld, Germany: CLV, 2000), p. 88.]


The discovery of the structure of DNA transformed biology profoundly, catalysing the sequencing of the human genome and engendering a new view of biology as an information science. Two features of DNA structure account for much of its remarkable impact on science: its digital nature and its complementarity, whereby one strand of the helix binds perfectly with its partner. DNA has two types of digital information--the genes that encode proteins, which are the molecular machines of life, and the gene regulatory networks that specify the behaviour of the genes.

http://www.ncbi.nlm.nih.gov/pubmed/12540920


"The basic flaw of all evolutionary views is the origin of the information in living beings. It has never been shown that a coding system and semantic information could originate by itself in a material medium, and the information theorems predict that this will never be possible. A purely material origin of life is thus precluded." - Werner Gitt, former Director, former head of the Department of Information Technology at the German Federal Institute of Physics and Technology (Physikalisch-Technische Bundesanstalt [PTB], in Braunschweig

Three prerequisites must be fulfilled in order for the German Ministerium to award the title "Director and Professor" at a German research institute, on the recommendation of the Praesidium. The person concerned must be: 1. A scientist (i.e., it is most definitely an academic title). 2. One who has published a significant number of original research papers in the technical literature. 3 .Must head a department in his area of expertise, in which several working scientists are employed.


"It was already clear that the genetic code is not merely an abstraction, but also the embodiment of life's mechanisms; the consecutive triplets of nucleotides in DNA (called codons) are inherited but they also guide the construction of proteins. So it is disappointing, but not surprising, that the origin of the genetic code is still as obscure as the origin of life itself." - John Maddox, "The Genetic Code by Numbers," Nature, Vol. 367, 13 January 1994, p. 111.


"We estimate that approximately 73% of all protein-coding SNVs and approximately 86% of SNVs predicted to be deleterious arose in the past 5,000-10,000?years." - Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants http://www.nature.com/nature/journal/v493/n7431/full/nature11690.html


The Linguistics of DNA Words, Sentences, Grammar, Phonetics and Semantics http://www.genetics.org/search?fulltext=information&submit=yes&x=0&y=0


Quantitative linguistic study of DNA sequences "A new family of compound Poisson distribution functions from quantitative linguistics is used to study the linguistic features of DNA sequences that go beyond the Zipf's law." http://www.sciencedirect.com/science/article/pii/S0378437102017879


Linguistics Features of Noncoding DNA Sequences http://cps.bu.edu/hes/articles/mbghpss94.pdf Complexity Matters "Evolutionary biologists have been loosely divided into two camps. One group believes that all characteristics of an organism are equally malleable by evolutionary pressures, with the result that an organism can in theory take any shape. The other camp has the view that there are fundamental properties of each organism that are quite immutable. In his commentary, Wagner discusses new work on the complexity of organisms and a paper by Waxman and Peck in this week's issue and argues that these results tip the balance in favor of the group that believes in a fundamentally immutable set of characteristics for each organism." http://www.sciencemag.org/content/279/5354/1158.summary


Scientists discover double meaning in genetic code: "Scientists have discovered a second code hiding within DNA. The second code contains information that changes how scientists read the instructions contained in DNA and interpret mutations to make sense of health and disease. Genomes use the genetic code to write two separate languages. One describes how proteins are made, and the other instructs the cell on how genes are controlled. One language is written on top of the other." http://www.sciencedaily.com/releases/2013/12/131212142151.htm


Module 6: Digital DNA http://www.cs.ubc.ca/~condon/cpsc101/notes/digital-dna.pdf


The digital code of DNA. http://www.ncbi.nlm.nih.gov/pubmed/12540920


"Information theory tells us that the only known way to decrease the entropy of an isolated system is by having intelligence in that system. [See, for example, Charles H. Bennett, "Demons, Engines and the Second Law," - Scientific American, Vol. 257, November 1987, pp. 108-116.] Because the universe is far from its maximum entropy level, a vast intelligence is the only known means by which the universe could have been brought into being. [See also "Second Law of Thermodynamics" on page 31.]


"Any living being possesses an enormous amount of "intelligence," very much more than is necessary to build the most magnificent of cathedrals. Today, this "intelligence" is called "information," but it is still the same thing. It is not programmed as in a computer, but rather it is condensed on a molecular scale in the chromosomal DNA or in that of any other organelle in each cell. This "intelligence" is the sine qua non of life. If absent, no living being is imaginable. Where does it come from? This is a problem which concerns both biologists and philosophers and, at present, science seems incapable of solving it." - Pierre P. Grasse, The Evolution of Living Organisms, 1977, p. 168


"Information is a non-physical fundamental entity, which the laws of physics and matter cannot produce. Information is a product of a non-physical mind. No physical thing is itself information. Observing something allows us to gain knowledge of it's properties, which we can convey to someone else, thus producing information by sharing the knowledge we have gained by observation, investigation, or study." - Gitt Werner, former head of the Department of Information Technology at the German Federal Institute of Physics and Technology (Physikalisch-Technische Bundesanstalt [PTB], in Braunschweig https://www.ptb.de/cms/en.html). Seven years later he was promoted to Director and Professor at PTB. https://www.youtube.com/watch?v=DA0Ojxr4pv0


"Information is information, neither matter nor energy. Any materialism which disregards this, will not survive one day." - Norbert Wiener, Mathematician, Cybernetics; or, Control and Communication in the Animal and the Machine, 2nd edition (Cambridge, Massachusetts: MIT Press, 1948), p. 132.


"Even the biology based on a materialistic philosophy, which discarded all vitalistic and metaphysical components, did not readily accept the reduction of biology to physics ... Information is neither a physical nor a chemical principle like energy and matter, even though the latter are required as carriers." - East German scientist J. Peil

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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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