DNA stores literally coded information
https://reasonandscience.catsboard.com/t1281-dna-stores-literally-coded-information
Paul Davies & Jeremy England • The Origins of Life: Do we need a new theory for how life began?
Paul Davies at 15:10
For me is the real challenge of explaining the origin of life: how do those systems uh develop information management overview. So I think um for me the definition of life is uh just to boil it down to a pity phrase its sort of chemistry plus information
https://www.youtube.com/watch?v=R9IU2ZWrkhg
Craig Venter: Life at the speed of light 2013 page 13
DNA is the software of life.
https://3lib.net/book/4978378/b560db
A A Travers DNA information: from digital code to analogue structure 2012 Jun 28
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.
http://www.ncbi.nlm.nih.gov/pubmed/22615471
George M Church Next-generation digital information storage in DNA 2012 Sep 28
DNA is among the most dense and stable information media known. The development of new technologies in both DNA synthesis and sequencing make DNA an increasingly feasible digital storage medium. We developed a strategy to encode arbitrary digital information in DNA, wrote a 5.27-megabit book using DNA microchips, and read the book by using next-generation DNA sequencing.
http://www.ncbi.nlm.nih.gov/pubmed/22903519
Richard Dawkins River Out of Eden: A Darwinian View of Life 1996
What is truly revolutionary about molecular biology in the post-Watson-Crick era is that it has become digital. After Watson and Crick, we know that genes themselves, within their minute internal structure, are long strings of pure digital information. What is more, they are truly digital, in the full and strong sense of computers and compact disks, not in the weak sense of the nervous system. The genetic code is not a binary code as in computers, nor an eight-level code as in some telephone systems, but a quaternary code, with four symbols. The machine code of the genes is uncannily computerlike. Apart from differences in jargon, the pages of a molecular-biology journal might be interchanged with those of a computer-engineering journal. . . .Our genetic system, which is the universal system of all life on the planet, is digital to the core. With word-for-word accuracy, you could encode the whole of the New Testament in those parts of the human genome that are at present filled with “junk” DNA – that is, DNA not used, at least in the ordinary way, by the body. Every cell in your body contains the equivalent of forty-six immense data tapes, reeling off digital characters via numerous reading heads working simultaneously. In every cell, these tapes – the chromosomes – contain the same information, but the reading heads in different kinds of cells seek out different parts of the database for their own specialist purposes. Genes are pure information – information that can be encoded, recoded and decoded, without any degradation or change of meaning. Pure information can be copied and, since it is digital information, the fidelity of the copying can be immense. DNA characters are copied with an accuracy that rivals anything modern engineers can do. What lies at the heart of every living thing is not a fire, warm breath, not a ‘spark of life’. It is information, words, instructions…Think of a billion discrete digital characters…If you want to understand life think about technology – Richard Dawkins (Dawkins 1996, 112)
https://3lib.net/book/807573/de593a
Richard Dawkins on the origins of life (1 of 5) Sep 29, 2008
Afther the seventh minute of his speech, Dawkins admits that : Can you think of any other class of molecule, that has that property, of folding itself up, into a uniquely characteristic enzyme, of which there is a enormous repertoire, capable of catalyzing a enormous repertoir of chemical reactions, and this is in itself to be absolutely determined by a digital code.
https://www.youtube.com/watch?v=wa55s9Gs_Eg#t=433
Leroy Hood The digital code of DNA 23 January 2003
Hubert Yockey, the worlds' foremost biophysicist and foremost authority on biological information contradicts you 100%.:
"Information, transcription, translation, code, redundancy, synonymous, messenger, editing, and proofreading are all appropriate terms in biology. They take their meaning from information theory (Shannon, 1948) AND ARE NOT SYNONYMS, METAPHORS, OR ANALOGIES." (Hubert P. Yockey, Information Theory, Evolution, and the Origin of Life, Cambridge University Press, 2005)
"It is important to understand that WE ARE NOT REASONING BY ANALOGY. the sequence hypothesis [that the exact order of symbols records the information] APPLIES DIRECTLY TO THE PROTEIN AND THE GENETIC TEXT AS WELL AS TO WRITTEN LANGUAGE AND THEREFORE THE TREATMENT IS MATHEMATICALLY IDENTICAL."
Yockey continued, "Like all messages, _the life message is NON-MATERIAL_ but has an information content measurable in bits and bytes".
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.
The discovery of the double helix in 1953 immediately raised questions about how biological information isencoded in DNA. A remarkable feature of the structure is that DNA can accommodate almost any sequence of base pairs — any combination of the bases adenine (A), cytosine (C), guanine (G) and thymine (T) — and, hence any digital message or information. During the following decade it was discovered that each gene encodes a complementary RNA transcript, called messenger RNA (mRNA), made up of A, C, G and uracil (U), instead of T. The four bases of the DNA and RNA alphabets are related to the 20 amino acids of the protein alphabet by a triplet code — each three letters (or ‘codons’) in a gene encodes one amino acid. For example, AGT encodes the amino acid serine. The dictionary of DNA letters that make up the amino acids is called the genetic code. There are 64 different triplets or codons, 61 of which encode an amino acid (different triplets can encode the same amino acid), and three of which are used for ‘punctuation’ in that they signal the termination of the growing protein chain. The molecular complementary of the double helix — whereby each base on one strand of DNA pairs with its complementary base on the partner strand (A with T, and C with G) — has profound implications for biology. As implied by James Watson and Francis Crick in their landmark paper, base pairing suggests a template copying mechanism that accounts for the fidelity in copying of genetic material during DNA replication . It also underpins the synthesis of mRNA from the DNA template, as well as processes of repairing damaged DNA.
The digital nature of biological information
The value of having an entire genome sequence is that one can initiate the study of a biological system with a precisely definable digital core of information for that organism — a fully delineated genetic source code. The challenge, then, is in deciphering what information is encoded within the digital code. The genome encodes two main types of digital information — the genes that encode the protein and RNA molecular machines of life, and the regulatory networks that specify how these genes are expressed in time, space and amplitude. It is the regulatory networks and not the genes themselves that play the critical role in making organisms different from one another.Development is the elaboration of an organism from a single cell (the fertilized egg) to an adult (for humans this is 10^14 cells of thousands of different types). Physiology is the triggering of specific functional programmes (for example, the immune response) by environmental cues. Regulatory networks are crucial in each of these aspects of biology. Regulatory networks are composed of two main types of components: transcription factors and the DNA sites to which they bind in the control regions of genes, such as promoters, enhancers and silencers. The control regions of individual genes serve as information processors to integrate the information inherent in the concentrations of different transcription factors into signals that mediate gene expression. The collection of the transcription factors and their cognate DNA-binding sites in the control regions of genes that carry out a particular developmental or physiological function constitute these regulatory networks.
http://www.nature.com/nature/journal/v421/n6921/full/nature01410.html
Genetic code
The genetic code is the set of rules by which information encoded in genetic material (DNA or RNA sequences) is translated into proteins (amino acid sequences) by living cells.
https://www.sciencedaily.com/terms/genetic_code.htm
What is DNA?
The information in DNA is stored as a code made up of four chemical bases: adenine (A), guanine (G), cytosine (C), and thymine (T).
https://www.thoughtco.com/microinjection-375568#:~:text=The%20information%20in%20DNA%20is%20stored%20as%20a,information%20available%20for%20building%20and%20maintaining%20an%20organism.[/url]
V A Ratner The genetic language: grammar, semantics, evolution 1993 May 29
The genetic language is a collection of rules and regularities of genetic information coding for genetic texts. It is defined by alphabet, grammar, collection of punctuation marks and regulatory sites, semantics.
http://www.ncbi.nlm.nih.gov/pubmed/8335231
Katrin Weigmann The code, the text and the language of God 2004 Feb 5
In his book The Language of Life, George Beadle wrote: “... the deciphering of the DNA code has revealed a language... as old as life itself, a language that is the most living language of all” (Beadle & Beadle, 1966).
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1298980/
Wikipedia:
Biological organisms contain genetic material that is used to control their function and development. This is DNA which contains units named genes that can produce proteins through a code (genetic code) in which a series of triplets (codons) of four possible nucleotides are translated into one of twenty possible amino acids. A sequence of codons results in a corresponding sequence of amino acids that form a protein.
https://en.wikipedia.org/wiki/Genetic_code
The Genetic Code
The sequence of bases in DNA operates as a true code in that it contains the information necessary to build a protein expressed in a four-letter alphabet of bases which is transcribed to mRNA and then translated to the twenty-amino-acid alphabet necessary to build the protein. Saying that it is a true code involves the idea that the code is free and unconstrained; any of the four bases can be placed in any of the positions in the sequence of bases. Their sequence is not determined by the chemical bonding. There are hydrogen bonds between the base pairs and each base is bonded to the sugar phosphate backbone, but there are no bonds along the longitudional axis of DNA. The bases occur in the complementary base pairs A-T and G-C, but along the sequence on one side the bases can occur in any order, like the letters of a language used to compose words and sentences.
To further illustrate what is meant by a true code, consider the magnetic letters fixed to the magnetic board at right. The letters are held to the board by the magnetic forces, but those forces do not impose any specific ordering of the letters. The letters can be arranged to spell out a meaningful message in the English language (code) or to form a meaningless sequence like the one at bottom.
http://hyperphysics.phy-astr.gsu.edu/hbase/organic/gencode.html
Genetic Entropy: Sanford 2005 page 52 and 53:
This “complex interwoven (poly-fuctional) network” throughout the entire DNA code makes the human genome severely poly-constrained to random mutations (Sanford; Genetic Entropy, 2005; page 141). This means the DNA code is now much more severely limited in its chance of ever having a hypothetical beneficial mutation since almost the entire DNA code is now proven to be intimately connected to many other parts of the DNA code. Thus even though a random mutation to DNA may be able to change one part of an organism for the better, it is now proven much more likely to harm many other parts of the organism that depend on that one particular part being as it originally was. Since evolution was forced, by the established proof of Mendelian genetics, to no longer view the whole organism as to what natural selection works upon, but to view the whole organism as a multiple independent collection of genes that can be selected or discarded as natural selection sees fit, this “complex interwoven network” finding is extremely bad news, if not absolutely crushing, for the “Junk DNA” population genetics scenario of evolution (modern neo-Darwinian synthesis) developed by Haldane, Fisher and Wright . We now know that in yeast DNA alone there are more than 300 nano machines at work performing various tasks in the cell, many of which are performed concurrently. Yet concurrency in info processing systems cannot arise without pre-knowledge of tasks requiring coordinated action!
http://www.doesgodexist.org/NovDec09/Information-Function.html
Harold R. Booher, Ph.D. The Scientific Case for Intelligent Design A Synopsis of Stephen Meyer’s Signature in the Cell February 2010
Literature from those who posture in favor of creation abounds with examples of the tremendous odds against chance producing a meaningful code. For instance, the estimated number of elementary particles in the universe is 10^80. The most rapid events occur at an amazing 10^45 per second. Thirty billion years contains only 10^18 seconds. By totaling those, we find that the maximum elementary particle events in 30 billion years could only be 10^143. Yet, the simplest known free-living organism, Mycoplasma genitalium, has 470 genes that code for 470 proteins that average 347 amino acids in length. The odds against just one specified protein of that length are 1:10^451.
The probability of useful DNA, RNA, or proteins occurring by chance is extremely small. Calculations vary somewhat but all are extremely small (highly improbable). If one is to assume a hypothetical prebiotic soup to start there are at least three combinational hurdles (requirements) to overcome. Each of these requirements decreases the chance of forming a workable protein. First, all amino acids must form a chemical bond (peptide bond) when joining with other amino acids in the protein chain. Assuming, for example a short protein molecule of 150 amino acids, the probability of building a 150 amino acids chain in which all linkages are peptide linkages would be roughly 1 chance in 10^45. The second requirement is that functioning proteins tolerate only left-handed amino acids, yet in abiotic amino acid production the right-handed and left-handed isomers are produced in nearly the same frequency. The probability of building a 150-amino-acid chain at random in which all bonds are peptide bonds and all amino acids are L-form is roughly 1 chance in 10^90. The third requirement for functioning proteins is that the amino acids must link up like letters in a meaningful sentence, i.e. in a functionally specified sequential arrangement. The chance for this happening at random for a 150 amino acid chain is approximately 1 chance in 10^195. It would appear impossible for chance to build even one functional protein considering how small the likelihood is. By way of comparison to get a feeling of just how low this probability is consider that there are only 10^65 atoms in our galaxy..
http://www.arn.org/docs/booher/scientific-case-for-ID.html
DNA is a communication system because the triplets are encoded into Messenger RNA and decoded into amino acids and proteins. For example the base pairs GGG (Guanine-Guanine-Guanine) are instructions to make the amino acid Glycine which is then assembled into proteins by the ribosomes.
http://cosmicfingerprints.com/faq/#code
Perry Marshall: Is DNA a Code?
1. Code is defined as communication between an encoder (a “writer” or “speaker”) and a decoder (a “reader” or “listener”) using agreed upon symbols.
2. DNA's definition as a literal code (and not a figurative one) is nearly universal in the entire body of biological literature since the 1960's.
3. DNA code has much in common with human language and computer languages
4. DNA transcription is an encoding / decoding mechanism isomorphic with Claude Shannon's 1948 model: The sequence of base pairs is encoded into messenger RNA which is decoded into proteins.
5. Information theory terms and ideas applied to DNA are not metaphorical, but in fact quite literal in every way. In other words, the information theory argument for design is not based on analogy at all. It is direct application of mathematics to DNA, which by definition is a code.
https://evo2.org/dna-atheists/dna-code/
Barbieri: Code Biology February 2018
"...there is no deterministic link between codons and amino acids because any codon can be associated with any amino acid. This means that the rules of the genetic code do not descend from chemical necessity and in this sense they are arbitrary."
"...we have the experimental evidence that the genetic code is a real code, a code that is compatible with the laws of physics and chemistry but is not dictated by them."
https://www.sciencedirect.com/journal/biosystems/vol/164/suppl/C
Alberts: The Molecular Biology of the Cell et al, p367
The relationship between a sequence of DNA and the sequence of the corresponding protein is called the genetic code…the genetic code is deciphered by a complex apparatus that interprets the nucleic acid sequence.
Genes VIII, by Lewin, p21-22
JIAN-JUN SHU A new integrated symmetrical table for genetic codes 2017
For the formation of proteins in living organism cells, it is found that each amino acid can be specified by either a minimum of one codon or up to a maximum of six possible codons. In other words, different codons specify the different number of amino acids. A table for genetic codes is a representation of translation for illustrating the different amino acids with their respectively specifying codons, that is, a set of rules by which information encoded in genetic material (RNA sequences) is translated into proteins (amino acid sequences) by living cells. There are a total of 64 possible codons, but there are only 20 amino acids specified by them.
https://arxiv.org/ftp/arxiv/papers/1703/1703.03787.pdf
Specification (technical standard)
A specification often refers to a set of documented requirements to be satisfied by a material, design, product, or service. A specification is often a type of technical standard.
https://en.wikipedia.org/wiki/Specification_(technical_standard)
ERICO What Is The Difference Between a Code, Standard, Regulation and Specification in the Electrical Industry? Nov 13, 2018
A code is a set of rules that serve as generally accepted guidelines recommended for the industry to follow.
https://blog.nvent.com/erico-what-is-the-difference-between-a-code-standard-regulation-and-specification-in-the-electrical-industry/
David L Abel Three subsets of sequence complexity and their relevance to biopolymeric information 11 August 2005
Genes are not analogous to messages; genes are messages.
https://link.springer.com/article/10.1186/1742-4682-2-29
Berg JM Biochemistry. 5th edition 2002
Lewin Genes VIII, by , p21-22
The relationship between a sequence of DNA and the sequence of the corresponding protein is called the genetic code…the genetic code is deciphered by a complex apparatus that interprets the nucleic acid sequence.
https://www.ncbi.nlm.nih.gov/books/NBK22358/#:~:text=The%20genetic%20codeis%20the%20relation%20between%20the%20sequence,features%20of%20the%20genetic%20code%20by%201961%3A%201.
David L Abel Dichotomy in the definition of prescriptive information suggests both prescribed data and prescribed algorithms: biosemiotics applications in genomic systems 2012 Mar 14
"Functional Information (FI)" has now been formalized into two subsets: Descriptive Information (DI) and Prescriptive Information (PI). This formalization of definitions precludes the prevailing confusion of informational terms in the literature. The more specific and accurate term "Prescriptive Information (PI)" has been championed by Abel to define the sources and nature of programming controls, regulation and algorithmic processing. Such prescriptions are ubiquitously instantiated into all known living cells
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3319427/
Paul E. Griffiths Genetic, epigenetic and exogenetic information in development and evolution 18 August 2017
We would expect to find that instructions written in the genetic code are read by gene regulatory networks to make an organism. But the genetic code runs out of steam when it has specified the linear structure of proteins
https://royalsocietypublishing.org/doi/10.1098/rsfs.2016.0152
Peter R. Wills DNA as information 13 March 2016
The biological significance of DNA lies in the role it plays as a carrier of information, especially across generations of reproducing organisms, and within cells as a coded repository of system specification and stability. DNA in organisms functions as information and that the internal DNA-dependent dynamics of cells embody functional information processing, that is, computation DNA-based molecular biological computation can be said to control, perhaps even ‘direct’, the entire panoply of biochemical events occurring in cells. The obvious way in which information is stored in DNA, as sequences of letters drawn predominantly from the standard four-letter {A, C, G, T} nucleotide alphabet, has been understood since the discovery of the substance's dual-linear-polymer, base-paired molecular structure and its mode of complementary chain copying. DNA is represented in these abstract terms, as information comprising a sequence of arbitrary symbols. Changes in the DNA sequence of an organism's genome translate in a regular causative way into biological changes in the concrete physical world. There is a causative connection between DNA sequence information, which is an arbitrary abstraction of material property, and the reality of events in the physical world of molecules embodying the sequence.
https://royalsocietypublishing.org/doi/full/10.1098/rsta.2015.0417
Paul Davies Origin of Life, page 18
Biological complexity is instructed complexity or, to use modern parlance, it is information-based complexity. Inside each and every one of us lies a message. Decrypted, the message contains instructions on how to make a human being. Inside each and every one of us lies a message. It is inscribed in an ancient code, its beginnings lost in the mists of time. Decrypted, the message contains instructions on how to make a human being. The message isn't written in ink or type, but in atoms, strung together in an elaborately arranged sequence to form DNA, short for deoxyribonucleic acid. It is the most extraordinary molecule on Earth. Although DNA is a material structure, it is pregnant with meaning. The arrangement of the atoms along the helical strands of your DNA determines how you look and even, to a certain extent, how you feel and behave. DNA is nothing less than a blueprint, or more accurately an algorithm or instruction manual, for building a living, breathing, thinking human being. We share this magic molecule with almost all other life forms on Earth. From fungi to flies, from bacteria to bears, organisms are sculpted according to their respective DNA instructions. Each individual's DNA differs from others in their species (with the exception of identical twins), and differs even more from that of other species. But the essential structure – the chemical make-up, the double helix architecture – is universal.
https://3lib.net/book/5597371/98ee4e
JAG BHALLA DNA Is Multibillion-Year-Old Software14 May, 2015
Nature invented (sic) software billions of years before we did. “The origin of life is really the origin of software,” says Gregory Chaitin. Life requires what software does (it’s foundationally algorithmic).
1. “DNA is multibillion-year-old software,” says Chaitin (inventor of mathematical metabiology). We’re surrounded by software, but couldn’t see it until we had suitable thinking tools.
2. Alan Turing described modern software in 1936, inspiring John Von Neumann to connect software to biology. Before DNA was understood, Von Neumann saw that self-reproducing automata needed software. We now know DNA stores information; it's a biochemical version of Turning’s software tape, but more generally: All that lives must process information. Biology's basic building blocks are processes that make decisions.
http://bigthink.com/errors-we-live-by/dna-is-multibillion-year-old-software
In signal transduction, in short, we find all the essential components of a code: two independents worlds of molecules (first messengers and second messengers), and a set of adaptors that create a mapping between them, and the proof that the mapping is arbitrary because its rules can be changed in many different ways. What we see operating in cells is not like a code, but genuinely is a code—therefore its best efficient explanation is intelligence.
…the conversion of the information in [messenger] RNA represents a translation of the information into another language that uses quite different symbols.
Only INTELLIGENCE specifies a set of rules for specific requirements.
Paul Davies reinforced the point that obtaining the building blocks would not explain their arrangement:
‘… just as bricks alone don’t make a house, so it takes more than a random collection of amino acids to make life. Like house bricks, the building blocks of life have to be assembled in a very specific and exceedingly elaborate way before they have the desired function.’
An analogy is written language. Natural objects in forms resembling the English alphabet (circles, straight lines, etc.) abound in nature, but this fact does not help to understand the origin of information (such as that in Shakespeare’s plays). The reason is that this task requires intelligence both to create the information (the play) and then to design and build the machinery required to translate that information into symbols (the written text). What must be explained is the source of the information in the text (the words and ideas), not the existence of circles and straight lines. Likewise, it is not enough to explain the origin of the amino acids, which correspond to the letters. Rather, even if they were produced readily, the source of the information that directs the assembly of the amino acids contained in the genome must be explained.
“DNA is not a special life-giving molecule, but a genetic databank that transmits its information using a mathematical code. Most of the workings of the cell are best described, not in terms of material stuff — hardware — but as information, or software. Trying to make life by mixing chemicals in a test tube is like soldering switches and wires in an attempt to produce Windows 98. It won’t work because it addresses the problem at the wrong conceptual level.” Inside each and every one of us lies a message. It is inscribed in an ancient code, its beginnings lost in the mists of time. Decrypted, the message contains instructions on how to make a human being. Although DNA is a material structure, it is pregnant with meaning. The arrangement of the atoms along the helical strands of your DNA determines how you look and even, to a certain extent, how you feel and behave. DNA is nothing less than a blueprint—or, more accurately, an algorithm or instruction manual—for building a living, breathing, thinking human being. So far, I have been somewhat cavalier in the use of the term “information.” Computer scientists draw a distinction between syntax and semantics. Syntactic information is simply raw data, perhaps arranged according to rules of grammar, whereas semantic information has some sort of context or meaning. Information per se doesn’t have to mean anything. Snowflakes contain syntactic information in the specific arrangement of their hexagonal shapes, but these patterns have no semantic content, no meaning for anything beyond the structure itself. By contrast, the distinctive feature of biological information is that it is replete with meaning. DNA stores the instructions needed to build a functioning organism; it is a blueprint or an algorithm for a specified, predetermined product. Snowflakes don’t code for, or symbolize, anything, whereas genes most definitely do. To explain life fully, it is not enough simply to identify a source of free energy, or negative entropy, to provide biological information. We also have to understand how semantic information comes into being. It is the quality, not the mere existence, of information that is the real mystery here. All that stuff about conflict with the second law of thermodynamics was mostly a red herring.
In a living organism we see the power of software, or information processing, refined to an incredible degree. Cells are not hard-wired, like kites. Rather, the information flow couples the chalk of nucleic acids to the cheese of proteins using the genetic code. Stored energy is then released and forces are harnessed to carry out the programmed instructions, as with the radio-controlled plane. Viewed this way, the problem of the origin of life reduces to one of understanding how encoded software emerged spontaneously from hardware. How did it happen? How did nature “go digital”? We are dealing here not with a simple matter of refinement and adaptation, an amplification of complexity, or even the husbanding of information, but a fundamental change of concept. It is like trying to explain how a kite can evolve into a radio-controlled aircraft. Can the laws of nature as we presently comprehend them account for such a transition? I do not believe they can.
Fact two: not all random sequences are potential genomes. Far from it. In fact, only a tiny, tiny fraction of all possible random sequences would be even remotely biologically functional. A functioning genome is a random sequence, but it is not just any random sequence. It belongs to a very, very special subset of random sequences—namely, those that encode biologically relevant information. All random sequences of the same length encode about the same amount of information, but the quality of that information is crucial: in the vast majority of cases it would be, biologically speaking, complete gobbledygook.
“DNA is not a special life-giving molecule, but a genetic databank that transmits its information using a mathematical code. Most of the workings of the cell are best described, not in terms of material stuff — hardware — but as information, or software. Trying to make life by mixing chemicals in a test tube is like soldering switches and wires in an attempt to produce Windows 98. It won’t work because it addresses the problem at the wrong conceptual level.”
Inside each and every one of us lies a message. It is inscribed in an ancient code, its beginnings lost in the mists of time. Decrypted, the message contains instructions on how to make a human being.
Although DNA is a material structure, it is pregnant with meaning. The arrangement of the atoms along the helical strands of your DNA determines how you look and even, to a certain extent, how you feel and behave. DNA is nothing less than a blueprint—or, more accurately, an algorithm or instruction manual—for building a living, breathing, thinking human being.
Nucleic acids store life’s software; the proteins are the real workers and constitute the hardware. The two chemical realms can support each other only because there is a highly specific and refined communication channel between them mediated by a code, the so-called genetic code.
JAMES J. S. JOHNSON DNA and RNA: Providential Coding to 'Revere' God FEBRUARY 28, 2011
When accurately describing what happens inside a eukaryotic cell’s nucleus or mitochondrion, evolutionary geneticists routinely describe what they see using terms like code (e.g., genetic code, protein coding, coding regions), encode, codon, anti-codon, decode, transcription, translation, blueprint, program, information, instruction, control, edit, decipher, messenger, reading, proofreading, signal, alphabet, letter, language, gene expression, information, surveillance (for detecting nonsense), etc. It is important to recognize that these genetic message-oriented terms were not imposed on the evolutionists by the creationists!
genetic science reveals God’s purposeful encoding of genetic messages, with mind-bogglingly complex instructions on how to build living things from the biomolecular level upward, with those same encoded messages being efficiently decoded and recognized with sufficient accuracy to produce responsive compliance with those biomolecular instructions!
a coded message is no good at all if the intended recipient cannot understand its encoded meaning. Accordingly, every code-based message must be informationally devised (i.e., created), encoded, and sent to the intended readers. The readers must then decode the message, recognize the information it contains, and act on that information in a way that corresponds to the original purpose of the message’s creator. It is vital that the intended recipient understand the sender’s meaning, because the message itself is unrecognizable unless both sender and receiver share a common understanding of what the words (or other symbols) mean.
Consider the following message: “One if by land, two if by sea.” What does that sequence of words signify? Because that message used a language shared by the sender (Robert Newman, with the help of John Pulling) and receivers (those awaiting word on the movement of British troops), it provided a recognizable warning that “the Regulars [British soldiers] are coming” by water, not by land. Two lanterns lit in the Old North Church on the night of April 18, 1775, provided a signal—but it was recognizable as such only to those who knew the “language” shared by Paul Revere and his allies.
This principle of coded information transfer is illustrated at the sub-cellular level. If a protein-coding “message” borne by a portion of DNA cannot be transferred by RNA and translated on ribosomes providentially fitted for the task, the DNA’s instructions cannot be complied with, and that would mean no protein synthesis—which can be a fatal failure for whatever life form is involved, whether girl or gecko, boy or bacterium.
http://www.icr.org/article/dna-rna-providential-coding-revere/
Vjtorley Is The Genetic Code A Real Code? February 15, 2013
If amino acids were randomly assigned to triplet codons, then there would be 1.5 x 10^84 possible genetic codes to choose from. However, the genetic code used by all known forms of life is nearly universal with few minor variations. This suggests that a single evolutionary history underlies the origin of the genetic code. Many hypotheses on the evolutionary origins of the universal genetic code have been proposed.
In responding to the “code skeptics,” we need to keep in mind that they are bound by their own methodology to explain the origin of the genetic code in non-teleological, causal terms. They need to explain how things happened in the way that they suppose. Thus if a code-skeptic were to argue that living things have the code they do because it is one which accurately and efficiently translates information in a way that withstands the impact of noise, then he/she is illicitly substituting a teleological explanation for an efficient causal one. We need to ask the skeptic: how did Nature arrive at such an ideal code as the one we find in living things today?
By contrast, a “top-down” explanation of life goes beyond such reductionistic accounts. On a top-down account, it makes perfect sense to say that the genetic code has the properties it has because they help it to withstand the impact of noise while accurately and efficiently translating information. The “because” here is a teleological one. A teleological explanation like this ties in perfectly well with intelligent agency: normally the question we ask an agent when they do something is: “Why did you do it that way?” The question of how the agent did it is of secondary importance, and it may be the case that if the agent is a very intelligent one, we might not even understand his/her “How” explanation. But we would still want to know “Why?” And in the case of the genetic code, we have an answer to that question.
We currently lack even a plausible natural process which could have generated the genetic code. On the other hand, we know that intelligent agents can generate codes. The default hypothesis should therefore be that the code we find in living things is the product of an Intelligent Agent.
http://www.uncommondescent.com/intelligent-design/is-the-genetic-code-a-real-code/
Aaron Saenz Messages Coded Into DNA Of Venter Synthetic Bacteria May 24, 2010
Craig Venter has proven that DNA and that complex coded information system is fundamentally the same as a computer operating system for biological organisms as he has been able to convert the biological code to computer code. He ... in fact ... calls DNA ... the software of life. Now, while it is true that Craig clings to the evolutionary idea, he cannot answer the simple question ... how did that complex coded software system originate. The reason he can't answer this question is that he refuses to accept the obvious fact that complex coded software systems require intelligence to be produced. Just like he has used human intelligence to map the genome and convert biological code into computer code.
https://singularityhub.com/2010/05/24/venters-newest-synthetic-bacteria-has-secret-messages-coded-in-its-dna/
Katrin Weigmann The code, the text and the language of God 2004 Feb 5
Common language talks about DNA as 'information' or 'a code'. For a very long time, scientists suspected that something—some kind of plan, specificity or driving force—resided within the sperm and/or egg, such that a snake developed from a snake egg and humans created human offspring. But it was only in the late 1940s and 1950s, when cyberneticists, physicists and mathematicians entered the field of molecular biology, that scientists came to interpret this 'something' as information. The physicist Erwin Schrödinger probably coined the term 'code' when he described living organisms in terms of their molecular and atomic structure, in his influential book What is Life (Schrödinger, 1944). The complete pattern of the future development of an organism and its function when mature, Schrödinger wrote, is contained in the chromosomes in the form of a 'code'. His writings had a strong influence on both Francis Crick and James Watson and their later discovery of the structure of DNA. “Schrödinger probably wasn't the first, but he was the first one I'd read to say that there must be a code of some kind that allowed molecules in cells to carry information,” Watson said in an interview with Scientific American (Watson, 2003). Indeed, Watson and Crick, in a paper on the implications of their DNA structure, picked up Schrödinger's metaphor when they wrote that “it therefore seems likely that the precise sequence of the bases is the code which carries the genetical information.”
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1298980/
DNA as software: DNA is binary just like the base language in computers 24 APRIL 2008
On 26 June 2000, when Francis Collins, Director of the National Human Genome Research Institute, announced the completion of the first draft in a major media event at the White House, he said “Today, we celebrate the revelation of the first draft of the human book of life” and declared that this breakthrough lets humans for the first time read “our own instruction book.”
http://colchambers.blogspot.com.br/2008/04/dna-as-software-dna-is-binary-just-like.html
Could you communicate in another language without learning it? 30 APRIL 2008
Ok, heres's another thing that amazed me when I found it out. I probably learnt it years agon cos I just checked http://en.wikipedia.org/wiki/DNA and found it called complementary base pairing which rings a bell to me. Going back over it I see that it's effectively a binary code. Just like the code that runs in computers. What's the point then. Well it's just this. How fascinating that the very code that runs computers bascially defines 1's and 0's and so does the very code that runs all species that we know of. That just seems amazing. Taking it further, the code that a programmer writes has a similar impact on the program its written for as DNA does for its host cell. Object oriented code for example works in a simiilar way to how proteins are made in a cell. As a programmer I like writing object oriented code. That's code that describes objects so if I wrote a program for a human I would write a class for a cell. I'd describe how the cell functions and what things it can do etc. then I'd describe lots of different kinds of cells. they'd have the same fundamental attributes of the basic cell class but they'd be a little different. A blood cell wouldn't have a nucleus (no dna), a young cell would be able to grow and change easily (say an osteoblast) an older cell wouldn't (an osteoclast). So how does dna work. Well it codes for proteins. Proteins make enzymes. Proteins are buidling blocks like the keratin in your nails and hair, they build cell walls. Enzymes are workers. The lactase in your stomach that breaks down the milk sugar lactose. Some people don't have this enzyme, their dna doesn't describe how to make it so they're lactose intolerant and can't have dairy products. how fascinating that the code for our bodies can be talked about in similar terms as the code I use to write computer programs. Who'd have thought it!
there is intention in the genetic code, and the genetic code uses arbitrary symbolism. the specific DNA sequences together with biochemistry to decode the sequences - has specific purposes. Thus, the DNA sequences and the biochemistry that ends up with the growth of my eyes exists in order to produce an eyes - which themselves exists so that I can see. In other words, this code was produced so that I can see. Contrast this with the tree rings. When you cut down a tree you can find out how old the tree is by counting the rings, so the rings contain information about the age of the tree. But there was no intention for the tree rings to contain that information, it is a chance by-product of the way a tree grows. The information in the DNA sequences that are the instructions for building an eye are by contrast there with the intention of building an eye. Furthermore, they are arbitrary, in the sense that other instructions to build an eye would do just as well, provided they built an eye.
https://colchambers.blogspot.com/2008/04/
DNA Writer
https://earthsciweb.org/js/bio/dna-writer/
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."
Biosemiosis: The Onset of Information on Earth
The Information Tetrahedron
The Information Tetrahedron is a visual aid for understanding translation. It is a model of the material conditions required to translate any form of recorded information, including the information recorded in DNA. The translation of an informational medium enables the production of effects that are not determined by the material properties of the medium being translated.Instead, those effects are determined elsewhere within the system of translation.
My comment: Why not by an intelligent designer ?
This relational architecture – with one arrangement of matter evoking an effect, while another arrangement of matter determines what the effect will be – establishes a physical discontinuity in the system. This discontinuity enables prescriptive control of effects that are not limited by local dynamics. Such effects can only be derived from the contingent organization of the individual systems that translate information.
My comment: The system of translation ITSELF and its origin is which origin has to be explained. The prescribing source must therefore be OUTSIDE of the system. We only know intelligence to be a capable informer and prescriber os a complex system with specific purposes.
To organize the first living cell implies the capacity to specify objects among alternatives. In short, the capacity to construct a cellular object made of x, y and z, requires the capacity to specify x, y, and z among other objects. Given that no physical object inherently specifies any other object, the act of specification is accomplished by the use of a representational medium (i.e. memory).
Nature demonstrates unambiguously how a representation is established in the natural world. An object is established as a representation when a second object physically determines what is being represented (i.e. its referent) and the natural discontinuity between the representation and its referent is preserved by the organization of the system.
This discontinuous association is a semiotic mechanism. It establishes the local independence (non-determinism) required to specify referents that are not derived from the properties of the representation.
My comment: In other words, it is not dependent on physical necessity.
A system that is capable of discontinuous association is limited only (in principle) by what is physically possible. This open set of potential outcomes is the physicochemical basis of both the origin and diversity of form in the living kingdom.
My comment: An open set of outcomes means, the set up of the genetic code is arbitrary. (based on random choice or personal whim, rather than any reason or system, aka physical necessity)
Because the effects of translation are not determined by local dynamics, they are subject to error, change, and noise. A rational distinction is therefore made between the functional and non-functional output of semiotic systems. Functional products are described as being the result of information; non-functional products are generally described as being the result of error and noise.
My comment: Mind is a set of Cognitive faculties including consciousness , perception, thinking , judgment, and memory .
The products of these systems include communication, sensory perception, replication, homeostasis, evolution, and culture. These examples reflect the entirety of the living kingdom, and are completely absent in the remaining inanimate world.
https://web.archive.org/web/20170316041716/http://biosemiosis.org/
DNA ultimately came from a mind, who had to make decisions, and be extraordinarily intelligent.
This claim can be falsified. Show one, just ONE example of coded, specified, complex information, and you top the claim.
We can quantify the information carrying capacity of nucleic acids in the following way. Each position can be one of four bases, corresponding to two bits of information (22 = 4). Thus, a chain of 5100 nucleotides corresponds to 2 × 5100 = 10,200 bits, or 1275 bytes (1 byte = 8 bits). The E. coli genome is a single DNA molecule consisting of two chains of 4.6 million nucleotides, corresponding to 9.2 million bits, or 1.15 megabytes, of information
Scientists have been looking to unlock the memory storage potential of DNA strands for a decade now. Over at Harvard it looks like they've finally cracked it with a breakthrough that allows over 700 terabytes of data to be stored on a single gram of DNA. Treating the genetic code much like the binary system traditional computer memory uses, they've successfully replicated the storage capacity of over 14,000 Bluray discs, or 151 kilograms of hard drives on a surface area smaller than the tip of your little finger.
https://www.prote.in/en/feed/2012/11/dna-hard-drives#.UoGXXeLQ7gE
1. In cells, information is encoded through the genetic code which is a set of rules, stored in DNA sequences of nucleotide triplets called codons. They are used to translate genetic information into amino acid polypeptide sequences, which make proteins ( the molecular machines, the working horses of the cell ). In life, this is done by over 25 extremely complex molecular machine systems, which do as well error check and repair to maintain genetic stability, and minimizing replication, transcription and translation errors, and permit organisms to pass accurately genetic information to their offspring, and survive.
2. A code is a system of rules where a symbol, letters, words, or even sounds, gestures, or images, are assigned to something else. Transmitting information, for example, can be done through the translation of the symbols of the alphabetic letters, to symbols of kanji, logographic characters used in Japan.
3. Assigning meaning of characters through a code system, where symbols of one language are assigned to symbols of another language that mean the same, requires a common agreement of meaning in order to establish communication, trough encoding, sending, and decoding. Semantics, Synthax, and pragmatics are always set up by intelligence.
4. The assignment of codons (triplet nucleotides) to amino acids must be pre-established by a mind. And so, the information which is sent through the system, as well as the communication channels that permit encoding, sending, and decoding. This system had to be set-up prior life began because life depends on it. The origin of such complex communication systems is best explained by an intelligent designer.
1. In biology the genetic code is the assignment ( a cipher) of 64 triplet codons to 20 amino acids.
2. The assignment of a word to represent something, like the word chair to an object to sit down, is always of mental origin.On top of that, the translation of a word in one language, to another language, is also 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.
3. Since we know only of intelligence to be able to do so, this assignment is best explained by the deliberate, arbitrary action of a non-human intelligent agency.
1. Genetic and epigenetic information is characterized containing prescriptive codified information, which result in functional outcomes due to the right particular specified complex sequence of triplet codons and ultimately the translated sequencing of amino acid building blocks into protein strings. The sequencing of nucleotides in DNA also prescribes highly specific regulatory micro RNAs and other epigenetic factors.
2. Algorithms, prescribing functional instructions, digital programming, using symbols and coding systems are abstract and non-physical, and originate always from thought—from conscious or intelligent activity.
3. Therefore, genetic and epigenetic information comes from an intelligent mind. Since there was no human mind present to create life, it must have been a supernatural agency.
1. The pattern in DNA is a code.
2. All codes we know the origin of com from a intelligent mind
3. Therefore we have 100% inference that DNA comes from a intelligent mind, and 0% inference that it is not.
1. DNA stores coded information.
2. All codes com from intelligence.
3. Therefore, DNA comes from a mind.
1. Symbols are defined as: something which represents something else.
2. Symbols carry thoughts (or messages) from a personal, intelligent, mind. No exceptions.
3. Scientific inquiry has discovered that DNA carries encoded symbolic instructions.
Claim: The genetic code is so in a metaphorical sense
Reply: Life on earth is the product of information recorded inside the cell. When this information is translated by cellular machinery, it organizes inanimate matter (carbon, hydrogen, nitrogen, etc) into all the living things on earth. The mystery of life’s origin is therefore equal to the mystery of information. Where did the information come from that organized the very first living cell on earth? Did this information come together as an incredible chance event in chemical history, or was it the result of a deliberate act of design? To organize the first living cell, one set of objects must encode the information in a series of representations, and the other set of objects must specify what is being represented. This is how a "recipe" for the cell can exist in a universe where no object inherently means (represents or specifies) any other object. It requires both a representation and the means to interpret it. But there is a third requirement. The organization of the system must also preserve the natural discontinuity that exists between the representations and their effects. By doing so, a group of arbitrary relationships are established that otherwise wouldn't exist. That set of relationships is what we now call The Genetic Code. The unique physical conditions described here are the universal requirements of translation. They were proposed in theory, confirmed by experiment, and are not even controversial. They are also something that the living cell shares with every other instance of translated information ever known to exist. The genetic translation system provides objective physical evidence of the first irreducible organic system on earth, and from it, all other organic systems follow. Moreover, this system is not the product of Darwinian evolution. Instead, it is the source of evolution (i.e. the physical conditions that enable life's capacity to change and adapt over time) and as the first instance of specification on earth, it marks the rise of the genome and the starting point of heredity. And as a final indication of just how profound the appearance of this system was, an almost impossible observation remains – not only must these objects arise from a non-information (inanimate) environment, but the details of their construction must also be simultaneously encoded in the very information that they make possible. Without these things, life on earth would simply not exist. There are two distinct categories of semiotic systems. One category uses representations where the arrangement of the medium (like a pheromone) is reducible to the physical properties of the medium itself; the other uses representations that have a spatial (dimensional) orientation and are not reducible to their physical make-up (like the words on this page). The first type is found throughout the living kingdom. The second type is found nowhere but in recorded language and mathematics (and in the genetic code). This leads to an undeniable observation of physical reality; the singularly-unique material conditions required for dimensional semiosis, which would ostensibly not exist on Earth until the rise of human intelligence, were entirely evident at the very origin of life. They are the physical means by which the living cell became organized.
Is the Genetic Code a) an information-bearing sequence of DNA nucleotides or b) a translation program?
DNA stores literally coded information
https://reasonandscience.catsboard.com/t1281-dna-stores-literally-coded-information
The genetic code, insurmountable problem for non-intelligent origin
https://reasonandscience.catsboard.com/t2363-the-genetic-code-unsurmountable-problem-for-non-intelligent-origin
The genetic code cannot arise through natural selection
https://reasonandscience.catsboard.com/t1405-the-genetic-code-cannot-arise-through-natural-selection
Coded information comes always from a mind
https://reasonandscience.catsboard.com/t1312-coded-information-comes-always-from-a-mind
The five levels of information in DNA
https://reasonandscience.catsboard.com/t1311-the-five-levels-of-information-in-dna
The language of the genetic code
https://reasonandscience.catsboard.com/t1472-the-language-of-the-genetic-code
The different genetic codes
https://reasonandscience.catsboard.com/t2277-the-different-genetic-codes
More:
Francis Crick Nobel Lecture Nobel Lecture, On the Genetic Code December 11, 1962
[url=https://www.nobelprize.org/prizes/medicine/1962/crick/lecture/]https://www.nobelprize.org/prizes/medicine/1962/cr
https://reasonandscience.catsboard.com/t1281-dna-stores-literally-coded-information
Paul Davies & Jeremy England • The Origins of Life: Do we need a new theory for how life began?
Paul Davies at 15:10
For me is the real challenge of explaining the origin of life: how do those systems uh develop information management overview. So I think um for me the definition of life is uh just to boil it down to a pity phrase its sort of chemistry plus information
https://www.youtube.com/watch?v=R9IU2ZWrkhg
Craig Venter: Life at the speed of light 2013 page 13
DNA is the software of life.
https://3lib.net/book/4978378/b560db
A A Travers DNA information: from digital code to analogue structure 2012 Jun 28
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.
http://www.ncbi.nlm.nih.gov/pubmed/22615471
George M Church Next-generation digital information storage in DNA 2012 Sep 28
DNA is among the most dense and stable information media known. The development of new technologies in both DNA synthesis and sequencing make DNA an increasingly feasible digital storage medium. We developed a strategy to encode arbitrary digital information in DNA, wrote a 5.27-megabit book using DNA microchips, and read the book by using next-generation DNA sequencing.
http://www.ncbi.nlm.nih.gov/pubmed/22903519
Richard Dawkins River Out of Eden: A Darwinian View of Life 1996
What is truly revolutionary about molecular biology in the post-Watson-Crick era is that it has become digital. After Watson and Crick, we know that genes themselves, within their minute internal structure, are long strings of pure digital information. What is more, they are truly digital, in the full and strong sense of computers and compact disks, not in the weak sense of the nervous system. The genetic code is not a binary code as in computers, nor an eight-level code as in some telephone systems, but a quaternary code, with four symbols. The machine code of the genes is uncannily computerlike. Apart from differences in jargon, the pages of a molecular-biology journal might be interchanged with those of a computer-engineering journal. . . .Our genetic system, which is the universal system of all life on the planet, is digital to the core. With word-for-word accuracy, you could encode the whole of the New Testament in those parts of the human genome that are at present filled with “junk” DNA – that is, DNA not used, at least in the ordinary way, by the body. Every cell in your body contains the equivalent of forty-six immense data tapes, reeling off digital characters via numerous reading heads working simultaneously. In every cell, these tapes – the chromosomes – contain the same information, but the reading heads in different kinds of cells seek out different parts of the database for their own specialist purposes. Genes are pure information – information that can be encoded, recoded and decoded, without any degradation or change of meaning. Pure information can be copied and, since it is digital information, the fidelity of the copying can be immense. DNA characters are copied with an accuracy that rivals anything modern engineers can do. What lies at the heart of every living thing is not a fire, warm breath, not a ‘spark of life’. It is information, words, instructions…Think of a billion discrete digital characters…If you want to understand life think about technology – Richard Dawkins (Dawkins 1996, 112)
https://3lib.net/book/807573/de593a
Richard Dawkins on the origins of life (1 of 5) Sep 29, 2008
Afther the seventh minute of his speech, Dawkins admits that : Can you think of any other class of molecule, that has that property, of folding itself up, into a uniquely characteristic enzyme, of which there is a enormous repertoire, capable of catalyzing a enormous repertoir of chemical reactions, and this is in itself to be absolutely determined by a digital code.
https://www.youtube.com/watch?v=wa55s9Gs_Eg#t=433
Leroy Hood The digital code of DNA 23 January 2003
Hubert Yockey, the worlds' foremost biophysicist and foremost authority on biological information contradicts you 100%.:
"Information, transcription, translation, code, redundancy, synonymous, messenger, editing, and proofreading are all appropriate terms in biology. They take their meaning from information theory (Shannon, 1948) AND ARE NOT SYNONYMS, METAPHORS, OR ANALOGIES." (Hubert P. Yockey, Information Theory, Evolution, and the Origin of Life, Cambridge University Press, 2005)
"It is important to understand that WE ARE NOT REASONING BY ANALOGY. the sequence hypothesis [that the exact order of symbols records the information] APPLIES DIRECTLY TO THE PROTEIN AND THE GENETIC TEXT AS WELL AS TO WRITTEN LANGUAGE AND THEREFORE THE TREATMENT IS MATHEMATICALLY IDENTICAL."
Yockey continued, "Like all messages, _the life message is NON-MATERIAL_ but has an information content measurable in bits and bytes".
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.
The discovery of the double helix in 1953 immediately raised questions about how biological information isencoded in DNA. A remarkable feature of the structure is that DNA can accommodate almost any sequence of base pairs — any combination of the bases adenine (A), cytosine (C), guanine (G) and thymine (T) — and, hence any digital message or information. During the following decade it was discovered that each gene encodes a complementary RNA transcript, called messenger RNA (mRNA), made up of A, C, G and uracil (U), instead of T. The four bases of the DNA and RNA alphabets are related to the 20 amino acids of the protein alphabet by a triplet code — each three letters (or ‘codons’) in a gene encodes one amino acid. For example, AGT encodes the amino acid serine. The dictionary of DNA letters that make up the amino acids is called the genetic code. There are 64 different triplets or codons, 61 of which encode an amino acid (different triplets can encode the same amino acid), and three of which are used for ‘punctuation’ in that they signal the termination of the growing protein chain. The molecular complementary of the double helix — whereby each base on one strand of DNA pairs with its complementary base on the partner strand (A with T, and C with G) — has profound implications for biology. As implied by James Watson and Francis Crick in their landmark paper, base pairing suggests a template copying mechanism that accounts for the fidelity in copying of genetic material during DNA replication . It also underpins the synthesis of mRNA from the DNA template, as well as processes of repairing damaged DNA.
The digital nature of biological information
The value of having an entire genome sequence is that one can initiate the study of a biological system with a precisely definable digital core of information for that organism — a fully delineated genetic source code. The challenge, then, is in deciphering what information is encoded within the digital code. The genome encodes two main types of digital information — the genes that encode the protein and RNA molecular machines of life, and the regulatory networks that specify how these genes are expressed in time, space and amplitude. It is the regulatory networks and not the genes themselves that play the critical role in making organisms different from one another.Development is the elaboration of an organism from a single cell (the fertilized egg) to an adult (for humans this is 10^14 cells of thousands of different types). Physiology is the triggering of specific functional programmes (for example, the immune response) by environmental cues. Regulatory networks are crucial in each of these aspects of biology. Regulatory networks are composed of two main types of components: transcription factors and the DNA sites to which they bind in the control regions of genes, such as promoters, enhancers and silencers. The control regions of individual genes serve as information processors to integrate the information inherent in the concentrations of different transcription factors into signals that mediate gene expression. The collection of the transcription factors and their cognate DNA-binding sites in the control regions of genes that carry out a particular developmental or physiological function constitute these regulatory networks.
http://www.nature.com/nature/journal/v421/n6921/full/nature01410.html
Genetic code
The genetic code is the set of rules by which information encoded in genetic material (DNA or RNA sequences) is translated into proteins (amino acid sequences) by living cells.
https://www.sciencedaily.com/terms/genetic_code.htm
What is DNA?
The information in DNA is stored as a code made up of four chemical bases: adenine (A), guanine (G), cytosine (C), and thymine (T).
https://www.thoughtco.com/microinjection-375568#:~:text=The%20information%20in%20DNA%20is%20stored%20as%20a,information%20available%20for%20building%20and%20maintaining%20an%20organism.[/url]
V A Ratner The genetic language: grammar, semantics, evolution 1993 May 29
The genetic language is a collection of rules and regularities of genetic information coding for genetic texts. It is defined by alphabet, grammar, collection of punctuation marks and regulatory sites, semantics.
http://www.ncbi.nlm.nih.gov/pubmed/8335231
Katrin Weigmann The code, the text and the language of God 2004 Feb 5
In his book The Language of Life, George Beadle wrote: “... the deciphering of the DNA code has revealed a language... as old as life itself, a language that is the most living language of all” (Beadle & Beadle, 1966).
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1298980/
Wikipedia:
Biological organisms contain genetic material that is used to control their function and development. This is DNA which contains units named genes that can produce proteins through a code (genetic code) in which a series of triplets (codons) of four possible nucleotides are translated into one of twenty possible amino acids. A sequence of codons results in a corresponding sequence of amino acids that form a protein.
https://en.wikipedia.org/wiki/Genetic_code
The Genetic Code
The sequence of bases in DNA operates as a true code in that it contains the information necessary to build a protein expressed in a four-letter alphabet of bases which is transcribed to mRNA and then translated to the twenty-amino-acid alphabet necessary to build the protein. Saying that it is a true code involves the idea that the code is free and unconstrained; any of the four bases can be placed in any of the positions in the sequence of bases. Their sequence is not determined by the chemical bonding. There are hydrogen bonds between the base pairs and each base is bonded to the sugar phosphate backbone, but there are no bonds along the longitudional axis of DNA. The bases occur in the complementary base pairs A-T and G-C, but along the sequence on one side the bases can occur in any order, like the letters of a language used to compose words and sentences.
To further illustrate what is meant by a true code, consider the magnetic letters fixed to the magnetic board at right. The letters are held to the board by the magnetic forces, but those forces do not impose any specific ordering of the letters. The letters can be arranged to spell out a meaningful message in the English language (code) or to form a meaningless sequence like the one at bottom.
http://hyperphysics.phy-astr.gsu.edu/hbase/organic/gencode.html
Genetic Entropy: Sanford 2005 page 52 and 53:
This “complex interwoven (poly-fuctional) network” throughout the entire DNA code makes the human genome severely poly-constrained to random mutations (Sanford; Genetic Entropy, 2005; page 141). This means the DNA code is now much more severely limited in its chance of ever having a hypothetical beneficial mutation since almost the entire DNA code is now proven to be intimately connected to many other parts of the DNA code. Thus even though a random mutation to DNA may be able to change one part of an organism for the better, it is now proven much more likely to harm many other parts of the organism that depend on that one particular part being as it originally was. Since evolution was forced, by the established proof of Mendelian genetics, to no longer view the whole organism as to what natural selection works upon, but to view the whole organism as a multiple independent collection of genes that can be selected or discarded as natural selection sees fit, this “complex interwoven network” finding is extremely bad news, if not absolutely crushing, for the “Junk DNA” population genetics scenario of evolution (modern neo-Darwinian synthesis) developed by Haldane, Fisher and Wright . We now know that in yeast DNA alone there are more than 300 nano machines at work performing various tasks in the cell, many of which are performed concurrently. Yet concurrency in info processing systems cannot arise without pre-knowledge of tasks requiring coordinated action!
http://www.doesgodexist.org/NovDec09/Information-Function.html
Harold R. Booher, Ph.D. The Scientific Case for Intelligent Design A Synopsis of Stephen Meyer’s Signature in the Cell February 2010
Literature from those who posture in favor of creation abounds with examples of the tremendous odds against chance producing a meaningful code. For instance, the estimated number of elementary particles in the universe is 10^80. The most rapid events occur at an amazing 10^45 per second. Thirty billion years contains only 10^18 seconds. By totaling those, we find that the maximum elementary particle events in 30 billion years could only be 10^143. Yet, the simplest known free-living organism, Mycoplasma genitalium, has 470 genes that code for 470 proteins that average 347 amino acids in length. The odds against just one specified protein of that length are 1:10^451.
The probability of useful DNA, RNA, or proteins occurring by chance is extremely small. Calculations vary somewhat but all are extremely small (highly improbable). If one is to assume a hypothetical prebiotic soup to start there are at least three combinational hurdles (requirements) to overcome. Each of these requirements decreases the chance of forming a workable protein. First, all amino acids must form a chemical bond (peptide bond) when joining with other amino acids in the protein chain. Assuming, for example a short protein molecule of 150 amino acids, the probability of building a 150 amino acids chain in which all linkages are peptide linkages would be roughly 1 chance in 10^45. The second requirement is that functioning proteins tolerate only left-handed amino acids, yet in abiotic amino acid production the right-handed and left-handed isomers are produced in nearly the same frequency. The probability of building a 150-amino-acid chain at random in which all bonds are peptide bonds and all amino acids are L-form is roughly 1 chance in 10^90. The third requirement for functioning proteins is that the amino acids must link up like letters in a meaningful sentence, i.e. in a functionally specified sequential arrangement. The chance for this happening at random for a 150 amino acid chain is approximately 1 chance in 10^195. It would appear impossible for chance to build even one functional protein considering how small the likelihood is. By way of comparison to get a feeling of just how low this probability is consider that there are only 10^65 atoms in our galaxy..
http://www.arn.org/docs/booher/scientific-case-for-ID.html
DNA is a communication system because the triplets are encoded into Messenger RNA and decoded into amino acids and proteins. For example the base pairs GGG (Guanine-Guanine-Guanine) are instructions to make the amino acid Glycine which is then assembled into proteins by the ribosomes.
http://cosmicfingerprints.com/faq/#code
Perry Marshall: Is DNA a Code?
1. Code is defined as communication between an encoder (a “writer” or “speaker”) and a decoder (a “reader” or “listener”) using agreed upon symbols.
2. DNA's definition as a literal code (and not a figurative one) is nearly universal in the entire body of biological literature since the 1960's.
3. DNA code has much in common with human language and computer languages
4. DNA transcription is an encoding / decoding mechanism isomorphic with Claude Shannon's 1948 model: The sequence of base pairs is encoded into messenger RNA which is decoded into proteins.
5. Information theory terms and ideas applied to DNA are not metaphorical, but in fact quite literal in every way. In other words, the information theory argument for design is not based on analogy at all. It is direct application of mathematics to DNA, which by definition is a code.
https://evo2.org/dna-atheists/dna-code/
Barbieri: Code Biology February 2018
"...there is no deterministic link between codons and amino acids because any codon can be associated with any amino acid. This means that the rules of the genetic code do not descend from chemical necessity and in this sense they are arbitrary."
"...we have the experimental evidence that the genetic code is a real code, a code that is compatible with the laws of physics and chemistry but is not dictated by them."
https://www.sciencedirect.com/journal/biosystems/vol/164/suppl/C
Alberts: The Molecular Biology of the Cell et al, p367
The relationship between a sequence of DNA and the sequence of the corresponding protein is called the genetic code…the genetic code is deciphered by a complex apparatus that interprets the nucleic acid sequence.
Genes VIII, by Lewin, p21-22
JIAN-JUN SHU A new integrated symmetrical table for genetic codes 2017
For the formation of proteins in living organism cells, it is found that each amino acid can be specified by either a minimum of one codon or up to a maximum of six possible codons. In other words, different codons specify the different number of amino acids. A table for genetic codes is a representation of translation for illustrating the different amino acids with their respectively specifying codons, that is, a set of rules by which information encoded in genetic material (RNA sequences) is translated into proteins (amino acid sequences) by living cells. There are a total of 64 possible codons, but there are only 20 amino acids specified by them.
https://arxiv.org/ftp/arxiv/papers/1703/1703.03787.pdf
Specification (technical standard)
A specification often refers to a set of documented requirements to be satisfied by a material, design, product, or service. A specification is often a type of technical standard.
https://en.wikipedia.org/wiki/Specification_(technical_standard)
ERICO What Is The Difference Between a Code, Standard, Regulation and Specification in the Electrical Industry? Nov 13, 2018
A code is a set of rules that serve as generally accepted guidelines recommended for the industry to follow.
https://blog.nvent.com/erico-what-is-the-difference-between-a-code-standard-regulation-and-specification-in-the-electrical-industry/
David L Abel Three subsets of sequence complexity and their relevance to biopolymeric information 11 August 2005
Genes are not analogous to messages; genes are messages.
https://link.springer.com/article/10.1186/1742-4682-2-29
Berg JM Biochemistry. 5th edition 2002
Lewin Genes VIII, by , p21-22
The relationship between a sequence of DNA and the sequence of the corresponding protein is called the genetic code…the genetic code is deciphered by a complex apparatus that interprets the nucleic acid sequence.
https://www.ncbi.nlm.nih.gov/books/NBK22358/#:~:text=The%20genetic%20codeis%20the%20relation%20between%20the%20sequence,features%20of%20the%20genetic%20code%20by%201961%3A%201.
David L Abel Dichotomy in the definition of prescriptive information suggests both prescribed data and prescribed algorithms: biosemiotics applications in genomic systems 2012 Mar 14
"Functional Information (FI)" has now been formalized into two subsets: Descriptive Information (DI) and Prescriptive Information (PI). This formalization of definitions precludes the prevailing confusion of informational terms in the literature. The more specific and accurate term "Prescriptive Information (PI)" has been championed by Abel to define the sources and nature of programming controls, regulation and algorithmic processing. Such prescriptions are ubiquitously instantiated into all known living cells
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3319427/
Paul E. Griffiths Genetic, epigenetic and exogenetic information in development and evolution 18 August 2017
We would expect to find that instructions written in the genetic code are read by gene regulatory networks to make an organism. But the genetic code runs out of steam when it has specified the linear structure of proteins
https://royalsocietypublishing.org/doi/10.1098/rsfs.2016.0152
Peter R. Wills DNA as information 13 March 2016
The biological significance of DNA lies in the role it plays as a carrier of information, especially across generations of reproducing organisms, and within cells as a coded repository of system specification and stability. DNA in organisms functions as information and that the internal DNA-dependent dynamics of cells embody functional information processing, that is, computation DNA-based molecular biological computation can be said to control, perhaps even ‘direct’, the entire panoply of biochemical events occurring in cells. The obvious way in which information is stored in DNA, as sequences of letters drawn predominantly from the standard four-letter {A, C, G, T} nucleotide alphabet, has been understood since the discovery of the substance's dual-linear-polymer, base-paired molecular structure and its mode of complementary chain copying. DNA is represented in these abstract terms, as information comprising a sequence of arbitrary symbols. Changes in the DNA sequence of an organism's genome translate in a regular causative way into biological changes in the concrete physical world. There is a causative connection between DNA sequence information, which is an arbitrary abstraction of material property, and the reality of events in the physical world of molecules embodying the sequence.
https://royalsocietypublishing.org/doi/full/10.1098/rsta.2015.0417
Paul Davies Origin of Life, page 18
Biological complexity is instructed complexity or, to use modern parlance, it is information-based complexity. Inside each and every one of us lies a message. Decrypted, the message contains instructions on how to make a human being. Inside each and every one of us lies a message. It is inscribed in an ancient code, its beginnings lost in the mists of time. Decrypted, the message contains instructions on how to make a human being. The message isn't written in ink or type, but in atoms, strung together in an elaborately arranged sequence to form DNA, short for deoxyribonucleic acid. It is the most extraordinary molecule on Earth. Although DNA is a material structure, it is pregnant with meaning. The arrangement of the atoms along the helical strands of your DNA determines how you look and even, to a certain extent, how you feel and behave. DNA is nothing less than a blueprint, or more accurately an algorithm or instruction manual, for building a living, breathing, thinking human being. We share this magic molecule with almost all other life forms on Earth. From fungi to flies, from bacteria to bears, organisms are sculpted according to their respective DNA instructions. Each individual's DNA differs from others in their species (with the exception of identical twins), and differs even more from that of other species. But the essential structure – the chemical make-up, the double helix architecture – is universal.
https://3lib.net/book/5597371/98ee4e
JAG BHALLA DNA Is Multibillion-Year-Old Software14 May, 2015
Nature invented (sic) software billions of years before we did. “The origin of life is really the origin of software,” says Gregory Chaitin. Life requires what software does (it’s foundationally algorithmic).
1. “DNA is multibillion-year-old software,” says Chaitin (inventor of mathematical metabiology). We’re surrounded by software, but couldn’t see it until we had suitable thinking tools.
2. Alan Turing described modern software in 1936, inspiring John Von Neumann to connect software to biology. Before DNA was understood, Von Neumann saw that self-reproducing automata needed software. We now know DNA stores information; it's a biochemical version of Turning’s software tape, but more generally: All that lives must process information. Biology's basic building blocks are processes that make decisions.
http://bigthink.com/errors-we-live-by/dna-is-multibillion-year-old-software
In signal transduction, in short, we find all the essential components of a code: two independents worlds of molecules (first messengers and second messengers), and a set of adaptors that create a mapping between them, and the proof that the mapping is arbitrary because its rules can be changed in many different ways. What we see operating in cells is not like a code, but genuinely is a code—therefore its best efficient explanation is intelligence.
…the conversion of the information in [messenger] RNA represents a translation of the information into another language that uses quite different symbols.
Only INTELLIGENCE specifies a set of rules for specific requirements.
Paul Davies reinforced the point that obtaining the building blocks would not explain their arrangement:
‘… just as bricks alone don’t make a house, so it takes more than a random collection of amino acids to make life. Like house bricks, the building blocks of life have to be assembled in a very specific and exceedingly elaborate way before they have the desired function.’
An analogy is written language. Natural objects in forms resembling the English alphabet (circles, straight lines, etc.) abound in nature, but this fact does not help to understand the origin of information (such as that in Shakespeare’s plays). The reason is that this task requires intelligence both to create the information (the play) and then to design and build the machinery required to translate that information into symbols (the written text). What must be explained is the source of the information in the text (the words and ideas), not the existence of circles and straight lines. Likewise, it is not enough to explain the origin of the amino acids, which correspond to the letters. Rather, even if they were produced readily, the source of the information that directs the assembly of the amino acids contained in the genome must be explained.
“DNA is not a special life-giving molecule, but a genetic databank that transmits its information using a mathematical code. Most of the workings of the cell are best described, not in terms of material stuff — hardware — but as information, or software. Trying to make life by mixing chemicals in a test tube is like soldering switches and wires in an attempt to produce Windows 98. It won’t work because it addresses the problem at the wrong conceptual level.” Inside each and every one of us lies a message. It is inscribed in an ancient code, its beginnings lost in the mists of time. Decrypted, the message contains instructions on how to make a human being. Although DNA is a material structure, it is pregnant with meaning. The arrangement of the atoms along the helical strands of your DNA determines how you look and even, to a certain extent, how you feel and behave. DNA is nothing less than a blueprint—or, more accurately, an algorithm or instruction manual—for building a living, breathing, thinking human being. So far, I have been somewhat cavalier in the use of the term “information.” Computer scientists draw a distinction between syntax and semantics. Syntactic information is simply raw data, perhaps arranged according to rules of grammar, whereas semantic information has some sort of context or meaning. Information per se doesn’t have to mean anything. Snowflakes contain syntactic information in the specific arrangement of their hexagonal shapes, but these patterns have no semantic content, no meaning for anything beyond the structure itself. By contrast, the distinctive feature of biological information is that it is replete with meaning. DNA stores the instructions needed to build a functioning organism; it is a blueprint or an algorithm for a specified, predetermined product. Snowflakes don’t code for, or symbolize, anything, whereas genes most definitely do. To explain life fully, it is not enough simply to identify a source of free energy, or negative entropy, to provide biological information. We also have to understand how semantic information comes into being. It is the quality, not the mere existence, of information that is the real mystery here. All that stuff about conflict with the second law of thermodynamics was mostly a red herring.
In a living organism we see the power of software, or information processing, refined to an incredible degree. Cells are not hard-wired, like kites. Rather, the information flow couples the chalk of nucleic acids to the cheese of proteins using the genetic code. Stored energy is then released and forces are harnessed to carry out the programmed instructions, as with the radio-controlled plane. Viewed this way, the problem of the origin of life reduces to one of understanding how encoded software emerged spontaneously from hardware. How did it happen? How did nature “go digital”? We are dealing here not with a simple matter of refinement and adaptation, an amplification of complexity, or even the husbanding of information, but a fundamental change of concept. It is like trying to explain how a kite can evolve into a radio-controlled aircraft. Can the laws of nature as we presently comprehend them account for such a transition? I do not believe they can.
Fact two: not all random sequences are potential genomes. Far from it. In fact, only a tiny, tiny fraction of all possible random sequences would be even remotely biologically functional. A functioning genome is a random sequence, but it is not just any random sequence. It belongs to a very, very special subset of random sequences—namely, those that encode biologically relevant information. All random sequences of the same length encode about the same amount of information, but the quality of that information is crucial: in the vast majority of cases it would be, biologically speaking, complete gobbledygook.
“DNA is not a special life-giving molecule, but a genetic databank that transmits its information using a mathematical code. Most of the workings of the cell are best described, not in terms of material stuff — hardware — but as information, or software. Trying to make life by mixing chemicals in a test tube is like soldering switches and wires in an attempt to produce Windows 98. It won’t work because it addresses the problem at the wrong conceptual level.”
Inside each and every one of us lies a message. It is inscribed in an ancient code, its beginnings lost in the mists of time. Decrypted, the message contains instructions on how to make a human being.
Although DNA is a material structure, it is pregnant with meaning. The arrangement of the atoms along the helical strands of your DNA determines how you look and even, to a certain extent, how you feel and behave. DNA is nothing less than a blueprint—or, more accurately, an algorithm or instruction manual—for building a living, breathing, thinking human being.
Nucleic acids store life’s software; the proteins are the real workers and constitute the hardware. The two chemical realms can support each other only because there is a highly specific and refined communication channel between them mediated by a code, the so-called genetic code.
JAMES J. S. JOHNSON DNA and RNA: Providential Coding to 'Revere' God FEBRUARY 28, 2011
When accurately describing what happens inside a eukaryotic cell’s nucleus or mitochondrion, evolutionary geneticists routinely describe what they see using terms like code (e.g., genetic code, protein coding, coding regions), encode, codon, anti-codon, decode, transcription, translation, blueprint, program, information, instruction, control, edit, decipher, messenger, reading, proofreading, signal, alphabet, letter, language, gene expression, information, surveillance (for detecting nonsense), etc. It is important to recognize that these genetic message-oriented terms were not imposed on the evolutionists by the creationists!
genetic science reveals God’s purposeful encoding of genetic messages, with mind-bogglingly complex instructions on how to build living things from the biomolecular level upward, with those same encoded messages being efficiently decoded and recognized with sufficient accuracy to produce responsive compliance with those biomolecular instructions!
a coded message is no good at all if the intended recipient cannot understand its encoded meaning. Accordingly, every code-based message must be informationally devised (i.e., created), encoded, and sent to the intended readers. The readers must then decode the message, recognize the information it contains, and act on that information in a way that corresponds to the original purpose of the message’s creator. It is vital that the intended recipient understand the sender’s meaning, because the message itself is unrecognizable unless both sender and receiver share a common understanding of what the words (or other symbols) mean.
Consider the following message: “One if by land, two if by sea.” What does that sequence of words signify? Because that message used a language shared by the sender (Robert Newman, with the help of John Pulling) and receivers (those awaiting word on the movement of British troops), it provided a recognizable warning that “the Regulars [British soldiers] are coming” by water, not by land. Two lanterns lit in the Old North Church on the night of April 18, 1775, provided a signal—but it was recognizable as such only to those who knew the “language” shared by Paul Revere and his allies.
This principle of coded information transfer is illustrated at the sub-cellular level. If a protein-coding “message” borne by a portion of DNA cannot be transferred by RNA and translated on ribosomes providentially fitted for the task, the DNA’s instructions cannot be complied with, and that would mean no protein synthesis—which can be a fatal failure for whatever life form is involved, whether girl or gecko, boy or bacterium.
http://www.icr.org/article/dna-rna-providential-coding-revere/
Vjtorley Is The Genetic Code A Real Code? February 15, 2013
If amino acids were randomly assigned to triplet codons, then there would be 1.5 x 10^84 possible genetic codes to choose from. However, the genetic code used by all known forms of life is nearly universal with few minor variations. This suggests that a single evolutionary history underlies the origin of the genetic code. Many hypotheses on the evolutionary origins of the universal genetic code have been proposed.
In responding to the “code skeptics,” we need to keep in mind that they are bound by their own methodology to explain the origin of the genetic code in non-teleological, causal terms. They need to explain how things happened in the way that they suppose. Thus if a code-skeptic were to argue that living things have the code they do because it is one which accurately and efficiently translates information in a way that withstands the impact of noise, then he/she is illicitly substituting a teleological explanation for an efficient causal one. We need to ask the skeptic: how did Nature arrive at such an ideal code as the one we find in living things today?
By contrast, a “top-down” explanation of life goes beyond such reductionistic accounts. On a top-down account, it makes perfect sense to say that the genetic code has the properties it has because they help it to withstand the impact of noise while accurately and efficiently translating information. The “because” here is a teleological one. A teleological explanation like this ties in perfectly well with intelligent agency: normally the question we ask an agent when they do something is: “Why did you do it that way?” The question of how the agent did it is of secondary importance, and it may be the case that if the agent is a very intelligent one, we might not even understand his/her “How” explanation. But we would still want to know “Why?” And in the case of the genetic code, we have an answer to that question.
We currently lack even a plausible natural process which could have generated the genetic code. On the other hand, we know that intelligent agents can generate codes. The default hypothesis should therefore be that the code we find in living things is the product of an Intelligent Agent.
http://www.uncommondescent.com/intelligent-design/is-the-genetic-code-a-real-code/
Aaron Saenz Messages Coded Into DNA Of Venter Synthetic Bacteria May 24, 2010
Craig Venter has proven that DNA and that complex coded information system is fundamentally the same as a computer operating system for biological organisms as he has been able to convert the biological code to computer code. He ... in fact ... calls DNA ... the software of life. Now, while it is true that Craig clings to the evolutionary idea, he cannot answer the simple question ... how did that complex coded software system originate. The reason he can't answer this question is that he refuses to accept the obvious fact that complex coded software systems require intelligence to be produced. Just like he has used human intelligence to map the genome and convert biological code into computer code.
https://singularityhub.com/2010/05/24/venters-newest-synthetic-bacteria-has-secret-messages-coded-in-its-dna/
Katrin Weigmann The code, the text and the language of God 2004 Feb 5
Common language talks about DNA as 'information' or 'a code'. For a very long time, scientists suspected that something—some kind of plan, specificity or driving force—resided within the sperm and/or egg, such that a snake developed from a snake egg and humans created human offspring. But it was only in the late 1940s and 1950s, when cyberneticists, physicists and mathematicians entered the field of molecular biology, that scientists came to interpret this 'something' as information. The physicist Erwin Schrödinger probably coined the term 'code' when he described living organisms in terms of their molecular and atomic structure, in his influential book What is Life (Schrödinger, 1944). The complete pattern of the future development of an organism and its function when mature, Schrödinger wrote, is contained in the chromosomes in the form of a 'code'. His writings had a strong influence on both Francis Crick and James Watson and their later discovery of the structure of DNA. “Schrödinger probably wasn't the first, but he was the first one I'd read to say that there must be a code of some kind that allowed molecules in cells to carry information,” Watson said in an interview with Scientific American (Watson, 2003). Indeed, Watson and Crick, in a paper on the implications of their DNA structure, picked up Schrödinger's metaphor when they wrote that “it therefore seems likely that the precise sequence of the bases is the code which carries the genetical information.”
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1298980/
DNA as software: DNA is binary just like the base language in computers 24 APRIL 2008
On 26 June 2000, when Francis Collins, Director of the National Human Genome Research Institute, announced the completion of the first draft in a major media event at the White House, he said “Today, we celebrate the revelation of the first draft of the human book of life” and declared that this breakthrough lets humans for the first time read “our own instruction book.”
http://colchambers.blogspot.com.br/2008/04/dna-as-software-dna-is-binary-just-like.html
Could you communicate in another language without learning it? 30 APRIL 2008
Ok, heres's another thing that amazed me when I found it out. I probably learnt it years agon cos I just checked http://en.wikipedia.org/wiki/DNA and found it called complementary base pairing which rings a bell to me. Going back over it I see that it's effectively a binary code. Just like the code that runs in computers. What's the point then. Well it's just this. How fascinating that the very code that runs computers bascially defines 1's and 0's and so does the very code that runs all species that we know of. That just seems amazing. Taking it further, the code that a programmer writes has a similar impact on the program its written for as DNA does for its host cell. Object oriented code for example works in a simiilar way to how proteins are made in a cell. As a programmer I like writing object oriented code. That's code that describes objects so if I wrote a program for a human I would write a class for a cell. I'd describe how the cell functions and what things it can do etc. then I'd describe lots of different kinds of cells. they'd have the same fundamental attributes of the basic cell class but they'd be a little different. A blood cell wouldn't have a nucleus (no dna), a young cell would be able to grow and change easily (say an osteoblast) an older cell wouldn't (an osteoclast). So how does dna work. Well it codes for proteins. Proteins make enzymes. Proteins are buidling blocks like the keratin in your nails and hair, they build cell walls. Enzymes are workers. The lactase in your stomach that breaks down the milk sugar lactose. Some people don't have this enzyme, their dna doesn't describe how to make it so they're lactose intolerant and can't have dairy products. how fascinating that the code for our bodies can be talked about in similar terms as the code I use to write computer programs. Who'd have thought it!
there is intention in the genetic code, and the genetic code uses arbitrary symbolism. the specific DNA sequences together with biochemistry to decode the sequences - has specific purposes. Thus, the DNA sequences and the biochemistry that ends up with the growth of my eyes exists in order to produce an eyes - which themselves exists so that I can see. In other words, this code was produced so that I can see. Contrast this with the tree rings. When you cut down a tree you can find out how old the tree is by counting the rings, so the rings contain information about the age of the tree. But there was no intention for the tree rings to contain that information, it is a chance by-product of the way a tree grows. The information in the DNA sequences that are the instructions for building an eye are by contrast there with the intention of building an eye. Furthermore, they are arbitrary, in the sense that other instructions to build an eye would do just as well, provided they built an eye.
https://colchambers.blogspot.com/2008/04/
DNA Writer
https://earthsciweb.org/js/bio/dna-writer/
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."
Biosemiosis: The Onset of Information on Earth
The Information Tetrahedron
The Information Tetrahedron is a visual aid for understanding translation. It is a model of the material conditions required to translate any form of recorded information, including the information recorded in DNA. The translation of an informational medium enables the production of effects that are not determined by the material properties of the medium being translated.Instead, those effects are determined elsewhere within the system of translation.
My comment: Why not by an intelligent designer ?
This relational architecture – with one arrangement of matter evoking an effect, while another arrangement of matter determines what the effect will be – establishes a physical discontinuity in the system. This discontinuity enables prescriptive control of effects that are not limited by local dynamics. Such effects can only be derived from the contingent organization of the individual systems that translate information.
My comment: The system of translation ITSELF and its origin is which origin has to be explained. The prescribing source must therefore be OUTSIDE of the system. We only know intelligence to be a capable informer and prescriber os a complex system with specific purposes.
To organize the first living cell implies the capacity to specify objects among alternatives. In short, the capacity to construct a cellular object made of x, y and z, requires the capacity to specify x, y, and z among other objects. Given that no physical object inherently specifies any other object, the act of specification is accomplished by the use of a representational medium (i.e. memory).
Nature demonstrates unambiguously how a representation is established in the natural world. An object is established as a representation when a second object physically determines what is being represented (i.e. its referent) and the natural discontinuity between the representation and its referent is preserved by the organization of the system.
This discontinuous association is a semiotic mechanism. It establishes the local independence (non-determinism) required to specify referents that are not derived from the properties of the representation.
My comment: In other words, it is not dependent on physical necessity.
A system that is capable of discontinuous association is limited only (in principle) by what is physically possible. This open set of potential outcomes is the physicochemical basis of both the origin and diversity of form in the living kingdom.
My comment: An open set of outcomes means, the set up of the genetic code is arbitrary. (based on random choice or personal whim, rather than any reason or system, aka physical necessity)
Because the effects of translation are not determined by local dynamics, they are subject to error, change, and noise. A rational distinction is therefore made between the functional and non-functional output of semiotic systems. Functional products are described as being the result of information; non-functional products are generally described as being the result of error and noise.
My comment: Mind is a set of Cognitive faculties including consciousness , perception, thinking , judgment, and memory .
The products of these systems include communication, sensory perception, replication, homeostasis, evolution, and culture. These examples reflect the entirety of the living kingdom, and are completely absent in the remaining inanimate world.
https://web.archive.org/web/20170316041716/http://biosemiosis.org/
DNA ultimately came from a mind, who had to make decisions, and be extraordinarily intelligent.
This claim can be falsified. Show one, just ONE example of coded, specified, complex information, and you top the claim.
We can quantify the information carrying capacity of nucleic acids in the following way. Each position can be one of four bases, corresponding to two bits of information (22 = 4). Thus, a chain of 5100 nucleotides corresponds to 2 × 5100 = 10,200 bits, or 1275 bytes (1 byte = 8 bits). The E. coli genome is a single DNA molecule consisting of two chains of 4.6 million nucleotides, corresponding to 9.2 million bits, or 1.15 megabytes, of information
Scientists have been looking to unlock the memory storage potential of DNA strands for a decade now. Over at Harvard it looks like they've finally cracked it with a breakthrough that allows over 700 terabytes of data to be stored on a single gram of DNA. Treating the genetic code much like the binary system traditional computer memory uses, they've successfully replicated the storage capacity of over 14,000 Bluray discs, or 151 kilograms of hard drives on a surface area smaller than the tip of your little finger.
https://www.prote.in/en/feed/2012/11/dna-hard-drives#.UoGXXeLQ7gE
1. In cells, information is encoded through the genetic code which is a set of rules, stored in DNA sequences of nucleotide triplets called codons. They are used to translate genetic information into amino acid polypeptide sequences, which make proteins ( the molecular machines, the working horses of the cell ). In life, this is done by over 25 extremely complex molecular machine systems, which do as well error check and repair to maintain genetic stability, and minimizing replication, transcription and translation errors, and permit organisms to pass accurately genetic information to their offspring, and survive.
2. A code is a system of rules where a symbol, letters, words, or even sounds, gestures, or images, are assigned to something else. Transmitting information, for example, can be done through the translation of the symbols of the alphabetic letters, to symbols of kanji, logographic characters used in Japan.
3. Assigning meaning of characters through a code system, where symbols of one language are assigned to symbols of another language that mean the same, requires a common agreement of meaning in order to establish communication, trough encoding, sending, and decoding. Semantics, Synthax, and pragmatics are always set up by intelligence.
4. The assignment of codons (triplet nucleotides) to amino acids must be pre-established by a mind. And so, the information which is sent through the system, as well as the communication channels that permit encoding, sending, and decoding. This system had to be set-up prior life began because life depends on it. The origin of such complex communication systems is best explained by an intelligent designer.
1. In biology the genetic code is the assignment ( a cipher) of 64 triplet codons to 20 amino acids.
2. The assignment of a word to represent something, like the word chair to an object to sit down, is always of mental origin.On top of that, the translation of a word in one language, to another language, is also 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.
3. Since we know only of intelligence to be able to do so, this assignment is best explained by the deliberate, arbitrary action of a non-human intelligent agency.
1. Genetic and epigenetic information is characterized containing prescriptive codified information, which result in functional outcomes due to the right particular specified complex sequence of triplet codons and ultimately the translated sequencing of amino acid building blocks into protein strings. The sequencing of nucleotides in DNA also prescribes highly specific regulatory micro RNAs and other epigenetic factors.
2. Algorithms, prescribing functional instructions, digital programming, using symbols and coding systems are abstract and non-physical, and originate always from thought—from conscious or intelligent activity.
3. Therefore, genetic and epigenetic information comes from an intelligent mind. Since there was no human mind present to create life, it must have been a supernatural agency.
1. The pattern in DNA is a code.
2. All codes we know the origin of com from a intelligent mind
3. Therefore we have 100% inference that DNA comes from a intelligent mind, and 0% inference that it is not.
1. DNA stores coded information.
2. All codes com from intelligence.
3. Therefore, DNA comes from a mind.
1. Symbols are defined as: something which represents something else.
2. Symbols carry thoughts (or messages) from a personal, intelligent, mind. No exceptions.
3. Scientific inquiry has discovered that DNA carries encoded symbolic instructions.
Claim: The genetic code is so in a metaphorical sense
Reply: Life on earth is the product of information recorded inside the cell. When this information is translated by cellular machinery, it organizes inanimate matter (carbon, hydrogen, nitrogen, etc) into all the living things on earth. The mystery of life’s origin is therefore equal to the mystery of information. Where did the information come from that organized the very first living cell on earth? Did this information come together as an incredible chance event in chemical history, or was it the result of a deliberate act of design? To organize the first living cell, one set of objects must encode the information in a series of representations, and the other set of objects must specify what is being represented. This is how a "recipe" for the cell can exist in a universe where no object inherently means (represents or specifies) any other object. It requires both a representation and the means to interpret it. But there is a third requirement. The organization of the system must also preserve the natural discontinuity that exists between the representations and their effects. By doing so, a group of arbitrary relationships are established that otherwise wouldn't exist. That set of relationships is what we now call The Genetic Code. The unique physical conditions described here are the universal requirements of translation. They were proposed in theory, confirmed by experiment, and are not even controversial. They are also something that the living cell shares with every other instance of translated information ever known to exist. The genetic translation system provides objective physical evidence of the first irreducible organic system on earth, and from it, all other organic systems follow. Moreover, this system is not the product of Darwinian evolution. Instead, it is the source of evolution (i.e. the physical conditions that enable life's capacity to change and adapt over time) and as the first instance of specification on earth, it marks the rise of the genome and the starting point of heredity. And as a final indication of just how profound the appearance of this system was, an almost impossible observation remains – not only must these objects arise from a non-information (inanimate) environment, but the details of their construction must also be simultaneously encoded in the very information that they make possible. Without these things, life on earth would simply not exist. There are two distinct categories of semiotic systems. One category uses representations where the arrangement of the medium (like a pheromone) is reducible to the physical properties of the medium itself; the other uses representations that have a spatial (dimensional) orientation and are not reducible to their physical make-up (like the words on this page). The first type is found throughout the living kingdom. The second type is found nowhere but in recorded language and mathematics (and in the genetic code). This leads to an undeniable observation of physical reality; the singularly-unique material conditions required for dimensional semiosis, which would ostensibly not exist on Earth until the rise of human intelligence, were entirely evident at the very origin of life. They are the physical means by which the living cell became organized.
Is the Genetic Code a) an information-bearing sequence of DNA nucleotides or b) a translation program?
DNA stores literally coded information
https://reasonandscience.catsboard.com/t1281-dna-stores-literally-coded-information
The genetic code, insurmountable problem for non-intelligent origin
https://reasonandscience.catsboard.com/t2363-the-genetic-code-unsurmountable-problem-for-non-intelligent-origin
The genetic code cannot arise through natural selection
https://reasonandscience.catsboard.com/t1405-the-genetic-code-cannot-arise-through-natural-selection
Coded information comes always from a mind
https://reasonandscience.catsboard.com/t1312-coded-information-comes-always-from-a-mind
The five levels of information in DNA
https://reasonandscience.catsboard.com/t1311-the-five-levels-of-information-in-dna
The language of the genetic code
https://reasonandscience.catsboard.com/t1472-the-language-of-the-genetic-code
The different genetic codes
https://reasonandscience.catsboard.com/t2277-the-different-genetic-codes
More:
Francis Crick Nobel Lecture Nobel Lecture, On the Genetic Code December 11, 1962
[url=https://www.nobelprize.org/prizes/medicine/1962/crick/lecture/]https://www.nobelprize.org/prizes/medicine/1962/cr
Last edited by Otangelo on Mon Aug 01, 2022 6:57 am; edited 135 times in total
