The five levels of information in DNA
The language of the genetic code
The scientific laws of information
Wanna Build a Cell? A DVD Player Might Be Easier
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).
[The genetic language: grammar, semantics, evolution]
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.
The digital code of DNA
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.
DNA information: from digital code to analogue structure
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.
Next-generation digital information storage in DNA
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.
The code, the text and the language of God
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).
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.
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.
DNA Is Multibillion-Year-Old Software
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.
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.’63
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.
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!
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..
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.
Theist: The DNA code is written by a intelligent mind.
Atheist : Emergent properties, and physical reactions, are perfectly capable to produce the code stored in DNA.
Theist : There is no known natural mechanism ( aka no intelligence involved ) to encode the information stored in DNA
Atheist: God of the gaps argument. Argument from ignorance. Because we don't know yet, does not mean, Godidit.
Theist : "The sentence you are reading now was written by a intelligent mind"
Atheist: "Emergent properties, and physical reactions are perfectly capable to screen these letters to the monitor"
Theist : "There is no known natural mechanism ( aka no intelligence involved ) to type these letters and they to appear on the screen"
Atheist: "Argument of the gaps. Argument from ignorance. Because we don't know yet, that does not mean, a intelligence did it"
TRANSLATE YOUR TEXT TO DNA CODE
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."
DNA and RNA: Providential Coding to 'Revere' God
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.
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.
River Out of Eden: A Darwinian View of Life, Dawkins writes:
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)
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.
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.
The organism follows the rules of the Genetic Code. GGG = Glycine, CGG = Arginine, AGC = Serine, etc. Note that GGG is not literally Glycine, it is symbolic instructions
to make Glycine.
Just like computer codes, the genetic code is arbitrary. There is no law of physics that says “1” has to mean “on” and “0” has to mean “off.” There’s no law of physics that says 10000001 has to code for the letter “A.” Similarly, there is no law of physics that says three Guanine molecules in a row have to code for Glycine. In both cases, the communication system operates from a freely chosen, fixed set of rules.
In all communication systems it is possible to label the encoder, the message and the decoder and determine the rules of the code.
The rules of communication systems are defined in advance by conscious minds. There are no known exceptions to this. Therefore we have 100% inference that the Genetic Code was designed by a conscious mind.
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.
Code, by definition, implies intelligence and the genetic code is real code, mathematically identical to that of language, computer codes etc. all of which can only arise by intelligent convention of symbologies. The genome contains meta information and there is now evidence of meta-programming as well. Meta info is information on information and we now know the genome contains such structures. But meta information cannot arise without knowledge of the original information.Meta programming is even more solid evidence of intelligence at work.
Rutgers University professor Sungchul Ji’s excellent paper “The Linguistics of DNA: Words, Sentences, Grammar, Phonetics, and Semantics” starts off
“Biologic systems and processes cannot be fully accounted for in terms of the principles and laws of physics and chemistry alone, but they require in addition the principles of semiotics—the science of symbols and signs, including linguistics.” Ji identifies 13 characteristics of human language. DNA shares 10 of them. Cells edit DNA. Theyalso communicate with each other and literally speak a language he called “cellese,” described as “a self-organizing system of molecules, some of which encode, act as signs for, or trigger, gene-directed cell processes.” This comparison between cell language and human language is not a loosey-goosey analogy; it’s formal and literal. Human language and cell language both employ multilayered symbols. Dr. Ji explains this similarity in his paper: “Bacterial chemical conversations also include assignment of contextual meaning to words and sentences (semantic) and conduction of dialogue (pragmatic)—the fundamental aspects of linguistic communication.” This is true of genetic material. Signals between cells do this as well.*
Nucleotides in DNA contain four different nitrogenous bases: Thymine, Cytosine, Adenine, or Guanine. The order of nucleotides along DNA polymers encode the genetic information carried by DNA. DNA polymers can be tens of millions of nucleotides long. At these lengths, the four letter nucleotide alphabet can encode nearly unlimited information. DNA is organized language of coded information. The symbols when read give a message or instructions. DNA is not just a pattern developed like a snowflake. It is information coded as symbolic representation of actual 3D implementation. It is a language that requires decision making and thought between a transmitter and receiver. The symbols contain an alphabet, grammar, meaning, intent and even error correction. You can even store it like computer data. The information is expressed through matter and energy. DNA is designed language. Natural patterns can not achieve cell to mammal morphology. Intelligence is required. All information is carried by a code of symbols that are material in nature.
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.
DNA stores coded information.
All codes com from intelligence.
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.
Just show ONE example of instructional information, that cannot be tracked back to intelligence, and you win. Just one.
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.
Last edited by Admin on Mon Feb 06, 2017 8:19 am; edited 57 times in total