DNA - the instructional blueprint of life
https://reasonandscience.catsboard.com/t2544-dna-the-instructional-blueprint-of-life
"DNA contains the complete genetic blueprint for human life."
Source: Alberts, B., Johnson, A., Lewis, J., et al. Molecular Biology of the Cell. 4th edition. New York: Garland Science; 2002. The Structure and Function of DNA. Available from: https://www.ncbi.nlm.nih.gov/books/NBK26821/
"The genome has been impressively stable over centuries of human existence. The complete sequencing of the human genome made it possible to read nature's complete genetic blueprint for building a human being."
Source: Check Hayden E. Human genome at ten: Life is complicated. Nature. 2010;464(7289):664-667. doi:10.1038/464664a. Available from: https://www.nature.com/articles/464664a
Both of these excerpts describe DNA as containing the "blueprint" for human life. The first comes from a textbook of cell biology, indicating DNA provides the complete genetic information guiding human development and function. The second comes from a Nature paper published when the first full human genome sequence draft was completed, highlighting that reading the genome allows us to see the blueprint that guides our biological construction. These quotes reinforce the idea of DNA as an informational molecule that contains assembly instructions encoded in its sequence.
Cells in our body make use of our DNA library to extract blueprints that contain the instructions to build structures and molecular machines called proteins.
https://www.mpg.de/16227844/0107-mozg-keeping-sperm-cells-on-track-151300-x?c=2249
The term biological information comprises not only genetic information, but also the "blueprint" information that is contained in cellular entities such as membranes or organelles. 13
In the same way that the most inspiring concept of an architect cannot be realised unless she prepares a blueprint, an organism, no matter how efficient, cannot have a second generation unless it contains within itself the blueprint of its own construction. Living things are essentially their cells and the set of proteins, which cells produce and control the way other cells of the organism behave. The cells of all living things hence contain a blueprint, in the form of a long (very long – billions of units long) ticker tape that carries the code for the proteins. The DNA molecule is the tape, and the code for the proteins are bits of DNA, called the genes. And the genes are built up of three-letter words of an alphabet of four kinds of chemical groups, the letters, called the bases.12
The genome provides a precise biological blueprint of life. 11
Genetic Information as Instructional Content
https://www.jstor.org/stable/10.1086/498472?seq=1
FROM DNA TO GENES, AN INSTRUCTION MANUAL FOR THE HUMAN BODY
https://servier.com/en/news/from-dna-to-genes-an-instruction-manual-for-the-human-body/
The field of information systems, with its role in living systems, is constantly evolving ( Corning and Kline 1998 ). Shannon and Weaver (1949) defined information as the capacity to reduce statistical uncertainty in the communication of messages between a sender and a receiver; however, this definition bears no relationship to natural systems, such as living organisms, that are “ informed thermodynamic systems ” ( Wicken 1987 ). Later information theorists introduced structural or functional information to account for the self-organizing capabilities of living systems, and instructional information, which is a physical array ( Brooks and Wiley 1988 ). However, linkages with the field of semiotics established a much more compatible approach to biological information ( Salthe 1998 ). Within this trend, control information is defined as the capacity to control the acquisition, disposition, and utilization of matter, energy, and information flows in purposive (cybernetic) processes.
1. Without information the inflow of energy would not lead to self-organization. Information in this sense is more than information in the Shannon and Weaver (1949 ) sense; it is functional and can be thought of as information in both an “ instructional ” and “ control ” sense, as it requires information that creates complex structures — for example, enzymatic proteins — and metabolic pathways that productively channel the flow of energy both within an organism and between the latter and its environment.
2. Blueprints, instructional information, and master plans, which permit the autonomous self-organization and control of complex machines and factories upon these are both always tracked back to an intelligent source which made both for purposeful, specific goals.
3. The Blueprint and instructional information stored in DNA, which directs the make and controls biological cells and organisms - the origin of both is, therefore, best explained by intelligent design.
DNA Is Called The Blueprint Of Life: Here’s Why
OCTOBER 26, 2017
DNA is called the blueprint of life because it is the instruction manual to create, grow, function and reproduce life on Earth similar to a blueprint of a house. 10
https://sciencetrends.com/dna-called-blueprint-life-heres/
BLUEPRINT How DNA makes us who we are
DNA is the major systematic force, the blueprint, that makes us who we are.
https://www.amazon.com/Blueprint-How-DNA-Makes-Press/dp/0262039168
A blueprint is a reproduction of a technical drawing using a contact print process on light-sensitive sheets. Introduced by Sir John Herschel in 1842,the process allowed rapid, and accurate, production of an unlimited number of copies. It was widely used for over a century for the reproduction of specification drawings used in construction and industry.
Blueprints direct the construction of Buildings, DNA directs the " construction" of cells and organisms. DNA is an informational code that directs the development and function of cells and organisms. Segments of DNA called genes code for the formation of specific proteins. The complex information in the DNA regulates which proteins are made at which time and in what quantity.
Life's Irreducible Structure
21 JUNE 1968
DNA Acts as a Blueprint But there remains a fundamental point to be considered. A printed page may be a mere jumble of words, and it has then no information content. So the improbability count gives the possible, rather than the actual, information content of a page. And this applies also to the information content attributed to a DNA molecule; the sequence of the bases is deemed meaningful only because we assume with Watson and Crick that this arrangement generates the structure of the offspring by endowing it with its own information content. This brings us at last to the point that I aimed at when I undertook to analyze the information content of DNA: Can the control of morphogenesis by DNA be likened to the designing and shaping of a machine by the engineer? We have seen that physiology interprets the organism as a complex network of mechanisms, and that an organism is-like a machine-a system under dual control. Its structure is that of a boundary condition harnessing the physicalchemical substances within the organism in the service of physiological functions. Thus, in generating an organism, DNA initiates and controls the growth of a mechanism that will work as a boundary condition within a system under dual control. And I may add that DNA itself is such a system, since every system conveying information is under dual control, for every such system restricts and orders, in the service of conveying its information, extensive resources of particulars that would otherwise be left at random, and thereby acts as a boundary condition. In the case of DNA this boundary condition is a blueprint of the growing organism 7
http://science.sciencemag.org.sci-hub.tw/content/160/3834/1308
Ribosome: The cell city's factories
16th May 2002
Messenger RNA acts as a blueprint, like a barcode. This blueprint is interpreted by machines on a production line, which are called ribosomes, to assemble the correct sequence of amino acids. 8
https://www.open.edu/openlearn/nature-environment/natural-history/ribosome-the-cell-citys-factories
Stephen Meyer, Signature of the Cell, page 73
Biologists tell us that DNA stores and transmits “genetic information,” that it expresses a “genetic message,” that it stores “assembly instructions,” a “genetic blueprint,” or “digital code.” 1
Builders have a blueprint or floor plan and electrical engineers have a wiring diagram, each of which determines the arrangement of lower-level parts. DNA stores information using a four-character chemical alphabet. Strings of precisely sequenced chemicals called nucleotide bases store and transmit the assembly instructions—the information—for building the crucial protein molecules and machines the cell needs to survive.
http://www.signatureinthecell.com/
Why is DNA called the blueprint of life?
Oct 27, 2014
DNA is called the blueprint of life because it contains the instructions needed for an organism to grow, develop, survive and reproduce. DNA does this by controlling protein synthesis. Proteins do most of the work in cells, and are the basic unit of structure and function in the cells of organisms. 2
https://socratic.org/questions/why-is-dna-called-the-blueprint-of-life
Why is DNA called the blueprint of life?
Shawn Burgess, Ph.D.:My research area involves studying developmental processes and their relation to human genetic disease.
Because all the information necessary to make a living organism is stored in the DNA. No other part of the cell contains a permanent record of how to make a new cell, or a new tissue, or a new organism. 3
https://www.genome.gov/dnaday/q.cfm?aid=762&year=2009
DNA: Blueprint for Life
It is the genetic blueprint, or recipe, for making all living things. Almost every cell in your body contains DNA and all the information needed to make you what you are, from the way you look to which hand you write with. 4
https://web.archive.org/web/20170602134258/http://www.microbeworld.org/interesting-facts/dna-blueprint-for-life
DNA Is Blueprint, Contractor And Construction Worker For New Structures
DNA is the blueprint of all life, giving instruction and function to organisms ranging from simple one-celled bacteria to complex human beings. Now researchers have used DNA as the blueprint, contractor and construction worker to build a 3-D structure out of gold, a lifeless material. Using just one kind of nanoparticle the researchers built two very different crystalline structures by changing one thing -- the strands of synthesized DNA attached to the tiny gold spheres. 5
The Touchstone of Life, page 146
The RNAs are not unlike prints that are transcribed from a master plan—working blueprints for everyday use—and the second-tier decoding is very much like a language translation. 6
Considering that the functional parts of a living cell are proteins and RNA molecules and that the instructions for making these parts are encoded by genes, we can define the necessary elements to keep a minimal cell alive by knowing its complete gene set, which has been called a minimal genome (Mushegian, 1999).
The generation of meaningful information in molecular systems
13 March 2016
An organism's DNA, synonymous now with its genome sequence, is often described as its ‘blueprint’ and the DNA acronym is used colloquially to refer to the embedded determinants of the character of any system, biological or not. The closest the blueprint metaphor has ever approached reality in molecular biology is in the work of Gibson et al., who substituted a synthetic DNA blueprint for the genome of a Mycoplasma capricolum cell, thereby providing the organic structure of the cell with the opportunity to construct a new strain 9
http://rsta.royalsocietypublishing.org/content/374/2063/20150066
What does DNA do?
DNA provides instructions for making proteins
https://www.yourgenome.org/facts/what-does-dna-do
What Is the Function and Structure of DNA?
The function of DNA is to store all of the genetic information that an organism needs to develop, function, and reproduce.
https://www.ancestry.com/lp/dna-function
DNA
DNA) is a molecule composed of two chains that coil around each other to form a double helix carrying the genetic instructions used in the growth, development, functioning, and reproduction of all known living organisms and many viruses.
https://en.wikipedia.org/wiki/DNA
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 central problem in biology
DNA is an information storage device like an HD and contains a genetic code ( formed by three DNA nucleotides, so-called triplets, or codons). Three-letter combinations from the four-letter alphabet of DNA bases ( Adenine, Thymine, Guanine and Cytosine ) form the genetic code. Each triplet codon can be compared to the letter of the alphabet, like the letter A. It is a combinatorial scheme in which 4 nucleotides arranged 3-at-a-time specify 20 different amino acids. It is used to form a biological instruction manual ( blueprint ) for the construction of proteins, cells, organisms, and instructing organisms how to grow, develop, survive and reproduce. Every triplet of nucleotides in a nucleic acid sequence specifies a single amino acid of a polypeptide chain of proteins. In other words, it instructs which of the twenty amino acids used in proteins is used in each position of the protein polypeptide chain. This specification, from triplet codon to amino acid, is called a cypher. It is like a translation from one language to another. These base triplets specify one of the letters of the 20 letter alphabet of amino acids. With three letters out of four possible, there are 4^3 = 64 possibilities. So the code is redundant but in a purposeful way. The redundancy takes care of the majority of single-base errors in coding. That means, more than one triplet can code for a particular amino acid (a possibility inherent in the fact that there are 64 possible triplets out of 4 base pairs and only 20 amino acids to be coded for)
There is a lot to be explained. That is:
- the origin of the hardware:
DNA, mRNA, amino acids, the gene regulatory network, the machinery of transcription and translation, tRNA, tRNA Synthase, in more advanced organisms, spliceosomes, and error check and repair mechanisms along the way. How did the transition from random occurrence of the building blocks, RNA, DNA, amino acids, lipids, on early earth occur, to the hypercomplex synthesis in cells, and precise arrangement of information flow ?
- the four-fold problem of the software ( information, alphabet, codes, and translation system ):
- the origin and selection of the alphabet, the four nucleobases, and not more or less
- the origin of the genetic code, the ‘dictionary’, the collection of rules, based on 64 codon triplets
- the origin of the instructional blueprint which directs the synthesis of proteins, and and instructing organisms how to grow, develop, survive and reproduce.
- the origin of the cypher, or the coding assignments—i.e., which triplets code for which amino acids, from 64 codons to 20 amino acids, and its redundancy, and robustness and error-proneness.
The DNA molecule is the hardware ( information storage device )
The genetic code ( software ) is composed of three-letter combinations from the four-letter alphabet of DNA bases ( adenine, thymine, guanine, cytosine ). Each triplet is called codon. It is the triplet recipe of these bases that make up the ‘dictionary’. It is a collection of rules. 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 biological instruction manual, blueprint ( information ), is composed of the genetic code ( software ) . The sequences of triplet codons are also called a code, which is confusing since the specific instructional codon sequence composed of three DNA bases is which instruct the ribosome about how to compose the sequence of amino acids of proteins is not the same as the dictionary which forms the collection of rules, which is also called genetic code. They are different things. The instructional blueprint or specific codon sequence contains the information necessary to build a protein, is first transcribed to messenger RNA, and afterwards translated to the twenty-amino-acid alphabet necessary to build the protein.
http://web.archive.org/web/20131209121838/http://gencodesignal.org/faq/
The confusion comes from the ambiguity in using the term “genetic code”. Here is a quote from Francis Crick, who seems to be the one who coined this term:
Unfortunately the phrase “genetic code” is now used in two quite distinct ways. Laymen often use it to mean the entire genetic message in an organism. Molecular biologists usually mean the little dictionary that shows how to relate the four-letter language of the nucleic acids to the twenty-letter language of the proteins, just as the Morse code relates the language of dots and dashes to the twenty-six letters of the alphabet… The proper technical term for such a translation is, strictly speaking, not a code but a cypher. In the same way, the Morse code should really be called the Morse cypher. I did not know this at the time, which was fortunate because “genetic code” sounds a lot more intriguing than “genetic cypher” (from “What Mad Pursuit”, 1988)
The specification, from triplet codon to amino acid, is called a cypher. It is like a translation from one language to another. We can use for example the google translate program. We write the English word language, and the program translates it and we can get the word "Sprache", in German, which is equivalent to the word "language" in English. As in all translations, there must be someone or something, that is bilingual, in this case, to turn the coded instructions written in nucleic acid language into a result written in the amino-acid language.
In Cells the adaptor molecule, tRNA, performs this task. One end of the tRNA mirrors the code on the codons on the messenger RNA and the other end is attached to the amino acid that is coded for. the correct amino acid is attached to the correct tRNA by an enzyme called amino acid tRNA Synthase..
This raises a huge - an even tougher problem concerning the coding assignments—i.e., which triplets code for which amino acids. How did these designations come about? Because nucleic-acid bases and amino acids don’t recognize each other directly but have to deal via the tRNA chemical intermediary, there is no obvious reason why particular triplets should go with particular amino acids. Other translations are conceivable. Coded instructions are a good idea, but the actual code seems to be pretty arbitrary. Perhaps it is simply a frozen accident, a random choice that just locked itself in, with no deeper significance? That is what Crick proposed. How could that not be called just an "ad-hoc" assertion, face no other reasonable or likely explanation? - unless, of course, we permit the divine into the picture.
1. Stephen Meyer, Signature of the Cell, page 73
2. https://socratic.org/questions/why-is-dna-called-the-blueprint-of-life
3. https://www.genome.gov/dnaday/q.cfm?aid=762&year=2009
4. https://web.archive.org/web/20170602134258/http://www.microbeworld.org/interesting-facts/dna-blueprint-for-life
5. https://www.sciencedaily.com/releases/2008/01/080130130652.htm
6. The Touchstone of Life, page 146
7. http://science.sciencemag.org.sci-hub.tw/content/160/3834/1308
8. http://www.open.edu/openlearn/nature-environment/natural-history/ribosome-the-cell-citys-factories
9. http://rsta.royalsocietypublishing.org/content/374/2063/20150066
10. https://sciencetrends.com/dna-called-blueprint-life-heres/
11. https://advances.sciencemag.org/content/3/10/e1701484
12. https://www.thestatesman.com/supplements/science_supplements/ancestry-genetic-code-1502937176.html
13. https://sci-hub.ren/10.1007/bf00700435
https://reasonandscience.catsboard.com/t2544-dna-the-instructional-blueprint-of-life
"DNA contains the complete genetic blueprint for human life."
Source: Alberts, B., Johnson, A., Lewis, J., et al. Molecular Biology of the Cell. 4th edition. New York: Garland Science; 2002. The Structure and Function of DNA. Available from: https://www.ncbi.nlm.nih.gov/books/NBK26821/
"The genome has been impressively stable over centuries of human existence. The complete sequencing of the human genome made it possible to read nature's complete genetic blueprint for building a human being."
Source: Check Hayden E. Human genome at ten: Life is complicated. Nature. 2010;464(7289):664-667. doi:10.1038/464664a. Available from: https://www.nature.com/articles/464664a
Both of these excerpts describe DNA as containing the "blueprint" for human life. The first comes from a textbook of cell biology, indicating DNA provides the complete genetic information guiding human development and function. The second comes from a Nature paper published when the first full human genome sequence draft was completed, highlighting that reading the genome allows us to see the blueprint that guides our biological construction. These quotes reinforce the idea of DNA as an informational molecule that contains assembly instructions encoded in its sequence.
Cells in our body make use of our DNA library to extract blueprints that contain the instructions to build structures and molecular machines called proteins.
https://www.mpg.de/16227844/0107-mozg-keeping-sperm-cells-on-track-151300-x?c=2249
The term biological information comprises not only genetic information, but also the "blueprint" information that is contained in cellular entities such as membranes or organelles. 13
In the same way that the most inspiring concept of an architect cannot be realised unless she prepares a blueprint, an organism, no matter how efficient, cannot have a second generation unless it contains within itself the blueprint of its own construction. Living things are essentially their cells and the set of proteins, which cells produce and control the way other cells of the organism behave. The cells of all living things hence contain a blueprint, in the form of a long (very long – billions of units long) ticker tape that carries the code for the proteins. The DNA molecule is the tape, and the code for the proteins are bits of DNA, called the genes. And the genes are built up of three-letter words of an alphabet of four kinds of chemical groups, the letters, called the bases.12
The genome provides a precise biological blueprint of life. 11
Genetic Information as Instructional Content
https://www.jstor.org/stable/10.1086/498472?seq=1
FROM DNA TO GENES, AN INSTRUCTION MANUAL FOR THE HUMAN BODY
https://servier.com/en/news/from-dna-to-genes-an-instruction-manual-for-the-human-body/
The field of information systems, with its role in living systems, is constantly evolving ( Corning and Kline 1998 ). Shannon and Weaver (1949) defined information as the capacity to reduce statistical uncertainty in the communication of messages between a sender and a receiver; however, this definition bears no relationship to natural systems, such as living organisms, that are “ informed thermodynamic systems ” ( Wicken 1987 ). Later information theorists introduced structural or functional information to account for the self-organizing capabilities of living systems, and instructional information, which is a physical array ( Brooks and Wiley 1988 ). However, linkages with the field of semiotics established a much more compatible approach to biological information ( Salthe 1998 ). Within this trend, control information is defined as the capacity to control the acquisition, disposition, and utilization of matter, energy, and information flows in purposive (cybernetic) processes.
1. Without information the inflow of energy would not lead to self-organization. Information in this sense is more than information in the Shannon and Weaver (1949 ) sense; it is functional and can be thought of as information in both an “ instructional ” and “ control ” sense, as it requires information that creates complex structures — for example, enzymatic proteins — and metabolic pathways that productively channel the flow of energy both within an organism and between the latter and its environment.
2. Blueprints, instructional information, and master plans, which permit the autonomous self-organization and control of complex machines and factories upon these are both always tracked back to an intelligent source which made both for purposeful, specific goals.
3. The Blueprint and instructional information stored in DNA, which directs the make and controls biological cells and organisms - the origin of both is, therefore, best explained by intelligent design.
DNA Is Called The Blueprint Of Life: Here’s Why
OCTOBER 26, 2017
DNA is called the blueprint of life because it is the instruction manual to create, grow, function and reproduce life on Earth similar to a blueprint of a house. 10
https://sciencetrends.com/dna-called-blueprint-life-heres/
BLUEPRINT How DNA makes us who we are
DNA is the major systematic force, the blueprint, that makes us who we are.
https://www.amazon.com/Blueprint-How-DNA-Makes-Press/dp/0262039168
A blueprint is a reproduction of a technical drawing using a contact print process on light-sensitive sheets. Introduced by Sir John Herschel in 1842,the process allowed rapid, and accurate, production of an unlimited number of copies. It was widely used for over a century for the reproduction of specification drawings used in construction and industry.
Blueprints direct the construction of Buildings, DNA directs the " construction" of cells and organisms. DNA is an informational code that directs the development and function of cells and organisms. Segments of DNA called genes code for the formation of specific proteins. The complex information in the DNA regulates which proteins are made at which time and in what quantity.
Life's Irreducible Structure
21 JUNE 1968
DNA Acts as a Blueprint But there remains a fundamental point to be considered. A printed page may be a mere jumble of words, and it has then no information content. So the improbability count gives the possible, rather than the actual, information content of a page. And this applies also to the information content attributed to a DNA molecule; the sequence of the bases is deemed meaningful only because we assume with Watson and Crick that this arrangement generates the structure of the offspring by endowing it with its own information content. This brings us at last to the point that I aimed at when I undertook to analyze the information content of DNA: Can the control of morphogenesis by DNA be likened to the designing and shaping of a machine by the engineer? We have seen that physiology interprets the organism as a complex network of mechanisms, and that an organism is-like a machine-a system under dual control. Its structure is that of a boundary condition harnessing the physicalchemical substances within the organism in the service of physiological functions. Thus, in generating an organism, DNA initiates and controls the growth of a mechanism that will work as a boundary condition within a system under dual control. And I may add that DNA itself is such a system, since every system conveying information is under dual control, for every such system restricts and orders, in the service of conveying its information, extensive resources of particulars that would otherwise be left at random, and thereby acts as a boundary condition. In the case of DNA this boundary condition is a blueprint of the growing organism 7
http://science.sciencemag.org.sci-hub.tw/content/160/3834/1308
Ribosome: The cell city's factories
16th May 2002
Messenger RNA acts as a blueprint, like a barcode. This blueprint is interpreted by machines on a production line, which are called ribosomes, to assemble the correct sequence of amino acids. 8
https://www.open.edu/openlearn/nature-environment/natural-history/ribosome-the-cell-citys-factories
Stephen Meyer, Signature of the Cell, page 73
Biologists tell us that DNA stores and transmits “genetic information,” that it expresses a “genetic message,” that it stores “assembly instructions,” a “genetic blueprint,” or “digital code.” 1
Builders have a blueprint or floor plan and electrical engineers have a wiring diagram, each of which determines the arrangement of lower-level parts. DNA stores information using a four-character chemical alphabet. Strings of precisely sequenced chemicals called nucleotide bases store and transmit the assembly instructions—the information—for building the crucial protein molecules and machines the cell needs to survive.
http://www.signatureinthecell.com/
Why is DNA called the blueprint of life?
Oct 27, 2014
DNA is called the blueprint of life because it contains the instructions needed for an organism to grow, develop, survive and reproduce. DNA does this by controlling protein synthesis. Proteins do most of the work in cells, and are the basic unit of structure and function in the cells of organisms. 2
https://socratic.org/questions/why-is-dna-called-the-blueprint-of-life
Why is DNA called the blueprint of life?
Shawn Burgess, Ph.D.:My research area involves studying developmental processes and their relation to human genetic disease.
Because all the information necessary to make a living organism is stored in the DNA. No other part of the cell contains a permanent record of how to make a new cell, or a new tissue, or a new organism. 3
https://www.genome.gov/dnaday/q.cfm?aid=762&year=2009
DNA: Blueprint for Life
It is the genetic blueprint, or recipe, for making all living things. Almost every cell in your body contains DNA and all the information needed to make you what you are, from the way you look to which hand you write with. 4
https://web.archive.org/web/20170602134258/http://www.microbeworld.org/interesting-facts/dna-blueprint-for-life
DNA Is Blueprint, Contractor And Construction Worker For New Structures
DNA is the blueprint of all life, giving instruction and function to organisms ranging from simple one-celled bacteria to complex human beings. Now researchers have used DNA as the blueprint, contractor and construction worker to build a 3-D structure out of gold, a lifeless material. Using just one kind of nanoparticle the researchers built two very different crystalline structures by changing one thing -- the strands of synthesized DNA attached to the tiny gold spheres. 5
The Touchstone of Life, page 146
The RNAs are not unlike prints that are transcribed from a master plan—working blueprints for everyday use—and the second-tier decoding is very much like a language translation. 6
Considering that the functional parts of a living cell are proteins and RNA molecules and that the instructions for making these parts are encoded by genes, we can define the necessary elements to keep a minimal cell alive by knowing its complete gene set, which has been called a minimal genome (Mushegian, 1999).
The generation of meaningful information in molecular systems
13 March 2016
An organism's DNA, synonymous now with its genome sequence, is often described as its ‘blueprint’ and the DNA acronym is used colloquially to refer to the embedded determinants of the character of any system, biological or not. The closest the blueprint metaphor has ever approached reality in molecular biology is in the work of Gibson et al., who substituted a synthetic DNA blueprint for the genome of a Mycoplasma capricolum cell, thereby providing the organic structure of the cell with the opportunity to construct a new strain 9
http://rsta.royalsocietypublishing.org/content/374/2063/20150066
What does DNA do?
DNA provides instructions for making proteins
https://www.yourgenome.org/facts/what-does-dna-do
What Is the Function and Structure of DNA?
The function of DNA is to store all of the genetic information that an organism needs to develop, function, and reproduce.
https://www.ancestry.com/lp/dna-function
DNA
DNA) is a molecule composed of two chains that coil around each other to form a double helix carrying the genetic instructions used in the growth, development, functioning, and reproduction of all known living organisms and many viruses.
https://en.wikipedia.org/wiki/DNA
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 central problem in biology
DNA is an information storage device like an HD and contains a genetic code ( formed by three DNA nucleotides, so-called triplets, or codons). Three-letter combinations from the four-letter alphabet of DNA bases ( Adenine, Thymine, Guanine and Cytosine ) form the genetic code. Each triplet codon can be compared to the letter of the alphabet, like the letter A. It is a combinatorial scheme in which 4 nucleotides arranged 3-at-a-time specify 20 different amino acids. It is used to form a biological instruction manual ( blueprint ) for the construction of proteins, cells, organisms, and instructing organisms how to grow, develop, survive and reproduce. Every triplet of nucleotides in a nucleic acid sequence specifies a single amino acid of a polypeptide chain of proteins. In other words, it instructs which of the twenty amino acids used in proteins is used in each position of the protein polypeptide chain. This specification, from triplet codon to amino acid, is called a cypher. It is like a translation from one language to another. These base triplets specify one of the letters of the 20 letter alphabet of amino acids. With three letters out of four possible, there are 4^3 = 64 possibilities. So the code is redundant but in a purposeful way. The redundancy takes care of the majority of single-base errors in coding. That means, more than one triplet can code for a particular amino acid (a possibility inherent in the fact that there are 64 possible triplets out of 4 base pairs and only 20 amino acids to be coded for)
There is a lot to be explained. That is:
- the origin of the hardware:
DNA, mRNA, amino acids, the gene regulatory network, the machinery of transcription and translation, tRNA, tRNA Synthase, in more advanced organisms, spliceosomes, and error check and repair mechanisms along the way. How did the transition from random occurrence of the building blocks, RNA, DNA, amino acids, lipids, on early earth occur, to the hypercomplex synthesis in cells, and precise arrangement of information flow ?
- the four-fold problem of the software ( information, alphabet, codes, and translation system ):
- the origin and selection of the alphabet, the four nucleobases, and not more or less
- the origin of the genetic code, the ‘dictionary’, the collection of rules, based on 64 codon triplets
- the origin of the instructional blueprint which directs the synthesis of proteins, and and instructing organisms how to grow, develop, survive and reproduce.
- the origin of the cypher, or the coding assignments—i.e., which triplets code for which amino acids, from 64 codons to 20 amino acids, and its redundancy, and robustness and error-proneness.
The DNA molecule is the hardware ( information storage device )
The genetic code ( software ) is composed of three-letter combinations from the four-letter alphabet of DNA bases ( adenine, thymine, guanine, cytosine ). Each triplet is called codon. It is the triplet recipe of these bases that make up the ‘dictionary’. It is a collection of rules. 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 biological instruction manual, blueprint ( information ), is composed of the genetic code ( software ) . The sequences of triplet codons are also called a code, which is confusing since the specific instructional codon sequence composed of three DNA bases is which instruct the ribosome about how to compose the sequence of amino acids of proteins is not the same as the dictionary which forms the collection of rules, which is also called genetic code. They are different things. The instructional blueprint or specific codon sequence contains the information necessary to build a protein, is first transcribed to messenger RNA, and afterwards translated to the twenty-amino-acid alphabet necessary to build the protein.
http://web.archive.org/web/20131209121838/http://gencodesignal.org/faq/
The confusion comes from the ambiguity in using the term “genetic code”. Here is a quote from Francis Crick, who seems to be the one who coined this term:
Unfortunately the phrase “genetic code” is now used in two quite distinct ways. Laymen often use it to mean the entire genetic message in an organism. Molecular biologists usually mean the little dictionary that shows how to relate the four-letter language of the nucleic acids to the twenty-letter language of the proteins, just as the Morse code relates the language of dots and dashes to the twenty-six letters of the alphabet… The proper technical term for such a translation is, strictly speaking, not a code but a cypher. In the same way, the Morse code should really be called the Morse cypher. I did not know this at the time, which was fortunate because “genetic code” sounds a lot more intriguing than “genetic cypher” (from “What Mad Pursuit”, 1988)
The specification, from triplet codon to amino acid, is called a cypher. It is like a translation from one language to another. We can use for example the google translate program. We write the English word language, and the program translates it and we can get the word "Sprache", in German, which is equivalent to the word "language" in English. As in all translations, there must be someone or something, that is bilingual, in this case, to turn the coded instructions written in nucleic acid language into a result written in the amino-acid language.
In Cells the adaptor molecule, tRNA, performs this task. One end of the tRNA mirrors the code on the codons on the messenger RNA and the other end is attached to the amino acid that is coded for. the correct amino acid is attached to the correct tRNA by an enzyme called amino acid tRNA Synthase..
This raises a huge - an even tougher problem concerning the coding assignments—i.e., which triplets code for which amino acids. How did these designations come about? Because nucleic-acid bases and amino acids don’t recognize each other directly but have to deal via the tRNA chemical intermediary, there is no obvious reason why particular triplets should go with particular amino acids. Other translations are conceivable. Coded instructions are a good idea, but the actual code seems to be pretty arbitrary. Perhaps it is simply a frozen accident, a random choice that just locked itself in, with no deeper significance? That is what Crick proposed. How could that not be called just an "ad-hoc" assertion, face no other reasonable or likely explanation? - unless, of course, we permit the divine into the picture.
1. Stephen Meyer, Signature of the Cell, page 73
2. https://socratic.org/questions/why-is-dna-called-the-blueprint-of-life
3. https://www.genome.gov/dnaday/q.cfm?aid=762&year=2009
4. https://web.archive.org/web/20170602134258/http://www.microbeworld.org/interesting-facts/dna-blueprint-for-life
5. https://www.sciencedaily.com/releases/2008/01/080130130652.htm
6. The Touchstone of Life, page 146
7. http://science.sciencemag.org.sci-hub.tw/content/160/3834/1308
8. http://www.open.edu/openlearn/nature-environment/natural-history/ribosome-the-cell-citys-factories
9. http://rsta.royalsocietypublishing.org/content/374/2063/20150066
10. https://sciencetrends.com/dna-called-blueprint-life-heres/
11. https://advances.sciencemag.org/content/3/10/e1701484
12. https://www.thestatesman.com/supplements/science_supplements/ancestry-genetic-code-1502937176.html
13. https://sci-hub.ren/10.1007/bf00700435
Last edited by Otangelo on Sun Oct 22, 2023 8:12 am; edited 43 times in total
