I just uploaded a PDF version of the fundamental paper here "Enzymes and Molecular Machines Can Be Selected from Random Copolymers" to Academia.edu.
Enjoy.
(15 pages.!?)
Sunday, November 16, 2014
Monday, February 10, 2014
Where Are the Merozoans?
The universal spectacle implicitly revealed to us by mechanomeric selection is an inspiring one, in which, wherever in the universe monomers and copolymers can be accumulated, sooner or later two such acting as enzymes and replicases capable of replicating (copying) one another (not necessarily of the same copolymer class, polyaminoacyl or polyester or whatever) will initiate an explosion of such replication, and life will begin.
Call such simplest life "merozoan", and such simplest living things "merozoans".
And throw in natural selection over a billion years and you arrive at people arguing over whether God has testicles or not.
It might be asked then, "Where are the merozoans here on Earth?"
The first and most obvious and most satisying answer of course is that we are all merozoans, bacteria, archaeans and viruses, amoebas and algae, plants, fungi and animals, contemporary versions N.x.y: See for example my "The Dual-Copolymer Proof of Evolution".
And even contemporary bacteria, archaeans and viruses are complex products of long evolutions (note that infectiousness is generally a well-evolved process, hence the host-specificity of most viruses).
But is it not possible that simpler, and even the simplest, merozoans may still be among us?
It is true that they would be out-competed in most ecological niches by their more highly-evolved relatives, but cannot some such still be around, some perhaps tumbling around abyssal volcanic vents, and other more evolved ones even acting as infectious agents?
This seems worth looking into.
[20120212 I couldn't argue if someone wanted to go with "merobes" and "meroba".]
Call such simplest life "merozoan", and such simplest living things "merozoans".
And throw in natural selection over a billion years and you arrive at people arguing over whether God has testicles or not.
It might be asked then, "Where are the merozoans here on Earth?"
The first and most obvious and most satisying answer of course is that we are all merozoans, bacteria, archaeans and viruses, amoebas and algae, plants, fungi and animals, contemporary versions N.x.y: See for example my "The Dual-Copolymer Proof of Evolution".
And even contemporary bacteria, archaeans and viruses are complex products of long evolutions (note that infectiousness is generally a well-evolved process, hence the host-specificity of most viruses).
But is it not possible that simpler, and even the simplest, merozoans may still be among us?
It is true that they would be out-competed in most ecological niches by their more highly-evolved relatives, but cannot some such still be around, some perhaps tumbling around abyssal volcanic vents, and other more evolved ones even acting as infectious agents?
This seems worth looking into.
[20120212 I couldn't argue if someone wanted to go with "merobes" and "meroba".]
Friday, September 7, 2012
A Mechanomeric-Selective R&D Road-Map,
Part 1: Introduction
Functional copolymers such as the proteins are called "mechanomers" here, distinguishing such naturally-occurring mechanomers as "biopolymers" where convenient; the science of mechanomers is called "mechanomerics"; and applied mechanomerics is called "mechanomeric engineering", including "mechanomeric medicine".
Mechanomeric engineering requires some technique for developing mechanomers to perform desired functions, such as enzymes and molecular machines.
And just as proteins are developed in nature by variation of amino acid order—and therefore of conformation (coiled structure), and therefore of shape, mechanical properties and surface structure, and therefore of function—followed by selection, so too artificial mechanomers can be developed by selecting those performing desired functions from among random mechanomers, mechanomers with random monomer orders, and therefore random conformations, and therefore random shapes, mechanical properties and surface structures, and therefore random functions, in what is called here "mechanomeric selection (MeSe)".
The background to, critical argument for, procedures in referred to below, and some applications of mechanomeric selection are described in the report “Enzymes and Molecular Machines Can Be Selected from Random Copolymers”.
The present series of short reports describes a sequence of experiments including those procedures and groups thereof sufficient to establish mechanomeric selection on a firm foundation, starting with fundamental experiments and ending with several small but significant applications.
Those experiments and procedures and groups thereof number about forty, and fall naturally into seven phases, each of which shall be addressed in its own part of this series of eight short reports, as follows:
“Part 1: Introduction.” This very report.
“Part 2: Phase I: First Experiments: Incidences of Random Protein Well-Conformedness and Function.” The first phase of mechanomeric-selective research and developmental experiments, procedures and groups thereof described here assesses the incidences of well-conformedness and simple function in random protein stocks. But it begins with three sets of decisions with consequences for all remaining phases, about what industrial organic chemistry reactions; indicators and indicating reactions; and those monomers’ prosthetic groups. It chemically synthesizes and thermally tempers random proteins bearing those prosthetic groups. It weighs, assesses the numbers using osmosis, and calculates the average weights, lengths and gram numbers, of those proteins. It uses affinity chromatography using media bearing those prosthetic groups to assess the incidence of well-conformedness among those proteins. And it assesses the incidences of catalyses of those reactions among those proteins in so many assessments of the incidence of such simplest function among random mechanomers.
“Part 3: Phase II: Early Mechanomeric Selection: Mechanomerogenesis.” The second phase of mechanomeric-selective research and developmental experiments, procedures and groups thereof performs the fundamental early mechanomeric-selective procedure of mechanomerogenesis, allowing the self-selection or autoevolution of replicases. But it begins with two sets of decisions with consequences for all remaining phases, about what two mechanomer classes are to be at least originally employed in mechanomeric selection, and the corresponding polymerization reactions and monomers to be used with them. It chemically synthesizes test-mechanomers to be used in testing the functionality of the replicases resulting from mechanomerogenesis. It chemically synthesizes and thermally tempers random mechanomers of those classes; weighs, assesses the numbers using osmosis, and calculates the average weights, lengths and gram numbers of those mechanomers; uses affinity chromatography to assess the incidence of well-conformedness, and assesses the incidences of catalyses of the industrial and indicating reactions selected in the first phase, among those random mechanomers, all just as was done in the first phase with random proteins. It performs mechanomerogenesis. It assesses the functions of the replicases produced by mechanomerogenesis. And it assesses the incidences of direct replicability among random mechanomers of the classes used.
“Part 4: Phase III: Early Mechanomeric Selection: Merases” The third phase of mechanomeric-selective developmental experiments, procedures and groups thereof utilizes the replicases selected in the second phase to select the “merases”—polymerases, ligases and other enzymes—useful for mechanomeric selection itself, using affine-chromatographic and spectroscopic techniques to characterize and assess their functions.
“Part 5: Phase IV: Mechanomeric Indication.” The fourth phase of mechanomeric-selective developmental experiments, procedures and groups thereof selects various “indicases” conditionally and “chromases” unconditionally catalyzing the indicating reactions selected in the first phase. It begins with decisions with consequences for all remaining phases, about what species of viruses and bacteria and types of human cells are to be used in these phases. It selects indicases catalyzing those reactions only when complexed with and thus indicating the presences of those viruses and bacteria and cells. It then selects simpler chromases unconditionally catalyzing those indicating reactions and “conditional chromase inhibitors” which complexed with those chromases inhibit their catalyses but dissociate upon complexing with those viruses and bacteria and cells, affording more readily-selected equivalents to those indicases.
“Part 6: Phase V: Mechanomeric Cytotechnology.” The fifth phase of mechanomeric-selective developmental experiments, procedures and groups thereof selects “cytomers” or cell-affecting mechanomers needed for mechanomeric cytotechnology. “Cytoindicators” indicating viruses and bacteria of selected species and human cells of selected types were selected in the previous phase. The fifth phase selects “clastomers” killing only bacteria of those species and human cells of those types; “cytochelates” which bound to media allow very specific separations of chemicals, mechanomers, viruses, bacteria and human cells; “cytodifferentiators” inducing human cells of some easily-obtained and/or –cultured type (selected in the previous phase) to differentiate into cells of those types; and “blastomers” (growth hormones) inducing cells of those types to reproduce, all together allowing the beginning of the construction of the “cytopalettes” of cultures of cells of different types from different species (target, differential, key, representative and endangered) needed for functional and toxicity testing of mechanomers intended for medical or environmental use, some of which cultures themselves will have medical uses examined in the next phase.
“Part 7: Phase VI: Early Applications: Mechanomeric Medicine.” The sixth phase of mechanomeric-selective developmental experiments, procedures and groups thereof examines the medical uses of the cytomers and cytopalettes selected, produced and foreshadowed in the previous phase. It uses those cytomers to produce such cytopalette, and then uses that cytopalette to select mechanomeric antibiotics toxic to a pathogenic bacterium but not human cells or bacteria of other species, mechanomeric antivirals protecting cultures from viruses, and mechanomeric antineoplastics toxic to cancer cells but not to their parent or other human tissues or commensal bacteria.
“Part 8: Phase VII: Early Applications: Mechanomeric Engineering.” The seventh phase of mechanomeric-selective developmental experiments, procedures and groups thereof chooses the reactions and reactants and then selects the enzymes needed to chemically synthesize diamond, and to photosynthesize octane and glucose.
It is not suggested that mechanomeric-selective research and development must follow the above path in every step of the way, but something very closely approximating the sequence from the second through fourth phases described seems unavoidable. Plainly, such program is as massive as it is ambitious and promising, and not only needs to but should be carried out at every phase by multiple laboratories, openly cross-checking results and sharing technical problems and solutions.
Any and all points may be altered or refined in the course of writing this series of reports (not least nomenclatural—e.g., “conditional chromase inhibitor” is very clumsy)—which is a work in progress, so it behooves those interested to check back occasionally not only for the later parts as they are finished but for such revisions, which will be explicitly indicated in the course, although all such apparatus will be discarded upon the finishing, of the series.
Warning: Finally, even with the precautions with regard to mechanomer and mechanomeric monomer and polymerization reaction classes referred to in the report cited above and in Part 3 of this series of reports, all random mechanomer stocks should be treated as if they are Biosafety Level 4 pathogens: As the cited reports assert, nucleic acids should not be mechanomerically selected, to prevent unwanted genomic introductions; mechanomer classes mechanomers of which are to be selected should not use naturally-existing monomers, to prevent naturalizations of replicative systems; and mechanomer classes mechanomers of which are to be selected should be non-toxic and biodegradable; but even such safety precautions should not be considered adequate at the outset at least of mechanomeric selection, and all random mechanomer stocks should be treated as if they are Biosafety Level 4 pathogens, and all procedures involving such stocks carried out in the appropriate facilities, until experience, experiment and analysis prove such precaution unnecessary and lesser precautions adequate.
[20130517—moved the decision on mechanomer classes from Phase I where it didn't belong to Phase II.]
Keywords: amino acids, antibiotics, antineoplastics, antivirals, artificial photosynthesis, biopolymers, blastomers, chromases, clastomers, cytodifferentiators, cytoindicators, cytomers, cytopalettes, cytotechnology, enzymes, indicases, mechanomeric engineering, mechanomeric medicine, mechanomerics, mechanomeric selection, mechanomerogenesis, mechanomers, MeSe, merases, molecular machines, monomers, New Medicine, nucleic acids, photonomy, proteins, Singularity
Mechanomeric engineering requires some technique for developing mechanomers to perform desired functions, such as enzymes and molecular machines.
And just as proteins are developed in nature by variation of amino acid order—and therefore of conformation (coiled structure), and therefore of shape, mechanical properties and surface structure, and therefore of function—followed by selection, so too artificial mechanomers can be developed by selecting those performing desired functions from among random mechanomers, mechanomers with random monomer orders, and therefore random conformations, and therefore random shapes, mechanical properties and surface structures, and therefore random functions, in what is called here "mechanomeric selection (MeSe)".
The background to, critical argument for, procedures in referred to below, and some applications of mechanomeric selection are described in the report “Enzymes and Molecular Machines Can Be Selected from Random Copolymers”.
The present series of short reports describes a sequence of experiments including those procedures and groups thereof sufficient to establish mechanomeric selection on a firm foundation, starting with fundamental experiments and ending with several small but significant applications.
Those experiments and procedures and groups thereof number about forty, and fall naturally into seven phases, each of which shall be addressed in its own part of this series of eight short reports, as follows:
“Part 1: Introduction.” This very report.
“Part 2: Phase I: First Experiments: Incidences of Random Protein Well-Conformedness and Function.” The first phase of mechanomeric-selective research and developmental experiments, procedures and groups thereof described here assesses the incidences of well-conformedness and simple function in random protein stocks. But it begins with three sets of decisions with consequences for all remaining phases, about what industrial organic chemistry reactions; indicators and indicating reactions; and those monomers’ prosthetic groups. It chemically synthesizes and thermally tempers random proteins bearing those prosthetic groups. It weighs, assesses the numbers using osmosis, and calculates the average weights, lengths and gram numbers, of those proteins. It uses affinity chromatography using media bearing those prosthetic groups to assess the incidence of well-conformedness among those proteins. And it assesses the incidences of catalyses of those reactions among those proteins in so many assessments of the incidence of such simplest function among random mechanomers.
“Part 3: Phase II: Early Mechanomeric Selection: Mechanomerogenesis.” The second phase of mechanomeric-selective research and developmental experiments, procedures and groups thereof performs the fundamental early mechanomeric-selective procedure of mechanomerogenesis, allowing the self-selection or autoevolution of replicases. But it begins with two sets of decisions with consequences for all remaining phases, about what two mechanomer classes are to be at least originally employed in mechanomeric selection, and the corresponding polymerization reactions and monomers to be used with them. It chemically synthesizes test-mechanomers to be used in testing the functionality of the replicases resulting from mechanomerogenesis. It chemically synthesizes and thermally tempers random mechanomers of those classes; weighs, assesses the numbers using osmosis, and calculates the average weights, lengths and gram numbers of those mechanomers; uses affinity chromatography to assess the incidence of well-conformedness, and assesses the incidences of catalyses of the industrial and indicating reactions selected in the first phase, among those random mechanomers, all just as was done in the first phase with random proteins. It performs mechanomerogenesis. It assesses the functions of the replicases produced by mechanomerogenesis. And it assesses the incidences of direct replicability among random mechanomers of the classes used.
“Part 4: Phase III: Early Mechanomeric Selection: Merases” The third phase of mechanomeric-selective developmental experiments, procedures and groups thereof utilizes the replicases selected in the second phase to select the “merases”—polymerases, ligases and other enzymes—useful for mechanomeric selection itself, using affine-chromatographic and spectroscopic techniques to characterize and assess their functions.
“Part 5: Phase IV: Mechanomeric Indication.” The fourth phase of mechanomeric-selective developmental experiments, procedures and groups thereof selects various “indicases” conditionally and “chromases” unconditionally catalyzing the indicating reactions selected in the first phase. It begins with decisions with consequences for all remaining phases, about what species of viruses and bacteria and types of human cells are to be used in these phases. It selects indicases catalyzing those reactions only when complexed with and thus indicating the presences of those viruses and bacteria and cells. It then selects simpler chromases unconditionally catalyzing those indicating reactions and “conditional chromase inhibitors” which complexed with those chromases inhibit their catalyses but dissociate upon complexing with those viruses and bacteria and cells, affording more readily-selected equivalents to those indicases.
“Part 6: Phase V: Mechanomeric Cytotechnology.” The fifth phase of mechanomeric-selective developmental experiments, procedures and groups thereof selects “cytomers” or cell-affecting mechanomers needed for mechanomeric cytotechnology. “Cytoindicators” indicating viruses and bacteria of selected species and human cells of selected types were selected in the previous phase. The fifth phase selects “clastomers” killing only bacteria of those species and human cells of those types; “cytochelates” which bound to media allow very specific separations of chemicals, mechanomers, viruses, bacteria and human cells; “cytodifferentiators” inducing human cells of some easily-obtained and/or –cultured type (selected in the previous phase) to differentiate into cells of those types; and “blastomers” (growth hormones) inducing cells of those types to reproduce, all together allowing the beginning of the construction of the “cytopalettes” of cultures of cells of different types from different species (target, differential, key, representative and endangered) needed for functional and toxicity testing of mechanomers intended for medical or environmental use, some of which cultures themselves will have medical uses examined in the next phase.
“Part 7: Phase VI: Early Applications: Mechanomeric Medicine.” The sixth phase of mechanomeric-selective developmental experiments, procedures and groups thereof examines the medical uses of the cytomers and cytopalettes selected, produced and foreshadowed in the previous phase. It uses those cytomers to produce such cytopalette, and then uses that cytopalette to select mechanomeric antibiotics toxic to a pathogenic bacterium but not human cells or bacteria of other species, mechanomeric antivirals protecting cultures from viruses, and mechanomeric antineoplastics toxic to cancer cells but not to their parent or other human tissues or commensal bacteria.
“Part 8: Phase VII: Early Applications: Mechanomeric Engineering.” The seventh phase of mechanomeric-selective developmental experiments, procedures and groups thereof chooses the reactions and reactants and then selects the enzymes needed to chemically synthesize diamond, and to photosynthesize octane and glucose.
It is not suggested that mechanomeric-selective research and development must follow the above path in every step of the way, but something very closely approximating the sequence from the second through fourth phases described seems unavoidable. Plainly, such program is as massive as it is ambitious and promising, and not only needs to but should be carried out at every phase by multiple laboratories, openly cross-checking results and sharing technical problems and solutions.
Any and all points may be altered or refined in the course of writing this series of reports (not least nomenclatural—e.g., “conditional chromase inhibitor” is very clumsy)—which is a work in progress, so it behooves those interested to check back occasionally not only for the later parts as they are finished but for such revisions, which will be explicitly indicated in the course, although all such apparatus will be discarded upon the finishing, of the series.
Warning: Finally, even with the precautions with regard to mechanomer and mechanomeric monomer and polymerization reaction classes referred to in the report cited above and in Part 3 of this series of reports, all random mechanomer stocks should be treated as if they are Biosafety Level 4 pathogens: As the cited reports assert, nucleic acids should not be mechanomerically selected, to prevent unwanted genomic introductions; mechanomer classes mechanomers of which are to be selected should not use naturally-existing monomers, to prevent naturalizations of replicative systems; and mechanomer classes mechanomers of which are to be selected should be non-toxic and biodegradable; but even such safety precautions should not be considered adequate at the outset at least of mechanomeric selection, and all random mechanomer stocks should be treated as if they are Biosafety Level 4 pathogens, and all procedures involving such stocks carried out in the appropriate facilities, until experience, experiment and analysis prove such precaution unnecessary and lesser precautions adequate.
[20130517—moved the decision on mechanomer classes from Phase I where it didn't belong to Phase II.]
Keywords: amino acids, antibiotics, antineoplastics, antivirals, artificial photosynthesis, biopolymers, blastomers, chromases, clastomers, cytodifferentiators, cytoindicators, cytomers, cytopalettes, cytotechnology, enzymes, indicases, mechanomeric engineering, mechanomeric medicine, mechanomerics, mechanomeric selection, mechanomerogenesis, mechanomers, MeSe, merases, molecular machines, monomers, New Medicine, nucleic acids, photonomy, proteins, Singularity
Saturday, May 26, 2012
Photonomics: The Photosynthetic Economy
Enzymes photosynthesizing fuels, organic chemical industrial feedstocks, and bulk macronutrients (fats, sugars and amino acids) from air, seawater and sunlight will be readily developed by mechanomeric selection (MeSe).
The critical argument with regard to mechanomeric selection is presented here.
A very concise report giving the background to that argument, the argument itself, a technological description of mechanomeric selection, and a small number of brief descriptions of medical and industrial applications of that technology, including artificial photosynthesis, is presented here
And a more expansive and easier-going introduction to mechanomeric selection in the form of a pseudoblog/FAQ is presented here (start with the earliest post, in blog fashion).
Seawater should be used for artificial photosynthesis wherever possible to minimize usage of and impact on freshwater.
Such photosynthesis should not use the ordinary biological photosynthetic frequencies (blue and red) on land, to avoid competition with natural photosynthesis, and should probably best use solar UV both on land and at sea, to avoid such competition and since UV penetrates cloud well and is high-energy.
And such photosynthesis should be as decentralized as possible (eg, every building/complex, municipality, etc., should generate its own fuel as much as possible, for electrical and vehicle-fleet use), not least in implementation in the form of specialized ocean-going photosynthetic barge-fleets(which barges should be transparently-bottomed, to allow unused sunlight to pass through).
The mechanomeric selection of a photoenzyme for such photosynthesis will involve matricial mechanomeric selection (see the referenced report and pseudoblog/FAQ): matriciating (usually meaning chromatographically two-dimensionally arraying) replicated random mechanomers (functional copolymers) of some artificial class (to avoid unintended consequences), say polyesters or polysulfonamides; overlaying the replicated random mechanomer matrix so produced with seawater and if desired or needed a mixture of metal ions and organic chemicals (chromophores and electrophores) facilitating photonic absorption and electronic transmission and/or some desired substrate or reactant; exposing the functional matrix so produced to sunlight; and examining that matrix for the emergence of the desired product (best using mechanomeric indication by a previously-developed enzyme, an indicase, and its substrate or indicator together reacting to and therefore indicating the presence of that product by catalyzing an indicating reaction causing a color-change—see the referenced report and pseudoblog/FAQ); followed by extraction of the mechanomers from locations where that product is being produced; replication of those mechanomers; and their further testing for the desired catalysis, for example by further selections using different matriciations.
Desired photosyntheses might be broken down into sequences of simpler reactions and the enzymes (photosynthetic or otherwise) catalyzing those separately selected, but there should usually be at least an initial or parallel attempt at the easiest one-shot selection of a necessarily more complex enzyme (and therefore one occurring less frequently in random mechanomer stocks) capable of catalyzing all those reactions in sequence and therefore the entire sequence from air, seawater and sunlight to final product, such enzyme being simplest to use in practice.
Similarly, where such simpler enzymes are selected, it might be best to select them in order of needed catalytic sequence, and use each enzyme/complex selected as an additional component of the next selective matrix, in an attempt in each selection to select an enzyme which complexes with the previously-selected enzyme or complex and catalyzes the growing sequence of reactions most efficiently.
One of the most important artificial photosynthetic products will be glucose, for use in cellophane (biodegradable bagging/wrapping plastic), (cellulose) paper, and the textile rayon.
And another will be lignin precursors or equivalents for use in lignin and artificial wood syntheses for light and medium construction.
Note that selection and use of such enzymes for such photosynthesis of fuels, organic chemical industrial feedstocks, and bulk macronutrients will not only halt the alarming present-day massive industrial crustal-carbon fossil-fuel extraction and burning and consequent carbon dioxide emission and greenhouse warming, but will also remove carbon dioxide from the atmosphere and "fix" it into fuel and other stocks, helping palliate the impact of previous extraction and burning and emission and warming.
And once the fuel, organic chemical and food industries are retooled away from use of petroleum to that of photosynthetic products, we will have finally established the sustainable photosynthetic economy or photonomy.
Keywords: bionanotechnology, enzymes, mechanomeric selection, mechanomers, MeSe, photonomics, photonomy, photosynthesis, Singularity, sustainability
The critical argument with regard to mechanomeric selection is presented here.
A very concise report giving the background to that argument, the argument itself, a technological description of mechanomeric selection, and a small number of brief descriptions of medical and industrial applications of that technology, including artificial photosynthesis, is presented here
And a more expansive and easier-going introduction to mechanomeric selection in the form of a pseudoblog/FAQ is presented here (start with the earliest post, in blog fashion).
Seawater should be used for artificial photosynthesis wherever possible to minimize usage of and impact on freshwater.
Such photosynthesis should not use the ordinary biological photosynthetic frequencies (blue and red) on land, to avoid competition with natural photosynthesis, and should probably best use solar UV both on land and at sea, to avoid such competition and since UV penetrates cloud well and is high-energy.
And such photosynthesis should be as decentralized as possible (eg, every building/complex, municipality, etc., should generate its own fuel as much as possible, for electrical and vehicle-fleet use), not least in implementation in the form of specialized ocean-going photosynthetic barge-fleets(which barges should be transparently-bottomed, to allow unused sunlight to pass through).
The mechanomeric selection of a photoenzyme for such photosynthesis will involve matricial mechanomeric selection (see the referenced report and pseudoblog/FAQ): matriciating (usually meaning chromatographically two-dimensionally arraying) replicated random mechanomers (functional copolymers) of some artificial class (to avoid unintended consequences), say polyesters or polysulfonamides; overlaying the replicated random mechanomer matrix so produced with seawater and if desired or needed a mixture of metal ions and organic chemicals (chromophores and electrophores) facilitating photonic absorption and electronic transmission and/or some desired substrate or reactant; exposing the functional matrix so produced to sunlight; and examining that matrix for the emergence of the desired product (best using mechanomeric indication by a previously-developed enzyme, an indicase, and its substrate or indicator together reacting to and therefore indicating the presence of that product by catalyzing an indicating reaction causing a color-change—see the referenced report and pseudoblog/FAQ); followed by extraction of the mechanomers from locations where that product is being produced; replication of those mechanomers; and their further testing for the desired catalysis, for example by further selections using different matriciations.
Desired photosyntheses might be broken down into sequences of simpler reactions and the enzymes (photosynthetic or otherwise) catalyzing those separately selected, but there should usually be at least an initial or parallel attempt at the easiest one-shot selection of a necessarily more complex enzyme (and therefore one occurring less frequently in random mechanomer stocks) capable of catalyzing all those reactions in sequence and therefore the entire sequence from air, seawater and sunlight to final product, such enzyme being simplest to use in practice.
Similarly, where such simpler enzymes are selected, it might be best to select them in order of needed catalytic sequence, and use each enzyme/complex selected as an additional component of the next selective matrix, in an attempt in each selection to select an enzyme which complexes with the previously-selected enzyme or complex and catalyzes the growing sequence of reactions most efficiently.
One of the most important artificial photosynthetic products will be glucose, for use in cellophane (biodegradable bagging/wrapping plastic), (cellulose) paper, and the textile rayon.
And another will be lignin precursors or equivalents for use in lignin and artificial wood syntheses for light and medium construction.
Note that selection and use of such enzymes for such photosynthesis of fuels, organic chemical industrial feedstocks, and bulk macronutrients will not only halt the alarming present-day massive industrial crustal-carbon fossil-fuel extraction and burning and consequent carbon dioxide emission and greenhouse warming, but will also remove carbon dioxide from the atmosphere and "fix" it into fuel and other stocks, helping palliate the impact of previous extraction and burning and emission and warming.
And once the fuel, organic chemical and food industries are retooled away from use of petroleum to that of photosynthetic products, we will have finally established the sustainable photosynthetic economy or photonomy.
Keywords: bionanotechnology, enzymes, mechanomeric selection, mechanomers, MeSe, photonomics, photonomy, photosynthesis, Singularity, sustainability
Friday, March 23, 2012
Nanopaprika.eu - The International NanoScience Community:
Two Blog-Posts and a Featuring
I've put two blog-posts on Nanopaprika.eu - The International NanoScience Community (TINC):
"Enzymes and Molecular Machines Can Be Selected from Random Copolymers" gives just the critical argument with regard to mechanomeric selection from and a link to the report of the same name blogged here below.
"Random Mechanomers and Artificial Photosynthesis" is an expansion on the paragraph on that particular set of applications at the end of that report as well as the earlier standalone blog-post on my personal blog.
By way of reward, I guess, TINC "featured" me—like about half the membership:
Finally! recognition!
"Enzymes and Molecular Machines Can Be Selected from Random Copolymers" gives just the critical argument with regard to mechanomeric selection from and a link to the report of the same name blogged here below.
"Random Mechanomers and Artificial Photosynthesis" is an expansion on the paragraph on that particular set of applications at the end of that report as well as the earlier standalone blog-post on my personal blog.
By way of reward, I guess, TINC "featured" me—like about half the membership:
Finally! recognition!
Thursday, March 15, 2012
Enzymes and Molecular Machines
Can Be Selected from Random Copolymers
Most cell structures are formed or synthesized and most other cell functions are performed by the molecules called proteins.
Proteins are polymers, complex chain-like molecules each synthesized by the chemical bonding together or polymerizing of many smaller molecules called their monomers, and furthermore are copolymers, polymers consisting of monomers of more than one kind.
The monomers of the proteins are called amino acids, of which twenty different kinds are commonly incorporated into natural proteins.
The amino acids are small molecules, composed of only ten to twenty-seven atoms each, depending on kind, averaging about twenty, and averaging in mass about 2.35 * 10-22 gram, about one-quarter of one zeptogram (sextillionth of a gram), or 235 yoctograms (septillionths of a gram), about eight times as much as the three-atom water molecule, an oxygen atom single-bonded to each of two hydrogen atoms (an oxygen atom forms two single bonds or one double bond in a molecule, while a hydrogen atom forms one single), the total mass of which is about 2.99 * 10-23 gram, or thirty yoctograms.
Every amino acid molecule consists of a central carbon atom single-bonded to a hydrogen atom, an amino group, a carboxylic acid group and a prosthetic group (a carbon atom forms four single bonds in a molecule, or one double bond and two singles, or two double bonds, or one triple bond and one single). An amino group is composed of a nitrogen atom (which forms three single bonds, or one double and one single, or one triple) single-bonded to each of two hydrogen atoms. And a carboxylic acid group is composed of a carbonyl group or moiety, a carbon double-bonded to an oxygen atom, further single-bonded to a hydroxy or alcohol group, an oxygen atom single-bonded to a hydrogen atom. Such bonds and groups are of course the ordinary molecular bonds and functional groups of carbon chemistry, called "organic chemistry" due to life's taking such advantage of the ability of carbon to form large and stable molecules that most carbon on the face of the earth is or has been part of a living organism. And the amino acid amino and carboxylic acid groups are of course what give it its name.
Every amino acid is identical to every other in the above, regardless of kind, in a nine-atom moiety called here its invariant moiety, composed of its central carbon atom and the hydrogen atom and amino and carboxylic acid groups bonded to it. And an amino acid of one kind differs from one of another solely in the elemental composition (the kinds and number of atoms involved), structure (how those atoms are bonded together) and consequent properties of its prosthetic group.
The invariant moieties of the amino acids incorporated into a protein, minus water of polymerization (the equivalent of one molecule of water is lost for each amino acid incorporated into a protein, the hydroxyl group from the carboxylic acid group and a hydrogen from the amino group), comprise what is called its backbone, an elongated and repetitive structure in which each invariant moiety remnant incorporated forms a unit identical to every other (although of course the end-units each bear a free bonding group unused in polymerization). And the prosthetic groups of those amino acids become protein side-groups projecting from those protein backbone units and that backbone.
Proteins of different kinds and functions vary widely in the number of amino acids of which they are composed. But three hundred amino acids is a modal protein length and size. And a modal protein mass can be calculated based on that length and size by multiplying the average mass of an amino acid by three hundred, and then subtracting the combined masses of the two hundred and ninety-nine water molecule equivalents lost, amounting to about 6.16 * 10-20 gram, about sixty zeptograms, a little over two thousand times the mass of a water molecule. And the corresponding modal protein gram number, the number of such proteins contained in one gram thereof, can be calculated by dividing that mass into one gram, giving about 1.62 * 1019 or about sixteen quintillion such proteins per gram.
Proteins can rotate around their backbone single bonds, and therefore all along their backbones, and consequently twist and coil, but the proteins which perform the functions of the cell generally assume three-dimensional coiled structures or conformations specific to their kinds, stabilized in various ways. For example, attractions between positively- and negatively-charged moieties of molecules form what are called hydrogen bonds, which separately are weaker but collectively can be much stronger than any one molecular bond. Such bonds between nearby backbone units along the protein backbone cause the assumption of winding or helical conformations along the backbone, as well as sheet conformations involving multiple turns and side-by-side runs thereof. Such interactions and resulting conformations are not specific to any particular protein or moiety thereof, since every backbone unit is identical to and can form the same such bonds as any other, and any stretch of backbone could theoretically engage in any such conformation. Slightly more specifically, the backbone units and some side-groups hydrogen-bond water molecules, and proteins tend to coil in such a way as to present such water-soluble or hydrophilic moieties or groups on their surfaces, and hold those side-groups which cannot form such bonds inside, in water-insoluble or hydrophobic cores. But in most of the proteins which perform the functions of the cell, conformation is specified by side-group interactions, which depend on the kinds of side-groups available and the order in which they occur, which depend in turn on which amino acids are incorporated into the protein and the order in which they are incorporated.
That is, protein amino acid order determines protein conformation.
Protein conformation determines protein shape, whether globular, elongated or flattened, and whether solid, indented or hollow; protein mechanical properties, such as whether and how one part of a protein can bend or rotate with respect to the rest; and protein surface structure, the protein’s surface shape and pattern of exposed side-groups and backbone units.
And protein shape, mechanical properties and surface structure determine protein function:
Two proteins or other large molecules of complementary shape and surface charge-patterns upon being brought together will develop multiple attractions including hydrogen-bonds to one another, such fit and collective attraction being called an affinity and such collective bond a complex. Protein complexing is so generally specific in its requirements of complementary shape and charge-pattern as to be described as “lock-and-key”. And protein complexing is a fundamental mechanism of protein function: The conformation-determining attractions and bonds of and within the protein itself can be considered intramolecular or internal complexing. Cytostructural proteins complex with one another to form the internal structural framework of the cell called the cytoskeleton. And every cell contains protein enzymes catalyzing—accelerating—the chemical reactions used by that cell, which reactions would otherwise run too slowly to be of use: Body cells typically each synthesize thousands of different enzymes, and many molecules of each, each more or less specifically catalyzing its specific reaction operating upon its specific substrate(s) or reactant(s) (the phrase "lock-and-key" was first applied to enzyme specificity). And each enzyme catalyzes its reaction largely through, and its specificity is that of, not so much its complexing with its substrate(s) as with its reaction's rate-determining transition state, the highest-energy state through which that reaction must proceed, stabilizing and therefore lowering the energy of that state, allowing lower-energy passage through that state, increasing the probability that a given enzyme-substrate complex will have the energy needed to pass through that state, and therefore, in the cell or other reaction mixture where many such complexes are forming and dissociating, increasing the number of such able to pass through that state and their reactions proceed to completion at any given time, and therefore the overall rate of reaction. In addition, many enzymes catalyze water-sensitive reactions in their hydrophobic cores. More complicatedly, many if not most proteins function by virtue of conformation changes, changing back and forth between two or more conformations in the course and by way of function, a phenomenon called allostery, and complexing is frequently combined in protein function with allosteric conformation changes. Protein complexing of one molecule causing an allosteric conformation change in that protein enabling or preventing subsequent complexing of another molecule is a central mechanism of protein function and control in the cell; for example, some enzymes, including some acting as cell switches, sensors or governors, are activated or deactivated—turned on or off—by conformation changes caused by complexing with or dissociating from the appropriate molecules, some used specifically as signals. And other protein enzymes catalyze the degradation of fuel and use the energy yielded to repetitively alter their conformations and shapes, acting as motors and machines.
Proteins can become damaged in use and need replaced, and indeed are routinely depolymerized and their amino acids reused. Furthermore, proteins need to be passed down from one generation to the next. There is therefore a constant need for new copies of proteins. But proteins are not directly replicated or copied in nature. Instead, the copolymers called nucleic acids, synthesized from monomers called nucleotides, are used as templates to synthesize proteins as well as new copies of themselves. There are two (sub-) classes of nucleic acids, the deoxyribonucleic acids or DNAs or just DNA, and the ribonucleic acids or RNAs. Nucleic acids of each class are synthesized from nucleotides of a corresponding class, the deoxyribotides and the ribotides, respectively, of which there are only four kinds each. Nucleotides are larger and more complicated than amino acids, but every nucleotide molecule is identical to every other of its class in part, regardless of kind, in an invariant moiety bearing two bonding groups of different kinds, and a nucleotide of one kind differs from one of another of its class solely in the composition, structure and properties of a base or base moiety bonded to its invariant moiety, all analogous to amino acids. Nucleic acid strands have repetitively-structured backbones composed of the invariant moieties of the nucleotides incorporated into them minus water of polymerization, and side groups projecting from those backbones composed of those nucleotides’ base moieties, and free end bonding groups unused in polymerization, all analogous to proteins. And just as with proteins, nucleic acid side-group hydrogen-bonding and complexing play central roles in the form and function of nucleic acids in the cell, both perfectly analogously to the proteins, and also in a very specific way used in protein synthesis and nucleic acid replication: The nucleotides of either class consist of two pairs of kinds in each pair of which the base moiety become a side-group when a nucleotide of the one kind is incorporated into a nucleic acid will hydrogen-bond to the other when close enough and at the proper angle. In a nucleic acid which is multiply and sequentially complexed with itself or another nucleic acid the hydrogen-bonded bases or side-groups and the bonds between them are referred to collectively as base-pairs. And two nucleic acids of either class, or one of the one class and one of the other, with complementary nucleotide orders but antiparallel (opposite) directions, can hydrogen-bond base-pair-by-base-pair all along both strands, forming a fully-complexed double strand. DNA generally exists as such double strand, or as a set of such, each of which when wrapped around and compacted with and by proteins for transfer and becoming visible under a microscope during cell reproduction is called a chromosome, and is the very stuff of heredity or biological inheritance, passed from parents to and conferring their biological traits upon their offspring. It is and does so by serving as a permanent record of the amino acid orders of all the proteins synthesized by every cell of the body, every body cell containing the identical DNA(s) (but see the description of B cells below), encoding those orders by means of the genetic code, in which three-deoxyribotide sequences called codons represent amino acids, and sequences of codons called genes represent proteins.
In cell reproduction, the cell divides into two daughter cells, and two DNA double strands or sets thereof, one for each daughter cell, must be synthesized for each such possessed by the parent cell. Simplifying greatly, such DNA synthesis or copying or replication is accomplished by separation of its strands, hydrogen-bonding the complementary deoxyribotides to the newly-exposed ones, and polymerizing the new deoxyribotides into complementary new strands complexed with the old, in what is called, due to each new double strand produced being composed of one old and one new strand, semi-conservative replication.
In protein synthesis, and again simplifying greatly, the DNA double strand is separated in the region of the gene or protein-encoding sequence being used or expressed and the appropriate strand used as a template for the bonding of the complementary ribotides in the transcribing of that gene into in the synthesis of a complementarily-encoded RNA primary transcript, which after post-transcriptional processing including the removal of segments and splicing together of the remainder then serves as a messenger RNA template for protein synthesis, the codons of that RNA complexing with complementary anticodons of transfer RNAs, each of which have been previously bonded to the corresponding amino acids, and which amino acids are then transferred from those RNAs to the growing protein, in the (usually repeated) synthesizing of or translating of that RNA into (usually many copies of) the encoded protein, the process controlled and catalyzed by the protein-and-RNA complex called the ribosome.
Every living thing of every species on our planet uses nucleic acids and the genetic code to synthesize its proteins in transcription and translation, and to inherit and pass on its proteins' amino acid orders and therefore its biological traits in heredity, proving beyond a reasonable doubt that all living things of every species on our planet are related. Since all living things and species are related, we must share a common ancestry. And such common ancestry and later divergence of species is called evolution. Evolution proceeds through mutation or change of trait caused by change of protein caused by change of gene, which last is the only kind of change which can be inherited, those changes which are fatal or otherwise disadvantageous being correspondingly unlikely to be inherited, while those which are advantageous preferentially so, in both negative and positive natural selection.
Evolution is therefore an organism-, cell-, trait- and nucleic-acid-based development of proteins by variation of amino acid order followed by selection.
The leukocytes or white blood cells (called so because they’re not red) called B cells, which synthesize the proteins called antibodies, comprise one exception to the rule that every body cell contains the identical DNA: Antibodies play a central role in the body's immunity to infection, by their complexings with or recognitions of antigen, mostly proteins upon the surfaces of invading microbes. Free antibodies secreted by B cells into the lymph and blood complex with foreign cells and trigger a complex, sequential and cascading biochemical attack by a group of blood proteins called the complement system, ending in among other things the construction of fatal protein pore complexes—holes—in the outer membranes of those cells. Antibodies complex with antigen at a relatively small antigen binding site on the antibody surface comprised of several adjacent runs of protein. During B cell development in early childhood the antigen binding site codon sequences in the antibody gene of each immature B cell are themselves produced by random and imprecise genetic recombinations of short codon sequences from a preexisting pool of such present in DNA. Cells with encoding errors from such recombination are either re-recombined or destroyed, while those which continue to mature encode and synthesize antibodies with antigen binding sites which vary from cell to cell. Such cells undergo further negative selection re-recombining or destroying those which recognize the body's own "self" proteins and cells. And the surviving cells reproduce to form a population of B cells consisting of millions of different B cell sub-populations or clones in the body each clone synthesizing its own specific antibody and all therefore collectively synthesizing millions of different antibodies. Each B cell synthesizes and exposes on its surface something on the order of a hundred thousand copies of the antibody specific to its clone. And such cells upon recognition of antigen are variously stimulated to reproduce, to secretion of free antibodies into lymph and blood, and to other immune activities, including further recombinations, selections and reproductions fine-tuning recognition of antigen.
Antibody development and function are therefore cell- and nucleic-acid-based developments of proteins by variation of amino acid order followed by selection.
Such functional copolymers as the proteins are called "mechanomers" here (distinguishing naturally-occurring mechanomers as "biopolymers" where convenient); the science of mechanomers is called "mechanomerics"; and applied mechanomerics is called "mechanomeric engineering", including "mechanomeric medicine".
Mechanomeric engineering requires some technique for developing mechanomers to perform desired functions, such as enzymes and molecular machines.
And just as proteins are developed in nature by variation of amino acid order—and therefore of protein conformation (coiled structure), and therefore of shape, mechanical properties and surface structure, and therefore of function—followed by selection, so too artificial mechanomers can be developed by selecting those performing desired functions from among random mechanomers, mechanomers with random monomer orders, conformations, shapes, mechanical properties, surface structures and functions, in what is called here "mechanomeric selection".
Evolution's scale, in numbers of mechanomers/biopolymers and selections and across time, keeps it from being proof that mechanomeric selection is a practicable technology.
However, the development of each individual's antibody complement in childhood, and still more such development in the even smaller and faster system of the duck embryo in the egg, and the function of those antibodies, and most of all the medical exploitation of such development and function in vaccination and the medical and industrial development and use of antisera and monoclonal antibodies, all furnish so many everyday small-scale proofs that proteins performing such more or less simple complexings or molecular recognitions as antibodies can be developed by random synthesis followed by selection.
Enzyme function furnishing so many more examples of such complexings, enzymes can therefore be developed likewise.
Proteins performing any equally simple functions or small combinations thereof likewise.
Biopolymers of the other important class of such, the nucleic acids, likewise, within the limitations imposed by their smaller numbers of kind of monomers (and smaller variations in structure between those).
And mechanomers of other classes likewise.
Nucleic acids should in fact not be mechanomerically selected, to prevent unwanted genomic introductions. Mechanomer classes mechanomers of which are to be selected should not use naturally-existing monomers, to prevent naturalizations of replicative systems (see below). And mechanomer classes mechanomers of which are to be selected should be non-toxic and biodegradable.
Random polymerization of a mixture of monomers of the different kinds of the appropriate class will produce a mixture of different random mechanomers of the desired class, a random mechanomer stock, and replication or molecular copying of the mechanomers in such stock a mixture of many replicands of each of those mechanomers, a mixture of many mechanomeric clones, a replicated random mechanomer stock. Such stocks will be the fundamental tools of mechanomeric selection. And such polymerization and replication will be catalyzed by enzymes, at least one polymerase and replicase respectively, both of another class of mechanomer than that of those being synthesized to avoid unwanted operations upon those enzymes themselves, both operating in the same direction along and continuously upon the growing mechanomer during its synthesis to insure that the replicands have the same conformations as the original, and both themselves mechanomerically selected in early mechanomeric selection (see below).
Mass properties of mechanomers significant to mechanomeric selection include (1) incidence of well-conformedness and (2) coincidence and incidence of function among random mechanomers or in random mechanomer stocks; (3) gestation (-time) of mechanomeric function (time for detectable effect to accumulate, taken here to be that of an enzyme); and (4) incidence of degradative enzymes among random mechanomers or in random mechanomer stocks:
(1) Incidence of well-conformedness: Proteins generally each assume a single stable conformation, or change between two or three conformations by way and in course of function, but perhaps fewer than one in one billion random amino acid orders will specify such well-conformed proteins, and such incidence is taken here to be that of well-conformed mechanomers in random mechanomer stocks. Many mechanomeric functions might be performed by mechanomers which do not assume such conformations (if only because conformed by complexing by way and in course of function), and such incidence will be adequate for the selection of mechanomers performing the simplest functions anyway (see below), but selection of mechanomers performing more complex functions will require use of some technique(s) for increasing such incidence. Three such techniques, in order of increasing complexity and decrease in synthesis of poorly-conformed mechanomers, are what are called here "diagonalization", "fuzzy replication" and "splicing":
Diagonalization: Chromatographing random mechanomers along one side of a square medium or matrix and then at a right angle to the original direction until the spectrum lies largely along and is enriched in well-conformed mechanomers along the diagonal, well-conformed mechanomers being more sharply localized in chromatography, such mechanomers extracted and the procedure repeated, using different media.
Fuzzy replication: Using an inaccurate or fuzzy replicase—see below—to replicate an original well-conformed mechanomer, perhaps with a function similar or even identical in part to that desired, and synthesize a random mechanomer stock, analogous to evolution.
Splicing: Of random or fuzzily-replicated segments into the appropriate areas of otherwise well-conformed mechanomers, analogous to antibody antigen binding site development, followed by replication to insure that those mechanomers assume the conformations they would have assumed upon continuous polymerization and will upon replication for production.
(2) Coincidence and incidence of function: Proteins vary widely in the numbers and orders of the amino acids of which they are composed, but three hundred amino acids is a modal protein length and size, and if all proteins with all possible amino acid orders of that length were synthesized, the total mass of protein synthesized would be several hundred powers of ten times the mass of our galaxy. Plainly, if each and every protein function could be performed by only one specific protein with one specific amino acid order, no biological process or artificial procedure could ever develop such. But the evolution of proteins and other mechanomers, and the development and function of antibodies in the body, and vaccination and the development and use of antisera and monoclonal antibodies, all prove not only that mechanomers with different monomer orders can share a given function but that there must be a fantastically high degree of coincidence of function among them. Hundreds out of the millions of different antibodies in the body typically complex with a given antigen, which incidence of one in ten thousand is taken here to be that of such simplest function among well-conformed random mechanomers (taking the restriction of antibody complexing to its antigen binding site alone to cancel out multiple antibody complexing of different parts of antigen). And the greater the number of functions performed by a mechanomer, and the greater their complexities, the lower will be such incidence of such mechanomer, the incidence with two sites performing such functions taken here to be about one in ten thousand squared or one in one hundred million, and the incidence with three one in ten thousand cubed or one in one trillion.
(3) Gestation time: Ten thousand random proteins three hundred amino acids in length will collectively mass a little over six hundred attograms, which stock if replicated to one gram will average about 1.6 quadrillion replicands and one hundred micrograms of each protein, which replicands if of an enzyme each molecule of which produces ten product molecules per second each with the mass of an amino acid will take about four and a half minutes to produce one milligram of such, while one trillion such proteins will mass a little over sixty nanograms, which replicated to one gram will average about sixteen million replicands and a picogram of each, which as such enzyme will take about ten months to produce one microgram of product.
(4) Incidence of degradative enzymes: Depolymerases depolymerizing and other enzymes degrading mechanomers of their own class will occur in every random mechanomer stock and make it unstable. Such reactions and enzymes for the most part will be simple ones, the collective incidence of such enzymes in such stocks will be correspondingly high, such stocks will be correspondingly unstable, and such problems will be exacerbated by replication. Random mechanomer stocks should therefore be freshly prepared for mechanomeric selection. If such stock must be stored it should be kept cold, decreasing reaction rates in general, and dry, if depolymerization incorporates solvent into the free monomers, as with proteins, amino acids and water. Such stock might also be matriciated (see below), separating most mechanomers in the stock and causing degradative enzymes to preferentially degrade their own replicands, and even bound after matriciation to some matrix, fixing the mechanomers in place and completely halting such degradation.
What is called here "matricial mechanomeric selection", analogous to antibiotic sensitivity testing, will be the simplest and most common form of such selection, at its own simplest matriciating (spreading and arraying) a sample of a replicated random mechanomer stock across or through or into a thin layer; overlaying that replicated random mechanomer matrix with any materials and subjecting it to any other conditions needed for the desired function; analyzing that matrix identifying locations in which the desired function is being performed; extracting the mechanomers from those locations for further replication and testing, perhaps by another round of such selection (using a different matriciation to redistribute the mechanomers in the sample—see below); and replicating the mechanomer finally selected for its performance of the desired function for production.
Matriciation must be ordered—for example by affine chromatography, chromatographing a sample of a replicated random mechanomer stock using one chromatographic medium and blotting the resulting linear chromatogram into one side of a different medium and chromatographing that a right angle to the first, forming a square or two-dimensional matrix, perhaps itself blotted into a final test matrix and medium—to localize the replicands and effects of each different mechanomer in its characteristic location on the matrix, maximizing concentration of effect and minimizing gestation (time for effect to accumulate to detectability) and analytical sensitivity needed; to perform parallel testing of mechanomers under different or incompatible conditions, using identical matriciations of multiple samples of a replicated random mechanomer stock and comparing mechanomer behaviors at their identical locations from matrix to matrix; to perform parallel recovery of mechanomers from a matrix parallel to a test matrix from which it would be difficult or impossible to recover the tested mechanomers; and as noted above to separate mechanomers and therefore decrease mechanomeric interactions on and in the matrix, causing enzymes degrading mechanomers of their own class to preferentially degrade their own replicands.
Matricial analysis will of course use infrared spectroscopy and nuclear magnetic resonance imaging where appropriate.
It will also use "orthogonal analysis", by "orthogonalization" or third-dimensional separation of the matrix, for example by blotting the matrix into one end of and separating its components using a very wide chromatographic column (and orthogonal standards inoculated into the margin of the original square matrix marking in the orthogonal matrix or column planes or bands of interest).
But matricial analysis will above all use what is called here "mechanomeric indication", overlaying the matrix with a previously-selected enzyme, called here an "indicase", which under some condition resulting from the performance of the desired mechanomeric function catalyzes a reaction converting a substrate, called here an "indicator", causing a color-change on the matrix. Such indicase will be readily developed by overlaying a replicated random mechanomer matrix with indicator, then subjecting that matrix to the desired condition, and noting where indicator was not converted and no color-change took place until that condition was applied. Mechanomeric indication by its analysis at the molecular level, analysis by complexing, cumulative indication as colored indicator accumulates, and ability to use the product of one indicase to trigger another to amplify indication, will render most mechanomeric selection amenable to being performed as matricial mechanomeric selection. Even though in such selection of any mechanomer the function of which is more complex than that of a simple enzyme catalyzing the indicating reaction, false indications by any given indicase will outnumber true, making advisable the development and simultaneous use of multiple indicases in such selection, and selecting only from regions on the matrix where multiple indication is taking place.
What is called here "mechanomeric evolution", freely mixing unreplicated random mechanomers and monomers with a replicase complexed with a previously-selected what is called here "conditional replicase inhibitor" which inhibits replication except under some condition resulting from the performance of the desired mechanomeric function, will test the greatest possible number of random mechanomers at a time for a desired function and therefore facilitate the selection of mechanomers performing more complex functions occurring more infrequently in random mechanomer stocks. Such conditional replicase inhibitor will be readily developed by first developing an indicase which converts colored indicator to colorless, then overlaying two parallel random mechanomer matrices with monomers, replicase and that indicase, subjecting one such matrix to some condition resulting from the desired function, and observing where in the latter indicator color persists. Mechanomeric evolutionary system sizes will be limited by same-class replicase-pair takeovers (see below), and in such selection of any mechanomer the function of which is more complex than that of a mechanomer disinhibiting the replicase, false evolutions will outnumber true.
The enzymes and other mechanomers needed for mechanomeric selection will themselves be mechanomerically selected, in what is called here "early mechanomeric selection":
Replication being a more complex function than and indeed including polymerization, replicases must be more complex and therefore occur more rarely in random mechanomer stocks than polymerases, but cross-class replicase pairs, one from each of two mechanomer classes replicating mechanomers of the other, will evolve in what is called here “mechanomerogenesis”, in which random mechanomers and monomers of both classes are mixed, and such replicases upon encountering one another engage in a more or less exponential course of mutual replication (with, note, a more or less exponentially-increasing heat of replication), with the first such event and pair likely taking over the system. Many such events will produce same-class pairs, which pairs will also limit mechanomeric evolutionary system sizes (see above), and many cross-class replicases produced will be incapable of replicating mechanomers incorporating monomers of all the kinds of the appropriate class supplied, and more or less inaccurate or fuzzy in their replication of the mechanomers they can replicate (such reduced-monomer-set replicases will often be workable until better ones are developed, and such fuzzy replicases will be useful for increasing the incidence of well-conformed mechanomers in random mechanomer stocks—see above).
Once a workable replicase pair is selected, at least one polymerase of each class polymerizing monomers of the other will be selected by matricial mechanomeric selection, using random mechanomers synthesized by purely-chemical (non-enzyme-catalyzed) polymerization and then replicated. Such polymerase pairs must operate in the same directions as their classmate replicases, although replicases and polymerases operating in both directions will be selected to select mechanomers which in the course of synthesis coil in such ways as to bury the ends first synthesized and prevent replication, as well as those which vary in their conformations depending on direction of synthesis.
Finally, sets of mechanomers—growth hormones stimulating cell reproduction and cytodifferentiators converting cells of a sample type to those of others—will be selected and refined and expanded which allow construction of cytopalettes, sets of cultures of cells of different types, for use in matricial mechanomeric selective matricial overlays in parallel testing of mechanomers for toxicity (including environmental safety). Cytopalettes will include multicytotypic such as neuromuscular junctional cultures. Cytopalettes cultured from cell samples from individual patients will allow the custom selection of mechanomeric pharmaceuticals for use in idiotherapies, individual or customized therapies of refractory infections and idiopathic diseases, including cancers (see below). And such cells and tissues will also be used for replenishment and replacement, and the engineering of organs for (more or less) autotransplantation.
The utility of mechanomeric selection is highlighted by its applications to itself above in mechanomerogenesis and other early mechanomeric selection (including the selection of cytopalette mechanomers), mechanomeric indication, and mechanomeric evolution.
There are, of course, many other relatively easily foreseeable applications for such technology, in particular with regard to medicine and industry.
Mechanomers specifically toxic to microbes of a given species but not to those of other species or to humans will be mechanomerically selected. At its simplest, such selection will take the form of parallel matricial mechanomeric selection: overlaying a set of parallel identical replicated random mechanomer matrices with, respectively, a culture of the microbes in question, cultures of microbes of as many other species as practicable, both human commensals (to avoid for example disturbing normal human gastrointestinal microflora and possibly facilitating fulminating toxic overgrowths) and a selection of environmentally-significant species, and cytopalette cultures of as many different human cell types from as many different humans as practicable; observing for regions where on the first matrix the microbial cells die but on the others no cells do, deaths signaled by mechanomeric indication for greatest sensitivity; extracting the random mechanomers from those regions from yet another parallel matrix; re-matriciating the mechanomers from each such region using different media to separate them; and repeating, until a specific and effective antimicrobial is selected. Multiple agents should be selected to overcome microbial resistance to any one such and to reduce the amount of each such agent needed and therefore any side-effects therefrom. And note that such selection of antimicrobials will enjoy even greater flexibility than microbes themselves do in their developments of resistances to antimicrobials, since it will be limited neither to starting from naturally-existing mechanomers nor to mechanomers of naturally-existing classes. Furthermore, it will be much faster than the microbial development of antimicrobial resistance.
Mechanomers preventing viral destruction of cells will be mechanomerically selected. At its simplest, such selection will take the form of parallel matricial mechanomeric selection: overlaying a set of parallel identical replicated random mechanomer matrices with, respectively, cytopalette cultures of as many different human cell types from as many different humans as practicable, and cultures of human microbial commensals (to avoid for example disturbing normal human gastrointestinal microflora and possibly facilitating fulminating toxic overgrowths); overlaying the human cell matrices with a solution of the virus in question; observing for regions where on the human cell matrices the cells do not die but on the microbial matrices no cells do, deaths signaled by mechanomeric indication for greatest sensitivity; extracting the random mechanomers from those regions from yet another parallel matrix; re-matriciating the mechanomers from each such region using different media to separate them; and repeating, until a specific and effective antiviral is selected. And just as with the mechanomeric selection of antimicrobials, multiple agents should be selected to overcome viral resistance to any one such and to reduce the amount of each such agent needed and therefore any side-effects therefrom, and such selection of antivirals will enjoy even greater flexibility and speed than viruses themselves do in their developments of resistances to antivirals.
Cytopalettes cultured from cell samples from individual patients will allow the custom selection of mechanomeric pharmaceuticals for use in idiotherapies, individual or customized therapies of refractory infections and idiopathic diseases, including cancers.
Mechanomers toxic to cancer cells but not to cells of their parent (or other normal) cell types will be mechanomerically selected, for the individualized mechanomeric oncotherapies necessitated by the individualized nature of cancers. Cancer cells are mutated cells, with at least one and usually multiple DNA abnormalities and consequently abnormal messenger RNAs transcribed from those DNAs and abnormal proteins translated from those RNAs, and the differences between such DNAs, RNAs and proteins and their normal versions will allow the mechanomeric selection of mechanomers which are toxic to such cells only (e.g., lethal enzymes activated by complexing with such abnormal proteins only). At its simplest, such selection will take the form of parallel matricial mechanomeric selection: overlaying a set of parallel identical replicated random mechanomer matrices with, respectively, a culture of the cancer cells in question, perhaps a culture of the parent cell-type of that cancer, and cytopalette cultures of as many other (normal) cell types generated and cultured from the patient as practicable; observing for regions where on the first matrix the cancer cells die but on the others none do, deaths signaled by mechanomeric indication for greatest sensitivity; extracting the random mechanomers from those regions from yet another parallel matrix; re-matriciating the mechanomers from each such region using different media to separate them; and repeating, until a set of individualized antineoplastic or oncotherapeutic mechanomers is selected. It is unlikely that even with the use of multiple oncotherapeutic mechanomers that all the cells of a cancer will be killed, and indeed some if not most cancers more or less steadily and rapidly mutate, so the mechanomeric oncotherapies of such cancers will therefore involve not only multiple mechanomers but also one or more extra passes or rounds of such multiplex therapy, as the cancer reoccurs to be re-sampled and a new set of oncotheraputic mechanomers selected to deal with it, with the majority of such cells destroyed by each pass, and a genetically-different minority left (if any) to begin again (note that even if not directly destroyed, the cells of such cancer held in check long enough should become ever more mutated, function ever more poorly, with ever greater numbers of its cells being fatally mutated, or exhibiting mutated proteins detectable and those cells therefore destroyed by the immune system, in what might be called "neoplastic burnout").
Cytopalette cells and tissues will be used for replenishment and replacement of tissues lost to injury or illness, including senescence, as well as the construction of organs for (more or less) autotransplantation.
As far as industrial applications of mechanomeric selection go, many expensive and/or toxic and/or otherwise hazardous industrial chemical catalysts will of course be replaced by mechanomerically selected enzymes. Such enzymes will catalyze many reactions at lower temperatures and pressures than at present, lowering energy use and cost, and many others in water rather than more expensive and/or toxic and/or otherwise hazardous solvents. Such catalysis due to enzymatic specificity will furthermore reduce side-reactions and increase the efficiency and economy of such reactions. And it will also allow new reactions to be developed and run as well, such as higher-order ones involving greater numbers of reactants at a time.
Most importantly, mechanomerically selected enzymes will afford artificial photosynthesis of fuels, organic chemical industrial feedstocks, and bulk nutrients such as cooking-oils and sugar, reversing the dumping of crustal carbon into the atmosphere over the last several centuries.
Thus the first glimpses of the new medicine and photosynthetic economy that will be afforded to us by mechanomeric selection.
The above, the fourth version of an analysis begun in 1992 as a private study of senescence and gerontotherapy, was based principally on two secondary sources:
Hendrickson, James; Cram, Donald; and Hammond, George. Organic Chemistry. Third Edition. New York: McGraw-Hill Book Company, 1970. The classic introduction to the classic science.
Alberts, Bruce; Johnson, Alexander; Lewis, Julian; Raff, Martin; Roberts, Keith; and Walter, Peter. Molecular Biology of the Cell. Third/Fourth Editions. Garland Science, 1994/2002. A tidal-wave of information on the core functions of the biopolymers.
Any errors in fact or analysis are of course the present author’s.
Keywords: antibiotic, antisenescent, antiviral, bionanotechnology, engineering, enzyme, mechanomeric selection, mechanomers, medicine, MeSe, molecular machine, nanotechnology, oncotherapy, artificial photosynthesis, virotherapy
Wednesday, January 11, 2012
Nomenclatural Change: EMD -> MeSe
I'm in the process of changing the name of the technology here from "empirical mechanomeric development (EMD)" to "mechanomeric selection (MeSe)":
The new name is of course analogous to "natural selection", in the same fashion as the "mechanomeric evolution" and "mechanomeric abiogenesis" already used (and I'm not altogether sure the last shouldn't be changed to "mechanomerogenesis", either), and the new acronym (pronounced if need be "meh-seh") is as far as I can tell unique, unlike the old.
This nomenclatural change is no big deal; "empirical mechanomeric development (EMD)" was previously referred to by me in my rough drafts and notes as "empirical biopolymeric development (EBD)", before I coined the better general neologism for functional copolymers, whether natural or artificial, "mechanomers" (reserving "biopolymers" for the natural mechanomers), and before that as "stochastic biopolymeric development (SBD)", and before that . . . .
The main annoyance with regard to this nomenclatural change is that the verb "develop" must generally be replaced with or accompany the verb "select" throughout all texts.
But the new nomenclature and language are better, and that's what counts.
The new name is of course analogous to "natural selection", in the same fashion as the "mechanomeric evolution" and "mechanomeric abiogenesis" already used (and I'm not altogether sure the last shouldn't be changed to "mechanomerogenesis", either), and the new acronym (pronounced if need be "meh-seh") is as far as I can tell unique, unlike the old.
This nomenclatural change is no big deal; "empirical mechanomeric development (EMD)" was previously referred to by me in my rough drafts and notes as "empirical biopolymeric development (EBD)", before I coined the better general neologism for functional copolymers, whether natural or artificial, "mechanomers" (reserving "biopolymers" for the natural mechanomers), and before that as "stochastic biopolymeric development (SBD)", and before that . . . .
The main annoyance with regard to this nomenclatural change is that the verb "develop" must generally be replaced with or accompany the verb "select" throughout all texts.
But the new nomenclature and language are better, and that's what counts.
Monday, August 15, 2011
That Doesn't Sound Very Sexy
Well, then, what about the mechanomeric selection of photoenzymes affording artificial photosynthesis of fuels, organic chemical industrial feedstocks, and bulk macronutrients, halting the alarming present-day massive industrial crustal-carbon fossil-fuel extraction and burning and consequent carbon dioxide emission and greenhouse warming; removing carbon dioxide from the atmosphere and "fixing" it into fuel and other stocks (not to mention all-but-eternal plastics), helping palliate the impact of previous extraction and burning and emission and warming; breaking the hold of the Fossil Fuel Cartel over the world, with its price-fixing, price-gouging and other corruption; and establishing the sustainable photosynthetic economy?
What Industrial Applications Are There for MeSe?
Many expensive and/or toxic and/or otherwise hazardous industrial chemical catalysts will be replaced by mechanomerically-selected enzymes.
Such enzymes will catalyze many reactions at lower temperatures and pressures than at present, lowering energy use and cost, and many others in water rather than more expensive and/or toxic and/or otherwise hazardous solvents.
Such catalysis due to enzymatic specificity will furthermore reduce side-reactions and increase the efficiency and economy of such reactions.
And it will also allow new reactions to be developed and run as well, such as higher-order ones involving greater numbers of reactants at a time.
Such enzymes will catalyze many reactions at lower temperatures and pressures than at present, lowering energy use and cost, and many others in water rather than more expensive and/or toxic and/or otherwise hazardous solvents.
Such catalysis due to enzymatic specificity will furthermore reduce side-reactions and increase the efficiency and economy of such reactions.
And it will also allow new reactions to be developed and run as well, such as higher-order ones involving greater numbers of reactants at a time.
Saturday, February 19, 2011
Can Oncotherapeutic (Anticancer) Mechanomers Be Mechanomerically Selected?
Mechanomers toxic to cancer cells but not to cells of their parent (or other normal) types can be mechanomerically selected, for the individualized oncotherapies or idiotherapies necessitated by the individualized nature of cancers.
Cancer cells are mutated cells, with at least one and usually multiple abnormal biopolymers (DNAs, messenger RNAs and proteins), and the differences between such biopolymers and their normal parent biopolymers will allow the mechanomeric selection of mechanomers which are toxic to such cells only (e.g., lethal enzymes activated by complexing with such abnormal biopolymers only).
At its simplest, such selection will take the form of parallel matricial mechanomeric selection: overlaying a set of parallel identical replicated random mechanomer matrices with, respectively, a culture of the cancer cells in question, perhaps a culture of the parent cell-type of that cancer, and cytopalette cultures of as many other (normal) cell types generated and cultured from the patient as practicable; observing for regions where on the first matrix the cancer cells die but on the others none do, deaths signaled by mechanomeric indication for greatest sensitivity; extracting the random mechanomers from those regions from yet another parallel matrix; re-matriciating the mechanomers from each such region using different media to separate them; and repeating, until a set of individualized antineoplastic or oncotherapeutic mechanomers is selected.
It is unlikely that even with the use of multiple oncotherapeutic mechanomers that all the cells of a cancer will be killed, and indeed some if not most cancers more or less steadily mutate, so the mechanomeric oncotherapies of such cancers will therefore involve not only multiple mechanomers but also one or more extra passes or rounds of such multiplex therapy, as the cancer reoccurs to be re-sampled and a new set of oncotheraputic mechanomers selected to deal with it, with the majority of such cells destroyed by each pass, and a genetically-different minority left (if any) to begin again (note that even if not directly destroyed, the cells of such cancer held in check long enough should become ever more mutated, function ever more poorly, with ever greater numbers of its cells being fatally mutated, or exhibiting mutated biopolymers detectable and those cells therefore destroyed by the immune system, in "neoplastic burnout").
Cancer cells are mutated cells, with at least one and usually multiple abnormal biopolymers (DNAs, messenger RNAs and proteins), and the differences between such biopolymers and their normal parent biopolymers will allow the mechanomeric selection of mechanomers which are toxic to such cells only (e.g., lethal enzymes activated by complexing with such abnormal biopolymers only).
At its simplest, such selection will take the form of parallel matricial mechanomeric selection: overlaying a set of parallel identical replicated random mechanomer matrices with, respectively, a culture of the cancer cells in question, perhaps a culture of the parent cell-type of that cancer, and cytopalette cultures of as many other (normal) cell types generated and cultured from the patient as practicable; observing for regions where on the first matrix the cancer cells die but on the others none do, deaths signaled by mechanomeric indication for greatest sensitivity; extracting the random mechanomers from those regions from yet another parallel matrix; re-matriciating the mechanomers from each such region using different media to separate them; and repeating, until a set of individualized antineoplastic or oncotherapeutic mechanomers is selected.
It is unlikely that even with the use of multiple oncotherapeutic mechanomers that all the cells of a cancer will be killed, and indeed some if not most cancers more or less steadily mutate, so the mechanomeric oncotherapies of such cancers will therefore involve not only multiple mechanomers but also one or more extra passes or rounds of such multiplex therapy, as the cancer reoccurs to be re-sampled and a new set of oncotheraputic mechanomers selected to deal with it, with the majority of such cells destroyed by each pass, and a genetically-different minority left (if any) to begin again (note that even if not directly destroyed, the cells of such cancer held in check long enough should become ever more mutated, function ever more poorly, with ever greater numbers of its cells being fatally mutated, or exhibiting mutated biopolymers detectable and those cells therefore destroyed by the immune system, in "neoplastic burnout").
Can Mechanomeric Antivirals Be Mechanomerically Selected?
Mechanomers preventing viral destruction of cells can be mechanomerically selected.
At its simplest, such selection will take the form of parallel matricial mechanomeric selection: overlaying a set of parallel identical replicated random mechanomer matrices with, respectively, cytopalette cultures of as many different human cell types from as many different humans as practicable, and cultures of human microbial commensals (to avoid for example disturbing normal human gastrointestinal microflora and possibly facilitating fulminating toxic overgrowths); overlaying the human cell matrices with a solution of the virus in question; observing for regions where on the human cell matrices the cells do not die but on the microbial matrices no cells do, deaths signaled by mechanomeric indication for greatest sensitivity; extracting the random mechanomers from those regions from yet another parallel matrix; re-matriciating the mechanomers from each such region using different media to separate them; and repeating, until a specific and effective antiviral is developed.
Note that such antiviral selection is even more flexible than viral development of resistance to antivirals, since mechanomeric selection of antivirals is limited neither to starting from naturally-existing mechanomers nor to mechanomers of naturally-existing classes.
Furthermore, it will be much faster than the viral development of antiviral resistance.
At its simplest, such selection will take the form of parallel matricial mechanomeric selection: overlaying a set of parallel identical replicated random mechanomer matrices with, respectively, cytopalette cultures of as many different human cell types from as many different humans as practicable, and cultures of human microbial commensals (to avoid for example disturbing normal human gastrointestinal microflora and possibly facilitating fulminating toxic overgrowths); overlaying the human cell matrices with a solution of the virus in question; observing for regions where on the human cell matrices the cells do not die but on the microbial matrices no cells do, deaths signaled by mechanomeric indication for greatest sensitivity; extracting the random mechanomers from those regions from yet another parallel matrix; re-matriciating the mechanomers from each such region using different media to separate them; and repeating, until a specific and effective antiviral is developed.
Note that such antiviral selection is even more flexible than viral development of resistance to antivirals, since mechanomeric selection of antivirals is limited neither to starting from naturally-existing mechanomers nor to mechanomers of naturally-existing classes.
Furthermore, it will be much faster than the viral development of antiviral resistance.
Thursday, February 17, 2011
Can Mechanomeric Antibiotics Be Mechanomerically Selected?
Mechanomers specifically toxic to microbes of a given species but not to those of other species or to humans can be mechanomerically selected.
At its simplest, such development will take the form of parallel matricial mechanomeric selection: overlaying a set of parallel identical replicated random mechanomer matrices with, respectively, a culture of the microbes in question, cultures of microbes of as many other species as practicable, both human commensals (to avoid for example disturbing normal human gastrointestinal microflora and possibly facilitating fulminating toxic overgrowths) and a selection of environmentally-significant species, and cytopalette cultures of as many different human cell types from as many different humans as practicable; observing for regions where on the first matrix the microbial cells die but on the others no cells do, deaths signaled by mechanomeric indication for greatest sensitivity; extracting the random mechanomers from those regions from yet another parallel matrix; re-matriciating the mechanomers from each such region using different media to separate them; and repeating, until a specific and effective antimicrobial is developed.
Note that such antimicrobial selection is even more flexible than microbial development of resistance to antimicrobials, since mechanomeric selection of antimicrobials is limited neither to starting from naturally-existing mechanomers nor to mechanomers of naturally-existing classes.
Furthermore, it will be much faster than the microbial development of resistance to antimicrobials.
At its simplest, such development will take the form of parallel matricial mechanomeric selection: overlaying a set of parallel identical replicated random mechanomer matrices with, respectively, a culture of the microbes in question, cultures of microbes of as many other species as practicable, both human commensals (to avoid for example disturbing normal human gastrointestinal microflora and possibly facilitating fulminating toxic overgrowths) and a selection of environmentally-significant species, and cytopalette cultures of as many different human cell types from as many different humans as practicable; observing for regions where on the first matrix the microbial cells die but on the others no cells do, deaths signaled by mechanomeric indication for greatest sensitivity; extracting the random mechanomers from those regions from yet another parallel matrix; re-matriciating the mechanomers from each such region using different media to separate them; and repeating, until a specific and effective antimicrobial is developed.
Note that such antimicrobial selection is even more flexible than microbial development of resistance to antimicrobials, since mechanomeric selection of antimicrobials is limited neither to starting from naturally-existing mechanomers nor to mechanomers of naturally-existing classes.
Furthermore, it will be much faster than the microbial development of resistance to antimicrobials.
Mechanomeric Selection Should Be Useful
The utility of mechanomeric selection is highlighted by its applications to itself in mechanomeric indication, mechanomeric evolution, mechanomerogenesis and other early mechanomeric selection including the development of cytopalettes.
Will Any Other Mechanomers Be Useful for Mechanomeric Selection?
Sets of mechanomers—growth hormones stimulating cell reproduction and cytodifferentiators converting cells of a sample type to those of others—will be developed and refined and expanded which allow construction of cytopalettes, sets of cultures of cells of different types, for use in matricial mechanomeric selective matricial overlays in parallel testing of mechanomers for toxicity (including environmental safety). Cytopalettes will include multicytotypic such as neuromuscular junctional cultures. Cytopalettes cultured from cell samples from individual patients will allow the custom selection of mechanomeric pharmaceuticals for use in idiotherapies, individual or customized therapies of refractory infections and idiopathic diseases, including cancers. And such cells and tissues will be used for replenishment and replacement, and the engineering of organs for (more or less) autotransplantation. And mechanomeric indicases or indicating systems should be developed for use with cytopalette cultures to indicate cell death and disfunction.
Where Will We Get the Enzymes Needed for Mechanomeric Selection?
The mechanomeric selective enzymes and other mechanomers will themselves be mechanomerically selected, in what is called here "early mechanomeric selection":
Replication being a more complex function than and indeed including polymerization, replicases must be more complex and therefore occur more rarely in random mechanomer stocks than polymerases, but cross-class replicase pairs, one from each of two mechanomer classes replicating mechanomers of the other, will evolve in what is called here "mechanomerogenesis" (analogous to abiogenesis), in which random mechanomers and monomers of both classes are mixed, and such replicases upon encountering one another engage in a more or less exponential course of mutual replication (with a more or less exponentially-increasing heat of replication), with the first such event and pair likely taking over the system. Many such events will produce same-class pairs, which pairs will also limit mechanomeric evolutionary system sizes, and many cross-class replicases produced will be incapable of replicating mechanomers incorporating monomers of all the kinds of the appropriate class supplied, and more or less inaccurate or fuzzy in their replication of the mechanomers they can replicate (such reduced-monomer-set replicases will often be workable until better ones are developed, and such fuzzy replicases will be useful for increasing the incidence of well-conformed mechanomers in random mechanomer stocks).
Once a workable replicase pair is developed, at least one polymerase of each class polymerizing monomers of the other will be developed by matricial mechanomeric selection, using random mechanomers synthesized by purely-chemical (non-enzyme-catalyzed) polymerization and then replicated. Such polymerase pairs must operate in the same directions as their classmate replicases, although replicases and polymerases operating in both directions will be developed to mechanomerically select mechanomers which in the course of synthesis coil in such ways as to bury the ends first synthesized and prevent replication, as well as those which vary in their conformations depending on direction of synthesis.
Replication being a more complex function than and indeed including polymerization, replicases must be more complex and therefore occur more rarely in random mechanomer stocks than polymerases, but cross-class replicase pairs, one from each of two mechanomer classes replicating mechanomers of the other, will evolve in what is called here "mechanomerogenesis" (analogous to abiogenesis), in which random mechanomers and monomers of both classes are mixed, and such replicases upon encountering one another engage in a more or less exponential course of mutual replication (with a more or less exponentially-increasing heat of replication), with the first such event and pair likely taking over the system. Many such events will produce same-class pairs, which pairs will also limit mechanomeric evolutionary system sizes, and many cross-class replicases produced will be incapable of replicating mechanomers incorporating monomers of all the kinds of the appropriate class supplied, and more or less inaccurate or fuzzy in their replication of the mechanomers they can replicate (such reduced-monomer-set replicases will often be workable until better ones are developed, and such fuzzy replicases will be useful for increasing the incidence of well-conformed mechanomers in random mechanomer stocks).
Once a workable replicase pair is developed, at least one polymerase of each class polymerizing monomers of the other will be developed by matricial mechanomeric selection, using random mechanomers synthesized by purely-chemical (non-enzyme-catalyzed) polymerization and then replicated. Such polymerase pairs must operate in the same directions as their classmate replicases, although replicases and polymerases operating in both directions will be developed to mechanomerically select mechanomers which in the course of synthesis coil in such ways as to bury the ends first synthesized and prevent replication, as well as those which vary in their conformations depending on direction of synthesis.
Will There Be Any More Advanced or Powerful Methods of Mechanomeric Selection?
Mechanomeric evolution, freely mixing unreplicated random mechanomers and monomers with a replicase complexed with a previously-mechanomerically-selected conditional replicase inhibitor which inhibits replication except under some condition resulting from the performance of the desired mechanomeric function, will test the greatest possible number of random mechanomers at a time for a desired function and therefore facilitate the development of mechanomers performing more complex functions and therefore occurring more infrequently in random mechanomer stocks. Mechanomeric evolutionary system sizes will be limited by same-class replicase-pair takeovers, and in such selection of any mechanomer the function of which is more complex than that of a mechanomer disinhibiting the replicase, false evolutions will outnumber true.
Mechanomeric Indication Should Be Useful in Many Other Contexts than Empirical Mechanomeric Developmental Matricial Analysis, Shouldn't It?
Yes, mechanomeric indicases or indicating systems should comprise one of the largest classes of mechanomerically-selected mechanomers, for use in science, engineering and medicine.
How Will Mechanomers Performing Desired Functions Be Detected in the Matrix?
Matricial analysis will of course use infrared spectroscopy and nuclear magnetic resonance imaging where appropriate. It will also use orthogonal analysis, by orthogonalization or third-dimensional separation of the matrix, for example by blotting the matrix into one end of and separating its components using a very wide chromatographic column (and orthogonal standards inoculated into the margin of the original square matrix marking in the orthogonal matrix or column planes or bands of interest). But matricial analysis will above all use mechanomeric indication, overlaying the matrix with a previously-mechanomerically-selected enzyme, an indicase, which under some condition resulting from the performance of the desired mechanomeric function catalyzes a reaction causing a color-change on the matrix. Such technique by its analysis at the molecular level, analysis by complexing, cumulative indication as colored indicator accumulates, and ability to use the product of one indicase to trigger another to amplify indication, will render most mechanomeric selection amenable to being performed as matricial mechanomeric selection. In such selection of any mechanomer the function of which is more complex than that of a simple enzyme catalyzing the indicating reaction, false indications will outnumber true, so multiple indicases should be developed and used to signal both true and false positives.
Matriciation Should Be Ordered, Shouldn't It?
Matriciation must be ordered—for example by affine chromatography, chromatographing a sample of a replicated random mechanomer stock using one chromatographic medium and blotting the resulting linear chromatogram into one side of a different medium and chromatographing that a right angle to the first, forming a square or two-dimensional matrix, perhaps itself blotted into a final test matrix and medium—to localize the replicands and effects of each different mechanomer in its characteristic location on the matrix, maximizing concentration of effect and minimizing gestation time (time for effect to accumulate to detectability) and analytical sensitivity needed; to perform parallel testing of mechanomers under different or incompatible conditions, using identical matriciations of multiple samples of a replicated random mechanomer stock and comparing mechanomer behaviors at their identical locations from matrix to matrix; to perform parallel recovery of mechanomers from a matrix parallel to a test matrix from which it would be difficult or impossible to recover the tested mechanomers; and to separate most mechanomers and therefore decrease mechanomeric interactions on and in the matrix, causing enzymes degrading mechanomers of their own class to preferentially degrade their own replicands.
How Will These Random Mechanomer Stocks Be Tested for Mechanomers Performing Desired Functions?
Matricial mechanomeric selection, analogous to antibiotic sensitivity testing, will be the simplest and most common form of such selection, at its own simplest matriciating (spreading and arraying) a sample of a replicated random mechanomer stock across or through or into a thin layer; overlaying that matrix with any materials and subjecting it to any other conditions needed for the desired function; analyzing the matrix identifying locations in which the desired function is being performed; extracting the mechanomers from those locations for further replication and testing, perhaps by another round of such development (using a different matriciation to redistribute the mechanomers in the sample); and replicating the mechanomer finally selected for its performance of the desired function for production.
Will Random Mechanomer Stocks Be Stable?
Depolymerases and other enzymes degrading mechanomers of their own class will occur in every random mechanomer stock and make it unstable. Such reactions and enzymes for the most part will be simple ones, the collective incidence of such enzymes in such stocks will be correspondingly high, such stocks will be correspondingly unstable, and such problems will be exacerbated by replication. Random mechanomer stocks should therefore be freshly prepared for mechanomeric selection. But if such stock must be stored it should be kept cold, decreasing reaction rates in general; dry, if depolymerization incorporates solvent into the free monomers, as with proteins, amino acids and water; and matriciated, separating most mechanomers in the stock and causing degradative enzymes to preferentially degrade their own replicands.
What Range of Gestations or Developmental Times Are We Talking About Here?
Ten thousand random proteins three hundred amino acids in length will collectively mass a little over six hundred attograms, which stock if replicated to one gram will average about 1.6 quadrillion replicands and one hundred micrograms of each protein, which replicands if of an enzyme each molecule of which produces ten product molecules per second each with the mass of an amino acid will take about four and a half minutes to produce one milligram of such, while one trillion such proteins will mass a little over sixty nanograms, which replicated to one gram will average about sixteen million replicands and a picogram of each, which as such enzyme will take about ten months to produce one microgram of product.
How Frequently Should Mechanomers Exercising Desired Functions Occur in Well-Conformed Random Mechanomer Stocks?
Proteins vary widely in the numbers and orders of the amino acids of which they are composed, but three hundred amino acids is a typical natural protein length and size, and if all proteins with all possible amino acid orders of that length were synthesized, the total mass of protein synthesized would be several hundred powers of ten times the mass of our galaxy. Plainly, if each and every protein function could be performed by only one specific protein with one specific amino acid order, no biological process or artificial procedure could ever develop such. But the evolution of proteins and other mechanomers, and the development and function of antibodies in the body, and vaccination and the development and use of antisera and monoclonal antibodies, all prove not only that mechanomers with different monomer orders can share a given function but that there must be a fantastically high degree of coincidence of function among them. Hundreds out of the millions of different antibodies in the body typically complex with a given antigen, which incidence of one in ten thousand is taken here to be that of such simplest function among well-conformed random mechanomers (taking the restriction of antibody complexing to its antigen binding site alone to cancel out multiple antibody complexing of different parts of antigen). And the greater the number of functions performed by a mechanomer, and the greater their complexities, the lower will be such incidence of such mechanomer, the incidence with two sites performing such functions taken here to be about one in ten thousand squared or one in one hundred million, and the incidence with three one in ten thousand cubed or one in one trillion.
Is There Anything Else to the Synthesis of These Random Mechanomers?
Proteins generally each assume a single stable conformation, or change between two or three conformations by way and in course of function, but perhaps fewer than one in one billion random amino acid orders specify such well-conformed proteins, and such incidence is taken here to be that of well-conformed mechanomers in random mechanomer stocks. Many mechanomeric functions might be performed by mechanomers which do not assume such conformations (if only because conformed by complexing in course and by way of function), and such incidence will be adequate for the mechanomeric selection of mechanomers performing the simplest functions anyway, but selection of mechanomers performing more complex functions will require use of some technique(s) for increasing such incidence. Three such techniques, in order of increasing complexity and decrease in synthesis of poorly-conformed mechanomers, are diagonalization (chromatographing random mechanomers along one side of a square medium or matrix and then at a right angle to the original direction until the spectrum lies largely along and is enriched in well-conformed mechanomers along the diagonal, well-conformed mechanomers being more sharply localized in chromatography, such mechanomers extracted and the procedure repeated, using different media), fuzzy replication (using an inaccurate or fuzzy replicase to replicate an original well-conformed mechanomer, perhaps with a function similar or even identical in part to that desired, and synthesize a random mechanomer stock, analogous to evolution), and splicing (of random or fuzzily-replicated segments into the appropriate areas of otherwise well-conformed mechanomers, analogous to antibody antigen binding site development, followed by replication to insure that those mechanomers assume the conformations they would have assumed upon continuous polymerization and will upon replication for production).
Where Do We Get These Mechanomers?
Random polymerization of a mixture of monomers of the different kinds of the appropriate class will produce a mixture of different random mechanomers of the desired class, a random mechanomer stock, and replication or molecular copying of the mechanomers in such stock a mixture of many replicands of each of those mechanomers, a replicated random mechanomer stock. Such stocks will be the fundamental tools of mechanomeric selection. And such polymerization and replication will be catalyzed by enzymes, at least one polymerase and replicase respectively, both of another class of mechanomer than that of those being synthesized to avoid unwanted operations upon those enzymes themselves, both operating in the same direction along and continuously upon the growing mechanomer during its synthesis to insure that the replicands have the same conformations as the original, and both themselves mechanomerically selected, in early mechanomeric selection.
So We Can Mechanomerically Select Proteins?
Nucleic acids should not be mechanomerically selected, to prevent unwanted genomic introductions. Mechanomer classes mechanomers of which are to be mechanomerically selected should not use naturally-existing monomers, to prevent naturalizations of replicative systems. And mechanomers of classes mechanomers of which are to be mechanomerically selected should be non-toxic and biodegradable.
Prove It
Mechanomers are developed in nature by variation of monomer order—and therefore of conformation, and therefore of shape, mechanical properties and surface structure, and therefore of function—followed by selection.
Evolution's scale, in numbers of mechanomers and selections and in time, keeps it from being proof that mechanomeric selection is practicable; but the development of each individual's antibody (protein) complement, and still more each duck's in the egg, and still more the primary immune response, and most of all vaccination and the development and use of antisera and monoclonal antibodies, furnish so many everyday small-scale proofs that proteins performing such more or less simple complexings or molecular recognitions as antibodies can be mechanomerically selected. Enzymes being so many more examples of such complexings can therefore be selected likewise. Proteins performing any equally simple functions or small combinations thereof likewise. Nucleic acids likewise. And mechanomers of other classes likewise.
Evolution's scale, in numbers of mechanomers and selections and in time, keeps it from being proof that mechanomeric selection is practicable; but the development of each individual's antibody (protein) complement, and still more each duck's in the egg, and still more the primary immune response, and most of all vaccination and the development and use of antisera and monoclonal antibodies, furnish so many everyday small-scale proofs that proteins performing such more or less simple complexings or molecular recognitions as antibodies can be mechanomerically selected. Enzymes being so many more examples of such complexings can therefore be selected likewise. Proteins performing any equally simple functions or small combinations thereof likewise. Nucleic acids likewise. And mechanomers of other classes likewise.
Wednesday, February 16, 2011
Can We Develop Mechanomers to Perform Desired Functions?
Mechanomers performing desired functions, such as enzymes and molecular machines, can be selected from among random mechanomers, mechanomers with random monomer orders, and therefore random conformations, and therefore random shapes, mechanical properties and surface structures, and therefore random functions, in what we call here "mechanomeric selection" (abbreviated "MeSe", and pronounced "meh-seh" if need be).
Why Are We Talking about Proteins Again?
We take proteins, the workhorses of the living cell, to be the type or classic mechanomers and biopolymers.
How Do Proteins Function?
Two proteins or other large molecules of complementary shape and surface charge-patterns upon being brought together will develop multiple attractions including hydrogen-bonds to one another, such fit and collective attraction being called an affinity and such collective bond a complex.
Protein complexing is so generally specific in its requirements of complementary shape and charge-pattern as to be described as “lock-and-key”.
And protein complexing is a fundamental mechanism of protein function:
The conformation-determining attractions and bonds of and within the protein itself can be considered intramolecular or internal complexing.
Cytostructural proteins complex with one another to form the internal structural framework of the cell called the cytoskeleton.
And every cell contains protein enzymes catalyzing—accelerating—the chemical reactions used by that cell, which reactions would otherwise run too slowly to be of use:
Body cells typically each synthesize thousands of different enzymes, and many molecules of each, each more or less specifically catalyzing its specific reaction operating upon its specific substrate(s) or reactant(s) (the phrase "lock-and-key" was first applied to enzyme specificity). And each enzyme catalyzes its reaction largely through, and its specificity is that of, not so much its complexing with its substrate(s) as with its reaction's rate-determining transition state, the highest-energy state through which that reaction must proceed, stabilizing and therefore lowering the energy of that state, allowing lower-energy passage through that state, increasing the probability that a given enzyme-substrate complex will have the energy needed to pass through that state, and therefore, in the cell or other reaction mixture where many such complexes are forming and dissociating, increasing the number of such able to pass through that state and their reactions proceed to completion at any given time, and therefore the overall rate of reaction.
In addition, many enzymes catalyze water-sensitive reactions in their hydrophobic cores.
More complicatedly, many if not most proteins function by virtue of conformation changes, changing back and forth between two or more conformations in the course and by way of function, a phenomenon called allostery, and complexing is frequently combined in protein function with allosteric conformation changes. Protein complexing of one molecule causing an allosteric conformation change in that protein enabling or preventing subsequent complexing of another molecule is a central mechanism of protein function and control in the cell; for example, some enzymes, including some acting as cell switches, sensors or governors, are activated or deactivated—turned on or off—by conformation changes caused by complexing with or dissociating from the appropriate molecules, some used specifically as signals. And other protein enzymes catalyze the degradation of fuel and use the energy yielded to repetitively alter their conformations and shapes, acting as motors and machines.
Protein complexing is so generally specific in its requirements of complementary shape and charge-pattern as to be described as “lock-and-key”.
And protein complexing is a fundamental mechanism of protein function:
The conformation-determining attractions and bonds of and within the protein itself can be considered intramolecular or internal complexing.
Cytostructural proteins complex with one another to form the internal structural framework of the cell called the cytoskeleton.
And every cell contains protein enzymes catalyzing—accelerating—the chemical reactions used by that cell, which reactions would otherwise run too slowly to be of use:
Body cells typically each synthesize thousands of different enzymes, and many molecules of each, each more or less specifically catalyzing its specific reaction operating upon its specific substrate(s) or reactant(s) (the phrase "lock-and-key" was first applied to enzyme specificity). And each enzyme catalyzes its reaction largely through, and its specificity is that of, not so much its complexing with its substrate(s) as with its reaction's rate-determining transition state, the highest-energy state through which that reaction must proceed, stabilizing and therefore lowering the energy of that state, allowing lower-energy passage through that state, increasing the probability that a given enzyme-substrate complex will have the energy needed to pass through that state, and therefore, in the cell or other reaction mixture where many such complexes are forming and dissociating, increasing the number of such able to pass through that state and their reactions proceed to completion at any given time, and therefore the overall rate of reaction.
In addition, many enzymes catalyze water-sensitive reactions in their hydrophobic cores.
More complicatedly, many if not most proteins function by virtue of conformation changes, changing back and forth between two or more conformations in the course and by way of function, a phenomenon called allostery, and complexing is frequently combined in protein function with allosteric conformation changes. Protein complexing of one molecule causing an allosteric conformation change in that protein enabling or preventing subsequent complexing of another molecule is a central mechanism of protein function and control in the cell; for example, some enzymes, including some acting as cell switches, sensors or governors, are activated or deactivated—turned on or off—by conformation changes caused by complexing with or dissociating from the appropriate molecules, some used specifically as signals. And other protein enzymes catalyze the degradation of fuel and use the energy yielded to repetitively alter their conformations and shapes, acting as motors and machines.
Does Protein Conformation Matter?
Protein conformation determines protein shape, whether globular, elongated or flattened, and whether solid, indented or hollow; protein mechanical properties, such as whether and how one part of a protein can bend or rotate with respect to the rest; and protein surface structure, the protein’s surface shape and pattern of exposed side-groups and backbone units.
Do Protein Amino Acid Orders Matter?
Proteins can rotate around their backbone single bonds, and therefore all along their backbones, and consequently twist and coil, but the proteins which perform the functions of the cell generally assume three-dimensional coiled structures or conformations specific to their kinds, stabilized in various ways.
For example, attractions between positively- and negatively-charged moieties of molecules form what are called hydrogen bonds, which separately are weaker but collectively can be much stronger than any one molecular bond.
Such bonds between nearby backbone units along the protein backbone cause the assumption of winding or helical conformations along the backbone, as well as sheet conformations involving multiple turns and side-by-side runs thereof. Such interactions and resulting conformations are not specific to any particular protein or moiety thereof, since every backbone unit is identical to and can form the same such bonds as any other, and any stretch of backbone could theoretically engage in any such conformation.
Slightly more specifically, the backbone units and some side-groups hydrogen-bond water molecules, and proteins tend to coil in such a way as to present such water-soluble or hydrophilic moieties or groups on their surfaces, and hold those side-groups which cannot form such bonds inside, in water-insoluble or hydrophobic cores.
But in most of the proteins which perform the functions of the cell, conformation is specified by side-group interactions, which depend on the kinds of side-groups available and the order in which they occur, which depend in turn on which amino acids are incorporated into the protein and the order in which they are incorporated.
That is, protein amino acid order determines protein conformation.
For example, attractions between positively- and negatively-charged moieties of molecules form what are called hydrogen bonds, which separately are weaker but collectively can be much stronger than any one molecular bond.
Such bonds between nearby backbone units along the protein backbone cause the assumption of winding or helical conformations along the backbone, as well as sheet conformations involving multiple turns and side-by-side runs thereof. Such interactions and resulting conformations are not specific to any particular protein or moiety thereof, since every backbone unit is identical to and can form the same such bonds as any other, and any stretch of backbone could theoretically engage in any such conformation.
Slightly more specifically, the backbone units and some side-groups hydrogen-bond water molecules, and proteins tend to coil in such a way as to present such water-soluble or hydrophilic moieties or groups on their surfaces, and hold those side-groups which cannot form such bonds inside, in water-insoluble or hydrophobic cores.
But in most of the proteins which perform the functions of the cell, conformation is specified by side-group interactions, which depend on the kinds of side-groups available and the order in which they occur, which depend in turn on which amino acids are incorporated into the protein and the order in which they are incorporated.
That is, protein amino acid order determines protein conformation.
How Big Are Proteins?
Proteins of different kinds and functions vary widely in the number of amino acids of which they are composed.
But three hundred amino acids is a typical natural protein length and size.
And a typical average natural protein mass can be calculated based on that length and size by multiplying the average mass of an amino acid (see "What Are the Protein Monomers") times three hundred, and then subtracting the combined masses of the two hundred and ninety-nine water molecule equivalents lost ("What Are the Protein Monomers"), amounting to about 6.16 * 10-20 gram, about sixty zeptograms, a little over two thousand times the mass of a water molecule.
And the corresponding typical average natural protein gram number, the number of such proteins contained in one gram thereof, can be calculated by dividing that mass into one gram, giving about 1.62 * 1019 or about sixteen quintillion such proteins per gram.
But three hundred amino acids is a typical natural protein length and size.
And a typical average natural protein mass can be calculated based on that length and size by multiplying the average mass of an amino acid (see "What Are the Protein Monomers") times three hundred, and then subtracting the combined masses of the two hundred and ninety-nine water molecule equivalents lost ("What Are the Protein Monomers"), amounting to about 6.16 * 10-20 gram, about sixty zeptograms, a little over two thousand times the mass of a water molecule.
And the corresponding typical average natural protein gram number, the number of such proteins contained in one gram thereof, can be calculated by dividing that mass into one gram, giving about 1.62 * 1019 or about sixteen quintillion such proteins per gram.
How Do Their Amino Acids Fit into Proteins?
The invariant moieties of the amino acids incorporated into a protein, minus water of polymerization, comprise what is called its backbone, an elongated and repetitive structure in which each invariant moiety remnant incorporated forms a unit identical to every other (although of course the end-units each bear a free bonding group unused in polymerization).
And the prosthetic groups of those amino acids become protein side-groups projecting from those protein backbone units and that backbone.
And the prosthetic groups of those amino acids become protein side-groups projecting from those protein backbone units and that backbone.
What Are the Protein Monomers?
Proteins are synthesized from monomers called amino acids, of which there are twenty different kinds.
The amino acids are small molecules, composed of only ten to twenty-seven atoms each, depending on kind, averaging about twenty, and averaging in mass about 2.35 * 10-22 gram, about one-quarter of one zeptogram (sextillionth of a gram), or 235 yoctograms (septillionths of a gram), about eight times as much as the three-atom water molecule, an oxygen atom single-bonded to each of two hydrogen atoms (an oxygen atom forms two single bonds or one double bond in a molecule, while a hydrogen atom forms one single), the total mass of which is about 2.99 * 10-23 gram, or thirty yoctograms.
Every amino acid molecule consists of a central carbon atom single-bonded to a hydrogen atom, an amino group, a carboxylic acid group and a prosthetic group (a carbon atom forms four single bonds in a molecule, or one double bond and two singles, or two double bonds, or one triple bond and one single).
An amino group is composed of a nitrogen atom (which forms three single bonds, or one double and one single, or one triple) single-bonded to each of two hydrogen atoms.
And a carboxylic acid group is composed of a carbonyl group or moiety, a carbon double-bonded to an oxygen atom, further single-bonded to a hydroxy or alcohol group, an oxygen atom single-bonded to a hydrogen atom.
Such bonds and groups are of course the ordinary molecular bonds and functional groups of carbon chemistry, called "organic chemistry" due to life's taking such advantage of the ability of carbon to form large and stable molecules that all carbon on the face of the earth is or has been part of a living organism.
And the amino acid amino and carboxylic acid groups are of course what gives it its name.
Every amino acid is identical to every other in the above, regardless of kind, in a nine-atom moiety called here its invariant moiety, composed of its central carbon atom and the hydrogen atom and amino and carboxylic acid groups bonded to it.
And an amino acid of one kind differs from one of another solely in the elemental composition (the kinds and number of atoms involved), structure (how those atoms are bonded together) and consequent properties of its prosthetic group.
The amino acids are small molecules, composed of only ten to twenty-seven atoms each, depending on kind, averaging about twenty, and averaging in mass about 2.35 * 10-22 gram, about one-quarter of one zeptogram (sextillionth of a gram), or 235 yoctograms (septillionths of a gram), about eight times as much as the three-atom water molecule, an oxygen atom single-bonded to each of two hydrogen atoms (an oxygen atom forms two single bonds or one double bond in a molecule, while a hydrogen atom forms one single), the total mass of which is about 2.99 * 10-23 gram, or thirty yoctograms.
Every amino acid molecule consists of a central carbon atom single-bonded to a hydrogen atom, an amino group, a carboxylic acid group and a prosthetic group (a carbon atom forms four single bonds in a molecule, or one double bond and two singles, or two double bonds, or one triple bond and one single).
An amino group is composed of a nitrogen atom (which forms three single bonds, or one double and one single, or one triple) single-bonded to each of two hydrogen atoms.
And a carboxylic acid group is composed of a carbonyl group or moiety, a carbon double-bonded to an oxygen atom, further single-bonded to a hydroxy or alcohol group, an oxygen atom single-bonded to a hydrogen atom.
Such bonds and groups are of course the ordinary molecular bonds and functional groups of carbon chemistry, called "organic chemistry" due to life's taking such advantage of the ability of carbon to form large and stable molecules that all carbon on the face of the earth is or has been part of a living organism.
And the amino acid amino and carboxylic acid groups are of course what gives it its name.
Every amino acid is identical to every other in the above, regardless of kind, in a nine-atom moiety called here its invariant moiety, composed of its central carbon atom and the hydrogen atom and amino and carboxylic acid groups bonded to it.
And an amino acid of one kind differs from one of another solely in the elemental composition (the kinds and number of atoms involved), structure (how those atoms are bonded together) and consequent properties of its prosthetic group.
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