Purpose of the theory

Introduction

- Description of the mathematical model
- Parallel between the mathematics division and the translation of the mRNA .
- Why the Base 21
- Example using base 21

- The role of periodicals
- Division without any return and endless.
- Special property of the last figure of a Base
- Periodical stopped by the repetition of a same figure to the dividend
- Notion of complementary figures and sequences portraits
- (Concepts developed for the needs of the mathematical model)

- List of Sequences Portraits and complementary figures at the base 10
- List of possible quotients at the base 21
- (For all figures of the base).

- List of sequences portraits at the base 21
- (Those generating all the figures of the base, except the complementary figures))

- List of sequences portraits and complementary figures at the base 21.
- Protection of the integrity of the coded message.

- Basic programs
- IBPOLY-A.ba
- IBGEN-21.ba
- IBGEN-20.ba
- IBADN-21.ba
- IBADN-20.ba
- IBSEQUEN.ba
- IBTAB-CO.ba
- IBQUO-PO.ba

- Mathematical Model and Genetic Code
- (New approach concerning the understanding of genetic code and emergence of new features listed below)

- Correlation between the Mathematical Model and the Living.
- Codon: Instruction in 3 steps
- Non-specificity CODON - AMINO ACID.
- ( Degeneration of the code??? Questions to be asked )

- Quantification numbering of the RNAm bases and angular quantification of Amino Acids.
- Numerical classification of Amino Acids versus the Three-dimensional Shape of proteins.
- (Discussed with more details as provided under Chapter VI.).

Numerical classification of Amino Acids allows to update :

2 characteristics of classification

- The assignment of figures to Amino Acids: The first characteristic of classification, figures which

would represent the identification of amino acids. - The value of the figure given to the amino acid: Characteristic outcome of the first one, a value of

the figure which would be probably dependent on the role to play by the amino acid at the level of

angles in connection with the other amino acids.

- (Discussed with more details as provided under Chapter VI.).
- Division: its interpretation on the translation side of the mRNA
- Example of the implementation of the division concept in the automation process.
- Example of a pathway towards a detailed step by step understanding in the base 10.
- Schema of the path at the base 10
- Schema of the path at the base 21

- Example of the implementation of the division concept in the automation process.
- For a good automation of the division .
- Case of the complementary figures
- "Rule for the comprehension in the use of a complementary figure.”
- Application of the rule of comprehension regarding the use of a complementary figure.
- Case going from sequence 4 to sequence 5
- Case going from sequence 5 to sequence 4
- To see a more detailed image of what is happening at the level of the sequences portraits (See the table 7.1.5a " visualization of the rule of understanding in using the complementary figure)
- Example at the base 21 involving complementary figures.
- Representation under another form of the example 7.1.6 involving complementary figures and Fig. 7.1.7a - Application of the rule of the complementary figure at the base 21 ((example 7.1.6 reused)
- Example for calculation of positions for complementary figures .
- Table of positions for complementary figures
- "In summary", regarding the use of the complementary figure .

- The 3 sources contributing to the optimization of a good automation of the division when using sequences portraits.
- The first source: dividing into 2 parts.
- Properties of the mathematical model at the origin of the automation of the division.
- The implementation of certain criteria that support the automation of the division.

- First part: Properties of the mathematical model at the origin of the automation.
.
- The sequences portraits to remember (typical sequences portraits).
- The gap between the figures making up the sequences portraits (their role).
- The effect of inertia, emergent property which come out from the results of divisions performed from eligible combinations; results of inertia applied as a criterion .

- Second part: The implementation of certain criteria supporting the automation of the division.
- The presence of the complementary figure at the requested sequence portrait level during the processing of the manual or automated division .
- The choice made on the figure(or amino acid) to reach or as a wanted choice, at all the 3 positions at the level of the quotient .
- The increase of the inertia effect searched on the use of sequence portraits coming from eligible combinations.

- The second source: The selection of an ideal combination among those eligible. Ideal combination related to the selected sequences portraits with which we will operate.
- The third source: The construction of the mRNA. Construction using the tables of RNA Construction data recorded by using the mRNA constructs table on Excel file called "Construction of the mRNA Table" .

- The first source: dividing into 2 parts.
- Thorough explanation of the 3 sources.
- (contributing to an optimization of a good automated division during the use of sequencesportraits) .

- The first source: dividing into 2 parts.
- Properties of the mathematical model at the origin of the automation of the division.
- The implementation of certain criteria that support the automation of the division

- First part:
Properties of the mathematical model at the origin of the automation of the division.
- Typical sequences portraits.
- Table 7.3.1a - " Typical Sequences Portraits that are possible at the base 21".
- The gap between figures composing sequences portraits.
- Table 7.3.1b - Gaps between the figures composing the sequences portraits
- Table 7.3.1c – Schematic diagram of the ribosome, the holder of the division “First hypothesis” .
- Table 7.3.1d - Schematic diagram of the ribosome, the holder of the division “second hypothesis ".

- The effect of inertia:Emergent property which come out from the results of the divisions performed from
eligible combinations; results of inertia applied as a criterion.
- Mathematical visualization characterizing "the effect of inertia" Using the 7.3.1e table " Effect of inertia: Resistance against a malfunction of the division by the sequences portraits." .
- Setting up of the table of restD and flexibility .

Table 7.3.1f - Table of the restD of the sequences portraits. (portrait format) .

Table 7.3.1g - Table of restD of the sequences portrait. (landscape format). - Quotient (normal division) and quotient (sequences portraits division) .
- Some 9 comments for a further explanation of the table 7.3.1e in order to understand better.
- In the top part of the table. Table 7.3.1h -This table indicates the origin of the restD on line B and C of the table 7.31e.
- For the bottom part of the table. Table 7.3.1i - Example of the annex table IIa showing the origin of the restD providing the de- velopment of the table of the sequences portraits restD at the level of the tables 7.3.1f or 7.3.1g
- For a same quotient obtained for a same position.
- If the gap between the two restD for a given position.
- The acceptable gap so that we may have a same quotient. Table 7.3.1j - Table of a detailed construction of a mRNA for a figure (or a base) one at a time, taking into account the inertia.
- That is this detailed flexibility.
- For negative differences between restD.
- The role of the sequences portraits restD table.
- Range or bracket of 20 (table of 20) .

- Second Part: The implementation of certain criteria supporting the automation of the division.
- The presence of the complementary figure at the requested sequence portrait level during the processing of the manual or automated division .
- The choice made on the figure ( or amino acid ) to reach or as a wanted choice, at all the 3 positions at the level of the quotient.
- The increase of the inertia effect searched on the use of the sequence portraits coming from eligible combinations.

- The second source: Coming from the selection of an ideal combination among those being eligible.
- The selection of an ideal combination
- Behavior of eligible combinations at the level of a certain number of performed divisions.
- Compiled results based on 2 classification criteria.
- First classification criterion: "Compilation of the number of different results".
- Second criterion of classification: "Compilation of the number of peaks for different figures".

- The third source: The one coming from the construction of mRNA using RNA table and the mRNA
construction table.
- The role of the RNA table allows us to perform 2 tasks:.
- The first task: Role of combination eliminations.
- The second task: Role of construction of the mRNA.

- Illustration of a page forming a RNA table.
- Example of a graphic linked to a page of RNA table.
- Graphic linked at the bottom of a RNA table page .
- Construction table of the mRNA ( on Excel )

- The role of the RNA table allows us to perform 2 tasks:.

- Manual or automated division: Application at the base 21.
- Example of division at the base 21.
- Combination used 1 3 U O
- Combination used 3 9 Q O
- Combination used 1 3 7 O
- Combination used 1 Q E U
- Combination used 1 Q E O
- Combination used 1 Q E O
- Combination used 1 Q E O

- Case of the complementary figures
- The problem of the ideal combination.
- Step 1: Selection by the typical sequences portraits.
- Typical séquences portraits table.
- Calculation of the number of possible combinations from the dividends of 8 typical sequences portraits.
- List of possible combinations from the dividends of 8 typical séquences portraits.

- Step 2: Selection based on the graphics from RNA tables.
- Example of a page from a mRNA table.
- Graphic example linked to a page of RNA table.
- Graphic linked at the bottom of each of the 20 pages constituting a RNA table .

- List of combinations with at most 6 missing figures.

- Step 3: Selection from the best behavior of the remaining combinations.
- List of the 10 divisions: (Step 3: Selection from the best behavior).
- Example of division made by computer from the IBgen21.BA basic program.

- The 2 classification criteria of possible combinations.
- Distribution of the results of differences: Manual division versus division made by a computer at the level of the 10 divisions for the 15 combinations.
- Table listing the discrepancy.

- Application of 2 classification criteria.
- Table of classification according to 2 selection criteria . .....
- Three dimensional graphic ranking of the first 8 from the 15 remaining combinations.
- Three dimensional graphic ranking of the last 7 from the 15 remaining combinations.

- Distribution of the results of differences: Manual division versus division made by a computer at the level of the 10 divisions for the 15 combinations.

- The choice of the combination.
- Possible ways for the classification.

- Step 1: Selection by the typical sequences portraits.

- Description and Use of the Theoretical Mathematical Model(Use and Application of the model to the gene.)
- Its use (via the description of tools necessary to its use) )
- Regarding computer programs.
- Schema of organization.

- Division operation at the base 21 through the conversion table 10 / 21 .
- Conversion table base 10 / 21.
- Construction tables of mRNA.
- Construction card of mRNA.

- Regarding computer programs.
- Its application : (raising the problem of the construction of a gene).
- Explanation of the Table of RNA.
- Example about a table of RNA.
- Dummy example of the construction of a mRNA using the tables of RNA from the values assigned to the bases A, G, C, U and to a predetermined choice of amino acids to which have been also assigned values through the base 21.
- Conclusion.
- Pattern of distribution found in bacteria.
- Pattern of distribution found in animal cells.
- List of amino acids.

- Its use (via the description of tools necessary to its use) )
- Amino acids and three-dimensional shape versus theoretical model.
- Structure and purpose of the chapter.
- The "Why or the mathematical reason"
- Amino acids and three-dimensional shape.
- Existence of parameters allowing the development of the three-dimensional shape.
- The protein folding "matter of chance? "

- The dynamic features of an amino acid .
- Mechanical aspect of the internal movement of an amino acid.
- Internal movement of an amino acid.
- -Schema: Showing the mechanical aspect of the internal movement of an amino acid.

- Amino acid, seen from a different perspective.
- -Schema: View of the infrastructure of an amino acid from another perspective .

- Internal movement of an amino acid.
- Description and characterization of the peptide link between two amino acids.
- - Schema: Formation of the peptide link by elimination of a water molecule.
- - Schema: Internal mechanical aspect of the internal movement of several amino acids and partial character of a double bond of the peptide link.
- - Schema: Mechanical aspect of the internal movement of amino acids.

- Classification of amino acids.
- - List of 20 amino acids used in the composition of a protein (first part).
- - Continuation of the list of amino acids (second part).

- Mechanical aspect of the internal movement of an amino acid.
- Relationship between amino acids "Possible Classification" .
- Mathematical modal versus relationship between amino acids.
- - Table: Couples / Angles of direction (first part).
- - Table: Couples / Angles of direction (second part).

- Hypothesis on how to determine the angle of a pair of amino acids.
- Three-dimensional direction possibilities determined by the axes of an amino acid.
- -Schema: Representing the possibilities of three-dimensional directions determined by the 2 axes of rotation of an amino acid.

- Hypothesis of visualization of directions of an angle coming from a couple of amino acids.
- Neutralization of the angle of direction of the first amino acid and determination of the tridimensional angle by the second amino acid.
- Scheme: Hypothesis of visualization of direction of the angle coming from a couple of amino acids.

- Three-dimensional direction possibilities determined by the axes of an amino acid.

- Mathematical modal versus relationship between amino acids.
- Tridimensional shape versus the mathematical model (What does the mathematical model allow us to consider).
- What the current genetic code cannot even consider.

- The case of the addition of Poly - A (animal cell) to mRNA versus the theoretical model.
- Role of the poly – A : We no longer know!
- Figure VI a : Maturation of a mRNA.
- Meaning of Poly – A : in the context of the theory presented in this book.
- End of the sentence signal.
- Security measure.

- Figure VI b : Hypothesis on the Poly - A ensuring the achievement of a completion of the end of the sentence signal.

- Assessment of the number of adenine required in order to achieve the zero state
- (The evaluation is being done in 3 steps)

- First and third steps: Table showing the developed strands and the achieved results.
- Graphics : number of adenine used after the cut versus the addition for figures from 1 to 20.
- Second step: Input of calculation parameters in the computer with the Program - Poly-A.
- Testing frequency.
- Beginning of the verification.
- Labeling of amino acids.

- For the assessment of the number of adenine required in order to achieve the zero state.
- A frequency of verification at every 3 quotients was retained.
- Beginning of the verification in position 1 has been retained.
- A start of labeling in position 1 has been retained.

- Another occurrence about the input of the parameters.
- Results of the calculations with the computer: (see annex XV)
- Conclusion :
- Roles developed and assigned to the poly - A.
- Poly - U and a tryptophan operon.
- Case of the poly-U located at the end of mRNA coding for the tryptophan operon.
- Case of the poly - U located at the end of the tryptophan operon LEADER.
- Low concentration in tryptophan.
- High concentration in tryptophan.

- Epilogue.
- About the poly-A (poly-U) versus the current theory of the genetic code

- Cancer , types de dommage, réparation et non réparation
- ( Introduction et généralité )

- Le problème du cancer. ( Point de vue des connaissances actuelles )
- Définition du cancer.
- Type de cancer.
- Carcinome.
- Sarcome.
- Leucémie.
- Leucémie Aigue.
- Leucémie chronique.

- Définition : Leucémie chronique Myéloide (Myélome)
- Définition : Leucémie chronique Lymphoide (lymphome)

- Cancer : La théorie la plus acceptée actuellement.
- Agents cancérigènes responsables de dommages causés à l’ ADN .
- Agents physiques.
- Composés inorganiques.
- Composés organiques.
- Agents parasiteurs.

- Altération de l ’ ADN et Types de dommages.
- Altération de l’ ADN ( Type de mécanismes responsables)
- Type de dommages:
- Une base incorrecte sur un brin.
- Bases manquantes.
- Modification de bases.
- Le bris de un des 2 brins composant l’ ADN .
- Le bris des deux brins de l’ ADN.
- Cross – linking.

- Schématisation des dommages et réparations.
- Base incorrecte sur un brin ne pouvant former de liens hydrogène avec la base correspondante sur l’autre brin.
- Dommage dû à une erreur de réplication.
- Dommage dû à une désamination.
- Exemple de désamination :
- ( transition cytosine -> uracile )

- Bases manquantes ( dépurination )
- Modification des bases ( dimère de thymines )
- Types de réparation

- Excision.
- Photoréactivation.
- Postréplication recombinaison.
- SOS Repair.
- Résumé du point 1.6.3 ; Modification des bases.

- Le bris de un des deux brins composant l’ ADN.
- Le bris des deux brins de l’ ADN.
- Le cross-linking.
- Type d’adducteur causant les cross-linking.
- Cross-linking Interstrand ( avec adducteur moléculaire ).
- Cross-linking Intrastrand ( avec adducteur moléculaire ).
- Cross-linking ( avec adducteur protéinique ).

- Cross-linking et réparation.

- Type d’adducteur causant les cross-linking.

- Base incorrecte sur un brin ne pouvant former de liens hydrogène avec la base correspondante sur l’autre brin.
- Segmentation de l’ ADN et formation d’ ARNm incomplet.
- Dimère de thymines et fragmentation de l’ ADN.
- Rencontre de la polymérase III avec un dimère de thymines et hypothèse de formation d` ARNm incomplets ou de type brisé.
- Segmentation possible de l’ ADN contenant des dimères de thymines.
- Le premier type de segmentation
- ( Impliqué dans la recombinaison postréplicative)

- Schéma : Hypothèse de formation d’ARNm incomplets ou de type brisé.

- Le deuxième type de segmentation
- Schéma : Hypothèse de formation d’ARNm incomplets ou de type brisé.

- Hypothèse de formation d’ARNm incomplets ou de type brisé.
- Conditions nécessaires à la formation d’ARNm incomplets ou de type brisé.

- Le premier type de segmentation

- Autres types de dommages et fragmentation de l’ADN
- Le bris de un des 2 brins ==> segmentations possibles
- Le bris des 2 brins ==> segmentations possibles
- Le cross-linking ==> segmentations possibles
- Cas de l’anémie de Fanconi

- L’ expérience de strasbourg ou la preuve indirecte possible de l’existence dans le cytoplasme de la cellule, d’ ARNm incomplets traduits en protéines par les ribosomes.
- Syndrome de Cockayne.
- Xeroderma pigmentosum.

- Conclusion

- Dimère de thymines et fragmentation de l’ ADN.

- Cancer et Biomathématique
- Nouvelle approche théorique du cancer.
- Le problème du cancer : un non lieu.
- Le potentiel de la biomathématique et de la bioinformatique comme outil de travail.

- Approche biomathématique du cancer.
- - Figure 10 .A : Exemple d’ une division déclencheur de périodique.

- Hypothèse sur la boucle de procédure déduit à partir du modèle mathématique.
- Visualisation à partir du concept de la division.
- - Figure 10.b : Visualisation à partir du concept de la division.

- Visualisation au moyen du concept de la transposition de la division en procédé d’automatisation par le biais des séquences portraits.
- - Figure 10.c : Visualisation au moyen du procédé d’automatisation.

- Comment d’un point de vue hypothétique, le mécanisme d’un périodique peut-être expliqué ou compris au niveau d’une division effectuée au moyen des séquences portraits.
- - Figure 10.d : Visualisation de la boucle au niveau des séquences portraits.

- Visualisation à partir du concept de la division.

- Nouvelle approche théorique du cancer.

---FIN De ce que j'ai de traduit.-----

© Michel Dulac 2006-2021

Webmaster: Agena