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DNA Random Mutation Simulator v.1.1
Staff  

 

User's Guide

 

Introduction

This simulator is a program that allows simulating the effects of random mutations on a sub-set of a DNA strain of a genome. A DNA string is a sequence of A, C, T, G nucleotides (or bases). To simplify, DNA is composed of two parts: coding DNA (which contains genes codifying for proteins) and non coding DNA, or "junk DNA" (whose functions aren't yet well known). The non coding portion is the greatest part of DNA. The simulator deals with coding DNA only. Only point mutations will be considered, namely mutations substituting a nucleotide into another nucleotide. The user can decide how many mutations to apply at every step and see the result of that step. Moreover he can choice how many steps to run and see the final result. A triplet (or codon) of nucleotides (from the set A, C, T, G) determines an amino acid (e.g. AAG -> Lys - Lysine). Usually a set of triplets ending with a STOP codon defines a "gene". A same amino acid can be coded by different codons, according to the "genetic code". A gene is a "recipe" for a protein. The complex process from a gene to a protein is composed of two parts: (1) the transcription, the synthesis of mRNA from DNA and (2) the translation, the synthesis of protein from mRNA. The simulation ends when all genes are non functional.

 

What to do

It's easy. The user can choice the number of mutations (1, 4, 10, 100) and the type of display (DNA, mRNA, amino acids). Then the user hits the "Mutate" button and, after that the simulator has randomly drawn the mutation sites, he can see the output on the "DNA display window". The "Reset" button creates a new DNA string without mutations. Above the buttons there are the parameter's values. Many of them change during the simulation. Primary representation is DNA. Display can also be mRNA and amino acids (secondary representations). On the bottom right there is also a sort of Morse-code-like display of the genes. A fully functional gene is a continuous line. More the line is discontinuous or interrupted more the gene is defective. When all genes are non functional the program alerts that the simulation is finished and forces the user to Reset.

 

How the simulator works

This simulator considers only four different types of point mutations.

 

  • Beneficial Mutations (flagged by Cyan color). They happen when a base change convert the codon to a codon of a different amino acid getting a "better" gene (protein functionality is increased). These mutations are very rare and their implications are insignificant.
  • Neutral Mutations (flagged by Green color). They happen when a base change convert the codon to a codon of the same amino acid (protein functionality is preserved). A mutation in a STOP codon is considered neutral when changes a STOP codon into another STOP codon.
  • Dangerous Mutations (flagged by Yellow color). A mutation in a STOP codon is dangerous when changes a STOP codon into an  amino acid codon (protein with non functional "tail"). A mutation converting an amino acid into another amino acid is dangerous (protein may be non functional).
  • Lethal Mutations (flagged by Red color). A mutation converting a codon into a STOP codon is lethal (protein is incomplete and non functional, gene destroyed). When a third mutation adds to two pre-existing dangerous mutations in the same gene is considered lethal (protein non functional and gene inactive).

 

At every step the simulator calculates the CSI of the DNA strain. CSI is a concept introduced by Intelligent Design Theory. It represents a measure of the Complex Specified Information of a system, in this case a part of a genome. Its measure unit is "bits" (as digital information according to Shannon). When a gene is destroyed the overall CSI decreases (because the CSI of a non functional gene becomes zero). When all genes of the DNA string are destroyed the CSI is zero and that DNA strain is considered functionally destroyed (simulation end).

 

Conclusion

Neo-Darwinian macroevolution is based on random genetic mutations and natural selection. The program is "generous" with Darwinism in at least three senses:

 

  • Neutral mutations (happen when a base change convert the codon to a codon of the same amino acid) are practically neutral only for coding DNA. For non coding DNA it's likely they aren't neutral. In other words synonymous changes in molecular cellular operations aren't always neutral. May be synonymous substitutions are an additional way of encoding information.
  • Only the third consecutive dangerous mutation in a gene is flagged "lethal" and the gene is considered destroyed (non functional). Two dangerous mutations in a gene are considered tolerable by the simulator. May be reality is less generous.
  • The strain of genome is considered destroyed (CSI = 0 and "game over") when all its genes are non functional. In real life organisms fall ill (and die) for far less.

 

In spite of its "generosity", at the very end this simulator allows seeing as real "beneficial" mutations are practically inexistent. The consequence is that Darwinian macroevolution, fully based on them, cannot generate new information. De facto random mutations can only decrease information, namely the DNA CSI. During the simulation sessions the CSI value is always decreasing. Without creating new information, without adding new CSI from the outside, no system can increase its internal organization. As Norbert Wiener said: "The amount of information in a system is a measure of its organization degree" (Cybernetics, Introduction). As a consequence, the alleged macroevolution of biological systems (species), from common simpler ancestors is impossible by mean of genetic random mutations and natural selection.

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