Needless to say, but this post has been a long time coming. Shortly after my last post, I started working on a computer program that would simulate natural selection using organisms whose properties where based on its genome as opposed to simply programmed properties. Also, I wanted to make sure that the selection process on the organisms where as close to pure natural selection as possible, while staying away from artificial selection. In other words, I wanted to defining factor to be based on reproductive success, as opposed to a pre-programmed goal (such as fastest runner, etc.).
At first, the programming was going great, I had spent quite a few months working on it, and I had a working program and was beginning to compile samples and results. That's when everything went to hell. A seemingly insignificant crack on the side of my laptop eventually split the screen from the main body of laptop, which broke the cord between the screen and the main body, and sent a short circuit to the hard drive, destroying all the information contained. Not only did I loose the program, I also lost almost a years work in other programs, and 3D models (for a space station I was building with Orbiter).
Needless to say, loosing months and months of data, programs, and 3D models rather killed my enthusiasm. Eventually however, I did get back to re-creating the program. The first incarnation was made mostly at my work while I worked on the night shift, and one of my colleagues would always ask my if I was "playing with my dots" (the organisms in the program are represented by little squares). So when I started my new program, I decided to officially name it DOTS (DNA Over Time Simulator). It's not entirely the most accurate title, namely that the program also simulates RNA as well as DNA, in fact, when the program was first written, it only simulated RNA.
Introduction
Genes
| Alanine/A | GCT, GCC, GCA, GCG | Leucine/L | TTA, TTG, CTT, CTC, CTA, CTG |
| Arginine/R | CGT, CGC, CGA, CGG, AGA, AGG | Lysine/K | AAA, AAG |
| Asparagine/N | AAT, AAC | Methionine/M | ATG |
| Aspartic acid/D | GAT, GAC | Phenylalanine/F | TTT, TTC |
| Cysteine/C | TGT, TGC | Proline/P | CCT, CCC, CCA, CCG |
| Glutamine/Q | CAA, CAG | Serine/S | TCT, TCC, TCA, TCG, AGT, AGC |
| Glutamic acid/E | GAA, GAG | Threonine/T | ACT, ACC, ACA, ACG |
| Glycine/G | GGT, GGC, GGA, GGG | Tryptophan/W | TGG |
| Histidine/H | CAT, CAC | Tyrosine/Y | TAT, TAC |
| Isoleucine/I | ATT, ATC, ATA | Valine/V | GTT, GTC, GTA, GTG |
| START/M | ATG | STOP/* | TAG, TGA, TAA |
When the program is started, a list of genes is created. The code used for the genes is the same as used in all eukaryotic organisms[1]. RNA organisms in the program all use the same code, the only difference is that the nucleotide for Thymine (T) is written as a Uracil (U) instead, however this has no major effect on the coding itself. All genes are composed of an amino acid for Methionine (the start codon), and a stop marker. An example of a gene would be "MDDTWRKPRstop".
However since many of these amino acids can be expressed in different ways, there are many different strings of nucleotides that can code for those amino acids, for example:
| M D D T W R K P R * |
| ATG GAC GAC ACA TGG AGG AAG CCG CGT TGA |
| ATG GAC GAT ACC TGG AGG AAG CCA CGA TAA |
| ATG GAT GAC ACT TGG CGC AAA CCT CGC TAG |
Each gene that an organism has subtracts energy from the organism, based on the length of the gene. The longer the gene, the more energy it uses. At present, there are 9 different types of genes programmed. If a gene appears in an organism that doesn't appear as any of the functional gene lists, it will still subtract energy while providing no other effect on the organism, and is labeled as a Pseudogene. The different functional types of genes are:
Herbivore Genes: These extract energy from the environment. The amount of energy available to each organism is based on a number of factors. Firstly, is the maximum amount of energy the herbivore gene can extract. Secondly, the amount of surrounding squares that are unoccupied. Only squares that have no organisms (other then its own) can provide energy, so the more open squares, the more energy available. Conversely, the fewer organisms that surround each of those open squares allows for the open square to provide more energy itself. Lastly, there is a maximum amount of energy that each square can provide. For example, if the maximum amount available is set to 500, and the gene's maximum available energy was 700 (or the total of all the herbivore genes), then even if every square was open, and every square around those were open, then the organism could still only extract 500 from the environment.
Asexual Reproduction Genes: These allow an organism to reproduce independently of a mate, and are the most basic (and currently only) form of reproduction creating a clone of the parent organism. The more Asexual Reproduction Genes an organism has, the more offspring it can produce at a time (for example, if it has 3 genes, then it can produce 3 offspring at a time, assuming that many open squares are available). If an organism lacks an Asexual Reproduction Gene, then it will be sterile, and unable to reproduce.
Attack Genes: If there are other organisms surrounding the organism with an attack gene, it will randomly select one and try to kill it. Each Attack Gene that an organism has, adds one attack point to it.
Defense Genes: Each defense genes that an organism has, adds one defense point to it.
Carnivore Genes: These genes allow an organism to extract energy from any other organisms that it kills. The amount of energy extracted from a kill is based on the length of the prey's genome, and the efficiency of the gene. The more efficient the gene, or the longer the prey's genome, the more energy extracted. The amount available also depends on if the organism it is consuming is a herbivore (full efficiency), and omnivore (half efficiency), or another carnivore (fifth efficiency). If an organism has more then one carnivore gene, then the organism's total carnivore efficiency is an average of the genes efficiency.
Altruistic Genes: Organisms that contain one of these genes are stopped from attacking other organisms of the same species. Whether or not an organism is deemed as the same species, is based on how similar its genomes are. For example, if an organism shared 95% of its DNA in common with its prey, and its Altruistic Gene was set at 6%, then it would consider it the same species and would not attack. However, if the same organism had an Altruistic Gene set at just 4%, then it would deem the prey as another species, and continue its attack.
Transcription Error Protection Genes (TEP Genes): These genes control the amount of error during transcription when an organism reproduces. It a TEP Gene has a value of 1%, then there is a 1% chance every time a nucleotide is transcribed during reproduction, that a nucleotide will be duplicated, skipped, or changed. If an organism lacks a TEP Gene, then the chances of error sky-rocket, rendering it almost infertile, as any offspring of its will likely lack any functioning genes due to widespread error. If an organism contains multiple TEP genes, then the organism's Transcription Error will be an average of its TEP genes.
Offspring Energy Transfer Genes (OEP Genes): Organisms containing this gene, pass on a percentage of its energy to its offspring when it reproduces. The percentage of its energy that it passes on differs between each OEP Gene, and if an organism has more then one, then it averages the percentages between the genes.
Movement Genes: These genes give an organism the ability to move to an adjacent square. In herbivores, it will move the organism to the most open square available, in carnivores it moves it to an open square that is adjacent to other organisms. The more Movement Genes an organism has, the less energy is needed during movement.
Genes do not have to match the genes in the lists 100%. Genes that match only partially (down to a certain percentage, the default is a minimum 60% match), work with reduced effectiveness. In Herbivore Genes for example, a partially match reduces the amount of herbivore energy that the gene can extract from the environment. For Carnivore Genes, it reduces the genes carnivore efficiency. Another effect of a gene needing to be only partially matched is that a gene may match (or partially match) many different genes, and therefore a single gene may take on multiple abilities.
Below is an example of an organism and the genes it contains. It contains 1474 nucleotides (or 737 base pairs) contains both partial genes, a short pseudogene, and was born after 2442 turns:
| TTAGGGAAAAAAACCCCGGGATAACCAGGTCCAAAAGACTTTTTTCCCTC
AATCCCTTTTTTTGGGGCCCTATTGGTCCAGGTTTTCTGAAAAAAGGGAG CAAACTATTTCACTCCCTCCATTTTAGGGTATTTTTTGGGGGACGCCTCA
GTTTGATAAAGTGAGGGAGGTAAAATCCCATAAAAAACCCCCTGCGGAGT AACAAGGGGAAGTGGAGCCCCGGAGGATACCCGCCCTCAGTGGAAAGCAT
TTGTTCCCCTTCACCTCGGGGCCTCCTATGGGCGGGAGTCACCTTTCGTA GCATTTTTTTCACTAGCCGGTCCTGGTGGGCAACGAAAAACCGAGCTTGG
CGTAAAAAAAGTGATCGGCCAGGACCACCCGTTGCTTTTTGGCTCGAACC CTAAACCGGACAATAACTTCCGCGGGTTTTGGGGCTCCCCCAAAGGTGCC
GATTTGGCCTGTTATTGAAGGCGCCCAAAACCCCGAGGGGGTTTCCACGG GAGGGGATTTTGGGGCGGCGAAAAAGAGTTTCGCCGTAGAACCCCCAAGG
CTCCCCTAAAACCCCGCCGCTTTTTCTCAAAGCGGCATCTTGGGGGTTCC GAGGCGCAAGGGCCAATTTCACGGGAGGTATAGGTTCACTTCCATAGACA
CTCCGCGTTCCCGGTTAAAGTGCCCTCCATATCCAAGTGAAGGTATCTGT CATAAACGTTTTCCCAAGTACCCCCTAAAGGGCCTCCAAAGAAAGGGGGA
GTATTTGCAAAAGGGTTCATGGGGGATTTCCCGGAGGTTTCTTTCCCCCT AGCTCCCGTAAAAAACAAAACGTTGGTCGGGGGGGTCTTTTTGAGGGGGA
TCGAGGGCATTTTTTGTTTTGCAACCAGCCCCCCCAGAAAAACTCCCCCT GCCGGGTCCGGTGGTAGTCCTAAGGTGATAGGGATTTGTTGGCGGGGTGG
CGGCCCAGGCCACCATCAGGATTCCACTATCCCTAAACAACCGCCCCACC TTTTTCTGCTATTAAAACAAATTTTTTACTCCATTGGGCGCGCCCCAGCC
AAAAAGACGATAATTTTGTTTAAAAAATGAGGTAACCCGCGCGGGGTCGG GTTGTTTCCTCGCCCAATGTTTGCGGTTCCTTAACCCCAGTGGTCGTAAC
CAACAAAGGAGCGGGTTACAAACGCCAAGGAATTGGGGTCACCAGCATTG CCCCGCTTCGGGGCGCAGCCCTTCCGAAACCACCAACCAAAGCTTTAATA
GGGGCGAAGCCCCGCGTCGGGAAGGCTTTGGTGGTTGGTTTCGAAATTAT GCTCGAATCACAGTTTCCCTTTGGGGGGGCGGGGGGGCCCCAGGGTAAGA
CGAGCTTAGTGTCAAAGGGAAACCCCCCCGCCCCCCCGGGGTCCCATTCT AAACGGGGGGGGAAGCCCCTGTCCGGACAAAACTGTA
TTTGCCCCCCCCTTCGGGGACAGGCCTGTTTTGACAT |
The genes contained in the organism are:
| Herbivore Gene 1 100% | M H F F H * ATGCATTTTTTTCACTAG |
| | |
| Herbivore Gene 13 80% | M F A V P * ATGTTTGCGGTTCCTTAA |
| | |
| Pseudogene | M E * ATGGAGTAA |
| | |
| TEP Gene 1 100% | M C L W K * ATGTGTCTATGGAAGTGA |
| | |
| Herbivore Gene 1 80% + Asexual Reproduction Gene 1 60% | M H A F H * ATGCATGCTTTCCACTGA |
| | |
| Herbivore Gene 13 60% + Asexual Reproduction Gene 26 80% | M E G V K * ATGGAGGGAGTGAAATAG |
Organisms
After the list of genes are created, the program then creates the organisms. It starts with a creating a genome for a master organism, and then duplicates it across the grid. The grid the organisms live on consists of 50 rows and 100 columns, totaling 5000 squares. The starting genome consists of a Herbivore Gene, TEP Gene, an Asexual Reproduction Gene, and "junk DNA" spread out between and around the genes randomly. When the junk DNA is made, the letters "ATG" and "CAT" (the reverse synonym for ATG) are prevented from appearing so as no pseudogenes appear that would interfere with the starting three 3 genes, however if one of the working genes contain CAT in it, then a pseudogene will appear on the opposite side of the gene. The 3 active genes can appear in any order, and on other the 5' (5 prime, read left-to-right) or 3' (3 prime, read right-to-left) side of the genome. Below is an example of a first generation organism, it contains 1308 nucleotides (654 base pairs) and is the ancestor of the organism shown above:
| ATTTAGAGCGAACCGTGCGGCCGCTATTGATCAAGTTTCTGCTAACAGCG
TAAATCTCGCTTGGCACGCCGGCGATAACTAGTTCAAAGACGATTGTCGC AACTAAATCAGTTGACCTCTACAACCGGAACAGCCGAAGGAAGGAGGTGC
TTGATTTAGTCAACTGGAGATGTTGGCCTTGTCGGCTTCCTTCCTCCACG TTCTTTGCCGACTCAGTCGAAACGAATGCATTTCTTTCACTGAGTCTATC
AAGAAACGGCTGAGTCAGCTTTGCTTACGTAAAGAAAGTGACTCAGATAG CTCTCAAGAAAGAACGAAGCACACTCGGCGTACTGACAGCAGGCAACAGG
GAGAGTTCTTTCTTGCTTCGTGTGAGCCGCATGACTGTCGTCCGTTGTCC CACTCCCCAAAAGTAGGGGTTGACACTGTGAGGAATAACTGCCTTGGCTC
GTGAGGGGTTTTCATCCCCAACTGTGACACTCCTTATTGACGGAACCGAG GGTTAGACGACGCAACCCCAAAAAGTGCCCAATTTAGATTACTTCCATAG
CCAATCTGCTGCGTTGGGGTTTTTCACGGGTTAAATCTAATGAAGGTATC ACACATAAGAACCCGGAATTAGTCTCTTCCTAGGAAAAGGTCTATTTGTA
TGTGTATTCTTGGGCCTTAATCAGAGAAGGATCCTTTTCCAGATAAACAT TTAGATCAACTAGAGTTGCAGAGGCTCAGTCGCGAAACGCTCAGGGAGTC
AATCTAGTTGATCTCAACGTCTCCGAGTCAGCGCTTTGCGAGTCCCTCAG AGACTACAATACGTTATCTGTTGTAGAGCTTTTGTAATACCGTTGGTACC
TCTGATGTTATGCAATAGACAACATCTCGAAAACATTATGGCAACCATGG ACAAGTTCGGCTGTGCGCGTCGAGGAATCAAATGAGCGCGTTTGCTTGAC
TGTTCAAGCCGACACGCGCAGCTCCTTAGTTTACTCGCGCAAACGAACTG GGGCACAGTAAACTTCCCACCCAATAGAGAAGGTGATATCTAGCGACCTA
CCCGTGTCATTTGAAGGGTGGGTTATCTCTTCCACTATAGATCGCTGGAT ATCAGCCACGTCCGATCCACGTACGTGGCGTCCTCGCGTTCGCCAGTCTT
TAGTCGGTGCAGGCTAGGTGCATGCACCGCAGGAGCGCAAGCGGTCAGAA AGTGTTAAGAGAGAGTCAAGAAGTAAGTGCCTGCGACGGATATTCCGCCA
TCACAATTCTCTCTCAGTTCTTCATTCACGGACGCTGCCTATAAGGCGGT ATAG
TATC |
The genes contained in the organism are:
| Herbivore Gene 100% | M H F F H * ATGCATTTCTTTCACTGA |
|
|
|
| Asexual Reproduction Gene 100% | M S A F A * ATGAGCGCGTTTGCTTGA |
|
|
|
| TEP Gene 1 100% | M C L W K * ATGTGTCTATGGAAGTAA |
|
|
|
| Pseudogene | M H S F R L S R Q R S T S F L R L F R L * ATGCATTCGTTTCGACTGAGTCGGCAAAGAAGCACCTCCTTCCTTCGGCTGTTCCGGTTGTAG |
Virtually all of the organisms features and properties are encoded by its genome and the genes therein. The only properties that are coded separately are the organisms Life Expectancy (when it dies of old age), and its Age of Maturity (the age it can begin to reproduce). Each of these provide various advantages and disadvantages. The later the Life Expectancy, the more chances an organism will be able to reproduce, but the more energy the organism will need to reproduce. The earlier an organism matures, the sooner it can reproduce, however the later it matures, its attack points, defense points, and OET efficiency goes up.
Asexual Reproduction
When an organism reproduces, it transcribes the nucleotides of the 5' strand, and then mirrors it for the 3' side. Every time a transcription is made, there is a chance (as dictated by the organism's TEP genes) for error. The nucleotide may be altered, omitted, or be copied twice. Each type of error has an equal chance of occurring. Life Expectancy and Age of Maturity also can change during reproduction. Life Expectancy and Age of Maturity, separately, can either increase, decrease, or stay the same with equal chance of each happening. Below are the first 50 nucleotides of the 5' side of a first generation organism, and three 2nd generation offspring.
| First Generation | CACTATCCTCAGCTAACGATCCCACTATACTCTCACCAAGATTTTTAAGG |
| 9th point substitution | CACTATCCACAGCTAACGATCCCACTATACTCTCACCAAGATTTTTAAGG |
| 29th point deletion | CACTATCCTCAGCTAACGATCCCACTATCTCTCACCAAGATTTTTAAGGA |
| 37th point duplication | CACTATCCTCAGCTAACGATCCCACTATACTCTCACCCAAGATTTTTAAG |
Combat
If an organism contains at least 1 attack gene, it may attack an organism in an adjacent square (either horizontally, vertically or diagonally). In the program, the organism attacking is known as the predator, and the organism being attacked becomes the prey. If the prey has attack genes of its own, then the organisms attack properties are matched up against each other. If one organism's attack points are higher then the other, it does not guarantee victory. Each organisms attack points are multiplied by separate random numbers. Therefore a predator with an attack point value of 2 attacking a prey with an attack point value of 1 will be twice as likely to win, but not automatically guaranteed.
After the initial attack phase, comes an attack/defense phase. If the prey wins the attack phase of combat, then the roles in the attack/defense phase are reversed. The predator's attack points come up against the prey's defense points in the same style as the attack phase. The predator's attack points are multiplied by a random number, and the prey's defense points are multiplied by a separate random number, with the higher number winning. If the predator wins, then the prey is killed (and consumed if the predator is a carnivore/omnivore). If the predator loses, and the prey's defense is successful, then both sides survive. Both attacking and defending consume energy. If an organism's energy falls below zero as a result of the combat, then the organism dies.
Results
Speciation
 -output7.dfx  -output9.dfx | As the adjacent graph shows, that despite the fact that the scenario begins with just a single species, diversity increases rapidly and then fluctuates between 30 and 35 percent (with default TEP Genes set at 1%). The drop at the end is the result of a new gene evolving that incorporated an Attack Gene, a Asexual Reproduction Gene, and an Altruistic Gene, along with a slightly more efficient TEP Gene. This drop is typical when an organism evolves that has significant advantages over other organisms, and quickly replace the organisms without the advantage. In scenarios where a TEP gene emerges that is more effective then the starting one, diversity drops as the organisms containing the more efficient TEP gene quickly replaces those without (since their offspring are more likely to survive). Once they become the dominate group, new species take longer to evolve (due to less mutations each generation), those keeping the diversity down. For example, the scenario in output9.dfx, the organisms don't even reach 20% before a more efficient TEP Gene emerges. The average chance of transcription error drops down to 0.236%, however since this includes organisms lacking a TEP Gene (therefore having a transcription error of 20%), the actual efficiency of the TEP Gene is even higher then that (error rate of about 0.025%). The error protection of the gene is so powerful, that once the organisms with the gene takeover, the genetic diversity drops down to 0% (all organisms are the same species). Evolution still occurs, however the rate of change becomes very slow, and diversity remains low. |
Emergent Behavior and Phenomena
Along with the reproduction behaviors and combat behaviors programmed into the organisms by their genes, their are a few "emergent" behaviors that appear that result from the interactions between organisms, that are not coded in.
Base-pair Repetition: After a number of generations, it becomes apparent that many base-pair sequences begin to repeat themselves. In the two example organisms above, the first generation organism contains a total of 27 repetitions greater then 3, the longest of which was a sequence that lasted 5 spaces, and 6 sequences lasting 4 squares. While the organism from Turn #2442 contains a total of 85 repetitions greater then 3, the longest sequence lasting 8 spaces. The purpose of the repetitions seems to work as a safeguard against the formation of unwanted pseudogenes by stopping the formation of ATG sites. Due to the repetitions, potential sites for an ATG codons to appear (doublets of "AT" or "TG") decrease. If the first generation organism there are 103 possible sites for a single-point mutation to create an ATG codon, whereas the 2442 Turn organism contains just 85 sites, despite being 13% longer then the first generation organism.
 -World of organisms containing movement genes  -World of organisms lacking movement genes | Pack/Anti-Pack Formation: To the right is two screenshots of organisms after about 150 turns. In the top screenshot, the world started out with organisms containing Movement Genes. In the bottom screenshot, the organisms started without them. In the world populated by organisms containing Movement genes, the organisms spread out, forming a checkerboard pattern, however when they can no longer spread out, they begin to form into columns and files, forming patterns similar to that of coral. The emergent behavior is due simply to each organism looking to find the most open space possible. When there is enough space for each organism to have completely open adjacent squares, they form the checkerboard pattern, otherwise, they form the coral shape pattern. In scenarios where the organisms lack movement genes, the organisms do not spread out, and simple stay near other members of there species, former scattered clumps of organisms. When the clumps become too big and the organisms in the center can no longer provide energy for themselves (or can no longer reproduce), they die off and the clumps break apart into smaller clumps. |
Multiple Partial Genes: Along with base-pair repetition, another emergent property in the DNA of the organisms is the tendency for genes to evolve to make multiple partial matches, as opposed to a single 100% match. This is caused by the fact it is easier to modify existing genes then it is to create new ones. Below is an example of an omnivore that evolved after 1102 turns, and contains 665 base-pairs (1330 nucleotides), where most of its functioning genes have evolved towards incorporating multiple gene types as opposed to evolving genes that match 100%. The long Pseudogene at the end of the 3' side does not actually contain a stop codon, instead stopping only because it has hit the end of the genome:
| AGGTCCGGTCTAAATTAACTTTTTTCCTACCCCTTATTAAGGAAAAACCC
TCCAGGCCAGATTTAATTGAAAAAAGGATGGGGAATAATTCCTTTTTGGG CTCCCCAAGGAGGTGGCCTTATTAATCGGGGGGCTGTACATTTTACAAAT
GAGGGGTTCCTCCACCGGAATAATTAGCCCCCCGACATGTAAAATGTTTA AATAAAAAAACCCGTGTGCATGGAACCCTTAACTTAAAGTGTTCCGGAAA
TTATTTTTTTGGGCACACGTACCTTGGGAATTGAATTTCACAAGGCCTTT AGCGGCTGAAGCTATTATATACCTTCAGGAGCCTCGAATAAATCTTAACT
TCGCCGACTTCGATAATATATGGAAGTCCTCGGAGCTTATTTAGAATTGA GTTGGAGGTTTCTACGGAAAGAAATCAGCCGTTTGTATTCAAATACGTAT
CAACCTCCAAAGATGCCTTTCTTTAGTCGGCAAACATAAGTTTATGCATA TTTAAATGCTTTACTAGAAGAAACCACGGGGCCGAAACGCGCCCTTTTTT
AAATTTACGAAATGATCTTCTTTGGTGCCCCGGCTTTGCGCGGGAAAAAA AACGATGCGGAGAGCTCGCTAGAAAAATGCAGAAGAGGGCTTAAGCCGGA
TTGCTACGCCTCTCGAGCGATCTTTTTACGTCTTCTCCCGAATTCGGCCT AAATAGACGGCTGAAACGGCTCGGAAGTCTTATAGGTTTCAACTCTACTG
TTTATCTGCCGACTTTGCCGAGCCTTCAGAATATCCAAAGTTGAGATGAC GAGCAGAGCCACTCCCCCGAGGTATAAAAGTTTCTTGAAAGACCACCCTG
CTCGTCTCGGTGAGGGGGCTCCATATTTTCAAAGAACTTTCTGGTGGGAC TTCACCGAAGTCTGGGTTACAAGTTTATATCTTAATGCCTTGTCCGCAGT
AAGTGGCTTCAGACCCAATGTTCAAATATAGAATTACGGAACAGGCGTCA AGGGCTTTACACACAAACGGTAAACAGCGGGAATTAAAATTACCCCCCCG
TCCCGAAATGTGTGTTTGCCATTTGTCGCCCTTAATTTTAATGGGGGGGC GAAAAAATTTTTATTGGGACCCCCTTCAGACGGCGGCTACGTTTTTCTTT
CTTTTTTAAAAATAACCCTGGGGGAAGTCTGCCGCCGATGCAAAAAGAAA TGGTTAAAACGGCTTAGAGTACAAATCGCCTTTTGGCGAAAGCAGGACCC
ACCAATTTTGCCGAATCTCATGTTTAGCGGAAAACCGCTTTCGTCCTGGG GTAAAACCCCTGTTA
CATTTTGGGGACAAT |
The genes contained in the organism are:
| Herbivore Gene 33 60% | M E P L T * ATGGAACCCTTAACTTAA |
|
|
|
| Pseudogene | M L Y * ATGCTTTACTAG |
|
|
|
| Herbivore Gene 37 60% + Carnivore Gene 1 60% + Asexual Reproduction Gene 1 60% | M R R A R * ATGCGGAGAGCTCGCTAG |
|
|
|
| Attack Gene 5 60% + Asexual Reproduction Gene 42 60% | M Q K R A * ATGCAGAAGAGGGCTTAA |
| | |
| Herbivore Gene 1 80% + Herbivore Gene 15 60% + TEP Gene 16 60% | M P C P Q * ATGCCTTGTCCGCAGTAG |
| | |
| Pseudogene | M H T G F F I I C K M Y S P P I ATGCACACGGGTTTTTTTATTATTTGTAAAATGTACAGCCCCCCGATT N K A T S L G R G F S L I R G R AATAAGGCCACCTCCTTGGGGAGGGGTTTTTCCTTAATAAGGGGTAGG K K V N L D R T * AAAAAAGTTAATTTAGACCGGACCT |
|  -output6.dfx  -Omnivore "explosion" | Carnivore Rise and Falls: In early simulations when the program lacked an Age of Maturity (and thus could immediately reproduce), the scenarios often went through two major stages of development (see output2.dfx and output3.dfx). In the first stage, the world was dominated by herbivores. Once the herbivores evolved to a point where they couldn't extract any more energy from the environment and became densely populated, omnivores (and to a lesser degree carnivores) evolved and quickly took over. Carnivores and omnivores did emerge before this, however the population wasn't dense enough for them to take over. One of the immediate effects of the omnivores was a massive drop in the average age of the population from about half the average maximum age, to just over 1.5 turns, and the average life expectancy dropping as well (in output3.dfx in settled to an average of about 5 turns). After an Age of Maturity was introduced, the sudden onset of carnivores either happened much later, or not at all (the more common occurrence). However, even when omnivores/carnivores never took over, omnivores/carnivores often still appeared when the world became densely populated. However instead of a world dominated by omnivores forming, the carnivores would consume all the local organisms close to them, followed by their offspring doing the same, until the "explosion" of omnivores or carnivores expanded too far, and then would either die off from consuming all the local organisms or from killing each other. However once the herbivores had repopulated to area, any surviving omnivores (or any newly evolved ones) would repeat the cycle. In cases where the carnivores or omnivores contain altruistic genes, the omnivores would be able to spread out even farther without collapse, and even balance out with the herbivores. The omnivore/carnivore "explosions" can be seen in the data by short term rising and falling of omnivores and carnivores in the data. |
Genome Length
 - output5.dfx  - Genome composition by percent (output6.dfx) | In all but 1 output, there was a general increase in genome length over time, with the organisms at the end having longer genomes then the starting organisms (output1.dfx showed an increase of over 350 nucleotides). However, a longer genome is not always better. In many cases a shorter genome can be better. While shorter genomes seem to be more prone to the appearance of harmful pseudogenes (due to fewer repeating sequences), they are therefore also more likely to evolve new beneficial genes. This is exemplified the most by output4.dfx, that decreased by approximately 150 nucleotides over the span of its run. Decreases in genome length typically seem to occur during periods of large-scale change (such as the emergence of wide-spread carnivores in output2.dfx and output3.dfx), forming a pattern of long-term lengthening, interspaced with short periods of shortening. Also, along with longer genome lengths, there is a general increase in the percent of useful information over time as the organisms evolve to use more of their "junk" DNA. Also, most simulations also show a decrease in the amount of pseudogene information in the organisms, in both amount and percent. |
Future Development
Save Function: An ability to stop a simulation, save it, and re-open it later. This would allow for much longer simulation runs.
Multiple Environments: At current, the "world" consists of a single environment. An organism that can survive on one square, can survive on any other square. Multiple environments, such as a temperature gradient, or land/water areas may change the way creatures evolve, and create different niches for organisms to survive and evolve in, more similar to what is seen in reality.
New Genes: Along with new environments, new genes to allow organisms to survive in them, such as a gene for breathing in water, and another for breathing on land, or genes for surviving in different temperature zones. Also, a gene for eating decaying material, so when an organism dies (and is not consumed by a carnivore), it decays over time, and any organisms with a "scavenger" gene may consume the decaying material. New parenting genes, such as ones for herbivores to pass on energy to its offspring (similar to an OET gene, but continue to do so until the offspring has matured), or genes for organisms with attack genes to come to the defense of other members of its species.
Chromosomes: Along with the basic DNA structure currently modeled, have the ability of the organisms to evolve chromosomes. These chromosomes would have basic telomeres at the ends, and a centromere in the middle, similar in chromosomes in eukaryotes. Chromosomes would allow for newer types of error such as trisomy, etc.
Sexual Reproduction: Along with asexual reproduction, organisms containing chromosomes could also evolve sexual reproduction, mating with other members of its species, and have their offspring be a combination of their chromosomes.
Using Genes to Control Age: Instead of using a separate variable, outside of the organisms genome, to control lifespan and age of maturity, use genes to control them instead. Instead of having a pre-determined maximum age, have each organism need more energy as it gets older, and have a genes to control the rate of energy-requirement increase. Transcription error could also be reprogrammed to change with age, and have a greater chance of transcription error as the organism gets older. Similar with Age of Maturity, make the energy required to reproduce drop with age, and have the rate of drop be controlled by genes.
References
-
Elzanowski, Andrzej (Anjay), and Ostell, Jim. The Genetic Codes. (December 4th, 2007) In National Center for Biotechnology Information. Retrieved August 20th, 2008 from http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
Raw Data
Posts
