I decided to open a separate thread to post releases of Biogenesis X Mod, which explores
- alternative mutation mechanisms, and
- an alternative stress-based aging mechanism.
Last edit: AdaM 2015-02-15
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
There is no maximum life expectancy for organisms anymore
Aging mechanism was revised:
Organisms possess a stress level that determines how often the segments stop to work correctly. The higher the stress level the more often a segment will fail.
The stress level is determined as the ratio of the current energy to the energy needed for reproduction.
Organisms possess a stress resistance, the higher it is the less energy organisms can have without being affected by stress. The stress resistance can be set as a parameter instead of maximum age now in the menu World > Parameters > Organisms.
CHANGES
renamed "rubbing" into "friction"
BUGFIXES
division by 0 exception in painting the average color composition in the statistics window fixed
Last edit: AdaM 2015-02-15
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Mutations of an organism can now occur spontaneously. This prevents that evolution "gets stuck" if there are only very successful almost immortal organisms in the world that do not reproduce successfully. The rate of spontaneous mutations is controlled by the "spontaneous mutation probability" in the menu World > Parameters > Organisms.
Currently, spontaneous mutations are limited to splitting or merging segments and color changes of segments.
The average length of the yellow segments has an influence on how the parent organism's energy is distributed between parent and children during reproduction.
An organism with long yellow segments gives most of its energy to its children and keeps only a small amount for itself, producing stronger children but weakening itself. An organism with short yellow segments will transfer just a small amount of its own energy to its children that are weak, but stays relatively strong.
CHANGES
Growth and reproduction of an organism depends on the stress level now:
reproduction is allowed only if stress level <= REPRODUCTION_MAX_STRESS_LEVEL, which is currently set to 0.05
growth is allowed only if stress level <= GROW_MAX_STRESS_LEVEL, which is currently set to 0.1
Introduced minimum energy that describes how much of the organisms energy is bound to the body. In that way the bodies of dead organisms remain in the world and can decay like in versions 0.1.x.
The stress level is adjusted so that not fully grown organisms do not experience disadvantages unless they get attacked.
After reproduction, the body of the parent organism shrinks in order to remain unaffected by the loss of energy caused by reproduction.
BUGFIXES
decay energy was not read from edit box, fixed now
fixed freezing of organisms at the world borders (happened only sometimes)
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
The frequency of mutations is based on rates (i.e. average number of mutations per frame) now instead of probabilities.
All kinds of mutations are balanced now, i.e. they do not cause systematic drift in the genetic code when there is no selection.
Split/merge mutation can produce segments with an arbitrary color.
Adapted default segment probabilities slightly.
BUGFIXES
Split/merge mutations were not balanced and made organisms shrink on the long term - this is fixed now.
Preferences on mutation parameters and stress resistance are saved now.
Pasting the same genetic code from the clipboard was leading to identical mutations in all organisms created in that way (i.e. the organimsms mutated synchronously) - this is fixed now.
Last edit: AdaM 2015-02-15
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
"Split/merge mutations were not balanced and made organisms shrink on the long term - this is fixed now."
Are you sure about that? All organisms on my 292k~ time world are incredibly small.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I never tried to simulate so long, so I'm not perfecly sure about what happens on the very long time scale. The bug I was fixing made the organisms shrink much faster because segments were merged too often in comparison to splitting them. After a few hundred of these mutations even fully grown organisms had only a few segments (in numbers, not in length).
I tried simulating many split/merge mutations by setting
- major and minor mutation rate to 0
- spontaneous mutation rate to 1
- cyan segment probability to 0 (otherwise the organisms will move and you don't see anything)
Under these conditions I did not see that all organisms are small. Some are fully grown and reproduce.
Organisms in this version can be small if they are not fully grown (Energy is much smaller than Reproduction). This can happen if larger organisms use up most of the remaining CO2 in the world. You can also check whether the length of the segments is small in the Genetic Laboratory panel.
Are the organisms in your world just small and have many segments, or are there only a few segments left (like just 1 or 2)?
If you like you can attach a your world file to the next post, then I can have a look.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
The organisms are small and have many segments, all the ones I examined had from 6 to 12 segments. The largest segment size I managed to find is 15. I guess that's not small at all, is it...? Huh.
Alright, it's probably better if you take a look at it. I let the simulation run for a few more ticks and it's now at 296928 time. I used the default setting for everything and never messed with any of the organisms, I also never changed the amount of CO2/O2.
Ah, I see, I'll do just that. Well, thank you for taking a look at it anyway!
By the way, do you accept feature requests? What about a way to auto-update the Statistics window in real-time?
I imagine you could, for example, leave the current update button as the default option and put a checkbox so that people who get tired of constantly pressing the button could just kick back and enjoy the statistics updating in real-time.
Last edit: Raul 2015-04-10
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I decided to open a separate thread to post releases of Biogenesis X Mod, which explores
- alternative mutation mechanisms, and
- an alternative stress-based aging mechanism.
Last edit: AdaM 2015-02-15
VERSION 0.1.1 released 2014-12-14
NEW FEATURES
CHANGES
BUGFIXES
Last edit: AdaM 2015-02-15
VERSION 0.2.0 released 2014-12-18
NEW FEATURES
CHANGES
BUGFIXES
Last edit: AdaM 2015-02-15
VERSION 0.2.1 released 2015-01-03
NEW FEATURES
Currently, spontaneous mutations are limited to splitting or merging segments and color changes of segments.
An organism with long yellow segments gives most of its energy to its children and keeps only a small amount for itself, producing stronger children but weakening itself. An organism with short yellow segments will transfer just a small amount of its own energy to its children that are weak, but stays relatively strong.
CHANGES
BUGFIXES
VERSION 0.2.2 released 2015-01-27
CHANGES
BUGFIXES
Last edit: AdaM 2015-02-15
"Split/merge mutations were not balanced and made organisms shrink on the long term - this is fixed now."
Are you sure about that? All organisms on my 292k~ time world are incredibly small.
Hi Raul, thanks for the feedback.
I never tried to simulate so long, so I'm not perfecly sure about what happens on the very long time scale. The bug I was fixing made the organisms shrink much faster because segments were merged too often in comparison to splitting them. After a few hundred of these mutations even fully grown organisms had only a few segments (in numbers, not in length).
I tried simulating many split/merge mutations by setting
- major and minor mutation rate to 0
- spontaneous mutation rate to 1
- cyan segment probability to 0 (otherwise the organisms will move and you don't see anything)
Under these conditions I did not see that all organisms are small. Some are fully grown and reproduce.
Organisms in this version can be small if they are not fully grown (Energy is much smaller than Reproduction). This can happen if larger organisms use up most of the remaining CO2 in the world. You can also check whether the length of the segments is small in the Genetic Laboratory panel.
Are the organisms in your world just small and have many segments, or are there only a few segments left (like just 1 or 2)?
If you like you can attach a your world file to the next post, then I can have a look.
The organisms are small and have many segments, all the ones I examined had from 6 to 12 segments. The largest segment size I managed to find is 15. I guess that's not small at all, is it...? Huh.
Alright, it's probably better if you take a look at it. I let the simulation run for a few more ticks and it's now at 296928 time. I used the default setting for everything and never messed with any of the organisms, I also never changed the amount of CO2/O2.
looks normal to me. the very small organisms are not fully grown.
try to increase the spontaneous mutation rate, then you'll nicely see the effect of the split-merge mutation.
Ah, I see, I'll do just that. Well, thank you for taking a look at it anyway!
By the way, do you accept feature requests? What about a way to auto-update the Statistics window in real-time?
I imagine you could, for example, leave the current update button as the default option and put a checkbox so that people who get tired of constantly pressing the button could just kick back and enjoy the statistics updating in real-time.
Last edit: Raul 2015-04-10
Feel free to create a feature request here: https://sourceforge.net/p/biogenesis/feature-requests/
Personally, I think that this could be a nice minor improvement of the program.
Alright, thank you for the link. Hopefully someone'll eventually take a look at it, there's one other feature request there that nobody ever closed...
(Also, can't believe I've never bothered to check the "Tickets" menu, my bad)
I love it! fun to play with