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Newb question about mutation

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EricL:
Another very common thing to do is to use the auto-costs capability to keep the total sim population near a specific target value.  The program will increase costs when the population grows and decrease them when it shrinks to try to keep things in a specific range.  There are certain ramifications to be aware of when doing this w.r.t. the kind of selection pressure it represents, but it can be very useful for keeping the population of an evo-sim under control.

See: Top Ten Ways to speed up your Evo Sim.

shvarz:

--- Quote ---I'm a biochemist with a specialization in bioinformatics
--- End quote ---

Good to see another trained biologist here! This program is great if you want to play with evolution. I've been hooked up on it for 4.5 years and saw some amazing progress in its ability to model biological systems. Right now I'm fascinated by evolution of viruses, both in my day job and in DBs.

Welcome to the community!

Gambrinus:
Wow, its amazing the difference some of those settings makes.  I'm also very impressed with how helpful this community is.  But I'm curious.  Is there a way to pause the simulation and find the most mutated surviving individual?  I doubt there is because there is little use for such a feature but I'm just finding it difficult to isolate mutated individuals just to observe the changes.

MacadamiaNuts:
You can speed mutations a lot if at the start of a sim, in the Species tab, click on Mutation Rates and, for example, drop Copy Error from 5000 to 500 or lower.

Run the smallest sim with 10 max vegetables, 30 energy per cycle (this stuff is in General Settings), and repopulating 1 vegetable each 100 cycles. Optionally you may want to put dynamic costs thru the Custom costs button at the Costs tab. Put the low left bar full right so the costs respond faster. Also, at the ageing costs text fields, put an high value and Begin at cycle 4000 or so. That kills elders (and bots with reproduction disabled), and makes generations turn faster.

When you get used to the Species menu, start a sim with T_Preservans instead of Animal_minimalis. If T_Preservans still works, it used to be better for evolution simulations. Eventually mutations disable their recognition of bots of their same species, they turn carnivore and control better their population. Anyway, it's common for small sims with high mutation rates to stagnate and die.

EricL:
There isn't really a good way to find the "most mutated" extant organism.  It's not clear (to me at least) that there even is such a thing.  Let me explain.

The default mutation rates in DB are probably an order of magnitude or more higher than they should be.  Given this and the limited size of the sims and asexual reproduxction and what you get is that all the extant bots in a single evo sim will all usually have roughly about the same number of accumulated mutations down their line from the base organism.  Even well adapted bots mutate given the high mutation rate.  It's just that their mutations are not deleterious.   Generally, all the bots in a sim will all share a common ancestor within N generations (N typically less than 100).  This is just observation on my part of isolated single evo sims and is a function of our small worlds and limited CPU cycles..  Larger inter-connected sims such as Internet Mode (which you should try) change this dynamic considerably adn there I think we may be starting to see long term coexistance of mutiple evolved species from common ancestors.

Try out the graphs if you havn't already.  I assume you are already looking at the mutation history of individual bots via their properties dialogs...

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