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Genetic Distance

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EricL:

--- Quote from: shvarz ---I don't think your genetic distance is much help, however, because you don't know whether these mutations are just drift or were selected for.
--- End quote ---
So, I'll push back a little bit.  It's true I can't tell drift from selection.   But I think it can tell us something about genome simularity and number of generations of separation between bots or groups of extant bots.   I do think we can draw some conclusions.   For example, when the most recent common ancestor between two extant bots is far enough back that the probability of both of them being alive by chance is sufficiently low, I think it may be safe to conclude that something interesting has happened even if is simply geographic isolation or the founder effect.  

We know nothign today the ancestrial relatedness of bots in an evo sim.  At least this is a first step towards gtting some data.


--- Quote from: shvarz ---And without sexual reproduction genetic distance does not matter for defining species.
--- End quote ---
I don't get that.  Seems to me genetic distance is the only way to define a species when we are talking about  asexual reproducers since the fuzzy definitions we use for sexually reproducing species such as "can successfully mate with each other" don't apply.


--- Quote from: shvarz ---The mutation counter already tracks accumulation of mutations.
--- End quote ---
Yes, but how many those mutations are shared in common with other extant bots?  We don't know today.


--- Quote from: shvarz ---I think that just from the practical point of view we just need to know if there are distinct groups of bots co-existing in a sim.
--- End quote ---
Hopefully this will tell use that.


--- Quote from: shvarz ---So, I think the easiest thing to do is just create new species when bots don't have a common ancestor for N generations. We can start with 100 and see how it goes. I'm sure this will result in speciation, simply because sims run at different speeds.
--- End quote ---
That is the first blush algorithm yes, but there are details to work out.  What distance do we use to define the members of the new species?   What if there are extant bots in the middle?  I'd really prefer something that leveraged relatedness clumbs of bots.   Hopefully we can see them (if they exist - our simes may simply be too small and simple) given this capability.  My suspision is that in a mixing population, the tree gets pruned pretty short.  Namely that most or all bots in a sim generally share a relatively recent common ancestor unless physically isolated.

And yes, different sim speeds in teleporter connected sims will need to be taken into account.  The distance to designate a new species should probably require at least several times the average number of generations beween migration events.

EricL:

--- Quote from: Peter ---You mean something like this, screenshots of DB2.1 and at the bottom you see some text about a database file generated by DarwinBots and you see a graph made in excel, has DB made in earlier versions a database file?
To me it seems now a little like we're reinventing the wheel, so where is the database?
--- End quote ---
It was never a database.  It was a comma seperated file.  The term database is misleading.

The code is still there.  Look at the recording tab on the options dialog.  I've never mucked with it so it may work.  But it may not.

The info it records is limited and in particular does not record parent-offspring relationships nor does it maintain information about relatedness through extinct individuals.

Numsgil:

--- Quote from: Peter ---You mean something like this, screenshots of DB2.1 and at the bottom you see some text about a database file generated by DarwinBots and you see a graph made in excel, has DB made in earlier versions a database file?
To me it seems now a little like we're reinventing the wheel, so where is the database?
--- End quote ---

That's exactly what I'm talking about (well, the graph would look different, but the idea is the same), only the conclusions drawn from that graph are a little naive, I think.  You can still (unless it's been broken by accident) run the program with database logging enabled, it just takes up a lot of space.

EricL:

--- Quote from: EricL ---and in particular does not record parent-offspring relationships nor does it maintain information about relatedness through extinct individuals.
--- End quote ---
Actually, I stand corrected.  That info is in there, one line for every bot that ever lived if you want it.

Numsgil:
In the distant future it would be neat for IM if we kept a database on the server.  When a program syncs itself with the database to upload and download bots, it would also update the database with all the bots that have died in its sim since last update.  You could then build phylogenic trees for the whole megasim, examining all sorts of neat data.

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