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Messages - shvarz

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Biology / Re: human mutation rate
« on: April 06, 2011, 05:10:48 PM »
Well, they don't. There are fairly well-known biases in mutation rates, for example CpG sites are hot-spots with mutations happening about 10 times more likely there as in other places, but that's a completely different questions.

Biology / Re: human mutation rate
« on: April 05, 2011, 03:34:38 PM »
It's a wrong assumption. It appeared back when the only way to see a mutation was to observe its effect on fitness (which is usually negative). It's quite fair to say that most mutations are either neutral or effectively neutral (their effect is smaller than the reciprocal of the effective population size, see Kimura et al.).

The protein-coding part of the genome is only about 1-2%. The functional part of the genome is significantly larger (probably on the order of 20-30%) and will include a whole bunch of regulatory sequences and genome-maintenance sequences, but mutations there are much more likely to be neutral than in the protein-coding part of the genome. The functionality of most of those elements just doesn't depend upon the exact sequence.

Biology / Re: human mutation rate
« on: April 01, 2011, 12:11:57 PM »
A mutation in a functional part of the genome (which is certainly bigger than 5%) will not necessarily affect the functionality. Chances are very high that it will remain neutral or have a very small effect (positive or negative) on fitness.

« on: July 27, 2010, 09:41:19 AM »
Could someone share their current sim settings? I'd like to join.

Off Topic / Re: We need more members!
« on: July 22, 2010, 02:14:52 PM »
We've discussed this before (probably before either of you have joined  :P ): We need a fun and easy out-of-the-box experience, where a new user would just start the default sim and get some interesting things to watch. Bots from other members should enter the sim fairly often and be able to survive.

I have to admit that I was one of the main culprits as far as standardization of sim conditions went - my sims were always the most weird ones (they were fun though). But I've come to recognize the need for a community and we can't get a community if everyone is running very different sims.

So, I would suggest that you choose a sim that is most dear to your heart (and one that is stable and long-lasting), switch all your other sims to it and also post it here. We may also modify the download package so that it comes with this sim, with the hack and with instructions on how to start DB in this mode.

Off Topic / Re: We need more members!
« on: July 22, 2010, 01:49:54 PM »
3 or 4 is pretty good. Are you guys running some more or less standard settings sim? Or everyone is just on their own?
I think I may join you soon, I have a home server that just stores files for now, but is always ON - would be good to put it to some use.

Off Topic / Re: We need more members!
« on: July 22, 2010, 01:17:20 PM »
It would be good enough even to get some activity from existing ones. It's no use sending people to a dead site - they'll just go away. Are there people currently running in internet mode? How many, how often?

Darwinbots3 / Re: alive ?
« on: July 21, 2010, 03:51:37 PM »
It's good to see that this thing is still (somewhat) alive.
Too bad not much is happening... at least on the surface...

Biology / A question on genetics and biology
« on: January 05, 2010, 02:33:36 PM »
What they probably meant in that program is that most genes in animals remain the same, but evolution mostly happens by changing the way these genes are regulated (which involves relatively small regions of DNA). So that two animals may look quite different, but most of their proteins are very closely related. The difference originates from the way proteins and higher level structures are assembled. Obviously bacteria, being very simple organisms, don't need these complex regulatory pathways (only multicellular organisms do).

Off Topic / Stuff broken on the forum!
« on: April 10, 2009, 02:40:17 PM »
Wow, Bots is back!

That is weird indeed...
As far as I remember there are two places where DNA can have costs. One is "DNA upkeep" cost and the other is detailed costs for each type of command. Are you sure you disabled both?

Internet Mode Commentary / When was the last time...
« on: April 01, 2009, 03:26:37 PM »
Hey Nums, how are you doing these days? Anything new happening? Good to see at least some of the oldies sticking around here.

Quick question: Is it possible to give DB some king of "low priority" on my computer? I'd love to run DB, but I'm on computer a lot these days and can't take the computer getting sluggish because there's a population explosion going on in the background

This is very interesting, Peksa!
In my previous sims the bots' DNA grew long pretty fast, so I'm guessing one of the reasons for the stability of your DNA is high costs for DNA maintenance. Otherwise your bots would have accumulated a lot of junk DNA. So, it's not that surprising to see your bots to preserve most of DNA functionality - they can't really mess around with it much. Any mutations that knock out basic functions will be very deleterious. Usually in evolution there is a way around this - duplication. Once the "core" functionality is duplicated, then one of the versions is free to mutate and acquire new functionality. But it could never happen in your sim.
Still, interesting result.

P.S: By the way, it's more meaningful to count sim progress in number of bots born from the beginning, not in cycles.

Announcements / 2.44.1 Released
« on: November 30, 2008, 03:12:00 PM »
Wow, that is very-very sad...
Well, all the best to you Eric!

P.S: By the way, how about that lunch (or coffee) that we were planning to have some time? I'm moving out of state soon, so we need to get going on that. My treat

Biology / Cambrian explosion
« on: November 30, 2008, 03:07:20 PM »
One thing that DB definitely lacks is the ability to simulate millions of organisms for billions of cycles. So there is a hard-wired limit for you. That said, I think I heard somewhere that cambrian explosion was mainly due to abundance of oxygen in the atmosphere. Suddenly energy became much cheaper.
You can simulate this by turning down all the costs in your sim and I've actually tried that and it works - you get tons of weird bots this way, because selection is not so hard anymore. Your bot counts shoot up as well, so can't really run a sim this way for long.

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