Messages

46

Newbie / DB server

« on: November 26, 2008, 03:38:51 PM »

You can set up a local LAN, turn on file sharing, map a network drive from one computer to the other and assign a special folder for your bots. Then just use outgoing teleporters in both sims to save bots in there and incoming teleporters to load them back. No need for a server or an internet mode.

47

Suggestions / Mutation protection opinion

« on: November 23, 2008, 12:30:03 AM »

1:

Anyway, here's an example off the top of my head: amino acids can be coded for in way more ways than necessary. In some cases, the amino acid will be coded for by DNA made from mostly As & Ts, while in other cases, the amino acid can be coded for using mostly Gs and Cs. Guanine and cytosine have 3 hydrogen bonds connecting them, while Adenine and thymine only have two. This makes G-C base pairs less susceptible to mutations and, sure enough, bacteria that dry out regularly and need to halt their metabolism have a far larger amount of Guanine and Cytosine in their DNA, to protect it from mutations, than their less hardy cousins.

First, the protective effect of such mechanisms is pretty small and is designed for very specific conditions. Second, we already have a similar mechanism in place. There are different mutation rates for different kinds of mutations. These rates can be mutated and, therefore, bots can evolve to protect their DNA.


3:
But how are they inserted?

There are insertion mutations that insert random stuff in random places.

48

Suggestions / Mutation protection opinion

« on: November 21, 2008, 12:59:26 AM »

1: There's nothing there about protection from mutation. The hypermutation process exists only in higher vertebrates in cells of immune system. It's a nice example, but it's rather an exception than the rule. I don't see this as evidence for immediate implementation of this feature. I stand by my original statement - in general cells have no mechanisms to protect certain areas from mutation.

2. To some extent - yes, but it really gets out of hand. With a small number of people running IM, this is like having a bucket of water and a frying pan. Anything that can live in one, cannot live in the other, so might as well disconnect from IM - nothing is being transferred.

3. They can be inserted one by one randomly.

49

Suggestions / Mutation protection opinion

« on: November 19, 2008, 07:36:29 PM »

Reason 1: There is mutation protection in nature- in fact, almost all mutations in nature cause a mutation in relatively unimportant genes that lead to, for example, formation of an extra limb, as opposed to missing important metabolism pathways.

I assume that this is the main reason, because you put it first. What can I tell you - it's just wrong. There is no mutation protection in nature, at least not in the way you are picturing it. DNA polymerase has no idea what DNA it is copying - it makes mutations everywhere with equal probability. If effect of the mutation happens to be very severe, then the organism just dies (maybe even at embryonic stage) and we don't see it. In this sense, DB already has mutation protection, as most of mutations that you see in evo-sims are mild mutations, not drastically crippling the bot.

Also, IMO, DB should always provide flexibility and features over simplicity and instant entertainment. DB has a very specific niche in games, mainly for people already familiar with CS or Biology.

I'm all for features, but at some point it just becomes a mess. In fact, it's already a causing a mess in IM - when I ran my sim in IM mode most of the bots that came in from internet died almost immediately, because conditions in different sims are so drastically different. What I'm saying is that there is a fine balance between usability and functionality. Saying "just add a tick-mark" does not automatically solve things.

cond, start stop etc all can be created through mutations and they can be moved around and deleted by mutations, so these are not meta-commands.

50

Suggestions / Mutation protection opinion

« on: November 19, 2008, 02:15:32 PM »

After following the development of this program for the last 6 years or so, I've come to the conclusion that a well-thought-out feature does not really need a tick-mark. We have plenty of those in options now, and most of them just confuse the hell out of new users. That's all they do.

I still have not heard a good reason for this "protection from mutations". Why do we need it? Give me one most important reason.

P.S: Maybe I'm missing something, but I thought that metadata or metatags are comments seen by us and by the program, but not by bots. In that light I'm confused by your last paragraph.

P.P.S: And, as mentioned in the other thread, the whole discussion is moot if we don't have a programmer to implement it. Eric is away doing some other fun things, and we don't have anyone else at the time.

51

Suggestions / Mutation protection opinion

« on: November 18, 2008, 01:55:16 PM »

Sorry, I've been away awhile and just now noticed this topic. I also apologize for not carefully reading all the proposals and the original DB3 topic. And I also apologize for posting in a separate thread - for some reason I'm not allowed to comment in the original one.

I voted for "another option" because I agree with Cyberduke - it is not clear what this option is trying to achieve. He proposed two different possibilities: 1) for us to make some DNA unmutable; 2) for bots to evolve protection of their DNA. I think these are vastly different goals and require vastly different approaches.

1) For us to make some DNA "protected" from mutation - this is for our convenience sake. Bots should suffer no penalty for that and should not even know that such protection exists. So clean metadata is the best approach here.

2) For bots to evolve protection of specific DNA regions. Seems like people are thinking that bots should be able to protect certain areas of their genome but not others. This is NOT how real DNA replicates. There may be some fancy exceptions, but in general organisms have a generic mechanism for DNA replication and mutation rate is the general feature of the organism. So, I'm completely against this idea!

3) For bots to evolve general rates of mutations. This already exists in the code - mutation rates can mutate and change. I think it would be fair to charge a little extra for lower mutation rates.

52

Off Topic / Wikipedia page in danger

« on: November 14, 2008, 05:44:12 PM »

I was looking for something completely different on wikipedia, when I stumbled on the page dedicated to Darwinbots. Turns out, as of yesterday it is scheduled to be deleted in four days due to

No references to reliable sources; very few Google hits (3,100 after omitting Wikipedia and Blogspot) to support the significance of this software.

Now, if anyone has any experience in dealing with wikipedia people, maybe they should try to stop that. If no one else volunteers, then I'll give it a try over weekend.

http://en.wikipedia.org/wiki/Darwinbots

53

Off Topic / Spore

« on: September 16, 2008, 08:41:27 PM »

So, a year later and "Spore" is out! What do you think?  Total F-up is what I think. There is nothing about evolution there, just the same creationist-type stereotypes about evolution. New features appear appear out of nowhere, evolution is directed toward intelligence, simplistic "survival of the strongest", no historical influence. At any point you can take your creature, disassemble it completely and create a completely different one.

Oh, and the actual gameplay is fun, but ultimately non-novel and with no depth to it. It's like a Mr. Potato Head crossed with PacMan. Waste of money I say, get it through torrent just to take a look and delete it the next day!

54

Tips and Tricks / Random Stuff

« on: July 15, 2008, 02:37:26 PM »

I'm just having fun with internet mode, which recently worked OK for me. My sim is very diverse with different bots and different veggies dominating at different times, sometimes in "rock-paper-scissors" scenarios. The local folder where I save bots also proves to be very useful, as it now often re-seeds the sim with "new" bots (veggies don't usually go extinct for me).

I'm just having fun with internet mode, which recently worked OK for me. My sim is very diverse with different bots and different veggies dominating at different times, sometimes in "rock-paper-scissors" scenarios. The local folder where I save bots also proves to be very useful, as it now often re-seeds the sim with "new" bots (veggies don't usually go extinct for me).

55

Off Topic / Can't upload files

« on: July 11, 2008, 01:53:54 PM »

Nope, did not help. Still gets stuck at "Uploading file".

Duh, it says "Max.single file 8Mb"!  Did you just add it now?  What should I do with the 10Mb file?  I'd like to report a bug, but my sim (even compressed) is above the limit. If people used RAR, then I could split it into two archives, but the regular Windows zip archivator does not do that.

56

Off Topic / Can't upload files

« on: July 10, 2008, 02:23:45 PM »

The file is about 10 Mb, it's in zip format.

I just tried uploading a smaller file and it worked, so I guess it's a size limit.

57

Off Topic / Can't upload files

« on: July 09, 2008, 02:12:11 PM »

Just like the title says - I can't upload any files to the board. It gets stuck at "uploading" and never finishes. I tried both Firefox and IE - nothing works.

58

Internet Mode Commentary / The State of the Simulation

« on: June 12, 2008, 02:06:49 PM »

Backuping your bots works!
I have local teleporters that save and load bots to/from local folder.
I originally had a system of Duplo/Alga shellular that was evolving for a long time, several months. I had >1200 bots backed up during that time. Then Eric introduced SeaSnake. The snake itself could not make it in my sim, but Alga minimalis infected with Snake genome could. They came in and wiped out my previous sim completely. For the last month I only had these Alga minimalis in my sim.  I also changed conditions a lot by adding shapes, modifying energy flow and tweaking costs.
Just an hour ago the local teleporter brought in a Duplo that was saved over three months ago and that Duplo is doing so great, it multiplied to >600 bots.  This is fun!  Let's see what happens now.

59

Biology / .delgene in Real Life

« on: June 04, 2008, 12:40:33 AM »

By the way, bacteria and their viruses can also generate diversity in their DNA "at will":
http://biology.plosjournals.org/perlserv/?...0060131#special

60

Internet Mode Commentary / The State of the Simulation

« on: May 30, 2008, 05:44:23 PM »

And just to illustrate the level of diversity that I see, here's a pic of two more sub-species (notice the difference in color) that exist in the same sim at the same time with the stuff I posted above.  If only we had more coherent sims connected to each other...