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Author Topic:   Evolution Generator Program
Percy
Member
Posts: 18470
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.8


Message 16 of 59 (572073)
08-03-2010 1:58 PM
Reply to: Message 11 by ICANT
08-03-2010 1:15 PM


Re: Evolution Generator
Hi ICANT, thanks for trying it out, I figured you'd be on vacation already.

Just to save time, try starting with a very short line of text, like maybe "Jesus loves us." Set the number of mutations to 2 and the number of offspring to 10, then try selecting the 2 to 4 strings that have the highest number of matching characters in each generation and let me know what happens. The fittest strings are those with the largest number of matching letters.

It doesn't matter whether you select parents or offspring, all you're doing is selecting which strings contribute to the next generation. Sometimes the parents are more fit than any of the offspring.

--Percy


This message is a reply to:
 Message 11 by ICANT, posted 08-03-2010 1:15 PM ICANT has responded

Replies to this message:
 Message 20 by Blue Jay, posted 08-03-2010 6:01 PM Percy has acknowledged this reply
 Message 21 by ICANT, posted 08-03-2010 6:34 PM Percy has responded

    
Taq
Member
Posts: 7864
Joined: 03-06-2009
Member Rating: 4.3


Message 17 of 59 (572080)
08-03-2010 3:26 PM


Schneider's EvJ program
You guys might be interested in Thomas D. Schneider's EvJ program which can be found here. He used this same program to show how biological information arises in evolving systems through the evolution of a binding protein and a binding site for that protein. You can find the article here.
  
Wounded King
Member (Idle past 2257 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 18 of 59 (572086)
08-03-2010 5:15 PM
Reply to: Message 10 by Aware Wolf
08-03-2010 12:42 PM


Re: Evolution Generator
The best I was able to come up with was a picture that mutated. I started with a grid of 20x20 squares, each with a random color. Its offspring would mutate by having a random number of squares change its color to a new random color. The human operator would choose a child picture to be the new parent, all other children died away. The selection pressure then became whatever the human wanted it to be. I was hoping that the random picture itself would suggest something. “Hey, that kind of looks like an apple/fork/lightning bolt/whatever”. The human would then select that child, and as he kept making selections, a nice picture of an apple/whatever would appear.

I seem to remember there was an online experiment along these lines. By using hundreds/thousands of web users it got around the attention span issues you mentioned.

TTFN,

WK


This message is a reply to:
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Blue Jay
Member (Idle past 860 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 19 of 59 (572088)
08-03-2010 5:35 PM
Reply to: Message 11 by ICANT
08-03-2010 1:15 PM


Re: Evolution Generator
Hi, ICANT.

Percy already answered, but I thought I would provide an extra conceptual explanation.

ICANT writes:

...I did random selection of a child for each generation

The selection process is not supposed to be random. If you randomize it, you remove the benefit of selection from the model, and all you get is random evolution, which is not what the ToE proposes.

Random mutation + random selection = random evolution.

Random mutation + discriminate selection = evolution proposed by ToE.

I hope that helped.


-Bluejay (a.k.a. Mantis, Thylacosmilus)

Darwin loves you.


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Blue Jay
Member (Idle past 860 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 20 of 59 (572091)
08-03-2010 6:01 PM
Reply to: Message 16 by Percy
08-03-2010 1:58 PM


Re: Evolution Generator
Hi, Percy.

I made the entire alphabet in 65 generations, with 10 offspring per parent, using the rule that I select all individuals with the highest number of matches each generation, and by dialing down the mutation rate when the next generation didn't improve over the last. I also set a ceiling of selecting 15 individuals, because 150 is a huge generation to deal with.

The whole thing took about 15 minutes.

(P.S. I've just started studying this week for my candidacy exams, so the insertion of occasional mindless, monotonous things in the middle of my study day is a nice break for my brain. )


-Bluejay (a.k.a. Mantis, Thylacosmilus)

Darwin loves you.


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 Message 16 by Percy, posted 08-03-2010 1:58 PM Percy has acknowledged this reply

  
ICANT
Member
Posts: 6187
From: SSC
Joined: 03-12-2007


Message 21 of 59 (572104)
08-03-2010 6:34 PM
Reply to: Message 16 by Percy
08-03-2010 1:58 PM


Re: Evolution Generator
Hi Percy,

Percy writes:

Hi ICANT, thanks for trying it out, I figured you'd be on vacation already.

I am on vacation.

My wife just is not packed and ready to leave the house yet.

I did one using JesUS loVEs ME.

I set it to 2 mutations and 5 OFFspring.

I selected the highest humber from each parent.

By the time I got to 50 generations I was getting 9's in some of the OFFspring.

Continuing the same process when I reached 100 generations the highest number was 8.

Since I had used upper and lower case letters the most perfect matches I had was 3.

What would a letter match represent as far as DNA information is concerned?

Is it supposed to represent new information or changed information in the string?

God Bless,


"John 5:39 (KJS) Search the scriptures; for in them ye think ye have eternal life: and they are they which testify of me."
This message is a reply to:
 Message 16 by Percy, posted 08-03-2010 1:58 PM Percy has responded

Replies to this message:
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Percy
Member
Posts: 18470
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.8


Message 22 of 59 (572107)
08-03-2010 7:05 PM
Reply to: Message 21 by ICANT
08-03-2010 6:34 PM


Re: Evolution Generator
Hi ICANT!

When the program checks whether letters match it doesn't care about upper and lower case. An upper case "J" will match a lower case "j". I did this on purpose because it is actually somewhat analogous to nucleotides in DNA where, for example, the amino acid arginine is coded for by both CGA and CGG - it doesn't matter whether the last letter is A or G, you still get arginine. So it doesn't matter whether it's a lower case or capital "J", it's still Jesus. Ancient Hebrew didn't have upper and lower case, did it? I'm not sure.

So it sounds like you were able to use selection to get closer and closer to the target phrase, "JesUS loVEs ME," though you couldn't quite get all the way there. That's quite a dramatic difference from the random selection you were using before.

As the string changes the information is new in the sense that it is information that was not there before.

--Percy


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 Message 21 by ICANT, posted 08-03-2010 6:34 PM ICANT has responded

Replies to this message:
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Aware Wolf
Member (Idle past 650 days)
Posts: 154
From: New Hampshire, USA
Joined: 02-13-2009


Message 23 of 59 (572122)
08-03-2010 9:26 PM
Reply to: Message 18 by Wounded King
08-03-2010 5:15 PM


Re: Evolution Generator
Interesting. I felt that the concept was a good one; I just lacked the time to prove it.
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CosmicChimp
Member
Posts: 306
From: Muenchen Bayern Deutschland
Joined: 06-15-2007


Message 24 of 59 (572126)
08-03-2010 10:45 PM
Reply to: Message 2 by Percy
08-03-2010 7:16 AM


Re: Evolution Generator
I've been messing around with it, highly addictive, but in an Asperger's syndrome kind of way. Makes it feel as though you're playing the god of natural selection.

To get anywhere you have to exert too much user input. you should make it a bit more manageable.


This message is a reply to:
 Message 2 by Percy, posted 08-03-2010 7:16 AM Percy has acknowledged this reply

  
ICANT
Member
Posts: 6187
From: SSC
Joined: 03-12-2007


Message 25 of 59 (572186)
08-04-2010 12:57 PM
Reply to: Message 22 by Percy
08-03-2010 7:05 PM


Re: Evolution Generator
Hi Percy,

Still not on the road, so I got some questions.

I will assume that Peter Marshals program is biased to support his worldview.

Now I have some questions about your generator.

If I set the mutations at 10 per generation using 15 parents how many of those mutations are:

Good mutations?

Netural mutations?

Delentious mutations?

How many get repaired by the automatic process in DNA?

God Bless,


"John 5:39 (KJS) Search the scriptures; for in them ye think ye have eternal life: and they are they which testify of me."
This message is a reply to:
 Message 22 by Percy, posted 08-03-2010 7:05 PM Percy has responded

Replies to this message:
 Message 26 by Wounded King, posted 08-04-2010 1:43 PM ICANT has not yet responded
 Message 29 by Percy, posted 08-04-2010 3:35 PM ICANT has responded
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Wounded King
Member (Idle past 2257 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 26 of 59 (572195)
08-04-2010 1:43 PM
Reply to: Message 25 by ICANT
08-04-2010 12:57 PM


Re: Evolution Generator
Hi ICANT,

I'm not Percy but I think that the answers to your questions are kind of what the programis there to address.

How many get repaired by the automatic process in DNA?

I think you should view these as mutations that have got as far as being incorporated into an embryo, i.e. have not been targetted by DNA repair mechanisms. The repair processes are not part of the model. DNA repair doesn' t operate across generations so it isn't particularly relevant.

As to the proportions of good bad and neutral mutations, you could probably estimate this quite simply by considering the mutation rate and the number of characters available in the alphabet that Percy is using. Alternatively you could just run the program through few iterations and make your own observations on the rates of beneficial/neutral/deleterious mutations, that is kind of one of the points of such a program surely?

Just a quick run at 10 10 as the settings gave me 5 beneficial, 5 deleterious and I didn't bother to count the neutrals but it should be around 10 since I had a target string about 20 characters long. One thing to bear in mind, as Percy pointed out, is that as your sequence gets closer to the target these proportions will change dramatically at the same mutation rate, with many more deleterious mutations arising.

TTFN,

WK


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ringo
Member
Posts: 16613
From: frozen wasteland
Joined: 03-23-2005
Member Rating: 3.0


Message 27 of 59 (572198)
08-04-2010 2:03 PM
Reply to: Message 2 by Percy
08-03-2010 7:16 AM


Re: Evolution Generator
I can't run the program at 10 mutations at all. It just waits and waits and never produces a result.


Life is like a Hot Wheels car. Sometimes it goes behind the couch and you can't find it.
This message is a reply to:
 Message 2 by Percy, posted 08-03-2010 7:16 AM Percy has responded

Replies to this message:
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Percy
Member
Posts: 18470
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.8


Message 28 of 59 (572208)
08-04-2010 3:30 PM
Reply to: Message 27 by ringo
08-04-2010 2:03 PM


Re: Evolution Generator
ringo writes:

I can't run the program at 10 mutations at all. It just waits and waits and never produces a result.

Can I guess that your target string was shorter than 10 characters?

This is a bug, I should be detecting pathological cases, but anyway, try a longer string and see if it works.

--Percy


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Percy
Member
Posts: 18470
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.8


Message 29 of 59 (572209)
08-04-2010 3:35 PM
Reply to: Message 25 by ICANT
08-04-2010 12:57 PM


Re: Evolution Generator
ICANT writes:

If I set the mutations at 10 per generation using 15 parents how many of those mutations are:

Good mutations?

A good mutation is any character position where the letter was black and is now red.

Neutral mutations?

A neutral mutation is any character position where the letter changes but not color.

Deleterious mutations

A deleterious mutation is any character position where the letter was red and is now black.

--Percy


This message is a reply to:
 Message 25 by ICANT, posted 08-04-2010 12:57 PM ICANT has responded

Replies to this message:
 Message 33 by ICANT, posted 08-23-2010 5:51 PM Percy has responded

    
Taq
Member
Posts: 7864
Joined: 03-06-2009
Member Rating: 4.3


Message 30 of 59 (572213)
08-04-2010 4:28 PM
Reply to: Message 25 by ICANT
08-04-2010 12:57 PM


Re: Evolution Generator
I will assume that Peter Marshals program is biased to support his worldview.

THE IRONY!!!! IT BURNS!!!!!!!!


This message is a reply to:
 Message 25 by ICANT, posted 08-04-2010 12:57 PM ICANT has not yet responded

  
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