Evolution Generator Program

I written a simple evolution generator program. You can find it here: It is a much more accurate representation than Marshall's of what evolution is really like. ICANT referenced Perry Marshall's program over at the When does design become intelligent? (AS OF 8/2/10 - CLOSING COMMENTS ONLY) thread, see this reply to ICANT that has the link's to Marshall's program: Message 635I would appreciate feedback on the program.--PercyEdited by Percy, : Clarify.

Yeah, you're right, but I wanted to be as similar to Marshall's program as possible, and with the number of matches displayed next to the select box I find I can go through 40 generations in five minutes with little problem, usually selecting between 2 and 4 strings to contribute to the next generation. Agreed, and I hope to add an "automatic" option. I agree, but it takes it to another level of time committment, and then it gets out of the realm of what ICANT might possibly understand. An understandable illustration for the average layperson was my goal, something that when someone mentions Marshall's program you could come straight back with a link to my program. That's why I made sure they looked very similar. I wouldn't have any problem varying the mutation rate automatically. One approach would be to track progress toward the goal and to reduce the mutation rate when it leveled off. Another approach would be to measure number of mutations against number of correct letters. Of course, you could quickly go through so many generations in an automatic mode that keeping the mutation rate high in the early stages wouldn't be necessary.Another improvement would be to have multiple targets, which would bring the program a little closer to actual evolution. You would quickly observe that random changes early in the process would direct lines of descent toward different niches.Wish I had serious time for this, there's so much that could be done.--Percy

Yeah, it's just Perl, but it could just as easily have been PhP. I'm faster in Perl.
--Percy

About number 1, that will vary, sometimes you're luckier than others. About number 2, getting the final few letters to match is the toughest, because there's only one right answer. In the real world there are millions of correct answers, and even creationists must acknowledge this because everyone's DNA is different. This is very easy, and I considered doing it, but I was afraid what I had was already too different from Marshall's program to be easily understood. This, too, is relatively easy. It would reflect a changing environment. It would show how organisms could get caught between needing a high mutation rate to keep up with a changing environment but not so high that fitness is undermined.--Percy

Thanks for finding this, typo, it's fixed now.--Percy

I was hoping to make something that was only incrementally more complicated than Perry's program but that gave a more accurate picture of how evolution works. I vaguely remember The Blind Watchmaker, but it's been over 20 years. I recall that he had a chapter about an evolution program, and I guess that's the WEASEL program you mention. Neat stuff, I still have the book on my shelf. At the time I read it I was carrying on a snail-mail debate with a fundamentalist Christian I'd met on an airplane and I sent her a copy. I'm sure she found it worked great as a paperweight.--Percy

Yeah, I can see the problems you faced. It would probably work great if selection was automated, but then it wouldn't provide any insights to the people watching it. They'd just gradually see a picture emerge.--Percy

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

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

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

A good mutation is any character position where the letter was black and is now red. A neutral mutation is any character position where the letter changes but not color. A deleterious mutation is any character position where the letter was red and is now black.--Percy

Bug is fixed.--PercyEdited by Percy, : Change author.

Here's a copy of the program, knock yourself out.--Percy

---

#!C:/Perl/bin/perl.exe
#!/usr/bin/perl

use strict;

use CGI;

my @LegalChars = ('a'..'z', 'A'..'Z', '0'..'9', ' ', '!', ',', '.', ';', ':', '"', chr(39));

print "Content-type: text/html\n\n";

my $p = new CGI;

my $styleSection = <<HERE;
<style type="text/css">
.style1 {
        font-family: Verdana, Arial;
	font-size: 10pt;
	font-weight: bold;
}
.style2 {
        font-family: courier;
	font-size: 10pt;
	font-weight: bold;
}
.style3 {
        font-family: Verdana, Arial;
        font-size: 12pt;
        font-weight: bold;
}
</style>
HERE

my $introText =
  (qq(Select some target text to represent favorable characteristics, then beginning with a) .
   qq(random string of letters and spaces the generator automatically adds random mutations) .
   qq(while you do the selection.));

my $descriptiveText = <<HERE;
<center>Discussion</center>

First a few explanatory words about what you're seeing in the display.  After you enter the target
text and click "Begin" the program generates a random starting string as the first parent, the
common ancestor of all subsequent organisms.  You can select the number of mutations per offspring
and the number of offspring per parent.  The text of each parent and
offspring has the matching characters highlighted in red.  Select the organisms you want to
contribute to the next generation by checking the select boxes.  The number of matching characters
is displayed next to the select box.

Natural selection permits the survival to reproduce of those best fitted to the environment.
In nature survival is dictated by how well an organism is fit to cope with the environment, such
as possessing fur for cold, or speed or disguise to elude predators.

In this simple computer program an organism is a string of text, and its fitness is measured by
how closely it matches the target string.  Notice that because the strings are relatively short,
maybe a hundred characters at most, that if you set the number of mutations as 10 that you're
chaning 10% of the genome in each offspring.  That's an enormous mutation rate for such a small
genome, and you'll find that while a high mutation rate is good for rapidly approaching the
target text in the beginning, that as you get closer you'll have to reduce the mutation rate.

This is similar to real life, where a high mutation rate such as can be caused by high radition is
fatal.  Evolution works through small incremental changes, and this program works best in
the same way.
HERE

my $command = $p->param('command');
my $startOver = $p->param('startover');

if ($command eq '' || $startOver) {

print <<HERE;
<html>
<head>
<title>Evolution Demonstrator</title>
<meta http-equiv="Content-type" content="text/html; charset=ISO-8859-1">
$styleSection
</head>

<body class=style1>
<form action="Evolution.cgi" enctype="multipart/form-data" method="post">
<input type="hidden" name="cnt" value="">

<center>
<blockquote>
<span class="style3">Evolution Demonstrator</span>

<p /> 
$introText
<p /> 

Enter the target text in the box below, then click Begin.

</blockquote>
</center>

<table border="1" align="center" class=style2>
<tr>
  <td>
    Target:
  <td>
    <script>var cleared=false;</script>
    <input type=text name=target value="Enter the target text used to measure fitness here" size=60
     onfocus="if (!cleared) {this.value='';cleared=true}">
  <td>
<tr>
  <td>
    Parent:
  <td>
  <td>
<tr>
  <td>
    Offspring of
Parent:
  <td>
  <td>
<tr>
  <td>
  <td align=right>
    Number of mutations:
  <td>
    <input type="radio" name="mutations" value="1" checked="true"/>1
    <input type="radio" name="mutations" value="2" />2
    <input type="radio" name="mutations" value="5" />5
    <input type="radio" name="mutations" value="10" />10
<tr>
  <td>
  <td align=right>
    Number of offspring per parent:
  <td>
    <input type="radio" name="offspring" value="1" checked="true"/>1
    <input type="radio" name="offspring" value="2" />2
    <input type="radio" name="offspring" value="5" />5
    <input type="radio" name="offspring" value="10" />10
<tr>
  <td colspan=3 align=center>
    <input type="submit" name="command" value="Begin">         
    <input type="submit" name="reset" value="Reset Form">
</table>

 <div align="center">

    <input type="hidden" name="total_mutations" value="0" />
    <input type="hidden" name="checksum" value="" />
    <span class="style1">Demonstrate evolution for yourself with the Evolution Generator</span></p>
 </div>
 <blockquote>
    $descriptiveText
 </blockquote>
</form>
</body>
</html>
HERE

} elsif ($command eq 'Begin') {

  my $targetText = $p->param('target');
  my $lengthTargetText = length($targetText);
  my $randomStartString = join '', (map {$LegalChars[int(rand(@LegalChars))]} (1..$lengthTargetText));
  $p->param('parentsel-1' => $randomStartString);
  $p->param('gennum' => 1);

  PresentNextGeneration($targetText);
} elsif ($command eq 'Create Next Generation') {
  my $targetText = $p->param('target');
  PresentNextGeneration($targetText);
} else {
  print "Error, sorry, apologies, etc...
\n";
}

exit(0);

sub PresentNextGeneration {

  my ($targetText) = @_;
  my $targetTextEncoded = $targetText;
  $targetTextEncoded =~ s/"/"/g;

  my $numMutations = $p->param('mutations');
  my %NumMutationsChecked;
  $NumMutationsChecked{$numMutations} = 'checked';

  my $numOffspring = $p->param('offspring');
  my %NumOffspringChecked;
  $NumOffspringChecked{$numOffspring} = 'checked';

  # Fetch parents
  my @Parents;
  map {push(@Parents, $p->param($_)) if $_ =~ /^parentsel-/} $p->param;

print <<HERE;
<html>
<head>
<title>Evolution Generator</title>
<meta http-equiv="Content-type" content="text/html; charset=ISO-8859-1">
$styleSection
</head>

<body class=style1>
HERE

  if (@Parents == 0) {
    print (qq(<blockquote><center>) .
           qq(You didn't select anyone to contribute to the next generation and everyone has died. ) .
           qq(You're population has gone extinct.

) .
           qq(Click your back button if you'd like to select one or more organisms to contribute ) .
           qq(to the next generation and try again.) .
           qq(</center></blockquote>));
    exit(0);
  }

  my $genNum = $p->param('gennum');
  my $nextGenNum = $genNum + 1;

print <<HERE;
<form action="Evolution.cgi" enctype="multipart/form-data" method="post">
<input type="hidden" name="cnt" value="">

<center>
<blockquote>
<span class="style3">Evolution Demonstrator</span>

<p /> 
$introText
<p /> 

Select the parents and offpsring to produce the next generation, then click Generate.
</blockquote>
</center>

<table border="1" align="center" class=style2>
<tr>
  <td>
    Number of
Generations:
  <td>
    $genNum
    <input type=hidden name=gennum value=$nextGenNum>
  <td>
<tr>
  <td>
    Target:
  <td>
    $targetTextEncoded
    <input type=hidden name=target value="$targetTextEncoded">
  <td>
    Select:
HERE

  my $count = 1;
  foreach (@Parents) {
    my $parentString = $_;
    my ($parentStringProcessed, $numMatches) = ProcessString($parentString, $targetText);
    my $parentStringEncoded = $parentString;
    $parentStringEncoded =~ s/"/"/g;
    print <<HERE;
<tr>
  <td>
    Parent $count:
  <td>
    $parentStringProcessed
  <td>
    <input type=checkbox name=parentsel-1 value="$parentStringEncoded"> $numMatches
HERE

    foreach (1..$numOffspring) {
      my $offspring = GenOffspring($parentString, $numMutations);
      my ($offspringProcessed, $numMatches) = ProcessString($offspring, $targetText);
      my $offspringEncoded = $offspring;
      $offspringEncoded =~ s/"/"/g;
      print <<HERE;
<tr>
  <td>
    Offspring $_:
  <td>
    $offspringProcessed
  <td>
    <input type=checkbox name=parentsel-$_ value="$offspringEncoded"> $numMatches
HERE

    }
    $count++;
  }

print <<HERE;
<tr>
  <td>
  <td align=right>
    Number of mutations:
  <td>
    <input type="radio" name="mutations" value="1" $NumMutationsChecked{1}/>1
    <input type="radio" name="mutations" value="2" $NumMutationsChecked{2}/>2
    <input type="radio" name="mutations" value="5" $NumMutationsChecked{5}/>5
    <input type="radio" name="mutations" value="10" $NumMutationsChecked{10}/>10
<tr>
  <td>
  <td align=right>
    Number of offspring per parent:
  <td>
    <input type="radio" name="offspring" value="1" $NumOffspringChecked{1}/>1
    <input type="radio" name="offspring" value="2" $NumOffspringChecked{2}/>2
    <input type="radio" name="offspring" value="5" $NumOffspringChecked{5}/>5
    <input type="radio" name="offspring" value="10" $NumOffspringChecked{10}/>10
<tr>
  <td colspan=3 align=center>
    <input type="submit" name="command" value="Create Next Generation">
               
    <input type="submit" name="startover" value="Start Over">
               
    <input type="submit" name="reset" value="Reset">
</table>

 <div align="center">

    <input type="hidden" name="total_mutations" value="0" />
    <input type="hidden" name="checksum" value="" />
    <span class="style1">Demonstrate evolution for yourself with the Evolution Generator</span></p>
 </div>
 <blockquote>
    $descriptiveText
 </blockquote>
</form>
</body>
</html>
HERE

}

sub GenOffspring {
  my ($parent, $numMutations) = @_;
  my %Positions;
  my $parentLen = length($parent);
  return '' if $parentLen == 0;
  if ($numMutations >= $parentLen) {
    $numMutations = $parentLen;
    map {$Positions{$_} = 1} (0..$numMutations-1);
  } else {
    foreach (1..$numMutations) {
      my $pos;
      do {
        $pos = int(rand($parentLen));
      } until !$Positions{$pos};
      $Positions{$pos} = 1;
    }
  }
  my @Parent = split(//, $parent);
  foreach (keys %Positions) {
    @Parent[$_] = $LegalChars[int(rand(@LegalChars))];
  }
  my $offspring = join '', @Parent;
  return $offspring;
}

sub ProcessString {
  my ($trialString, $targetText) = @_;
  my @TrialString = split(//, $trialString);
  my @TargetString = split(//, $targetText);
  my $numMatches = 0;
  for (my $i=0; $i<@TrialString; $i++) {
    if (lc($TrialString[$i]) eq lc($TargetString[$i])) {
      if ($TrialString[$i] eq ' ') {
        $TrialString[$i] = "<font color=red>_</font>";
      } else {
        $TrialString[$i] = "<font color=red>$TrialString[$i]</font>";
      }
      $numMatches++;
    }
    $TrialString[$i] =~ s/"/"/;
  }
  return ((join '', @TrialString), $numMatches);
}

Those would be excellent improvements, though you don't really want to change the environment as rapidly as every 10 generations, but the rate of environmental change can be a variable. The source is in Message 34, go for it.--PercyEdited by Percy, : Add comment.

Hi Bolder-dash,Your concerns were addressed earlier in the thread, particularly in Message 4. An excerpt: You are welcome to make all the improvements you like. Let me know when you're done and I'll be glad to make it available here. The original source appears in Message 34.But before you go to any trouble please be aware that there are many excellent evolution simulation programs available on the web. They lack the simplicity and layperson-level understandability of my program, but they do an excellent job addressing the concerns you raise. If you want links to them just ask. I don't know the links off the top of my head, but I'm sure other participants in this thread do.--Percy