Random mutations shot down on this site.

Hoot Mon writes:Now, on the issue of speciation and the role of drift, I wrote in Message 15:

quote:

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Two British evolutionary biologists, Nick Smith & Adam Eyre-Walker (Adaptive protein evolution in Drosophila, Nature, 2002) have studied adaptive protein evolution in two fruit-fly species, D. melanogaster and D. yakuba. They determined that the two species separated about 6 million years ago, and that 45% of the separation could be attributed to natural selection. The remaining 55% of the protein differences were determined to be selection-neutral, and these difference were attributed to genetic drift.

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They are taling about speciation here.

I wish I could get you to examine Smith and Eyre-Walker’s Science article, reference above. They found 55% of the protein differences between two fruit fly species to be attributable to drift. And please see the work of Daniel Hartl, also referenced above. He often stresses the non-adaptive aspects of speciation.

Doddy writes:I'm with Hoot Mon on this one.

For there to be random mating, each tree in the forest should have equal chance of being pollinated by every other tree, which does not happen due to the long distances in the population.

This is not sexual selection, because there is no selection of mates by either party. Just luck of the wind and insects usually.

Doddy writes:Let me quote the definition on wikipedia:

quote:

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Random mating involves the mating of individuals regardless of any physical, genetic, or social preference. In other words, the mating between two organims is not influenced by any environmental, heriditary, or social interaction. Hence, potential mates have an equal chance of being selected.

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That is what random mating means. And, no species does it...so what?

For there to be random mating, each tree in the forest should have equal chance of being pollinated by every other tree, which does not happen due to the long distances in the population.

Doddy writes:I must be missing something....

Hoot Mon writes:I think you are wrong. I bothered to go get the whole article through my public library. Try it. You would be impressed with their drift v. selection model.

Doddy writes:Sorry, I'm fairly sure that it does. All genetics simulations that I've encountered do this when set to random mating.

As one of the assumptions of the HWP, random mating is described. Infinite population size can't be observed in any species either, but that doesn't mean it is a useless definition....But, it appears we are both using different definitions - I refer to the theoretical, and you to the real-world.

Percy writes:Can you imagine any species in the known universe where an individual has an equal chance of mating with all other living individuals of its species? No, of course not. So obviously that's not what random mating means.

Hoot Mon writes:Two British evolutionary biologists, Nick Smith & Adam Eyre-Walker (Adaptive protein evolution in Drosophila, Nature, 2002) have studied adaptive protein evolution in two fruit-fly species D. melanogaster and D. yakuba. They determined that the two species separated about 6 million years ago, and that 45% of the separation could be attributed to natural selection. The remaining 55% of the protein differences were determined to be selection-neutral, and these difference were attributed to genetic drift.

Hoot Mon writes:To me, this is a credible attempt to differentiate, as casual factors attending microevolution, the actions of natural selection from those of drift.

Hoot Mon writes:But you obviously didn't read my Message 43, in which I made clear to Quetzal my mistaken conflation of speciation with microevolution. You're just ankle biting again.

Hoot Mon writes:Yes, Percey, I went there, but I haven't run the generator yet because I was disappointed by this claim...

Let's say you want the word Brown to evolve into the word Black. Shouldn't be too hard, should it? Only four letters need to change after all. But even if you could get the mutations to concentrate just on those four letters, you'd still get a mis-spelled word, which natural selection would eliminate before it ever evolved into the correct spelling.Let's try it, one mutation at a time:Brown > Brorn > Brorb > BrorW > qrorW > qKorW > qKoJW > qKoyW > qFoyW > qjoyW > qjTyW

Brown to Black Genetic Algorithm Program with extremely weak selection writes:nclx65% perl ga.pl
Generation 1: Brown
Generation 2: Bhown Browg Bwown Bxown BrFwn
Generation 3: Bhogn Bxoin BwoYn Bkown BroTg
Generation 4: Bhfgn Bhodn Boogn Bnoin Bhohn
Generation 5: Bhfdn Bmfgn Bhfgs Bhocn Bhfgu
Generation 6: Bhfdn Bhfgk Bhfdf Bifgn BhYdn
Generation 7: Bhagk Bhddn Bhcdf Bhfdh Bifgl
Generation 8: Boagk Bhddk Biagl Bmcdf Bhagi
Generation 9: Biddk Biafl Boagl Bhddk Bmcdg
Generation 10: Bhbdk Bmcdi Bhddk Biddi Boagm
Generation 11: Bhbck Bmcdl Bhbbk Brbdk Biddm
Generation 12: Bhack Bhbbk Bibdm Bmcdo Biddm
Generation 13: Bkbbk Fhack Brbbk Bidcm Biddj
Generation 14: Bkbbk Bkbbm Brbbk Bidcm Ciddj
Generation 15: Bkabk Ckbbk Bkbbm Bpbbk Jkbbk
Generation 16: Dkbbk Bgabk Bpbbk Bkabf Ckbbh
Generation 17: Bpbbk Bpbak Bkadf Ckbbh Dpbbk
Generation 18: Dnbbk Bpbbj Bpbbj Bmadf Dpbbk
Generation 19: Bmadh Bmadn Dobbk Bpbdj Bpbbl
Generation 20: Blbbl Bmadh Dkbbk Bjadn Bmadq
Generation 21: Blbbl Bmadm Bmach Ckbbk Bldbl
Generation 22: Bmadj Blach Ckbdk Ckbbm Cibbk
Generation 23: Blach Blcch Bibbk Bqadj Cpbbk
Generation 24: Blacm Blach Blacf Blcch Bgbbk
Generation 25: Bkach Blcci Blace Bpach Blaim
Generation 26: Bkcci Bkcci Bkaeh Boach Blccg
Generation 27: Boacl Dkaeh Bfcci Bdach Bccci
Generation 28: Boacm Bjach Boacg Dkaei Dkaeh
Generation 29: Bmacg Bjacg Bjcch Dkaeh Dkaeh
Generation 30: Bmacg Bmacf Dmacg Bmacq Bmacr
Generation 31: Dmacg Dmabg Dmccg Bmaar Bmaar
Generation 32: Bmabg Dmabm Dmacg Diacg Fmacg
Generation 33: Bmabg Cmacg Fmabm Dnacg Bmdbg
Generation 34: Bmacg Cmabg Cmacp Bmdbn Bhabg
Generation 35: Bmabg Bhabm Cmaeg Bhabh Ciabg
Generation 36: Bhabm Ckaeg Bhabh Cmbeg Ciabg
Generation 37: Bhabk Ciabk Bhabm Bhabo Bhaah
Generation 38: Cjabk Biabm Bhabj Bjaah Beabk
Generation 39: Ckabk Cjabk Biabk Bqabk Ahabj
Generation 40: Clabk Boabk Aiabk Biaek Fkabk
Generation 41: Alabk Bkabk Clbbk Boabk Aiadk
Generation 42: Aladk Amabk Alaak Boabk Boadk
Generation 43: Alaal Alafk Biadk Anaak Amabn
Generation 44: Alaak Alafk Alaah Anaaj Amabn
Generation 45: Amaaj Anabj Aiaak Aldak Agaak
Generation 46: Anaej Aiaak Aldek Aoaak Aldal
Generation 47: Alaak Aldal Algek Aieak AlZek
Generation 48: Aleak Cldal Algbk Algek AlZek
Generation 49: Claal Alcbk Albek Alcek Cldak
Generation 50: Alcck Claal Albfk Dlcek Alcbh
Generation 51: Alcck Dlaek Dlcck Albfh Alcce
Generation 52: Aldck Dlahk Albfm Dlccg Dlchk
Generation 53: Albcm Ajdck Clbfm Dlccn AlZck
Generation 54: Aldcm Ajdck Clafm Blbfm Djdck
Generation 55: Agdck Ajdfk Claff Djfck Dpdck
Generation 56: Amdck Ajdbk Ajffk Cnaff Drdck
Generation 57: Ajdck Ajcbk Gmdck Amhck Imdck
Generation 58: Ejdck Ajebk Gmdck Cmhck Gndck
Generation 59: Gldck Ajebi Gndck AjYbk Cmhch
Generation 60: Cmbch Endck Endck Gldbk Fndck
Generation 61: Andck Cibch Fmdck Gmbch Fndcl
Generation 62: Ajdck Andck Bndcl Cibcm Andak
Generation 63: Andck Aodck Andcl Anddk Bodcl
Generation 64: Boacl Bkdcl Andck Apdck Bodbl
Generation 65: Boack Boacl Bkdcl Aidck Cpdck
Generation 66: Coack Bkdck Bkdcl Boacg Bfacl
Generation 67: Aoack Bkdbk Bndck Bkdcl Bndcl
Generation 68: Bkdak Dkdcl Bkdch Aeack Bhdbk
Generation 69: Bkdbk Dkddl Ekdcl Ceack Bkdan
Generation 70: Ekacl Dkdcl Bkdbh Ekdcl Bkdbo
Generation 71: Ekacl Dkdcl Epacl Eeacl Bkdgh
Generation 72: Akacl Emacl Ekagl Ekecl Egacl
Generation 73: Amacl Akacp Epacl Ekafl Egacl
Generation 74: Akacm Bgacl Amacd Akaap Enafl
Generation 75: Akabm Akacf Bracl Enael Akfcm
Generation 76: Bracl Anacf Braci Enael Enaem
Generation 77: Bnaci Bracl Dnael Enaek Brbcl
Generation 78: Bmaci Emaek Fnaek Dhael Dncel
Generation 79: Bnaek Fnadk Doael Emdek Hmaek
Generation 80: Bnaek Biaek Bmdek Fnadk Fnadk
Generation 81: Biaak Bhaek Bmdel Bnaik Eiaek
Generation 82: Biaak Biaek Bhaak Bmdbl Bmdel
Generation 83: Bjaak Bmdcl Biaai Btaak Bmdil
Generation 84: Bmccl Bmdcj Bjagk Bpaak Ejaak
Generation 85: Bjack Blccl Elaak Bjagk BpaakSuccess! Here's the final generation:Generation 86: Black Blbcl Bjack Bjaak Bqack

Brown to Black Genetic Algorithm Program with extremely strong selection writes:nclx65% perl ga.pl
Generation 1: Brown
Generation 2: Bxown BroKn Brywn Bgown Brhwn
Generation 3: Bxown BxoBn BVown BxowJ BxRwn
Generation 4: BTown BxowY Bxoun BxoWn Bxosn
Generation 5: BToNn BToww BTowD BTojn BTokn
Generation 6: BToIn BTozn BUoNn BRoNn BNoNn
Generation 7: BTogn BToIK BTojn BOoIn BaoIn
Generation 8: BTogk Byogn BTogb BMogn BTogm
Generation 9: BVogk BTXgk BTolk Blogn BMocn
Generation 10: Blogk BPogk BVosk Bdogk BVokk
Generation 11: BloSk Blolk BlNgk Blojk BloWk
Generation 12: Block BlGSk BloJk Blouk BloIk
Generation 13: BlVck plock BloMk Xlock BloekSuccess! Here's the final generation:Generation 14: Black Block BlLck BlEck BlVWk

#! /dv/tools/bin/perl

use strict;

my $originalWord = "Brown";

my $targetWord = "Black";

my $numOffspring = 10;

my $numSelectedOffspring = 5;

my $maxGenerations = 100;

if (length($originalWord) != length($targetWord)) {
  print ("Length of orginal word ($originalWord) and target\n" .
         "word ($targetWord) are not the same, this program\n" .
         "can not yet handle different word lengths.\n");
  exit;
}

my $wordLength = length($originalWord);

my $letters = "abcdefghijklmnopqrstuvwxyz" .
              "ABCDEFGHIJKLMNOPQRSTUVWXYZ";

my @Letters = split(//, $letters);

my $numLetters = @Letters;

my @ThisGeneration = ($originalWord);

PrintGeneration(1, @ThisGeneration);

for (my $gen=2; $gen<=$maxGenerations; $gen++) {
  my (@NextGeneration, @SelectedNextGeneration);
  foreach my $word(@ThisGeneration) {
    for (my $i=0; $i<$numOffspring; $i++) {
      my $offspring = $word;
      substr($offspring, int(rand($wordLength)), 1) =
        $Letters[int(rand($numLetters))];
      push(@NextGeneration,
           [Evaluate2($offspring), $offspring]);
    }
  }
  @NextGeneration =
    sort {($a)->[0] <=> ($b)->[0]} @NextGeneration;

  for (my $i=0; $i<$numSelectedOffspring; $i++) {
    push(@SelectedNextGeneration, $NextGeneration[$i]->[1]);
  }
  @ThisGeneration = @SelectedNextGeneration;
  if (Success(@ThisGeneration)) {
    print "\nSuccess!  Here's the final generation:\n\n";
    PrintGeneration($gen, @ThisGeneration);
    last;
  } else {
    PrintGeneration($gen, @ThisGeneration);
  }
}

exit(0);

##################################################

sub PrintGeneration {
  my ($gen, @Generation) = @_;
  print "Generation $gen: " . (join " ", @Generation) . "\n";
}

# Uses count of number of correct letters, higher is better
sub Evaluate1 {
  my ($word) = @_;
  my $sum = 0;
  for (my $i=0; $i < $wordLength; $i++) {
    if (substr($word, $i, 1) eq substr($targetWord, $i, 1)) {
      $sum++;
    }
  }
  return $sum;
}

# Uses summation of differences of letter ordinals,
# lower is better
sub Evaluate2 {
  my ($word) = @_;
  my $sum = 0;
  for (my $i=0; $i < $wordLength; $i++) {
    my $diff = ord(substr($word, $i, 1)) -
               ord(substr($targetWord, $i, 1));
    if ($diff < 0) { $diff = -$diff; }
    $sum += $diff;
  }
  return $sum;
}

sub Success {
  foreach my $word(@_) {
    if ($word eq $targetWord) {
      return 1;
    }
  }
  return 0;
}

Wounded King writes:I'm pretty sure Perry would categorise all of those intermediate changes as 'fatal' mutations, even though you have done the first thing he said was impossible.

DigDug Master writes:If anyone had bothered to run the generator you would see there is a natural selection element.

Ironicly, even though it seems nobody agrees with the site, you would all rather bicker amongst each other then seriusly attempt to reason and explain why it's inaccurate. I'm an open minded person, why not dignify the subject with some clear answers.