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dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: Mar. 29 2009,08:24   

In the past, I've worked with the ECJ package from Sean Luke's group at George Mason University. It has support for (mu, lamda)-ES built in. I might have time to build a weasel in ECJ. I think it might be a matter of setting up the parameter file right, all the code is already there.

--------------
I知 referring to evolution, not changes in allele frequencies. - Cornelius Hunter
I知 not an evolutionist, I知 a change in allele frequentist! - Nakashima

  
dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: Mar. 29 2009,08:45   

Not specifically Weasel...

I just read this paper on sexual selection in GA. I was thinking of trying to reproduce (ahem) some of the results. It seems the researchers made a bunch of changes to the standard GA, and I'd like to see which were responsible for the positive variations they report.

--------------
I知 referring to evolution, not changes in allele frequencies. - Cornelius Hunter
I知 not an evolutionist, I知 a change in allele frequentist! - Nakashima

  
Wesley R. Elsberry



Posts: 4504
Joined: May 2002

(Permalink) Posted: June 10 2009,20:11   

The antievolutionist software, Mendel's Accountant, asserts that it "allows realistic numerical simulation of the mutation/selection process over time".

Discussion at Theology Web, though, indicates that the program may not deliver results in accordance with known population genetics.

Gary Hurd suggested that this would be a good topic for a TOA FAQ. We can use this thread to help coordinate people working on an analysis of Mendel's Accountant.

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
AnsgarSeraph



Posts: 11
Joined: June 2009

(Permalink) Posted: June 10 2009,22:07   

Hi, all

I'm another migrant from TWeb; I've got Mendel's Accountant set up on a 32-bit and a 64-bit system. I certainly won't be much help with any actual knowledge but I'm very willing to run simulations for anyone who doesn't have/doesn't want Mendel set up on their computer.

I've found that Mendel will allow my 4GB setup to run small populations (~1000) for about 40,000 generations or larger populations (~10,000) for less than 10,000 generations. I plan on purchasing some extra RAM soon so I might be able to extend the runs a bit. I did not see much difference in latitude running a 64-bit setup but extra RAM might change that.

The user manual for Mendel's Accountant is here. If helpful, I can (hopefully) attach screen grabs of the advanced Mendel settings so people don't need to hunt through the manual.

祐am

  
AnsgarSeraph



Posts: 11
Joined: June 2009

(Permalink) Posted: June 10 2009,22:10   

Sorry. The manual is HERE:

Mendel's Accountant User Manual

There is also a Linux how-to but the SourceForge page does not have the tarball listed. Some advanced features of MENDEL require Linux. They are almost certainly unnecessary for a FAQ but I'll e-mail the maintainer of the code (Dr. Brewer, I think) and try to get that.

祐am

  
Dr.GH



Posts: 1956
Joined: May 2002

(Permalink) Posted: June 10 2009,22:36   

Howdy Sam. Glad to see you here. I'll assume that you have seen the prior discussion on this site starting about about here.

I hope to be away all day tomorrow, so I hope that everyone will start right to work while I go fishing.  :D

--------------
"Science is the horse that pulls the cart of philosophy."

L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

   
Richardthughes



Posts: 10228
Joined: Jan. 2006

(Permalink) Posted: June 10 2009,22:46   

Also:

http://www.facebook.com/group.php?gid=5381573897

--------------
"Richardthughes, you magnificent bastard, I stand in awe of you..." : Arden Chatfield
"You magnificent bastard! " : Louis
"ATBC poster child", "I have to agree with Rich.." : DaveTard
"I bow to your superior skills" : deadman_932
"...it was Richardthughes making me lie in bed.." : Kristine

  
utidjian



Posts: 185
Joined: Oct. 2007

(Permalink) Posted: June 11 2009,00:18   

Ok... I downloaded the .exe files. Both the earlier version and the update from sourceforge.

I am running Linux (Fedora 10) on a Intel iMac with 1G of RAM.

I unpacked the files with Wine. First the older version and then the newer one. Man it installs a lot of stuff.

The Linux source is in
/home/utidjian/.wine/drive_c/Mendel/Source
on my system. Not much in there.

listing:
Code Sample

[utidjian@istrain Source]$ ls -ogh
total 416K
-rw-rw-rw- 1 4.5K 2008-09-13 17:38 common.h
-rw-rw-rw- 1 587 2008-09-07 22:00 Interface back-end.lnk
-rw-rw-rw- 1 661 2008-09-07 22:00 Interface front-end.lnk
-rw-rw-rw- 1 985 2008-09-01 20:51 Makefile
-rw-rw-rw- 1 165K 2008-10-01 06:15 mendel.f
-rw-rw-rw- 1 163K 2008-09-05 22:00 mendel.f.bak
-rw-rw-rw- 1 1.9K 2008-09-18 18:57 mendel.in
-rw-rw-rw- 1 1.5K 2008-09-04 03:20 mpi_mendel.f
-rw-rw-rw- 1 42K 2006-03-01 13:02 random_pkg.f90
-rw-rw-rw- 1 1.3K 2007-01-15 09:50 sort.f90


The main file in there is mendel.f. Lots of comments. I can "read" Fortran but I don't know diddly about Population Genetics.

Time for bed.

-DU-

--------------
Being laughed at doesn't mean you're progressing along some line. It probably just means you're saying some stupid shit -stevestory

  
Zachriel



Posts: 2598
Joined: Sep. 2006

(Permalink) Posted: June 11 2009,07:08   

I upgraded to Mendel 1.4.1. It acts differently with the parameters I tried in the original version. I started with the defaults changing only the fraction of beneficial mutations and maximum effect of beneficial mutations parameters.

    1.0000000 frac_fav_mutn
    1.0000000 max_fav_fitness_gain


Now the fitness increases in a linear fashion. So they must have fixed a major bug in between versions. I'll continue to test over the next few days.

--------------
Tard Acquisition and Repository Department

   
Dr.GH



Posts: 1956
Joined: May 2002

(Permalink) Posted: June 11 2009,11:22   

I collected the various "articles" writen about MA;

Larry Vardiman
2008. 典he "Fatal Flaws" of Darwinian Theory Acts & Facts. 37 (7): 6. Institute of Creation Research
http://www.icr.org/article/fatal-flaws-darwinian-theory/

Money quote:
 
Quote
溺endel's Accountant provides overwhelming empirical evidence that all of the "fatal flaws" inherent in evolutionary genetic theory are real. This leaves evolutionary genetic theory effectively falsified--with a degree of certainty that should satisfy any reasonable and open-minded person.


John Sanford, John Baumgardner, Wesley Brewer, Paul Gibson, Walter ReMine
2008a 填sing Numerical Simulation to Test the Validity of Neo-Darwinian Theory In A. A. Snelling (Ed.) (2008). Proceedings of the Sixth International Conference on Creationism (pp. 165175). Pittsburgh, PA: Creation Science Fellowship and Dallas, TX: Institute for Creation Research.
Download PDF


Baumgardner, J., Sanford, J., Brewer, W., Gibson, P., & ReMine, W.
2008b 溺endel痴 Accountant: A new population genetics simulation tool for studying mutation and natural selection. In A. A. Snelling (Ed.), Proceedings of the sixth international conference on creationism (pp. 8798). Pittsburgh, Pennsylvania: Creation Science Fellowship & Dallas, Texas: Institute for Creation Research.
Download PDF

Sanford, J., Baumgardner, J., Gibson, P., Brewer, W., & ReMine, W.
(2007a). Mendel痴 Accountant: A biologically realistic forward-time population genetics program. Scalable Computing: Practice and Experience 8(2), 147165. http://www.scpe.org.
Download PDF

Sanford, J., Baumgardner, J., Gibson, P., Brewer, W., & ReMine, W.
(2007b). Using computer simulation to understand mutation accumulation dynamics and genetic load. In Y. Shi, G. D. van Albada, J. Dongarra, & P. M. A. Sloot (Eds.), International Conference on Computer Sscience 2007, Part II, Lecture Notes in Computational Science 4488 (pp. 386392). Springer-Verlag: Berlin, Heidelberg.
Download PDF

Edited by Dr.GH on June 11 2009,09:33

--------------
"Science is the horse that pulls the cart of philosophy."

L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

   
Wesley R. Elsberry



Posts: 4504
Joined: May 2002

(Permalink) Posted: June 11 2009,11:29   

So, how much "evolution sucks" verbiage was generated by the people running the pre-1.4.1 versions? Was there any notice that people should re-run their experiments due to a pretty drastic change in program behavior?

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
Dr.GH



Posts: 1956
Joined: May 2002

(Permalink) Posted: June 11 2009,11:35   

Quote (Wesley R. Elsberry @ June 11 2009,09:29)
So, how much "evolution sucks" verbiage was generated by the people running the pre-1.4.1 versions? Was there any notice that people should re-run their experiments due to a pretty drastic change in program behavior?

Exactly!

PS: The links all work now, and I am going fishing.

--------------
"Science is the horse that pulls the cart of philosophy."

L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

   
AnsgarSeraph



Posts: 11
Joined: June 2009

(Permalink) Posted: June 11 2009,11:41   

Quote (Wesley R. Elsberry @ June 11 2009,11:29)
So, how much "evolution sucks" verbiage was generated by the people running the pre-1.4.1 versions? Was there any notice that people should re-run their experiments due to a pretty drastic change in program behavior?

To be fair (to a shoddy program? How odd), v. 1.4.1 still "demonstrates" all the genetic entropy problems that Sanford makes noise about. Whatever they fixed in terms of beneficial mutations, our runs at TWeb using 1.4.1 indicate that it's nowhere near enough; a 90% beneficial mutation rate with default "maximal benefit effect" still reduces fitness in a linear manner.

祐am

  
AnsgarSeraph



Posts: 11
Joined: June 2009

(Permalink) Posted: June 11 2009,11:45   

Quote (Wesley R. Elsberry @ June 11 2009,11:29)
So, how much "evolution sucks" verbiage was generated by the people running the pre-1.4.1 versions? Was there any notice that people should re-run their experiments due to a pretty drastic change in program behavior?

To be fair (to a shoddy program? How odd), v. 1.4.1 still "demonstrates" all the genetic entropy problems that Sanford makes noise about. Whatever they fixed in terms of beneficial mutations, our runs at TWeb using 1.4.1 indicate that it's nowhere near enough; a 90% beneficial mutation rate with default "maximal benefit effect" still reduces fitness in a linear manner.

祐am

  
utidjian



Posts: 185
Joined: Oct. 2007

(Permalink) Posted: June 11 2009,12:17   

Is anyone else playing with the source (or even reading it)?
I also found this file in the Source folder:

Code Sample

[utidjian@buttle Source]$ cat mendel.in
       1000    pop_size
        500    num_generations
          1    fitness_distrib_type:exponential_mutation_effect
          2    selection_scheme:unrestricted_probability_selection
         23    haploid_chromosome_number
       1000    num_linkage_subunits
   0.000000    pop_growth_rate
          0    pop_growth_model:fixed_population
  3.000e+08    haploid_genome_size
  6.0000000    offspring_per_female
  0.0000000    fraction_random_death
  0.0000000    fraction_self_fertilization
 10.0000000    new_mutn_per_offspring
  0.0010000    high_impact_mutn_fraction
  0.1000000    high_impact_mutn_threshold
  0.0010000    uniform_fitness_effect_del
  0.0000000    multiplicative_weighting
  1.000e-05    tracking_threshold
  0.0000000    fraction_recessive
  0.0000000    recessive_hetero_expression
  0.5000000    dominant_hetero_expression
  0.0000000    frac_fav_mutn
  0.0010000    max_fav_fitness_gain
  0.2000000    heritability
  0.0000000    non_scaling_noise
  0.5000000    partial_truncation_value
          0    num_contrasting_alleles
  0.0000000    initial_alleles_mean_effect
  0.9000000    linked_mutn_se_fraction
  1.0000000    se_scaling_factor
          0    synergistic_epistasis
          0    clonal_reproduction
          0    clonal_haploid
          1    dynamic_linkage
          0    fitness_dependent_fertility
          0    is_parallel
          0    bottleneck_yes
       1000    bottleneck_generation
        100    bottleneck_pop_size
        500    num_bottleneck_generations
          0    num_initial_fav_mutn
          1    num_indiv_exchanged
          1    migration_generations
          1    migration_model
          1 homogenous_tribes
      47469 max_tracked_mutn_per_indiv
         42 random_number_seed
          0 write_dump
          0 restart_case
          1 restart_dump_number
test01 case_id
/.
          2 num_tribes
          2 num_procs
          0 plot_avg_data
          0 restart_case_id
          1 restart_append
batch run_queue
          0 c_engine


Anything interesting in there?

-DU-

--------------
Being laughed at doesn't mean you're progressing along some line. It probably just means you're saying some stupid shit -stevestory

  
midwifetoad



Posts: 3568
Joined: Mar. 2008

(Permalink) Posted: June 11 2009,12:37   

Quote (Richardthughes @ Mar. 27 2009,17:08)
Pharyngula on "Weasel":

http://scienceblogs.com/pharyng....put.php

Quote
As Ian Musgrave shows, the program is trivial, and even us biologists can whip one out in minutes.


Even non-biologists...

http://www.itatsi.com

--------------
罵et痴 not make a joke of ourselves.

Pat Robertson

  
Wesley R. Elsberry



Posts: 4504
Joined: May 2002

(Permalink) Posted: June 11 2009,12:41   

If anybody is trying to install MA, but has a more recent Perl and unchecks the Perl install, be warned that the CGI has a fixed location that it expects to launch the Perl executable from, C:\Mendel\Perl\bin\perl.exe

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
AnsgarSeraph



Posts: 11
Joined: June 2009

(Permalink) Posted: June 11 2009,12:52   

Quote (utidjian @ June 11 2009,12:17)
Is anyone else playing with the source (or even reading it)?
I also found this file in the Source folder:

Code Sample

47469 max_tracked_mutn_per_indiv


Anything interesting in there?

-DU-

That number is considerably higher than the input parameters on my runs; ranging from a population of 1000 to a population of 10,000, I think the highest setting on my runs for that was ~25,000 tracked mutations per individual. I'm not sure how they calculate for that parameter. This might be one of the limiting factors in testing MENDEL, as I have already run up against a "Favorable mutation count exceeds limit" error.

祐am

  
Steve Schaffner



Posts: 13
Joined: June 2009

(Permalink) Posted: June 11 2009,13:02   

I may have missed something, but I haven't seen anything in the v. 1.4.1 runs that was clearly wrong, i.e. that suggested a bug in the implementation (other than the broken option for fixed selection coefficient). Which doesn't mean there aren't any bugs, but they are not obvious.

What is clear is that the default parameters for beneficial alleles are very low. Their justification for having such a low maximum beneficial effect strikes me as plausible-sounding nonsense.

It's also clear that their basic model is not one from evolutionary biology. The essential process they're modeling is the accumulation of mildly deleterious mutations, ones that have such a small functional effect that they are invisible to natural selection. This only occurs because the population starts out in a state of genetic perfection, compared to which the new mutations are deleterious. A real population would never have become that optimized, precisely because the different choices of allele are indistinguishable by NS.

For those who have the program running . . . Can it provide more output? Comparing results with theory would be much more straightforward if one could count only the number of mutations that have fixed, rather than all present in the population; it would also be useful to see the allele frequency spectrum. (And if it can't do those things, then it is of no interest as a population genetics tool.)

  
AnsgarSeraph



Posts: 11
Joined: June 2009

(Permalink) Posted: June 11 2009,13:23   

Quote (Steve Schaffner @ June 11 2009,13:02)
For those who have the program running . . . Can it provide more output? Comparing results with theory would be much more straightforward if one could count only the number of mutations that have fixed, rather than all present in the population; it would also be useful to see the allele frequency spectrum. (And if it can't do those things, then it is of no interest as a population genetics tool.)

Is the allele frequency spectrum you're looking for in here?

Box.net - human1 sample Folder

I think what you're looking for might be titled "human1_plm.png".

The output files in MENDEL do give a count for the number of fixed alleles; it's near the bottom of the output file and looks like this:

Code Sample

Allele summary statistics (tracked mutations only):
   (Statistics are based on       891517 tracked deleterious mutations
                        and            0 tracked   favorable mutations.)
    Very rare   Polymorphic     Fixed      Total
      (0-1%)      (1-99%)      (100%)
       15107        8202           0       23309 deleterious
           0           0           0           0 favorable


祐am

  
Henry J



Posts: 4079
Joined: Mar. 2005

(Permalink) Posted: June 11 2009,13:27   

Quote
I can "read" Fortran

I used to be able to do that, but college was decades ago and the language probably "evolved" since then.

Quote
Anything interesting in there?

-DU-

Yes:

Quote
10.0000000    new_mutn_per_offspring

I'm no biologist, but that sounds high to me.

Henry

  
midwifetoad



Posts: 3568
Joined: Mar. 2008

(Permalink) Posted: June 11 2009,13:40   

Quote
What is clear is that the default parameters for beneficial alleles are very low. Their justification for having such a low maximum beneficial effect strikes me as plausible-sounding nonsense.


From my own dabbling I think the only really critical factor in getting a GA to "work" is an effective fitness function. Assuming at least some offspring are viable, the fitness function must be able to see and score alleles, either by seeing them directly of by having some means of scoring phenotypes.

All the other aspects are pretty much irrelevant.

My own effort tries to evolve a population of letter strings that "look like" words, without having a fixed target. The trick is having a fitness function that can score relative wordness without requiring enormous computational resourses.

--------------
罵et痴 not make a joke of ourselves.

Pat Robertson

  
Wesley R. Elsberry



Posts: 4504
Joined: May 2002

(Permalink) Posted: June 11 2009,13:46   

I just ran Zachriel's modified parameter set under v1.2.1 and v.1.4.1. Both used exactly the same "mendel.in" configuration file. Only one each, but the v1.4.1 run does go to completion and shows the accumulation and fixation of favorable mutations. The v1.2.1 run, by contrast, shows a declining population that only lasts to generation 31. The value for "before sel: geno fitness" looks particularly strange; in the final generation, the value was -90.5. In the v1.4.1 run, that value was never less than 1.0, and at generation 500 had reached a little over 20. I'm assuming at the moment that the "fitness" value is always with respect to the original absolute value at the start of the run.

Whatever else may be going on, it does seem that MA treatment of favorable mutations changed rather radically between those versions. I wouldn't want to validate v1.4.1 on this basis, but it comparatively is doing a much better job than v1.2.1, and I think my earlier comment stands: outcomes of experiments performed with MA v1.2.1 (and perhaps earlier versions) should be treated with skepticism until independently confirmed, preferably with a package that can be validated against actual popgen results.

ETA: Using Mendel's Accountant v.1.2.1 is like using a bank that inexplicably only records your withdrawals and fails to record your deposits.

Edited by Wesley R. Elsberry on June 11 2009,13:57

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
oldmanintheskydidntdoit



Posts: 4999
Joined: July 2006

(Permalink) Posted: June 11 2009,13:47   

Quote (midwifetoad @ June 11 2009,13:40)
The trick is having a fitness function that can score relative wordness without requiring enormous computational resourses.

I wonder if google could help, after all it "suggests" words when it cannot match your search term. No suggestion = not "wordy" enough.

OK it's probably not practical, not for running quickly anyway.

Still....

--------------
I also mentioned that He'd have to give me a thorough explanation as to *why* I must "eat human babies".
FTK

if there are even critical flaws in Gauger痴 work, the evo mat narrative cannot stand
Gordon Mullings

  
midwifetoad



Posts: 3568
Joined: Mar. 2008

(Permalink) Posted: June 11 2009,13:51   

Quote (oldmanintheskydidntdoit @ June 11 2009,13:47)
Quote (midwifetoad @ June 11 2009,13:40)
The trick is having a fitness function that can score relative wordness without requiring enormous computational resourses.

I wonder if google could help, after all it "suggests" words when it cannot match your search term. No suggestion = not "wordy" enough.

OK it's probably not practical, not for running quickly anyway.

Still....

Google runs pretty quickly for me. I'm a bit in awe of their ability to suggest words from misspellings, but after my experience evolving words I think I know how they do it. Or at least one approach that doesn't require a supercomputer.

I think my approach is more effective than that used by most spelling checkers.

--------------
罵et痴 not make a joke of ourselves.

Pat Robertson

  
sledgehammer



Posts: 531
Joined: Sep. 2008

(Permalink) Posted: June 11 2009,14:05   

I haven't run the program, but perusing the description of the algorithm, it seem to me that this section that describes how fitness is assigned is the part that determines the ultimate behavior of the model. They clearly have built in an asymmetry in the fitness of beneficial vs deleterious mutations, and their justifications of the asymmetry smell fishy to me, but IANAB. (bolding mine)
 
Quote
To provide users of Mendel even more flexibility in specifying the fitness effect distribution, we have chosen to use a
form of the Weibull function [12] that is a generalization of the more usual exponential function. Our function, expressed
by eq. (3.1), maps a random number x, drawn from a set of uniformly distributed random numbers, to a fitness effect d(x)
for a given random mutation.
d(x) = (dsf) exp(?ax^gamma), 0 < x < 1. (3.1)
Here (dsf) is the scale factor which is equal to the extreme value which d(x) assumes when x = 0. We allow this scale
factor to have two separate values, one for deleterious mutations and the other for favorable ones.
These scale factors are meaningful relative to the initial fitness value assumed for the population before we introduce new mutations. In Mendel we assume this initial fitness value to be 1.0. For deleterious mutations, since lethal mutations exist, we choose dsf del = ?1. For favorable mutations, we allow the user to specify the (positive) scale factor dsf fav. Normally, this would be a small value (e.g., 0.01 to 0.1), since it is only in very special situations that a single beneficial mutation would
have a very large effect.

The parameters a and gamma, both positive real numbers, determine the shape of the fitness effect distribution. We applythe same values of a and gamma to both favorable and deleterious mutations. The parameter a determines the minimum absolute values for d(x), realized when x = 1. We choose to make the minimum absolute value of d(x) the inverse of the haploid genome size G (measured in number of nucleotides) by choosing a = loge(G). For example, for the human genome, G = 3 ラ 109, which means that for the case of deleterious mutations, d(1) = ?1/G = ?3 ラ 10?10. For large genomes,
this minimum value is essentially 0. For organisms with smaller genomes such as yeast, which has a value for G on
the order of 107, the minimum absolute effect is larger. This is consistent with the expectation that each nucleotide in a smaller genome on average plays a greater relative role in the organism痴 fitness.
The second parameter gamma, can be viewed as ontrolling the fraction of mutations that have a large absolute fitness
effect. Instead of specifying gamma directly, we select two quantities that are more intuitive and together define gamma. The first is theta, a threshold value that defines a 塗igh-impact mutation. The second is q, the fraction of mutations that exceed this threshold in their effect. For example, a user can first define a high-impact mutation as one that results in 10% or more change in fitness (theta = 0.1) relative to the scale factor and then specify that 0.001 of all mutations (q = 0.001) be in this category. Inside the code the value of is computed that satisfies these requirements. We reiterate that Mendel uses the same value for gamma, and thus the same values for theta and q, for both favorable and deleterious mutations. Figure 3.1 shows the effect of the parameter q on the shape of the distribution of fitness effect. Note that for each of the cases displayed the large majority of mutations are nearly neutral, that is, they have very small effects. Since a utation痴 effect on fitness can be measured experimentally only if it is sufficiently large, our strategy for parameterizing the fitness effect distribution in terms of high-impact situtations provides a means for the Mendel user to relate the numerical model input more directly to available data regarding the actual measurable frequencies of mutations in a given biological context.

Part of the justification for asymmetry is that some mutations are lethal, meaning that individual has zero probability of reproducing. OK, but the maximum fitness benefit of a beneficial mutation is "a very small number like 0.001", which is then subject to "heritability factor", typically 0.2, and other probabilities that severely limit its ability to propagate.
To make matters worse, for some unjustified reason, the same distribution for beneficial and deleterious is used, after severely skewing the results with the above.
Again, IANOB, but it seems to me that a single beneficial mutation can, in many situations like disease resistance, blonde hair, big boobs, etc, virtually guarantee mating success, just like a deleterious mutation can be reproductively lethal.
I can see easily how the skewed treatment of beneficial vs deleterious mutations could virtually guarantee "genetic entropy", as evidenced by monotonically decreasing population fitness caused by accumulation of deleterious mutational load.

ETA source.  link is above
Sanford, J., Baumgardner, J., Gibson, P., Brewer, W., & ReMine, W.
(2007a). Mendel痴 Accountant: A biologically realistic forward-time population genetics program. Scalable Computing: Practice and Experience 8(2), 147165.

--------------
The majority of the stupid is invincible and guaranteed for all time. The terror of their tyranny is alleviated by their lack of consistency. -A. Einstein (H/T, JAD)
If evolution is true, you could not know that it's true because your brain is nothing but chemicals. ?Think about that. -K. Hovind

  
Zachriel



Posts: 2598
Joined: Sep. 2006

(Permalink) Posted: June 11 2009,14:12   

Quote (AnsgarSeraph @ June 11 2009,11:41)
 
Quote (Wesley R. Elsberry @ June 11 2009,11:29)
So, how much "evolution sucks" verbiage was generated by the people running the pre-1.4.1 versions? Was there any notice that people should re-run their experiments due to a pretty drastic change in program behavior?

To be fair (to a shoddy program? How odd), v. 1.4.1 still "demonstrates" all the genetic entropy problems that Sanford makes noise about. Whatever they fixed in terms of beneficial mutations, our runs at TWeb using 1.4.1 indicate that it's nowhere near enough; a 90% beneficial mutation rate with default "maximal benefit effect" still reduces fitness in a linear manner.

祐am

I think a key to understanding Mendel's Accountant is the so-called "Maximal beneficial mutation effects". It defaults to an extremely low number.

Quote
Mendel's Accountant User Manual: Maximal beneficial mutation effects A realistic upper limit must be placed upon beneficial mutations. This is because a single nucleotide change can expand total biological functionality of an organism only to a limited degree. The larger the genome and the greater the total genomic information, the less a single nucleotide is likely to increase the total. Researchers must make a judgment for themselves of what is a reasonable maximal value for a single base change. The MENDEL default value for this limit is 0.001. This limit implies that a single point mutation can increase total biological functionality by as much as 0.1%. In a genome such as man痴, assuming only 10% of the genome is functional, such a maximal impact point mutation might be viewed as equivalent to adding 300,000 new information-bearing base pairs each of which had the genome-wide average fitness contribution. Researchers need to honestly define the upper limit they feel is realistic for their species. However it should be obvious that, in all cases, the upper limit for beneficial mutation effects ought to correspond to a very small fraction of the total genomic information (i.e. a small number relative to one).

There is something wrong with the analysis. They're comparing the selective value of a change to adding thousands of new bases to the genome. But adding 10% to a genome doesn't necessarily make an organism 10% fitter. On the other hand, a small change can often have a very high selective value. Consider a mutation making someone resistant to plague. Maybe he just tastes bad to fleas.

Also, I'm not sure what the number is supposed to represent. Does a value of 1 mean a change in fitness of 1? Shouldn't this scale with absolute fitness? Or is it a fractional? So does 1 represent 100% or a doubling of fitness? PS. I'm guessing the former, but my Accounting time has been somewhat limited.

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Tard Acquisition and Repository Department

   
sledgehammer



Posts: 531
Joined: Sep. 2008

(Permalink) Posted: June 11 2009,14:23   

Call me skeptical, but I think  that they put the various "hooks" to skew the beneficial vs deleterious effects into the program for one reason only.

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The majority of the stupid is invincible and guaranteed for all time. The terror of their tyranny is alleviated by their lack of consistency. -A. Einstein (H/T, JAD)
If evolution is true, you could not know that it's true because your brain is nothing but chemicals. ?Think about that. -K. Hovind

  
Wesley R. Elsberry



Posts: 4504
Joined: May 2002

(Permalink) Posted: June 11 2009,15:02   

Has anyone seen anything in MA that deals with compensatory mutations?

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"You can't teach an old dogma new tricks." - Dorothy Parker

    
deadman_932



Posts: 3094
Joined: May 2006

(Permalink) Posted: June 11 2009,15:57   

For those that need a fair (and free!) Population Genetics text, here's one available in PDF form, in a RAR-compressed file, for personal use:


Alan R. Templeton, 撤opulation Genetics and Microevolutionary Theory
Wiley-Liss; 1st edition (September 29, 2006) 705 pages

http://depositfiles.com/en/files/2390240 (8.05 MB)

Click on "free downloading" and wait for 60-second clock countdown, then download PDF to a folder, and un-rar.

If you need a (clean) free PDF reader, try Foxit : http://www.foxitsoftware.com/pdf/reader/reader-interstitial.html

Sanford's "genomic (mutational) meltdown" scenarios are a hoot. Even DaveScot was bright enough to see that Sanford's proposed mutation rates were out of line with reality: fast-reproducing sexual species that have existed a few million should have all been extinct by now, but they're not. Sanford inflates deleterious mutation rates and disregards compensatory mechanisms.

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AtBC Award for Thoroughness in the Face of Creationism

  
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