Wright, Fisher, and the Weasel

Posted on February 25, 2016 by Joe Felsenstein

Richard Dawkins’s computer simulation algorithm explores how long it takes a 28-letter-long phrase to evolve to become the phrase “Methinks it is like a weasel”. The Weasel program has a single example of the phrase which produces a number of offspring, with each letter subject to mutation, where there are 27 possible letters, the 26 letters A-Z and a space. The offspring that is closest to that target replaces the single parent. The purpose of the program is to show that creationist orators who argue that evolutionary biology explains adaptations by “chance” are misleading their audiences. Pure random mutation without any selection would lead to a random sequence of 28-letter phrases. There are $27^{28}$ possible 28-letter phrases, so it should take about $10^{40}$ different phrases before we found the target. That is without arranging that the phrase that replaces the parent is the one closest to the target. Once that highly nonrandom condition is imposed, the number of generations to success drops dramatically, from $10^{40}$ to mere thousands.

Although Dawkins’s Weasel algorithm is a dramatic success at making clear the difference between pure “chance” and selection, it differs from standard evolutionary models. It has only one haploid adult in each generation, and since the offspring that is most fit is always chosen, the strength of selection is in effect infinite. How does this compare to the standard Wright-Fisher model of theoretical population genetics?

The Wright-Fisher model, developed 85 years ago, independently, by two founders of theoretical population genetics, is somewhat similar. But it has an infinite number of newborns, precisely $N$ of whom survive to adulthood. In its simplest form, with asexual haploids, the adult survivors each produce an infinitely large, but equal, number of offspring. In that infinitely large offspring population, mutations occur exactly in the expected frequencies. Each genotype has a fitness, and the proportions of the genotypes change according to them, exactly as expected. Since there are an infinite number of offspring, there is no genetic drift at that stage. Then finally a random sample of $N$ of the survivors is chosen to become the adults of this new generation.

In one case we get fairly close to the Weasel. That is when $N = 1$ , so that there is only one adult individual. Now for some theory, part of which I explained before, in a comment here. We first assume that a match of one letter to the target multiplies the fitness by a factor of $1+s$ , and that this holds no matter how many other letters match. This is the fitness scheme in the genetic algorithm program by keiths. A phrase that has $k$ matches to the target has fitness $(1+s)^k$ . We also assume that mutation occurs independently in each letter of each offspring with probability $u$ , and produces one of the other 26 possibilities, chosen uniformly at random. This too is what happens in keiths’s program. If a letter matches the target, there is a probability $u$ that it will cease to match after mutation. If it does not match, there is a probability $u/26$ that it will match after mutation.

The interesting property of these assumptions is that, in the Wright-Fisher model with $N = 1$ , each site evolves independently because neither its mutational process nor its selection coefficients depend on the the state of the other sites. So we can simply ask about the evolution of one site.

If the site matches, after mutation $1-u$ of the offspring will still match, and $u$ of them will not. Selection results in a ratio of $(1+s)(1-u)\,:\,u$ of matching to nonmatching letters. Dividing by the sum of these, the probability of ending up with a nonmatch is then $u$ divided by the sum, or

$q \ = \ u\big/\left((1+s)(1-u)+u\right) \ = \ u \big/ (1 + s(1-u))$

Similarly if a letter does not match, after mutation the ratio of nonmatches to matches is $\frac{u}{26}\,:\,1-\frac{u}{26}$ . After selection the ratio is $(1+s)\frac{u}{26}\,:\,1-\frac{u}{26}$ . Dividing by the sum of these, the probability of ending up with a match is

$p \ = \ \frac{u}{26}(1+s) \bigg/\left( \frac{u}{26}(1+s) + \left(1 - \frac{u}{26}\right)\right) \ = \ u(1+s) \big/ (26 + us)$

Thus, what we see at one position in the 28-letter phrase is that if it is not matched, it has probability $p$ of changing to a match, and if it is matched, it has probability $q$ of changing to not being matched. This is a simple 2-state Markov process. I’m going to leave out the further analysis — I can explain any point in the comments. Suffice it to say that

1. The probability, in the long run, of a position matching is $p/(p+q)$ .

2. This is independent in each of the 28 positions. So the number of matches will, in the long run, be a Binomial variate with 28 trials each with probability $p/(p+q)$ .

3. The “relaxation time” of this system, the number of generations to approach the long-term equilibrium, will be roughly $1/(p+q)$ .

4. At what value of $s$ do we expect selection to overcome genetic drift? There is no value where drift does not occur, but we can roughly say that when the equilibrium frequency $p/(p+q)$ is twice as great as the no-selection value of 1/27, that selection is then having a noticeable effect. The equation for this value is a quadratic equation in $s$ whose coefficients involve $u$ as well. If $u$ is much smaller than $s$ , then this value of $s$ is close to 0.44.

5. The probability of a match at a particular position, one which started out not matching, will be after $t$ generations

$P(t) \ = \ \frac{p}{p+q} (1\:-\:(1-p-q)^t)$

and the probability of a nonmatch given that one started out matching is

$Q(t) \ = \ \frac{q}{p+q} (1\:-\:(1-p-q)^t)$

I don’t have the energy to see whether the runs of keiths’s program verify this, but I hope others will.

291 thoughts on “Wright, Fisher, and the Weasel”

dazz
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on February 27, 2016 at 9:40 pm said:

petrushka: Mean fitness: 16.04

This is average number of matches, right?
petrushka
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on February 27, 2016 at 9:40 pm said:

Keiths uses 50000.

I can change it.
petrushka
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on February 27, 2016 at 9:42 pm said:

dazz: This is average number of matches, right?

That’s the way I read it.

I took one term of statistics in 1970, and haven’t seen a C compiler since 1995.

I’m a bit under-educated and rusty.
petrushka
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on February 27, 2016 at 9:51 pm said:

With 1000 children per generation:

Generation: 7040 Number of survivors per generation: 1

Selection: ON Coefficient: 5.00 Mutation rate: 0.036

Mean fitness: 16.04 Standard Deviation: 2.78
petrushka
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on February 27, 2016 at 9:54 pm said:

Another run:
Mean fitness: 15.59 Standard Deviation: 2.65

and another:
Mean fitness: 15.68 Standard Deviation: 2.87
Tom English
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on February 27, 2016 at 9:55 pm said:

petrushka:
Throwing away the first 2000:

Generation: 7010 Number of survivors per generation: 1

Selection: ONCoefficient: 5.00 Mutation rate: 0.036
Mean fitness: 16.04 Standard Deviation: 2.70

Doing this with the data, again, from the red run above, I get a mean of 15.934730538922155 and a standard deviation of 2.575163769620239. The histogram isn’t so pretty this time, so I probably was just lucky with the black one above.
petrushka
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on February 27, 2016 at 10:01 pm said:

Keiths will have to look at my SD code in the context of his program and tell us if it is done correctly, and if I’m using the right snapshot of his run.
Tom English
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on February 27, 2016 at 10:03 pm said:

petrushka,

petrushka:
Another run:
Mean fitness: 15.59 Standard Deviation: 2.65

This is looking reasonable. The standard deviation is telling you to do some longer runs, if you want to see if the mean observation is close to the theoretical mean.

Joe’s interested also in the time for “relaxation,” and that will take many short runs (but I would rather take a shot at analysis before getting into that).
Tom English
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on February 27, 2016 at 10:10 pm said:

dazz:

petrushka: Mean fitness: 16.04

This is average number of matches, right?

Joe pointed out that I shouldn’t have called it fitness, and he was right.
dazz
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on February 27, 2016 at 10:14 pm said:

Tom English: This is average number of matches, right?

Joe pointed out that I shouldn’t have called it fitness, and he was right.

Oh, I thought petrushka was running keiths’ algo, not yours, and I also got lost in translation and somehow thought mean = median. I’m on a roll, duh!
Tom English
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on February 27, 2016 at 10:15 pm said:

Mung: I’m thinking more along the lines of converting it into another language. I do have Python installed, I should probably just bite the bullet and use it. If I did convert it to another language I can’t see myself posting it anywhere but here. Just thought I’d ask first.

Thanks. Implementing it in a different language is a good way to study it.
petrushka
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on February 27, 2016 at 10:17 pm said:

I am running keiths’ program. I just added code to calculate the mean and sd. Saves time comparing it with Tom’s.

I just added the caveat that I am not a wizard. I’m pretty sure I got it right, but I wouldn’t ship it.
dazz
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on February 27, 2016 at 10:21 pm said:

petrushka:
I am running keiths’ program. I just added code to calculate the mean and sd. Saves time comparing it with Tom’s.

I just added the caveat that I am not a wizard. I’m pretty sure I got it right, but I wouldn’t ship it.

Do you have a windows build please? I can’t get it to compile on MinGW
petrushka
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on February 27, 2016 at 10:29 pm said:

http://www.filedropper.com/keithssd

This is one I modified to display mean and sd.

It is also modified to default to 1000 children and a mutation rate of .0357.

These can be changed interactively.
dazz
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on February 27, 2016 at 10:49 pm said:

petrushka,

Thank you! I almost have the code compiled in MinGW, apparently conio is not available in it’s compiler :/ Might just remove that even if I can’t change params on the fly
petrushka
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on February 27, 2016 at 10:56 pm said:

It’s possible that conio.lib might sneak it’s way to your computer. If you wished it.

Lcc-win is free and takes about five minutes to download and install.

Keiths got it working on Win-7.

I have it working on win-10 and XP.
dazz
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on February 27, 2016 at 11:10 pm said:

petrushka:
It’s possible that conio.lib might sneak it’s way to your computer. If you wished it.

Lcc-win is free and takes about five minutes to download and install.

Keiths got it working on Win-7.

I have it working on win-10 and XP.

Thanks
Mung
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on February 27, 2016 at 11:11 pm said:

On Windows you might try installing Git for Windows and running from a git bash prompt.

ETA: Nope.

ks-drift-weasel.c:6:24: fatal error: sys/select.h: No such file or directory

ks-drift-weasel.c:7:21: fatal error: termios.h: No such file or directory
petrushka
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on February 27, 2016 at 11:14 pm said:

I’ll be out for the evening, leaving in a while. I think I’ll leave a download for my sd modification. I did not rename it, so it might sit on top of any previous code.

http://www.filedropper.com/keiths

This is keiths.c
dazz
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on February 27, 2016 at 11:24 pm said:

Mung:
On Windows you might try installing Git for Windows and running from a git bash prompt.

ETA: Nope.

ks-drift-weasel.c:6:24: fatal error: sys/select.h: No such file or directory

ks-drift-weasel.c:7:21: fatal error: termios.h: No such file or directory

Those are the linux i/o libs. Might still compile with petrushka’s tweaks

http://pastebin.com/raw/hE14eHGN

Thanks for the suggestion, I’m rather incompetent in C
CharlieM
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on February 27, 2016 at 11:24 pm said:

Joe Felsenstein:
CharlieM, the whole point of the Weasel algorithm is to show that evolutionary theory is not a theory of evolution “by chance”. dazz’s remark is sarcastic, which you missed.

I didn’t miss the sarcasm.

Joe Felsenstein:The Weasel refutes the statements in many lectures by creationists, statements that assure their audiences that evolutionary biologists explain adaptations as occurring “by chance”.If their audience believes that statement, they will of course immediately reject evolutionary biology as nonsense.After all, random genotypes will have such a small probability of producing exquisitely adapted phenotypes, that we will not ever see anything like the adaptations that we do see.The Weasel is a teaching demonstration showing that the processes evolutionary biologists envision are very, very far from random.That the statements of the creationist debaters are massively misleading.

Are there any such critics of evolutionary theory who still think that it is composed only of chance mechanisms or would descibe it as such?

Joe Felsenstein:You seem to have countered with the objection that the Weasel model is of processes that are very, very far from random. Well, um yes, of course.

Yes of course its not random. I’m making an observation that Weasel is modelling a process that has a target to aim at.

And as I see that Mung has started a thread to prevent the diversions that my post will inevitably bring if I keep getting responses, I’m happy to continue over there.
petrushka
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on February 28, 2016 at 2:37 am said:

dazz: Those are the linux i/o libs. Might still compile with petrushka’s tweaks
http://pastebin.com/raw/hE14eHGN
Thanks for the suggestion, I’m rather incompetent in C

I’m back,if anyone cares. The more recent versions of keiths’ code will compile without file errors, but you need to edit the dot c file and add a line at the top that says #define WINDOWS
Flint
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on February 28, 2016 at 2:58 am said:

CharlieM: Yes of course its not random.I’mmaking an observation that Weasel is modelling a process that has a target to aim at.

Here I think is where the ambiguity sets in. In the Dawkins example, the exact target is specified at the start, and all iterations are compared with that target. This doesn’t resemble evolution, it’s simply an illustration of the power of selection. The question is, if the “target” were more general, like “produce a grammatically correct sentence” would that count as a pre-specified target?

After all, biological evolution also has a pre-specified target in this sense – produce an organism capable of surviving long enough to breed in any environment available to be colonized.
petrushka
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on February 28, 2016 at 3:08 am said:

In the Joe F model, the target is irrelevant except as a way of measuring drift. It’s just a mathematical abstraction. What’s important is the mathematics of the selection coefficient.
dazz
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on February 28, 2016 at 10:25 am said:

petrushka: I’m back,if anyone cares. The more recent versions of keiths’ code will compile without file errors, but you need to edit the dot c file and adda line at the top that says #define WINDOWS

lcc worked like a charm, thanks again
Allan Miller
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on February 28, 2016 at 11:10 am said:

petrushka,

Throwing away the first 2000:

Strictly speaking, the number discarded should be variable, based on s and u – according to Joe’s OP point (3), equilibrium takes 1/(p+q) generations, with p and q both having u and s terms.
CharlieM
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on February 28, 2016 at 11:55 am said:

Flint: Here I think is where the ambiguity sets in. In the Dawkins example, the exact target is specified at the start, and all iterations are compared with that target. This doesn’t resemble evolution, it’s simply an illustration of the power of selection. The question is, if the “target” were more general, like “produce a grammatically correct sentence” would that count as a pre-specified target?

After all, biological evolution also has a pre-specified target in this sense – produce an organism capable of surviving long enough to breed in any environment available to be colonized.

That is food for thought. This would give the Weasel algorithm an unimaginable number of targets to aim for, not just one pre-specified target.

Can the Weasel algorithm be adjusted to test this? Has it ever been tried previously?
dazz
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on February 28, 2016 at 12:22 pm said:

CharlieM: That is food for thought. This would give the Weasel algorithm an unimaginable number of targets to aim for, not just one pre-specified target.

Can the Weasel algorithm be adjusted to test this? Has it ever been tried previously?

The GA to calculate PI by combining digits and arithmetic symbols did exactly that. There are literally an infinitude of possible arithmetic expressions, and since PI is infinite it’s impossible to reach the “target”, just find better and better solutions

http://theskepticalzone.com/wp/math-genome-fun-2-upb-and-beyond/
Alan Fox
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on February 28, 2016 at 1:01 pm said:

CharlieM: Can the Weasel algorithm be adjusted to test this? Has it ever been tried previously?

Dawkins, after presenting his “Weasel” program on pp 46 – 50 of Blind Watchmaker, went on to describe ‘Biomorph Land’, his attempt to develop a more realistic computer model of selection. In one way, it is a pretty good model of artificial (or indeed, sexual) selection, with the operator playing the rôle of God, the environment, selective breeder or choosy mate.
petrushka
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on February 28, 2016 at 1:16 pm said:

CharlieM: That is food for thought. This would give the Weasel algorithm an unimaginable number of targets to aim for, not just one pre-specified target.

I have a web game in which the “target” is all the words in the Scrabble dictionary. One of the regulars at AtBC did something similar.

Not an unimaginable number, but over a hundred thousand possible targets. Works in five languages. Glad you asked.

The more targets, the better.
petrushka
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on February 28, 2016 at 2:21 pm said:

Allan Miller:
petrushka,
Strictly speaking, the number discarded should be variable, based on s and u – according to Joe’s OP point (3), equilibrium takes 1/(p+q) generations, with p and q both having u and s terms.

I’ve done something wrong. Using mutation rate of .0357 and selection coefficient of 5, I get a relaxation time of 69.

cs = CHARSET_SIZE - 1; u = mutation_rate; s = selection_coefficient; q = u / (1 + (s * (1 - u))); p = (u * (1 + s)) / (cs + (u * s)); eq = 1 / (p + q);
phoodoo
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on February 28, 2016 at 2:32 pm said:

Holy shit, I see the stupidity here hasn’t abaded one bit.

A program, which has in place a solution (a never changing solution!), and which simply picks things that match that solution, is an example of how evolution is not random.

Fucking hell. What a waste of an education.
Allan Miller
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on February 28, 2016 at 2:45 pm said:

phoodoo,

Let us not detain you further, then.
Allan Miller
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on February 28, 2016 at 2:49 pm said:

petrushka,

It may be the units for ‘generations’. 5000 births/deaths in a steady state population of 1000 would be 5 generations (phoodoo’s back to set that one straight!).
petrushka
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on February 28, 2016 at 2:55 pm said:

In keiths’ code, a generation is independent of child population size.
dazz
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on February 28, 2016 at 3:14 pm said:

phoodoo: A program, which has in place a solution (a never changing solution!)

First statement, first blunder. Pathetic
Mung
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on February 28, 2016 at 4:32 pm said:

Hi Tom,

Was it your intent to have this refer to your constants at the top of the file?

Evolve(n_offspring=1000, selection=s, alphabet_size=27)

Line 100

ETA: ah. I think I see you are just using the constants for defaults.
Joe Felsenstein
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on February 28, 2016 at 4:50 pm said:

I am so glad that Mung started a new thread so that all the meaningless baiting about “it’s a search” and “it has a target built in” can happen there and not here …

For those who want to see an evolutionary simulation which does not have a target built in, there are genetic algorithms that do not have any detailed specification of the goal genotype or phenotype built in, but achieve remarkable adaptations:

(1) Karl Sims (site here) had a genetic algorithm that described organisms made of blocks and links that existed in a simulated physics. They were under selection (to pick a dramatic case) to swim through the medium to the right. Starting with phenotypes that could barely wiggle, they evolve to “swim” in all sorts of fascinating ways. Sims’s code is not available but there is an imitation of it called breve that is available from Jonathan Klein (here).

(2) A similar effort called Boxcar2d evolves imaginary vehicles that move to the right across a 2-dimensional landscape. It will be found here.

I have mentioned these here before.
phoodoo
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on February 28, 2016 at 5:01 pm said:

Joe Felsenstein,

How well did the boxcar2d algorithm do at creating a better antibiotic for staph infection?

I am guessing not so good. Funny how all these so called random algorithms only do the thing they are supposed to do.

Gee, I wonder why people think they are searches Joe?
keiths
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on February 28, 2016 at 5:53 pm said:

phoodoo,

Holy shit, I see the stupidity here hasn’t abaded one bit.

Indeed, you seem to carry it with you wherever you go.

Perhaps cracking a book or two would help ‘abade’ it.
Tom English
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on February 28, 2016 at 5:54 pm said:

Mung:
Hi Tom,

Was it your intent to have this refer to your constants at the top of the file?

Evolve(n_offspring=1000, selection=s, alphabet_size=27)

Line 100

ETA: ah. I think I see you are just using the constants for defaults.

Your ETA is correct. It was a lapse in judgment. I was shooting for a combination of ease of use and compact code, when I should have favored flexibility and explicitness in use. I’ll post a no-constants version on my blog, and send you a PM.
keiths
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on February 28, 2016 at 6:00 pm said:

petrushka:

Throwing away the first 2000:

Allan:

Strictly speaking, the number discarded should be variable, based on s and u – according to Joe’s OP point (3), equilibrium takes 1/(p+q) generations, with p and q both having u and s terms.

Strictly speaking, you don’t have to discard anything. The mean will approach the ‘true’ value over time anyway. Discarding the initial generations just speeds up the process somewhat.

I implemented the ‘c’ command — the one that resets the histogram — as a convenience, not as a necessity.
keiths
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on February 28, 2016 at 6:04 pm said:

Allan:

It may be the units for ‘generations’. 5000 births/deaths in a steady state population of 1000 would be 5 generations (phoodoo’s back to set that one straight!).

petrushka:

In keiths’ code, a generation is independent of child population size.

That’s right. The generations are non-overlapping, which is why the Wright-Fisher model is applicable.
Mung
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on February 28, 2016 at 6:19 pm said:

Hi Tom.

I like being able to change the settings at the top of the file but if the program uses the constants then there’s not much point in setting defaults, lol. Whatever you come up with I’ll try not to bitch about it because off the cuff I couldn’t think of a better way. 🙂
Mung
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on February 28, 2016 at 6:24 pm said:

Joe Felsenstein: I am so glad that Mung started a new thread so that all the meaningless baiting about “it’s a search” and “it has a target built in” can happen there and not here …

Thanks. Now if folks can just resist the temptation to respond to baiting in this thread. Please.
keiths
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on February 28, 2016 at 6:31 pm said:

Joe:

For those who want to see an evolutionary simulation which does not have a target built in, there are genetic algorithms that do not have any detailed specification of the goal genotype or phenotype built in, but achieve remarkable adaptations:

And as dazz mentioned, the GA in this thread also qualifies:

Math Genome Fun 2, UPB and beyond?

The solutions the GA comes up with are completely different depending on the constant being approximated and the digits available to the GA. It’s obvious that the solutions are not being “smuggled” in.
petrushka
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on February 28, 2016 at 6:35 pm said:

keiths:
Allan:
petrushka:
That’s right. The generations are non-overlapping, which is why the Wright-Fisher model is applicable.

maybe you could take a look at this and see if anything’s wrong.

http://www.filedropper.com/keiths-petru
petrushka
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on February 28, 2016 at 6:44 pm said:

http://www.labbookpages.co.uk/teaching/evoHW/files/ehw3.pdf

Look at Thompson’s tone discriminator.
keiths
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on February 28, 2016 at 8:33 pm said:

petrushka,

maybe you could take a look at this and see if anything’s wrong.

Are you asking about the relaxation time computation?

If so, I think your code is correct, but I don’t know the basis of the 1/(p+q) formula. Joe, could you elaborate?
Joe Felsenstein
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on February 28, 2016 at 9:22 pm said:

keiths:
petrushka,

Are you asking about the relaxation time computation?

If so, I think your code is correct, but I don’t know the basis of the 1/(p+q) formula.Joe, could you elaborate?

I showed in the OP my formulas for the probability of change from nonmatch to match in $t$ generations. Basically the probability of match rises from $0$ to $p$ in the first generation. The asymptotic value is $p/(p+q)$ . Thus in one generation it goes a fraction

$p \big/ \left(p / (p+q)\right) \ = \ p+q$

of the way to that asymptote. If it continued changing by the amount $p$ it would then reach the asymptote in $1/(p+q)$ generations. Of course, it doesn’t do that, it changes by less as it approaches the asymptote. But the $1/(p+q)$ time is a reasonable indication of how fast it is changing.

A similar calculation can be done for the case where we start with a match, It gives the same answer for the relaxation time.