http://exploringourmatrix.blog...

* We can predict that the family of the Kingdom of BUG will form a nested hierarchy of descent that can be discerned within any generation or between generations.
* We can predict that the family of the Kingdom of BUG will form a nested hierarchy with other families, such as the Fjords of BUR and the Isles of BUM.
* We can determine that all families share a common ancestor.
* As neutral drift occurs at a statistically constant rate, we can determine how long any two populations diverged from their common ancestor.
* We can detect selection due to its rapid rate of fixation (compared to the known rate of neutral drift and fixation).
* That rare selective traits can become fixated in a population long before many neutral traits are fixed.

Biology is much more complicated, but geneticists employ a vast array of statistical tools to devise and test valid scientific hypotheses.

I appreciate being made aware of the issues surrounding fixation.

Added a new image showing evolution's Founder Effect. Many of the patterns we see are due to stochastic processes.

I've added another Result to Killer Rabbits, this time the other extreme so that we can hopefully grasp the entire process in a single visual. I hope it helps.

Genome = 8, Field = 4

The process is very chaotic with these small numbers, so I ran the simulation three or four times so that everything could be captured in a single screen shot. Take a look at this Result.

Once the BUR mutation occurs, it predominates in only a couple of Generations. But importantly, notice that the Genome still has substantial remnants of the Founding Genome. Also notice all the various mutations that were tried. But that have disapppeared!

2 L
3 Y S
4 J B
5 X Q
6 R A
7 B* R!
8 V W B
9 D O
10 K

But of all these, only the R! and D persist. Only a single change to the Junk Genome remains after 10 Generations. The rest were tried and discarded. Meanwhile, selection for fitness preserved the BUR strain.

Fixation occurs at a slow, constant rate in such populations. In fact, evolution can try all those letter positions with the vast majority being lost to neutral drift. Try to grasp this last concept.

And so we have come complete circle and pretty much confirmed Kimura's mathematical result that I mentioned in the first post to this thread.

We expect a BUG mutation once in every 100 Generations or so. Perhaps in a hundred generations, or maybe in a few hundred. After a thousand generations, Purity = 95% reliably. Here's the first couple of hundred letters with Generation = 1000.

BUT,,,,,,,,,,,,,,,,,,,,,,,,,G,,,,,,,,,,,,,,,,,,,,,
,,,F,,,,,,,,,,,,,,,,O,,,,,,,,,,,,,,,R,,,,,,,,,,,,,
 ,,,,,,,,,,,,,,,,,,,,,,,A,,,,,,,,,,,,,,,,,,,,,,,,,,
,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
 ,,,,,,,,,O,,L,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,

The large majority of the sequence is identical to the Founding Genome and to other populations that diverged from that Founding Genome.

You indicated that the junk would be scrambled by the time the BUG mutation occurred. You based this on the expectation that evolution would have to more-or-less try each letter position. You are extrapolating from how a single sequence might work. But most of those mutations will not be fixed in a population of sequences. Fixation occurs at a slow, constant rate in such populations. In fact, evolution can try all those letter positions with the vast majority being lost to neutral drift. Try to grasp this last concept.

Wonders for Oyarsa: I hadn't thought of the case where mutations were likely enough that a good one was probable each generation (though to get the next step you need to wait for the new one to dominate).

That's not the case under consideration. With a Genome of 2000 and a population of only ~100, we definitely do not expect beneficial mutations each Generation, but a very irregular appearance after many Generations.

Wonders for Oyarsa: If the probability of a good mutation per mutation is 1/n, and the population is n, then you will get a good mutation with only minimal cost to the junk.

In our example, the Genome size is 20+ times the size of the Field. (The Field is actually a crowding limit and the population rarely exceeds this value.) Within the limitations of our program, the Genome was very large compared to the Field, and it provides results contrary to your expectation.

Wonders for Oyarsa: I'm still far from convinced, however, that good mutations in a human/chimp ancestor would be anywhere on the order of 1/n.

You were the one making claims. This is why I originally suggested you try to disprove your own intuition, rather than merely attempt to support it.

So population size would be as strong of a driving force behind evolution as time.

I'm still far from convinced, however, that good mutations in a human/chimp ancestor would be anywhere on the order of 1/n.