On the frustration of trying to educate IDiots

Theme

Mutation

-definition
-mutation types
-mutation rates
-phylogeny
-controversies
The Intelligent Design Creationists are remarkably ignorant about evolution so, over the past two decades, we have tried to explain a little bit about modern concepts of evolution. My latest attempt was to describe how modern evolutionary theory (and evidence) is consistent with the differences in DNA sequence between humans and chimpanzees. This required a brief explanation of Neutral Theory, population genetics, and random genetic drift, along with a description of mutation rates.

It didn't work. Creationists like Vincent Torley and Sal Cordova came up with all kinds of reasons why they couldn't believe the explanation. They were joined by Branko Kozulic, a biochemist who decided to help Vincent Torley come up with criticisms that used the right words.

Their latest attempt is at: Branko Kozulic responds to Professor Moran.

This is a continuation of an earlier post, A short post on fixation, to which Professor Moran replied here. He has asked Dr. Kozulic to contact him directly; Dr. Kozulic is now answering that request as co-author of the present post. We asked Professor Moran to answer three questions relating to the fixation of neutral mutations. But before dealing with his answers, let’s confirm that both sides agree that the key point at issue here is the fixation of neutral mutations in the human lineage, subsequent to its divergence from the lineage leading to chimpanzees.

Yes, that's the key point.

There's a lot of gibberish in that post—Nick Matzke calls it the worst post ever on Uncommon Descent—but I'll try and answer the questions.

Here at the first two questions ....

The crux of our dispute with Professor Moran, as agreed by both sides (see above) is the feasibility of 22 million neutral mutations being fixed in the human population, over a period of five million years. These mutations are nucleotide mutations. Professor Moran is kindly asked to answer the following two questions.

First, since we are talking about nucleotide mutations here, why doesn’t he apply the value for the mutation rate per nucleotide in his calculation?

I've described the human mutation rate in a series of posts from last year.

What Is a Mutation?
Estimating the Human Mutation Rate: Biochemical Method
Estimating the Human Mutation Rate: Phylogenetic Method
Estimating the Human Mutation Rate: Direct Method

There are several different ways of expressing the mutation rate. The typical population genetics definition is the number of mutations per nucleotide per generation. In humans, this value is about 2 × 10^-8 mutations per nucleotide per generation. It's easier to convert this to the actual number of mutations in order to simplify teaching.

Thus, the number of mutations is 2 × 10^-8 mutations per base pair times the size of the diploid human genome (2 × 3.2 × 10⁹ bp). This equals about 128 mutations per generation. (I calculated 130 mutations per generation in Estimating the Human Mutation Rate: Biochemical Method).

This value is called μ (mu) in population genetics calculations. It doesn't matter whether you use the per nucleotide mutation rate or the overall mutation rate as long as you keep the units correct.

Our second, related question is: since the dispute between us is not about the fixation rate of individual genomes(?), then why does he use the value for the mutation rate per individual genome?

The definition of mutation rate refers to a single generation. If you want to know the total number of mutations in the population then you have to multiply by the effective population size (N_e). Torley and Kozulic do this quite frequently in their posts, so I don't know why they are confused. If the population size is 10,000 then the total number of new mutations in the population every generation is N_eμ or 130 × 10,000 = 1.3 million. [Most textbooks treat μ as the mutations rate per haploid genome so the total number of mutations is 2N_eμ, It doesn't matter, as long as you keep the units straight.)

This is the key to understanding why the rate of fixation of neutral alleles in a population is equal to the mutation rate since if all of the mutations are neutral (a fair assumption in the case of the human and chimp genomes) then the probability of fixation for each mutation is 1/N_e (diploid). The rate of substitution (fixation) of neutral alleles is then N_eμ × 1/N_e = μ.

That's the whole point of the discussion. The population size is not relevant. You can't do the calculation unless μ is the mutation rate per generation per individual.

The third question is a bit complicated because it seems to be based on an even more serious misunderstanding of population genetics. Recall that the probability of fixation of a neutral allele is 1/N_e (diploid). What that means is that the vast majority of neutral alleles are lost before they ever become fixed. It also means that the time to fixation is very long (about 4N_e generations for diploid calculations). For an evolving population of 10,000 individuals (effective population size) this means that when a neutral allele is fixed it will take about 40,000 generations, or over one million years for humans and chimpanzees.

During that time, the populations will contain a great deal of variation as alleles are being fixed and lost. In fact, it was the discovery of this enormous amount of variation that led to the development of Neutral Theory [The Cause of Variation in a Population].

Here's the third question from Torely and Kozulic.

Let us now consider two hypothetical models:

1. In every human generation there was just a single couple that left descendants (effective population size 2Ne = 2), while all others were infertile or killed, so all new 100 mutations that appeared (scattered across some 3,000,000,000 possible sites in the genome) were fixed in the descendants.
2. In all individuals of one generation (2Ne can have any value), all the new mutations were of the same type and happened at the same sites, so regardless of which individuals mated, all descendants acquired the same mutations. This same process continued for thousands of generations, with various mutations.

The first model would require continual inbreeding, and the second, continual miracles. Neither model appears credible to us; nor do we believe Professor Moran would espouse either of these models. It is important to note, however, that that both models have one thing in common, which is why they both work: all of the mutations fix without having to pass through the polymorphic state. We suspect that Professor Moran’s back-of-the-envelope-calculations which he referred to (see the footnote below), share this same feature. We would therefore kindly ask Professor Moran to provide a numerical value for Ne that does the job, for a model that’s capable of delivering what he needs, which is: 100 new mutations being fixed in each human generation over a period of 5,000,000 years.

I certainly do not think that the fixation of neutral alleles avoids the situation where the alleles persist in polymorphic states for long periods of time. That would be totally contrary to the evidence. All populations contain enormous amounts of variation that cannot be explained by natural selection.

In my calculation, values of N_e are irrelevant so any value will work equally well as long as you realize that you start with an ancestral population containing existing variation. I'm not sure why Torley and Kozulic are so confused by this since they've read some population biology textbooks. Perhaps they are imagining a situation where the ancestral population consists entirely of clones (homogeneous) and no new alleles are fixed for the first million years of evolution?

There are more questions but they don't have anything to do with teaching about why the human and chimps genomes differ. Let them grasp that point before we move on to other questions.

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