R. David Pogge and his 'Mutation Math' email

R. David Pogge posted an email he received in response to his essay Chimps are like Us, which I have already rebutted. The email's author, "Doug", agrees with Pogge's claims but expands on them, much to Pogge's glee. Let us see if the glee was warranted...

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Mutation Math

It is difficult to compute exactly how different two strands of DNA are.
We are going to comment on this email before you read it because, frankly, we are afraid you might not make it all the way through the email. Math turns some people off. This is why we try to avoid using mathematical arguments whenever possible. But, in the October newsletter, where we talked about the published 4% difference between human DNA and chimp DNA, the devil made us do it.

Indeed. Apparently, the Devil made R. David Pogge produce intellectually dishonest propaganda in a sad attempt to prop up his religio-political ideology by attacking evolution.

Evolutionists were minimizing the difference between us and chimps to try to prove we have a close common ancestor. We wanted to show that the difference is really very large, and that one can present numbers in a variety of ways to minimize or maximize differences.

No, evolutionists were analyzing the difference, and Pogge engaged in some silly tomfoolery to try to minimize what data analyses indicate.

Doug argues that the differences are actually even larger than we said, and uses a mathematical argument to back up his position.

As is par for the course in creationist writings, his “mathematical argument” is, as was Pogge’s original diatribe, premised on a substandard understanding of the issues.

We suspect most of you won’t be able to follow it.

Because, after all, creationist software engineers know all about everything, and they know that you commoners are just too dumb to understand this stuff. That is why you will just have to believe whatever R. David Pogge tells you to think. Bad move.

We present it to you primarily to show just how difficult it is to make sense of the numbers.

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Hello,
You might be interested in some explanations for some of the details related to the recent Newsletter. They actually strengthen your case.
The 35 million substitutions represents ~1.25% of the genome. The remaining 5 million indels are, on average, roughly fifteen bases long. This means that there are about 75 million bases (i.e., ~2.75% of the entire genome) accounted for by these indels. The sum of these is 4%. Some of these indels are hundreds of bases long. And many of them involve complex additions to the genome ( i.e., not simply the replication of an existing genomic neighborhood). Note that such indels should NOT be treated as if they are a single mutation event.

Here is where “Doug” demonstrates a typical creationist trait – making an incorrect claim yet stating it as a fact. The real fact is that indels ARE, and should be, treated as one time events.

For example:
abcdefghij <- originalabccccccdefghij <- single indel/single mutationabcdefghdefghij <- single indel/single mutationabcindeldefghij <- single indel/multiple mutations

Case in point – ‘Doug’ presents multiple scenarios – multiple events – as indicating a single one! In a single indel with multiple mutations, the indel itself is still just a single event. ‘Doug’, like Pogge and others, is trying to muddle things up with creationist math.

… some information addressing another point you made on "Chimps Like Us":
"DNA contains the biological instructions for making proteins. If 29% of the proteins are identical, that means that 71% are different, doesn't it? If the DNA is 96% the same, why are 71% of the proteins it produces different?"
Suppose we have two "alignable" genomes (i.e., no indels).

You can align genomes with indels just as you can align genomes without. ‘Doug’, like Pogge and most other creationists, clearly has no direct or relevant knowledge of the things he is discussing. As we will see below, he incorrectly believes that all mutations occur in genes. A fairly ignorant – yet common - belief among creationists.

the chance of a single bp being different is 4% (i.e., 1 - 0.96).Suppose that the chance of a single bp substitution effecting [sic] a change in protein is x.Suppose that the average number of bp's coding a single protein are N.Suppose that the chance of a protein being identical is 29%.

Whaa? Suppose? The 29% number is an empirical figure…

We have the following equation:(1 - 0.04x)^N = 0.29
I expect that you follow.

… that renders the above moot.

Finally, you mistakenly think that "[in] the last 4,000 years of recorded human history, there would have been about 20,000 mutations." In fact, the expected number of mutations would be proportional to the total number of humans born within the last 4,000 years!

First, Pogge’s original “estimate” of 20,000 mutations in the last 4,000 years was premised in his rather ridiculous interpretation of a sentence, which made him think that there must be a disproportionate number of mutations in the human genome (compared to the chimp).
Second, there is no relevance on the proportionality issue, since, for example, the rate of accumulation of neutral mutations is proportional to the mutation rate, regardless of population size. ‘Doug’ might have known this, had he any basic understanding of population genetics. But consider this - if a fellow creationist can find flaws in Pogge's reasoning, well...

Based on a stable pre-historic population size of one hundred thousand, we observe that the number of mutations experienced by that population in six million years is roughly the same as the number of mutations experienced by the historic human population in the last two thousand years (see http://www.census.gov/ipc/www/worldhis.html). In the first case, the population is compressed in size and expanded in time. In the second, it is compressed in time and expanded in size.

Which, again, is rendered moot by actual population genetics.

Note, however, that the same number of mutations does not indicate the same degree of evolution. Evolution requires the "fixation" of those mutations, and it likely requires the accumulation of numerous mutations (i.e., sequential mutation-on-top-of-mutation).

Erroneous assumption on top of erroneous assumption plus baseless assertion equals creationist certainty!

Not much else to say on this scienceagainstevolution.org travesty.