This is most obvious with the Intelligent Design Creationists because they like to use science-sounding jargon to convince us that they know what they are talking about. They claim that they can refute evolutionary biology using scientific evidence. Instead they just reveal their ignorance.
They've been doing it for decades in spite of the fact that many people have tried to educate them. I don't get it.
Recently, I tried to explain how the difference between the chimpanzee and human genomes is consistent with what we know about population genetics, mutation rates, and Neutral Theory. I was aware of the fact that this stuff would all be news to most Intelligent Design Creationists but it was still an opportunity to try, once again, to teach them about modern evolutionary theory.
Recall the the fundamentals of population genetics were worked out in the 1920s and 1930s and that Neutral Theory is about 45 years old. I think it's about time that Intelligent Design Creationists learn about them, no?
The only person to take up the challenge was a philosopher, Vincent Torley. Let's see how he does at: Fixation: the neutral theory’s Achilles’ heel?. He starts with,
The neutral theory of evolution appears to have won out over its rival, neo-Darwinian selection theory (see here and here). However, the neutral theory makes a very specific prediction about the rate at which mutations are fixed in a population, which I think warrants more testing and scrutiny. The evidence for this prediction which I’ve seen to date is frankly underwhelming.There are several errors and/or misconceptions in this paragraph. First, Neutral Theory did not replace (win out over) natural selection. Neutral Theory refers to the fact that most new mutations may be neutral. If so, their frequency in the population will be governed by random genetic drift, described in the early 20th century. Random genetic drift is now seen as an important mechanism of evolution along with natural selection.
Second, Neutral Theory, per se, does not predict the rate of fixation of neutral alleles.1 That was what population genetics told us 80 years ago. What Neutral Theory says is that this may be the dominant form of evolution.
Third, I think we'll see that Vincent Torley never actually looks at the evidence for fixation of neutral alleles in a population so he really can't have an informed opinion.
Torley goes on to quote several internet sources in an attempt to understand, and explain, the concepts of neutral alleles and fixation rates. One of them is an article from talk.origins by Chris Colby. It's 20 years old. That's an indication of how long we've been trying to teach this stuff to creationists on the internet. The fact that Torley is relying on selected internet articles indicates that he doesn't have any books on evolution or population genetics. That's not a surprise.
Torley seems to get the idea that the overall rate of fixation of neutral alleles will be the same as the mutation rate per generation. That's just simplified population genetics. Now he's in a position to understand my post so he says ...
What Professor Moran is saying here is that 121 mutations are being fixed in the human population, in each successive generation. Since 185,200 generations have elapsed since the human and chimpanzee lines diverged, this means that 22.4 million mutations have become fixed in the human lineage since our ancestors diverged from the line leading to chimps. That’s a staggering number.Since he can't be surprised by the number of generations, he must be "staggered" by the idea that there might be 121 new mutations per generation and that population genetics predicts fixation of 121 alleles per generation.
To his credit, he seems to have read (scanned?) my posts on the mutation rate in humans. Those are the post where I presented some of the evidence for the mutation rate.
Professor Moran thinks we shouldn’t be surprised. The rate of fixation is supported by three converging lines of evidence, as he explains, in a post titled, stimating the Human Mutation Rate: Direct Method (February 22, 2013):Now let's be clear here. What I'm doing is describing two methods of directly calculating the mutation rate. One of them relies on our knowledge of DNA replication and repair and the other relies on direct sequencing of parents and childeren and counting the number of mutations. The result is between 70 and 130 new mutations per generation.
There are basically three ways to estimate the mutation rate in the human lineage. I refer to them as the Biochemical Method, the Phylogenetic Method, and the Direct Method.
The Biochemical Method is based on our knowledge of biochemistry and DNA replication as well as estimates of the number of cell divisions between zygote and egg. It gives a value of 130 mutations per generation. The Phylogenetic Method depends on the fact that most mutations are neutral and that the rate of fixation of alleles is equal to the mutation rate. It also relies on a correct phylogeny. The Phylogenetic Method gives values between 112-160 mutations per generation. These two methods are pretty much in agreement.
The Direct Method involves sequencing the entire genomes of related individuals (e.g. mother, father, child) and simply counting the new mutations in the offspring. [Moran then cites a paper by Xue et al. (2009) which estimates the mutation rate at 103 mutations per generation.]
The third method relies on our understanding of population genetics and the idea that most alleles are fixed by random genetic drift. When we plug in the numbers, we get a mutation rate that agrees with the direct measurements.
I did not present any independent evidence to support the idea the fixation rate is the same as the mutation rate. In the case of the Phylogenetic Method, I just pointed out that, if this were true (a reasonable assumption), then the mutation rate agrees pretty much with the other methods.
Vincent Torley says,
With the greatest respect to Professor Moran, none of these methods counts as an observation of the rate at which mutations get fixed in the human population. Inferring how many mutations must have taken place from an assumed time at which the human and chimp lineages diverged, is not the same thing as observing the rate at which mutations get fixed in the human line. And observing how many mutations occur in the space of one generation, from parent to child, is not the same thing as observing the rate at which mutations occur in the human population as a whole.That's correct. My posts were about the mutation rate and not the fixation rate. However, the fact that humans and chimpanzees descend from a common ancestor several million years ago is just that, a fact. It would be perverse (IDiotic?) to believe otherwise.
Professor Moran might respond that according to the mathematical assumptions underlying the neutral theory of evolution, the rate at which mutations get passed on from parent to child is the same as the rate at which mutations get fixed in the population as a whole. That may be so; but it does not mean that an observation of the former automatically counts as an observation of the latter. The equation of the two rates only occurs within a particular theory of evolution: the neutral theory. If we are to test this theory properly, then, we need a population in which we can observe mutations getting fixed, and see if the rate accords with the mutation rate from parent to offspring.Again, this is correct. It's population genetics theory that says the fixation rate should equal the mutation rate if the alleles are neutral. I was presenting evidence for the mutation rate.
The fact that the predictions of evolutionary theory and our knowledge of the mutation rate gives the right number for the number of differences between chimpanzees and humans, lends support to the theory but, strictly speaking, it is not a direct demonstration of fixation rates. (BTW, Torely never tells us the latest Intelligent Design Creationist version of population genetics so we can see if it works any better.)
Although I’m happy to be proved wrong, the claim that more than 100 mutations get fixed in the entire human population, in each passing generation, strikes me as implausible. I’m tempted to ask: where are all these mutations that are fixed in the human population in 2014, but were not fixed in the human population one generation ago, in 1987? Has anyone identified them?A near as I can tell, this is all new stuff to Vincent Torley. He acts like he's never thought of it before. Judging by this paragraph, he has a lot more thinking to do. Perhaps, he should have done it before posting?
The time taken for these mutations to get fixed also seems extraordinary. We are told that for a population of N organisms, it takes (4*Ne) generations for a mutation to get fixed in the population, where Ne is the effective size of the human population. For most of human history, the effective population size appears to have been around 10,000, even though the actual human population size is thought to have been considerably higher (350,000 from the Middle Pleistocene onwards, according to a 2008 article by Professor John Hawks). Four times 10,000 equals 40,000 generations, and if we use Professor Moran’s figure of 27.5 years per generation, that’s equivalent to 1,100,000 years ago.No, Vincent, you are not the only one who finds the basics of evolution "extraordinary" and "suspicious." Just about everyone who posts on Uncommon Descent and Evolution News & Views is as ignorant as you.
Let me spell that out: if we take a typical mutation out of the 100-odd mutations which (according to the neutral theory of evolution) got fixed in the human population within the last generation (from 1987 to 2014), we will find that that mutation first appeared in the human lineage some 1,100,000 years ago.
Am I the only one who thinks this figure is absolutely extraordinary? And for that matter, doesn’t the notion of a mutation that takes one million years to fix sound a little suspicious?
Do you really think the argument from ignorance carries any weight?
Should we trust mathematical estimates of how long it takes mutations to get fixed in the human population, given the enormous environmental upheavals (e.g. Ice Ages, the Toba eruption, and so on) that we’ve faced in the past million years?The mathematics is solid. If Vincent Torley understood population genetics, he would realize that environmental upheavals don't make much difference.
And what about this? Anthropologist John Hawks estimates that positive selection in the past 5,000 years has occurred at a rate roughly 100 times higher than any other period of human evolution. He adds: “We are more different genetically from people living 5,000 years ago than they were different from Neanderthals.” All this hyper-evolution has been occurring at a time when the human population has been higher than ever before – which means that it should take much, much longer for mutations to get fixed in the population! So how does that work? Go figure.John Hawks is probably wrong but in any case his argument is irrelevant. He's talking about the small number of alleles that might be fixed by natural selection and not the vast majority of neutral alleles that are fixed by random genetic drift.
Of course, I realize that testing the predictions of the neutral theory of evolution regarding how many mutations get fixed in the population in each generation, and how long it takes for a new mutation to get fixed, might be rather impractical for a long-lived, slow-reproducing species like Homo sapiens.It's ludicrous to think that the people who comment on Uncommon Descent are going to help him. (Read the comments to see for yourself.)
So I’d be very interested to hear from any readers with a biology background. How do the predictions of the neutral theory check out when applied to bacteria? What about simple eukaryotes? Have any studies been done for animals? Which ones? Over to you.
Vincent Torley seems to think that population genetics and Neutral Theory are just idle speculations with no evidence to support them. That's very insulting to all the thousands of scientists who have been studying evolution for the past forty years. Does he really think that evolutionary theory rest on such a shaky foundation?
Fortunately for Torley, there are a number of papers that answer his question. The one that I talk about in class is from Richard Lenski's long-term evolution experiment. Recall that mutation rates are about 10-10 per generation. If the fixation rates of neutral alleles was equal to the mutation rate then (as predicted by population genetics) then this should be observable in the experiment run by Lenski (now 60,000 generations).
The result is just what you expect. The total number of neutral allele fixations is 35 in the bacterial cultures and this correspond to a mutation rate of 0.9 × 10-10 or only slightly lower than what is predicted. There are lots of references in the paper and lots of other papers in the literature.
Wielgoss, S., Barrick, J. E., Tenaillon, O., Cruveiller, S., Chane-Woon-Ming, B., Médigue, C., Lenski, R. E. and D. Schneider (2011) Mutation rate inferred from synonymous substitutions in a long-term evolution experiment with Escherichia coli. G3: Genes, Genomes, Genetics 1, 183-186. [doi: 10.1534/g3.111.000406]
1. We know that the modern theory is Nearly-Neutral Theory but that's a lesson for another time.