An Intelligent Design Creationist explains why chimpanzees and humans are so similar

The genomes of chimpanzees and bonobos are remarkably similar to the human genome. In terms of sequence similarity, they are more than 98% identical in the regions that can be aligned. This, of course, is due to the fact that they descend from a common ancestor in the recent past (about 5 million years ago).

Intelligent Design Creationists don't agree. Many of them do not accent common descent and macroevolution so they make up stories that account for the similarity based on what they think god might have been thinking when he created chimps and humans.

But the scientific evidence for evolution is much stronger than just overall sequence similarity. The number of differences (about 50 million substitutions) corresponds pretty closely with what we expect from evolutionary theory (population genetics) and known mutation rates [Why are the human and chimpanzee/bonobo genomes so similar?]. If the Intelligent Design Creationists are going to dismiss this confirmation of evolutionary theory then they are going to have to be much more inventive.

It's been four weeks since I posted my original calculations and no creationist has responded until now. I mentioned this the other day when I was discussing Vincent Torley's strange views about macroevolution [What do Intelligent Design Creationists really think about macroevolution?].

I guess Torley is embarrassed by the fact that although some of his colleagues pretend to be scientists they didn't dare respond to my post. Torley is a philosopher but he isn't afraid to tackle science questions as we saw in his attempt to refute macroevolution.

Now he thinks he can respond to my post about the evidence that chimps and humans descend from a common ancestor [So, why are the human and chimpanzee/bonobo genomes so similar? A reply to Professor Larry Moran]. This is going to be fun.

Vincent Torley starts off by telling us that he accepts the common ancestry of chimpanzees, bonobos, and humans. He agrees that many Intelligent Design Creationists do not accept common descent, but he's not one of them. Then he explains how the creator made these species so that it looks like evolution.

In his post, Professor Moran (acting as devil’s advocate) proposes the intelligent design hypothesis that “the intelligent designer created a model primate and then tweaked it a little bit to give chimps, humans, orangutans, etc.” However, he argues that this hypothesis fails to explain “the fact that humans are more similar to chimps/bonobos than to gorillas and all three are about the same genetic distance from orangutans.” On the contrary, I think it’s very easy to explain that fact: all one needs to posit is three successive acts of tweaking, over the course of geological time: a first act, which led to the divergence of African great apes from orangutans; a second act, which caused the African great apes to split into two lineages (the line leading to gorillas and the line leading to humans, chimps and bonobos); and finally, a third act, which led humans to split off from the ancestors of chimps and bonobos.

"Why would a Designer do it that way?" you ask. "Why not just make a human being in a single step?" The short answer is that the Designer wasn’t just making human beings, but the entire panoply of life-forms on Earth, including all of the great apes. Successive tweakings would have meant less work on the Designer’s part, whereas a single tweaking causing a simultaneous radiation of orangutans, gorillas, chimps, bonobos and humans from a common ancestor would have necessitated considerable duplication of effort (e.g. inducing identical mutations in different lineages of African great apes), which would have been uneconomical. If we suppose that the Designer operates according to a "minimum effort" principle, then successive tweakings would have been the way to go.

Interesting. One imagines the creator visiting Africa about 15 million years ago and fiddling with the genome of the ape ancestor so that two distinct species are formed. One leads eventually to orangutans and their extinct relatives and the other is the progenitor of the other extant apes and their extinct relatives.

Then the creator gets busy with beetles, or other planets, and lets things evolve on their own for a while, accumulating and fixing alleles at the rate we expect for evolution. Then the creator comes back for a visit about five million years later, having gotten bored with beetles. He (she?) tweaks the genome of some African ape so that a new species arises. The old one is the ancestor of modern gorillas and all the other related species that have gone extinct and the new species becomes the ancestor of chimps, bonobos and humans.

Now the creator turns his attention elsewhere for a few million years as those ape species evolve (insects need attention and his creation on Titan is in peril). Back he (she?) comes about five million years ago to tweak another two species into existence—one that will give rise, by evolution, to several species of Australopithicus, several species of Paranthropus, and several species of Homo (Homo habilis, Homo erectus, Homo heidelbergensis, and Homo sapiens. The other will eventually lead to over-sexed bonobos, the main goal of the exercise, I assume.

I think that what Vincent Torley is saying is that this is all consistent with the data I posted because most of the time these species are evolving just as we would expect. That's why the sequence differences between chimps and humans corresponds to what we expect from evolutionary theory. The reason this is misleading is because it omits the key mutations that god inserted every five million years or so in order to make modern gorillas.

There is, of course, no evidence that Torley's scenario is true and no evidence that a creator exists. I thank Vincent Torley for showing us just how ridiculous the Intelligent Design Creationist movement has become if this is the best they can do.

Professor Moran makes the remarkable claim that 130 mutations are fixed in the human population, in each generation. Here are a few reasons why I’m doubtful, even after reading his posts on the subject (see here, here and here):

(a) most mutations will be lost due to drift, so a mutation will have to appear many times before it gets fixed in the population;
(b) necessarily, the mutation rate will always be much greater than the fixation rate;
(c) nearly neutral mutations cannot be fixed except by a bottleneck.

I owe the above points to a skeptical biologist who kindly offered me some advice about fixation. As I’m not a scientist, I shall pursue the matter no further. Instead, I’d like to invite other readers to weigh in. Is Professor Moran’s figure credible?

A classic argument from ignorance. Vincent Torley doesn't understand evolution (population genetics) therefore he's "doubtful" of any result that he can't understand even though it seems consistent with the scenario he proposes above.

Professor Moran is also assuming that chimps and humans diverged a little over five million years ago. He might like to read the online articles, What is the human mutation rate? (November 4, 2010) and A longer timescale for human evolution (August 10, 2012), by paleoanthropologist John Hawks, who places the human-chimp divergence at about ten million years ago, but I’ll let that pass for now.

It's possible that our estimate of the human mutation rate is off by a factor of two (i.e. 70 per generation instead of 130 per generation) [see Theme: Mutation for a thorough discussion¹). Personally, I doubt it but if it turns out to be the case then chimps and humans may have diverged ten million years ago. It would then still be true that the differences between chimps and humans is what we expect if they evolved from a common ancestor at a slower mutation rate.

I shall also overlook the fact that Professor Moran severely underestimates the genetic differences between humans and chimps. As Jon Cohen explains in an article in Science (Vol. 316, 29 June 2007) titled, Relative Differences: The Myth of 1%, these differences include "35 million base-pair changes, 5 million indels in each species, and 689 extra genes in humans," although he adds that many of these may have no functional meaning, and he points out that many of the extra genes in human beings are probably the result of duplication. Cohen comments: "Researchers are finding that on top of the 1% distinction, chunks of missing DNA, extra genes, altered connections in gene networks, and the very structure of chromosomes confound any quantification of ‘humanness’ versus ‘chimpness.’" Indeed, Professor Moran himself acknowledges in another post that "[t]here are about 90 million base pair differences as insertion and deletions (Margues-Bonet et al., 2009)," but he goes on to add that the indels (insertions and deletions) “may only represent 90,000 mutational events if the average length of an insertion/deletion is 1kb (1000 bp)." Still, 90,000 is a pretty small number, compared to his estimate of 22.4 million mutations that have occurred in the human line.

There have been plenty of insertions, deletions, and chromosomal rearrangements in the lineages leading to chimps and humans. If you want to count a deletion of 1000bp as 1000 differences then be my guest. It doesn't change the fact that we can examine the rate of single nucleotide substitutions as a close proxy for the total number of mutations and arrive at a figure that's remarkably close to that predicted by evolutionary theory.

Counting the deletion as 1000 separate mutation events events doesn't make any sense, even for a creationist.

I could also point out that the claim made by Professor Moran that the DNA of humans and chimps is 98.6% identical in areas where it can be aligned is misleading, taken on its own: what it overlooks is the fact that, as creationist geneticist Jeffrey Tomkins (who obtained his Ph.D. from Clemson University) has recently demonstrated, the chromosomes of chimpanzees display "an overall genome average of only 70 percent similarity to human chromosomes" (Human and Chimp DNA–Nearly Identical, Acts & Facts 43 (2)).

The claim that the human and chimp genomes are only 70% similar in overall sequence is too silly too waste time on. Besides, as I already explained, it's the rate of substitution in the regions that can be aligned that has to be explained. Why is this rate so similar to what evolutionary theory predicts?

I might add (h/t StephenB) that Professor Moran has overlooked the fact that humans have 23 pairs of chromosomes, whereas chimpanzees (and other great apes) have 24. However, Dr. Jeffrey Tomkins has published an article titled, Alleged Human Chromosome 2 "Fusion Site" Encodes an Active DNA Binding Domain Inside a Complex and Highly Expressed Gene—Negating Fusion (Answers Research Journal 6 (2013):367–375). Allow me to quote from the abstract:

Irrelevant. (And boring.)

Leaving aside these points, the real flaw in Professor Moran’s analysis is that he assumes that the essential differences between humans and chimpanzees reside in the 22.4 million-plus mutations – for the most part, neutral or near-neutral – that have occurred in the human line since our ancestors split off from chimpanzees. This is where I must respectfully disagree with him.

I assumed no such thing. I'm just asking creationists to account for the fact that there's powerful evidence of evolution in the sequence comparisons. It's not just the overall similarity but the number of differences that support an evolutionary explanation.

So far, the only "reasonable" thing that Vincent Torley has said is that he agrees that most of the changes are due to evolution but that god tweaked a few other spots every five million years in order to make sure that bonobos appeared on his favorite planet. (Although he clearly liked beetles better.)

These [orphan genes] are the genes that I’m really interested in. Can a neutral theory of evolution, such as the one espoused by Professor Moran, account for their origin?

That's a discussion for another time. We first need to prove that all potential orphan genes are really functioning genes and we're quite a long way from that. If they aren't, then Neutral Theory is a good foundation for explaining the origin of things that look like functional genes but aren't.

The rest of Torley's post is about what creationists think of species. I don't feel the need to discuss it. He concludes with ...

I shall stop there for today. In conclusion, I’d like to point out that Professor Moran nowhere addressed the problem of the origin of orphan genes in his reply, so he didn’t really answer the first argument in my previous post, which was that we cannot claim to understand macroevolution until we ascertain the origin of the hundreds of chemically unique proteins and orphan genes that characterize each species.

I didn't discuss orphan genes because it's irrelevant to either of the points I was making. It has nothing to do with the question of human/chimp sequence similarity and it has nothing to do with the abundant evidence in support of macroevolution.

Besides, I don't accept his premise that there are hundreds of unique genes that characterize each species.

To Professor Moran’s credit, he did attempt to answer my second argument (why is there so much stasis in the fossil record?), by suggesting that even large populations will still change slowly in their diversity, as new alleles increase in frequency and old ones are lost, but that morphological change is “more likely to occur during speciation events when the new daughter population (species) is quite small and rapid fixation of rare alleles is more likely.” But as I argued previously, why, during the times of environmental upheaval described by Professor Prothero, don’t we see a diversification of niches? Why don’t species branch off? Why do we instead see morphological stasis persisting for millions of years? That remains an unsolved mystery.

Nope, it's not a mystery.

Finally, it seems to me that Professor Moran has solved the “time” question (my third argument) only in a trivial sense: he has calculated that the requisite number of mutations separating humans and chimps could have gotten fixed in the human line. I have to say I found his claim that in the last five million years, 22.4 million mutations have become fixed in the lineage leading to human beings, utterly astonishing. But even supposing that this figure is correct, what it overlooks is that the mutations accounting for the essential differences between humans and chimps aren’t your ordinary, run-of-the-mill mutations. Many of them seem to have involved orphan genes, which means that until we can explain how these genes arise, we lack an adequate account of macroevolution.

In other words, Vincent Torley is "astonished" that the differences between the genome sequences of chimps and humans correspond to what we would expect if they evolved from a common ancestor.

Why am I not surprised that a creationist doesn't understand evolution?

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1. Vincent Torley could have read this as well.