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Saturday, February 25, 2023

How Intelligent Design Creationists try to deal with the similarity between human and chimp genomes

The initial measurement of the difference between the human and chimp genomes was based on aligning 2.4 billion base pairs in the two genomes. This gave a difference of 1.23% by counting base pair substitutions and small deletions and insertions (indels). However, if you look at larger indels, including genes, you can come up with bigger values because you can count the total number of base pairs in each indel; for example, a deletion of 1,000 bp will be equivalent to 1,000 SNPs.

Depending on how many of these large deletions and insertions you detect, the difference between the human and chimp genomes can be 4%, 10%, or even 20%. Intelligent Design Creationists seize upon these different ways of comparing the genomes as evidence that the case for common ancestry is weak. You can hear Casey Luskin try to argue against evolution in one of the latest podcasts from ID The Future [Chimp and Human Genomes: An Evolution Myth Unravels].

Luskin mentions a short paper published in Science in 2007 where Jon Cohen supposedly exposes the "myth of 1%" (Cohen, 2007). According to Cohen, the actual value is more than 6% and Luskin jumps all over this in order to make the point that "evolutionists" were wrong.

Luskin conveniently forgets to mention that even using these larger percentage differences allows us to infer that humans and chimps shared a common ancestor about 6-7 million years ago and to infer more distant relationships with other mammals that are consistent with the fossil record (see figure). The Twin Nested Hierarchy (sequence plus fossils) is the most powerful evidence supporting the common ancestry of humans and other species. Evolution explains the Twin Nested Hierarchy but I don't know of any other explanation that accounts for these observations—creationists certainly don't have one.

The main problem with debates over the exact percentage is that it obscures the real issue when it comes to inferring evolution. What we're concerned about is not the total number of nucleotide differences but the number of mutations that gave rise to those differences. In that sense, a single base pair substitution is the same as a single deletion of 1000 bp.

According to Luskin, "Your percent DNA similarity between two species really doesn't tell you anything about whether or not they are genetically related." He says that common design can explain the similarities. That's true up to a point, you could argue that the mystery designer used common features to design chimps and humans then tweaked the design to make them slightly different. That might work as an explanation for two species, such as humans and chimps, but it's much harder to explain the overall pattern of differences when you look at a lot of species. How do creationists explain that the number of differences between the genomes of multiple species just happen to correlate with their presumed evolutionary relationships based on the fossil record?

I suppose they could argue that what we're seeing is merely the handiwork of the designer who first built a mammal prototype then started experimenting with slight modifications to create working models of rodents, bats, and ungulates. Each of these other prototypes were then adjusted using small changes to make smaller groups (families, genera) and then species. Presumably this was done over several million years of experimenting and adjusting in order to account for transitional fossils and dating technology.

But in addition to being mere speculation based on the presumption of a designer, there's one other problem with this model. The differences between genomes aren't just due to specific modifications that create distinct species as the designer model predicts. Instead, the evidence shows that they are mostly concentrated in parts of the genome that are not under strong selection. What this means is that most of the mutations are effectively neutral and thus the affected DNA should be evolving at the neutral rate, which, according to population genetics, is equivalent to the mutation rate. This prediction turned out to be correct and changes at the neutral rate are what gives rise to the approximate molecular clock.1 (See Calculating time of divergence using genome sequences and mutation rates (humans vs other apes).)

What this means is that our current understanding of evolution has enormous explanatory power. It satisfactorily accounts for the data on genome differences in a way that no competing model can. If Intelligent Design Creationists expect to be taken seriously as scientists then they have to do more than come up with hand-waving arguments about the possible motives of the designer. Instead, they have to explain why those differences just happen to fall in line with known mutation rates, which then give times of divergence from common ancestors that just happen to correlate with the fossil record.

1. It's important to keep in mind that the changes we see when we compare genomes are due to the combination of mutation and fixation of alleles by random genetic drift.

Cohen, J. (2007) Relative Differences: The Myth of 1%. Science 316:1836. [doi: 10.1126/science.316.5833.1836


SPARC said...

I wonder if Luskin's reasoning doesn't force him to view his parents as members of a distant species.

Wade said...

There is the possibility that much of the design was done by student designers who just made changes at random because they didn't really believe in biochemistry but were instead adherents of the great philosopher Norman Vincent Peale and The Power of Positive Thinking.

Joe Felsenstein said...

When a creationist announces that the fraction of difference between humans and chimps is not 1% but is Much Bigger Than That, ask them about the fraction of difference between humans and gorillas. That will turn out to be even larger. And with orangutangs, even larger than that. They never seem to make those comparisons. I wonder: why not?

gert korthof said...

Intelligent Design supporters are in good company: the famous Erich von Daniken claims in his latest book 'Evolution is Wrong':
"the amino acid sequence of the 231 proteins discovered in humans and apes differs by 83 percent."

Furthermore, a strong argument that humans and the great apes cannot be closely related is this fact: humans have 46 chromosomes and chimp, gorilla and orangutan have 48 chromosomes!

Matthew said...

And since a predetermined conclusion allows interpreting absolutely anything as support for your position, let's not forget that a post on Evolution News & Views by Cornelius Hunter declared that the close relationship between chimps and humans was evidence FOR intelligent design:
"In recent decades the genomes of humans and chimps have been determined, and in an evolutionary paradigm they make no sense. One of the main problems is that the genes of the two species are almost identical. They are only about 1-to-2 percent different and, if you’re an evolutionist, this means you have to believe that the evolution of humans from a small, primitive, ape-like creature was caused by only a tiny modification of the genome."

Anonymous said...

Jeffrey Tomkins responding to Dennis Venema argues that the human vitellogenin pseudogene has only 14% identity with the chicken vitellogenin gene, he argues that any two random genetic sequences will have 25% similarity because DNA has only 4 nitrogenous bases and the vitellogenin pseudogene has only a 39% match to the vitellogenin gene and this results in a 14% identity on a scale of 0 to 100. How do you refute this

here is the Answersingenesis article:

Larry Moran said...


Hunter's argument makes no sense (duh!). The data shows that chimps and humans differ by only 1-2% so whether you believe in a creator or in evolution makes no difference - in both cases it only takes a tiny modification of the genome to change chimps into humans and vice versa.

Intelligent Design Creationism has been around for thirty years. You would think that by now they could have come up with better arguments.

Larry Moran said...


Tomkins is correct. If the similarity between any two nucleic acid sequences is only 25% then you cannot conclude that they share a common ancestor. In the case of the vitellogenin genes, this similarity is 39%, which is well above the cutoff of 25% so the sequences are very likely to be related.

If these were just random alignments between the chicken vitellogenin genes and any fragment of the human genome, you would be right to question whether this was just a coincidence but that's not what the authors of the study did. They looked specifically at the same region of the mammalian genomes (wallaby, opossum, dog, human) where the chicken genes are located in the chicken genome.

The similarities (39%) are located right where they should be if the mammalian genes are old pseudogenes. Not only that, the authors reported that there are no other similar matches anywhere else in the genome. That seems like pretty good data to me.

Robert Byers said...

Two points that actually matter on this.
First its a great point that if us/primates are o little different then it undercuts the great evolution that must of happened since we are quite different. the dna is not what it should be in difference if we seaparted so long ago and so much in important poinys.
The second more importany point is we do have the primate body. biblical creationists, more easily then ID folks, must see the primate was made before the man. So god in making the man was making a copy of another creature. Another kind. yet unique in biology for such a exact bodyplan likeness. SO the creationist must conclude we do not have our our bodyplan that represents us . iNstead because we uniquely are made in Gods image we can not have a bodyplan to show that in the common blueprint of biology. So we alone are renting another creatures body. having a identical bodyplan with primates is the evidence of our unique origin. A creationist must reason this way and , like me , desire as exact a dna score as primates. its close enough to demand we got thier bodyplan. case closed.
We simply can't have our own and so have the best one in biology for fun and profit. there is no better bodyplan than the primate sorry to the eagle. It is wrong to seek DNA differences from primates. not needed and undesirable if one thinks carefully about it.

Paul Nelson said...

“The problem is that similarity and difference are relational and oppositional concepts. We can study how similar and how different we are from the apes and we can examine the patterns of those similarities and differences, but the meanings we attach to the results are by no means self-evident... It is not that difficult to tell a human from an ape, after all. The human is the one walking, talking, sweating, praying, building, reading, trading, crying, dancing, writing, cooking, joking, working, decorating, shaving, driving a car, or playing football. Quite literally, from the top of our head (where the hair is continually growing, unlike gorillas) to the tips of our toes (the stoutest of which is non-opposable), one can tell the human part from the ape part quite readily if one knows what to look for. Our eye- whites, small canine teeth, evaporative heat loss, short arms and long legs, breasts, knees, and of course, our cognitive communication abilities and the productive anatomies of our tongue and throat are all dead giveaways. However, they are not readily apparent in a genetic comparison.”

Jonathan Marks, “What is the Viewpoint of Hemoglobin, and Does It Matter?” History and Philosophy of the Life Sciences 31 (2009):241-262; pp. 244, 246.

John Harshman said...

A few minor points:

1. I think the chimp genome paper's 1.23% figure was based on differences in aligned sites only, not on indels, however short.

2. The measure that counts an indel of 1000 bases as 1000 differences was, I believe, introduced by Roy Britten. Can't immediately summon up the paper in which he did that.

3. 25% similarity results from randomized sequences only under the Juke-Cantor model, or any other with equal expected base frequencies. Consider, for example, an extreme bias of frequency in which A is 90% and C, G, T are all at 3.3%. Randomized sequences will still be exceedingly similar.

Anonymous said...

He's still around? I read his and Sitchin's books in my late teens and was initially convinced but once I started reading science, and especially biology, I realized how wrong they were.
-César D.

John Harshman said...

The measure that counts an indel of 1000 bases as 1000 differences was, I believe, introduced by Roy Britten. This may be it, though I think I encountered it in another of his publications:

It's a silly way to measure divergence if you're thinking in evolutionary terms, but if you're interested in the melting point of cross-species duplex DNA, it's probably better.

Bayesian Bouffant, FCD said...

"He says that common design can explain the similarities. That's true up to a point, you could argue that the mystery designer used common features to design chimps and humans then tweaked the design to make them slightly different."

This does not appear to have any explanatory power. Why would a 'mystery designer' want to reuse code? I can understand why a human designer might do so; to conserve effort and materials. But this motivation completely fails if one is to postulate that the designer might be omniscient and omnipotent. Therefore, if the Creationist is to continue on and eventually get around to pointing out that their putative designer is the Christian God, they have left behind the argument that got them there.

bill4 said...

ID or not, Blind Watchmaker Evolutionists haven't proven their case.

dean said...

It's becoming more evident that "Intelligent Design proponents" needs to be replaced by "willing to lie repeatedly about science proponents".

Scott said...

Of note, to follow on Joe's comment, I have yet to see the ID creationists expand their comparisons to, say, pairs of taxa that they believe to have been descended from a 'common Kind' post-ark.
My suspicion is that they understand that THOSE percentages would increase at the same rate as the percentages seen between humans and chimps, which would be just as problematic for them.

Scott said...

To follow on Joe's comment - I find it curious that the ID creationists do not expand their 'research' by comparing pairs of taxa that they have pre-concluded are related via post-flood descent from an 'original Kind'.

Joe Felsenstein said...

@Scott: Yes, it would be interesting to note what fraction of difference they find between different species that are of the same "kind". They only have about 200 years for these to evolve after the Ark. It would also be interesting to know whether the fans of the Ark see natural selection as having any role in those species' differing adaptations.