Human vs Chimp: an honest evaluation of our genetic differences

Several anti-creationists have made a hobby out of attacking creationists. Their best efforts, however, have generally failed. For example, see:

Sanford 2013 Critic ignores reality of Genetic Entropy: the author of a landmark book on genomic decay responds to unsustainable criticisms creation.com 7 Mar 2013.

Price, Carter, and Sanford 2020, Responding to supposed refutations of genetic entropy from the ‘experts’, creation.com, 1 Dec 2020.

Unperturbed, "Gutsick Gibbon" has recently tried to discredit Dr Jeffrey Tomkins and his work on human-chimp genetic similarities:

"80% Chimpanzee" | The Bogus Creationism of Jeffery Tomkins" 26 May 2023 youtube.com/watch?v=QtTHlqhRQi0.

In my analysis of her analysis, I note several flaws in her logic. Note, however, that I deliberately ignored several of her main objections. This was not because I do not have answers, mind you, but because I wanted to focus on the most salient questions. Ignored were questions about why God would have included all the chimp-like non-coding DNA when he made humans and questions about properly weighting samples.

The most recent comparison I am aware of claimed 96.6% similarity between humans and chimps:

Seaman and Buggs 2020 FluentDNA: nucleotide visualization of whole genomes, annotations, and alignments, Frontiers in Genetics 30;11:292.

This comes from the laboratory of Richard Buggs. This is much higher than Tomkins' estimates, that, with one exception, are generally in the 80s. However, I know the first author on that paper, so I called him up to discuss his methods. Sure enough, he used entirely different methodology than earlier work from that same laboratory (which arrived at an estimate of ~85%). To reach the higher percentage similarity, they cut out everything humans and chimps do not share, including the centromeres, telomeres, copy number variations of many annotated genes, and hundreds of thousands of small insertions and deletions that must be included to align the two genomes. This "apples to apples" comparison is fine, as long as everybody acknowledges that the true similarity is necessarily less than 96.6%. Yet, if the percent similarity is much less than 99%, there is no way, mathematically, to explain how so many millions of difference arose in the (imagined) 6.5 million years since our last common ancestor.

Additional links:

The Waiting Time Problem, BiblicalGenetics.com, 8 Jun 2021.

Hierachical clustering complicates baraminiological analysis

Carter 2021 Robert Carter gets everything wrong? Responding to even more ridiculous aspersions, creation.com, 10 July 2021.

“Dr. Rob Carter Gets Everything Wrong (with Gutsick Gibbon)” 20 May 2021.

Sibley and Alquist. 1991. The Phylogeny and Classification of Birds.

King and Wilson. 1975. Evolution at two levels in humans and chimpanzees, Science 188(4184):107–116.

Moorjani et al. 2016. Variation in the molecular clock of primates, PNAS 113(38):10607–10612.

Sibley and Ahlquist. 1984. The phylogeny of the hominoid primates, as indicated by DNA-DNA hybridization, J Mol Evol 20(1):2–15.

Sibley, Comstock, and Ahlquist. 1990. DNA hybridization evidence of hominoid phylogeny: a reanalysis of the data, J Mol Evol 30(3):202–36.

Wikipedia page on DNA reassociation kinetics.

Bergman and Tomkins 2012 Is the human genome nearly identical to chimpanzee?—a reassessment of the literature, Journal of Creation 26(1):54–60,

Tomkins and Bergman 2012 Genomic monkey business—estimates of nearly identical human–chimp DNA similarity re-evaluated using omitted data, Journal of Creation 26(1):94–100,

Tomkins 2013 Comprehensive analysis of chimpanzee and human chromosomes reveals average DNA similarity of 70%. Answers Research Journal 8:379–390.