Human vs Chimp: an honest evaluation of our genetic differences

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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. The version of BLAST he used for this paper had a flaw in the algorithm that only manifested when using extremely large data sets. Tomkins corresponded with the bioinformatics group at the NIH to get the BLASTN algorithm fixed, which they eventually did. Gutsick Gibbon claims her collaborator is the one who pointed it out. Personally, I do not know the order of events, but either way, the bug was fixed. See the notes on Tomkins 2016 below.
• Tomkins 2015 Documented anomaly in recent versions of the BLASTN algorithm and a complete reanalysis of chimpanzee and human genome-wide DNA similarity using Nucmer and LASTZ. Answers Research Journal 8:379–390.
• Tomkins 2016 Analysis of 101 chimpanzee trace read data sets: assessment of their overall similarity to human and possible contamination with human DNA. Answers Research Journal 9:294–298. This was a repeat of the 2013 paper, but after the bug was fixed. This is why Tomkins did not change his methods to allow for gaps. See the next entry, however.
• Tomkins 2018 Comparison of 18,000 de novo assembled chimpanzee contigs to the human genome yields average BLASTN alignment identities of 84%. Answers Research Journal 11:205–209. Here, Tomkins used long read chimp PacBio contigs, BLASTing them against the human genome with very liberal gap extension set. That study gave an average alignment similarity of 84%. Note that one of the main complaints is that Tomkins did not allow for gaps in his several papers. This is clearly not true. At least, the issue was certainly addressed five years ago. Note also that Tomkins ran his jobs on a local server, which took months to run and complete. Neither he nor I know exactly what she did, nor do I have a strong desire to attempt to repeat her methods. The fact that her ungapped human-to-human BLAST searches yield a percent similarity in the 80s is highly suspicious. If this is the case, BLAST is generally useless and I would assume this would be general knowledge. Nevertheless, this is less important than the fact that the human-chimp identity is demonstrably less than 96.6%.
• “They Lied to Us? (Humans & Chimps: Part 1) | The Creation Podcast: Episode 40” 10 Jan 2023.
• Lake County Forest Preserves: Fort Hill Trail
• Quentin Road Baptist Church, Exploring God’s Oceans (on In Grace TV), Dayspring Bible College and Seminary
• Midwest Creation Fellowship (Chicago area: north, south, and central), Quad-Cities Creation Science Association (Iowa)