Why the Similarity Percentage of Chimp and Human DNA Is Deceptive

Photo by Eric Erbe, digital colorization by Christopher Pooley, both of USDA, ARS, EMU., Public domain, via Wikimedia Commons

What Is a Genome?

The genome is the entire DNA sequence for an organism—it contains all the adenines (A), cytosines (C), guanines (G), and thymines (T). The A’s , C’s, G’s, and T’s are arranged in a specific order to code for the genes but are also important in parts of the genome that act to regulate when certain genes are turned on/off (like a switch). When I was a college student, the evolutionary textbook for my molecular genetics class suggested that bacterial genomes were smaller than humans’ genomes because of descent with modification.8 However, Table 1 shows various genome sizes from viruses through humans. If Darwinian evolution were true, then there would be no exceptions like the largest genome on record belonging to a fern (notice also that the largest virus genome is larger than the smallest bacterial genome). The number of genomes that an organism carries is also different from organism to organism. On average, bacteria carry roughly one copy of their genome (often referred to as haploid), while humans carry two copies of the genome (called diploid).9 Even more interesting are certain plant species that carry even more genomes per cell, such as some strawberries that carry eight copies (called octaploid).10 Sometimes, genomes are referenced based on the percentage of G’s and C’s in the sequence (called G/C content). The most important aspect to a genome is the sequence of the letters because they code for the different proteins making up the organism.

How Is DNA Sequenced and Compared?

Sequencing DNA became widespread in the 1970s with the discovery of the particular method pioneered by Fred Sanger (who won the Nobel prize for this discovery).12 Initially, DNA sequencing was complex, dideoxyribonucleotide triphosphates (ddNTPs) were placed in separate tubes and run in separate lanes on a radiograph gel. The next significant advancement with DNA sequencing came when different dyes were incorporated and recorded by a computer giving a readout. When the computers were added to the process, our ability to sequence entire genomes became easier. Initially, individual genes were sequenced, followed by entire genomes for viruses, before finally sequencing entire bacterial genomes. Today, the method of next generation sequencing (NGS) allows scientists to sequence multiple genomes simultaneously through either paired-end sequencing using an Illumina platform (see image using bacterial genome) or obtaining long-reads on something like a PacBio. When the human genome was originally sequenced, it took a team of dedicated researchers across several laboratories approximately 10 years to finish. Using today’s NGS, we can obtain a single human genome in one lab, from one machine, in just a few days. As a result, the cost of DNA sequencing has dropped and our access to DNA sequence has expanded exponentially.

Nataschamt, CC BY-SA 4.0, via Wikimedia Commons

Traditionally, scientists measure percent similarity for two DNA sequences (or more) using a computer algorithm called Basic Local Alignment Search Tool (or BLAST for short).13 The BLAST algorithm finds the maximal alignment between two DNA sequences and reports it as a percentage. However, it is important to distinguish two similar DNA sequences from two identical DNA sequences because similar and identical are not synonyms. Furthermore, there are sequences that cannot align using BLAST because the differences are so strong—so how can those be classified? Simply put: Sequences without any alignment are not classified as having any matches nor are they described otherwise—they are not addressed. In summary, there are identical sequences, similar sequences that can match to a certain extent, and sequences that have no sequence matching whatsoever. Let’s consider the simple bacterium Escherichia coli to understand the differences between identical and similar as it relates to DNA percentages.

What Escherichia coli Is: The Good and the Bad

Escherichia coli is the best understood organism on the planet. It was originally called Bacterium coli commune when first isolated by pediatrician Theodor Escherich in 1886.14 Some have said, “There are only two kinds of bacteria. One is Escherichia coli and the other is not.”15 It was identified as a commensal, enteric bacteria that we now know provides us with vitamin K. What identifies E. coli from other enterics is that it is a Gram-negative, facultative anaerobe (bacteria capable of respiring oxygen and other chemicals), ferments the carbohydrate lactose, and usually does not grow aerobically on citrate media (aka citrate negative).16 In the 1970s, Carl Woese began sequencing the 16S ribosomal RNA (rRNA) gene from organisms and used this for classification purposes (each species has a unique 16S sequence).17 Everything that meets these biochemical test requirements (with the exception of the genera Shigella spp. that are simply citrate positive) along with carrying the specific sequence for the 16S rRNA gene are classified as E. coli—including harmless ones (non-pathogens or commensals) and ones that cause disease (pathogens) (more below).18

What We Learned from Sequencing E. coli

The first E. coli genome sequenced was for the non-pathogenic serotype K-12 strain MG1655 originally isolated from a convalescing diphtheria patient (referred hereafter as MG1655) and was significant for its time.19^, 20 MG1655 is used in biotechnology responsible for medical breakthroughs like insulin production for diabetics or industrial chemicals like acetone.21 The MG1655 genome is 4,639,221 base pairs (simplified in millions of base pairs as 4.64 Mbp) and has a GC-content of 50.8%. MG1655 is a Gram-negative, facultative anaerobe, fermenting lactose, is citrate negative, and its 16S rRNA gene sequence matches our understanding of E. coli. When MG1655 was first sequenced, most scientists thought that sequencing one strain of E. coli was sufficient to understand every strain of E. coli. It was not long before we began investigating more E. coli isolated from other sources that things began falling apart. But it is first important to discuss what scientists mean when they say that certain genomes share similar DNA sequences.

After sequencing the commensal MG1655, scientists sequenced the pathogenic E. coli known as O157:H7 strain EDL933 (referred hereafter as EDL933).22 EDL933 was isolated from an outbreak of hemolytic uremic syndrome in 1983.23 When EDL933 was sequenced, it was already known to have virulence factors (e.g., toxin genes and/or a pathogenicity island, which is a stretch of DNA carrying multiple toxins that were probably acquired from an outside source like a bacteriophage) that were absent from commensal E. coli (e.g., MG1655). In terms of how the EDL933 genome might compare with the genome of commensal MG1655, it was thought that the only difference between MG1655 and EDL933 would be the presence of virulence genes in EDL933 (both integrated on the bacterial chromosome as well as its plasmid pO157). To the contrary, the EDL933 genome size was considerably larger than the MG1655 genome (nearly 1Mbp!): The size of the EDL933 genome is 5,528,445 bp (with a plasmid, pO157, that is only 92,077 bp). Even the authors stated, “Our findings reveal a surprising level of diversity between two members of the species E. coli.”24 In looking at just the comparison between these two members of E. coli (from information provided in the EDL933 genome sequence publication), several things are already worth noting. If MG1655 and EDL933 have significant differences, then what do the differences mean? To address those differences, here is an example to help understand what is seen at the DNA level.

Initial Differences Among E. coli

The base pair difference between MG1655 and EDL933 is 889,224—this number represents about a 19.2% difference. Putting this difference another way, one in five nucleotides is different between these strains. Even with this many differences, both strains still share DNA (called a backbone) that is 4.1 Megabases. Having this common backbone means that there are base pairs unique to both commensal MG1655 and pathogenic EDL933—there are base pairs present in only MG1655 and base pairs present in only EDL933. From the backbone of the E. coli genome, there are 75,168 single nucleotide polymorphisms (today referred to as single nucleotide variants) between MG1655 and EDL933. The number of polymorphisms is less than a 2% difference in the parts of the genome that are highly similar between both strains.25 Keep in mind that both of these strains are still Gram-negative, facultative anaerobes, fermenting lactose, citrate negative, and have nearly identical 16S rRNA gene sequences (one nucleotide difference, still the same species by all measures)!

Second (and possibly most interesting), there are genes unique to the pathogen EDL933 besides the virulence factors. The authors of the paper for the genome sequence of EDL933 stated that there were 528 genes unique to MG1655 and 1,387 “new genes” in EDL933. Some of the unique genes in EDL933 allow it the ability to grow on the carbohydrate N-aceltylgalactosamine (i.e., MG1655 lacks these genes entirely). The idea of knowing what defines E. coli (by whether it is a Gram-negative, facultative anaerobe, fermenting lactose, is citrate negative, and its 16S rRNA gene sequence) began to unravel as we entertained the idea that E. coli carried a certain set of “required” genes and could also carry other miscellaneous genes without falling outside the traditional definition. It seems that there are certain sets of genes always found inside of what is called E. coli in addition to certain sets of genes that are never found in an E. coli genome.

Third, only 911 proteins were identical between the ~4,600 genes in MG1655 and ~5,600 genes in EDL933—that’s 19.8% in MG1655 and 16.2% in EDL933. The percentages of identical proteins means that approximately only one in five proteins is identical (100% the same) for two members of the same species! Even more surprising than how few identical proteins exist between these strains is that the authors suggest a most recent common ancestor between these E. coli was 4.5 million years ago (which is not based on Scripture). For only 911 proteins being identical after 4.5 million years is shocking because both strains still meet the core definition for what makes E. coli. Given these three observations, some initial conclusions can be drawn before updating this information with even more recent genome sequences available.

Measuring percent similarity between two strains of E. coli is complicated because of the different sizes of their genomes (the number of base pairs for MG1655 divided by the number of base pairs for EDL933, which is 83.915%) or the number of identical base pairs between the core E. coli backbone they identified (the total backbone minus the single nucleotide polymorphisms divided by the core backbone base pairs, which is 98.167%). When I was in graduate school, we asked ourselves whether MG1655 was the same as EDL933 for these reasons. We told ourselves that they were similar where they were identical but that they remained different strains of E. coli because of how many gene differences there are (and it was not just the virulence genes that made these strains so different—e.g., I published significant differences in what they competed for during colonization of the mammalian intestine).26 The idea of any given bacterial species containing nearly identical DNA sequences was becoming unhinged with just the second E. coli genome sequenced. But what about additional E. coli genomes to sequence? Does more DNA sequencing provide the answer?

Even Less DNA Similarity Among E. coli

The third E. coli genome sequenced was a strain that causes urinary tract infections called CFT073 (serotype O6:H1:K? ).27 The genome of CFT073 has 5,231,428 base pairs (without a plasmid, unlike EDL933) and was significantly different from both MG1655 and EDL933. The authors stated in the second sentence of the paper abstract: “A three-way genome comparison of the CFT073, enterohemorrhagic E. coli EDL933, and laboratory strain MG1655 reveals that, amazingly, only 39.2% of their combined (nonredundant) set of proteins actually are common to all three strains” (see Figure 1). In this three-way comparison, the idea of a core backbone to the genome decreased to about 40% because of an additional E. coli genome being compared. Take note of what the authors of the paper were suggesting: Modern day members of the same species can have a percent similarity as low as 40%! Remember that the current positivistic philosophy of modern science thought they could rescue percent similarity by sequencing more strains of E. coli. But did this extra sequencing help the evolutionary problems for a percent similarity used within a given species? Keep in mind: E. coli is the best understood organism on the planet. How much worse can a percent similarity get?

Figure 1. Genome comparison between MG1655, EDL933, and CFT073 adapted from Welch RA et al. 2002.

While several other E. coli genome sequences were published around the time of CFT073, the first paper reporting sequences of multiple E. coli strains had eight genome sequences and compared them with the other available E. coli genomes (a total of 17 genomes were included for this comparison).28 In performing this analysis, the authors found that all E. coli genomes sequenced only shared ~2,200 genes—though the gene content for each genome ranged from 4,238 genes (MG1655) up to 5,589 (CFT073). From their comparative genomic analysis, the authors concluded that there may be approximately 13,000 different genes that could be found in all E. coli genomes on the planet today—while still all being called E. coli.

About the time of the previous comparative genomic analysis, a new sequencing technology was developed that allowed more genomes to be sequenced with greater frequency and efficiency (called next generation sequencing, or NGS). The labs that reported the initial eight genomes have since obtained over 600 genomes (Table 1). Of the over 600 sequences they deposited in Genbank, no two were identical. If we began the process of comparing genomes by using Venn diagrams, the first couple genomes sequenced only had between 60% and 70% similarity or overlap. As there were more genomes sequenced, the area of overlap has continued to decrease. However, the amount of overlap in that Venn diagram has reached a limit given the number of E. coli genome sequences available. Several years ago, I contacted one of the genome scientists to ask how many nucleotides he had found to define E. coli. The response I received was that E. coli has about 2.5 million nucleotides. When he said 2.5 million nucleotides, consider that those 2.5 million did not need to be in order on the genome but only that they were present somewhere in the genome for something we know and call E. coli.

If No Two E. coli Genomes Are Identical , Then Humans and Chimpanzees Did Not Share Common Ancestors

Our understanding of the E. coli genome has advanced significantly in recent years. To date, there are 29,031 whole genome sequences for Escherichia coli in Genbank (including scaffold, chromosome, or complete for the filter, retrieved on May 4, 2025, https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=562&assembly_level=1:3).29 Most importantly, no two E. coli genomes are identical. Among those genomes most closely related might be the strain that I sequenced, which was passaged through a mouse intestine and found to have minor differences compared to its original genome.30 If we had stopped sequencing E. coli genomes after the first one (MG1655), we might have a slightly different perspective about what E. coli is. However, by sequencing the vast number of E. coli genomes, we have a sufficient number of genomes in Genbank to draw conclusions about genome similarities that extends beyond understanding what E. coli is—we can learn how useful genome similarities are in the origins debate.

By sequencing the vast number of E. coli genomes, we have a sufficient number of genomes in Genbank to draw conclusions about genome similarities that extends beyond understanding what E. coli is—we can learn how useful genome similarities are in the origins debate.

First, the understanding we had about what defines E. coli from traditional biochemical tests is valid still: a Gram-negative, facultative anaerobe, fermenting lactose, that is usually citrate negative (Bergey’s manual).31 If we think about it, the bigger surprise should be expecting sequencing genomes to tell us something different than what the central dogma of molecular biology upholds: Enzymes have DNA sequences that should be relatively similar. Perhaps the shock is with the differences in gene content and regulatory regions. The idea of allowing the central dogma of molecular biology to inform our thoughts on percent similarities extends well beyond E. coli and into every living thing on the planet.

Consider the visible anatomical similarities between humans and chimpanzees as an example of expecting DNA similarities. If there are anatomical similarities and DNA codes for structural features in organisms, then the expectation is that there will be significant DNA sequence similarities between these organisms (saying there are no DNA similarities would violate our anatomical observations and the central dogma of molecular biology). Second, the number of genes defining E. coli fits well within the number of known nucleotides (i.e., the 2.5 million), but there might be value in modifying the E. coli definition—it might also be helpful to define E. coli by what it cannot do because it never has those genes. For example, E. coli has never been found to perform photosynthesis, methanogenesis, grow on polysaccharides, or glow in the dark. In comparing humans with other living things, we have to acknowledge some simple observations like our inability to make a cell wall made of cellulose. These functions are never present in the E. coli that we have been testing biochemically for years and is worth considering inclusion in the definition of what E. coli is. Upon closer analysis, we already can see that E. coli is usually citrate negative, but why not also include that E. coli is photosynthesis negative? Including other features helps define what we are able to see about E. coli in the mammalian intestine and marine ecosystems.32 Finally, the percent differences for all E. coli genomes can vary by as much as half and still be called the same organism because it shares the same 2.5 million nucleotides. There are some profound implications for this final point as it relates to percent similarities use for so-called human evolution and comparisons with nonhuman primate genomes.

Summing It Up

The percent differences for all E. coli genomes can vary by as much as half.

The main conclusion is that percent similarities between biblical kinds (or taxonomic families) carry little significance (unlike what evolutionists would have us think). According to evolutionary estimates, E. coli came into existence between 10 and 50 million years ago. Keep in mind that E. coli is present in all land animals and the majority of fish in the oceans, so evolutionists would need to consider coevolution of these organisms since these are symbiotic relationships. If coevolution is how these symbiotic relationships must happen, we must keep in mind that bacteria are supposed to be proof of evolution happening today. What does not make sense is that a single-cell bacterium like E. coli remains the same for 10 to 50 million years since evolutionists claim that bacteria evolve today rapidly. But if the bacteria are evolving rapidly, can there be any meaning behind a similarity between a human and a chimpanzee (or other nonhuman primate) on that same timeline? If the bacteria evolve quickly, then the humans and chimpanzees must also evolve quickly.33 The issue centers on the evolutionists’ usage of these percent similarities as part of their argument. Furthermore, it must be highlighted that E. coli has a far lower percentage of similarity among itself (near 50%, depending on the strains) as a single species than humans and chimpanzees have between themselves by either the creationist or evolutionist estimates (between 80% to 98%–99%). That amount of change in a genome sequence happening for something like bacteria means that genomic entropy is real.34 And if we know that there is such wide genetic diversity in E. coli and that it evolves quickly, then the timescale for humans and chimpanzees must be much shorter than previously thought. A difference of 1–2% cannot exist for 10–50 million years because organisms like E. coli have evolved (in their worldview) and have far greater percent difference between the organisms. Using this evolutionary logic in drawing a conclusion from a supposed 1–2% difference would put humans and chimpanzees having only been created within the past several thousand years (and I doubt that is what they are trying to promote).35

The Numbers Game

A related issue that must be addressed by evolutionists concerning these vanishingly small genome differences is that there could be an organism with only 1% similarity (for an outlandish example) that shares common ancestry with other organisms. Let’s pretend that organism A and organism B are “similar” and share 1% of the genome, which is 1,000,000,000 base pairs in size. Having a 1% similarity means that 10,000,000 nucleotides are the same. Looking at only numbers, the use of percent similarity obscures truly big differences. For example, it is generally thought that bathroom cleaning products are effective at killing 99.9% of the germs (Figure 2). However, most people do not realize that 99.9% of the millions of bacteria on a surface still means that there are thousands of bacteria left on that same surface—the percentage is misleading in advertising as much as it is misleading in an evolutionary worldview. And just like we should not abandon the use of disinfectants, we should also not abandon using percent similarities. We must remind ourselves of the limitations of each and use them within reason. In contrast with the evolutionary worldview, the biblical concept of kind fits well with a limited number of DNA nucleotides that comprises the genome for a given kind. Given this extreme perspective of thought, we should realize and call out evolutionists because they would cite a 1% similarity between organisms as proof of evolution if they needed to because it is not about the evidence.

Figure 2. Disinfectants often claim to kill 99.9% of the germs. But the 99.9% number obscures how many germs are actually left behind. Still use disinfectant, but do not assume it is as effective as you may think.

DNA Similarities Support Design

Genome comparisons and percent similarities demonstrate the faith that we exercise: either in God’s Word or man’s word. No amount of evidence will convince an evolutionist just like the Pharisees who witnessed the healing of the sick and accused Jesus of being demon possessed. Ultimately, Christians can stand confidently on the authority of Scripture because all good science supports Scripture.